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-rw-r--r--.github/workflows/duplicates.yml2
-rw-r--r--.github/workflows/pkgcheck.yml2
-rw-r--r--.github/workflows/repoman.yml22
-rw-r--r--CONTRIBUTING.md83
-rw-r--r--README.md1
-rw-r--r--app-arch/libdeflate/Manifest1
-rw-r--r--app-arch/libdeflate/libdeflate-1.11.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.9.ebuild2
-rw-r--r--app-arch/libdeflate/libdeflate-9999.ebuild4
-rw-r--r--app-office/visidata/Manifest3
-rw-r--r--app-office/visidata/metadata.xml4
-rw-r--r--app-office/visidata/visidata-1.5.2.ebuild60
-rw-r--r--app-office/visidata/visidata-2.8.ebuild (renamed from app-office/visidata/visidata-2.1.1.ebuild)7
-rw-r--r--dev-cpp/blitz/blitz-9999.ebuild48
-rw-r--r--dev-libs/asmjit/Manifest1
-rw-r--r--dev-libs/asmjit/asmjit-1.0_p22092020.ebuild34
-rw-r--r--dev-libs/asmjit/asmjit-9999.ebuild34
-rw-r--r--dev-libs/asmjit/metadata.xml31
-rw-r--r--dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild30
-rw-r--r--dev-perl/Bio-EnsEMBL/Manifest1
-rw-r--r--dev-perl/Bio-EnsEMBL/metadata.xml12
-rw-r--r--dev-python/annexremote/Manifest4
-rw-r--r--dev-python/annexremote/annexremote-1.5.0.ebuild9
-rw-r--r--dev-python/annexremote/annexremote-1.6.0.ebuild9
-rw-r--r--dev-python/annexremote/metadata.xml1
-rw-r--r--dev-python/anys/Manifest2
-rw-r--r--dev-python/anys/anys-0.2.0.ebuild28
-rw-r--r--dev-python/anys/anys-0.2.1.ebuild28
-rw-r--r--dev-python/anys/files/anys-0.2.0-coverage.patch10
-rw-r--r--dev-python/anys/metadata.xml16
-rw-r--r--dev-python/asciitree/Manifest1
-rw-r--r--dev-python/asciitree/asciitree-0.3.3.ebuild19
-rw-r--r--dev-python/asciitree/metadata.xml (renamed from sci-biology/symap/metadata.xml)6
-rw-r--r--dev-python/astroscrappy/Manifest2
-rw-r--r--dev-python/astroscrappy/astroscrappy-1.1.0.ebuild (renamed from dev-python/astroscrappy/astroscrappy-1.0.8.ebuild)7
-rw-r--r--dev-python/bokeh/Manifest11
-rw-r--r--dev-python/bokeh/bokeh-2.2.1-r1.ebuild85
-rw-r--r--dev-python/bokeh/bokeh-2.2.2-r1.ebuild85
-rw-r--r--dev-python/bokeh/bokeh-2.2.3.ebuild85
-rw-r--r--dev-python/bokeh/bokeh-2.3.0.ebuild85
-rw-r--r--dev-python/bokeh/bokeh-2.3.2.ebuild85
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild (renamed from dev-python/bokeh/bokeh-2.3.1.ebuild)32
-rw-r--r--dev-python/bokeh/files/bokeh-2.2.1-conftest_py.patch56
-rw-r--r--dev-python/cadquery-ocp/Manifest1
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild195
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild63
-rw-r--r--dev-python/cadquery/Manifest1
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild58
-rw-r--r--dev-python/ccdproc/Manifest2
-rw-r--r--dev-python/ccdproc/ccdproc-2.3.0.ebuild (renamed from dev-python/ccdproc/ccdproc-2.1.0.ebuild)14
-rw-r--r--dev-python/click-didyoumean/Manifest2
-rw-r--r--dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild24
-rw-r--r--dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild22
-rw-r--r--dev-python/click-didyoumean/metadata.xml16
-rw-r--r--dev-python/dandi-schema/Manifest4
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.4.3.ebuild46
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.5.1.ebuild42
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.5.3.ebuild42
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.6.0.ebuild42
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch11
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch10
-rw-r--r--dev-python/dandi-schema/metadata.xml26
-rw-r--r--dev-python/fiona/Manifest3
-rw-r--r--dev-python/fiona/fiona-1.8.21.ebuild (renamed from dev-python/fiona/fiona-1.8.20.ebuild)8
-rw-r--r--dev-python/fscacher/Manifest2
-rw-r--r--dev-python/fscacher/files/fscacher-0.1.4-coverage.patch9
-rw-r--r--dev-python/fscacher/files/fscacher-0.2.0-coverage.patch10
-rw-r--r--dev-python/fscacher/fscacher-0.1.4.ebuild32
-rw-r--r--dev-python/fscacher/fscacher-0.2.0.ebuild31
-rw-r--r--dev-python/fscacher/metadata.xml23
-rw-r--r--dev-python/fslpy/Manifest2
-rw-r--r--dev-python/fslpy/files/fslpy-3-remove_dataclasses_req.patch8
-rw-r--r--dev-python/fslpy/fslpy-2.8.4.ebuild42
-rw-r--r--dev-python/fslpy/fslpy-3.4.0.ebuild46
-rw-r--r--dev-python/geopandas/geopandas-0.10.2.ebuild2
-rw-r--r--dev-python/gmsh_interop/Manifest2
-rw-r--r--dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild (renamed from dev-python/gmsh_interop/gmsh_interop-2019.1.ebuild)10
-rw-r--r--dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch10
-rw-r--r--dev-python/hdmf/files/hdmf-3.1.1-versions.patch21
-rw-r--r--dev-python/hdmf/hdmf-3.1.1-r1.ebuild (renamed from dev-python/hdmf/hdmf-3.1.1.ebuild)4
-rw-r--r--dev-python/interleave/Manifest1
-rw-r--r--dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch18
-rw-r--r--dev-python/interleave/interleave-0.2.0.ebuild25
-rw-r--r--dev-python/interleave/metadata.xml21
-rw-r--r--dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch90
-rw-r--r--dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild (renamed from dev-python/keyrings_alt/keyrings_alt-4.1.0.ebuild)8
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch91
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch92
-rw-r--r--dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild (renamed from dev-python/llvmlite/llvmlite-0.38.0.ebuild)4
-rw-r--r--dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild (renamed from dev-python/llvmlite/llvmlite-0.37.0.ebuild)6
-rw-r--r--dev-python/meshio/Manifest1
-rw-r--r--dev-python/meshio/meshio-4.4.6.ebuild26
-rw-r--r--dev-python/meshpy/Manifest3
-rw-r--r--dev-python/meshpy/meshpy-2018.2.1_p1.ebuild51
-rw-r--r--dev-python/meshpy/meshpy-2020.1.ebuild (renamed from dev-python/meshpy/meshpy-2018.2.1.ebuild)24
-rw-r--r--dev-python/multimethod/Manifest1
-rw-r--r--dev-python/multimethod/metadata.xml (renamed from dev-python/meshio/metadata.xml)3
-rw-r--r--dev-python/multimethod/multimethod-1.8.ebuild20
-rw-r--r--dev-python/nptyping/Manifest1
-rw-r--r--dev-python/nptyping/metadata.xml13
-rw-r--r--dev-python/nptyping/nptyping-1.4.3.ebuild27
-rw-r--r--dev-python/numba/Manifest2
-rw-r--r--dev-python/numba/numba-0.55.0.ebuild2
-rw-r--r--dev-python/numcodecs/Manifest2
-rw-r--r--dev-python/numcodecs/metadata.xml16
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.0.ebuild35
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.1.ebuild35
-rw-r--r--dev-python/nwbinspector/Manifest1
-rw-r--r--dev-python/nwbinspector/metadata.xml16
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.3.9.ebuild28
-rw-r--r--dev-python/pynndescent/Manifest2
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.6.ebuild (renamed from dev-python/pynndescent/pynndescent-0.5.2.ebuild)9
-rw-r--r--dev-python/pynwb/Manifest2
-rw-r--r--dev-python/pynwb/files/pynwb-2.0.0-versions.patch21
-rw-r--r--dev-python/pynwb/metadata.xml20
-rw-r--r--dev-python/pynwb/pynwb-2.0.0.ebuild46
-rw-r--r--dev-python/pynwb/pynwb-2.0.0_p0.ebuild47
-rw-r--r--dev-python/pyout/Manifest2
-rw-r--r--dev-python/pyout/metadata.xml24
-rw-r--r--dev-python/pyout/pyout-0.7.1.ebuild32
-rw-r--r--dev-python/pyout/pyout-0.7.2.ebuild32
-rw-r--r--dev-python/pyparsing/Manifest1
-rw-r--r--dev-python/pyparsing/metadata.xml21
-rw-r--r--dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild29
-rw-r--r--dev-python/python-gantt/Manifest1
-rw-r--r--dev-python/python-gantt/python-gantt-0.6.0.ebuild26
-rw-r--r--dev-python/python-igraph/Manifest2
-rw-r--r--dev-python/python-igraph/python-igraph-0.8.2.ebuild36
-rw-r--r--dev-python/python-igraph/python-igraph-0.8.3.ebuild36
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild5
-rw-r--r--dev-python/pyvista/Manifest2
-rw-r--r--dev-python/pyvista/pyvista-0.33.2.ebuild (renamed from dev-python/pyvista/pyvista-0.31.1.ebuild)7
-rw-r--r--dev-python/pyvote/pyvote-0.1.ebuild9
-rw-r--r--dev-python/rasterio/rasterio-1.2.10-r1.ebuild (renamed from dev-python/rasterio/rasterio-1.2.10.ebuild)9
-rw-r--r--dev-python/rasterstats/rasterstats-0.16.0.ebuild2
-rw-r--r--dev-python/reproject/Manifest2
-rw-r--r--dev-python/reproject/reproject-0.8.ebuild (renamed from dev-python/reproject/reproject-0.7.1.ebuild)15
-rw-r--r--dev-python/repsep_utils/metadata.xml4
-rw-r--r--dev-python/snakemake/metadata.xml4
-rw-r--r--dev-python/snakemake/snakemake-5.32.2.ebuild6
-rw-r--r--dev-python/sphinx-argparse/Manifest2
-rw-r--r--dev-python/sphinx-argparse/sphinx-argparse-0.2.5.ebuild41
-rw-r--r--dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild27
-rw-r--r--dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild4
-rw-r--r--dev-python/trimesh/Manifest2
-rw-r--r--dev-python/trimesh/metadata.xml22
-rw-r--r--dev-python/trimesh/trimesh-3.9.1.ebuild52
-rw-r--r--dev-python/trimesh/trimesh-3.9.42.ebuild65
-rw-r--r--dev-python/typish/Manifest2
-rw-r--r--dev-python/typish/metadata.xml20
-rw-r--r--dev-python/typish/typish-1.9.3.ebuild30
-rw-r--r--dev-python/umap-learn/Manifest4
-rw-r--r--dev-python/umap-learn/umap-learn-0.4.6.ebuild28
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.0.ebuild28
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.1.ebuild28
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.2.ebuild26
-rw-r--r--dev-python/zarr/Manifest3
-rw-r--r--dev-python/zarr/metadata.xml16
-rw-r--r--dev-python/zarr/zarr-2.11.1.ebuild61
-rw-r--r--dev-python/zarr/zarr-2.11.3.ebuild62
-rw-r--r--dev-python/zarr/zarr-2.12.0.ebuild62
-rw-r--r--dev-util/Tensile/Manifest1
-rw-r--r--dev-util/Tensile/Tensile-4.0.0-r1.ebuild62
-rw-r--r--dev-util/Tensile/Tensile-4.0.0.ebuild62
-rw-r--r--dev-util/Tensile/files/Tensile-4.0.0-cmake.patch38
-rw-r--r--dev-util/Tensile/files/Tensile-4.0.0-locate-commands.patch62
-rw-r--r--dev-util/Tensile/files/Tensile-4.0.0-output-currentISA.patch22
-rw-r--r--dev-util/Tensile/files/Tensile-4.0.0-setup.py-cmake.patch13
-rw-r--r--dev-util/Tensile/metadata.xml11
-rw-r--r--dev-vcs/dandi-cli/Manifest3
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild87
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild87
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild89
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch30
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch46
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch13
-rw-r--r--dev-vcs/dandi-cli/metadata.xml26
-rw-r--r--licenses/Artistic-Manatee50
-rw-r--r--licenses/OBO-Edit9
-rw-r--r--media-libs/embree-bin/embree-bin-3.12.0.ebuild2
-rw-r--r--media-libs/embree-bin/embree-bin-3.12.1.ebuild2
-rw-r--r--media-libs/embree-bin/embree-bin-3.12.2.ebuild2
-rw-r--r--media-libs/embree-bin/embree-bin-3.13.0.ebuild2
-rw-r--r--net-misc/cernbox-client/Manifest2
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild)3
-rw-r--r--profiles/package.mask6
-rw-r--r--sci-astronomy/libthesky/Manifest2
-rw-r--r--sci-astronomy/libthesky/libthesky-0.4.2.ebuild (renamed from sci-astronomy/libthesky/libthesky-0.4.1-r1.ebuild)10
-rw-r--r--sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild2
-rw-r--r--sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild2
-rw-r--r--sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild2
-rw-r--r--sci-biology/GAL/GAL-0.2.2_p20200508.ebuild19
-rw-r--r--sci-biology/GAL/files/Build.PL.patch24
-rw-r--r--sci-biology/LINKS/LINKS-1.8.7.ebuild50
-rw-r--r--sci-biology/LINKS/LINKS-2.0.1.ebuild21
-rw-r--r--sci-biology/LINKS/Manifest2
-rw-r--r--sci-biology/MolBioLib/Manifest1
-rw-r--r--sci-biology/MolBioLib/MolBioLib-5.ebuild40
-rw-r--r--sci-biology/MolBioLib/metadata.xml15
-rw-r--r--sci-biology/OBO-Edit/Manifest1
-rw-r--r--sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild73
-rw-r--r--sci-biology/OBO-Edit/files/response.varfile10
-rw-r--r--sci-biology/OBO-Edit/metadata.xml15
-rw-r--r--sci-biology/SOAPdenovo2/Manifest1
-rw-r--r--sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild40
-rw-r--r--sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch204
-rw-r--r--sci-biology/SOAPdenovo2/files/soapdenovo2.122
-rw-r--r--sci-biology/SOAPdenovo2/metadata.xml12
-rw-r--r--sci-biology/SPAdes/Manifest8
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.1.ebuild55
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.3.ebuild36
-rw-r--r--sci-biology/Trinotate/Manifest2
-rw-r--r--sci-biology/Trinotate/Trinotate-3.2.2.ebuild (renamed from sci-biology/Trinotate/Trinotate-3.2.1.ebuild)9
-rw-r--r--sci-biology/afni/Manifest2
-rw-r--r--sci-biology/afni/afni-20.1.16.ebuild14
-rw-r--r--sci-biology/afni/afni-20.3.03.ebuild20
-rw-r--r--sci-biology/afni/afni-22.0.21.ebuild (renamed from sci-biology/afni/afni-19.3.12.ebuild)45
-rw-r--r--sci-biology/afni/afni-9999.ebuild70
-rw-r--r--sci-biology/afni/files/afni-20.1.16-python.patch2
-rw-r--r--sci-biology/afni/files/afni-20.3.03-python.patch11
-rw-r--r--sci-biology/aghermann/aghermann-1.1.2-r2.ebuild4
-rw-r--r--sci-biology/ants/ants-2.3.4.ebuild2
-rw-r--r--sci-biology/arachne/Manifest1
-rw-r--r--sci-biology/arachne/arachne-46233.ebuild39
-rw-r--r--sci-biology/arachne/metadata.xml12
-rw-r--r--sci-biology/bambus/bambus-2.33-r2.ebuild (renamed from sci-biology/bambus/bambus-2.33.ebuild)30
-rw-r--r--sci-biology/behaviopy/Manifest2
-rw-r--r--sci-biology/behaviopy/behaviopy-0.2.ebuild (renamed from sci-biology/behaviopy/behaviopy-0.1.ebuild)18
-rw-r--r--sci-biology/behaviopy/behaviopy-9999.ebuild46
-rw-r--r--sci-biology/blasr/blasr-5.3.5.ebuild2
-rw-r--r--sci-biology/canu/canu-2.1.1.ebuild5
-rw-r--r--sci-biology/chiron/chiron-0.6.1.1.ebuild6
-rw-r--r--sci-biology/cortex_var/Manifest2
-rw-r--r--sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild51
-rw-r--r--sci-biology/cortex_var/metadata.xml15
-rw-r--r--sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild3
-rw-r--r--sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild3
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-rw-r--r--sci-biology/gffread/Manifest4
-rw-r--r--sci-biology/gffread/gffread-0.12.7.ebuild (renamed from sci-biology/gffread/gffread-0.11.0.ebuild)10
-rw-r--r--sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild3
-rw-r--r--sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild10
-rw-r--r--sci-biology/longstitch/longstitch-1.0.1.ebuild9
-rw-r--r--sci-biology/manatee-igs/Manifest1
-rw-r--r--sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild65
-rw-r--r--sci-biology/manatee-igs/metadata.xml15
-rw-r--r--sci-biology/manatee-jcvi/Manifest1
-rw-r--r--sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild54
-rw-r--r--sci-biology/manatee-jcvi/metadata.xml15
-rw-r--r--sci-biology/mappy/Manifest2
-rw-r--r--sci-biology/mappy/mappy-2.24.ebuild (renamed from sci-biology/mappy/mappy-2.17.ebuild)6
-rw-r--r--sci-biology/mmseqs2/Manifest1
-rw-r--r--sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch40
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-rw-r--r--sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild55
-rw-r--r--sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild4
-rw-r--r--sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild4
-rw-r--r--sci-biology/mrsfast/Manifest1
-rw-r--r--sci-biology/mrsfast/metadata.xml11
-rw-r--r--sci-biology/mrsfast/mrsfast-3.4.2.ebuild28
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild5
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild5
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild5
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-rwxr-xr-xscripts/setup-and-run-repoman.sh30
430 files changed, 3634 insertions, 7101 deletions
diff --git a/.github/workflows/duplicates.yml b/.github/workflows/duplicates.yml
index 0a1f34a9d..c6cc040f0 100644
--- a/.github/workflows/duplicates.yml
+++ b/.github/workflows/duplicates.yml
@@ -5,8 +5,6 @@ on:
branches: [ master ]
pull_request:
branches: [ master ]
- schedule:
- - cron: '0 0 * * *'
jobs:
build:
diff --git a/.github/workflows/pkgcheck.yml b/.github/workflows/pkgcheck.yml
index e3abc3de6..c7440aef2 100644
--- a/.github/workflows/pkgcheck.yml
+++ b/.github/workflows/pkgcheck.yml
@@ -5,8 +5,6 @@ on:
branches: [ master ]
pull_request:
branches: [ master ]
- schedule:
- - cron: '0 0 * * *'
jobs:
build:
diff --git a/.github/workflows/repoman.yml b/.github/workflows/repoman.yml
deleted file mode 100644
index afea3ae53..000000000
--- a/.github/workflows/repoman.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-name: repoman
-
-on:
- push:
- branches: [ master ]
- pull_request:
- branches: [ master ]
- schedule:
- - cron: '0 0 * * *'
-
-jobs:
- build:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Setup master gentoo repository
- run: |
- ./scripts/setup-master-gentoo.sh
- - name: Setup and run Repoman
- run: |
- ./scripts/setup-and-run-repoman.sh
-
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f46087c06..f414ef5b5 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -36,32 +36,27 @@ Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=po
Now git will sign your commits to the overlay by using the gpg key.
-* **Install [hub](http://hub.github.com/)**, the *command-line wrapper for git that makes you better at GitHub*.
+* **Install [pkgdev](https://github.com/pkgcore/pkgdev)**, *A repository commit helper*
-*hub* can be used equivalent to to *git* and upstream even recommends *"alias git='hub'*.
+*pkgdev* sanitizes your commit in a convenient way and runs QA checks.
- emerge dev-vcs/hub
-
-* **Install [repo-commit](https://bitbucket.org/gentoo/repo-commit/)**, *A repository commit helper*
-
-*repo-commit* sanitizes your commit in a convenient way.
-
- emerge app-portage/repo-commit
+ emerge dev-util/pkgdev
---
## Contributing ebuilds
+### Fork the overlay
+In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by clicking the "Fork" button in the top right of our GitHub page.
+
### Clone the overlay
-Create a local checkout of the overlay
+Create a local checkout of your fork, where `USERNAME` is your GitHub username.
- hub clone gentoo-science/sci
+ git clone git@github.com:USERNAME/sci.git
-### Fork the overlay
-In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
+To conveniently update your fork later, add the main repository as a second remote
- cd sci
- hub fork
+ git remote add upstream git@github.com:gentoo/sci.git
### Branch out for contribution
It is always convenient for development as well as for the review and merging process, if the development is done in branches. Let's branch the overlay into a local branch named PACKAGE_NAME.
@@ -71,37 +66,38 @@ It is always convenient for development as well as for the review and merging pr
For the fastest process during merging it is best to have a single branch per package.
### Work on the package
-Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
+Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[pkgcheck](https://pkgcore.github.io/pkgcheck/man/pkgcheck.html)** to do a static analysis of your work.
This can be done with
- repoman full
+ pkgcheck scan --net
### Commit your work
Once *all* reported problems are resolved, you can commit it
- repo-commit "Here we write a comprehensible commit message"
+ pkgdev commit --all
-### Push to Github and make a pull request
+### Push to GitHub and make a pull request
In order to facilitate potential reverts of mistakes, we prefer to keep the git history as linear as possible. For this, always rebase your changes on the latest remote changes.
- hub pull --rebase=preserve github master
+ git pull --rebase=merges upstream master
+
+Next we push back the changes in the PACKAGE_NAME branch to our fork.
-Next we push back the changes in the PACKAGE_NAME branch to our fork and send a pull-request to the overlay maintainers.
+ pkgdev push YOUR_GITHUB_USER PACKAGE_NAME
- hub push YOUR_GITHUB_USER PACKAGE_NAME
- hub pull-request
+Now we are ready to create a Pull Request, go to your GitHub fork and press "Contribute" --> "Open pull request".
-Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
+Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't hesitate to ping them again. In case you need to include some improvements, just commit your work again using `pkgdev commit` and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
### What's next?
-If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
+If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ Libera. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
----
## Ebuild recommendations
As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
-* **Aim for writing EAPI=7 ebuilds.** For certain eclasses, EAPI=7 is not allowed yet. In such cases you may use EAPI=6. We will not accept EAPI<6 ebuilds.
+* **Aim for writing EAPI=8 ebuilds.** For certain eclasses, `EAPI=8` is not allowed yet. In such cases you may use `EAPI=7`. We will not accept `EAPI<=6` ebuilds.
* **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
----
@@ -109,46 +105,21 @@ As the Gentoo Science overlay is a constant work-in-progress, we have some recom
**It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**
-
-
### Prerequisite
-Make sure you have both repos (github & gentoo.org) as remotes defined.
-
- git remote -v
-
-should give
-
->github git@github.com:gentoo-science/sci.git (fetch)
->
->github git@github.com:gentoo-science/sci.git (push)
->
->origin git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
->
->origin git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
-
+Install `app-portage/pram`
### Review process
-In the beginning you should review the pull request on github directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
+In the beginning you should review the pull request on GitHub directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
#### Checking out the pull-request as local branch
Once everything is fine or you like to fix the rest yourself, simply use the following command to get the pull-request in a new branch in your repo.
- hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
-
-#### Testing and repoman check
-Now check the package by building and installing it, and run *repoman* in the package dir. Remember, when merging a pull request you take the responsibility for the quality of the commit.
-
-#### Merge the pull-request branch into master
-If this is also fine, merge the branch into the master
-
- git checkout master
- git merge USER-BRANCH
-
-#### Merging the two remote HEADs
-Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
+ pram -r gentoo/sci PULLREQUEST-NUMBER
+#### Testing and pkgcheck check
+Now check the package by building and installing it, and run *pkgcheck* in the package directory. Remember, when merging a pull request you take the responsibility for the quality of the commit.
---
#### Contribution to the document
diff --git a/README.md b/README.md
index e7618050b..3904770a0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
# The [Gentoo Science Project](https://wiki.gentoo.org/wiki/Project:Science) Repository
[![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
-[![repoman](https://github.com/gentoo/sci/workflows/repoman/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Arepoman)
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diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
index f2e2fae94..f26d506d5 100644
--- a/app-arch/libdeflate/Manifest
+++ b/app-arch/libdeflate/Manifest
@@ -1,3 +1,4 @@
+DIST libdeflate-1.11.tar.gz 162862 BLAKE2B 70ee15bdbe697083f84eef4bfce069b3bff8499a8daf53037a52fd247a47cd04867c1d93265e1b88232da52919ad15333e90d787dff05f7d8e5abe7a9613a07a SHA512 71badc0d934dde5fa79c0d8661b3a38a45d7189fba6f1c77986b2fb6baa03233b8474f0a83f004242410421c2063d2f98f02ca4f8a7a7a14cc7bcd3a9be4fbbc
DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb
DIST libdeflate-1.6.tar.gz 139031 BLAKE2B c9390408322dc71f27d86fb69e0dd47996a725a3f4ddbe1d395e07dcd1b1f2b6fde1a9decfa8d7a0bd841defff67a659b1f2efd2609db7d79626e038cb44e020 SHA512 b7225c7defb3e9b1177c434aa0de80e525de06160894282e9d3e736d6c17d2ee107e321042104a67dfa3649d982a022ee30fe30380259b8aa65ac75d1d02e334
DIST libdeflate-1.7.tar.gz 144143 BLAKE2B 6aa947a4e2489f5a3e5681d56c2272b0a694981ed2607fa4112d90a8b4565ba1066364ffcac2fe8836bacbbad0346bce5efea54b4abae55022a33ee7d983e570 SHA512 82b297af2d3128a244e561893cce1d3664de410469ba6745c3f68fc3a1962c62467c427f3857bb679578e0f704cd0eba1a64b13c30505addd310ff9af1883068
diff --git a/app-arch/libdeflate/libdeflate-1.11.ebuild b/app-arch/libdeflate/libdeflate-1.11.ebuild
new file mode 100644
index 000000000..9e7344b22
--- /dev/null
+++ b/app-arch/libdeflate/libdeflate-1.11.ebuild
@@ -0,0 +1,28 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
+HOMEPAGE="https://github.com/ebiggers/libdeflate"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
+else
+ SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="static-libs test"
+RESTRICT="!test? ( test )"
+
+src_install() {
+ emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
+ if ! use static-libs; then
+ find "${ED}" -name '*.a' -delete || die
+ fi
+ dodoc NEWS.md README.md
+}
diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild b/app-arch/libdeflate/libdeflate-1.9.ebuild
index 9f66534f1..ef7ead774 100644
--- a/app-arch/libdeflate/libdeflate-1.9.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.9.ebuild
@@ -24,5 +24,5 @@ src_install() {
if ! use static-libs; then
find "${ED}" -name '*.a' -delete || die
fi
- dodoc NEWS README.md
+ dodoc NEWS,d README.md
}
diff --git a/app-arch/libdeflate/libdeflate-9999.ebuild b/app-arch/libdeflate/libdeflate-9999.ebuild
index bfafcfecd..35aff28c3 100644
--- a/app-arch/libdeflate/libdeflate-9999.ebuild
+++ b/app-arch/libdeflate/libdeflate-9999.ebuild
@@ -1,7 +1,7 @@
# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
HOMEPAGE="https://github.com/ebiggers/libdeflate"
@@ -24,5 +24,5 @@ src_install() {
if ! use static-libs; then
find "${ED}" -name '*.a' -delete || die
fi
- dodoc NEWS README.md
+ dodoc NEWS.md README.md
}
diff --git a/app-office/visidata/Manifest b/app-office/visidata/Manifest
index 42921ce64..125ed2aa0 100644
--- a/app-office/visidata/Manifest
+++ b/app-office/visidata/Manifest
@@ -1,2 +1 @@
-DIST visidata-1.5.2.tar.gz 637598 BLAKE2B 47ef05280cec9fdb3620759b7c2089de7d2e42a4a1d1a13d14b5e59555c8de6091ceab1fb72ab4ee45dc7611741ffdc6eeefcab5e4755485b6d18d48327fe639 SHA512 36f11c207f391d06095dfab75fe4a638e562cd20bc29f72a6e5df1dcc87ab46f2834ffbdb561fb9e4e07fdd50dc5b34c619bbc4bc3d34ce350428e7330ea252c
-DIST visidata-2.1.1.tar.gz 952448 BLAKE2B c58378b9d653b50532f4f7209d08fbe4146a91907e7ca145580254784ea676b74554e9a8be69f7ae86842bf9548b16e28aa04fc8ecd42bfaee2f28e908cdddb9 SHA512 ade237622a1ac394fa2f287994c439330560062327b32a26adf129e3cae548a883ab1e76698233136aa6368b1823c4914e6912031c5b4221283d224ad2852bc7
+DIST visidata-2.8.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3
diff --git a/app-office/visidata/metadata.xml b/app-office/visidata/metadata.xml
index baa3633f0..67a30f446 100644
--- a/app-office/visidata/metadata.xml
+++ b/app-office/visidata/metadata.xml
@@ -5,10 +5,6 @@
<email>chr@chymera.eu</email>
<name>Horea Christian</name>
</maintainer>
- <maintainer type="project">
- <email>proxy-maint@gentoo.org</email>
- <name>Proxy Maintainers</name>
- </maintainer>
<longdescription lang="en">
VisiData is an interactive multitool for tabular data. It combines the
clarity of a spreadsheet, the efficiency of the terminal, and the power
diff --git a/app-office/visidata/visidata-1.5.2.ebuild b/app-office/visidata/visidata-1.5.2.ebuild
deleted file mode 100644
index f9da52b26..000000000
--- a/app-office/visidata/visidata-1.5.2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
-HOMEPAGE="http://visidata.org"
-SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]"
-DEPEND=""
-BDEPEND="
- test? (
- dev-vcs/git
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- $(python_gen_impl_dep sqlite)
- ${RDEPEND}
- )
-"
-
-python_test() {
- rm tests/golden/load-http.tsv || die "Could not remove network-dependent test."
- git init || die "Git init failed."
- git add tests/golden/ || die "Git add failed."
- dev/test.sh || die "Tests failed."
- rm .git -rf || die "Could not clean up git test directory."
-}
-
-pkg_postinst() {
- optfeature "integration with yaml" dev-python/pyyaml
- optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
- optfeature "integration with png" dev-python/pypng
- optfeature "integration with http" dev-python/requests
- optfeature "integration with postgres" dev-python/psycopg
- optfeature "integration with xlsx" dev-python/openpyxl
- optfeature "integration with xls" dev-python/xlrd
- optfeature "integration with hdf5" dev-python/h5py
- optfeature "integration with ttf/otf" dev-python/fonttools
- optfeature "integration with xml/htm/html" dev-python/lxml
- optfeature "integration with dta (Stata)" dev-python/pandas
- optfeature "integration with shapefiles" sci-libs/pyshp
- optfeature "integration with namestand" dev-python/graphviz
- #optfeature "integration with mbtiles" mapbox-vector-tile
- #optfeature "integration with xpt (SAS)" xport
- #optfeature "integration with sas7bdat (SAS)" sas7bdat
- #optfeature "integration with sav (SPSS)" savReaderWriter
-}
diff --git a/app-office/visidata/visidata-2.1.1.ebuild b/app-office/visidata/visidata-2.8.ebuild
index a214036d8..bb35b1c03 100644
--- a/app-office/visidata/visidata-2.1.1.ebuild
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 optfeature
@@ -20,6 +20,7 @@ RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]"
BDEPEND="
test? (
dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/odfpy[${PYTHON_USEDEP}]
dev-python/openpyxl[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/pytest[${PYTHON_USEDEP}]
diff --git a/dev-cpp/blitz/blitz-9999.ebuild b/dev-cpp/blitz/blitz-9999.ebuild
deleted file mode 100644
index cb92e37f0..000000000
--- a/dev-cpp/blitz/blitz-9999.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake git-r3 python-any-r1
-
-DESCRIPTION="Multi-dimensional array library for C++"
-HOMEPAGE="https://github.com/blitzpp/blitz"
-EGIT_REPO_URI="https://github.com/blitzpp/blitz"
-
-LICENSE="BSD LGPL-3+"
-SLOT="0"
-IUSE="boost doc test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="
- ${PYTHON_DEPS}
- doc? ( app-doc/doxygen[dot] )
-"
-DEPEND="
- boost? ( dev-libs/boost:=[static-libs(-)] )
-"
-
-src_configure() {
- local mycmakeargs=(
- -DBUILD_DOC=$(usex doc)
- -DBUILD_TESTING=$(usex test)
- -DENABLE_SERIALISATION=$(usex boost)
- )
- use doc && mycmakeargs+=( -DDISABLE_REFMAN_PDF=ON )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- use doc && cmake_build blitz-doc
- use test && cmake_build testsuite benchmark examples
-}
-
-src_install() {
- cmake_src_install
- if use doc ; then
- find "${D}" -type f \( -name "*.md5" -o -name "*.map" \) -delete || die
- fi
-}
diff --git a/dev-libs/asmjit/Manifest b/dev-libs/asmjit/Manifest
deleted file mode 100644
index 8733ba51c..000000000
--- a/dev-libs/asmjit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST asmjit-1.0_p22092020.tar.gz 601680 BLAKE2B dcbfc7f5385bc12d70e4c0418c89fed4453e3b08e88ccae78775d5b65d0eaada1fc12809732a77fde8b50966aacfa487e213e96754e2b7846836dcd5057a1c0b SHA512 fae457eef331edb8b9ecec23630d109500751e9ff0a7c8081c962d76c67ce68ea5813189185537f916946ce2c9c84c1574799315952f776b703019783632c4cf
diff --git a/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild b/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild
deleted file mode 100644
index 097ccfb7e..000000000
--- a/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
-HOMEPAGE="https://asmjit.com/"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/asmjit/asmjit"
-else
- COMMIT=b49d685cd9e2e4488f55ce6004306a79bdea056b
- SRC_URI="https://github.com/asmjit/asmjit/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="natvis static-libs test"
-RESTRICT="!test? ( test )"
-
-src_configure() {
- local mycmakeargs=(
- -DASMJIT_EMBED=$(usex static-libs)
- -DASMJIT_BUILD_X86=ON
- -DASMJIT_NO_NATVIS=$(usex natvis)
- -DASMJIT_TEST=$(usex test)
- )
- cmake_src_configure
-}
diff --git a/dev-libs/asmjit/asmjit-9999.ebuild b/dev-libs/asmjit/asmjit-9999.ebuild
deleted file mode 100644
index 097ccfb7e..000000000
--- a/dev-libs/asmjit/asmjit-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
-HOMEPAGE="https://asmjit.com/"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/asmjit/asmjit"
-else
- COMMIT=b49d685cd9e2e4488f55ce6004306a79bdea056b
- SRC_URI="https://github.com/asmjit/asmjit/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="natvis static-libs test"
-RESTRICT="!test? ( test )"
-
-src_configure() {
- local mycmakeargs=(
- -DASMJIT_EMBED=$(usex static-libs)
- -DASMJIT_BUILD_X86=ON
- -DASMJIT_NO_NATVIS=$(usex natvis)
- -DASMJIT_TEST=$(usex test)
- )
- cmake_src_configure
-}
diff --git a/dev-libs/asmjit/metadata.xml b/dev-libs/asmjit/metadata.xml
deleted file mode 100644
index d8cc7be33..000000000
--- a/dev-libs/asmjit/metadata.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>xarthisius@gentoo.org</email>
- <name>Kacper Kowalik</name>
- </maintainer>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- AsmJit is complete x86/x64 JIT-Assembler for C++ language. It supports
- 32/64-bit x86 processors including all usable extensions (FPU, MMX,
- 3dNow, SSE, SSE2, SSE3 and SSE4) through type-safe API that mimics Intel
- assembler syntax and eliminates nearly all common mistakes that can be
- done by developers.
-
- AsmJit contains also high-level code generation classes that can be used
- as a portable way to create JIT code that should run on all supported
- architectures. High-level classes can handle various function
- calling-conventions, register allocation and 32/64-bit mode differences.
- </longdescription>
- <use>
- <flag name="natvis">build natvis files</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
deleted file mode 100644
index f2d7c6a54..000000000
--- a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MODULE_AUTHOR=""
-inherit perl-module
-
-DESCRIPTION="EnsEMBL Perl API aka ensembl-api exposing Bio::EnsEMBL::Registry"
-HOMEPAGE="https://www.ensembl.org/index.html"
-SRC_URI="ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-
-S="${WORKDIR}"
-
-src_install(){
- perl_set_version
- find . -name t | xargs rm -rf || die
- find . -name test.pl | xargs rm -f || die
- find . -name \*.example | xargs rm -f || die
- find . -name \*.json | xargs rm -f || die
- find . -name README* | xargs rm -rf || die
- find . -name \*.conf | xargs rm -f || die
- find . -name travisci | xargs rm -rf || die
- find . -name sql | xargs rm -rf || die
- find . -name modules | while read d; do pushd "$d"; perl_domodule -r *; popd; done || die
-}
diff --git a/dev-perl/Bio-EnsEMBL/Manifest b/dev-perl/Bio-EnsEMBL/Manifest
deleted file mode 100644
index 29ccdd889..000000000
--- a/dev-perl/Bio-EnsEMBL/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ensembl-api.tar.gz 69757923 BLAKE2B 78b0f688667ffc501e14b8633416582dbf8921edfd8aea5eef98f403bdadf9b78c2ceeebcc2b8d89ebaaaef5b3f32a0c3066ee899a1ac94dafb19f70bc15d96c SHA512 bb70e70221a945902d937c2cdd811d1c39cf477ae8c1825bfb08681f2051a39d47ae91f305bfee12c3c2ced4b56b7756549c39d93bb16f8b6a23d793d0813e5f
diff --git a/dev-perl/Bio-EnsEMBL/metadata.xml b/dev-perl/Bio-EnsEMBL/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-perl/Bio-EnsEMBL/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/annexremote/Manifest b/dev-python/annexremote/Manifest
index f60f5eca8..c5eac671a 100644
--- a/dev-python/annexremote/Manifest
+++ b/dev-python/annexremote/Manifest
@@ -1,2 +1,2 @@
-DIST annexremote-1.5.0.tar.gz 65988 BLAKE2B a8ebbe8d4d3bfa7bcdfec3c43ec76788f3b4006804c715c5baf40f7e999a9a28052428ecee9ad865e8216ecf51ebbaf4728f73f622ac6b49edafbf623255419d SHA512 b0d2b3f41046f43ff49ca1d629a34e0d80c200a28bf13a3cf4f138204afa9fb7b04b6d8b9851bb201438fc6ef692d43dbaa96cf129855978fb40fdecf8818b67
-DIST annexremote-1.6.0.tar.gz 66805 BLAKE2B 6663e7ff3e223ac49a2e57ffaab20097bd91f1f8a679e15b7aa0ddd60411f99a602eaa6a7dc2e3f93b57bdff49fc70b3ddfd27f5f48ea89d97c8091fa6f7584b SHA512 657d9f53ebf1f0ad87aae758736ea3e5695e2c0f7ba111bd0810482126e4b38b292abc49fc3c2b55d6e63a42eab90aeaf64c4f287bbfbaa169070aed1356c430
+DIST annexremote-1.5.0.tar.gz 73544 BLAKE2B f5b528faf3d390f9bba6fb97768318ab04224cf05941a2606d49edda7bde30d743bf8e492f277986c0eda62f4000e1446e048d932df436cc2075b1f3e536c7d2 SHA512 7307f5ead82d449eda8b27a83f314b112bfe243a50f556397aed0f563452db6b4ba06b68aacaa27ff722ec9ccd2bdc489a3a8f4f3d849354757bd2fff8ae50d0
+DIST annexremote-1.6.0.tar.gz 74199 BLAKE2B 27956c5ea4789a1bd22bfabe6e0da8a5c8700ba50c3c28610b364d6b358f195124667381094c7786a825fae4464a340b36fd61cd09956477101c7bfd54ba8166 SHA512 1320e06fb3bebe65cce872af6adfb702d9d44cad1671ab8fd432137eb44f22cbd35744b889f11900379da2512fb79da0972c0326fcf3e51c6a404fe497e20ea4
diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild
index 94549009e..b35e3c274 100644
--- a/dev-python/annexremote/annexremote-1.5.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,20 +6,15 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-MY_PN="AnnexRemote"
-MY_P="${MY_PN}-${PV}"
-
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="https://github.com/Lykos153/AnnexRemote/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-S="${WORKDIR}/${MY_P}"
-
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
${COMMON_DEPEND}
diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild
index 94549009e..b35e3c274 100644
--- a/dev-python/annexremote/annexremote-1.6.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,20 +6,15 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-MY_PN="AnnexRemote"
-MY_P="${MY_PN}-${PV}"
-
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="https://github.com/Lykos153/AnnexRemote/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-S="${WORKDIR}/${MY_P}"
-
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
${COMMON_DEPEND}
diff --git a/dev-python/annexremote/metadata.xml b/dev-python/annexremote/metadata.xml
index 0c1ee80ae..a4bcc5d17 100644
--- a/dev-python/annexremote/metadata.xml
+++ b/dev-python/annexremote/metadata.xml
@@ -17,5 +17,6 @@
</longdescription>
<upstream>
<remote-id type="github">Lykos153/AnnexRemote</remote-id>
+ <remote-id type="pypi">annexremote</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/anys/Manifest b/dev-python/anys/Manifest
new file mode 100644
index 000000000..d5c7418ba
--- /dev/null
+++ b/dev-python/anys/Manifest
@@ -0,0 +1,2 @@
+DIST anys-0.2.0.tar.gz 17799 BLAKE2B d481c43df1a3161f75a32b6fc7a38d3e18dc996f05dd08abb3891ca9570a2a841b159547f1c6889b73d2476a141404baba4ad3e10c318bc2e230c9d136b02ff6 SHA512 72bdc9df4cd805604f5497418a90738fccbc0ffd2dddf81324fe50d0d8ab13e036ff829e284dea8473427af396f02ceb01a191ad7d6946427478a12c04ca2ffd
+DIST anys-0.2.1.tar.gz 17850 BLAKE2B c7eda2e245108f9a0a0263af45589d7b0df78767517e9b56768626e43badc5100f01a844d17b10e34a19c0a0fbfa951ba97a374cb8951e7a5560e11867b12d78 SHA512 5a46d9e8aa97401f11dcc7a26a3d8dc759c59b5485222cb6ba1df3d4b2d8d67455102943f044850d289cd3e32bcaf6413ed4a4dfbee26c049a6ef32dfa5cd87e
diff --git a/dev-python/anys/anys-0.2.0.ebuild b/dev-python/anys/anys-0.2.0.ebuild
new file mode 100644
index 000000000..0d2fec35f
--- /dev/null
+++ b/dev-python/anys/anys-0.2.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+inherit distutils-r1
+
+DESCRIPTION="Matchers for pytest"
+HOMEPAGE="https://github.com/jwodder/anys"
+SRC_URI="https://github.com/jwodder/anys/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.2.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
new file mode 100644
index 000000000..783fc75ce
--- /dev/null
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+inherit distutils-r1
+
+DESCRIPTION="Matchers for pytest"
+HOMEPAGE="https://github.com/jwodder/anys"
+SRC_URI="https://github.com/jwodder/anys/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.2.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/anys/files/anys-0.2.0-coverage.patch b/dev-python/anys/files/anys-0.2.0-coverage.patch
new file mode 100644
index 000000000..8091ded2d
--- /dev/null
+++ b/dev-python/anys/files/anys-0.2.0-coverage.patch
@@ -0,0 +1,10 @@
+--- a/tox.ini 2021-09-27 06:43:49.569561395 -0400
++++ b/tox.ini 2021-09-27 06:47:36.549815529 -0400
+@@ -30,7 +30,6 @@
+ mypy src test
+
+ [pytest]
+-addopts = --cov=anys --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
+
diff --git a/dev-python/anys/metadata.xml b/dev-python/anys/metadata.xml
new file mode 100644
index 000000000..f0a7bb068
--- /dev/null
+++ b/dev-python/anys/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">jwodder/anys</remote-id>
+ <remote-id type="pypi">anys</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/asciitree/Manifest b/dev-python/asciitree/Manifest
new file mode 100644
index 000000000..5ea004309
--- /dev/null
+++ b/dev-python/asciitree/Manifest
@@ -0,0 +1 @@
+DIST asciitree-0.3.3.tar.gz 8765 BLAKE2B 85b935d9a0df286cd14bb7828335608a2fa2b7acd83707ab61ba29ca58b452a378758ec3553d2845a2536150fd0c9c2bfeb25e95d6bdf02c3d023156e1065e8e SHA512 82ec368db5c3302640860aadeefc89ef2bc74a4336a46729d2688591454b6c1ab1f1fe9fc5305bc956c9998f27bca9e55aeee3bfb82bdf24a67955953e7e37f0
diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild
new file mode 100644
index 000000000..0ced423c8
--- /dev/null
+++ b/dev-python/asciitree/asciitree-0.3.3.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="ASCII trees in python"
+HOMEPAGE="https://github.com/mbr/asciitree"
+SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/0.3.3.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+distutils_enable_tests pytest
diff --git a/sci-biology/symap/metadata.xml b/dev-python/asciitree/metadata.xml
index ae9640ffb..f6f63a810 100644
--- a/sci-biology/symap/metadata.xml
+++ b/dev-python/asciitree/metadata.xml
@@ -1,6 +1,10 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
diff --git a/dev-python/astroscrappy/Manifest b/dev-python/astroscrappy/Manifest
index a4c5a9984..e18b6655d 100644
--- a/dev-python/astroscrappy/Manifest
+++ b/dev-python/astroscrappy/Manifest
@@ -1 +1 @@
-DIST astroscrappy-1.0.8.tar.gz 449193 BLAKE2B 0c4fda8055c5e50ff2fcc0adab17eb118b62f843cf5ca8c5d4c10bc7970efbfffd48a6c262a9bbc7bcda0c9e95237d3c3fe7121f56a7edfe26235ac351336466 SHA512 876ceb9596478930ebc9287657dcc6ff922a45daf56aa201255116247ca1a5029915292c189a5c740aed70093b050522c69186149ef721eda1669f7b5b3bd404
+DIST astroscrappy-1.1.0.tar.gz 368489 BLAKE2B d39caedd8a6b4346959c8af8546fee5fc69d41348f1743911af4c6d5755d5e8b6cdf603907d0962807d65a584422eb8c7355ada1b95c11221c735a1c94a24c5a SHA512 f6e8f7aa2eb930c5def05d33f8eb0788b15f53dda0cd583daae262e02d49b4d57e56b46562583aebf25c5e38295a62caf464b797f78deaf07962ebfca8862f8b
diff --git a/dev-python/astroscrappy/astroscrappy-1.0.8.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
index d71e7d1ac..f4ef741da 100644
--- a/dev-python/astroscrappy/astroscrappy-1.0.8.ebuild
+++ b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -24,6 +24,7 @@ RDEPEND="
>=dev-python/astropy-2.0[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
# Requires self to already be installed
#distutils_enable_sphinx docs dev-python/sphinx-astropy
diff --git a/dev-python/bokeh/Manifest b/dev-python/bokeh/Manifest
index 1a38ac66c..54357f721 100644
--- a/dev-python/bokeh/Manifest
+++ b/dev-python/bokeh/Manifest
@@ -1,9 +1,2 @@
-DIST bokeh-2.2.1.tar.gz 8845855 BLAKE2B 54846c4033a57677a197ee736266993401e00da791b0b2202e2d1683cb044d26f0ab958340f3ed2603bc78100e30b09aa7e569fff26eb235ebcb53beb7720b3a SHA512 8f58196468750f8fa24b4a8165ecb1407e61cfe207f1e0c82f0efc83d7b41f1db73ae56363e52bccc3b1f1cb9cc93f1a3ab40af0bb4b981e8b241c4c19c7b900
-DIST bokeh-2.2.2.tar.gz 8847568 BLAKE2B b279e72106ec7771fbdad6709d529e5b5e23152eae6feeae2b5cddceeba1d9db5def6c1f99cb884739536b2ecbe33060531a229f8838bcf4fa69aadf42053619 SHA512 5a53a11e3252dd904c5a436733f520251b7990bf2f112315cd5c76f0d26a6733888a36f73954c3339647981971400fc815710a3a9a753db4c9cdf10c5e2a1643
-DIST bokeh-2.2.3.tar.gz 8848373 BLAKE2B 4bae1e729980bced589c256213df22cabc08b8105113698b0e5eefd37760506a625212931dcafb8c00f1a2fce1b77a48b4802ede4a3f09c73f09b8dbe39a1a81 SHA512 7d7cf6b4207644894c8a358e235f2901f65b453f3324c1b766ddca67b287e13e82df67c193ba87123d5b3b855f7ba29c01e2113fb787dd60c39bef6ba7c95aba
-DIST bokeh-2.3.0.tar.gz 10617724 BLAKE2B ee20260b17a9d2fd13df0dab92d317b0c3a1709945e85bd0697f66d9d4363422fbb3efc29f0b402d5c8f7fab1e2f9d6903bc4da7951af88a7cf101ae85c1a535 SHA512 9e584810ffd1cc66b2c97ffbd527cb0fe4a7c63dd0cc9ddae29beae167db9c4333c2323928a91117ac226e401997dd2b2d6f8968c0618c3b40c70c6bac334c95
-DIST bokeh-2.3.1.tar.gz 10627152 BLAKE2B 30833fb83eae60bc6b92faa3128cce8a9f2bab84179d1565acf9f08b35c39540a2a6cc2a70a5f611d2a6aeede4ce6328851ac11261fab0a491976e570456c3a8 SHA512 fd9f03ae267b4cae5cc6fdae2217ef67c27bc297c00e59971bdc8ae53389a15ea80005ed7547b4761836070e53bdbc4ec2038fc0e7624788254d8bc311b765df
-DIST bokeh-2.3.2.tar.gz 10662248 BLAKE2B c289ae8d1fddd470d838d0afe8eae46d62755c8986af79784df08af4c839129f039deca85ad5dbfedcb97163a7f630063859aeaa25e0e9a7c0c65839d2b9acee SHA512 58321d318ad69a1caee130870c5e31e59bab3c99faf070a752ee9cd506400de2007f17363930fad86af5014fb42fd80b9e9bef109c5da8d8bd83edd8d3ca3aa9
-DIST conftest-bokeh-2.3.0.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
-DIST conftest-bokeh-2.3.1.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
-DIST conftest-bokeh-2.3.2.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
+DIST bokeh-2.4.2.tar.gz 17693785 BLAKE2B 295f79032ded6c63b16a1a95fe81e9850e21a5b1962786b8c99836789d4d267eb9bd51cc3b27b01c03944eb481493f61e6925d4c86a4cef67da7f18afd394de3 SHA512 d1939c095f6109d54060f6963dcbe3ff38c5132ac47d8c468b36a78f894454812838a40ae208af2f9723b02d46ae6eb3d77080ca1b19d8153eb73b89afda6864
+DIST conftest-bokeh-2.4.2.py 1788 BLAKE2B f50dd660a1a55338de345db246d493d4f6d8aad339dbe3dee48921575bfe65c0ecf018e759cca095b28b91423833506137e3d6b16a80a954f09ef953c3db495a SHA512 2b76430f09f39282e2e421c3de7f2a1a9bf2968930b729397374c61c2c6c70aa24e34e5d3a0269e8665bd8909642dc32465579e16802f583b3c17f381a7b8768
diff --git a/dev-python/bokeh/bokeh-2.2.1-r1.ebuild b/dev-python/bokeh/bokeh-2.2.1-r1.ebuild
deleted file mode 100644
index 8381bfbdd..000000000
--- a/dev-python/bokeh/bokeh-2.2.1-r1.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-# upstream hasn't tested python 3.8 fully
-PYTHON_COMPAT=( python3_{6..8} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Statistical and interactive HTML plots for Python"
-HOMEPAGE="https://bokeh.org/
- https://github.com/bokeh/bokeh
-"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
-RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
-"
-BDEPEND="
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/flaky[${PYTHON_USEDEP}]
- dev-python/ipython_genutils[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/nbconvert[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/selenium[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-PATCHES=(
- "${FILESDIR}"/${PN}-2.2.1-conftest_py.patch
-)
-
-python_test() {
- # disable tests having network calls
- local SKIP_TESTS=" \
- not (test___init__ and TestWarnings and test_filters) and \
- not (test_json__subcommands and test_no_script) and \
- not (test_standalone and Test_autoload_static) and \
- not test_nodejs_compile_javascript and \
- not test_nodejs_compile_less and \
- not test_inline_extension and \
- not (test_model and test_select) and \
- not test_tornado__server and \
- not test_client_server and \
- not test_webdriver and \
- not test_export and \
- not test_server and \
- not test_bundle and \
- not test_ext \
- "
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "integration with amazon S3" dev-python/boto
- optfeature "pypi integration to publish packages" dev-python/twine
- optfeature "js library usage" net-libs/nodejs
-}
diff --git a/dev-python/bokeh/bokeh-2.2.2-r1.ebuild b/dev-python/bokeh/bokeh-2.2.2-r1.ebuild
deleted file mode 100644
index 8381bfbdd..000000000
--- a/dev-python/bokeh/bokeh-2.2.2-r1.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-# upstream hasn't tested python 3.8 fully
-PYTHON_COMPAT=( python3_{6..8} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Statistical and interactive HTML plots for Python"
-HOMEPAGE="https://bokeh.org/
- https://github.com/bokeh/bokeh
-"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
-RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
-"
-BDEPEND="
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/flaky[${PYTHON_USEDEP}]
- dev-python/ipython_genutils[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/nbconvert[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/selenium[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-PATCHES=(
- "${FILESDIR}"/${PN}-2.2.1-conftest_py.patch
-)
-
-python_test() {
- # disable tests having network calls
- local SKIP_TESTS=" \
- not (test___init__ and TestWarnings and test_filters) and \
- not (test_json__subcommands and test_no_script) and \
- not (test_standalone and Test_autoload_static) and \
- not test_nodejs_compile_javascript and \
- not test_nodejs_compile_less and \
- not test_inline_extension and \
- not (test_model and test_select) and \
- not test_tornado__server and \
- not test_client_server and \
- not test_webdriver and \
- not test_export and \
- not test_server and \
- not test_bundle and \
- not test_ext \
- "
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "integration with amazon S3" dev-python/boto
- optfeature "pypi integration to publish packages" dev-python/twine
- optfeature "js library usage" net-libs/nodejs
-}
diff --git a/dev-python/bokeh/bokeh-2.2.3.ebuild b/dev-python/bokeh/bokeh-2.2.3.ebuild
deleted file mode 100644
index 8381bfbdd..000000000
--- a/dev-python/bokeh/bokeh-2.2.3.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-# upstream hasn't tested python 3.8 fully
-PYTHON_COMPAT=( python3_{6..8} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Statistical and interactive HTML plots for Python"
-HOMEPAGE="https://bokeh.org/
- https://github.com/bokeh/bokeh
-"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
-RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
-"
-BDEPEND="
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/flaky[${PYTHON_USEDEP}]
- dev-python/ipython_genutils[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/nbconvert[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/selenium[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-PATCHES=(
- "${FILESDIR}"/${PN}-2.2.1-conftest_py.patch
-)
-
-python_test() {
- # disable tests having network calls
- local SKIP_TESTS=" \
- not (test___init__ and TestWarnings and test_filters) and \
- not (test_json__subcommands and test_no_script) and \
- not (test_standalone and Test_autoload_static) and \
- not test_nodejs_compile_javascript and \
- not test_nodejs_compile_less and \
- not test_inline_extension and \
- not (test_model and test_select) and \
- not test_tornado__server and \
- not test_client_server and \
- not test_webdriver and \
- not test_export and \
- not test_server and \
- not test_bundle and \
- not test_ext \
- "
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "integration with amazon S3" dev-python/boto
- optfeature "pypi integration to publish packages" dev-python/twine
- optfeature "js library usage" net-libs/nodejs
-}
diff --git a/dev-python/bokeh/bokeh-2.3.0.ebuild b/dev-python/bokeh/bokeh-2.3.0.ebuild
deleted file mode 100644
index 8c00f2092..000000000
--- a/dev-python/bokeh/bokeh-2.3.0.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Statistical and interactive HTML plots for Python"
-HOMEPAGE="https://bokeh.org/"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz
- https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py
-"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
-RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
-"
-BDEPEND="
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/flaky[${PYTHON_USEDEP}]
- dev-python/ipython_genutils[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/nbconvert[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/selenium[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all(){
- cp "${DISTDIR}"/conftest-${P}.py "${S}"/conftest.py || die
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- # disable tests having network calls
- local SKIP_TESTS=" \
- not (test___init__ and TestWarnings and test_filters) and \
- not (test_json__subcommands and test_no_script) and \
- not (test_standalone and Test_autoload_static) and \
- not test_nodejs_compile_javascript and \
- not test_nodejs_compile_less and \
- not test_inline_extension and \
- not (test_model and test_select) and \
- not test_tornado__server and \
- not test_client_server and \
- not test_webdriver and \
- not test_export and \
- not test_server and \
- not test_bundle and \
- not test_ext \
- "
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "integration with amazon S3" dev-python/boto
- optfeature "pypi integration to publish packages" dev-python/twine
- optfeature "js library usage" net-libs/nodejs
-}
diff --git a/dev-python/bokeh/bokeh-2.3.2.ebuild b/dev-python/bokeh/bokeh-2.3.2.ebuild
deleted file mode 100644
index 8c00f2092..000000000
--- a/dev-python/bokeh/bokeh-2.3.2.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Statistical and interactive HTML plots for Python"
-HOMEPAGE="https://bokeh.org/"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz
- https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py
-"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
-RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
-"
-BDEPEND="
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/flaky[${PYTHON_USEDEP}]
- dev-python/ipython_genutils[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/nbconvert[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/selenium[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all(){
- cp "${DISTDIR}"/conftest-${P}.py "${S}"/conftest.py || die
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- # disable tests having network calls
- local SKIP_TESTS=" \
- not (test___init__ and TestWarnings and test_filters) and \
- not (test_json__subcommands and test_no_script) and \
- not (test_standalone and Test_autoload_static) and \
- not test_nodejs_compile_javascript and \
- not test_nodejs_compile_less and \
- not test_inline_extension and \
- not (test_model and test_select) and \
- not test_tornado__server and \
- not test_client_server and \
- not test_webdriver and \
- not test_export and \
- not test_server and \
- not test_bundle and \
- not test_ext \
- "
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "integration with amazon S3" dev-python/boto
- optfeature "pypi integration to publish packages" dev-python/twine
- optfeature "js library usage" net-libs/nodejs
-}
diff --git a/dev-python/bokeh/bokeh-2.3.1.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
index 8c00f2092..d6dfa1901 100644
--- a/dev-python/bokeh/bokeh-2.3.1.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
DISTUTILS_IN_SOURCE_BUILD=1
inherit distutils-r1 optfeature
@@ -18,20 +18,14 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-# upstream authoritative dependencies
-# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
RDEPEND="
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- >=www-servers/tornado-5[${PYTHON_USEDEP}]
+ >=dev-python/jinja-2.9[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.11.3[${PYTHON_USEDEP}]
+ >=dev-python/packaging-16.8[${PYTHON_USEDEP}]
+ >=dev-python/pillow-7.1.0[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
+ >=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}]
+ >=www-servers/tornado-5.1[${PYTHON_USEDEP}]
"
BDEPEND="
test? (
@@ -72,10 +66,10 @@ python_test() {
not test_export and \
not test_server and \
not test_bundle and \
- not test_ext \
+ not test_ext and \
+ not test_detect_current_filename \
"
- pytest -m "not sampledata" tests/unit -k \
- "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
+ epytest -m "not sampledata" tests/unit -k "${SKIP_TESTS}"
}
pkg_postinst() {
diff --git a/dev-python/bokeh/files/bokeh-2.2.1-conftest_py.patch b/dev-python/bokeh/files/bokeh-2.2.1-conftest_py.patch
deleted file mode 100644
index 5dfb43c8e..000000000
--- a/dev-python/bokeh/files/bokeh-2.2.1-conftest_py.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/conftest.py b/conftest.py
-new file mode 100644
-index 0000000..795da89
---- /dev/null
-+++ b/conftest.py
-@@ -0,0 +1,50 @@
-+#-----------------------------------------------------------------------------
-+# Copyright (c) 2012 - 2020, Anaconda, Inc., and Bokeh Contributors.
-+# All rights reserved.
-+#
-+# The full license is in the file LICENSE.txt, distributed with this software.
-+#-----------------------------------------------------------------------------
-+
-+pytest_plugins = (
-+ "bokeh._testing.plugins.ipython",
-+ "bokeh._testing.plugins.managed_server_loop",
-+ "bokeh._testing.plugins.pandas",
-+)
-+
-+# Standard library imports
-+from inspect import iscoroutinefunction
-+from typing import List
-+
-+# External imports
-+import _pytest
-+import pytest
-+
-+
-+def pytest_collection_modifyitems(items: List[_pytest.nodes.Item]) -> None:
-+ for item in items:
-+ if iscoroutinefunction(item.obj):
-+ item.add_marker(pytest.mark.asyncio)
-+
-+# Unfortunately these seem to all need to be centrally defined at the top level
-+def pytest_addoption(parser: _pytest.config.argparsing.Parser) -> None:
-+
-+ # plugins/selenium
-+ parser.addoption(
-+ "--driver", choices=('chrome', 'firefox', 'safari'), default='chrome', help='webdriver implementation')
-+
-+ # plugins/bokeh_server
-+ parser.addoption(
-+ "--bokeh-port", dest="bokeh_port", type=int, default=5006, help="port on which Bokeh server resides"
-+ )
-+
-+ # plugins/jupyter_notebook
-+ parser.addoption(
-+ "--notebook-port", type=int, default=6007, help="port on which Jupyter Notebook server resides"
-+ )
-+
-+ parser.addoption(
-+ "--examples-log-file", dest="log_file", metavar="path", action="store", default='examples.log', help="where to write the complete log"
-+ )
-+ parser.addoption(
-+ "--no-js", action="store_true", default=False,
-+ help="only run python code and skip js")
diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest
index 2fdce96f0..4818fac84 100644
--- a/dev-python/cadquery-ocp/Manifest
+++ b/dev-python/cadquery-ocp/Manifest
@@ -1 +1,2 @@
DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8
+DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
new file mode 100644
index 000000000..064952018
--- /dev/null
+++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
+inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
+
+MY_PN=OCP
+MY_PV="${PV//_/-}"
+MY_P="${MY_PN}-${MY_PV}"
+OCCT_PV=$(ver_cut 1-3)
+
+DESCRIPTION="Python wrapper for OCCT generated using pywrap"
+HOMEPAGE="https://github.com/CadQuery/OCP"
+SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file
+# generated by the src_prepare() phase. OCP currently requires opencascade
+# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also:
+# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994
+BDEPEND="
+ >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}]
+ >=dev-util/cmake-3.16
+"
+RDEPEND="
+ ${PYTHON_DEPS}
+ sci-libs/opencascade:0/7.5[json,tbb,vtk]
+ >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
+"
+DEPEND="${RDEPEND}
+ $(python_gen_cond_dep '
+ >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]')
+"
+
+S="${WORKDIR}/${MY_P}"
+
+# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare().
+CMAKE_IN_SOURCE_BUILD=True
+
+# Ensure the path returned by get_llvm_prefix() contains clang.
+llvm_check_deps() {
+ has_version -r "sys-devel/clang:${LLVM_SLOT}"
+}
+
+cadquery-ocp_check_reqs() {
+ CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE}
+}
+
+pkg_pretend() {
+ cadquery-ocp_check_reqs
+}
+
+pkg_setup() {
+ cadquery-ocp_check_reqs
+ llvm_pkg_setup
+ python-single-r1_pkg_setup
+}
+
+# OCP currently requires manual configuration, compilation, and installation
+# loosely inspired by the conda-specific "build-bindings-job.yml" file.
+#
+# Note that the cmake_src_prepare() function called below handles user patches.
+src_prepare() {
+ # Most recently installed version of Clang.
+ local _CLANG_VERSION="$(CPP=clang clang-fullversion)"
+
+ # Most recently installed version (excluding trailing patch) of VTK.
+ local _VTK_VERSION="$(best_version -r sci-libs/vtk)"
+ _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")"
+
+ # Absolute dirname of the most recently installed Clang include directory,
+ # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also:
+ # https://bugs.gentoo.org/619490
+ local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include"
+
+ # Absolute filename of the most recently installed Clang shared library.
+ local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so"
+
+ # Absolute dirname of OCCT's include and shared library directories.
+ local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade"
+ local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade"
+
+ # Absolute dirname of a temporary directory to store symbol tables for this
+ # OCCT version dumped below by the "dump_symbols.py" script.
+ local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols"
+ local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux"
+
+ # Absolute dirname of VTK's include directory,
+ local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}"
+
+ # Ensure the above paths exist as a crude sanity test.
+ test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found."
+ test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found."
+ test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found."
+ test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found."
+ test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found."
+
+ # "dev-python/clang-python" atom targeting this Clang version.
+ local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}"
+
+ # Ensure "dev-python/clang-python" targets this Clang version.
+ has_version -r "=${_CLANG_PYTHON_ATOM}" ||
+ die "${_CLANG_PYTHON_ATOM} not installed."
+
+ # Remove all vendored paths.
+ rm -r conda opencascade pywrap *.dat || die
+
+ # Inject a symlink to OCCT's include directory.
+ ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die
+
+ # Inject a symlink from OCCT's shared library directory into this temporary
+ # directory as required by the "dump_symbols.py" script.
+ mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die
+ ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die
+
+ # Update all hardcoded OCCT shared library versions in "dump_symbols.py".
+ sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \
+ dump_symbols.py || die
+
+ # Dump (i.e., generate) symbol tables for this OCCT version.
+ einfo 'Dumping OCCT symbol tables...'
+ ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die
+
+ # Generate OCCT bindings in the "OCP/" subdirectory.
+ einfo 'Building OCP CMake binary tree...'
+ ${EPYTHON} -m bindgen \
+ --verbose \
+ --njobs $(makeopts_jobs) \
+ --libclang "${_CLANG_LIB_FILE}" \
+ --include "${_CLANG_INCLUDE_DIR}" \
+ --include "${_VTK_INCLUDE_DIR}" \
+ all ocp.toml || die
+
+ # Remove the source "FindOpenCascade.cmake" after generating bindings,
+ # which copied that file to the target "OCP/FindOpenCascade.cmake".
+ rm FindOpenCascade.cmake || die
+
+ #FIXME: Submit an issue recommending upstream replace their
+ #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level
+ #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl
+ # find_package(vtk 9 CONFIG REQUIRED)
+ # if(TARGET VTK::VTK)
+ # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES)
+ # endif()
+
+ # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with
+ # standard OCCT paths derived above. That file is both fundamentally
+ # broken and useless, as the ${CASROOT} environment variable and
+ # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file
+ # already reliably identify all requisite OpenCASCADE paths. Failure to
+ # patch this file results in src_configure() failures resembling:
+ # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES)
+ sed -i \
+ -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \
+ -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \
+ -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \
+ OCP/FindOpenCascade.cmake || die
+
+ # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed
+ # as an absolute path both here and below to minimize eclass issues.
+ CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -B "${S}/OCP.build"
+ -DPYTHON_EXECUTABLE="${PYTHON}"
+ -Wno-dev
+ )
+
+ CMAKE_USE_DIR="${S}/OCP" cmake_src_configure
+}
+
+src_compile() {
+ CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile
+}
+
+# OCP currently ships no test suite, so we synthesize a crude import unit test.
+src_test() {
+ PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \
+ 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ'
+}
+
+src_install() {
+ python_moduleinto .
+ python_domodule "${S}/OCP.build/"OCP*.so
+}
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
index a203693d6..e5aef7ccf 100644
--- a/dev-python/cadquery-pywrap/Manifest
+++ b/dev-python/cadquery-pywrap/Manifest
@@ -1 +1,2 @@
DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872
+DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
new file mode 100644
index 000000000..b2213cef7
--- /dev/null
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit llvm distutils-r1
+
+DESCRIPTION="C++ binding generator based on libclang and pybind11"
+HOMEPAGE="https://github.com/CadQuery/pywrap"
+
+#FIXME: Uncomment on bumping to the next stable release.
+# MY_PN=occt
+# MY_PV=$(ver_cut 1-2)
+# MY_P="${MY_PN}${MY_PV}"
+# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz"
+
+# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.3 has yet to be
+# officially released. We instead package a commit known to work as expected.
+MY_COMMIT="66e7376d3a27444393fc99acbdbef40bbc7031ae"
+SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+# Dependencies are intentionally listed in "setup.py" order.
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/logzero[${PYTHON_USEDEP}]
+ dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/clang-python[${PYTHON_USEDEP}]
+ dev-python/cymbal[${PYTHON_USEDEP}]
+ dev-python/toml[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/toposort[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/schema[${PYTHON_USEDEP}]
+ sci-libs/vtk
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/pywrap-${MY_COMMIT}"
+
+src_prepare() {
+ #FIXME: Submit an upstream issue. This violates PEP 440 standards.
+ # Sanitize the "bindgen" version to avoid Gentoo QA notices.
+ sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die
+
+ # Replace conda- with Gentoo-specific prefix dirnames.
+ sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py ||
+ die
+
+ # Reduce all hardcoded header includes to noops.
+ sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die
+
+ distutils-r1_src_prepare
+}
diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest
index ae1e31fa3..380c3e6ae 100644
--- a/dev-python/cadquery/Manifest
+++ b/dev-python/cadquery/Manifest
@@ -1 +1,2 @@
DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3
+DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
new file mode 100644
index 000000000..26aa07b6d
--- /dev/null
+++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_SINGLE_IMPL=1
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python parametric CAD scripting framework based on OCCT"
+HOMEPAGE="https://cadquery.readthedocs.io"
+
+# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but
+# CadQuery 2.2 has yet to be officially released. We instead package a commit
+# known to work as expected with OCCT 7.5.2.
+MY_COMMIT="803a05e78c233fdb537a8604c3f2b56a52179bbe"
+
+#FIXME: Uncomment on bumping to the next stable release.
+# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz"
+SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its
+# Anaconda focus, "setup.py" currently fails to list dependencies.
+BDEPEND="
+ test? (
+ $(python_gen_cond_dep '
+ dev-python/docutils[${PYTHON_USEDEP}]
+ dev-python/path-py[${PYTHON_USEDEP}]
+ ')
+ )
+"
+RDEPEND="
+ >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}]
+ dev-python/ezdxf[${PYTHON_USEDEP}]
+ dev-python/ipython[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/nptyping[${PYTHON_USEDEP}]
+ sci-libs/nlopt[python,${PYTHON_USEDEP}]
+ dev-python/multimethod[${PYTHON_USEDEP}]
+ dev-python/typish[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}-${MY_COMMIT}"
+
+distutils_enable_tests pytest
+
+#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints".
+# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints
diff --git a/dev-python/ccdproc/Manifest b/dev-python/ccdproc/Manifest
index 8220136aa..e952c66af 100644
--- a/dev-python/ccdproc/Manifest
+++ b/dev-python/ccdproc/Manifest
@@ -1 +1 @@
-DIST ccdproc-2.1.0.tar.gz 604227 BLAKE2B 0c570722b7efc15969c0887341721faa320ff6967a6f6bd218e56ec6f17ee13bc987c0d22a3d681ba51d85f0e51b532c7287fb77a6ad4ba799c3ca9d7f9ef5b7 SHA512 25fea4e3f750c70d4d952bf99c3846a0e7ec0ac22adf6fd9a3dfced5399ab3a40846396367abf397835a2f243b6a25e73baa9ef11861bb0374ccaaa5e4190ff6
+DIST ccdproc-2.3.0.tar.gz 617350 BLAKE2B 750c9690fecd8f02ce0ca46681ac5959aa6a3810f20204b4698418767df63186a3b47f454fa17357c7fb57f6e6e8e06eab456633c05dcb17502773a023d327cc SHA512 bf68d7c98bb3208f3fab44e85a4dc21e64070b12d1b4e78275e1674e99c99d6a9ae1ff6a1bfeba8fd9cb91ec37ddac8ca8ae8c75e6e8ad15b8ddb713f01e4ff6
diff --git a/dev-python/ccdproc/ccdproc-2.1.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
index be1c00c5f..015dd2910 100644
--- a/dev-python/ccdproc/ccdproc-2.1.0.ebuild
+++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -27,12 +27,12 @@ RESTRICT="test"
BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]"
RDEPEND="
- >=dev-python/astropy-2.0[${PYTHON_USEDEP}]
- dev-python/astroscrappy[${PYTHON_USEDEP}]
- dev-python/reproject[${PYTHON_USEDEP}]
+ >=dev-python/astropy-4.0.6[${PYTHON_USEDEP}]
+ >=dev-python/astroscrappy-1.0.8[${PYTHON_USEDEP}]
+ >=dev-python/reproject-0.7[${PYTHON_USEDEP}]
sci-libs/scikit-image[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
-distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib dev-python/pytest-doctestplus
distutils_enable_tests pytest
diff --git a/dev-python/click-didyoumean/Manifest b/dev-python/click-didyoumean/Manifest
new file mode 100644
index 000000000..5c8198fe3
--- /dev/null
+++ b/dev-python/click-didyoumean/Manifest
@@ -0,0 +1,2 @@
+DIST click-didyoumean-0.2.0.tar.gz 309305 BLAKE2B 498571996758c57e015dd2f5de8966ace78defb2b1f9faa5a99c6020fb143bafa03e240f183f46a962dc9a3d39e1e9a7a49855f6f6e2dfd5452c546f015b17ce SHA512 690438809d103d2f2b54fc1dabb912b359f5355ba242bb37ef420cd8fcc3ed226911d7216acdcb3574bb0e93231c3a3ca7b00e9e99365955387cfeddeed449ae
+DIST click-didyoumean-0.3.0.tar.gz 309301 BLAKE2B 2b667b5e94dd690e5b7a2e96b83197f52e201b002a32fff4a8dbb4bd5497d5b816b40d9da98729821e1d17a795a3776c1553a746aa4c4144cf7fe6540768e1ca SHA512 4927ee392f27950c3f7ef5e0f1d5a5e2421172f3e9d34ec76986c9c7ea698cfa1981678a06fb8682577d6ed04c242c42bdd1d796d7623a1c99dfdbdb61c80fca
diff --git a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
new file mode 100644
index 000000000..b9a65c5d8
--- /dev/null
+++ b/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( pypy3 python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Enable git-like did-you-mean feature in click"
+HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
+SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+# Tests actually pass, but not included in archive:
+# https://github.com/click-contrib/click-didyoumean/issues/11
+DEPEND="
+ dev-python/click
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild
new file mode 100644
index 000000000..9fe4373c8
--- /dev/null
+++ b/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+PYTHON_COMPAT=( pypy3 python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Enable git-like did-you-mean feature in click"
+HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
+SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+DEPEND="
+ dev-python/click
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/click-didyoumean/metadata.xml b/dev-python/click-didyoumean/metadata.xml
new file mode 100644
index 000000000..d206a1b1c
--- /dev/null
+++ b/dev-python/click-didyoumean/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">click-contrib/click-didyoumean</remote-id>
+ <remote-id type="pypi">click-didyoumean</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
new file mode 100644
index 000000000..cb098f9b4
--- /dev/null
+++ b/dev-python/dandi-schema/Manifest
@@ -0,0 +1,4 @@
+DIST dandi-schema-0.4.3.tar.gz 51831 BLAKE2B 177a0ec148c1e823abdaa2b7e60d971c17a7f49bc72b69b16989e32ed014cf6df6378530be7fa142ca49662134a169b21903e9c49d9849ee944dfa9462fe6c3a SHA512 3d6c8f8cf86c933a04017f34a3832d642cf4ee27fd3edf6cf57ceab2e0ad6a1b82c245e4e27283913db941f86877996256604d345c1ee798acca2981ee046b5e
+DIST dandi-schema-0.5.1.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804
+DIST dandi-schema-0.5.3.tar.gz 56222 BLAKE2B 3b23c93330f621a5a050c9e5b597fd8b9046a66465c16f26b5216d443547a0c8d07a491213cde90c411f5cda6f6c6b2a23d1c0f4b2d7a1e7336c55e5768d3338 SHA512 bf0d434ac6d8e5584ba9f31dd179e5402c13c89257bc87c2d34b03483e9ab85d9b616391a40c64ad853e6774f950ecc58d3f3fde29305586d5faa387dc5b3e80
+DIST dandi-schema-0.6.0.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd
diff --git a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild
new file mode 100644
index 000000000..cf3c8a34f
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+DEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+ "${FILESDIR}/${PN}-0.3.4-versioningit.patch"
+)
+
+src_configure() {
+ echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
new file mode 100644
index 000000000..19a906634
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+)
+
+src_configure() {
+ echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild
new file mode 100644
index 000000000..19a906634
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+)
+
+src_configure() {
+ echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
new file mode 100644
index 000000000..19a906634
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+)
+
+src_configure() {
+ echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch
new file mode 100644
index 000000000..a9c7b6c2b
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch
@@ -0,0 +1,11 @@
+--- a/tox.ini 2021-09-22 19:31:20.534576095 -0400
++++ b/tox.ini 2021-09-26 16:11:30.080164191 -0400
+@@ -17,7 +17,7 @@
+ flake8 --config=setup.cfg {posargs} dandischema setup.py
+
+ [pytest]
+-addopts = --cov=dandischema --tb=short --durations=10
++addopts = --tb=short --durations=10
+ filterwarnings = error
+
+ [coverage:run]
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
new file mode 100644
index 000000000..589091756
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
@@ -0,0 +1,10 @@
+--- a/setup.py 2021-09-22 19:31:20.533576086 -0400
++++ b/setup.py 2021-09-23 07:42:02.856983656 -0400
+@@ -21,7 +21,7 @@
+
+ # Give setuptools a hint to complain if it's too old a version
+ # Should match pyproject.toml
+-SETUP_REQUIRES = ["setuptools >= 42.0.0", "versioningit ~= 0.1.0"]
++SETUP_REQUIRES = ["setuptools >= 42.0.0"]
+ # This enables setuptools to install wheel on-the-fly
+ SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
diff --git a/dev-python/dandi-schema/metadata.xml b/dev-python/dandi-schema/metadata.xml
new file mode 100644
index 000000000..91cb893fc
--- /dev/null
+++ b/dev-python/dandi-schema/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ A Python library for maintaining and managing DANDI metadata schemata.
+ The library helps create and validate DANDI schema-compliant metadata
+ for Dandisets and assets. Every Dandiset and associated asset has a
+ metadata object that can be retrieved using the DANDI API. This
+ library uses Pydantic to implement all the metadata classes. Schemas
+ are generated on schema modifications and placed into this repository.
+ Dandischema generates JSON schema definitions and also an associated
+ context.json file for JSON-LD compliance of the metadata models.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">dandi/dandi-schema</remote-id>
+ <remote-id type="pypi">dandischema</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest
index 6f48f8721..2140ef1a5 100644
--- a/dev-python/fiona/Manifest
+++ b/dev-python/fiona/Manifest
@@ -1 +1,2 @@
-DIST fiona-1.8.20.tar.gz 269491 BLAKE2B 0778a0824e3ecd70fc7a153a4be4631c04e70dc6218c3c78e7ddffae01db22a081f8f8b7f44cce37f864e32277b88596263d6ac640293c93e6a14ec7a932aa04 SHA512 4864f3c48903b34c6b4d2cf5dcdc5ebb6e155e32e7e138bdf17756a823f36a0985162c211127b283235569235c830e11abd330c229b2bb8de6cee053fe3204d7
+DIST fiona-1.8.21.tar.gz 270166 BLAKE2B 752957f3cc3ed6a35713536e90cdbc542d73de9718e878a449f71c9b9a2150b4ead90ff5d9ce254a6adcfcf7deb61b4483e7cf5bfee12997e581fd0a3ffc767e SHA512 c77cedae67fb7e2b6b6a84aeef39ce5424ccb38b13774f7c2e9bd5934836a6abe6759eeea1d4a8cfc83c5111442f2028d18dd79af209e11618789de2149e7885
+
diff --git a/dev-python/fiona/fiona-1.8.20.ebuild b/dev-python/fiona/fiona-1.8.21.ebuild
index 1127afa70..51ded0d37 100644
--- a/dev-python/fiona/fiona-1.8.20.ebuild
+++ b/dev-python/fiona/fiona-1.8.21.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ sci-libs/gdal[geos,sqlite]
dev-python/attrs[${PYTHON_USEDEP}]
dev-python/click-plugins[${PYTHON_USEDEP}]
dev-python/cligj[${PYTHON_USEDEP}]
@@ -24,11 +24,12 @@ RDEPEND="
dev-python/six[${PYTHON_USEDEP}]
dev-python/certifi[${PYTHON_USEDEP}]
"
+
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
test? (
dev-python/boto3[${PYTHON_USEDEP}]
- sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ sci-libs/gdal[geos,sqlite]
)
"
@@ -56,6 +57,9 @@ python_test() {
tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK]
tests/test_drvsupport.py::test_write_or_driver_error[DGN]
+ # failure in flatgeobuf impl
+ tests/test_drvsupport.py::test_no_append_driver_cannot_append[FlatGeobuf]
+
# geos
#tests/test_collection.py::test_mask_polygon_triangle
#tests/test_collection.py::test_mask_polygon_triangle
diff --git a/dev-python/fscacher/Manifest b/dev-python/fscacher/Manifest
new file mode 100644
index 000000000..67c5c736e
--- /dev/null
+++ b/dev-python/fscacher/Manifest
@@ -0,0 +1,2 @@
+DIST fscacher-0.1.4.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c
+DIST fscacher-0.2.0.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e
diff --git a/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch b/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch
new file mode 100644
index 000000000..ce87d33b3
--- /dev/null
+++ b/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch
@@ -0,0 +1,9 @@
+--- a/tox.ini 2021-09-27 01:00:33.935464308 -0400
++++ b/tox.ini 2021-09-27 02:48:34.349729243 -0400
+@@ -27,7 +27,6 @@
+ asv run {posargs}
+
+ [pytest]
+-addopts = --cov=fscacher --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
diff --git a/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch b/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch
new file mode 100644
index 000000000..c5c7f85e2
--- /dev/null
+++ b/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch
@@ -0,0 +1,10 @@
+--- a/tox.ini 2021-09-27 01:00:33.935464308 -0400
++++ b/tox.ini 2021-09-27 02:48:34.349729243 -0400
+@@ -31,7 +31,6 @@
+ asv run --strict {posargs} HEAD^1..HEAD
+
+ [pytest]
+-addopts = --cov=fscacher --no-cov-on-fail
+ filterwarnings =
+ error
+ ignore:The distutils package is deprecated:DeprecationWarning:joblib
diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild
new file mode 100644
index 000000000..3f55c8604
--- /dev/null
+++ b/dev-python/fscacher/fscacher-0.1.4.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Cache results of operations on heavy file trees"
+HOMEPAGE="https://github.com/con/fscacher"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.1.4-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild
new file mode 100644
index 000000000..bb632800e
--- /dev/null
+++ b/dev-python/fscacher/fscacher-0.2.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Cache results of operations on heavy file trees"
+HOMEPAGE="https://github.com/con/fscacher"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.2.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/fscacher/metadata.xml b/dev-python/fscacher/metadata.xml
new file mode 100644
index 000000000..460ce9d09
--- /dev/null
+++ b/dev-python/fscacher/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ fscacher provides a cache and decorator for memoizing functions whose
+ outputs depend upon the contents of a file argument. If you have a
+ function `foo()` that takes a file path as its first argument, and if
+ the behavior of `foo()` is pure in the contents of the path and the
+ values of its other arguments, fscacher can help cache that function,
+ </longdescription>
+ <upstream>
+ <remote-id type="github">con/fscacher</remote-id>
+ <remote-id type="pypi">fscacher</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest
index 895961b9b..196e885ac 100644
--- a/dev-python/fslpy/Manifest
+++ b/dev-python/fslpy/Manifest
@@ -1,3 +1 @@
-DIST fslpy-2.8.4.tar.gz 4655735 BLAKE2B 3ab673b724c375e2cdc0caf797e1d528381fdfc0cef1e09f8d5348f34502c6da0d311e51172cb7f0402219110d72ab8aa3cfbb3cb108aa894171f4b6d6f4e7e3 SHA512 43acb95fdfc23e1810d372c945a9080e784106f2c1f65c096962681f3e0f6d4b3b7c3b59bb8b4c196cf9df6093ff01e4cce3a50e16e8a64f1f97739ded84c6e5
-DIST fslpy-3.4.0.tar.gz 4691622 BLAKE2B 95cb246aafe7210fcaf5dd11336ad1ba9afca27c50fec23a56bbcd5658d6a0f28ef15e71816f1a0d77949d6232f15325b85331a16b50578d8cdeb7f4da94a326 SHA512 4e860e70fc3681c6c7e1869e9b9f8ed7d63fbf9496dd302493670e2aac730cc5ef72e246264b4b8f448a85b0dd78282778fd4516d2751fd1d9b7be0d11db89e9
DIST fslpy-3.8.1.tar.gz 4698603 BLAKE2B 33740081a065b6684b864eaf50910a38e26ce7aa10d18bf8faaeaf34ee87dfa22e8f2ee3cebc5681f2356cfb519a59ba07232a3cfb81526258ef92f3ced893ea SHA512 1b5d945f6aae6557e892e5700f228170bab8a235c77d06b162fc2afc16663f3bdbe18e54e4e20dad46ac873ccbf0cdc2649e5ac1c53e17b0d78c45e91e8a1896
diff --git a/dev-python/fslpy/files/fslpy-3-remove_dataclasses_req.patch b/dev-python/fslpy/files/fslpy-3-remove_dataclasses_req.patch
deleted file mode 100644
index eb2a0480d..000000000
--- a/dev-python/fslpy/files/fslpy-3-remove_dataclasses_req.patch
+++ /dev/null
@@ -1,8 +0,0 @@
-diff -Naur fslpy-3.4.0.orig/requirements.txt fslpy-3.4.0/requirements.txt
---- fslpy-3.4.0.orig/requirements.txt 2021-02-18 21:38:49.826829560 -0500
-+++ fslpy-3.4.0/requirements.txt 2021-02-18 21:38:55.475829863 -0500
-@@ -3,4 +3,3 @@
- numpy>=1
- scipy>=0.18
- six>=1
--dataclasses
diff --git a/dev-python/fslpy/fslpy-2.8.4.ebuild b/dev-python/fslpy/fslpy-2.8.4.ebuild
deleted file mode 100644
index ed427ded2..000000000
--- a/dev-python/fslpy/fslpy-2.8.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="The FSL Python Library"
-HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
-SRC_URI="https://github.com/pauldmccarthy/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
- test? (
- dev-python/pytest[${PYTHON_USEDEP}]
- )
- dev-python/setuptools[${PYTHON_USEDEP}]
-"
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/indexed_gzip[${PYTHON_USEDEP}]
- =dev-python/numpy-1*[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- =dev-python/six-1*[${PYTHON_USEDEP}]
- dev-python/trimesh[${PYTHON_USEDEP}]
- =dev-python/wxpython-4*[${PYTHON_USEDEP}]
- sci-libs/rtree[${PYTHON_USEDEP}]
- >=sci-libs/nibabel-2.3.1[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-
-PATCHES=( "${FILESDIR}/fslpy-2.7.0-coverage.patch" )
-
-python_test() {
- virtx pytest --niters=50 -m "not (dicomtest or longtest or fsltest)" --verbose || die
-}
diff --git a/dev-python/fslpy/fslpy-3.4.0.ebuild b/dev-python/fslpy/fslpy-3.4.0.ebuild
deleted file mode 100644
index 59e17f0cf..000000000
--- a/dev-python/fslpy/fslpy-3.4.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="The FSL Python Library"
-HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
-SRC_URI="https://github.com/pauldmccarthy/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/indexed_gzip[${PYTHON_USEDEP}]
- =dev-python/numpy-1*[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- =dev-python/six-1*[${PYTHON_USEDEP}]
- dev-python/trimesh[${PYTHON_USEDEP}]
- =dev-python/wxpython-4*[${PYTHON_USEDEP}]
- sci-libs/rtree[${PYTHON_USEDEP}]
- >=sci-libs/nibabel-2.3.1[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- !<sci-biology/fsl-6.0.4
-"
-
-DEPEND="
- !<sci-biology/fsl-6.0.4
-"
-
-PATCHES=(
- "${FILESDIR}/fslpy-2.7.0-coverage.patch"
- "${FILESDIR}/fslpy-3-remove_dataclasses_req.patch"
-)
-
-distutils_enable_tests pytest
-
-python_test() {
- virtx pytest --niters=50 -m "not (dicomtest or longtest or fsltest)" --verbose || die
-}
diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.10.2.ebuild
index 6dde1c23f..e63aaa1bc 100644
--- a/dev-python/geopandas/geopandas-0.10.2.ebuild
+++ b/dev-python/geopandas/geopandas-0.10.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/pandas[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
dev-python/fiona[${PYTHON_USEDEP}]
dev-python/pyproj[${PYTHON_USEDEP}]"
diff --git a/dev-python/gmsh_interop/Manifest b/dev-python/gmsh_interop/Manifest
index fd0494716..2780b9e2e 100644
--- a/dev-python/gmsh_interop/Manifest
+++ b/dev-python/gmsh_interop/Manifest
@@ -1 +1 @@
-DIST gmsh_interop-2019.1.tar.gz 12009 BLAKE2B 5e5becd169d9fc729d5f25a2fdd39ebe27ef8ec5ab959745a946955f9cb636b12cb5525e4b1e30224e28b20c16c352d6e22af44aef20ab3754b8f3d0c43cd242 SHA512 4602ec6e889b692daf919630dc5ae1af3100cf535e187df4d548256895466054dd79689a949d1ed24dea535f71fda8faec9fb9c7095e94b3118baf06df23b951
+DIST gmsh_interop-2021.1.1.tar.gz 24654 BLAKE2B c2959a6b2b7950d4f1bbc4961e3c77c5f28b7ccc53d74410fe851782b471feea14235828f5882bdc57ad8f93719e6e9591cbe0d336670d0f79c77ddfb6486a28 SHA512 b60694dad4bd6e79bc8417812f1df9568599b9f0adfab5f5d2e56b9d1667ff3fd9893b6dc0d1a22ba1aefc7fa214c45aa97464f78af1713dd85eab0a6102ea5c
diff --git a/dev-python/gmsh_interop/gmsh_interop-2019.1.ebuild b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
index 3a3069255..785646336 100644
--- a/dev-python/gmsh_interop/gmsh_interop-2019.1.ebuild
+++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{6..8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,14 +16,12 @@ SLOT="0"
KEYWORDS="~amd64"
RDEPEND="${PYTHON_DEPS}
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.6.0[${PYTHON_USEDEP}]
dev-python/pytools[${PYTHON_USEDEP}]
sci-libs/gmsh[blas]
"
BDEPEND="
test? (
- dev-python/hopcroftkarp[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
)
"
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
deleted file mode 100644
index 989332bb5..000000000
--- a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/setup.py 2021-09-24 00:51:55.892741725 -0400
-+++ b/setup.py 2021-10-27 14:33:20.733741241 -0400
-@@ -23,7 +23,7 @@
- 'scipy>=1.1,<2',
- 'pandas>=1.0.5,<2',
- 'ruamel.yaml>=0.16,<1',
-- 'jsonschema>=2.6.0,<4',
-+ 'jsonschema>=2.6.0',
- 'setuptools',
- ]
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
new file mode 100644
index 000000000..58822989d
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
@@ -0,0 +1,21 @@
+--- a/setup.py 2022-01-31 02:48:24.645837186 -0500
++++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
+@@ -12,12 +12,12 @@
+ schema_dir = 'common/hdmf-common-schema/common'
+
+ reqs = [
+- 'h5py>=2.10,<4',
+- 'numpy>=1.16,<1.22',
+- 'scipy>=1.1,<2',
+- 'pandas>=1.0.5,<2',
+- 'ruamel.yaml>=0.16,<1',
+- 'jsonschema>=2.6.0,<4',
++ 'h5py',
++ 'numpy',
++ 'scipy',
++ 'pandas',
++ 'ruamel.yaml',
++ 'jsonschema',
+ 'setuptools',
+ ]
+
diff --git a/dev-python/hdmf/hdmf-3.1.1.ebuild b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index 1731b0d90..76d40c95f 100644
--- a/dev-python/hdmf/hdmf-3.1.1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -28,5 +28,5 @@ BDEPEND=""
distutils_enable_tests pytest
PATCHES=(
- "${FILESDIR}/${PN}-3.1.1-new_jsonschema.patch"
+ "${FILESDIR}/${PN}-3.1.1-versions.patch"
)
diff --git a/dev-python/interleave/Manifest b/dev-python/interleave/Manifest
new file mode 100644
index 000000000..6040d8f7d
--- /dev/null
+++ b/dev-python/interleave/Manifest
@@ -0,0 +1 @@
+DIST interleave-0.2.0.tar.gz 15879 BLAKE2B 72056882821415b68f404e757098b8cb89968feef717fec61bae7a92d97d90a68a2e2aff490c5acc07d55410c28c6310b6882d122f0be64eaada4348ddf6c588 SHA512 ed47603fb0b917e7355c9e461584b5c92ba4beef2416e602da0c8b70f36d9d5d5bc57fa3a71bb00e96e35bd580873dca10cdd19280ace7b717765a8386576a0f
diff --git a/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch b/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch
new file mode 100644
index 000000000..5f358f6aa
--- /dev/null
+++ b/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch
@@ -0,0 +1,18 @@
+--- a/tox.ini
++++ b/tox.ini
+@@ -8,8 +8,6 @@
+ passenv = CI
+ deps =
+ pytest~=7.0
+- pytest-cov~=3.0
+- pytest-rerunfailures~=10.0
+ commands =
+ pytest {posargs} test
+
+@@ -31,7 +29,6 @@
+ mypy src test
+
+ [pytest]
+-addopts = --cov=interleave --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild
new file mode 100644
index 000000000..c8a9c9ca1
--- /dev/null
+++ b/dev-python/interleave/interleave-0.2.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10})
+
+inherit distutils-r1
+
+DESCRIPTION="Yield from multiple iterators as values become available"
+HOMEPAGE="https://github.com/jwodder/interleave"
+SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${PN}-0.2.0-drop-coverage.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/interleave/metadata.xml b/dev-python/interleave/metadata.xml
new file mode 100644
index 000000000..66b4383b6
--- /dev/null
+++ b/dev-python/interleave/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The interleave package provides a function of the same name that
+ takes a number of iterators, runs them in separate threads, and
+ yields the values produced as soon as each one is available.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">jwodder/interleave</remote-id>
+ <remote-id type="pypi">interleave</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch b/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch
new file mode 100644
index 000000000..e0ca3a012
--- /dev/null
+++ b/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch
@@ -0,0 +1,90 @@
+diff --git a/keyrings/alt/file.py b/keyrings/alt/file.py
+index 37c837f..866e8d0 100644
+--- a/keyrings/alt/file.py
++++ b/keyrings/alt/file.py
+@@ -44,8 +44,12 @@ class Encrypted:
+ """
+ Create the cipher object to encrypt or decrypt a payload.
+ """
+- from Cryptodome.Protocol.KDF import PBKDF2
+- from Cryptodome.Cipher import AES
++ try:
++ from Cryptodome.Protocol.KDF import PBKDF2
++ from Cryptodome.Cipher import AES
++ except ImportError:
++ from Crypto.Protocol.KDF import PBKDF2
++ from Crypto.Cipher import AES
+
+ pw = PBKDF2(password, salt, dkLen=self.block_size)
+ return AES.new(pw[: self.block_size], AES.MODE_CFB, IV)
+@@ -79,7 +83,12 @@ class EncryptedKeyring(Encrypted, Keyring):
+ __import__('Cryptodome.Protocol.KDF')
+ __import__('Cryptodome.Random')
+ except ImportError: # pragma: no cover
+- raise RuntimeError("pycryptodomex required")
++ try:
++ __import__('Crypto.Cipher.AES')
++ __import__('Crypto.Protocol.KDF')
++ __import__('Crypto.Random')
++ except ImportError:
++ raise RuntimeError("pycryptodomex or pycryptodome required")
+ if not json: # pragma: no cover
+ raise RuntimeError("JSON implementation such as simplejson required.")
+ return 0.6
+@@ -190,10 +199,16 @@ class EncryptedKeyring(Encrypted, Keyring):
+
+ def encrypt(self, password, assoc=None):
+ # encrypt password, ignore associated data
+- from Cryptodome.Random import get_random_bytes
++ try:
++ from Cryptodome.Random import get_random_bytes
++ except ImportError:
++ from Crypto.Random import get_random_bytes
+
+ salt = get_random_bytes(self.block_size)
+- from Cryptodome.Cipher import AES
++ try:
++ from Cryptodome.Cipher import AES
++ except ImportError:
++ from Crypto.Cipher import AES
+
+ IV = get_random_bytes(AES.block_size)
+ cipher = self._create_cipher(self.keyring_key, salt, IV)
+diff --git a/tests/test_crypto.py b/tests/test_crypto.py
+index cfc782a..7396023 100644
+--- a/tests/test_crypto.py
++++ b/tests/test_crypto.py
+@@ -14,7 +14,12 @@ def is_crypto_supported():
+ __import__('Cryptodome.Protocol.KDF')
+ __import__('Cryptodome.Random')
+ except ImportError:
+- return False
++ try:
++ __import__('Crypto.Cipher.AES')
++ __import__('Crypto.Protocol.KDF')
++ __import__('Crypto.Random')
++ except ImportError:
++ return False
+ return True
+
+
+diff --git a/tests/test_file.py b/tests/test_file.py
+index 62192da..3f813f0 100644
+--- a/tests/test_file.py
++++ b/tests/test_file.py
+@@ -157,7 +157,14 @@ class FileKeyringTests(BackendBasicTests):
+ class TestEncryptedFileKeyring(FileKeyringTests):
+ @pytest.fixture(autouse=True)
+ def crypt_fixture(self, monkeypatch):
+- pytest.importorskip('Cryptodome')
++ try:
++ import Cryptodome
++ except ImportError:
++ try:
++ import Crypto
++ except ImportError:
++ pytest.skip("Neither pycryptodome nor pycryptodomex are available",
++ allow_module_level=True)
+ fake_getpass = mock.Mock(return_value='abcdef')
+ monkeypatch.setattr(getpass, 'getpass', fake_getpass)
+
diff --git a/dev-python/keyrings_alt/keyrings_alt-4.1.0.ebuild b/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
index 247679bb6..290c2f434 100644
--- a/dev-python/keyrings_alt/keyrings_alt-4.1.0.ebuild
+++ b/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( pypy3 python3_{8..10} )
+
inherit distutils-r1
MY_PN="keyrings.alt"
@@ -21,5 +23,9 @@ DEPEND=""
S="${WORKDIR}/${MY_P}"
+# Patch sumbitted upstream:
+# https://github.com/jaraco/keyrings.alt/pull/46
+PATCHES=( "${FILESDIR}/${P}-pycryptodome.patch" )
+
distutils_enable_tests pytest
distutils_enable_sphinx docs
diff --git a/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch
new file mode 100644
index 000000000..ed104ab99
--- /dev/null
+++ b/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch
@@ -0,0 +1,91 @@
+From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
+From: Richard Barnes <rbarnes@umn.edu>
+Date: Wed, 1 Dec 2021 10:29:08 -0700
+Subject: [PATCH] Enable LLVM-12 and LLVM-13
+
+---
+ ffi/build.py | 5 ++---
+ ffi/targets.cpp | 2 ++
+ llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
+ 3 files changed, 20 insertions(+), 6 deletions(-)
+
+diff --git a/ffi/build.py b/ffi/build.py
+index 6408bf5f..95e33c64 100755
+--- a/ffi/build.py
++++ b/ffi/build.py
+@@ -162,9 +162,8 @@ def main_posix(kind, library_ext):
+ print(msg)
+ print(warning + '\n')
+ else:
+-
+- if not out.startswith('11'):
+- msg = ("Building llvmlite requires LLVM 11.x.x, got "
++ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')):
++ msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
+ "{!r}. Be sure to set LLVM_CONFIG to the right executable "
+ "path.\nRead the documentation at "
+ "http://llvmlite.pydata.org/ for more information about "
+diff --git a/ffi/targets.cpp b/ffi/targets.cpp
+index 1ce472c2..4ba33e79 100644
+--- a/ffi/targets.cpp
++++ b/ffi/targets.cpp
+@@ -233,6 +233,8 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T,
+ rm = Reloc::DynamicNoPIC;
+
+ TargetOptions opt;
++#if LLVM_VERSION_MAJOR < 12
+ opt.PrintMachineCode = PrintMC;
++#endif
+
+ bool jit = JIT;
+diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py
+index 80495787..fee2372a 100644
+--- a/llvmlite/tests/test_binding.py
++++ b/llvmlite/tests/test_binding.py
+@@ -18,6 +18,16 @@
+ from llvmlite.tests import TestCase
+
+
++def clean_string_whitespace(x: str) -> str:
++ # Remove trailing whitespace from the end of each line
++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
++ # Remove intermediate blank lines
++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
++ # Remove extraneous whitespace from the beginning and end of the string
++ x = x.strip()
++ return x
++
++
+ # arvm7l needs extra ABI symbols to link successfully
+ if platform.machine() == 'armv7l':
+ llvm.load_library_permanently('libgcc_s.so.1')
+@@ -158,7 +168,7 @@ def no_de_locale():
+ target triple = "unknown-unknown-unknown"
+ target datalayout = ""
+
+-define i32 @"foo"()
++define i32 @"foo"()
+ {
+ "<>!*''#":
+ ret i32 12345
+@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self):
+ bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
+ bd.ret(ir.Constant(ir.IntType(32), 12345))
+ asm = str(mod)
+- self.assertEqual(asm, asm_nonalphanum_blocklabel)
++ self.assertEqual(
++ clean_string_whitespace(asm),
++ clean_string_whitespace(asm_nonalphanum_blocklabel)
++ )
+
+ def test_global_context(self):
+ gcontext1 = llvm.context.get_global_context()
+@@ -509,7 +522,7 @@ def test_set_option(self):
+ def test_version(self):
+ major, minor, patch = llvm.llvm_version_info
+ # one of these can be valid
+- valid = [(11,)]
++ valid = [(11,), (12,), (13,)]
+ self.assertIn((major,), valid)
+ self.assertIn(patch, range(10))
+
diff --git a/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch
new file mode 100644
index 000000000..6630652c2
--- /dev/null
+++ b/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch
@@ -0,0 +1,92 @@
+From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
+From: Richard Barnes <rbarnes@umn.edu>
+Date: Wed, 1 Dec 2021 10:29:08 -0700
+Subject: [PATCH] Enable LLVM-12 and LLVM-13
+
+---
+ ffi/build.py | 5 ++---
+ ffi/targets.cpp | 2 ++
+ llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
+ 3 files changed, 20 insertions(+), 6 deletions(-)
+
+diff --git a/ffi/build.py b/ffi/build.py
+index 6408bf5f..95e33c64 100755
+--- a/ffi/build.py
++++ b/ffi/build.py
+@@ -162,9 +162,8 @@ def main_posix(kind, library_ext):
+ print(msg)
+ print(warning + '\n')
+ else:
+-
+- if not out.startswith('11'):
+- msg = ("Building llvmlite requires LLVM 11.x.x, got "
++ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')):
++ msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
+ "{!r}. Be sure to set LLVM_CONFIG to the right executable "
+ "path.\nRead the documentation at "
+ "http://llvmlite.pydata.org/ for more information about "
+diff --git a/ffi/targets.cpp b/ffi/targets.cpp
+index 1ce472c2..4ba33e79 100644
+--- a/ffi/targets.cpp
++++ b/ffi/targets.cpp
+@@ -233,7 +233,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T,
+ rm = Reloc::DynamicNoPIC;
+
+ TargetOptions opt;
++#if LLVM_VERSION_MAJOR < 12
+ opt.PrintMachineCode = PrintMC;
++#endif
+ opt.MCOptions.ABIName = ABIName;
+
+ bool jit = JIT;
+diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py
+index 80495787..fee2372a 100644
+--- a/llvmlite/tests/test_binding.py
++++ b/llvmlite/tests/test_binding.py
+@@ -18,6 +18,16 @@
+ from llvmlite.tests import TestCase
+
+
++def clean_string_whitespace(x: str) -> str:
++ # Remove trailing whitespace from the end of each line
++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
++ # Remove intermediate blank lines
++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
++ # Remove extraneous whitespace from the beginning and end of the string
++ x = x.strip()
++ return x
++
++
+ # arvm7l needs extra ABI symbols to link successfully
+ if platform.machine() == 'armv7l':
+ llvm.load_library_permanently('libgcc_s.so.1')
+@@ -158,7 +168,7 @@ def no_de_locale():
+ target triple = "unknown-unknown-unknown"
+ target datalayout = ""
+
+-define i32 @"foo"()
++define i32 @"foo"()
+ {
+ "<>!*''#":
+ ret i32 12345
+@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self):
+ bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
+ bd.ret(ir.Constant(ir.IntType(32), 12345))
+ asm = str(mod)
+- self.assertEqual(asm, asm_nonalphanum_blocklabel)
++ self.assertEqual(
++ clean_string_whitespace(asm),
++ clean_string_whitespace(asm_nonalphanum_blocklabel)
++ )
+
+ def test_global_context(self):
+ gcontext1 = llvm.context.get_global_context()
+@@ -509,7 +522,7 @@ def test_set_option(self):
+ def test_version(self):
+ major, minor, patch = llvm.llvm_version_info
+ # one of these can be valid
+- valid = [(11,)]
++ valid = [(11,), (12,), (13,)]
+ self.assertIn((major,), valid)
+ self.assertIn(patch, range(10))
+
diff --git a/dev-python/llvmlite/llvmlite-0.38.0.ebuild b/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild
index cadbc5407..607c1bb0b 100644
--- a/dev-python/llvmlite/llvmlite-0.38.0.ebuild
+++ b/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="examples"
-LLVM_MAX_SLOT=11
+LLVM_MAX_SLOT=12
RDEPEND="
sys-devel/llvm:${LLVM_MAX_SLOT}
@@ -24,6 +24,8 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
+PATCHES=( "${FILESDIR}/${P}-llvm12.patch" )
+
src_prepare() {
sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
distutils-r1_src_prepare
diff --git a/dev-python/llvmlite/llvmlite-0.37.0.ebuild b/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild
index d76175444..607c1bb0b 100644
--- a/dev-python/llvmlite/llvmlite-0.37.0.ebuild
+++ b/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="examples"
-LLVM_MAX_SLOT=11
+LLVM_MAX_SLOT=12
RDEPEND="
sys-devel/llvm:${LLVM_MAX_SLOT}
@@ -24,6 +24,8 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
+PATCHES=( "${FILESDIR}/${P}-llvm12.patch" )
+
src_prepare() {
sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
distutils-r1_src_prepare
diff --git a/dev-python/meshio/Manifest b/dev-python/meshio/Manifest
deleted file mode 100644
index 191a8e4aa..000000000
--- a/dev-python/meshio/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST meshio-4.4.6.tar.gz 482071 BLAKE2B f8d410ad7293b5e7f9debbb1e4dc9050304731bee1091b4480aeace006a92bb8f7cec2fc442d0f5b20d492ae859bb76cbb52b6be26f06be2558bc42a27d9cd96 SHA512 624f551b017b6c4e44efc5db0fb6d08a161ceef64d1317264eaf3ba0f36202b93c3fa959ab34ce8212c01083ae570b3db25c7445eee2d51feaf84726984e2770
diff --git a/dev-python/meshio/meshio-4.4.6.ebuild b/dev-python/meshio/meshio-4.4.6.ebuild
deleted file mode 100644
index ec5af300f..000000000
--- a/dev-python/meshio/meshio-4.4.6.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
-
-inherit distutils-r1
-
-DESCRIPTION="Python input/output for many mesh formats"
-HOMEPAGE="https://pypi.org/project/meshio"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-BDEPEND="
- test? (
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/netcdf4-python[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/meshpy/Manifest b/dev-python/meshpy/Manifest
index 82dd9c18b..b39e4ba75 100644
--- a/dev-python/meshpy/Manifest
+++ b/dev-python/meshpy/Manifest
@@ -1,2 +1 @@
-DIST meshpy-2018.2.1.tar.gz 493048 BLAKE2B 78a84bdf8af6228f991a8f724131dfe4f32cff156cb3c148894d4b2c07bfa30d192fc2830f5161cdc555c45aeff4a1189862a6e627bb1bfb4170b5f819b4538a SHA512 779a6fe6694eb381a32cb7304091402a11c019dbde75391c36aa9e76c57ee8b76f2215856c2998e58a7cee2b77626661f8b6518f54e5e6f2112f79acb3151d9d
-DIST meshpy-2018.2.1_p1.tar.gz 494699 BLAKE2B 2f8ca25e193437d5e4fd01c5ebbd6c1a6cb38103754455bec91d120484b89451bc9d34157a369ffcfb248ab4d993e1e0b015f20b80a558f97934f9302152aedf SHA512 9f830a32d8c7c32f34eb0dbdf7341bf49d03451957ea8b319639f6afc15fdfe43a8852a1049878fd1827822016aefca05794a588d6d3fd26c9471d52783e8f81
+DIST meshpy-2020.1.tar.gz 482475 BLAKE2B fe59de6fae837db584c38ee0f8ad7d9e242624df360fa0c0eb2778f1d2ea6233e6f92f113014dfc73f570dbb47c65582775ec3c615cd887b5aefdb7030794b90 SHA512 d328a546f14db44a40e885554cf3bfff1e522a1ce38b312acaf6ac7ddc6fd909299fb78793229482ec51ccb2484baee13c2c09406be937a073555cc120f6f2df
diff --git a/dev-python/meshpy/meshpy-2018.2.1_p1.ebuild b/dev-python/meshpy/meshpy-2018.2.1_p1.ebuild
deleted file mode 100644
index 6985305a0..000000000
--- a/dev-python/meshpy/meshpy-2018.2.1_p1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-MY_PN="MeshPy"
-
-DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python"
-HOMEPAGE="https://mathema.tician.de/software/meshpy
- https://pypi.python.org/pypi/MeshPy
-"
-
-COMMIT=6f4f9418f5f02b414d561bd8de710c4f1349ea72
-SRC_URI="https://github.com/inducer/meshpy/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${PN}-${COMMIT}
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-RDEPEND="
- dev-libs/boost[python,${PYTHON_USEDEP}]
- dev-python/gmsh_interop[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pybind11[${PYTHON_USEDEP}]
- dev-python/pytools[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- sci-libs/gmsh
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
- sed 's:delay=10:delay=1:g' -i aksetup_helper.py || die
-
-# echo "BOOST_PYTHON_LIBNAME = ['boost_${EPYTHON}-mt']">> "${S}"/siteconf.py
-
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- distutils_install_for_testing
- pytest -vv || die "tests failed with ${EPYTHON}"
-}
diff --git a/dev-python/meshpy/meshpy-2018.2.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild
index 5df9336ad..191589690 100644
--- a/dev-python/meshpy/meshpy-2018.2.1.ebuild
+++ b/dev-python/meshpy/meshpy-2020.1.ebuild
@@ -1,24 +1,27 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{6..8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
+MY_PN="MeshPy"
+
DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python"
HOMEPAGE="https://mathema.tician.de/software/meshpy
https://pypi.python.org/pypi/MeshPy
"
-
SRC_URI="https://github.com/inducer/meshpy/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="test"
+
+# ModuleNotFoundError: No module named 'meshpy._internals'
+RESTRICT="test"
RDEPEND="
dev-libs/boost[python,${PYTHON_USEDEP}]
@@ -26,22 +29,13 @@ RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
dev-python/pytools[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
sci-libs/gmsh
"
DEPEND="${RDEPEND}"
-distutils_enable_tests pytest
+distutils_enable_tests --install pytest
python_prepare_all() {
sed 's:delay=10:delay=1:g' -i aksetup_helper.py || die
-
-# echo "BOOST_PYTHON_LIBNAME = ['boost_${EPYTHON}-mt']">> "${S}"/siteconf.py
-
distutils-r1_python_prepare_all
}
-
-python_test() {
- distutils_install_for_testing
- pytest -vv || die "tests failed with ${EPYTHON}"
-}
diff --git a/dev-python/multimethod/Manifest b/dev-python/multimethod/Manifest
new file mode 100644
index 000000000..2b7c7d4a6
--- /dev/null
+++ b/dev-python/multimethod/Manifest
@@ -0,0 +1 @@
+DIST multimethod-1.8.gh.tar.gz 15364 BLAKE2B e16a42a9d35387b4a972e0b88299af215df20dd5025ad5a2fa4314410f667ba4cea401c0d050dfa3e45612117774c4a6627f6b84c33bc55ed0e4c4ec42f5fec3 SHA512 433a2c72a6c98129df70aa09d1e640f2f23be6c42236cb88ad4ef9dee89406a9b6a2c01771b2b7e69ffa8d6b6cae05a8e0cd273d77c2eed86c5b8ee0c6887c8c
diff --git a/dev-python/meshio/metadata.xml b/dev-python/multimethod/metadata.xml
index 1bfb9f30f..cd5b00a2b 100644
--- a/dev-python/meshio/metadata.xml
+++ b/dev-python/multimethod/metadata.xml
@@ -7,7 +7,6 @@
</maintainer>
<stabilize-allarches/>
<upstream>
- <remote-id type="pypi">meshio</remote-id>
- <remote-id type="github">nschloe/meshio</remote-id>
+ <remote-id type="github">coady/multimethod</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild
new file mode 100644
index 000000000..4d3c7837c
--- /dev/null
+++ b/dev-python/multimethod/multimethod-1.8.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library allowing Python function overloads based on argument types"
+HOMEPAGE="https://github.com/coady/multimethod"
+
+SRC_URI="https://github.com/coady/multimethod/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests pytest
diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest
deleted file mode 100644
index 585f387a9..000000000
--- a/dev-python/nptyping/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nptyping-1.4.3.tar.gz 47943 BLAKE2B 0e4acfc1bd9cc3cae98c6aebab3c4c1aa47a7547adaacb3835a4cb0150cc11a628ce84e30e3d811ca93a33f0b97f0ebd320b8bd0be2bd2e8651154526a69cdf6 SHA512 1cfec2215965902b9df2b4b440a37fc6241734b6befb76feac509c688073f1dda67f5832673aab3f9d718ce0aebc916b6b3b5218bb74f21118a19722b630a7fe
diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml
deleted file mode 100644
index 7b2aa8131..000000000
--- a/dev-python/nptyping/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="pypi">nptyping</remote-id>
- <remote-id type="github">ramonhagenaars/nptyping</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/nptyping/nptyping-1.4.3.ebuild b/dev-python/nptyping/nptyping-1.4.3.ebuild
deleted file mode 100644
index b2d6ad271..000000000
--- a/dev-python/nptyping/nptyping-1.4.3.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit distutils-r1
-
-DESCRIPTION="Type hints for NumPy"
-HOMEPAGE="https://pypi.org/project/nptyping"
-
-# Prefer GitHub. Upstream failed to push its source tarball to PyPI.
-SRC_URI="https://github.com/ramonhagenaars/nptyping/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- >=dev-python/typish-1.7.0[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}"
-
-#FIXME: Enabling tests requires packaging additional packages (e.g., "xenon").
-RESTRICT="test"
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index 05834c652..a4d39c09c 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1,2 +1,2 @@
DIST numba-0.54.0.tar.gz 2263302 BLAKE2B 24747fcf23f686460fdd8df4784a3bccd6c41f07ff7e657f797a2959066254c079b05ec4460a7cbafef9482f463aa000ee28f8f09339cd7568a0c85b52bc4437 SHA512 ad1142e8c772660b7cbbd17566b9dc96784057467b5cc546f88e2215c9428905e1f6da05ffe104f4ad526f5131fedfa9057745d5458c3293a8cd8e01a49d0fad
-DIST numba-0.55.0.tar.gz 2335694 BLAKE2B 38b0b6f1aa0a903db4a3a8185d5e0b81a5eb87be8db3e5f176e3e2dcd0b1777a473826742d975de2ff7cb5acbd7c3fd3c2e8a5a9d1199cb335b95bc5b913b085 SHA512 cbf758c2b928537968dc70e2f6a97ff14ced0954b7b61a091ace921866adaa1ed17a31cc7d27aa43f071b32c473508e13eb56f1cb6473aeaa00c04f5e7484f86
+DIST numba-0.55.0.tar.gz 2335687 BLAKE2B 439206cb94149226f54eb988bcc9cefb815f734b0bfa01888f7ba16525ae2cbab39ee929a655086a47a3c3bc540e8589bdbf119cc084e876d9b61da1017bdfe9 SHA512 3651d1d06c5f325459ab73c07f501c12b3081d97d0f92d0120c8cfb312092658bbebc91f8340786f7b10cd43a95e278085cbba6d199cb3d0b5f71987ee7e5776
diff --git a/dev-python/numba/numba-0.55.0.ebuild b/dev-python/numba/numba-0.55.0.ebuild
index c700339ad..342c3894f 100644
--- a/dev-python/numba/numba-0.55.0.ebuild
+++ b/dev-python/numba/numba-0.55.0.ebuild
@@ -23,7 +23,7 @@ RDEPEND="
<=dev-python/llvmlite-0.39.0
>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
<dev-python/numpy-1.22[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2019.5 )
+ threads? ( >=dev-cpp/tbb-2021.1 )
"
BDEPEND="
dev-python/pip[${PYTHON_USEDEP}]
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
new file mode 100644
index 000000000..761068546
--- /dev/null
+++ b/dev-python/numcodecs/Manifest
@@ -0,0 +1,2 @@
+DIST numcodecs-0.9.0.tar.gz 4514267 BLAKE2B d7042ff0296a8246f063f55f31d790fcfbd59de07c08ff0d57e1bd4c7094c6f375ef55714866061f449dcca87d39abd36c56218d23aca0fd6bcfae491fb10097 SHA512 1525e5a7f7a7427752d3ccfbbb82b7afbfc90fcbc2c9e886e31d286c64478d85747de7e6bf16a8e980af96cf952d1202a15affa02cf6a22b4aac3725a0c8a65f
+DIST numcodecs-0.9.1.tar.gz 4514374 BLAKE2B b418ee0fd27cb5f7bf8def3b124f31af7c0e2e2610dca55351c105933f7471e2465f24fa24e53ee607abcf26d690ba2b368e77618c703a4dbc8a926be48c9c1d SHA512 639cc5a5656e026f85e893009831f98420e3818f73bab95f0afd0a5bd64c901082826921e40c1b6e1f75cad82b3be2cf36787fa74ba7f0fd011dac070b24e0f8
diff --git a/dev-python/numcodecs/metadata.xml b/dev-python/numcodecs/metadata.xml
new file mode 100644
index 000000000..ab018028a
--- /dev/null
+++ b/dev-python/numcodecs/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">zarr-developers/numcodecs</remote-id>
+ <remote-id type="pypi">numcodecs</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/numcodecs/numcodecs-0.9.0.ebuild b/dev-python/numcodecs/numcodecs-0.9.0.ebuild
new file mode 100644
index 000000000..7219b5b7b
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.9.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Fails to collect tests for yet unknown reasons:
+# https://github.com/zarr-developers/numcodecs/issues/304
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/cython[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/numcodecs/numcodecs-0.9.1.ebuild b/dev-python/numcodecs/numcodecs-0.9.1.ebuild
new file mode 100644
index 000000000..7219b5b7b
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.9.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Fails to collect tests for yet unknown reasons:
+# https://github.com/zarr-developers/numcodecs/issues/304
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/cython[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
new file mode 100644
index 000000000..f5e2c79b7
--- /dev/null
+++ b/dev-python/nwbinspector/Manifest
@@ -0,0 +1 @@
+DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e
diff --git a/dev-python/nwbinspector/metadata.xml b/dev-python/nwbinspector/metadata.xml
new file mode 100644
index 000000000..ccdbc7f6d
--- /dev/null
+++ b/dev-python/nwbinspector/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">NeurodataWithoutBorders/nwbinspector</remote-id>
+ <remote-id type="pypi">nwbinspector</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
new file mode 100644
index 000000000..1e0352b88
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
@@ -0,0 +1,28 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
diff --git a/dev-python/pynndescent/Manifest b/dev-python/pynndescent/Manifest
index d3d33643f..a92be64b7 100644
--- a/dev-python/pynndescent/Manifest
+++ b/dev-python/pynndescent/Manifest
@@ -1 +1 @@
-DIST pynndescent-0.5.2.tar.gz 1148182 BLAKE2B 64cff5fe0d92b2d735564b7e3a1dc62c64bcaec33d8d5bfaffbcf61423ff1cef388dd2335479dff5af7f50848dbe8d9640a22add54b2b90a979cb13d0894b371 SHA512 b38bbf8aab91d4278572a6446e4750022e2b2bc82e7a8f7754b8ec74c0ae1f7795364ef4e22cd6bd39071056ebacaedeb79981620e3143d3c9060a1520c85aae
+DIST pynndescent-0.5.6.tar.gz 1135907 BLAKE2B 53f09045b14b3026ff1a2fa1ed27a4ce75f23e9c25ca0469c5ce207a51a25c778a7c2d3af51c3a724e1c0cd4eb148b3a8e73b6d39e819fc9c4cb0549240623be SHA512 9556754d4edbdfe442abf6b95b1970b8c606616a0012fc7a6875e1dfbe9a98b21b317eee84836c2b521dffb0db4e19ba6c8f1f9009498d43153ffda0f0a3b820
diff --git a/dev-python/pynndescent/pynndescent-0.5.2.ebuild b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
index 3eeb7ae79..1e9eb00e4 100644
--- a/dev-python/pynndescent/pynndescent-0.5.2.ebuild
+++ b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -15,9 +15,10 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-RDEPEND="${PYTHON_DEPS}
+RDEPEND="
dev-python/joblib[${PYTHON_USEDEP}]
>=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
>=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
>=dev-python/scipy-1.0[${PYTHON_USEDEP}]
>=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}]
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
new file mode 100644
index 000000000..16b7c7287
--- /dev/null
+++ b/dev-python/pynwb/Manifest
@@ -0,0 +1,2 @@
+DIST pynwb-2.0.0.post0.dev5.tar.gz 450799 BLAKE2B 02aef74992dda44139e776eebf3d29924caa46bfc2a12da400ceaadff5856295b6205c6ad230483935e713eed9dd868b9109c2d51d7c69291dc93db806ef4761 SHA512 840a33cd0a2de5c491e785530e4dab589945015b9a60384ed127a27fbfe4c527b1b10d74a9ffe2a795a29c3bba65aafd007975973a2da68fca73bf71260b7b8b
+DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a
diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
new file mode 100644
index 000000000..d09c50594
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
@@ -0,0 +1,21 @@
+diff --git a/setup.py b/tmp/setup.py
+index 39e75824..f7948f64 100755
+--- a/setup.py
++++ b/setup.py
+@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
+ schema_dir = 'nwb-schema/core'
+
+ reqs = [
+- 'h5py>=2.9,<4',
+- 'hdmf>=3.1.1,<4',
+- 'numpy>=1.16,<1.22',
+- 'pandas>=1.0.5,<2',
+- 'python-dateutil>=2.7,<3',
++ 'h5py',
++ 'hdmf',
++ 'numpy',
++ 'pandas',
++ 'python-dateutil',
+ 'setuptools'
+ ]
+
diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
new file mode 100644
index 000000000..99512b574
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ PyNWB is a Python package for working with NWB files. It provides a
+ high-level API for efficiently working with Neurodata stored in the NWB
+ format. Neurodata Without Borders: Neurophysiology (NWB:N) is a project
+ to develop a unified data format for cellular-based neurophysiology
+ data, focused on the dynamics of groups of neurons measured under a
+ large range of experimental conditions.
+ </longdescription>
+</pkgmetadata>
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild
new file mode 100644
index 000000000..d9afd62e7
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3(-)]
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${P}-versions.patch"
+ )
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/dandi/dandischema/issues/87
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+ # Reported upstream and fixed in newer version:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1412#issuecomment-934153799
+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_dandi_read
+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_read
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
new file mode 100644
index 000000000..25672015c
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+MY_PV="${PV/_p/.post}.dev5"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/latest/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3(-)]
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.0.0-versions.patch"
+ )
+
+S="${WORKDIR}/${MY_P}"
+
+EPYTEST_DESELECT=(
+ # Reported upsream
+ # https://github.com/dandi/dandischema/issues/87
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pyout/Manifest b/dev-python/pyout/Manifest
new file mode 100644
index 000000000..551424495
--- /dev/null
+++ b/dev-python/pyout/Manifest
@@ -0,0 +1,2 @@
+DIST pyout-0.7.1.tar.gz 180439 BLAKE2B b64808edfa013c8460961afacbe70caad4f3c0520d8b87656e909e278534bf111154fd31a186f95246d3084671c841ea421ed52118ddeee3f08f21106f2f80b1 SHA512 66338ce6dbf1e4ee6a187993609f762fcd2f8dddd981bc976b3240b6ecd461ba1fd47b9f08b91fc29853ce88e26158c7047de0adfcf28a0dd66869adfad5ab71
+DIST pyout-0.7.2.tar.gz 181753 BLAKE2B 780e536921151f81097e5dee7c74cfa086153f916fc9b9fd684f01008ada34102ba33ee7bdd3dd8cc4ccf89a8d9821ec0aecdbd87bc356abf25c6e4fe32d4c5a SHA512 e7be6f7829f6b09ead64c596cfdecfa45073af0a1da15401702327e141bbfae10e7968ee5e332358aa04bfc7ddf71b7b6caf2d5877aca8514e4ba544d3b1670a
diff --git a/dev-python/pyout/metadata.xml b/dev-python/pyout/metadata.xml
new file mode 100644
index 000000000..712a48169
--- /dev/null
+++ b/dev-python/pyout/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ pyout is a Python package that defines an interface for writing
+ structured records as a table in a terminal. It is being developed to
+ replace custom code for displaying tabular data in in ReproMan and
+ DataLad. See the Examples folder for how to get started. A primary
+ goal of the interface is the separation of content from style and
+ presentation.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">pyout/pyout</remote-id>
+ <remote-id type="pypi">pyout</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyout/pyout-0.7.1.ebuild b/dev-python/pyout/pyout-0.7.1.ebuild
new file mode 100644
index 000000000..6cf80ec85
--- /dev/null
+++ b/dev-python/pyout/pyout-0.7.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Terminal styling for structured data"
+HOMEPAGE="https://github.com/pyout/pyout"
+SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/blessings[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ dev-python/pytest-timeout[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ sed -i -e '/pytest-runner/d' setup.py || die
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/pyout/pyout-0.7.2.ebuild b/dev-python/pyout/pyout-0.7.2.ebuild
new file mode 100644
index 000000000..6cf80ec85
--- /dev/null
+++ b/dev-python/pyout/pyout-0.7.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Terminal styling for structured data"
+HOMEPAGE="https://github.com/pyout/pyout"
+SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/blessings[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ dev-python/pytest-timeout[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ sed -i -e '/pytest-runner/d' setup.py || die
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/pyparsing/Manifest b/dev-python/pyparsing/Manifest
new file mode 100644
index 000000000..736d09882
--- /dev/null
+++ b/dev-python/pyparsing/Manifest
@@ -0,0 +1 @@
+DIST pyparsing_2.4.7.tar.gz 648158 BLAKE2B 24525b4ee7876e245b9eb270f0e3e22fe2d8b398f9777ad3b3657b8a1227dcbd25983aa64a3f3018debdbffc1a042c732e6b3a09800e081c7acac7b97da15317 SHA512 c7a546729f86a2b5176e2482b566b9fd715b03e495aaef4d720b21307bb03f385dbc849247f8d266cb3d92be0a83c34ce4995b655ce85318355d5a0d42d6991e
diff --git a/dev-python/pyparsing/metadata.xml b/dev-python/pyparsing/metadata.xml
new file mode 100644
index 000000000..2692e21d7
--- /dev/null
+++ b/dev-python/pyparsing/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The pyparsing module is an alternative approach to creating and
+ executing simple grammars, vs. the traditional lex/yacc approach, or the
+ use of regular expressions. The pyparsing module provides a library of
+ classes that client code uses to construct the grammar directly in
+ Python code.
+ </longdescription>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="sourceforge">pyparsing</remote-id>
+ <remote-id type="pypi">pyparsing</remote-id>
+ <remote-id type="github">pyparsing/pyparsing</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild b/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild
new file mode 100644
index 000000000..55da214a2
--- /dev/null
+++ b/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2004-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# please keep this ebuild at EAPI 7 -- sys-apps/portage dep
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
+inherit distutils-r1
+
+MY_P=${P/-/_}
+DESCRIPTION="Easy-to-use Python module for text parsing"
+HOMEPAGE="https://github.com/pyparsing/pyparsing https://pypi.org/project/pyparsing/"
+SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz"
+S=${WORKDIR}/${PN}-${MY_P}
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~x64-cygwin ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
+IUSE="examples"
+
+distutils_enable_tests setup.py
+
+python_install_all() {
+ if use examples; then
+ docompress -x /usr/share/doc/${PF}/examples
+ dodoc -r examples
+ fi
+ distutils-r1_python_install_all
+}
diff --git a/dev-python/python-gantt/Manifest b/dev-python/python-gantt/Manifest
index fe170a0a7..607c0bbc8 100644
--- a/dev-python/python-gantt/Manifest
+++ b/dev-python/python-gantt/Manifest
@@ -1,2 +1 @@
-DIST python-gantt-0.6.0.tar.gz 53522 BLAKE2B e66b6ae0609372e66e8858c4f3c356d774fea879b5a1bee9f2c62fec4c8f3bc99fa79a5066df469d24448c8b2f0bf9f9493b6099f71db75e3fbc87b351af8a1d SHA512 916595bc572bac3b8c2e593d18d4087446b0de7a08902788c1c5c97496518e75c6c4e82434709bf80753da04f307bde7b543e7f0a4b4d5cdaf66f31da2772f9f
DIST python-gantt-0.6.0_p20200809.tar.gz 32423 BLAKE2B e1e34276707d757e5c8386a75318863550dc7cabc1fa9cee161043ec757633819ac2efbd237b20d8497ce2b037aa72f44396dbcbd4c206f264eef4601985323a SHA512 62811ab5ac8aa26bdfa2ec10b621e1aeae84612e628be6555eb71548694dce4d474cc8d0bd56d5db8a40ffee4ac161c8aa11b7a250f8260df6a8175b3672e50b
diff --git a/dev-python/python-gantt/python-gantt-0.6.0.ebuild b/dev-python/python-gantt/python-gantt-0.6.0.ebuild
deleted file mode 100644
index 2c8347c49..000000000
--- a/dev-python/python-gantt/python-gantt-0.6.0.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Draw Gantt charts from Python"
-HOMEPAGE="https://pypi.org/project/python-gantt/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/svgwrite[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests nose
-
-python_test() {
- nosetests -v || die "nose tests fail with ${EPYTHON}"
-}
diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest
index e8ec2f978..bb22f152b 100644
--- a/dev-python/python-igraph/Manifest
+++ b/dev-python/python-igraph/Manifest
@@ -1,3 +1 @@
-DIST python-igraph-0.8.2.tar.gz 3970354 BLAKE2B 2107a147ad98fa0b1a6c4f7332167a4256225615b9ef457e7c4b39c63cbe97456b4952e7c208ab0712365e1103eb541f4f8d0f0554470132b05b57bcc8f1dc67 SHA512 669d44081de2f0e1d0ef5b06e1cced193a9a0686e3e5e58b8334fd6eef14df3226cd0f7902f88289e575c822516e85b442c89ca9ec73a0d9d48ac8522347a30a
-DIST python-igraph-0.8.3.tar.gz 4059460 BLAKE2B 795dee8a72450c8d6ccf88188f663f54b3e7b551de2ceff8f7104a97f64741f8e5a02e2ef9b3d4e09806c26ba85e75c39c9ab99dc5019437db780f23dc1bb629 SHA512 5015a339ac4f0aa9a08942396f97c667602c760491cccb85ff8ef807f1be47d4e3c66a4145c5064c19ec8657ddac02a9ae88f460ab2e1c3394348de100879c90
DIST python-igraph-0.9.0.tar.gz 3366754 BLAKE2B baab83753bea4ee880564fe189b246c2ce0647a74ea1a41299062c3a2e203ec155abe1a3680c228d62a28e7bbf263e60e4529f151094b916ce4a1cae9f360705 SHA512 bd6071fc20c6c8f65034c71be6083e66367eb3047f376eb603e590da3606338fbd9890a2a74b8e0547fba2900c353f952683ea69b4d996f5643e84ee1c450b03
diff --git a/dev-python/python-igraph/python-igraph-0.8.2.ebuild b/dev-python/python-igraph/python-igraph-0.8.2.ebuild
deleted file mode 100644
index 0b2883896..000000000
--- a/dev-python/python-igraph/python-igraph-0.8.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for igraph"
-HOMEPAGE="https://igraph.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-libs/igraph
- dev-python/texttable[${PYTHON_USEDEP}]
- dev-python/pycairo[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- test? (
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/ipywidgets[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_compile() {
- distutils-r1_python_compile --use-pkg-config
-}
diff --git a/dev-python/python-igraph/python-igraph-0.8.3.ebuild b/dev-python/python-igraph/python-igraph-0.8.3.ebuild
deleted file mode 100644
index 749126cdc..000000000
--- a/dev-python/python-igraph/python-igraph-0.8.3.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for igraph"
-HOMEPAGE="https://igraph.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-libs/igraph
- dev-python/texttable[${PYTHON_USEDEP}]
- dev-python/pycairo[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- test? (
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/ipywidgets[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_compile() {
- distutils-r1_python_compile --use-pkg-config
-}
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
index 7b3ad5e3f..cf51f4e9b 100644
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
+++ b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
@@ -4,7 +4,6 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_SINGLE_IMPL=1
inherit distutils-r1
@@ -17,8 +16,7 @@ SLOT="0"
KEYWORDS="~amd64"
RDEPEND="
- sci-libs/pytorch[python,${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
+ sci-libs/pytorch[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/future[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
@@ -28,5 +26,4 @@ RDEPEND="
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/typing-extensions[${PYTHON_USEDEP}]
dev-python/ratelimit[${PYTHON_USEDEP}]
- ')
"
diff --git a/dev-python/pyvista/Manifest b/dev-python/pyvista/Manifest
index b4d7a9196..0fa9b89d4 100644
--- a/dev-python/pyvista/Manifest
+++ b/dev-python/pyvista/Manifest
@@ -1 +1 @@
-DIST pyvista-0.31.1.tar.gz 1249426 BLAKE2B 1f52f5bf5a5bc7bee1197a8b31c8806eae9c6ca03f45b8db601625134f9ce8fd301bc8032923f31ae0e75292c1126fb65076e48a5bc11f6838d6d2b42c75fddf SHA512 f184f667759bf85801831372a91e12617c223c745c2acf778cb7b42f6a1812719714caba322ff3013cb2ed0cb32f72ddcdb279989e93b67fe8a503b85314da71
+DIST pyvista-0.33.2.tar.gz 1383071 BLAKE2B bebd90489ac37566dc9f9161ce9348d48bc758c8dfe6ffa4f7d3085061f49db30dcc515d4a2c6f470150667f23e498a165f8492391b42115556b17868d684865 SHA512 bf6a6d921bcb5f86e4fb05c42ff50d90cb24800d930bd41d7d13b112b476dcaf6888d598354ca50e58313e05682a92160dbdfe633955f48f8895d464669aeb59
diff --git a/dev-python/pyvista/pyvista-0.31.1.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild
index 1ba6d0882..c8b5a59dc 100644
--- a/dev-python/pyvista/pyvista-0.31.1.ebuild
+++ b/dev-python/pyvista/pyvista-0.33.2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1"
@@ -23,10 +23,7 @@ RDEPEND="
dev-python/imageio[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pillow[${PYTHON_USEDEP}]
- !>=dev-python/meshio-5.0.0[${PYTHON_USEDEP}]
- >=dev-python/meshio-4.0.3[${PYTHON_USEDEP}]
>=dev-python/scooby-0.5.1[${PYTHON_USEDEP}]
- >=dev-python/transforms3d-0.3.1[${PYTHON_USEDEP}]
')
"
DEPEND="${RDEPEND}"
diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild
index df94c55f4..b7ef458e2 100644
--- a/dev-python/pyvote/pyvote-0.1.ebuild
+++ b/dev-python/pyvote/pyvote-0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -14,10 +14,7 @@ SRC_URI="https://github.com/TheChymera/pyvote/archive/${PV}.tar.gz -> ${P}.tar.g
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-DEPEND=""
RDEPEND="
dev-python/argh[${PYTHON_USEDEP}]
dev-python/mpmath[${PYTHON_USEDEP}]
diff --git a/dev-python/rasterio/rasterio-1.2.10.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
index 625e4a7da..7ae9776c7 100644
--- a/dev-python/rasterio/rasterio-1.2.10.ebuild
+++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
dev-python/affine[${PYTHON_USEDEP}]
dev-python/attrs[${PYTHON_USEDEP}]
dev-python/certifi[${PYTHON_USEDEP}]
@@ -26,13 +26,15 @@ RDEPEND="
dev-python/click-plugins[${PYTHON_USEDEP}]
dev-python/snuggs[${PYTHON_USEDEP}]
"
+
#DEPEND="${RDEPEND}"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
test? (
dev-python/boto3[${PYTHON_USEDEP}]
dev-python/hypothesis[${PYTHON_USEDEP}]
- sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
+ sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
)
"
@@ -43,6 +45,9 @@ python_test() {
# disable tests failing for unknown reason
tests/test_env.py::test_rio_env_no_credentials
tests/test_rio_info.py::test_info_azure_unsigned
+
+ tests/test__env.py::test_search_debian_gdal_data
+ tests/test__env.py::test_search_gdal_data_debian
tests/test_warp.py::test_reproject_resampling[Resampling.cubic]
tests/test_warp.py::test_reproject_resampling[Resampling.lanczos]
tests/test_warp.py::test_reproject_resampling_alpha[Resampling.cubic]
diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
index ccaa17351..3567cdb42 100644
--- a/dev-python/rasterstats/rasterstats-0.16.0.ebuild
+++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/affine[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/rasterio[${PYTHON_USEDEP}]
dev-python/cligj[${PYTHON_USEDEP}]
diff --git a/dev-python/reproject/Manifest b/dev-python/reproject/Manifest
index 848284dcf..76c6dd3c9 100644
--- a/dev-python/reproject/Manifest
+++ b/dev-python/reproject/Manifest
@@ -1 +1 @@
-DIST reproject-0.7.1.tar.gz 770363 BLAKE2B 6df020b3cf594993a8660e335e528e9edd58c6104c546c01cb6a7a55df6f9ba6888a702c447a494065aa7da3aff7532ac6fd4f301f7f324976e6e0e3f001b0ce SHA512 7316a0b7bbf0dca9991b3298d0f5f308c4d88ba0c31b3cad28058d963ceac8fbb4b2d35d8fab1f379d767024159bbdb7408c18161bf3790325e599c75e603114
+DIST reproject-0.8.tar.gz 774255 BLAKE2B bf66cf2038f436567b6b0a66cc19608c96f98d2bf1624aa33c7b07e1e42c8bfdecc46072d410699f2a0c2f3db52a0ee04d0ce64f58464fd1abd28e33d704933d SHA512 48fba585de3fc67fdb39390390021e6e8295297e31d2c3fccbead53a592f512232ef182e8914906f21190108f87266faf5ad57d5982a76a50c30eeca630fd6ed
diff --git a/dev-python/reproject/reproject-0.7.1.ebuild b/dev-python/reproject/reproject-0.8.ebuild
index 33ca7691c..2daccec83 100644
--- a/dev-python/reproject/reproject-0.7.1.ebuild
+++ b/dev-python/reproject/reproject-0.8.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -28,10 +28,11 @@ BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]"
RDEPEND="
>=dev-python/astropy-3.2[${PYTHON_USEDEP}]
- dev-python/astropy-healpix[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
+ >=dev-python/astropy-healpix-0.6[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.14[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.1[${PYTHON_USEDEP}]
"
-distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib
+# requires self to be installed
+# distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib
distutils_enable_tests --install pytest
diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml
index 0090cc810..aa31ba351 100644
--- a/dev-python/repsep_utils/metadata.xml
+++ b/dev-python/repsep_utils/metadata.xml
@@ -5,10 +5,6 @@
<email>chr@chymera.eu</email>
<name>Horea Christian</name>
</maintainer>
- <maintainer type="project">
- <email>python@gentoo.org</email>
- <name>Python</name>
- </maintainer>
<longdescription lang="en">
Utilities for compiling and developing RepSeP-style articles, such as the
reference implementation. The package contains generic boilerplate code for
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index cff648bf6..440b5758f 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/metadata.xml
@@ -5,10 +5,6 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
- <maintainer type="project">
- <email>python@gentoo.org</email>
- <name>Python</name>
- </maintainer>
<upstream>
<remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
<remote-id type="pypi">snakemake</remote-id>
diff --git a/dev-python/snakemake/snakemake-5.32.2.ebuild b/dev-python/snakemake/snakemake-5.32.2.ebuild
index 312699378..59d2f061a 100644
--- a/dev-python/snakemake/snakemake-5.32.2.ebuild
+++ b/dev-python/snakemake/snakemake-5.32.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -32,7 +32,7 @@ BDEPEND="test? (
RDEPEND="
dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/configargparse[${PYTHON_USEDEP}]
+ dev-python/ConfigArgParse[${PYTHON_USEDEP}]
dev-python/datrie[${PYTHON_USEDEP}]
dev-python/docutils[${PYTHON_USEDEP}]
dev-python/GitPython[${PYTHON_USEDEP}]
diff --git a/dev-python/sphinx-argparse/Manifest b/dev-python/sphinx-argparse/Manifest
index a0e62eccf..cc6a6ba19 100644
--- a/dev-python/sphinx-argparse/Manifest
+++ b/dev-python/sphinx-argparse/Manifest
@@ -1 +1 @@
-DIST sphinx-argparse-0.2.5.tar.gz 24890 BLAKE2B 870329d588c5c1131bb104e548e6f1caf673b6b4ffa9cb074a9a6e769f90d8d351ec14ce05f902d10ce4ae2336e05a119a386ea154faf2a5c57ba240514c9b92 SHA512 8e946947c9d018c10d7283b19c49cf19bf5813ba5c227bf3aac21752e5ecddf4653ec2bb1e2b67b8c1c3d8eb50ede55acc5b0e0071297433a2468606d3baa0b1
+DIST sphinx-argparse-0.3.1.tar.gz 42953 BLAKE2B 76c74a270a638b1b894548bc898918fbfa5fde6bcf1ccbf5e69a3daaada829bc1ae27ad8befd18e834646dc2fc3b025f36807c2be894911cc0c6d65294174898 SHA512 3d289c90165eb6a3d7a94dff8e6a429a49eb404ce373e80e007a0cd9abaae1e1236f5393df2fbf11701c349dade9d199640dc398064da4fd50a58a90eb3f8f12
diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.2.5.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.2.5.ebuild
deleted file mode 100644
index 33cb3ae66..000000000
--- a/dev-python/sphinx-argparse/sphinx-argparse-0.2.5.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2020-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Sphinx extension that automatically documents argparse commands and options"
-HOMEPAGE="https://pypi.org/project/sphinx-argparse/
- https://github.com/alex-rudakov/sphinx-argparse"
-SRC_URI="https://github.com/alex-rudakov/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="
- ${DEPEND}
- dev-python/sphinx[${PYTHON_USEDEP}]
- dev-python/commonmark[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-# requires self to build own documentation
-distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse
-
-python_prepare_all() {
- # test fails, skip it until a fix is found:
- # AssertionError: assert [{'action_groups': [{'description': None,\n 'options': [{'default': None,\n
- sed -i -e 's:test_parse_nested:_&:' \
- -e 's:test_parse_nested_traversal:_&:' \
- test/test_parser.py || die
-
- # needs test files in workdir to compile docs for some reason
- cp -r test "${WORKDIR}/test/" || die
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild
new file mode 100644
index 000000000..5b380202e
--- /dev/null
+++ b/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 2020-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+inherit distutils-r1
+
+DESCRIPTION="Sphinx extension that automatically documents argparse commands and options"
+HOMEPAGE="https://pypi.org/project/sphinx-argparse/
+ https://github.com/ashb/sphinx-argparse"
+SRC_URI="https://github.com/ashb/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ dev-python/commonmark[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+# requires self to build own documentation
+distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse
diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
index cdb82f956..7680d8206 100644
--- a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
+++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/trimesh/Manifest b/dev-python/trimesh/Manifest
deleted file mode 100644
index dc63d312d..000000000
--- a/dev-python/trimesh/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST trimesh-3.9.1.tar.gz 10407978 BLAKE2B e16829d9f99d1d88bc924004d7187d086a04d1cc91fefb1e32e1a22d8774469b492d3240b902ec2fbd1f085fa43e2b9196b4d077c8856037cfd0447beaa13c4d SHA512 ef278acf894abff6b64223934d669558a2c0bfaa611607c908810df67597f635d50786b6e18651e30ee70dee88163ec9a624f4d8e13a3a9b171782ee04498bc2
-DIST trimesh-3.9.42.tar.gz 10626604 BLAKE2B 3b6c8caeb50b2fa3f540638f4e9cf228e64e9d8c41b2908689d6122ac1444ecfa67bd622afc9df0c02af3936bfee712aa55a8afb65ba6f0f4711872cbf801e5f SHA512 fa5e048ef5baba51466be1a3c16924fd89ca4047b05e630c2980345c6e8a1bdf7ce5819858dd7ed95e9aef6a0bb6ca4a5ae605e8d0279f5ccd7529c3a143bf18
diff --git a/dev-python/trimesh/metadata.xml b/dev-python/trimesh/metadata.xml
deleted file mode 100644
index 2a4942b0a..000000000
--- a/dev-python/trimesh/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@chymera.eu</email>
- <name>Horea Christian</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- Trimesh is a pure Python library for loading and using triangular meshes
- with an emphasis on single- body watertight surfaces. The goal of the
- library is to provide a full featured and well tested Trimesh object which
- allows for easy manipulation and analysis, in the style of the Polygon
- object in the Shapely library.
- </longdescription>
- <use>
- <flag name="extra">Extra functionality for advanced mesh preparation</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-python/trimesh/trimesh-3.9.1.ebuild b/dev-python/trimesh/trimesh-3.9.1.ebuild
deleted file mode 100644
index 5376fadd6..000000000
--- a/dev-python/trimesh/trimesh-3.9.1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for loading and using triangular meshes."
-HOMEPAGE="https://trimsh.org/"
-SRC_URI="https://github.com/mikedh/trimesh/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="extra"
-
-DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="
- extra? (
- dev-libs/xxhash
- dev-python/colorlog[${PYTHON_USEDEP}]
- dev-python/chardet[${PYTHON_USEDEP}]
- dev-python/lxml[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyglet[${PYTHON_USEDEP}]
- dev-python/pycollada[${PYTHON_USEDEP}]
- dev-python/psutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/svg-path[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
- sci-libs/rtree[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-python_test() {
- if use extra; then
- pytest -vv || die
- else
- cd tests || die
- pytest -p no:warnings $(grep -v '^#' basic.list) || die
- fi
-}
diff --git a/dev-python/trimesh/trimesh-3.9.42.ebuild b/dev-python/trimesh/trimesh-3.9.42.ebuild
deleted file mode 100644
index 3ec15c516..000000000
--- a/dev-python/trimesh/trimesh-3.9.42.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for loading and using triangular meshes."
-HOMEPAGE="https://trimsh.org/"
-SRC_URI="https://github.com/mikedh/trimesh/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="extra"
-
-DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="
- extra? (
- dev-libs/xxhash
- dev-python/colorlog[${PYTHON_USEDEP}]
- dev-python/chardet[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/lxml[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
- dev-python/pyglet[${PYTHON_USEDEP}]
- dev-python/pycollada[${PYTHON_USEDEP}]
- dev-python/psutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/svg-path[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
- sci-libs/rtree[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-# TODO: package pypandoc
-# distutils_enable_sphinx docs \
-# dev-python/sphinx_rtd_theme \
-# dev-python/numpy \
-# dev-python/scipy \
-# dev-python/networkx \
-# dev-python/recommonmark \
-# dev-python/jupyter \
-# dev-python/pyopenssl \
-# dev-python/autodocsumm \
-# dev-python/jinja2 \
-# dev-python/matplotlib
-
-python_test() {
- if use extra; then
- epytest
- else
- cd tests || die
- epytest -p no:warnings $(grep -v '^#' basic.list)
- fi
-}
diff --git a/dev-python/typish/Manifest b/dev-python/typish/Manifest
index 672b11f96..809dd7e09 100644
--- a/dev-python/typish/Manifest
+++ b/dev-python/typish/Manifest
@@ -1 +1 @@
-DIST typish-1.9.3.tar.gz 22997 BLAKE2B f399f5d9b3ae8f85f3b719de77d675b142ac45b6535f66d9d0d999411bc5bfc9100523667ea4c1d2be60c15a4bf35ec931ded9e1181a4545bbaa9b96fb27d0dd SHA512 baad9d2229ac289c4eb1d6e64bac0313efd4680f42a95270e0c1141d511392e6a95a5fea767943ddf432f5f0d48d95a05bbf26e06df188079ac177d321e4fa5c
+DIST typish-1.9.3.gh.tar.gz 22997 BLAKE2B f399f5d9b3ae8f85f3b719de77d675b142ac45b6535f66d9d0d999411bc5bfc9100523667ea4c1d2be60c15a4bf35ec931ded9e1181a4545bbaa9b96fb27d0dd SHA512 baad9d2229ac289c4eb1d6e64bac0313efd4680f42a95270e0c1141d511392e6a95a5fea767943ddf432f5f0d48d95a05bbf26e06df188079ac177d321e4fa5c
diff --git a/dev-python/typish/metadata.xml b/dev-python/typish/metadata.xml
index 4febcc126..603d0691e 100644
--- a/dev-python/typish/metadata.xml
+++ b/dev-python/typish/metadata.xml
@@ -1,13 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="pypi">typish</remote-id>
- <remote-id type="github">ramonhagenaars/typish</remote-id>
- </upstream>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">typish</remote-id>
+ <remote-id type="github">ramonhagenaars/typish</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
index f471f6836..3c32b1184 100644
--- a/dev-python/typish/typish-1.9.3.ebuild
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -1,21 +1,29 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
-
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-DESCRIPTION="Python functions for thorough checks on types"
-HOMEPAGE="https://pypi.org/project/typish"
-
-# Prefer GitHub. Upstream failed to push its source tarball to PyPI.
-SRC_URI="https://github.com/ramonhagenaars/typish/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+DESCRIPTION="Functionality for types"
+HOMEPAGE="https://pypi.org/project/typish/
+ https://github.com/ramonhagenaars/typish"
+SRC_URI="
+ https://github.com/ramonhagenaars/typish/archive/v${PV}.tar.gz
+ -> ${P}.gh.tar.gz
+"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+
+BDEPEND="
+ test? (
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/nptyping[${PYTHON_USEDEP}]
+ )
+"
-#FIXME: Tests require "nptyping" which circularly requires... "typish". *sigh*
-RESTRICT="test"
+distutils_enable_tests pytest
diff --git a/dev-python/umap-learn/Manifest b/dev-python/umap-learn/Manifest
index fb1d7bdca..911c8ce27 100644
--- a/dev-python/umap-learn/Manifest
+++ b/dev-python/umap-learn/Manifest
@@ -1,3 +1 @@
-DIST umap-learn-0.4.6.tar.gz 69894 BLAKE2B 9d2029f31e58e5e0e4b4b32aa8d26f3d8a4a22684e99bb06b623ff35c3e3ed9ac63e532c409c206b95a1d0e2079f8512294e43eb77389351e1145e6a7ba35025 SHA512 9f339ac55bb3e9326dd3b04e71dcdd9e22ea40b0240b62a7af629167eb18b7d5cf11cdfdcb0215cfe54ffe69026b234188c2f81c26f231fed741deeff3daa5e9
-DIST umap-learn-0.5.0.tar.gz 81722 BLAKE2B 9de88cbac480f97b2fee77fca9c43b99417c1ed0be222d92024d67379335ff2c376096b47ab151ffaa18f180a50e7289f6872e6ff03fabdad49c52f7781b1868 SHA512 cd4ccba452d773f1ea9875a35b4e3dc616e34d8707bfbba376964b1606bbf02903f8a6ed8387c77dc88d733c2a2f1bd3bc02908fd43a42441bf9043a1bdd8025
-DIST umap-learn-0.5.1.tar.gz 80906 BLAKE2B a09563847d24f9b0d8195af61949fb040d32cd9e4e28daad534e857aed76305a2ccf372a0f61d417204dc7c1d062468609f2a02529ad781d8e60d4329d8bdceb SHA512 39d21ef147516c920f3ff088889188a25ecf147dd090a61755cfd3f24321b232f53e6cb160011d518a38d08ed1d01cdb79d7bad1dfe714708fa798eb679c78f4
+DIST umap-learn-0.5.2.tar.gz 86805 BLAKE2B b1381647c947472a10472475477d3f4c91446606b1ee7235dd91c65606e4c54119a706864364845ad34d74db33760013f93fd6f2a3b7e75a5161bbbc216a2c5a SHA512 89d7e7680554c63429eee1c0702f6b0b03f5a29d7770af0630a15bd50aeeaa3c272d87f2380ec71a60accea96fe9936c7c807bfe4143c6afa1444741c865eef5
diff --git a/dev-python/umap-learn/umap-learn-0.4.6.ebuild b/dev-python/umap-learn/umap-learn-0.4.6.ebuild
deleted file mode 100644
index 665f1e204..000000000
--- a/dev-python/umap-learn/umap-learn-0.4.6.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Uniform Manifold Approximation and Projection"
-HOMEPAGE="https://umap-learn.readthedocs.io/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/numba[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pynndescent[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-# no tests in package
diff --git a/dev-python/umap-learn/umap-learn-0.5.0.ebuild b/dev-python/umap-learn/umap-learn-0.5.0.ebuild
deleted file mode 100644
index 37ca3ca45..000000000
--- a/dev-python/umap-learn/umap-learn-0.5.0.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Uniform Manifold Approximation and Projection"
-HOMEPAGE="https://umap-learn.readthedocs.io/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/numba[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pynndescent[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-# no tests in package
diff --git a/dev-python/umap-learn/umap-learn-0.5.1.ebuild b/dev-python/umap-learn/umap-learn-0.5.1.ebuild
deleted file mode 100644
index 37ca3ca45..000000000
--- a/dev-python/umap-learn/umap-learn-0.5.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="Uniform Manifold Approximation and Projection"
-HOMEPAGE="https://umap-learn.readthedocs.io/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/numba[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pynndescent[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-# no tests in package
diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
new file mode 100644
index 000000000..f0dc3dab5
--- /dev/null
+++ b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Uniform Manifold Approximation and Projection"
+HOMEPAGE="https://umap-learn.readthedocs.io/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-python/numba-0.49[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
+ >=dev-python/pynndescent-0.5[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/zarr/Manifest b/dev-python/zarr/Manifest
new file mode 100644
index 000000000..08592fdcc
--- /dev/null
+++ b/dev-python/zarr/Manifest
@@ -0,0 +1,3 @@
+DIST zarr-2.11.1.tar.gz 3492813 BLAKE2B ff31cc2d11f5f863770f91136694108ab76525c644dd57861a4a57ca03dae0bb8cde5c20a2654f3566ffb69900d581e7592f576b9c0d2746e4fb95ed6991c740 SHA512 e0079a69f65a1bc230049469f50bf52af036d85d84f7c163ecdc2a4a8d7b75b07b59c1fcdecd83f578682914a6463641e9341d2c18f939c57f1e78f298f6b7ea
+DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65
+DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
diff --git a/dev-python/zarr/metadata.xml b/dev-python/zarr/metadata.xml
new file mode 100644
index 000000000..036ff8b45
--- /dev/null
+++ b/dev-python/zarr/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">zarr-developers/zarr-python</remote-id>
+ <remote-id type="pypi">zarr</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild
new file mode 100644
index 000000000..8cb175408
--- /dev/null
+++ b/dev-python/zarr/zarr-2.11.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/asciitree[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/numcodecs[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+ zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild
new file mode 100644
index 000000000..1fa4e9af9
--- /dev/null
+++ b/dev-python/zarr/zarr-2.11.3.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/asciitree[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+ zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme
diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild
new file mode 100644
index 000000000..1fa4e9af9
--- /dev/null
+++ b/dev-python/zarr/zarr-2.12.0.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/asciitree[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+ zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme
diff --git a/dev-util/Tensile/Manifest b/dev-util/Tensile/Manifest
deleted file mode 100644
index 002a92399..000000000
--- a/dev-util/Tensile/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rocm-Tensile-4.0.0.tar.gz 9734773 BLAKE2B fe5c18371eb8f0d2d43955ad117e79ca2cec13fe49e7edd76f6ea61f9efc57fe6597523ec0b78d3dde1729f6ab755c0d371b2a7f067d0e66785fd230eb999d58 SHA512 096a49ae960f58d96f5d5c9a0efd0ec1564fdafdd8ced18a15f0588e06d5c5e522fc06e420368bfcde4e3312825dcfb0b119f4bdfc33db8397bf6214ecb253c4
diff --git a/dev-util/Tensile/Tensile-4.0.0-r1.ebuild b/dev-util/Tensile/Tensile-4.0.0-r1.ebuild
deleted file mode 100644
index ec2a738d9..000000000
--- a/dev-util/Tensile/Tensile-4.0.0-r1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Stretching GPU performance for GEMMs and tensor contractions"
-HOMEPAGE="https://github.com/ROCmSoftwarePlatform/Tensile"
-SRC_URI="https://github.com/ROCmSoftwarePlatform/Tensile/archive/rocm-${PV}.tar.gz -> rocm-Tensile-${PV}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-IUSE=""
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
- dev-util/hip"
-
-PATCHES=( "${FILESDIR}"/${PN}-4.0.0-cmake.patch
- "${FILESDIR}"/${PN}-4.0.0-setup.py-cmake.patch
- "${FILESDIR}"/${PN}-4.0.0-locate-commands.patch
- "${FILESDIR}"/${PN}-4.0.0-output-currentISA.patch )
-
-S="${WORKDIR}/${PN}-rocm-${PV}"
-CMAKE_USE_DIR="${WORKDIR}/Source"
-
-src_prepare() {
- distutils-r1_src_prepare
-
- mv ${PN}/Source "${WORKDIR}"/ || die
- sed -e "/ROCM_SMI_ROOT/s,lib,$(get_libdir)," \
- -i "${WORKDIR}"/Source/cmake/FindROCmSMI.cmake || die
- sed -r -e "/TENSILE_USE_LLVM/s/ON/OFF/" \
- -i "${WORKDIR}"/Source/CMakeLists.txt || die
-
- mv ${PN}/cmake "${T}"/ || die
-
- sed -e "/HipClangVersion/s/0,0,0/$(ver_rs 1-3 ,)/" \
- -e "/SourcePath/s,os\.path\.join.*$,\"${EPREFIX}/usr/share/${PN}\"," \
- -i ${PN}/Common.py || die
-
- sed -e "s|os\.path\.dirname.*$|\"${EPREFIX}/usr/share/Tensile\", end='')|" \
- -i ${PN}/__init__.py || die
-}
-
-src_install() {
- distutils-r1_src_install
-
- insinto /usr/$(get_libdir)/cmake/${PN}
- doins "${T}"/cmake/*.cmake
-
- insinto /usr/share/${PN}
- doins -r "${WORKDIR}"/Source/*
- dosym . /usr/share/${PN}/Source
-}
diff --git a/dev-util/Tensile/Tensile-4.0.0.ebuild b/dev-util/Tensile/Tensile-4.0.0.ebuild
deleted file mode 100644
index eda97d225..000000000
--- a/dev-util/Tensile/Tensile-4.0.0.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Stretching GPU performance for GEMMs and tensor contractions"
-HOMEPAGE="https://github.com/ROCmSoftwarePlatform/Tensile"
-SRC_URI="https://github.com/ROCmSoftwarePlatform/Tensile/archive/rocm-${PV}.tar.gz -> rocm-Tensile-${PV}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-IUSE=""
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
- dev-util/hip"
-
-PATCHES=( "${FILESDIR}"/${PN}-4.0.0-cmake.patch
- "${FILESDIR}"/${PN}-4.0.0-setup.py-cmake.patch
- "${FILESDIR}"/${PN}-4.0.0-locate-commands.patch
- "${FILESDIR}"/${PN}-4.0.0-output-currentISA.patch )
-
-S="${WORKDIR}/${PN}-rocm-${PVR}"
-CMAKE_USE_DIR="${WORKDIR}/Source"
-
-src_prepare() {
- distutils-r1_src_prepare
-
- mv ${PN}/Source "${WORKDIR}"/ || die
- sed -e "/ROCM_SMI_ROOT/s,lib,$(get_libdir)," \
- -i "${WORKDIR}"/Source/cmake/FindROCmSMI.cmake || die
- sed -r -e "/TENSILE_USE_LLVM/s/ON/OFF/" \
- -i "${WORKDIR}"/Source/CMakeLists.txt || die
-
- mv ${PN}/cmake "${T}"/ || die
-
- sed -e "/HipClangVersion/s/0,0,0/$(ver_rs 1-3 ,)/" \
- -e "/SourcePath/s,os\.path\.join.*$,\"${EPREFIX}/usr/share/${PN}\"," \
- -i ${PN}/Common.py || die
-
- sed -e "s|os\.path\.dirname.*$|\"${EPREFIX}/usr/share/Tensile\", end='')|" \
- -i ${PN}/__init__.py || die
-}
-
-src_install() {
- distutils-r1_src_install
-
- insinto /usr/$(get_libdir)/cmake/${PN}
- doins "${T}"/cmake/*.cmake
-
- insinto /usr/share/${PN}
- doins -r "${WORKDIR}"/Source/*
- dosym . /usr/share/${PN}/Source
-}
diff --git a/dev-util/Tensile/files/Tensile-4.0.0-cmake.patch b/dev-util/Tensile/files/Tensile-4.0.0-cmake.patch
deleted file mode 100644
index 0c39f747c..000000000
--- a/dev-util/Tensile/files/Tensile-4.0.0-cmake.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Index: Tensile-rocm-4.0.0/Tensile/cmake/TensileConfig.cmake
-===================================================================
---- Tensile-rocm-4.0.0.orig/Tensile/cmake/TensileConfig.cmake
-+++ Tensile-rocm-4.0.0/Tensile/cmake/TensileConfig.cmake
-@@ -26,7 +26,7 @@ if(NOT DEFINED Tensile_ROOT)
- get_filename_component(Tensile_PREFIX "${CMAKE_CURRENT_LIST_FILE}" PATH)
- get_filename_component(Tensile_PREFIX "${Tensile_PREFIX}" PATH)
-
--execute_process(COMMAND "${Tensile_PREFIX}/bin/TensileGetPath" OUTPUT_VARIABLE Tensile_ROOT)
-+execute_process(COMMAND "TensileGetPath" OUTPUT_VARIABLE Tensile_ROOT)
- endif()
- list(APPEND CMAKE_MODULE_PATH "${Tensile_ROOT}/Source/cmake/")
- list(APPEND CMAKE_MODULE_PATH "${Tensile_ROOT}/Source/")
-@@ -93,7 +93,7 @@ function(TensileCreateLibraryFiles
- set(Tensile_MERGE_FILES OFF)
- endif()
-
-- set(Script "${Tensile_ROOT}/bin/TensileCreateLibrary")
-+ set(Script "TensileCreateLibrary")
- message(STATUS "Tensile script: ${Script}")
-
- set(Options "--new-client-only" "--no-legacy-components")
-Index: Tensile-rocm-4.0.0/Tensile/Source/TensileCreateLibrary.cmake
-===================================================================
---- Tensile-rocm-4.0.0.orig/Tensile/Source/TensileCreateLibrary.cmake
-+++ Tensile-rocm-4.0.0/Tensile/Source/TensileCreateLibrary.cmake
-@@ -52,10 +52,7 @@ function(TensileCreateLibraryCmake
- message(STATUS "Tensile_ARCHITECTURE from TensileCreateLibraryCmake : ${Tensile_ARCHITECTURE}")
- message(STATUS "Tensile_LIBRARY_FORMAT from TensileCreateLibraryCmake : ${Tensile_LIBRARY_FORMAT}")
-
-- execute_process(COMMAND chmod 755 ${Tensile_ROOT}/bin/TensileCreateLibrary)
-- execute_process(COMMAND chmod 755 ${Tensile_ROOT}/bin/Tensile)
--
-- set(Tensile_CREATE_COMMAND "${Tensile_ROOT}/bin/TensileCreateLibrary")
-+ set(Tensile_CREATE_COMMAND "TensileCreateLibrary")
-
- set(Tensile_SOURCE_PATH "${PROJECT_BINARY_DIR}/Tensile")
- message(STATUS "Tensile_SOURCE_PATH=${Tensile_SOURCE_PATH}")
diff --git a/dev-util/Tensile/files/Tensile-4.0.0-locate-commands.patch b/dev-util/Tensile/files/Tensile-4.0.0-locate-commands.patch
deleted file mode 100644
index 78d467349..000000000
--- a/dev-util/Tensile/files/Tensile-4.0.0-locate-commands.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-Index: Tensile-rocm-4.0.0/Tensile/Common.py
-===================================================================
---- Tensile-rocm-4.0.0.orig/Tensile/Common.py
-+++ Tensile-rocm-4.0.0/Tensile/Common.py
-@@ -155,7 +155,7 @@ globalParameters["PrintTensorRef"] = 0
- globalParameters["PrintIndexAssignments"] = 0 # Print the tensor index assignment info
- globalParameters["PrintTensorRef"] = 0 # Print reference tensor. 0x1=after init; 0x2=after copy-back; 0x3=both
- globalParameters["PrintWinnersOnly"] = False # Only print the solutions which become the fastest
--globalParameters["PrintCodeCommands"] = False # print the commands used to generate the code objects (asm,link,hip-clang, etc)
-+globalParameters["PrintCodeCommands"] = True # print the commands used to generate the code objects (asm,link,hip-clang, etc)
-
- # TODO - remove this when NewClient is mainstream
- globalParameters["OldClientSourceTmp"] = True # Use an intermediate sourceTmp dir to detect file changes and minimize rebuilds on old client
-@@ -1521,14 +1521,14 @@ def assignGlobalParameters( config ):
- print2(" %24s: %8s (unspecified)" % (key, defaultValue))
-
- # ROCm Agent Enumerator Path
-- globalParameters["ROCmAgentEnumeratorPath"] = locateExe("/opt/rocm/bin", "rocm_agent_enumerator")
-+ globalParameters["ROCmAgentEnumeratorPath"] = locateExe("", "rocm_agent_enumerator")
- if "CxxCompiler" in config:
- globalParameters["CxxCompiler"] = config["CxxCompiler"]
-
- if "TENSILE_ROCM_ASSEMBLER_PATH" in os.environ:
- globalParameters["AssemblerPath"] = os.environ.get("TENSILE_ROCM_ASSEMBLER_PATH")
- elif globalParameters["AssemblerPath"] is None and globalParameters["CxxCompiler"] == "hipcc":
-- globalParameters["AssemblerPath"] = locateExe("/opt/rocm/llvm/bin", "clang++")
-+ globalParameters["AssemblerPath"] = locateExe("", "clang++")
- elif globalParameters["AssemblerPath"] is None and globalParameters["CxxCompiler"] == "hcc":
- globalParameters["AssemblerPath"] = locateExe("/opt/rocm/bin", "hcc")
-
-@@ -1536,8 +1536,8 @@ def assignGlobalParameters( config ):
- if globalParameters["CxxCompiler"] == "hcc":
- globalParameters["ExtractKernelPath"] = locateExe("/opt/rocm/bin", "extractkernel")
- else:
-- globalParameters["ExtractKernelPath"] = locateExe("/opt/rocm/hip/bin", "extractkernel")
-- globalParameters["ClangOffloadBundlerPath"] = locateExe("/opt/rocm/llvm/bin", "clang-offload-bundler")
-+ globalParameters["ExtractKernelPath"] = locateExe("", "extractkernel")
-+ globalParameters["ClangOffloadBundlerPath"] = locateExe("", "clang-offload-bundler")
-
- if "ROCmAgentEnumeratorPath" in config:
- globalParameters["ROCmAgentEnumeratorPath"] = config["ROCmAgentEnumeratorPath"]
-@@ -1579,20 +1579,6 @@ def assignGlobalParameters( config ):
- # Due to platform.linux_distribution() being deprecated, just try to run dpkg regardless.
- # The alternative would be to install the `distro` package.
- # See https://docs.python.org/3.7/library/platform.html#platform.linux_distribution
-- try:
-- if globalParameters["CxxCompiler"] == "hipcc":
-- output = subprocess.run(["dpkg", "-l", "hip-rocclr"], check=True, stdout=subprocess.PIPE).stdout.decode()
-- elif globalParameters["CxxCompiler"] == "hcc":
-- output = subprocess.run(["dpkg", "-l", "hcc"], check=True, stdout=subprocess.PIPE).stdout.decode()
--
-- for line in output.split('\n'):
-- if 'hipcc' in line:
-- globalParameters['HipClangVersion'] = line.split()[2]
-- elif 'hcc' in line:
-- globalParameters['HccVersion'] = line.split()[2]
--
-- except (subprocess.CalledProcessError, OSError) as e:
-- printWarning("Error: {} looking for package {}: {}".format('dpkg', 'hip-rocclr', e))
-
- for key in config:
- value = config[key]
diff --git a/dev-util/Tensile/files/Tensile-4.0.0-output-currentISA.patch b/dev-util/Tensile/files/Tensile-4.0.0-output-currentISA.patch
deleted file mode 100644
index a00f9fdca..000000000
--- a/dev-util/Tensile/files/Tensile-4.0.0-output-currentISA.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Index: Tensile-rocm-4.0.0/Tensile/TensileCreateLibrary.py
-===================================================================
---- Tensile-rocm-4.0.0.orig/Tensile/TensileCreateLibrary.py
-+++ Tensile-rocm-4.0.0/Tensile/TensileCreateLibrary.py
-@@ -132,7 +132,7 @@ def buildSourceCodeObjectFile(CxxCompile
- return globalParameters["AsmCaps"][arch]["SupportedISA"] and \
- globalParameters["AsmCaps"][arch]["SupportedSource"]
-
-- archs = ['gfx'+''.join(map(str,arch)) for arch in globalParameters['SupportedISA'] \
-+ archs = ['gfx'+''.join(map(str,arch)) for arch in [globalParameters['CurrentISA']] \
- if isSupported(arch)]
-
- archFlags = ['--amdgpu-target=' + arch for arch in archs]
-@@ -1004,7 +1004,7 @@ def buildObjectFileNames(solutionWriter,
- kernelHelperOjbNmaes = [ko.getKernelName() for ko in kernelHelperOjbs]
-
- # Source based kernels are built for all supported architectures
-- sourceArchs = ['gfx'+''.join(map(str,arch)) for arch in globalParameters['SupportedISA'] \
-+ sourceArchs = ['gfx'+''.join(map(str,arch)) for arch in [globalParameters['CurrentISA']] \
- if isSupported(arch)]
-
- # Asm based kernels target the configured ISA
diff --git a/dev-util/Tensile/files/Tensile-4.0.0-setup.py-cmake.patch b/dev-util/Tensile/files/Tensile-4.0.0-setup.py-cmake.patch
deleted file mode 100644
index e020842b2..000000000
--- a/dev-util/Tensile/files/Tensile-4.0.0-setup.py-cmake.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: Tensile-rocm-4.0.0/setup.py
-===================================================================
---- Tensile-rocm-4.0.0.orig/setup.py
-+++ Tensile-rocm-4.0.0/setup.py
-@@ -30,8 +30,6 @@ setup(
- install_requires=readRequirementsFromTxt(),
- python_requires='>=3.5',
- packages=["Tensile"],
-- package_data={ "Tensile": ["Tensile/cmake/*"] },
-- data_files=[ ("cmake", ["Tensile/cmake/TensileConfig.cmake", "Tensile/cmake/TensileConfigVersion.cmake"]) ],
- include_package_data=True,
- entry_points={"console_scripts": [
- # user runs a benchmark
diff --git a/dev-util/Tensile/metadata.xml b/dev-util/Tensile/metadata.xml
deleted file mode 100644
index 336bdb639..000000000
--- a/dev-util/Tensile/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>gentoo@holzke.net</email>
- <name>Wilfried Holzke</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
new file mode 100644
index 000000000..cce81b9b2
--- /dev/null
+++ b/dev-vcs/dandi-cli/Manifest
@@ -0,0 +1,3 @@
+DIST dandi-cli-0.37.0.tar.gz 212121 BLAKE2B a38077439edb9975b25eaffd299cba633b538d7c5a93aefeb35e8403e07896f1e93eb6b42790ca84ab20ddfe0ead850a000f857cfd3ef8c6342eb76952b95b62 SHA512 fe96b760bb8526cf2670be4523121b389ede82699a8b13a9b46e4511012ab15390d9aec35b5403fa4d52dd79738a37980bcc83755df738b4039ae56eb6ca0f14
+DIST dandi-cli-0.38.0.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054
+DIST dandi-cli-0.39.4.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild
new file mode 100644
index 000000000..08d652de9
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test etelemetry"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/click-didyoumean[${PYTHON_USEDEP}]
+ ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/fscacher[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/interleave[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pycryptodome[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyout[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/semantic_version[${PYTHON_USEDEP}]
+ dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/anys[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/pyfakefs[${PYTHON_USEDEP}]
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+ )
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+# Some tests require deep copy with git history
+# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299
+EPYTEST_DESELECT=(
+ "dandi/tests/test_utils.py::test_get_instance_dandi_with_api"
+ "dandi/tests/test_utils.py::test_get_instance_url"
+ "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old"
+ "dandi/tests/test_utils.py::test_get_instance_bad_cli_version"
+)
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch"
+ "${FILESDIR}/${PN}-0.37.0-pep517.patch"
+)
+
+src_prepare() {
+ if use etelemetry; then
+ default
+ else
+ eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
+ default
+ sed -i "/etelemetry/d" setup.cfg
+ fi
+}
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ epytest
+}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
new file mode 100644
index 000000000..08d652de9
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test etelemetry"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/click-didyoumean[${PYTHON_USEDEP}]
+ ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/fscacher[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/interleave[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pycryptodome[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyout[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/semantic_version[${PYTHON_USEDEP}]
+ dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/anys[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/pyfakefs[${PYTHON_USEDEP}]
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+ )
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+# Some tests require deep copy with git history
+# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299
+EPYTEST_DESELECT=(
+ "dandi/tests/test_utils.py::test_get_instance_dandi_with_api"
+ "dandi/tests/test_utils.py::test_get_instance_url"
+ "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old"
+ "dandi/tests/test_utils.py::test_get_instance_bad_cli_version"
+)
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch"
+ "${FILESDIR}/${PN}-0.37.0-pep517.patch"
+)
+
+src_prepare() {
+ if use etelemetry; then
+ default
+ else
+ eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
+ default
+ sed -i "/etelemetry/d" setup.cfg
+ fi
+}
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ epytest
+}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
new file mode 100644
index 000000000..11f322912
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
@@ -0,0 +1,89 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test etelemetry"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/click-didyoumean[${PYTHON_USEDEP}]
+ ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/fscacher[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/interleave[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pycryptodome[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyout[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/semantic_version[${PYTHON_USEDEP}]
+ dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+ test? (
+ dev-python/anys[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/pyfakefs[${PYTHON_USEDEP}]
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+ )
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+# Some tests require deep copy with git history
+# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299
+EPYTEST_DESELECT=(
+ "dandi/tests/test_utils.py::test_get_instance_dandi_with_api"
+ "dandi/tests/test_utils.py::test_get_instance_url"
+ "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old"
+ "dandi/tests/test_utils.py::test_get_instance_bad_cli_version"
+)
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch"
+ "${FILESDIR}/${PN}-0.37.0-pep517.patch"
+)
+
+src_prepare() {
+ if use etelemetry; then
+ default
+ else
+ eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
+ default
+ sed -i "/etelemetry/d" setup.cfg
+ fi
+}
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ epytest
+}
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch
new file mode 100644
index 000000000..6822e1abf
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch
@@ -0,0 +1,30 @@
+--- a/dandi/utils.py 2021-09-21 11:51:39.799524534 -0400
++++ b/dandi/utils.py 2021-10-06 04:58:00.506440719 -0400
+@@ -734,27 +734,4 @@
+ def check_dandi_version():
+ if os.environ.get("DANDI_NO_ET"):
+ return
+- try:
+- import etelemetry
+-
+- try:
+- etelemetry.check_available_version(
+- "dandi/dandi-cli", __version__, lgr=lgr, raise_exception=True
+- )
+- except etelemetry.client.BadVersionError:
+- # note: SystemExit is based of BaseException, so is not Exception
+- raise SystemExit(
+- "DANDI CLI has detected that you are using a version that is known to "
+- "contain bugs, is incompatible with our current data archive, or has "
+- "other significant performance limitations. "
+- "To continue using DANDI CLI, please upgrade your dandi client to a newer "
+- "version (e.g., using pip install --upgrade dandi if you installed using pip). "
+- "If you have any issues, please contact the DANDI "
+- "helpdesk at https://github.com/dandi/helpdesk/issues/new/choose ."
+- )
+- except Exception as exc:
+- lgr.warning(
+- "Failed to check for a more recent version available with etelemetry: %s",
+- exc,
+- )
+ os.environ["DANDI_NO_ET"] = "1"
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
new file mode 100644
index 000000000..4d4715f95
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
@@ -0,0 +1,46 @@
+From a363b68b79b3dd2004912640c90958882a918537 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
+Date: Wed, 4 May 2022 19:49:37 +0200
+Subject: [PATCH] Prepend to sys.path to fix versioneer in PEP517 mode
+
+Prepend the current directory to sys.path rather than appending it
+in order to fix the build in PEP517 mode properly. If the path
+is appended and versioneer is installed on the system, the system
+versioneer.py (i.e. the module used to install versioneer into projects)
+is imported rather than the local file, and the build fails:
+
+```
+Traceback (most recent call last):
+ File "/usr/lib/python-exec/python3.10/gpep517", line 4, in <module>
+ sys.exit(main())
+ File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 136, in main
+ return func(args)
+ File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 44, in build_wheel
+ wheel_name = backend.build_wheel(args.wheel_dir, args.config_json)
+ File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel
+ return self._build_with_temp_dir(['bdist_wheel'], '.whl',
+ File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir
+ self.run_setup()
+ File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
+ exec(compile(code, __file__, 'exec'), locals())
+ File "setup.py", line 32, in <module>
+ "version": versioneer.get_version(),
+AttributeError: module 'versioneer' has no attribute 'get_version'
+```
+---
+ setup.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index e8dddc985..05765009c 100755
+--- a/setup.py
++++ b/setup.py
+@@ -23,7 +23,7 @@
+ # This is needed for versioneer to be importable when building with PEP 517.
+ # See <https://github.com/warner/python-versioneer/issues/193> and links
+ # therein for more information.
+-sys.path.append(os.path.dirname(__file__))
++sys.path.insert(0, os.path.dirname(__file__))
+
+ try:
+ import versioneer
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
new file mode 100644
index 000000000..bcc3853d3
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
@@ -0,0 +1,13 @@
+--- a/setup.cfg 2021-10-06 11:44:40.549337707 -0400
++++ b/dsetup.cfg 2021-10-06 11:45:10.236935245 -0400
+@@ -30,8 +30,8 @@
+ appdirs
+ click
+ click-didyoumean
+- dandischema ~= 0.6.0
+- etelemetry >= 0.2.2
++ dandischema
++ etelemetry
+ fasteners
+ fscacher
+ # Specifying != might be what causes pip 19.3.1 first to install hdmf 1.5.1
diff --git a/dev-vcs/dandi-cli/metadata.xml b/dev-vcs/dandi-cli/metadata.xml
new file mode 100644
index 000000000..9565a2184
--- /dev/null
+++ b/dev-vcs/dandi-cli/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ This package provides a dandi command line utility with a basic interface
+ which should assist you in preparing and uploading your data to and/or
+ obtaining data from the http://dandiarchive.org . Each of the commands
+ has a set of options to alter their behavior. Please run
+ `dandi COMMAND --help` to get more information
+ </longdescription>
+ <use>
+ <flag name="etelemetry">version checking to respect server schema version</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">dandi/dandi-cli</remote-id>
+ <remote-id type="pypi">dandi</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/licenses/Artistic-Manatee b/licenses/Artistic-Manatee
deleted file mode 100644
index 266b5db33..000000000
--- a/licenses/Artistic-Manatee
+++ /dev/null
@@ -1,50 +0,0 @@
-The Artistic License
-
-Preamble
-
-The intent of this document is to state the conditions under which a Package may be copied, such that the Copyright Holder maintains some semblance of artistic control over the development of the package, while giving the users of the package the right to use and distribute the Package in a more-or-less customary fashion, plus the right to make reasonable modifications.
-
-Definitions:
-
- * "Package" refers to the collection of files distributed by the Copyright Holder, and derivatives of that collection of files created through textual modification.
- * "Standard Version" refers to such a Package if it has not been modified, or has been modified in accordance with the wishes of the Copyright Holder.
- * "Copyright Holder" is whoever is named in the copyright or copyrights for the package.
- * "You" is you, if you're thinking about copying or distributing this Package.
- * "Reasonable copying fee" is whatever you can justify on the basis of media cost, duplication charges, time of people involved, and so on. (You will not be required to justify it to the Copyright Holder, but only to the computing community at large as a market that must bear the fee.)
- * "Freely Available" means that no fee is charged for the item itself, though there may be fees involved in handling the item. It also means that recipients of the item may redistribute it under the same conditions they received it.
-
-1. You may make and give away verbatim copies of the source form of the Standard Version of this Package without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers.
-
-2. You may apply bug fixes, portability fixes and other modifications derived from the Public Domain or from the Copyright Holder. A Package modified in such a way shall still be considered the Standard Version.
-
-3. You may otherwise modify your copy of this Package in any way, provided that you insert a prominent notice in each changed file stating how and when you changed that file, and provided that you do at least ONE of the following:
-
- a) place your modifications in the Public Domain or otherwise make them Freely Available, such as by posting said modifications to Usenet or an equivalent medium, or placing the modifications on a major archive site such as ftp.uu.net, or by allowing the Copyright Holder to include your modifications in the Standard Version of the Package.
-
- b) use the modified Package only within your corporation or organization.
-
- c) rename any non-standard executables so the names do not conflict with standard executables, which must also be provided, and provide a separate manual page for each non-standard executable that clearly documents how it differs from the Standard Version.
-
- d) make other distribution arrangements with the Copyright Holder.
-
-4. You may distribute the programs of this Package in object code or executable form, provided that you do at least ONE of the following:
-
- a) distribute a Standard Version of the executables and library files, together with instructions (in the manual page or equivalent) on where to get the Standard Version.
-
- b) accompany the distribution with the machine-readable source of the Package with your modifications.
-
- c) accompany any non-standard executables with their corresponding Standard Version executables, giving the non-standard executables non-standard names, and clearly documenting the differences in manual pages (or equivalent), together with instructions on where to get the Standard Version.
-
- d) make other distribution arrangements with the Copyright Holder.
-
-5. You may charge a reasonable copying fee for any distribution of this Package. You may charge any fee you choose for support of this Package. You may not charge a fee for this Package itself. However, you may distribute this Package in aggregate with other (possibly commercial) programs as part of a larger (possibly commercial) software distribution provided that you do not advertise this Package as a product of your own.
-
-6. The scripts and library files supplied as input to or produced as output from the programs of this Package do not automatically fall under the copyright of this Package, but belong to whomever generated them, and may be sold commercially, and may be aggregated with this Package.
-
-7. C or perl subroutines supplied by you and linked into this Package shall not be considered part of this Package.
-
-8. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission.
-
-9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-The End
diff --git a/licenses/OBO-Edit b/licenses/OBO-Edit
deleted file mode 100644
index 4c2b496ae..000000000
--- a/licenses/OBO-Edit
+++ /dev/null
@@ -1,9 +0,0 @@
-OBO-Edit License Agreement
-Copyright (C) 2000-2007, Berkeley Bioinformatics and Ontologies Project
-Author: John Richter (jrichter@berkeleybop.org)
-
-OBO-Edit is hearby released to the public under the terms of the Artistic License
-contained in this archive in the file ARTISTIC_LICENSE.
-
-OBO-Edit makes use of the org.bbop toolkit, which is free to distribute and
-modify. \ No newline at end of file
diff --git a/media-libs/embree-bin/embree-bin-3.12.0.ebuild b/media-libs/embree-bin/embree-bin-3.12.0.ebuild
index 77e7a248a..479c2eb90 100644
--- a/media-libs/embree-bin/embree-bin-3.12.0.ebuild
+++ b/media-libs/embree-bin/embree-bin-3.12.0.ebuild
@@ -21,7 +21,7 @@ RDEPEND="
dev-lang/ispc
media-libs/glfw
media-libs/glu
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
virtual/opengl
x11-libs/libxcb
x11-libs/libX11
diff --git a/media-libs/embree-bin/embree-bin-3.12.1.ebuild b/media-libs/embree-bin/embree-bin-3.12.1.ebuild
index 77e7a248a..479c2eb90 100644
--- a/media-libs/embree-bin/embree-bin-3.12.1.ebuild
+++ b/media-libs/embree-bin/embree-bin-3.12.1.ebuild
@@ -21,7 +21,7 @@ RDEPEND="
dev-lang/ispc
media-libs/glfw
media-libs/glu
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
virtual/opengl
x11-libs/libxcb
x11-libs/libX11
diff --git a/media-libs/embree-bin/embree-bin-3.12.2.ebuild b/media-libs/embree-bin/embree-bin-3.12.2.ebuild
index 7b9d5d0dd..10bd17f02 100644
--- a/media-libs/embree-bin/embree-bin-3.12.2.ebuild
+++ b/media-libs/embree-bin/embree-bin-3.12.2.ebuild
@@ -22,7 +22,7 @@ RDEPEND="
dev-lang/ispc
media-libs/glfw
media-libs/glu
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
virtual/opengl
x11-libs/libxcb
x11-libs/libX11
diff --git a/media-libs/embree-bin/embree-bin-3.13.0.ebuild b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
index a1cf40c1a..ac7de32f4 100644
--- a/media-libs/embree-bin/embree-bin-3.13.0.ebuild
+++ b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
@@ -25,7 +25,7 @@ RDEPEND="
dev-lang/ispc
media-libs/glfw
media-libs/glu
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
virtual/opengl
x11-libs/libxcb
x11-libs/libX11
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index 05ff69f80..ad8668437 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,3 @@
DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2
-DIST ownCloud-2.9.2.6206.tar.xz 5759996 BLAKE2B c328ea261a4fddecf93837dbcac01aab0971542d8dfb3f5b0a32a8432ca0e0904c3f4fc81c5c7811da8b3af64b58e929c055e7cec0649f00049e037372948eec SHA512 d075a11ee92aa9771c631a766feddfa1a70907d7d341b58043e1ba96ac52786a6a750b15c2f9b7a0992fe02a45586cc3445755dc9df4cd267e72f070d2222f0f
+DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
diff --git a/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
index 27080cd72..c4eeaa7be 100644
--- a/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -73,7 +73,6 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
- -DSYSCONF_INSTALL_DIR="${EPREFIX}"/etc
-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
-DBUILD_TESTING=$(usex test)
diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..b338c8d20 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,9 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 May 2022)
+# Requires old and removed batik:1.9::gentoo
+# No updates since 2019
+# Mask for removal in 30 days
+dev-java/jeuclid-core
diff --git a/sci-astronomy/libthesky/Manifest b/sci-astronomy/libthesky/Manifest
index f29fbac70..aed369dea 100644
--- a/sci-astronomy/libthesky/Manifest
+++ b/sci-astronomy/libthesky/Manifest
@@ -1,2 +1,2 @@
-DIST libthesky-0.4.1.tar.gz 214547 BLAKE2B 4f3c8dbda236cd86505e1aa307546e39f9e615341605bed0bf5980ff04b6506dd33be3d037fa2913d80ffe858b0d6ae6ad5c9284d1bce43aeb1d6d78d7c36177 SHA512 a8e46c325c8c13a53177ae482ace79fa5de8507d1b052df412df7735692c19712915f78ebd0ecd83c1a0ed9d9b9d99f6065ae3c313ec4842d2223b28558abcb1
+DIST libthesky-0.4.2.tar.gz 217861 BLAKE2B 8197878a299b93e6c6f98aef5555bbbb4304ade0fff10714a4fb33cf6eac89ccd4ae24400f5ee0262dca877cf770e85525787ceca2b95700407ddd3f5fa5e133 SHA512 70bcc525d54f1645cff65fc0ac702fb0a19445d74fa3c567aa07fed027b966c4753146becb9efc46e81521d1788846c460c47ec88d6611cec0524c2dad7cb646
DIST libthesky-data-20160409.tar.bz2 3780265 BLAKE2B 9331156f7536d634f8523e776209190d73c10158800ff73694ac499292b2be80948810e6aaa531b51d878b5018f7304188b855fcbc976a1b1c285829555d2f4e SHA512 b790aa70b60c6c35db85a54de3487aa5ef47710121cb6c6c13069d4d8adba822b61449eb59ce7ec9203fb4d9cf33570222ec9a65b36ac21f5d4506cddd0b35a3
diff --git a/sci-astronomy/libthesky/libthesky-0.4.1-r1.ebuild b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
index bda782891..09f89265f 100644
--- a/sci-astronomy/libthesky/libthesky-0.4.1-r1.ebuild
+++ b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
CMAKE_BUILD_TYPE=Release
-inherit cmake fortran-2
CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
DESCRIPTION="Fortran library to compute positions of celestial bodies"
HOMEPAGE="http://libthesky.sourceforge.net/"
@@ -18,14 +18,12 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static-libs"
-DEPEND="~sci-libs/libsufr-0.7.5[static-libs?]"
+DEPEND="sci-libs/libsufr[static-libs?]"
RDEPEND="${DEPEND}"
src_unpack() {
default
-
gunzip -r "${S}"/man || die
-
mv "${WORKDIR}"/data "${S}" || die
}
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
index b882373e2..4b5476138 100644
--- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
+++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
index b882373e2..4b5476138 100644
--- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
+++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
index 0d53f2a90..e28aa18be 100644
--- a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
+++ b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
@@ -8,7 +8,7 @@ inherit check-reqs
DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-expression-data_generator"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="fairuse"
diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
index 1aa7e99be..f02907368 100644
--- a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module
@@ -10,16 +10,15 @@ COMMIT="94af39622aab5ba48eb693f2327f6e90f1d202ed"
DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
HOMEPAGE="https://github.com/The-Sequence-Ontology/GAL"
SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
LICENSE="( GPL-1+ Artistic )"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
RESTRICT="test"
DEPEND="
- >=dev-lang/perl-5.6.1
- dev-perl/Module-Build
dev-perl/Config-Std
virtual/perl-Data-Dumper
dev-perl/Data-Types
@@ -29,6 +28,7 @@ DEPEND="
dev-perl/Number-Format
virtual/perl-Scalar-List-Utils
dev-perl/Set-IntSpan-Fast
+ dev-perl/Statistics-Descriptive
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit
dev-perl/Text-Graph
@@ -36,7 +36,12 @@ DEPEND="
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
- dev-perl/URI"
+ dev-perl/URI
+ sci-biology/fasta
+"
RDEPEND="${DEPEND}"
+BDEPEND="dev-perl/Module-Build"
-S="${WORKDIR}/${PN}-${COMMIT}"
+PATCHES=(
+ "${FILESDIR}/Build.PL.patch"
+)
diff --git a/sci-biology/GAL/files/Build.PL.patch b/sci-biology/GAL/files/Build.PL.patch
index 6d881f249..eee4fb60d 100644
--- a/sci-biology/GAL/files/Build.PL.patch
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -1,16 +1,11 @@
-diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
---- GAL_0.2.2.orig/Build.PL 2014-01-30 01:35:11.000000000 +0100
-+++ GAL_0.2.2/Build.PL 2016-01-02 12:09:16.212623256 +0100
-@@ -6,26 +6,6 @@
- my $class = Module::Build->subclass
- (
- class => 'Module::Build::Custom',
-- code => q{
-- sub ACTION_build {
-- my $self = shift;
-- $self->SUPER::ACTION_build;
-- $self->dispatch('installdeps');
-- }
+diff --git a/Build.PL b/Build.PL
+index 5915ca8..61eceb3 100644
+--- a/Build.PL
++++ b/Build.PL
+@@ -12,19 +12,6 @@ my $class = Module::Build->subclass
+ $self->SUPER::ACTION_build;
+ $self->dispatch('installdeps');
+ }
- sub ACTION_install {
- my $self = shift;
- print "\n\nGAL does not do a system wide install\n\n";
@@ -24,7 +19,6 @@ diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
- print "remove the entire subroutine (ACTION_install) where this message\n";
- print "is printed run Build realclean and re-install.\n\n";
- }
-- },
+ },
);
- my $builder = $class->new(
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
deleted file mode 100644
index 898898b94..000000000
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
-HOMEPAGE="https://github.com/bcgsc/LINKS"
-SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RESTRICT="test"
-
-RDEPEND="
- >=dev-lang/perl-1.6
- dev-lang/swig
- dev-util/cppcheck
-"
-# sci-biology/btl_bloomfilter
-
-src_compile(){
- cd btllib | die "Cannot chdir to bundled btllib/"
- ./compile-wrappers || die "Failed to compile bundled btllib"
- # baah, this also does some kind of install
- # SUCCESS: sdsl was installed successfully!
- # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
- # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
- #
- # Sample programs can be found in the examples-directory.
- # A program 'example.cpp' can be compiled with the command:
- # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
- # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
- # example.cpp -lsdsl -ldivsufsort -ldivsufsort64
- #
- # Tests in the test-directory
- # A cheat sheet in the extras/cheatsheet-directory.
- # Have fun!
- # [2/3] Installing files.
- # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
- # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python
-}
-
-src_install(){
- sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
- sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
- dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
- dodoc README.md
-}
diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild
new file mode 100644
index 000000000..c1c9cc5d8
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS"
+SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${PV}/links-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/links-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-lang/perl-1.6
+ dev-util/cppcheck
+"
+DEPEND="${RDEPEND}
+ dev-lang/swig
+"
diff --git a/sci-biology/LINKS/Manifest b/sci-biology/LINKS/Manifest
index bc5133d76..e57aae29d 100644
--- a/sci-biology/LINKS/Manifest
+++ b/sci-biology/LINKS/Manifest
@@ -1 +1 @@
-DIST LINKS-1.8.7.tar.gz 13550877 BLAKE2B ee77f295b0dfc70494b985075c1be794492178c050117f7d775d9cfb2a0dc2ab96030fae2b05075955b03ed99683586fd1b0688a99cd741671be762021bc06e8 SHA512 1b869229275eddc7cb9ae2df1d4f9422741b845df50d438761a8afd4ea172244ded1a70e4fba42045e09a0ae23f8a64e2233d66a261698c13aba1b231576015c
+DIST LINKS-2.0.1.tar.gz 4566466 BLAKE2B 0713278c17b5d6fce3d6c0bbfffd2decd71599464b9d4c7da5b82997dfc6f2e1be7435dc26bc96eb6ce23ba0bd8136f8ca714e327de465137e0435ebdaa19d9c SHA512 2bbcc264da6dbe361d8224e2a123983c4f09a4b051490d599f193e3f02463e4e8ff2fadf72b8be2df6adee6db886b76d59eee179648cfed6a025c31d7fe2c696
diff --git a/sci-biology/MolBioLib/Manifest b/sci-biology/MolBioLib/Manifest
deleted file mode 100644
index fcfe68414..000000000
--- a/sci-biology/MolBioLib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MolBioLib_public.version5.tar.gz 2414384 BLAKE2B 845ac366ed41886cc0d3d96376dc9a97bae3d84bfc41d5f9e5be4fa274a6d64a981fcbcc12de28e1518212313af12330b08cac5488e7db9a2738c7846b981cb7 SHA512 056c38bcb65b845b32678fb8c5d758023154c07085414194e98e58281e61e475dca7321c8d684955c88bf459bc92c9d39f8b6091d0b804581e6f6e6ecabe3832
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
deleted file mode 100644
index bbbbeb605..000000000
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-
-inherit docs
-
-DESCRIPTION="C++11 framework for bioinformatics tasks"
-HOMEPAGE="https://sourceforge.net/projects/molbiolib"
-SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # does not build
-
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62)
-# which contains jsoncpp, also needs app-doc/doxygen
-DEPEND="
- dev-lang/perl
- sys-devel/gcc:*
- sys-devel/clang:*
- >=sci-biology/samtools-0.1.18:0.1-legacy
- <sci-biology/samtools-1:0.1-legacy"
-RDEPEND="${DEPEND}"
-CDEPEND="doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}"/MolBioLib
-
-src_compile(){
- perl MakeAllApps.pl || die
- docs_compile
-}
-
-src_install() {
- einstalldocs
- # TODO: install this
-}
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
deleted file mode 100644
index 3b9e38617..000000000
--- a/sci-biology/MolBioLib/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">molbiolib</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest
deleted file mode 100644
index 328ce0bca..000000000
--- a/sci-biology/OBO-Edit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST OBO-Edit_unix_install4j-2.3.1.sh 44841394 BLAKE2B cdde5fa8bd3ce505bc18471a3924f35f6bdcac426a260c65568cdc0a70027c86d095c05e85441e770b4a6d3d0d8de3da1a3808bc3c3758e51e708e60864c0ab4 SHA512 3a48c20c02727057e3dfc7e94cf5e414942a63a9b2339e2bc6bb19e8f45ac0289904e1e6cf7b83efa53bf32b7f188c36d0deb539e169710ea2f326c5ea323603
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
deleted file mode 100644
index 321d3901c..000000000
--- a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2
-
-MY_PV="${PV//./_}"
-
-DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
-HOMEPAGE="http://www.oboedit.org/" # no https, invalid certificate
-SRC_URI="https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/oboedit_${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh"
-
-LICENSE="OBO-Edit" # Artistic-like
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="app-arch/rpm2targz"
-RDEPEND="virtual/jre"
-
-S="${WORKDIR}"
-
-pkg_setup() {
- einfo "Fixing java access violations ..."
- # learned from bug #387227
- # opened a bug #402507 to get this .systemPrefs directory pre-created for everybody
- addpredict /opt/icedtea-bin-7.2.0/jre/.systemPrefs
- addpredict /usr/local/bin/OBO-Edit
-}
-
-src_prepare(){
- default
- dodir /opt/OBO-Edit2/.install4j /usr/bin
- cp "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh "${WORKDIR}" || die
-
- # /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile
- sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \
- sed -e "s#\"\${HOME}\"#"${HOME}"#g" | \
- sed -e "s@sys.symlinkDir=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \
- > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
- cp -r "${D}"/opt/OBO-Edit2/.install4j "${HOME}" || die
-
- # for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it
- # found via JAVA_HOME or similar variables
- # for other users it writes into $HOME/.java/.userPrefs/
-
- # trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work
- sed \
- -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${HOME}" -Dinstall4j.jvmDir="${HOME}" -Dsys.symlinkDir="${D}"/usr/bin -Djava.util.prefs.systemRoot="${HOME}"@" \
- -i "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh \
- || die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found"
-
- chmod u+rx "${WORKDIR}/${PN}"_unix_install4j-"${PV}".sh || die
-}
-
-src_install(){
- # it looks install4j removes the target installation direcotry before writing into it :((
- #
- # cat "${TMPDIR}"/.install4j/response.varfile
- # chmod a-w "${TMPDIR}"/.install4j/response.varfile
-
- INSTALL4J_KEEP_TEMP="yes" \
- sh "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \
- --varfile="${HOME}"/.install4j/response.varfile \
- --destination="${D}"/opt/OBO-Edit2 \
- -dir "${D}"/opt/OBO-Edit2 \
- || die "Failed to run the self-extracting ${WORKDIR}/${PN}_unix_install4j-${PV}.sh file"
-
- find . -name firstrun -delete || die
-
- echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die
- doenvd 99OBO-Edit
-}
diff --git a/sci-biology/OBO-Edit/files/response.varfile b/sci-biology/OBO-Edit/files/response.varfile
deleted file mode 100644
index 8c4361d01..000000000
--- a/sci-biology/OBO-Edit/files/response.varfile
+++ /dev/null
@@ -1,10 +0,0 @@
-#install4j response file for OBO-Edit2 2.1.1-b6
-#Tue Feb 07 03:08:04 MET 2012
-sys.component.89$Boolean=false
-createDesktopLinkAction$Boolean=false
-oboedit.memoryAlloc$Integer=3456
-sys.programGroupDisabled$Boolean=true
-sys.component.61$Boolean=true
-sys.symlinkDir="${D}"usr/bin
-sys.languageId=en
-sys.installationDir="${D}"opt/OBO-Edit2
diff --git a/sci-biology/OBO-Edit/metadata.xml b/sci-biology/OBO-Edit/metadata.xml
deleted file mode 100644
index acbbc35a4..000000000
--- a/sci-biology/OBO-Edit/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">geneontology</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest
deleted file mode 100644
index f732ff7a8..000000000
--- a/sci-biology/SOAPdenovo2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SOAPdenovo2-242.tar.gz 1534059 BLAKE2B e72b8b8005a807e1f949d092a1b582ed75ddbd3f4a1f014f86754ae69e279b93758693f36942e16183095fcfcc843a637fab39b08cfa6b8cbeffaf8b07c3050a SHA512 eaa2020aa9054588805bd69bb2e1d70be5bfcad31d52a33ed8f7accd4006db1ec980b20f846a6e1c0ee0ec8a493c38febb9022ce6a59c14d03fe43a3ca50569b
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
deleted file mode 100644
index 33fd4a2a3..000000000
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
-HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
- https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
-SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # fails to compile
-
-DEPEND="dev-libs/libaio
- sci-biology/samtools:0.1-legacy"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241
-
-src_prepare(){
- #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
- # this will be partly covered by
- # https://github.com/aquaskyline/SOAPdenovo2/pull/44
- #
- for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do
- sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die
- done
- rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
- sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
- standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
- sparsePregraph/*.a || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- default
-}
diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
deleted file mode 100644
index a710c2d86..000000000
--- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
+++ /dev/null
@@ -1,204 +0,0 @@
---- sparsePregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ sparsePregraph/Makefile 2018-04-22 22:07:47.303546845 +0200
-@@ -1,28 +1,28 @@
--CC= g++
-+CXX ?= g++
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS= -O3 -fomit-frame-pointer -w
-+CXXFLAGS ?= -O3 -fomit-frame-pointer -w
- endif
-
--DFLAGS=
--OBJS= build_graph.o build_edge.o multi_threads.o \
-- build_preArc.o pregraph_sparse.o io_func.o\
-- global.o convert_soapdenovo.o
--PROG=
--INCLUDES= -I./inc
--SUBDIRS= .
--LIBPATH= -L/usr/lib64
--LIBS= -pthread -lz -L./inc
-+DFLAGS =
-+OBJS = build_graph.o build_edge.o multi_threads.o \
-+ build_preArc.o pregraph_sparse.o io_func.o\
-+ global.o convert_soapdenovo.o
-+PROG =
-+INCLUDES = -I./inc
-+SUBDIRS = .
-+LIBPATH = -L/usr/lib64
-+LIBS = -pthread -lz -L./inc
- EXTRA_FLAGS=
--VERSION = 1.0.3
-+VERSION = 1.0.3
-
- ifdef 127mer
--CFLAGS += -D_127MER_
-+CXXFLAGS += -D_127MER_
- PROG = pregraph_sparse_127mer.v$(VERSION)
-
- else
--CFLAGS += -D_63MER_
-+CXXFLAGS += -D_63MER_
- PROG = pregraph_sparse_63mer.v$(VERSION)
- endif
-
-@@ -38,22 +38,22 @@
- endif
-
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
-
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS +=
-+CXXFLAGS +=
- endif
-
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
-
- .SUFFIXES:.cpp .o
-
- .cpp.o:
- @printf "Compiling $<... \r"
-- @$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
-+ @$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<"
-
- all: $(OBJS)
- @printf "$(PROG) objects generated. \n"
-@@ -66,7 +66,7 @@
-
- pregraph_sparse: clean envTest $(OBJS)
- @printf "Linking... \r"
-- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
-+ @$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
- @printf "$(PROG) compilation done. \n"
-
- clean:
---- Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ Makefile 2018-04-22 22:09:16.526124921 +0200
-@@ -1,17 +1,17 @@
- MAKEFLAGS += --no-print-directory
--CC = g++
-+CXX ?= g++
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS= -O3 -fomit-frame-pointer
-+CXXFLAGS ?= -O3 -fomit-frame-pointer
- endif
-
- SUBDIRS = sparsePregraph standardPregraph fusion
--PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
--INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc
-+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
-+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc
-
--LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
--LIBS= -pthread -lz -lm
-+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc
-+LIBS = -pthread -lz -lm
- EXTRA_FLAGS=
-
- BIT_ERR = 0
-@@ -25,15 +25,15 @@
- endif
-
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
-
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS +=
-+CXXFLAGS +=
- endif
-
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
-
-
-@@ -46,20 +46,20 @@
- SOAPdenovo-63mer:
- @cd sparsePregraph;make 63mer=1 debug=1;cd ..;
- @cd standardPregraph;make 63mer=1 debug=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- @cd sparsePregraph;make 127mer=1 debug=1;cd ..;
- @cd standardPregraph;make 127mer=1 debug=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- else
- SOAPdenovo-63mer:
- @cd sparsePregraph;make 63mer=1;cd ..;
- @cd standardPregraph;make 63mer=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- @cd sparsePregraph;make 127mer=1;cd ..;
- @cd standardPregraph;make 127mer=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- endif
-
- clean:
---- standardPregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ standardPregraph/Makefile 2018-04-22 22:10:33.108337752 +0200
-@@ -5,13 +5,13 @@
- #
- ###################################
-
--CC= gcc
-+CC ?= gcc
- GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2
-+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2
- else
--CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2
-+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2
- endif
- DFLAGS=
- OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
-@@ -24,12 +24,12 @@
- prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\
- readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
- cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
--PROG= SOAPdenovo-63mer
--INCLUDES= -Iinc
--SUBDIRS= .
--LIBPATH= -L/lib64 -L/usr/lib64 -L./inc
--LIBS= -pthread -lz -lm
--EXTRA_FLAGS=
-+PROG = SOAPdenovo-63mer
-+INCLUDES = -Iinc
-+SUBDIRS = .
-+LIBPATH = -L./inc
-+LIBS = -pthread -lz -lm
-+EXTRA_FLAGS =
-
- BIT_ERR = 0
- ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
---- fusion/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ fusion/Makefile 2018-04-22 22:11:21.209727636 +0200
-@@ -6,8 +6,8 @@
- libdir =
- mandir =
-
--CC = gcc
--CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w
-+CC ?= gcc
-+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w
- LIBS = -lm -lpthread
- INCDIRS = -Iinc/
- CFLAGS = ${CCOPT} ${INCDIRS}
diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1
deleted file mode 100644
index 337618ace..000000000
--- a/sci-biology/SOAPdenovo2/files/soapdenovo2.1
+++ /dev/null
@@ -1,22 +0,0 @@
-.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS"
-.SH NAME
-soapdenovo2 \- Short-read assembly method that can build a de novo draft assembly
-.SH SYNOPSIS
-.B soapdenovo_63mer soapdenovo_127mer
-
-.SH Introduction
-
-SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
-
-1) Support large kmer up to 127 to utilize long reads. Three version are provided.
- I. The 31mer version support kmer only <=31.
- II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31.
- III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63.
-
-Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version.
-
-For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site.
-
-.SH AUTHOR
-Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-
diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/SOAPdenovo2/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index e10186934..57f4fc569 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,4 +1,4 @@
-DIST SPAdes-3.15.1.tar.gz 13686155 BLAKE2B fb0ff0de93302268e1fc28199be3e14ef670aeab91fca82f2e895f899c9cd8d5380c31d4fe2e884737a917ff04a94cf55d25b91a27b47c91aa3e7c7408b9bd87 SHA512 b2ee4719937912f2b6326b67f602dc62f4be319ccf2774380a487da67fc2e32adcfa417ac5fcf4c5494f80152aab561b87e30a2d36abfe50ed1c48396b44d9d9
-DIST SPAdes-3.15.1_manual.html 78200 BLAKE2B b78da09ae94a46fbf4df19ba668276e6129083e7b50f66f86da137f8ed6435a2300b133be58fe25edb0cbb598aeb66e9310425574408bc419a3e3dff18893b15 SHA512 c3571abc87ffea1c54d7f0d42ce73955a7d101a4a61ecd104538832d193eab19c8813cf0a732f2bbe428724c24be283db89165900c2d49a7f3142770de4ca3b6
-DIST SPAdes-3.15.1_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
-DIST SPAdes-3.15.1_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
+DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4
+DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b
+DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
deleted file mode 100644
index 853524984..000000000
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="https://cab.spbu.ru/software/spades"
-SRC_URI="
- https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
- https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
- https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
- https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
-# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used,
-# not *.so or *.a are even used)
-#
-# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
-# existing packages
-# nlopt
-# llvm
-# python_libs
-# bamtools
-# ConsensusCore
-# ssw
-# jemalloc
-# htrie
-# getopt_pp
-# cppformat
-# cityhash
-# samtools
-# bwa
-
-# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary?
-# bwa-0.7.12
-# bwa-0.6.2
-
-src_compile(){
- PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
-
-src_install(){
- # BUG: move *.py files to standard site-packages/ subdirectories
- insinto /usr/share/"${PN}"
- dodoc "${DISTDIR}"/${P}_*manual.html
-}
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
new file mode 100644
index 000000000..553c21e21
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+ https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+ https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+ https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+ https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ dev-python/regex
+ ${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-util/cmake"
+
+src_install(){
+ einstalldocs
+ # WORKAROUND: This script does both compile and install in one go
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest
index 30ecd61fa..cb1b89168 100644
--- a/sci-biology/Trinotate/Manifest
+++ b/sci-biology/Trinotate/Manifest
@@ -1 +1 @@
-DIST Trinotate-3.2.1.tar.gz 29794455 BLAKE2B b630b4750540aeefaed598d34038ebc4bf0147f998d9a45038759b1f02cd210835b88cdc7e8e5b8e194ade05b410f8e76ea562c09dcbf09bfa56cfffafa207c3 SHA512 0c2c5021156651644cfcec09bdd19f45c4dd5ab5dd63effbacca3ffc13a32ff3b2050d8fe860e4302ade142f350c895303925542aa730c16abe0721654f8cad7
+DIST Trinotate-3.2.2.tar.gz 12902856 BLAKE2B 741b5b7386c5de646a4a1f3aa4ffc7ed9c4891e64a977efc5cd482eb0cd9315fbddc1db35f20f6fbbf136e28942542f72d33c078524971968a932f5af5d6551b SHA512 9e302eee948974c647fdcc6a352b17d55f3bd1331f6d3ddc49e0fc35f5603dcc370e9c6020e7b33dcd57324a954eab2ed3e81f2e34ef83af2fd97c793f1dfc48
diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
index ca61abdf4..794de03ae 100644
--- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
@@ -1,17 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${PN}-v${PV}"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
@@ -32,8 +33,6 @@ RDEPEND="${DEPEND}
# In the 'rnammer' software configuration, edit the rnammer script to point
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-S="${WORKDIR}/${PN}-${PN}-v${PV}"
-
src_install(){
perl_set_version
dobin Trinotate
diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index 2f909b5c4..e8caa43d1 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,3 +1,3 @@
-DIST afni-19.3.12.tar.gz 42337320 BLAKE2B f8f3347e38b7c4b3d720c3c49d5bc50f1057b1d3945e6a33b8415e84e7e539577e5eb351cfc61c53269b6a465619f900b9edcb25830ea056a53f54beb683b0ad SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371
DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6
DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65
+DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index e2ed432c8..e3e16f834 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -21,7 +21,7 @@ RDEPEND="dev-libs/expat
media-video/mpeg-tools
sci-libs/gsl
sys-devel/llvm:*
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
x11-libs/libGLw
x11-libs/libXft
x11-libs/libXi
@@ -46,17 +46,17 @@ src_prepare() {
# Unbundle imcat
sed -e "s/ imcat / /g" \
-i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
-e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
index 3185a297a..1d9043ebb 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -21,7 +21,7 @@ RDEPEND="dev-libs/expat
media-video/mpeg-tools
sci-libs/gsl
sys-devel/llvm:*
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
x11-libs/libGLw
x11-libs/libXft
x11-libs/libXi
@@ -39,28 +39,24 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-#PATCHES=(
-# "${FILESDIR}/${P}-python.patch"
-#)
-
src_prepare() {
- eapply "${FILESDIR}/${P}-python.patch" || die
+ eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
find -type f -exec sed -i -e "s/-lXp //g" {} +
cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
# Unbundle imcat
sed -e "s/ imcat / /g" \
-i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
-e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
index db19930fd..149deede8 100644
--- a/sci-biology/afni/afni-19.3.12.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -1,46 +1,49 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+# SUMA error: https://ppb.chymera.eu/4223de.log
+KEYWORDS=""
-RDEPEND="dev-libs/expat
+RDEPEND="
+ dev-libs/libf2c
+ dev-libs/expat
+ media-libs/freeglut
media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools
sci-libs/gsl
sys-devel/llvm:*
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
x11-libs/libGLw
x11-libs/libXft
x11-libs/libXi
x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+ x11-libs/motif
+"
DEPEND="${RDEPEND}
- app-shells/tcsh"
+ app-shells/tcsh
+"
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
+ # more easily applied here than via PATCHES at phase end.
+ eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
+ find -type f -exec sed -i -e "s/-lXp //g" {} + || die
cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
# Unbundle imcat
sed -e "s/ imcat / /g" \
@@ -52,11 +55,11 @@ src_prepare() {
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+ sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
+ default
}
src_compile() {
@@ -64,9 +67,9 @@ src_compile() {
}
src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
+ emake INSTALLDIR="${ED}/usr/bin" install install_plugins
+ emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
+ rm "${ED}/usr/bin/${CONFLICT}" || die
done
}
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
deleted file mode 100644
index c6e4c669b..000000000
--- a/sci-biology/afni/afni-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/AFNI/AFNI"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- virtual/jpeg:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${P}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
index 24ed98405..8c3e859f5 100644
--- a/sci-biology/afni/files/afni-20.1.16-python.patch
+++ b/sci-biology/afni/files/afni-20.1.16-python.patch
@@ -1,5 +1,5 @@
--- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
++++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
@@ -11,8 +11,6 @@
# ------------------------------
diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch
deleted file mode 100644
index 24ed98405..000000000
--- a/sci-biology/afni/files/afni-20.3.03-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration
diff --git a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
index 4606fa9df..b0ac5fe00 100644
--- a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
+++ b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,7 +13,7 @@ SRC_URI="http://johnhommer.com/code/aghermann/source/${P}.tar.xz"
LICENSE="GPL-2+"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
REQUIRED_USE="${LUA_REQUIRED_USE}"
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
index 756fde11d..95eb6355b 100644
--- a/sci-biology/ants/ants-2.3.4.ebuild
+++ b/sci-biology/ants/ants-2.3.4.ebuild
@@ -14,7 +14,7 @@ HOMEPAGE="http://stnava.github.io/ANTs/"
SRC_URI="
https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
test? (
- http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
+ http://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
)
"
diff --git a/sci-biology/arachne/Manifest b/sci-biology/arachne/Manifest
deleted file mode 100644
index c70683996..000000000
--- a/sci-biology/arachne/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST arachne-46233.tar.gz 5161566 BLAKE2B dc9381fae80477e4a2439e24cbcf9bc462c7a4effb06c26a9f74ad1740f86a96273c3dae142d0065aad08d6340e9508528c35ee6914a8405b66327bfc4ec89da SHA512 4ab293e7f4477dd6aeba7c6bc1a78d168cbb811d7f67cbcbc1eea094a7b6bd180bdde6fb1b7c8256ff473dba3d748a43bd426d971575f1c0793289a0b200dc2b
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
deleted file mode 100644
index b34d00134..000000000
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
-HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc openmp"
-
-DEPEND="dev-libs/xerces-c
- doc? ( virtual/latex-base app-text/dvipsk )"
-RDEPEND="${DEPEND}"
-
-# needs >=g++-4.7 but does not compile with 5.3.0
-
-# --disable-openmp to disable requirement for OpenMP-capable compiler
-src_configure() {
- local myconf=()
- use openmp || myconf+=( --disable-openmp )
- econf ${myconf[@]}
-}
-
-# set the following environment variables
-# http://www.broadinstitute.org/crd/wiki/index.php/Setup
-#
-# ARACHNE_PRE
-# ARACHNE_BIN_DIR
-# ARACHNE_PRETTY_HELP
-
-pkg_postinst(){
- einfo "Please add these to your ~/.bashrc"
- einfo "limit stacksize 100000"
- einfo "limit datasize unlimited"
-}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/arachne/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
index e92c8c8da..475c7f0b1 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module toolchain-funcs
@@ -66,28 +66,12 @@ src_prepare() {
einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
- cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
- sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
-}
-
-src_compile() {
- emake DESTDIR="${ED}/usr"
-
- # TODO:
- #ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
- # ld: warning: creating a DT_TEXTREL in object.
- #
- # * QA Notice: The following files contain runtime text relocations
- # * Text relocations force the dynamic linker to perform extra
- # * work at startup, waste system resources, and may pose a security
- # * risk. On some architectures, the code may not even function
- # * properly, if at all.
- # * For more information, see http://hardened.gentoo.org/pic-fix-guide.xml
- # * Please include the following list of files in your report:
- # * TEXTREL usr/bin/grommit
}
src_install() {
+ pushd src/TIGR_Foundation_CC || die
+ sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
+ popd || die
emake DESTDIR="${ED}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
@@ -102,13 +86,13 @@ src_install() {
done
rm "${ED}"/usr/lib/libTigrFoundation.a || die
- dodir /usr/share/doc/${P}
+ dodir /usr/share/doc/${PF}
mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
rmdir "${ED}"/usr/doc || die
dobin "${FILESDIR}"/goBambus.pl
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
- rm -rf "${ED}"/usr/lib || die
+ rm -r "${ED}"/usr/lib || die
}
pkg_postinst(){
diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest
index e5e6f36cd..916b93320 100644
--- a/sci-biology/behaviopy/Manifest
+++ b/sci-biology/behaviopy/Manifest
@@ -1 +1 @@
-DIST behaviopy-0.1.tar.gz 32986 BLAKE2B f0de67a59591f266906d0b21c8fedf1e847df47128f0cb45e10fca849c674cb95d1ef586f407c9775ccaad8a7300aa4d6a67f1a4cc77fa18af28ec0848b77605 SHA512 8cead97a6bf06b31b817999377e5460ec7b05b58a997bcad9c8947f6cd1ab48d2525600c0c6e18bd6e52fccd8a9358b5f36c9911d1fab0fb974dc6581a63949b
+DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc
diff --git a/sci-biology/behaviopy/behaviopy-0.1.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild
index 35bcaab6b..ca6700729 100644
--- a/sci-biology/behaviopy/behaviopy-0.1.ebuild
+++ b/sci-biology/behaviopy/behaviopy-0.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -13,11 +13,9 @@ SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.ta
LICENSE="GPL-3"
SLOT="0"
-IUSE="evaluation test"
+IUSE="evaluation"
KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
RDEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
@@ -25,17 +23,17 @@ RDEPEND="
dev-python/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- "
+"
-src_prepare() {
+python_prepare_all() {
if ! use evaluation; then
rm behaviopy/evaluation.py || die
fi
- default
+ distutils-r1_python_prepare_all
}
python_test() {
- cd behaviopy/examples
+ cd behaviopy/examples || die
echo "backend : Agg" > matplotlibrc || die
for i in *py; do
echo "Executing $i"
diff --git a/sci-biology/behaviopy/behaviopy-9999.ebuild b/sci-biology/behaviopy/behaviopy-9999.ebuild
deleted file mode 100644
index a4c087764..000000000
--- a/sci-biology/behaviopy/behaviopy-9999.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://github.com/TheChymera/behaviopy"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/TheChymera/behaviopy"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="evaluation test"
-KEYWORDS=""
-RESTRICT="!test? ( test )"
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
-RDEPEND="
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
- #evaluation? ( sci-biology/psychopy[${PYTHON_USEDEP}] )
-
-src_prepare() {
- if ! use evaluation; then
- rm behaviopy/evaluation.py || die
- fi
- default
-}
-
-python_test() {
- cd behaviopy/examples
- echo "backend : Agg" > matplotlibrc || die
- for i in *py; do
- echo "Executing $i"
- ${EPYTHON} $i || die
- done
-}
diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
index 8552bff9e..85e4ea66d 100644
--- a/sci-biology/blasr/blasr-5.3.5.ebuild
+++ b/sci-biology/blasr/blasr-5.3.5.ebuild
@@ -7,7 +7,7 @@ inherit meson
DESCRIPTION="The PacBio long read aligner"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="blasr"
SLOT="0"
diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index e14efe3af..987fb99f2 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -28,8 +28,7 @@ RDEPEND="${PYTHON_DEPS}
DEPEND="${RDEPEND}
>=virtual/jdk-1.8:*
dev-java/ant-core
- !sci-biology/wgs-assembler
- "
+"
# Detected file collision(s):
# * sci-biology/wgs-assembler-8.3_rc2:0::science
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild
index 645e4ed30..162a03129 100644
--- a/sci-biology/chiron/chiron-0.6.1.1.ebuild
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/sci-biology/cortex_var/Manifest b/sci-biology/cortex_var/Manifest
deleted file mode 100644
index 969e60d0a..000000000
--- a/sci-biology/cortex_var/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST CORTEX_release_v1.0.5.21.tgz 26902149 BLAKE2B 397d309fa941fd76ca51f58f20e036dd51548455ae2831738f03fed2293bb3f8dac7443282bba900b3f264a14e6bdacc23ff5460e713c05d4c5e5f11de021080 SHA512 92200cc1e886e519a8e54c9054a2901a03001091654a0534c7a92a5fa7a0ac43aba782b59731d588525902adf749cabca64cdb9cdb25c215be9afb01690215e3
-DIST cortex_var_user_manual.pdf 265899 BLAKE2B 83797183e88f0c17fe3a114c2912263bb84b4c2dca1a0a2a563c82fe377111d24a8ad726581f62b3e44a6cc714bcf58ffd8c18f9f5bd0eb9df6130bd49b296ee SHA512 e4ff442f9280e9eee384c2b82c75493bdb90589b354333fc8b2bee8cf9c9baa432ec09dce5325b2e12c1e1930971616065713858565d56f9a361c573ac0c4f65
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
deleted file mode 100644
index d368f5db3..000000000
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Genotype variant discovery without reference sequence"
-HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" # no https
-SRC_URI="
- https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz
- http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-# http://www.well.ox.ac.uk/project-stampy
-
-DEPEND="
- sci-biology/vcftools
- sci-libs/gsl
- sci-libs/htslib:0=
- dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/CORTEX_release_v${PV}"
-
-src_prepare(){
- default
- sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die
- sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
-}
-
-src_compile(){
- rm -rf libs/htslib libs/gsl-1.15 || die
- emake -C libs/string_buffer
- emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file
- emake NUM_COLS=1 MAXK=31 cortex_var
-}
-
-src_install(){
- bash install.sh || die
- perl_set_version
- perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
- echo \
- "PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
- > "${T}/99${PN}" || die
- doenvd "${T}/99${PN}"
- dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
-}
diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml
deleted file mode 100644
index a2867d6fd..000000000
--- a/sci-biology/cortex_var/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">cortexassembler</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
index df7ba43bb..0312eda29 100644
--- a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
+++ b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="BIDS data selection of wildtype animals from DARGCC article"
HOMEPAGE="https://academic.oup.com/cercor/article/28/7/2495/4975475"
SRC_URI="
https://zenodo.org/record/3885733/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
index 6385db093..227aafd54 100644
--- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
+++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -9,7 +9,6 @@ DESCRIPTION="BIDS data files released with the DRLFOM publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
https://zenodo.org/record/3598424/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="CC-BY-SA-4.0"
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
deleted file mode 100644
index ca3945442..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
+++ /dev/null
@@ -1,240 +0,0 @@
-From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:40:53 +1300
-Subject: [PATCH] Making sure fsl code and executable can find other executable
- and data in standard location.
-
----
- src/fast4/fast_two.cc | 8 ++++----
- src/feat5/feat_model.cc | 8 +++-----
- src/feat5/tsplot.cc | 7 +++----
- src/first/first_utils.cc | 4 ++--
- src/fnirt/fnirtfns.cpp | 11 ++++-------
- src/fslsurface/fslsurface_first.cc | 6 ++----
- src/fslsurface/fslsurfacemaths.cpp | 12 ------------
- src/libvis/miscpic.h | 7 +------
- src/melodic/meldata.cc | 4 ++--
- src/melodic/meloptions.cc | 8 --------
- src/melodic/meloptions.h | 1 -
- src/melodic/melreport.cc | 12 ++++++------
- src/melodic/melreport.h | 20 ++++++++++----------
- src/mm/mixture_model.cc | 4 ++--
- src/siena/siena_diff.cc | 28 +++++++++++++---------------
- src/topup/topupfns.cpp | 3 +--
- 16 files changed, 53 insertions(+), 90 deletions(-)
-
-diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
-index 592b5df..b525444 100644
---- a/src/fast4/fast_two.cc
-+++ b/src/fast4/fast_two.cc
-@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
- string csfPriorName, grayPriorName, whitePriorName;
- if(alternatePriors.unset())
- {
-- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
-+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
- csfPriorName = priorRootName+"csf";
- grayPriorName = priorRootName+"gray";
- whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
- if(bapused>0)
- {
- char reg[1024];
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
-diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
-index 399a13e..e15e43c 100644
---- a/src/feat5/feat_model.cc
-+++ b/src/feat5/feat_model.cc
-@@ -744,7 +744,7 @@ int main(int argc, char **argv)
- vector<int> G;
- vector<string> titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[10000], *FSLDIR;
-+ char fl[10000];
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -763,8 +763,6 @@ int main(int argc, char **argv)
- if (argc==3)
- motionparams=remmean(read_ascii_matrix(argv[2]));
-
-- FSLDIR=getenv("FSLDIR");
--
- fn = string(argv[1])+".fsf";
-
- level = atoi(find_line(fn, "fmri(level)", fl));
-@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
- writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
- writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
-
-- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
-+ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
- system(filename.c_str());
-
- return(0);
-@@ -2161,6 +2159,6 @@ char the_string[10000];
-
- fclose(outputfile);
-
-- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
-+ filename="wpng -q -overwrite " + filename;
- system(filename.c_str());
- }
-diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
-index ae191fd..3a02b55 100644
---- a/src/feat5/tsplot.cc
-+++ b/src/feat5/tsplot.cc
-@@ -293,7 +293,7 @@ int main(int argc, char **argv)
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> normalisedContrasts, model, triggers;
-- string fmriFileName, fslPath, featdir, vType, indexText;
-+ string fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@ volume<float> immask;
- if (argc<2) usage("");
- featdir=string(argv[1]);
- fmriFileName=featdir+"/filtered_func_data";
-- fslPath=string(getenv("FSLDIR"));
-
- string outputName(featdir);
-
-@@ -753,7 +752,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -768,7 +767,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat report */
-diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
-index 68be44b..85960f4 100644
---- a/src/first/first_utils.cc
-+++ b/src/first/first_utils.cc
-@@ -1954,8 +1954,8 @@ void do_work_bvars(){
- if (!surfaceVAout.value()) {
- // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
- volume<float> refim;
-- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
-+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
- volume<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> volnormals;
-diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
-index 24e26fd..77899e7 100644
---- a/src/fnirt/fnirtfns.cpp
-+++ b/src/fnirt/fnirtfns.cpp
-@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
- return(string(ref_fname));
- }
- else {
-- const char *fsldir_ptr = getenv("FSLDIR");
-- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
- else return(string(""));
- }
-@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
- NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
- eref_fname = ref_fname;
- }
-- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
-- const char *fsldir_ptr = getenv("FSLDIR");
-- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ catch(...) { // Didn't exist in current directory, try in .../data/standard
-+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- try {
- cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
- NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
-@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
- if (check_exist(ecfname)) return(ecfname);
- }
- if (!FNIRT::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (check_exist(ecfname)) return(ecfname);
- else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
-diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
-index faec642..b2ef794 100644
---- a/src/fslsurface/fslsurface_first.cc
-+++ b/src/fslsurface/fslsurface_first.cc
-@@ -500,8 +500,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-@@ -699,8 +698,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
-index eaf55eb..3dc184d 100644
---- a/src/fslsurface/fslsurfacemaths.cpp
-+++ b/src/fslsurface/fslsurfacemaths.cpp
-@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconFromBvars"){
- cout<<"do recon "<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
deleted file mode 100644
index 74bf19169..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
+++ /dev/null
@@ -1,255 +0,0 @@
-diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
-index a2f3855..5f440f2 100644
---- a/src/libvis/miscpic.h
-+++ b/src/libvis/miscpic.h
-@@ -90,12 +90,7 @@ namespace MISCPIC{
- markRight=false;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index 1749a45..c4ad234 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -992,7 +992,7 @@ namespace Melodic{
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1157,7 +1157,7 @@ namespace Melodic{
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
-index 08170c7..252e72b 100644
---- a/src/melodic/meloptions.cc
-+++ b/src/melodic/meloptions.cc
-@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
-diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
-index f546125..b964b7d 100644
---- a/src/melodic/meloptions.h
-+++ b/src/melodic/meloptions.h
-@@ -93,7 +93,6 @@ class MelodicOptions {
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
-index 141b6c2..2625059 100644
---- a/src/melodic/melreport.cc
-+++ b/src/melodic/melreport.cc
-@@ -84,8 +84,8 @@ namespace Melodic{
- IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -486,8 +486,8 @@ namespace Melodic{
-
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -665,8 +665,8 @@ namespace Melodic{
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
-index 574fc4c..e444681 100644
---- a/src/melodic/melreport.h
-+++ b/src/melodic/melreport.h
-@@ -104,21 +104,21 @@ namespace Melodic{
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@ namespace Melodic{
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
-diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
-index b8e6167..5f00693 100644
---- a/src/mm/mixture_model.cc
-+++ b/src/mm/mixture_model.cc
-@@ -2224,8 +2224,8 @@ namespace Mm {
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
-index e19193a..17d8701 100644
---- a/src/siena/siena_diff.cc
-+++ b/src/siena/siena_diff.cc
-@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@ if (argc<3)
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
-index 6873758..9e8b956 100644
---- a/src/topup/topupfns.cpp
-+++ b/src/topup/topupfns.cpp
-@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
---
-2.24.1
-
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index 4797c1298..cd91cf192 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -28,12 +28,8 @@ DEPEND="
dev-lang/tk:0=
>=virtual/lapack-3.8
>=virtual/blas-3.8
-
cuda? (
- || (
- ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
- )
+ =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
)
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
index c51a9d30e..d3ec1de1d 100644
--- a/sci-biology/fsl/fsl-6.0.5.ebuild
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -39,9 +39,7 @@ DEPEND="
>=virtual/lapack-3.8
>=virtual/blas-3.8
cuda? (
- || (
- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
- )
+ =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
)
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/gffread/Manifest b/sci-biology/gffread/Manifest
index ea0f27b53..999049e10 100644
--- a/sci-biology/gffread/Manifest
+++ b/sci-biology/gffread/Manifest
@@ -1,2 +1,2 @@
-DIST gclib-0.11.0.tar.gz 184895 BLAKE2B ea8434c8a68fc7d032341271ed55eab3dcc8618da0ea823f7e1588598275a775369d1b7e7ce38eba02437272c28b56543ac50a50f5b0a03d01f37e24e85bb53e SHA512 ec773a805141e8f0f98774760e0608aac6c66c7541d4777c8cb0edcf2172a4bc86a0f0c1f6f7459858b408f47d8b1f6eeb35c871668991424f74d55a9c19bce2
-DIST gffread-0.11.0.tar.gz 28887 BLAKE2B 0d9e89666770c64713d0edb256aa9f18b8d33cba941afbb14a82e26359bfa96044a1655678095a8468e1d1d651406fb0250b20696b4026c4a47892cc45785935 SHA512 79d8a376c892c1567c80a045b08b8f4c97d8778a46b89bcce0372e2e3d6b4bcfe746b64b2101fd8411d02a2d157585eb39d0e067a2aaeb5e8c1e1f7da21bc834
+DIST gclib-0.12.7.tar.gz 259314 BLAKE2B 9e3d4b535a7bbeb4b03360801a4ce4c81055d49525857cce306009e18f78709808732e24cb3dc3efa050b293c863d6f045f5fc3a5d3c14f3c6a2566acbc1f6f4 SHA512 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90
+DIST gffread-0.12.7.tar.gz 403734 BLAKE2B e925518fad8e1047d7e4a785338e51cd0317d8e26545587024ee2617a2e432426e80172c62b9d4103ec9da0d33d758105d8803cc82b4f74cf5dba07009aab477 SHA512 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b
diff --git a/sci-biology/gffread/gffread-0.11.0.ebuild b/sci-biology/gffread/gffread-0.12.7.ebuild
index 871d38d03..9758ccef0 100644
--- a/sci-biology/gffread/gffread-0.11.0.ebuild
+++ b/sci-biology/gffread/gffread-0.12.7.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
@@ -12,13 +12,8 @@ SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
src_prepare(){
- src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz
default
sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
cd .. && ln -s gclib-"${PV}" gclib || die
@@ -30,4 +25,5 @@ src_compile(){
src_install(){
dobin gffread
+ einstalldocs
}
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
index b8cc73c5a..d50ebf927 100644
--- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
+++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,6 @@ inherit check-reqs
DESCRIPTION="BIDS data files released with the IRSABI publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
https://zenodo.org/record/3601531/files/${P}.tar.xz
"
diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
index fe8fef44a..d146efd5a 100644
--- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
+++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,6 +13,7 @@ SRC_URI="
https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-bin.tar.gz
https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
"
+S="${WORKDIR}/TreeView-${PV}-bin"
LICENSE="GPL-2"
SLOT="0"
@@ -20,11 +21,10 @@ KEYWORDS="~amd64"
DEPEND="
>virtual/jdk-1.5:*
- !sci-biology/jtreeview"
+"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5:*"
-
-S="${WORKDIR}/TreeView-${PV}-bin"
+ >=virtual/jre-1.5:*
+"
# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild b/sci-biology/longstitch/longstitch-1.0.1.ebuild
index 6cd035d86..b14bdee87 100644
--- a/sci-biology/longstitch/longstitch-1.0.1.ebuild
+++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild
@@ -1,15 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
HOMEPAGE="https://github.com/bcgsc/LongStitch"
SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/LongStitch-${PV}"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
RESTRICT="test"
@@ -20,8 +21,6 @@ RDEPEND="
sci-biology/samtools
"
-S="${WORKDIR}"/LongStitch-"${PV}"
-
src_install(){
dobin longstitch
dodoc README.md LongStitch_overview.pdf
diff --git a/sci-biology/manatee-igs/Manifest b/sci-biology/manatee-igs/Manifest
deleted file mode 100644
index 89599e152..000000000
--- a/sci-biology/manatee-igs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST manatee-2.23.1_linux.tgz 19879146 BLAKE2B bd69d0d701c92ad4e4c8bbfdf8c9cb23184fa2778a924f71dd83e01901a8054296fb32adb58c5bb66d442b29c564c31c8690398479d214e020697726fc413a59 SHA512 50a76d36f69e3b8b80bcdf7fe28e1c9eb7c15bd8889bd8d130bc65f879ec99aa0caec6d0df495d7ab5804e6414599fc316073c9c55ecd1d370c5dd72aadd65ba
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
deleted file mode 100644
index 8a21f8f36..000000000
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
-HOMEPAGE="http://manatee.sourceforge.net/igs" # no https
-SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=dev-libs/expat-1.95.8
- >=media-libs/gd-2.0.34
- dev-perl/CGI
- dev-perl/Bio-DB-Das-Chado
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- dev-perl/XML-Simple
- dev-perl/XML-Writer
- dev-perl/HTML-Template
- dev-perl/Tree-DAG_Node
- virtual/perl-File-Spec
- virtual/perl-Data-Dumper
- dev-perl/GD
- dev-perl/GDTextUtil
- dev-perl/GDGraph
- virtual/perl-Storable
- dev-perl/Log-Log4perl
- dev-perl/Log-Cabin
- dev-perl/Date-Manip
- dev-perl/IO-Tee
- dev-perl/MLDBM
- dev-perl/JSON
- dev-perl/JSON-Any
- sci-biology/bioperl"
-RDEPEND="${DEPEND}
- >=virtual/mysql-5:*
- >=www-servers/apache-2.2"
-
-S="${WORKDIR}/manatee-${PV}_linux"
-
-src_prepare(){
- default
- find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
- find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
- find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
-}
-
-src_install(){
- dodir /var/www/localhost/cgi-bin
- cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
- dodir /var/www/localhost/htdocs/manatee
- cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
-
- einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
-
- einfo "You have to fetch the 1.1 GB large file from https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
- einfo "You need to update it regularly."
- einfo "Also fetch https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
-}
diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
deleted file mode 100644
index 8a3d26043..000000000
--- a/sci-biology/manatee-igs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">manatee</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/manatee-jcvi/Manifest b/sci-biology/manatee-jcvi/Manifest
deleted file mode 100644
index 9efd473f9..000000000
--- a/sci-biology/manatee-jcvi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST manatee-2.4.3.tgz 1840410 BLAKE2B e80b499e4a9a6fddc60851e1da126dc48356d675df36938f1ed1a920f19a5f76708fc4be295164ae69330d1978cebbf6e6b9c1f7c098e8049710a3e48eeee0d3 SHA512 0bfb9dff8bdaec1e602fdaa1ec6e2939cba1813ac639b95b9e2679e3473719ad74bb383ba54c56cf4dc0553eac002ea3955ae05a1bc87215c7553b9edb9f9fcf
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
deleted file mode 100644
index 7bc28decf..000000000
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Genome annotation tool"
-HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
-SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-${PV}/manatee-2.4.3.tgz"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=">=dev-libs/expat-1.95.8
- >=media-libs/gd-2.0.34
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- dev-perl/XML-Simple
- dev-perl/XML-Writer
- dev-perl/HTML-Template
- dev-perl/Tree-DAG_Node
- virtual/perl-File-Spec
- virtual/perl-Data-Dumper
- dev-perl/GD
- virtual/perl-Storable
- dev-perl/Log-Log4perl
- dev-perl/Log-Cabin
- dev-perl/IO-Tee
- dev-perl/MLDBM
- dev-perl/CGI
- dev-perl/DBI
- dev-perl/Apache-DBI
- dev-perl/Date-Manip
-"
-# dev-perl/CGI-Carp
-# dev-perl/CGI-Cookie
-# dev-perl/GD-Text
-# dev-perl/GD-Graph
-#
-RDEPEND="${DEPEND}
- >=virtual/mysql-5:*
- >=www-servers/apache-2.2"
-
-S="${WORKDIR}"/manatee-"${PV}"
-
-src_configure(){
- econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld
-}
-
-src_compile(){
- default
-}
diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/manatee-jcvi/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest
index 511c8e3d0..c39d0ea60 100644
--- a/sci-biology/mappy/Manifest
+++ b/sci-biology/mappy/Manifest
@@ -1 +1 @@
-DIST mappy-2.17.tar.gz 199280 BLAKE2B b79175016f26ed7f33bdff65cc5187c4c777849e5d89c44d0acb94d95189ccce7d89839cfc81c681d3bda6b29ae4ba1934205bd72472f7f228dbedc40dd78602 SHA512 399ceeb710f496c3d9bc409dcafb11122c5b93453dcfdf41c2f6d7d3a052d3600baff29ff08ed1322fcf10f1fc060434f9b0e79cb627c155d559f579b43dd267
+DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4
diff --git a/sci-biology/mappy/mappy-2.17.ebuild b/sci-biology/mappy/mappy-2.24.ebuild
index 15399c913..3e25ed1eb 100644
--- a/sci-biology/mappy/mappy-2.17.ebuild
+++ b/sci-biology/mappy/mappy-2.24.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest
new file mode 100644
index 000000000..dbfe85988
--- /dev/null
+++ b/sci-biology/mmseqs2/Manifest
@@ -0,0 +1 @@
+DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919
diff --git a/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
new file mode 100644
index 000000000..10884765c
--- /dev/null
+++ b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
@@ -0,0 +1,40 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1a677e3..df1d765 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -56,23 +56,29 @@ if (HAVE_AVX2)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q")
+ endif ()
+ set(X64 1)
+-elseif (HAVE_SSE4_1)
++endif ()
++if (HAVE_SSE4_1)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16")
+ set(X64 1)
+-elseif (HAVE_SSE2)
++endif ()
++if (HAVE_SSE2)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2")
+ set(DISABLE_IPS4O 1)
+ set(X64 1)
+-elseif (HAVE_POWER9)
++endif ()
++if (HAVE_POWER9)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx")
+ set(PPC64 1)
+-elseif (HAVE_POWER8)
++endif ()
++if (HAVE_POWER8)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx")
+ set(PPC64 1)
+-elseif (HAVE_ARM8)
++endif ()
++if (HAVE_ARM8)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd")
+ set(ARM 1)
+-elseif (HAVE_S390X)
++endif ()
++if (HAVE_S390X)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14")
+ set(ZARCH 1)
+ endif ()
diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml
new file mode 100644
index 000000000..c957d777e
--- /dev/null
+++ b/sci-biology/mmseqs2/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <upstream>
+ <remote-id type="github">soedinglab/mmseqs2</remote-id>
+ <doc>https://github.com/soedinglab/mmseqs2/wiki</doc>
+ </upstream>
+ <maintainer type="person">
+ <email>joel@generisbio.com</email>
+ <name>Joel Berendzen</name>
+ </maintainer>
+ <longdescription>
+ MMseqs2 (Many-against-Many sequence searching) is a software suite toi
+ search and cluster huge protein and nucleotide sequence sets.
+ MMseqs2 is open source GPL-licensed software implemented in C++.
+ The software is designed to run on multiple cores and servers
+ and exhibits very good scalability. MMseqs2 can run 10000 times
+ faster than BLAST. At 100 times its speed it achieves almost the
+ same sensitivity. It can perform profile searches with the same
+ sensitivity as PSI-BLAST at over 400 times its speed.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
new file mode 100644
index 000000000..6cbd139d8
--- /dev/null
+++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake
+
+MY_PN="MMseqs2"
+
+# Must be manually updated with each release
+COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e"
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${COMMIT}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
+
+RDEPEND="
+ app-arch/zstd[static-libs]
+ sys-libs/zlib
+ app-arch/bzip2
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-properly-handle-cpuflags.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411
+ -DBUILD_SHARED_LIBS=OFF
+ -DUSE_SYSTEM_ZSTD=ON
+ # Disable auto detection, build respecting cpu flags instead
+ -DNATIVE_ARCH=OFF
+ -DHAVE_AVX2="$(usex cpu_flags_x86_avx2)"
+ -DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)"
+ -DHAVE_SSE2="$(usex cpu_flags_x86_sse2)"
+ # We also have cpu flags for ppc/arm/s390x
+ -DVERSION_OVERRIDE=${PV}
+ )
+ cmake_src_configure
+}
+
+src_install(){
+ cmake_src_install
+ # move the bashcomp to correct dir
+ newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}"
+ rm -r "${ED}/usr/util/" || die
+}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
index 65963d55a..0709fb65d 100644
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
+++ b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
@@ -8,8 +8,8 @@ inherit check-reqs
DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
- hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
+ hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
"
LICENSE="fairuse"
diff --git a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
index 1ba2221aa..79c042a2a 100644
--- a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
+++ b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
@@ -8,8 +8,8 @@ inherit check-reqs
DESCRIPTION="A collection of mouse brain templates in NIfTI format"
HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
- hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
+ hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
"
LICENSE="fairuse"
diff --git a/sci-biology/mrsfast/Manifest b/sci-biology/mrsfast/Manifest
deleted file mode 100644
index b6da5c3dd..000000000
--- a/sci-biology/mrsfast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mrsfast-3.4.2.tar.gz 47451 BLAKE2B e8dc3d06ec53d036ef2b556fc536b5430c6bc392846341e86afcd3131f38cc2ac2a642e8f4cf97e2bb56039604b18e839f0bc3803665a713cdb13374eee0fb46 SHA512 3ca0e166a165b338a3949fea1f80c6e3f228e36663af3cd6de57eb22ac05fa0d8a4c5fa8c2ca5ee5ce8cfe17d7df05362f26a9ae77f9d117ea256461a3c3e9a0
diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml
deleted file mode 100644
index 309390097..000000000
--- a/sci-biology/mrsfast/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">mrsfast</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild b/sci-biology/mrsfast/mrsfast-3.4.2.ebuild
deleted file mode 100644
index 91f7d771c..000000000
--- a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Micro Read Fast Alignment Search Tool"
-HOMEPAGE="https://sfu-compbio.github.io/mrsfast/"
-SRC_URI="https://github.com/sfu-compbio/mrsfast/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-
-src_prepare() {
- default
- sed \
- -e "s:gcc:$(tc-getCC) ${LDFLAGS}:g" \
- -e '/^CFLAGS/d' \
- -e '/^LDFLAGS/d' \
- -i Makefile || die
- tc-export CC
-}
-
-src_install() {
- dobin ${PN}
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 623759901..527acfadf 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -61,7 +60,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index d4ae93742..e90652f38 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -55,7 +54,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index f0269f0b5..ddeeac07d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -55,7 +54,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index b232894b4..976ea3804 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -33,7 +33,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -56,7 +55,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 623759901..527acfadf 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -61,7 +60,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 6daf7b3f0..009085d15 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -36,7 +36,6 @@ RESTRICT="!test? ( test )"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -60,7 +59,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index e2db30639..604c9c638 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -64,7 +63,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 7df161c99..4d0d6363e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -64,7 +63,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest
index 580b087b0..5dd197214 100644
--- a/sci-biology/nilearn/Manifest
+++ b/sci-biology/nilearn/Manifest
@@ -1 +1,2 @@
-DIST nilearn-0.8.0.tar.gz 6603264 BLAKE2B f96621b68255722f89ac18cfc8b44e2dc5fc6d4bda2d867d5f83ba669f1c3369318e8458360071245398362122b501c70849741068f7bfa567e49a7f8cdeefa1 SHA512 6e7da3963cd29282ab77bbf1dbb5c1879897dae3d3296a8e0c57edc11a272d9e386914fc3af81d13b57199d64880f534806dca6851b5d8ddecae9083ec5df18e
+DIST nilearn-0.8.1.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4
+DIST nilearn-0.9.1.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571
diff --git a/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
new file mode 100644
index 000000000..6d13b76b1
--- /dev/null
+++ b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
@@ -0,0 +1,10 @@
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -78,7 +78,6 @@
+ doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS
+ junit_family = xunit2
+ addopts =
+- --doctest-modules
+ -s
+ -vv
+ --durations=0
diff --git a/sci-biology/nilearn/nilearn-0.8.0.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index a70e8d0fc..c73c9f519 100644
--- a/sci-biology/nilearn/nilearn-0.8.0.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -38,5 +38,5 @@ distutils_enable_tests pytest
python_test() {
echo "backend: Agg" > matplotlibrc
- MPLCONFIGDIR=. pytest -vv || die
+ MPLCONFIGDIR=. epytest
}
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild
new file mode 100644
index 000000000..7e3716791
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="http://nilearn.github.io/"
+SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+ >=dev-python/joblib-0.15[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+ >=dev-python/pandas-1[${PYTHON_USEDEP}]
+ >=dev-python/requests-2[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.5[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-3[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-tests.patch" )
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ "examples/05_glm_second_level/plot_second_level_association_test.py"
+ "examples/05_glm_second_level/plot_second_level_one_sample_test.py"
+ "examples/05_glm_second_level/plot_second_level_two_sample_test.py"
+)
+# Reported upstream:
+# https://github.com/nilearn/nilearn/issues/3232
+EPYTEST_DESELECT=(
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-psc]"
+)
+
+python_test() {
+ echo "backend: Agg" > matplotlibrc
+ MPLCONFIGDIR=. epytest
+}
diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild
deleted file mode 100644
index a9478fc8e..000000000
--- a/sci-biology/nilearn/nilearn-9999.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-EGIT_REPO_URI="https://github.com/nilearn/nilearn"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# Tests attempt to download external data.
-RESTRICT="test"
-
-BDEPEND="
- test? (
- dev-python/matplotlib[${PYTHON_USEDEP}]
- )
-"
-
-RDEPEND="
- >=dev-python/joblib-0.12[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.2[${PYTHON_USEDEP}]
- >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
- >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
- >=dev-python/requests-2[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_test() {
- echo "backend: Agg" > matplotlibrc
- MPLCONFIGDIR=. pytest -vv || die
-}
diff --git a/sci-biology/oases/Manifest b/sci-biology/oases/Manifest
deleted file mode 100644
index 031a5ff34..000000000
--- a/sci-biology/oases/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST OasesManual.pdf 113886 BLAKE2B aa8492887cea64e67966238e620b24aa5f90a8622a6de9bc4d4e1f56554f624c9ae7a19e0c46d83478849ec5d2ecb758fd8e253d8327d4d2bdcdda9db2e114a7 SHA512 c710a62cd1982060f723918f5f4de91adff12870d1682d0729035a3588ed37d26898c399c07b1b81b4b399c7ea1a14509784a6dbb9de6004bcadf6677cd5859f
-DIST oases_0.2.08.tgz 92037 BLAKE2B ff9762264d18c42e20b2208a057b073a2a960dab1ca17372db2fbf6f09094d3446ccd29a6038e17ee59b5adee9afe23cd59bbc4b640f57ce04141d2990b32b90 SHA512 e9a73a9227ce13995fcac7f456534a650099d8160d48d2d9831f3f05e482353c29dd76bbc74b0b451154eb5061ddb473649d21442941360f0e8c7623f6fe586c
diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch
deleted file mode 100644
index fcd0842ff..000000000
--- a/sci-biology/oases/files/Makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- a/Makefile 2016-04-10 22:34:31.976222662 +0200
-+++ b/Makefile 2016-04-10 22:37:49.636225327 +0200
-@@ -1,8 +1,8 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
-+CC ?= gcc
-+CFLAGS ?= -Wall
-+DEBUG ?= -g
- LIBS = -lm
--OPT = -O3
-+#OPT = -O3
- export MAXKMERLENGTH = 64
- export CATEGORIES = 2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/oases/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-0.2.08.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
index 9f8d8eeac..a2611bd74 100644
--- a/sci-biology/open-ephys-gui/Manifest
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -1,2 +1 @@
-DIST open-ephys-gui-0.5.2.2.tar.gz 64533170 BLAKE2B dc70c3eca6a8fbc7c4f6e84580fa6d5b31b837fedbdff20f532e3c01c764cbc3c51637e4fd678d048c78b6f79b4b4a5cd4d437125beeaf712f6f322e82579c85 SHA512 b6369bb0abd8ca18ff225cffab04a24915865647ee1ab5b6d83d5d6fbda3bc64d1b7db04c23deb8d29b8ff378e703b88cfa9d409f4cde62a3af34a7984427219
DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
deleted file mode 100644
index b4cbc6d8f..000000000
--- a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-inherit cmake
-
-DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
-HOMEPAGE="https://open-ephys.org/gui/"
-LICENSE="GPL-3"
-
-if [[ ${PV} == "9999" ]] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
- Suffix=$EGIT_BRANCH
- SubDir=${P}
-elif [[ ${PV} == "99999999" ]] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="development"
- Suffix=$EGIT_BRANCH
- SubDir=${P}
-else
- SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- Suffix=${PV}
- SubDir="plugin-GUI-${PV}"
- S="${WORKDIR}/$SubDir"
- KEYWORDS="~amd64 ~x86"
-fi
-
-SLOT="${PV}"
-IUSE="jack"
-
-BDEPEND="
- <sys-devel/gcc-9
-"
-DEPEND="
- media-libs/alsa-lib
- media-libs/freeglut
- media-libs/freetype
- x11-libs/libXrandr
- x11-libs/libXcursor
- x11-libs/libXinerama
- jack? ( media-sound/jack-audio-connection-kit )
-"
-RDEPEND="${DEPEND}"
-
-BUILD_DIR="$S/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
-
-QA_PREBUILT="opt/open-ephys-0.5.2.2/shared/*.so"
-QA_PRESTRIPPED="
- opt/open-ephys-0.5.2.2/plugins/*.so
- opt/open-ephys-0.5.2.2/open-ephys
-"
-
-src_prepare() {
- cmake_src_prepare
-
- if use jack; then
- sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
- fi
-}
-
-src_configure() {
- local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
- cmake_src_configure
-}
-
-src_install() {
- dodir opt/open-ephys-"$Suffix"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"$Suffix"/
- cp -R "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules "${ED}"/lib/udev/rules.d/
- dosym ../../opt/open-ephys-"$Suffix"/open-ephys usr/bin/open-ephys-"$Suffix"
-}
-
-pkg_postinst() {
- ewarn " "
- ewarn "You must restart the udev service in order to allow your computer to"
- ewarn "communicate with the Open Ephys acquisition board."
- ewarn " "
-}
diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
index 988f6ba6f..c43c10257 100644
--- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
+++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,6 @@ inherit check-reqs
DESCRIPTION="BIDS data files released with the OPFVTA publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
https://zenodo.org/record/3575149/files/${P}.tar.xz
"
diff --git a/sci-biology/primerD/Manifest b/sci-biology/primerD/Manifest
deleted file mode 100644
index 063af78cf..000000000
--- a/sci-biology/primerD/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST primerD.tar.gz 58132 BLAKE2B 4fdf1126649ba3bddb92852dacd14a4e4bf652715166f7c6d9ba23aa3ebe8ab7419cf939131e6bde09190c65e5ed04222172757ff642d7af9eb34bfadd9875eb SHA512 9f70ccb2a8304fe9e3a3885f2607969ca00483c1f3bb70ea3b5da709db0c43979cdd6bbf2b9ef805c13d215000afab2053fdeda66dc48006cb50f536886b86b2
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/primerD/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild
deleted file mode 100644
index 6d46832a9..000000000
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Design degenerate primers"
-HOMEPAGE="https://mblab.wustl.edu/software.html"
-SRC_URI="primerD.tar.gz"
-#SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz"
-# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
-# Unable to locally verify the issuer's authority.
-# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
-RESTRICT="fetch"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-# make: *** No rule to make target '/usr/include/linux/new.h', needed by 'Main.o'. Stop.
-KEYWORDS=""
-
-S="${WORKDIR}"/primerD
-
-src_prepare(){
- default
- sed -i -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" \
- -e "s:/usr/include/g++-3/stl_algobase.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_algobase.h:g" \
- -e "s:/usr/include/g++-3/stl_relops.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_relops.h:g" \
- -e "s:/usr/include/g++-3/stl_pair.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_pair.h:g" \
- -e "s:/usr/include/g++-3/type_traits.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/ext/type_traits.h:g" \
- -e "s:/usr/include/g++-3/stl_config.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/pstl/pstl_config.h:g" \
- -e "s:/usr/include/g++-3/:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/:g" \
- -e "s:/usr/include/_G_config.h:/usr/include/stdio.h:g" \
- -e "s:/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/:/usr/include/linux/:g" \
- Makefile || die
-
-}
-
-src_install(){
- dodoc README
- dobin primerD
-}
diff --git a/sci-biology/pufferfish/Manifest b/sci-biology/pufferfish/Manifest
deleted file mode 100644
index 4ca8429dc..000000000
--- a/sci-biology/pufferfish/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST htslib-pufferfish-1.4.0.tar.gz 1262620 BLAKE2B 7fff233fadd4737e416058a24d9dc916e5ecf1fa10c456cfb15001df7c664daedecdbcef49469dffb6516c47e00937cbe399a68032fcf18ab9070768d40d3091 SHA512 52ae9099ddadb1d0136f1a62825ff0539baf754302c735ea81b8748a1c349107766b2022cc59814728d366b6df2c9f1b93edf926c1a6a7af78a4f40c4e821c4c
-DIST pufferfish-1.4.0.tar.gz 3099274 BLAKE2B 65c26b02513840b3f7b6f381af674b59a21960fe56559b8d87dd22051fa02e7e5c06ab1ba1b9f81516f9831ea1b79492a9cc0e2d0b9258d9c21ddfb7ea162d69 SHA512 683bad5a5e3512c56c211af1270ea1e627d2483d601d20ef70f92087b37327463b36224eda38699231f8daa8c318d745757eed2a4190351ebb8b4a252fca6474
-DIST seqlib-pufferfish-1.4.0.tar.gz 315441 BLAKE2B b402f94837aeb43e4d443044c65d1c193ce7b24a8507b9a79da6cbfc5d7093d286ccd8573eca64c78bd3c65830dc11a18ec26dc619e7ab95d04a472c15ec70d7 SHA512 b3efa0511df9c39ed8021c1bf316f88fb6b51ebd745b7f799bc92edebf31ff7dbd466b83ba30a3381e411d36455f4074163267d4331c5fe16f2934762865d22f
-DIST setcover-pufferfish-1.4.0.tar.gz 33911 BLAKE2B 690cfca7e271490ef8b7119fe9fb7df3e7c06897eab52346b485c22a8a7b8e75d344a07f24dbf44aa68919793f942c8f5d1bd1932d2ce1a21a18631e3e64aecf SHA512 8954b38a183f81fff36663c6cbbef25fbf003045d93462933d09f0384f6e17fa726d48e9d94daa5195052e6ff9650aba4a2c8a6f0691f50c360462f02760e2a1
diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
deleted file mode 100644
index c86fe847f..000000000
--- a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 7f1516a..90f7cdd 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
-
-
- ExternalProject_Add(libseqlib
--GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git
--GIT_TAG master
- UPDATE_COMMAND ""
- UPDATE_DISCONNECTED 1
- BUILD_IN_SOURCE TRUE
--DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ./configure
-@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include &
- )
-
- ExternalProject_Add(libSetCover
-- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git
-- GIT_TAG master
- UPDATE_COMMAND ""
- CONFIGURE_COMMAND ""
- UPDATE_DISCONNECTED 1
- BUILD_IN_SOURCE TRUE
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- BUILD_COMMAND make -j8
diff --git a/sci-biology/pufferfish/metadata.xml b/sci-biology/pufferfish/metadata.xml
deleted file mode 100644
index 7b582e896..000000000
--- a/sci-biology/pufferfish/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">COMBINE-lab/pufferfish</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
deleted file mode 100644
index 588970e06..000000000
--- a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25"
-SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479"
-HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae"
-
-DESCRIPTION="Index for the colored, compacted, de Bruijn graph"
-HOMEPAGE="https://github.com/COMBINE-lab/pufferfish"
-SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz -> setcover-${P}.tar.gz
- https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz -> seqlib-${P}.tar.gz
- https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz -> htslib-${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="dev-cpp/tbb"
-
-S="${WORKDIR}/${PN}-salmon-v${PV}"
-
-PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" )
-
-src_prepare() {
- mkdir -p external/{setcover,seqlib}
- mv "../setcover-${SC_COMMIT}"/* external/setcover || die
- mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die
- mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die
- cmake_src_prepare
-}
diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
index 20c923eb0..d41c14a11 100644
--- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
+++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="A collection of rat brain templates in NIfTI format"
HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest
deleted file mode 100644
index 025cfe9ea..000000000
--- a/sci-biology/sailfish/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST jellyfish-2.2.5.tar.gz 1083486 BLAKE2B 545c110199cb2661656ddd558f5ee2b9715a78f6d33275f53aa5a9719247dff4421ef5dd37c3683a3423c8b79ff33395bf4e0ac86cade7480bc604a2b197e214 SHA512 7747030628f82562669c5021aeaca03d8dfc559dc9c3a407e2e4e8de633673f7cf9c60989c16f73deb8e88e7204a3fe84993209a2ebffcb34fd35eac7784e9ab
-DIST quasi-mph.zip 414036 BLAKE2B 414ccd806fc11fdc949ecf107db079e4ab0dec8f443f4ba27df9c4273bc3e01f9d4e7c377651a930cf28c77198526a7ed52eb65419a9c29d6cf12a6ecf268b6c SHA512 65d420af549ce138e6d240438919cbfb76a6f137d2767ba45c099c9a946ca04686fedca609a5ebe4c9d371d2587379f35d9e5dd591abe1afc4b7d433bb4f61c9
-DIST sailfish-0.10.0.tar.gz 1621862 BLAKE2B d04d8db99e1d191ad1bea690bf43f31d23d6505bc3e80399cfafbbf4e1404edf8a4bbe0532e2c47ec59a5a26f50509342a7143bc0b0c41c3a8723ec0f6e53bd4 SHA512 ec66cff89dac037b84deaf997b7769802f594e69820d42915fb830bfcd527786c9c466a9476bdf2b29b9f7481e98905acf580f4a766765bccaa1b0ced22c4bb2
-DIST sparsehash-2.0.2.tar.gz 321951 BLAKE2B 057776f89fe3ca4b826eec7a142a18106561e4a20eaf907b3996f4dc52f484b84196c3bf9cf6d8bc31bd09aec34fc68b5992560c5fbe8c279c94d18062a96855 SHA512 e086b8beb45f2aa395b5ae49aed8ebaed1cafc9a59ece862f64f067098e2b9c28efc5cfac6b26eea46e5fe6b3db1bfa1afc0b9656c48adc01c3c3d05a5b327e8
-DIST v1.0.tar.gz 86404 BLAKE2B ce59ff034cbd70a504ed8c2e42e552489cc07a80a7130149234294aa2c75329f15ff5c4da4709a40712e18762e160355de67f4f68810856f8bc8218ceffb671d SHA512 ba4b395374da16f9ac22dd3cbf96ab5a67ab4d64a312f382ace883633199bbbd5f7602abe768ac84f6ddf2611eaf2db3d402893bd5dad135d598b4b9853ccd6b
diff --git a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--set (Boost_USE_STATIC_LIBS ON)
--set (Boost_USE_MULTITHREADED ON)
--#set (Boost_USE_STATIC_RUNTIME OFF)
--
- find_package (ZLIB)
- if (NOT ZLIB_FOUND)
- message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
diff --git a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch b/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
deleted file mode 100644
index 985f83f4a..000000000
--- a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ee4b34c..3c58830 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -176,7 +176,7 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59")
-+set(Boost_ADDITIONAL_VERSIONS "1.72.0" "1.74.0" "1.75.0")
- find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
diff --git a/sci-biology/sailfish/files/sailfish-no-curl.patch b/sci-biology/sailfish/files/sailfish-no-curl.patch
deleted file mode 100644
index 2ec97808e..000000000
--- a/sci-biology/sailfish/files/sailfish-no-curl.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be4117..ee4b34c 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -230,9 +230,6 @@ elseif(FETCH_BOOST)
- message("Build system will fetch and build Boost")
- message("==================================================================")
- ExternalProject_Add(libboost
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz &&
-- tar xzf boost_1_59_0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-@@ -292,10 +289,6 @@ if (NOT JELLYFISH_FOUND)
- message("Build system will fetch and build Jellyfish")
- message("==================================================================")
- ExternalProject_Add(libjellyfish
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz &&
-- rm -fr jellyfish-2.2.5 &&
-- tar -xzvf jellyfish-2.2.5.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-@@ -335,11 +328,7 @@ if ("${TBB_COMPILER}" STREQUAL "gcc")
- endif()
-
- ExternalProject_Add(libtbb
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-- DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-- tar -xzvf tbb_20140724oss_src.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- PATCH_COMMAND "${TBB_PATCH_STEP}"
- CONFIGURE_COMMAND ""
-@@ -407,11 +396,6 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
- message("Build system will compile libgff")
- message("==================================================================")
- ExternalProject_Add(libgff
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
-- tar -xzvf libgff.tgz &&
-- rm -fr libgff &&
-- mv libgff-1.0 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -445,9 +429,6 @@ if (NOT HAVE_FAST_MALLOC)
- message("Build system will fetch and use JEMalloc")
- message("==================================================================")
- ExternalProject_Add(libjemalloc
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-- tar -xzf jemalloc-3.6.0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -465,9 +446,6 @@ endif ()
- message("Build system will fetch and build SparseHash")
- message("==================================================================")
- ExternalProject_Add(libsparsehash
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
-- tar -xzf sparsehash-2.0.2.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -487,7 +465,6 @@ ExternalProject_Add(libsparsehash
- #
- ####
- if(NOT FETCHED_RAPMAP)
-- exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
- set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
- endif()
-
-diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh
-deleted file mode 100755
-index cab05a1..0000000
---- a/scripts/fetchRapMap.sh
-+++ /dev/null
-@@ -1,37 +0,0 @@
--#!/bin/bash
--
--CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
--EXTERNAL_DIR=${CURR_DIR}/../external
--INSTALL_DIR=${CURR_DIR}/../external/install
--
--if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
-- rm -fr ${EXTERNAL_DIR}/RapMap
--fi
--
--if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/include/rapmap
--fi
--
--if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/src/rapmap
--fi
--
--mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip -o ${EXTERNAL_DIR}/rapmap.zip
--rm -fr ${EXTERNAL_DIR}/RapMap
--unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/RapMap-quasi-mph ${EXTERNAL_DIR}/RapMap
--
--mkdir -p ${INSTALL_DIR}/include/rapmap
--mkdir -p ${INSTALL_DIR}/src/rapmap
--
--rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
--rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h
--
--cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/emphf ${INSTALL_DIR}/include/rapmap
diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml
deleted file mode 100644
index 530333987..000000000
--- a/sci-biology/sailfish/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
- <upstream>
- <remote-id type="github">kingsfordgroup/sailfish</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
deleted file mode 100644
index 9fa4060ca..000000000
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
- https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
- https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
- https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
-"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- dev-cpp/sparsehash
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-BDEPEND="app-arch/unzip"
-# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch"
- "${FILESDIR}/${PN}-no-curl.patch"
- "${FILESDIR}/${PN}-allow-newer-boost.patch"
-)
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
- mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
- mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
- mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
- mkdir -p "${S}/external/install/src/rapmap"
- cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-}
-
-src_configure() {
- JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure
- # jellyfish2 instead of jellyfish
- find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die
- find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
deleted file mode 100644
index a76e8ee89..000000000
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" )
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-
- # jellyfish2 instead of jellyfish
- pushd external/install/include/rapmap
- find -type f -name "*.hpp" -exec sed -i -e 's/jellyfish/jellyfish2/g' {} + || die
- popd
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index cf8f50df3..37410d297 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,8 +1,10 @@
DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
+DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2
+DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d
DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST salmon-1.4.0.tar.gz 7061272 BLAKE2B d26685c0a1a888d1acc2d3b6789d572f5c3d811e20068fa923197b04c86ccdda3c9ddbe8cb6df99d6855dfdcdb90ac3b69371804c2fdc78b40469c205e1c96ed SHA512 9007899f91cef2589a965d2d039393e0a19b4fcea488b8f256431907323cadf2d182579ffc6203f19feafad4a72ddad1cbeee6a7acd81cd8d5a4fe890996c5ec
+DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6
DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
new file mode 100644
index 000000000..76ef25547
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
@@ -0,0 +1,116 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1be02ab..48ffda2 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -428,9 +428,9 @@ endif()
+ ##
+ # Set the latest version and look for what we need
+ ##
+-set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
++set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
+ if (NOT BOOST_RECONFIGURE)
+-find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
++find_package(Boost 1.59.0 COMPONENTS ALL)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
+ endif()
+
+ ## Try and find TBB first
+-find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
++find_package(TBB)
+
+ ## NOTE: we actually require at least 2019 U4 or greater
+ ## since we are using tbb::global_control. However, they
+@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+ ## source. Check before release if we can bump to the 2020
+ ## version (requires having tbb 2020 for OSX).
+ if (${TBB_FOUND})
+- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
+ message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
+ set(TBB_TARGET_EXISTED TRUE)
+- else()
+- set(TBB_TARGET_EXISTED FALSE)
+- endif()
+ else()
+ set(TBB_TARGET_EXISTED FALSE)
+ endif()
+@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
+ message("Build system will compile libgff")
+ message("==================================================================")
+ externalproject_add(libgff
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
+- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
+- tar -xzvf libgff.tgz
+ ##
+ #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+ #DOWNLOAD_NAME libff.tgz
+diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
+index c8b3eb5..b4c23da 100644
+--- a/cmake/Modules/FindTBB.cmake
++++ b/cmake/Modules/FindTBB.cmake
+@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
+ ##################################
+
+ if(TBB_INCLUDE_DIRS)
+- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
+ string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
+ TBB_VERSION_MAJOR "${_tbb_version_file}")
+ string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
+diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
+index d32e131..1b5cbf2 100755
+--- a/scripts/fetchPufferfish.sh
++++ b/scripts/fetchPufferfish.sh
+@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+ EXTERNAL_DIR=${CURR_DIR}/../external
+ INSTALL_DIR=${CURR_DIR}/../external/install
+
+-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
+- rm -fr ${EXTERNAL_DIR}/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
+- rm -fr ${INSTALL_DIR}/include/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
+- rm -fr ${INSTALL_DIR}/src/pufferfish
+-fi
+-
+ SVER=salmon-v1.6.0
+ #SVER=develop
+ #SVER=sketch-mode
+@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
+ EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
+
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
+-
+-hashcheck=""
+-if exists sha256sum; then
+- hashcheck="sha256sum"
+-elif exists shasum; then
+- hashcheck="shasum -a256"
+-else
+- unset hashcheck
+-fi
+-
+-if [ -z "${hashcheck-}" ]; then
+- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
+-else
+- if [[ $SVER != develop ]]; then
+- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
+- else
+- echo "not testing sha since pulling from develop"
+- fi
+-fi
+-
+-
+-rm -fr ${EXTERNAL_DIR}/pufferfish
+-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
+-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
+
+ mkdir -p ${INSTALL_DIR}/include/pufferfish
+
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
deleted file mode 100644
index 420cb2ae2..000000000
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RDEPEND="
- dev-libs/boost:=[threads(-)]
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- sci-biology/pufferfish
- dev-libs/cereal
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
-
-PATCHES=(
- "${FILESDIR}/${P}-do-not-fetch-pufferfish.patch"
- "${FILESDIR}/${P}-allow-newer-boost.patch"
-)
diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
new file mode 100644
index 000000000..6c19ff58f
--- /dev/null
+++ b/sci-biology/salmon/salmon-1.6.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI="
+ https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
+ https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
+"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-libs/boost:=
+ sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+ app-arch/bzip2
+ app-arch/xz-utils
+ >=dev-libs/jemalloc-5.0.1
+ >=dev-cpp/tbb-2018.20180312
+ dev-libs/cereal
+ sci-libs/io_lib[static-libs]
+"
+
+BDEPEND="
+ app-arch/unzip
+ net-misc/curl
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-find-boost.patch"
+)
+
+src_unpack() {
+ default
+ mkdir -p "${S}/external/install/lib" || die
+ mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
+ mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
+}
+
+src_prepare() {
+ cmake_src_prepare
+ sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
+ -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
+ -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DFETCH_BOOST=FALSE
+ -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
+ -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
+ -DBoost_ALL_FOUND=TRUE
+ -Dboost_headers_FOUND=TRUE
+ -DBoost_FOUND=TRUE
+ )
+ cmake_src_configure
+}
diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest
deleted file mode 100644
index 0c4fb09d1..000000000
--- a/sci-biology/sambamba/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lz4-sambamba-0.8.0.tar.gz 320972 BLAKE2B e9af776d3a867f551e20c2a3c234f2c9a27e729b972a0b40e25eee830f1c2a2975fe939de68459fda6d56a1b3a63e26937cfbf77fcbb2b711ecdbc9385069d91 SHA512 f51c5332fdc5a74bcd4f9597b187721cc2f33bc535c374c0ff47f438f79f6bec382e20462bb90d8be5f6bdf02ff5d7b4f5bf358bba55e03211ee566035ef3fbd
-DIST sambamba-0.8.0.tar.gz 630637 BLAKE2B ea51a86bb546de3792e6d8bc0494aa2afe525d3914d1cc15ad8d52ca1acd2d109f726154273e98ef0e6144266fc34048f8c5008fe5c50be093b4082fb3fac1b5 SHA512 2d74c5ca3188fe0628b4873891eebecb1f514474bb1a2a8aca4ca3f40275acfb0fda0de5e11097754d317cac39b982b6ae45c5dde457cd83d6f684596ca5a5ac
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
deleted file mode 100644
index 3c6df6245..000000000
--- a/sci-biology/sambamba/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">lomereiter/sambamba</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
deleted file mode 100644
index d5f7c1359..000000000
--- a/sci-biology/sambamba/sambamba-0.8.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz -> lz4-${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_unpack() {
- default
- rm -r "${S}/lz4" || die
- mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die
-}
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
deleted file mode 100644
index e655b10b0..000000000
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest
index d8c689507..d683d1d3b 100644
--- a/sci-biology/samri/Manifest
+++ b/sci-biology/samri/Manifest
@@ -1,2 +1 @@
-DIST samri-0.4.1.tar.gz 4115417 BLAKE2B 882b1fbf213f85919a790d669365498c06269a2cb37ba859606e0e4bd696116e954b6683dd636ff34406b2394b4ae3d743c1840a789a828ca3d535b27c0a80da SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf
DIST samri-0.5.tar.gz 4117149 BLAKE2B 1767d6d07726431e43dad5f843eee04bd5111dde3174905b79b938aa94dbb340ca3f3d6316c6720bf01212b87c895df47c965738dff70ec1debbbd542bb77043 SHA512 94fb981adf78b2062e1beac8433bca34e3db90964f720918603e2b89d617b4dfe9f4bc1591b6953e060553ea0014ebca4db62aa0f5b264feb084bc785a48c367
diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
deleted file mode 100644
index f94119541..000000000
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..8} )
-
-inherit distutils-r1 prefix
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="labbookdb test"
-KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${PYTHON_USEDEP}]
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
-"
-RDEPEND="
- dev-python/argh[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- media-gfx/blender
- >=sci-biology/fsl-5.0.9
- sci-biology/bru2nii
- sci-biology/mouse-brain-atlases
- labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
- sci-libs/nibabel[${PYTHON_USEDEP}]
- >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-biology/ants
- sci-biology/afni
- sci-biology/nilearn[${PYTHON_USEDEP}]
-"
-
-S="${WORKDIR}/SAMRI-${PV}"
-
-src_prepare() {
- distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
-}
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 84161f65f..4cc90a0ef 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7..8} )
+PYTHON_COMPAT=( python3_{8..9} )
inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/SAMRI-${PV}"
LICENSE="GPL-3"
SLOT="0"
-IUSE="+atlases labbookdb test"
KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
DEPEND="
test? (
- dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
)
@@ -36,26 +36,25 @@ RDEPEND="
>=media-gfx/blender-2.83.4
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
+ atlases? ( sci-biology/mouse-brain-templates )
labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
+ <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
sci-libs/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
"
-REQUIRED_USE="test? ( atlases )"
-
-S="${WORKDIR}/SAMRI-${PV}"
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
src_prepare() {
distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
}
@@ -68,5 +67,5 @@ python_test() {
sed -i -e \
"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
samri/pipelines/tests/test_repos.py || die
- pytest -vv -k "not longtime" || die
+ epytest -k "not longtime"
}
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
deleted file mode 100644
index 8dba8864c..000000000
--- a/sci-biology/samri/samri-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..8} )
-
-inherit distutils-r1 prefix git-r3
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS=""
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${PYTHON_USEDEP}]
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
- "
-RDEPEND="
- dev-python/argh[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- >=media-gfx/blender-2.83.4
- >=sci-biology/fsl-5.0.9
- sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
- labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
- sci-libs/nibabel[${PYTHON_USEDEP}]
- >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- sci-biology/ants
- sci-biology/afni
- sci-biology/nilearn[${PYTHON_USEDEP}]
-"
-
-REQUIRED_USE="test? ( atlases )"
-
-src_prepare() {
- distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
-}
-
-python_test() {
- distutils_install_for_testing
- export MPLBACKEND="agg"
- export PATH=${TEST_DIR}/scripts:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- pytest -vv -k "not longtime" || die
-}
diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
index 8216eada8..8e47fb775 100644
--- a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
+++ b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="
https://zenodo.org/record/3831124/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
index 17873ce56..9ab92211a 100644
--- a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
+++ b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="
https://zenodo.org/record/3823441/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
index 3122e2188..2c0d5f63d 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -20,9 +20,10 @@ LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-QA_PREBUILT="/opt/.*"
+QA_PREBUILT="*"
-pkg_setup() {
+src_unpack() {
+ default
use x86 && export S="${WORKDIR}"/${MY_P}_i686
use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
}
@@ -31,8 +32,7 @@ src_compile() {
}
src_install() {
- dobin samflag
- exeinto /opt/bin
- doexe ssaha2 ssaha2Build ssahaSNP
+ dobin samflag ssaha2 ssaha2Build ssahaSNP
dodoc README "${DISTDIR}"/ssaha2-manual.pdf
+ einstalldocs
}
diff --git a/sci-biology/stacks/Manifest b/sci-biology/stacks/Manifest
index 51adfa214..06b5c03ad 100644
--- a/sci-biology/stacks/Manifest
+++ b/sci-biology/stacks/Manifest
@@ -1 +1 @@
-DIST stacks-2.55.tar.gz 11716625 BLAKE2B ab359095a546a6ae946fd4196f7955b1e6f294c5ade94e1474984c435c3f2dd468fe8665afbcf201b567d2dd84b999bfc8f9ff7a6dd2712e6be0d4b0d609f0f6 SHA512 eb517f5d9a677095efe3000d0e88ee3be3a6abb725290a0fb1cdb9113a4f19d929dd8eb0d8ce3fd3f9d8234fc0b936523f06d754d5c428381fd97fcebbe89a0b
+DIST stacks-2.60.tar.gz 12135281 BLAKE2B 8d529ba75af4c78710bc36230ef7c564551cd2f2cb9c2ff2cfdc9372f5721bcb463b959b67b7082cdc95f88c772b4e6146cd0c48c25a7b4a6f21d8cdb3045b8e SHA512 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
diff --git a/sci-biology/stacks/stacks-2.55.ebuild b/sci-biology/stacks/stacks-2.60.ebuild
index becd91a5d..4de3f8da8 100644
--- a/sci-biology/stacks/stacks-2.55.ebuild
+++ b/sci-biology/stacks/stacks-2.60.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module webapp autotools
@@ -10,10 +10,8 @@ HOMEPAGE="http://creskolab.uoregon.edu/stacks"
SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
LICENSE="GPL-3"
-# SLOT="0" # webapp ebuilds do not set SLOT
-KEYWORDS=""
+KEYWORDS="~amd64"
-# No rule to make target test
RESTRICT="test"
DEPEND="
@@ -21,11 +19,14 @@ DEPEND="
dev-cpp/sparsehash
sci-biology/samtools:*
sci-biology/bamtools
- sci-biology/gmap" # Source code for both GMAP and GSNAP
+ sci-biology/gmap
+"
+
RDEPEND="${DEPEND}
dev-lang/perl
- >=dev-lang/php-5
- dev-perl/DBD-mysql"
+ >=dev-lang/php-5:*
+ dev-perl/DBD-mysql
+"
PATCHES=(
"${FILESDIR}/${PN}-make-install.patch"
@@ -41,17 +42,13 @@ src_prepare(){
src_configure() {
econf
- webapp_src_preinst
sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
}
src_install() {
- emake install DESTDIR="${ED}"
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install DESTDIR="${ED}"
- webapp_src_install || die "Failed running webapp_src_install"
-}
-
-pkg_postinst() {
- webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+ webapp_src_preinst
+ DESTDIR="${ED}" default
+ DESTDIR="${ED}" perl-module_src_install
+ dodir /usr/share/webapps/${PN}/${PV}
+ webapp_src_install
}
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
-
- getABIdate: $(OBJSD)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-
- getABIcomment: $(OBJSC)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
-
- alfsplit: $(ALFOBJ)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-
- RSOBJ = $(ALFBIN)/2rs.o
-
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
deleted file mode 100644
index 39537604e..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- gap5/zfio.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/gap5/zfio.c b/gap5/zfio.c
-index 35da12a..1b628e4 100644
---- a/gap5/zfio.c
-+++ b/gap5/zfio.c
-@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
- if (c != EOF)
- ungetc(c, zf->fp);
- } else {
-- c = gzgetc(zf->gz);
-+ c = gzgetc((gzFile)zf->gz);
- if (c != EOF)
- gzungetc(c, zf->gz);
- }
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
deleted file mode 100644
index b2ed35724..000000000
--- a/sci-biology/staden/staden-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2 subversion
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden/"
-ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-DEPEND="
- app-arch/xz-utils
- dev-lang/tk:0=
- dev-tcltk/tklib
- media-libs/libpng:0
- sci-biology/samtools:0
- >=sci-libs/io_lib-1.13.8
- sys-libs/zlib"
-RDEPEND="${DEPEND}
- >=dev-tcltk/iwidgets-4.0
- tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )
- net-misc/curl
- doc? ( sci-biology/staden_doc )"
-
-src_prepare() {
- default
- sed \
- -e 's:svnversion:false:' \
- -i configure.in || die
-}
-
-src_configure(){
- use debug && append-cflags "-DCACHE_REF_DEBUG"
- econf \
- $(use_enable X x) \
- $(use_enable amd64 64bit) \
- --with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-src_install() {
- default
- # install the LDPATH so that it appears in /etc/ld.so.conf after env-update
- # subsequently, apps linked against /usr/lib/staden can be run because
- # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
- # somehow for gap2caf, for example
- cat >> "${T}"/99staden <<- EOF
- STADENROOT="${EPREFIX}"/usr/share/staden
- LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
- EOF
- doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
- einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/subread/Manifest b/sci-biology/subread/Manifest
index 48a9f7ca3..8b4dcee7c 100644
--- a/sci-biology/subread/Manifest
+++ b/sci-biology/subread/Manifest
@@ -1 +1 @@
-DIST subread-2.0.1-source.tar.gz 23260381 BLAKE2B 498f898c9b5f5e0819fb7ae0a1407805fb3dc34cf5a07b4354d1493315a9e9190735916fb5c5587f972a67a7d47880e31dc3cc627e271dd2e452e856f5fd79c1 SHA512 e7548c426f75a5705a7c0538787007c5d3f23e4a4561022f192b3219f333483a02312986936cbbfcc8f9afa24cb4d91a1cc62fbebb6c6aef957568d5d8fa3505
+DIST subread-2.0.3-source.tar.gz 23304665 BLAKE2B 715907360f477a8ef69ba0465d6de1f23224da0c2095a21141f597a9cfe5c787cbafaa5d3c9cb04175f4d73cc4d184e13628541072d164596ee0b9b24175b501 SHA512 085d436d933c317555f36cbfb8e8c200ca15f20e56e48ae5427a673a74017dca7818320143a4841b78946685839931d48ae563b8b8e3ee6074581536cd0ff13b
diff --git a/sci-biology/subread/files/subread-2.0.1-fno-common.patch b/sci-biology/subread/files/subread-2.0.1-fno-common.patch
deleted file mode 100644
index 8f86840c5..000000000
--- a/sci-biology/subread/files/subread-2.0.1-fno-common.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/gene-algorithms.h
-+++ b/src/gene-algorithms.h
-@@ -60,7 +60,7 @@ void add_allvote_q(gene_allvote_t* allvote,int qid , int pos, gene_vote_number_t
-
- unsigned char get_next_char(FILE * fp);
-
--unsigned char * replica_index;
-+extern unsigned char * replica_index;
-
- extern double begin_ftime;
-
diff --git a/sci-biology/subread/subread-2.0.1.ebuild b/sci-biology/subread/subread-2.0.3.ebuild
index a16d0af5f..624509aa5 100644
--- a/sci-biology/subread/subread-2.0.1.ebuild
+++ b/sci-biology/subread/subread-2.0.3.ebuild
@@ -1,22 +1,20 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts"
HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/" # no https
SRC_URI="https://sourceforge.net/projects/subread/files/${P}/${P}-source.tar.gz"
+S="${S}-source"
LICENSE="GPL-3"
SLOT="0"
+KEYWORDS="~amd64"
DEPEND="sys-libs/zlib"
RDEPEND="${DEPEND}"
-S="${S}-source"
-
-PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
-
src_prepare(){
default
sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die
diff --git a/sci-biology/symap/Manifest b/sci-biology/symap/Manifest
deleted file mode 100644
index 4e5ac6ea6..000000000
--- a/sci-biology/symap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST symap-5.0.6.tar.gz 39447370 BLAKE2B 749769c36d7a46c11ab8bc874915b1dc2e4402b881c7f1fbd56353b4c0dc10cb20864c426c8bdb3ab28aa34d5f7d9bfbf8df66a99de34eebc13f3aa66b4a8d27 SHA512 356bebd7e1afeb78d00e748e1ec4488f180f1225aa3ca117b58cc381dc1d910241d54bc84d932ff6de955b6f4150043508fae6bc0f33c4486025aeb7deb010a8
diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild
deleted file mode 100644
index 58b444b3d..000000000
--- a/sci-biology/symap/symap-5.0.6.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP"
-SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-# error: package netscape.javascript does not exist
-KEYWORDS=""
-
-DEPEND="
- sci-biology/blat
- sci-biology/mummer
- sci-biology/muscle"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/SyMAP-${PV}/java"
-
-src_unpack() {
- default
- cd "${S}"
- tar xvf classes_ext.tar.gz
- cd ../
- tar xvf ext.tar.gz
-}
-
-src_prepare() {
- default
- sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die
-}
-
-src_compile() {
- emake class_dirs
- emake
-}
diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
index a03a130c2..18eec4e53 100644
--- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild
+++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="TIGR Foundation for C++"
HOMEPAGE="https://sourceforge.net/projects/amos/"
@@ -20,11 +20,7 @@ PATCHES=(
"${FILESDIR}/TigrFoundation-all-patches.patch"
)
-src_prepare(){
- sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
- default
-}
-
src_install(){
- emake install DESTDIR="${ED}/usr" # Makefile does not respect DESTDIR
+ sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
+ DESTDIR="${ED}/usr" emake install # Makefile does not respect DESTDIR
}
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest
index 815ffe565..153f208fd 100644
--- a/sci-biology/trinityrnaseq/Manifest
+++ b/sci-biology/trinityrnaseq/Manifest
@@ -1 +1 @@
-DIST trinityrnaseq-2.11.0.tar.gz 320752461 BLAKE2B 53327a49d31f7350e8fe820ac106f1cbe0577097852a63ea2154004d1945079f737f646c09d9907cfd45fb011845ea5e21eedf8fcda09e1db17d563fbdd0fd66 SHA512 9e9af2a16423ff8c063522c7acb6c8fc9386a95a7b58e01c94cd97971f71c3080cd5b2d34133bb501505d35cae05b77ff8423ad948324f49f9d4ddbb16629d20
+DIST trinityrnaseq-2.13.2.tar.gz 310355363 BLAKE2B 63055e11976a8d70b2c10b4859b25c8a27f23c05d1f5196eca137f281812aa54558b7eda343498a61af0c5aaa0e8d255e5d0a81e53c906859b455e0725180f95 SHA512 8399e12516d6d3cfde6803323b3bfb9ae249528fc79c08a6b290f42e7498783e6b300b89f9890570b28b2847ebe0f7894f59a888bf47d51190aad9e7c1ce54b7
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
deleted file mode 100644
index 9ecaf24f2..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
-SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.2.6:2
- >=sci-libs/htslib-1.2.1
- >=sci-biology/samtools-1.3:0
- >=sci-biology/trimmomatic-0.36
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All
- sci-biology/seqtools"
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-# has the following "plugins" (aka bundled 3rd-party code)
-# slclust
-# DEXseq_util
-# COLLECTL
-# ParaFly-0.1.0
-
-S="${WORKDIR}/${PN}-v${PV}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
-)
-
-src_compile(){
- emake all
- emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-}
-
-src_install(){
- dodoc Chrysalis/chrysalis.notes
- dodoc Changelog.txt
- perl_set_version
- dobin Trinity
- perl_domodule util/*.pl
- dobin Inchworm/bin/*
- cd Chrysalis/bin || die
- dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts
- cd ../../util/R || die
- insinto /usr/share/"${PN}"/R
- doins *.R
- cd ../PBS || die
- insinto /usr/share/"${PN}"/PBS
- doins *
- cd .. || die
- cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
- cd "${S}" || die
- perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm
- perl_domodule PerlLib/KmerGraphLib/*.pm
- perl_domodule PerlLib/CDNA/*.pm
- perl_domodule PerlLib/Simulate/*.pm
- perl_domodule PerlLib/CanvasXpress/*.pm
- chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
new file mode 100644
index 000000000..3b94d9713
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module
+
+DESCRIPTION="Transcriptome assembler for RNA-seq reads"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/parafly
+ >=sci-biology/jellyfish-2.2.6:2
+ >=sci-libs/htslib-1.2.1
+ >=sci-biology/samtools-1.3:0
+ >=sci-biology/trimmomatic-0.36
+ >=sci-biology/GAL-0.2.1
+ dev-perl/IO-All
+ sci-biology/seqtools
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
+)
+
+src_compile(){
+ # missing submodule for bamsifter
+ emake no_bamsifter
+ emake plugins
+}
+
+src_install(){
+ # fix the install path
+ sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \
+ -i util/support_scripts/trinity_installer.py || die
+ dodir /usr/bin
+ default
+}
diff --git a/sci-biology/vcflib/Manifest b/sci-biology/vcflib/Manifest
index 57b3d1f2b..a535ea547 100644
--- a/sci-biology/vcflib/Manifest
+++ b/sci-biology/vcflib/Manifest
@@ -1 +1 @@
-DIST vcflib-1.0.2-src.tar.gz 20881031 BLAKE2B 67e8fd60db3171fa05cac36306852134cc8c37a3e4715d141547773c3252569a01363298297978d89c015b1120ad0f0d05eb2b67b5ee7d01728f27f0049bc748 SHA512 7dadd2398d4054a1d7e7b520f192243f63c98a4fa184f7c6750dce9296356f4b45bdbb50f7de270a6c4c3aa76deec45980c363e19b22bea64590de711fdb7d71
+DIST vcflib-1.0.3.tar.gz 19213097 BLAKE2B 142685d494759d61e7b0ed40e9d91b78d7856038b6fb73f7f26f80152b0a85006bd6f3e9b5e7422e74841eb9a21e3a86efc3f63545e3fea7545fb91a7475b409 SHA512 16c7b3932fd4e6a985adbc1131dd0b48028501be3023d85fd57b4efccaf071a11ba6f49219df723f6eacc2787218e8f3f2b318e016633ce3e829139b698154a2
diff --git a/sci-biology/vcflib/vcflib-1.0.2.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild
index 272e69483..d4cf1e02f 100644
--- a/sci-biology/vcflib/vcflib-1.0.2.ebuild
+++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake toolchain-funcs
DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
HOMEPAGE="https://github.com/vcflib/vcflib"
-SRC_URI="https://github.com/vcflib/vcflib/releases/download/v${PV}/${P}-src.tar.gz"
-
-# vcflib is incorporated into several projects, such as freebayes
+SRC_URI="https://github.com/vcflib/vcflib/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT-with-advertising"
SLOT="0"
+# No proper release tarball for this release yet
KEYWORDS=""
IUSE="openmp"
@@ -22,10 +21,6 @@ DEPEND="
sci-biology/tabixpp
"
RDEPEND="${DEPEND}"
-# contains bundled sci-biology/htslib ?
-# see also ./include for possible traces of other bundled sw
-
-S="${WORKDIR}/${PN}"
src_prepare(){
cmake_src_prepare
@@ -47,7 +42,7 @@ src_prepare(){
src_compile(){
mycmakeargs=(
-DOPENMP="$(use_enable openmp)"
- -DHTSLIB_LOCAL=NO
+ -DHTSLIB_LOCAL=ON
)
cmake_src_compile
}
diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest
deleted file mode 100644
index 5209a3925..000000000
--- a/sci-biology/wcd/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST wcd-0.6.3_p20180430.tar.gz 368654 BLAKE2B c6936964d4dd2602e9fd735ddf70ed79e625b6dfa58972a1ba95532b36968da4345ef40d7ba68355f8f53308d0989124c1bbdce48e11d0240ccabc91787d3b61 SHA512 7c847607fcbeb20cb5dbf023968a9174a5d2fd876127a6008b878274ec2e1a6498e7c0a610e4f75473128236661848d6403f96fc868eec773be3a8e4e7dd7f4f
-DIST wcd.html 8448 BLAKE2B d1561925a0f299d12c177f499a95fbc314d558c18106642c49852bd96a104bdef5271b5ea1b4312e70936db6726ea3ea54e3a942d9c9c52e806b48137321cf05 SHA512 11156d4811b7716632fbd7b0330d918ae30b6dcc9ebbd59c95d445ba465504aa68d0fa9863b3ad4b5743c929f4558d1698af03c124fd02299ef13479a80555c2
-DIST wcd.pdf 275513 BLAKE2B 049d0d8b9d6db0e2754322f69903c5680a62c007a9abf5466b21a96f778a9f537a8ec91344d729961317ff6a8b484ca870f5ee0a78fa7cec8ae4ba2d7c5f1939 SHA512 ef2e0e8bbe49a5c5b304a305d8948b253ba2bf789790941600c5d5ba74351fe41e54a66dd189a33846304a8f2a8fa4c70025e516f3b73643da71030cbded63a2
diff --git a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch b/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
deleted file mode 100644
index 15d851577..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/auxcluster.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/auxcluster.c b/src/auxcluster.c
-index ac00a0f..e98f19f 100644
---- a/src/auxcluster.c
-+++ b/src/auxcluster.c
-@@ -2,6 +2,7 @@
-
- #include "common.h"
- #include "strings.h"
-+#include <string.h>
- #include "assert.h"
-
- extern SeqInfoPtr seqInfo;
diff --git a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch b/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
deleted file mode 100644
index d697d00b7..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index e986a91..ff87e29 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -7,7 +7,7 @@ wcd_CFLAGS += -DMPI
- endif
- if PTHREADS
- wcd_CFLAGS += -DPTHREADS
--wcd_LDFLAGS += -lpthread
-+wcd_LDADD = -lpthread
- endif
- if !COMPILER
- wcd_CFLAGS += -DNOINLINE
diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/wcd/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
deleted file mode 100644
index 6593d97ed..000000000
--- a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-COMMIT="aee525029bb661b633097e989c6fe2eaa93d2def"
-
-DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
-HOMEPAGE="https://shaze.github.io/wcdest/"
-SRC_URI="https://github.com/shaze/wcdest/archive/${COMMIT}.tar.gz -> ${P}.tar.gz
- http://www.bioinf.wits.ac.za/~scott/wcd.html
- http://www.bioinf.wits.ac.za/~scott/wcd.pdf"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="doc mpi threads"
-
-# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse,
-# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse)
-DEPEND="mpi? ( sys-cluster/mpich2 )"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-0.6.3-ldflags.patch
- "${FILESDIR}"/${PN}-0.6.3-impl-decl.patch
-)
-
-S="${WORKDIR}/${PN}est-${COMMIT}/code"
-
-src_configure(){
- econf \
- $(use_enable mpi) \
- $(use_enable threads pthreads)
-}
-
-src_compile() {
- default
- use doc && emake pdf info html
-}
-
-src_install() {
- use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
- emake install PREFIX=/usr LIBDIR="${D}"/usr/$(get_libdir)
- dodoc "${DISTDIR}"/wcd.*
-}
diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild
index b65625139..7d5f9147a 100644
--- a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild
+++ b/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild
@@ -30,7 +30,7 @@ RDEPEND="
sci-libs/hdf5
sci-libs/xdrfile
sys-devel/gcc[openmp,fortran]
- virtual/jpeg
+ media-libs/libjpeg-turbo
virtual/glu
virtual/opengl
x11-libs/libX11
diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild
index b65625139..7d5f9147a 100644
--- a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild
+++ b/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild
@@ -30,7 +30,7 @@ RDEPEND="
sci-libs/hdf5
sci-libs/xdrfile
sys-devel/gcc[openmp,fortran]
- virtual/jpeg
+ media-libs/libjpeg-turbo
virtual/glu
virtual/opengl
x11-libs/libX11
diff --git a/sci-chemistry/ctffind/ctffind-4.1.14.ebuild b/sci-chemistry/ctffind/ctffind-4.1.14.ebuild
index ae4ced4e5..a69a36308 100644
--- a/sci-chemistry/ctffind/ctffind-4.1.14.ebuild
+++ b/sci-chemistry/ctffind/ctffind-4.1.14.ebuild
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86"
DEPEND="
sci-libs/fftw:3.0
- virtual/jpeg
+ media-libs/libjpeg-turbo
media-libs/tiff
x11-libs/wxGTK:*
"
diff --git a/sci-chemistry/erkale/Manifest b/sci-chemistry/erkale/Manifest
new file mode 100644
index 000000000..c7ee5eb6b
--- /dev/null
+++ b/sci-chemistry/erkale/Manifest
@@ -0,0 +1 @@
+DIST erkale-0_p20220106.tar.gz 45625969 BLAKE2B 038c504008c1023064426b39c6266e3e26c7a09a47c595a4d1c1ebd70e43a9c8acef527fd47079ca95f337e0ea8c81370a43fb24c7f87887d1f1637c162449fe SHA512 f41b8e82703d7a8d4b9728d04e9deed471af608368b27c2ab6a42073426c3ae5bab3151efbebef6c3baeb1de839472d4ed7b2df430eaafd7e47962cbc06de48f
diff --git a/sci-chemistry/erkale/erkale-9999.ebuild b/sci-chemistry/erkale/erkale-0_p20220106.ebuild
index 11c7b05c6..1ed7ab033 100644
--- a/sci-chemistry/erkale/erkale-9999.ebuild
+++ b/sci-chemistry/erkale/erkale-0_p20220106.ebuild
@@ -1,17 +1,20 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit cmake flag-o-matic git-r3 multibuild toolchain-funcs
+inherit cmake flag-o-matic multibuild toolchain-funcs
+
+COMMIT="bfb9d499a45e1da78b32a9fd52a06fd0dafc52f8"
DESCRIPTION="Quantum chemistry program for atoms and molecules"
HOMEPAGE="https://github.com/susilehtola/erkale"
-EGIT_REPO_URI="https://github.com/susilehtola/erkale.git"
+SRC_URI="https://github.com/susilehtola/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
SLOT="0"
LICENSE="GPL-2"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE="openmp"
RDEPEND="
@@ -40,7 +43,7 @@ src_prepare() {
src_configure() {
my_configure() {
local OMP=OFF && [[ ${MULTIBUILD_VARIANT} == "omp" ]] && OMP=ON
- local basis="${EROOT}/usr/share/${PN}/basis"
+ local basis="${EPREFIX}/usr/share/${PN}/basis"
local mycmakeargs=(
-DUSE_OPENMP=${OMP}
-DBUILD_SHARED_LIBS=ON
diff --git a/sci-chemistry/module2/Manifest b/sci-chemistry/module2/Manifest
deleted file mode 100644
index 2bb0b7338..000000000
--- a/sci-chemistry/module2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MODULE2.tar.gz 1593965 SHA256 c98a32e2b9af109bf8cfc0670bff1350b97adf3ede4a44e33f6c977fb0348e48 SHA512 bae62229268affd7d9e059f4e7862ebe266d881d98b7a87b42c01591a6304be727bb516e3966666bd105341e131d739cc66f4352ecce69a13cce34fcf0baec39 WHIRLPOOL 77ada1b4e795f39a660a2b8edad98afa18bb31807a13c0005c9d7259e9c4a185c2f10d0bf7d65628217bb7a02d1ff2d97b51770f3b19875615001a5f517c3aee
diff --git a/sci-chemistry/module2/metadata.xml b/sci-chemistry/module2/metadata.xml
deleted file mode 100644
index 713d21566..000000000
--- a/sci-chemistry/module2/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>jlec@gentoo.org</email>
- </maintainer>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/module2/module2-0_pre20140717.ebuild b/sci-chemistry/module2/module2-0_pre20140717.ebuild
deleted file mode 100644
index d9123f318..000000000
--- a/sci-chemistry/module2/module2-0_pre20140717.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Residual dipolar coupling and residual chemical shift analysis software"
-HOMEPAGE="http://www.ibs.fr/science-213/scientific-output/software/module/?lang=en"
-SRC_URI="MODULE2.tar.gz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-
-RDEPEND="
- x11-libs/motif[abi_x86_32(-)]
- x11-libs/libX11[abi_x86_32(-)]
- x11-libs/libXext[abi_x86_32(-)]
- x11-libs/libXpm[abi_x86_32(-)]
- x11-libs/libXt[abi_x86_32(-)]
-"
-DEPEND="${RDEPEND}
-"
-
-RESTRICT="fetch splitdebug"
-
-S="${WORKDIR}"/MODULE2
-
-QA_PREBUILT="opt/bin/.*"
-
-pkg_nofetch() {
- elog "Please download ${A} from"
- elog "${HOMEPAGE}"
- elog "and place it into your DISTDIR folder"
-}
-
-src_install() {
- use prefix && \
- patchelf --set-rpath "${EPREFIX}"/usr/lib
- exeinto /opt/bin
- doexe module
- dosym module /opt/bin/${PN}
-
- dodoc -r MODULE2_manual_fichiers MODULE2_manual.htm
-
- insinto /usr/share/${PN}
- doins sample*
-}
diff --git a/sci-chemistry/pyquante/Manifest b/sci-chemistry/pyquante/Manifest
deleted file mode 100644
index af2e5e23d..000000000
--- a/sci-chemistry/pyquante/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyquante-2.1_p20190721.tar.gz 533943 BLAKE2B 6d443d052bc20150841e6e07b0a79120c421c281ac56b85c047ea8db0bd918ca607d42c94005b7e40e78e2b65e1675e0670dde2a135b43f43d6d2850e947b221 SHA512 d8df7ac4a2c4bf0528fefd79159c406387182d039f5557ec285de9120c8e4264404920672ddd640a51a1fff7585fa39e11eb43a99dc8e46094b9689f244e3008
diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml
deleted file mode 100644
index 9f3ad9572..000000000
--- a/sci-chemistry/pyquante/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">pyquante</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pyquante/pyquante-2.1_p20190721.ebuild b/sci-chemistry/pyquante/pyquante-2.1_p20190721.ebuild
deleted file mode 100644
index 1eee1d60a..000000000
--- a/sci-chemistry/pyquante/pyquante-2.1_p20190721.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9
-
-inherit distutils-r1
-
-COMMIT="6e34cb4480ae7dbd8c5e44d221d8b27584890c83"
-
-DESCRIPTION="Quantum chemistry package written in Python"
-HOMEPAGE="https://github.com/rpmuller/pyquante2"
-SRC_URI="https://github.com/rpmuller/pyquante2/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-# Fails to find self, even with --install
-RESTRICT="test"
-
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${PN}2-${COMMIT}"
-
-distutils_enable_sphinx docs --no-autodoc
-distutils_enable_tests --install pytest
-
-python_prepare_all() {
- # this has been renamed in newer versions of sphinx
- sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die
-
- distutils-r1_python_prepare_all
-}
diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild
index ab1a155c3..a74996b46 100644
--- a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild
+++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild
@@ -14,7 +14,7 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-DEPEND="app-arch/zstd sci-libs/hdf5"
+DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r2"
RDEPEND="${DEPEND}"
S=${WORKDIR}/${PN}-${COMMIT}
@@ -25,9 +25,3 @@ src_configure() {
)
cmake_src_configure
}
-
-src_install() {
- echo "HDF5_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/hdf5/plugin" >> 99h5zstd || die
- doenvd 99h5zstd
- cmake_src_install
-}
diff --git a/sci-libs/aocl-libm/Manifest b/sci-libs/aocl-libm/Manifest
index c27520623..3f320d8be 100644
--- a/sci-libs/aocl-libm/Manifest
+++ b/sci-libs/aocl-libm/Manifest
@@ -1,2 +1,2 @@
-DIST aocl-libm-linux-aocc-3.6.0-4.tar.gz 855788 BLAKE2B 39874a04bd010382e6b5f14066a7267bc7f999384211c4663ca191dbcc8d2a990597d1b140c6bcd4cb2b945ae8951c430572a9696edef505c6815c5acfad3166 SHA512 6f49cca01eab40ad06b6e3a4166eb83f355245e892171907f1315f5e60372aafd9bca5878dc1480fb102a3de4699369ce5931167ead00165fd1644c988f6c325
-DIST aocl-libm-linux-gcc-3.6.0-4.tar.gz 844698 BLAKE2B 1a72691d9351859f07abdf49663bd1da8932465cfcb0983ba594ad0d09375ca964abd196ab5f26a9eaf0c9f1bd343cbdc0b6b427d7648f148ff880aeb826770b SHA512 fc07d1b45864140cf87410ad3595c681598458a8dd9ef7625a9e520b5d10ab06dccb2551193d4d907b19b188cdb34ef16f587549b94324371ee1e04b612f1ee9
+DIST aocl-libm-linux-aocc-3.1.0.tar.gz 1234123 BLAKE2B d63c5e5a5e5445de59ed5726ae5cc285fa7e9416255b861f337c7f649d460d6f95d4deb2b635166a5ed99f216eefb47054b11f3949c54a2fb06c4fc7bc9098d7 SHA512 0806b50b2f20bfe05a3d3eff16be09c4597f07f1dad15861cb289f1f0850cc9ed53601d4cf41174f6ad1f67963a94f7a6fee66394f787d302bf1a9c7b17e45cc
+DIST aocl-libm-linux-gcc-3.1.0.tar.gz 1281295 BLAKE2B 953fbc381182afb7e3b26a93643f4ab18c9fb7b331d686bde75b63f512668a5045fa74209031849a4b3701fd51000c386c96ad7a3d4567913b68b04b9115351a SHA512 3df4700498713c510ff2cc04ad37db12b3b3c174caf6118bfd364f95899a10eeefca566d898c13fb3732f5b7390792f1c786c64dbf928ed9021b11546d5c04c9
diff --git a/sci-libs/aocl-libm/aocl-libm-3.6.0_p4.ebuild b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild
index f7a741abb..890414de2 100644
--- a/sci-libs/aocl-libm/aocl-libm-3.6.0_p4.ebuild
+++ b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild
@@ -1,19 +1,17 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
-MY_PV=${PV/_p/-}
-
DESCRIPTION="Optimized libm replacement from AMD for x86_64 architectures"
HOMEPAGE="https://developer.amd.com/amd-aocl/amd-math-library-libm/"
SRC_URI="
- aocc? ( aocl-libm-linux-aocc-${MY_PV}.tar.gz )
- !aocc? ( aocl-libm-linux-gcc-${MY_PV}.tar.gz )
+ aocc? ( aocl-libm-linux-aocc-${PV}.tar.gz )
+ !aocc? ( aocl-libm-linux-gcc-${PV}.tar.gz )
"
-S="${WORKDIR}"/amd-libm
+S="${WORKDIR}/amd-libm"
LICENSE="AMD"
SLOT="0"
@@ -36,15 +34,15 @@ src_prepare() {
sed -e "s/^CC =.*$/CC = $(tc-getCC)/" -i examples/Makefile || die
- cat <<- EOF > "${T}"/amdlibm.pc
- prefix=${EROOT}/usr
+ cat <<- EOF > "${T}"/amdlibm.pc || die
+ prefix=${EPREFIX}/usr
exec_prefix=\${prefix}
libdir=\${prefix}/$(get_libdir)
includedir=\${prefix}/include
Name: ${PN}
Description: ${DESCRIPTION}
- Version: ${MY_PV}
+ Version: ${PV}
Libs: -L\${libdir} -lamdlibm
Cflags: -I\${includedir}
EOF
@@ -61,9 +59,8 @@ src_install() {
doheader include/*
- dolib.so lib/libamdlibm.so
- use static-libs && \
- dolib.a lib/libamdlibm.a
+ dolib.so lib/*.so
+ use static-libs && dolib.a lib/*.a
if use examples; then
dodoc -r examples
diff --git a/sci-libs/arpack/Manifest b/sci-libs/arpack/Manifest
new file mode 100644
index 000000000..730cdcfdd
--- /dev/null
+++ b/sci-libs/arpack/Manifest
@@ -0,0 +1,3 @@
+DIST arpack-3.8.0_p20220604.gh.tar.gz 1012341 BLAKE2B 30f71c334f3ce8b24bce309cdfa5869fa4781baa1935dbd7772936f1f135e4d6a3b576f9fece8ba9ff48f053bac1d1328c4f5f5545cacaa568e1ea5695013e2f SHA512 f31c7bd45a82a8a64e1d041ca18eac9c50dac0ebecf845ad5e57c70d1c12ab36ab0630db224897bfe6181c0fff9152f1dea7b3a6a2eb53bfda2f2a590ca8a37b
+DIST arpack-tutorial.ps.gz 105599 BLAKE2B 99570e6a0cc1c020b9c271e8ce1cc224f69ff5333cc818c10b063dc8ffbaf66a9f5c6ede99541b4212286d422146b1c4e332eba7e1635c99efa0e4c2620f0630 SHA512 a7b8fefd1a572ed477ae208d49094c1c65c9368990d12de9b3528e33fed546c947659f74e54a810d04154b4a1b0f9a94bcba4db0cf59d379e20786a261066aa4
+DIST arpack-ug.ps.gz 248543 BLAKE2B ac010aef470060636fa00360636ba093f0d24d219fa927c79fb1726b798160eda74fa8b4be6c7dff94f5759efcf30afa99ad310e7959115e028738beb8aa125d SHA512 3349117fb10b07207ffbab2ffa31b406d026855ea4c16e8649b14c7d70bc94e11b5730672e34acd654817799136d4bd76569ac50ec78d787df5582d18ed61328
diff --git a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
new file mode 100644
index 000000000..b7a989641
--- /dev/null
+++ b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
@@ -0,0 +1,102 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+COMMIT="5eafea4328f1631eab28b1a20e757d1f0e21f8a6"
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit cmake flag-o-matic fortran-2 python-single-r1
+
+DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems"
+HOMEPAGE="
+ https://www.caam.rice.edu/software/ARPACK/
+ https://github.com/opencollab/arpack-ng
+"
+SRC_URI="
+ https://github.com/opencollab/${PN}-ng/archive/${COMMIT}.tar.gz -> ${PF}.gh.tar.gz
+ doc? (
+ http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz -> ${PN}-ug.ps.gz
+ http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz -> ${PN}-tutorial.ps.gz
+ )
+"
+S="${WORKDIR}/${PN}-ng-${COMMIT}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples icb icbexmm int64 mpi python"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+
+ icbexmm? ( dev-cpp/eigen )
+ mpi? ( virtual/mpi[fortran] )
+ icb? ( virtual/mpi[cxx] )
+ python? (
+ ${PYTHON_DEPS}
+ $(python_gen_cond_dep 'dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]')
+ )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+REQUIRED_USE="
+ icb? ( mpi )
+ python? (
+ ${PYTHON_REQUIRED_USE}
+ icbexmm
+ )
+"
+
+src_configure() {
+ append-fflags '-fallow-argument-mismatch'
+
+ local mycmakeargs=(
+ -DBUILD_SHARED_LIBS=ON
+ -DEXAMPLES=$(usex examples)
+ -DICB=$(usex icb)
+ -DICBEXMM=$(usex icbexmm)
+ -DINTERFACE64=$(usex int64)
+ -DMPI=$(usex mpi)
+ -DPYTHON3=$(usex python)
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ dodoc DOCUMENTS/*.doc
+ newdoc DOCUMENTS/README README.doc
+ use doc && dodoc "${WORKDIR}"/*.ps
+ if use examples; then
+ for i in BAND COMPLEX NONSYM SIMPLE SVD SYM ; do
+ exeinto "/usr/libexec/${PN}/examples/${i}"
+ doexe "${BUILD_DIR}/EXAMPLES/${i}"/*
+ done
+
+ if use mpi; then
+ exeinto "/usr/libexec/${PN}/examples/MPI"
+ doexe "${BUILD_DIR}"/PARPACK/EXAMPLES/MPI/*
+ fi
+
+ if use python; then
+ docinto examples/pyarpack
+ dodoc "${BUILD_DIR}"/*.py
+ fi
+ docompress -x "/usr/share/doc/${PF}/examples"
+ fi
+ if use icbexmm; then
+ exeinto "/usr/libexec/${PN}/examples/MATRIX_MARKET"
+ doexe "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm"
+ rm "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm" || die
+ docinto examples
+ dodoc -r "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET"
+ fi
+ if use python; then
+ python_domodule "${ED}/usr/$(get_libdir)/pyarpack"
+ rm -r "${ED}/usr/$(get_libdir)/pyarpack" || die
+ fi
+}
diff --git a/sci-libs/arpack/metadata.xml b/sci-libs/arpack/metadata.xml
new file mode 100644
index 000000000..9cd539912
--- /dev/null
+++ b/sci-libs/arpack/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The ARnoldi PACKage is a library of routines capable of solving large scale symmetric,
+ nonsymmetric, and generalized eigenproblems. The software is designed to compute a few
+ eigenvalues with user specified features such as those of largest real
+ part or largest magnitude. Storage requirements are on the order of
+ n*k locations. No auxiliary storage is required. A set of Schur basis
+ vectors for the desired k-dimensional eigen-space is computed which is
+ numerically orthogonal to working precision. Numerically accurate
+ eigenvectors are available on request.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">opencollab/arpack-ng</remote-id>
+ </upstream>
+ <use>
+ <flag name="icb">Enable support for *[ae]upd_c with ISO_C_BINDING</flag>
+ <flag name="icbexmm">Enable support for matrix market example based on ICB</flag>
+ <flag name="int64">Use the 64-bit integer interface (ILP64)</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-libs/clfft/clfft-2.12.2.ebuild b/sci-libs/clfft/clfft-2.12.2-r1.ebuild
index 9cfbc7f8a..8be3d24d0 100644
--- a/sci-libs/clfft/clfft-2.12.2.ebuild
+++ b/sci-libs/clfft/clfft-2.12.2-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
MY_PN="clFFT"
@@ -18,7 +18,7 @@ SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${
LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="callback_client +client test"
+IUSE="callback-client +client test"
RDEPEND="
virtual/opencl
@@ -38,7 +38,7 @@ S="${WORKDIR}/${MY_PN}-${PV}/src"
src_configure() {
local mycmakeargs=(
- -DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
+ -DBUILD_CALLBACK_CLIENT="$(usex callback-client)"
-DBUILD_CLIENT="$(usex client)"
-DBUILD_TEST="$(usex test)"
-DBoost_USE_STATIC_LIBS=OFF
diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild
index d78fc3e9e..10e6ed148 100644
--- a/sci-libs/clfft/clfft-9999.ebuild
+++ b/sci-libs/clfft/clfft-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
MY_PN="clFFT"
@@ -21,7 +21,7 @@ EGIT_BRANCH="develop"
LICENSE="Apache-2.0"
SLOT="0"
-IUSE="callback_client +client test"
+IUSE="callback-client +client test"
RDEPEND="
virtual/opencl
@@ -40,7 +40,7 @@ S="${WORKDIR}/${P}/src"
src_configure() {
local mycmakeargs=(
- -DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
+ -DBUILD_CALLBACK_CLIENT="$(usex callback-client)"
-DBUILD_CLIENT="$(usex client)"
-DBUILD_TEST="$(usex test)"
-DBoost_USE_STATIC_LIBS=OFF
diff --git a/sci-libs/clfft/metadata.xml b/sci-libs/clfft/metadata.xml
index e353d590c..911f5977b 100644
--- a/sci-libs/clfft/metadata.xml
+++ b/sci-libs/clfft/metadata.xml
@@ -18,7 +18,7 @@ clFFT is part of the clMath sofware library, which is the
successor of APPML.
</longdescription>
<use>
- <flag name="callback_client">
+ <flag name="callback-client">
Build a command line clFFT client program that tests callback functionality.
</flag>
<flag name="client">
diff --git a/sci-libs/iRODS/Manifest b/sci-libs/iRODS/Manifest
index 4efc24868..8466e3408 100644
--- a/sci-libs/iRODS/Manifest
+++ b/sci-libs/iRODS/Manifest
@@ -1 +1,2 @@
-DIST iRODS-4.2.8.tar.gz 1902368 BLAKE2B 7ecbf4da15bb15dba6dbcebb21b66b46f6906daa694c7d9d49fbcfbcc9b9eabffe805f7da411e6d3272c34e605cfed12525130c1cedfd58a6601401ec49a963a SHA512 0a57201f4404e0d023f68591842edd1f750050c16ca2b4fad4dcbdabfce77755540a13140d201bc3fea214dcf3d3c40a43fd079f09f0544e979330f04279a579
+DIST iRODS-4.2.11.tar.gz 2183164 BLAKE2B 8c87938e7c8aa731282bf64ec8e017fe0f9ee70c46f07b4c136973bf0ca50954898d93c045440c79eecab84d8adbda6905f1e8eae434c8094ca50ce9f2c1b5dc SHA512 6f938ecc5b872326a4b59b82f119f1c5526c438e7b5c44248b5bba735445e4bc8b287f3bc0eb53b684b17a247aff31cb48b0211a10fc92870d29bdef978715e5
+DIST iRODS-4.2.11_schema_messaging.tar.gz 454 BLAKE2B 09f1f48e22f05545233017db85b84472d0a84b3926b706af6d81cbaaf5d919f508856572daa6e5c61a5a4830527fb982df2df2eb11540a0c7841513eee206ee2 SHA512 d77b0e9d9f80b1513eacc9a86f14ffb02ff5172df41527c41cd49fea26831f11f2c87dc2ea21ae7ad5fb6e0399f8a72248d9accea65101a08158710c5012184a
diff --git a/sci-libs/iRODS/iRODS-4.2.11.ebuild b/sci-libs/iRODS/iRODS-4.2.11.ebuild
new file mode 100644
index 000000000..849a7c509
--- /dev/null
+++ b/sci-libs/iRODS/iRODS-4.2.11.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake llvm
+
+MESSAGING_COMMIT="24c73702c88e94c3b159dac97fe7a0640dfc209d"
+
+DESCRIPTION="Integrated Rule Oriented Data System, a data management software"
+HOMEPAGE="https://irods.org"
+SRC_URI="
+ https://github.com/irods/irods/archive/${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/irods/irods_schema_messaging/archive/${MESSAGING_COMMIT}.tar.gz -> ${P}_schema_messaging.tar.gz
+"
+S="${WORKDIR}/irods-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+# need the c++ version of avro
+KEYWORDS=""
+
+DEPEND="
+ app-arch/libarchive
+ dev-cpp/catch:0
+ dev-libs/avro-c
+ dev-libs/boost:=
+ dev-libs/jansson
+ dev-libs/json-c
+ dev-libs/libfmt
+ dev-libs/openssl
+ dev-libs/spdlog
+ sys-libs/libcxx
+ sys-libs/pam
+ net-libs/cppzmq
+ net-libs/zeromq
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ sys-devel/clang
+"
+
+src_unpack() {
+ default
+ mv "${WORKDIR}/irods_schema_messaging-${MESSAGING_COMMIT}/v1" "${S}/irods_schema_messaging/" || die
+}
+
+src_prepare() {
+ cmake_src_prepare
+ # use the correct lib dir
+ find . -name "CMakeLists.txt" -exec sed -i \
+ -e '/${IRODS_EXTERNALS_FULLPATH_.*}/s/\/lib\//\/lib64\//g' \
+ {} + || die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DIRODS_EXTERNALS_FULLPATH_CLANG="$(get_llvm_prefix)"
+ -DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="$(get_llvm_prefix)"
+ -DIRODS_EXTERNALS_FULLPATH_ARCHIVE="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_AVRO="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_BOOST="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_CATCH2="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_FMT="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_ZMQ="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_JANSSON="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_SPDLOG="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_CPPZMQ="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_JSON="${EPREFIX}/usr"
+ -DIRODS_EXTERNALS_FULLPATH_NANODBC="${EPREFIX}/usr"
+ # pretend we are Arch, otherwise fatal error
+ -DIRODS_LINUX_DISTRIBUTION_NAME="arch"
+ -DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR="1"
+ )
+ cmake_src_configure
+}
diff --git a/sci-libs/iRODS/iRODS-4.2.8.ebuild b/sci-libs/iRODS/iRODS-4.2.8.ebuild
deleted file mode 100644
index eba0c76e2..000000000
--- a/sci-libs/iRODS/iRODS-4.2.8.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Integrated Rule Oriented Data System, a data management software"
-HOMEPAGE="https://irods.org"
-SRC_URI="https://github.com/irods/irods/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND="sys-devel/clang"
-
-S="${WORKDIR}/irods-${PV}"
diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index c0a74b27f..bf9f0f021 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -40,7 +40,7 @@ RDEPEND="
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
sys-libs/zlib:0=
- virtual/jpeg:0=
+ media-libs/libjpeg-turbo:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
python? ( ${PYTHON_DEPS} )
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 8c9e48dba..3f6c759ec 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -51,7 +51,7 @@ RDEPEND="
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
sys-libs/zlib:0=
- virtual/jpeg:0=
+ media-libs/libjpeg-turbo:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
python? ( ${PYTHON_DEPS} )
diff --git a/sci-libs/libflame-amd/Manifest b/sci-libs/libflame-amd/Manifest
index 6da475e97..422282045 100644
--- a/sci-libs/libflame-amd/Manifest
+++ b/sci-libs/libflame-amd/Manifest
@@ -1 +1 @@
-DIST libflame-amd-2.2.tar.gz 28327573 BLAKE2B a53bef8c08bfb5ca14c145ac9ae11e6f41f9d0ef2755cab2b69df6103b2164a6786bb2e3e709faf7a11cad2b4a58310082637c6e5516a987bb65cb599837bfff SHA512 c68a9a1e37eac649d898f25bd5f4d89abecd3fdb8ff9c9678d4d2c0761660322f270f4508f93511f3db75ef074531a1c9824cc81ed88cfcec82bc9513d274ec0
+DIST libflame-amd-3.1.tar.gz 26635219 BLAKE2B 43f5db65bb53a818259e62e01d373ba8db2052c11b5839d28805e37e2b9033e16410efc4b6ce3379f3d92067511b834ef16dbca22987945608167a90e4f31871 SHA512 b6a05dbadd169e05645bc4ae456f00b6c84f2c3eeaf1e1bd74d273e540ca1f99915bd221427bce0e4f73fed050daf2db8902891451d5b2b9273af48c8e2f4479
diff --git a/sci-libs/libflame-amd/libflame-amd-2.2.ebuild b/sci-libs/libflame-amd/libflame-amd-2.2.ebuild
deleted file mode 100644
index 04830e5c3..000000000
--- a/sci-libs/libflame-amd/libflame-amd-2.2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2
-FORTRAN_NEED_OPENMP=1
-
-DESCRIPTION="AMD optimized high-performance object-based library for DLA computations"
-HOMEPAGE="https://developer.amd.com/amd-aocl/"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/amd/libflame"
-else
- SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/libflame-"${PV}"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-
-CPU_FLAGS=( sse3 )
-IUSE_CPU_FLAGS_X86="${CPU_FLAGS[@]/#/cpu_flags_x86_}"
-IUSE="scc static-libs supermatrix ${IUSE_CPU_FLAGS_X86[@]}"
-
-DEPEND="virtual/cblas"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-vcs/git"
-
-src_configure() {
- local myconf=(
- --disable-optimizations
- --enable-multithreading=openmp
- --enable-verbose-make-output
- --enable-lapack2flame
- --enable-cblas-interfaces
- --enable-max-arg-list-hack
- --enable-dynamic-build
- --enable-vector-intrinsics=$(usex cpu_flags_x86_sse3 sse none)
- $(use_enable static-libs static-build)
- $(use_enable scc)
- $(use_enable supermatrix)
- )
- econf "${myconf[@]}"
-}
-
-src_compile() {
- default
-}
-
-src_install() {
- emake -j1 DESTDIR="${D}" install
-}
diff --git a/sci-libs/libflame-amd/libflame-amd-9999.ebuild b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild
index 04830e5c3..cdadccb5c 100644
--- a/sci-libs/libflame-amd/libflame-amd-9999.ebuild
+++ b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild
@@ -1,29 +1,23 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit fortran-2
FORTRAN_NEED_OPENMP=1
DESCRIPTION="AMD optimized high-performance object-based library for DLA computations"
HOMEPAGE="https://developer.amd.com/amd-aocl/"
+SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/libflame-${PV}"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/amd/libflame"
-else
- SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/libflame-"${PV}"
- KEYWORDS="~amd64"
-fi
-
+KEYWORDS="~amd64"
LICENSE="BSD"
SLOT="0"
CPU_FLAGS=( sse3 )
IUSE_CPU_FLAGS_X86="${CPU_FLAGS[@]/#/cpu_flags_x86_}"
-IUSE="scc static-libs supermatrix ${IUSE_CPU_FLAGS_X86[@]}"
+IUSE="scc supermatrix ${IUSE_CPU_FLAGS_X86[@]}"
DEPEND="virtual/cblas"
RDEPEND="${DEPEND}"
@@ -39,17 +33,14 @@ src_configure() {
--enable-max-arg-list-hack
--enable-dynamic-build
--enable-vector-intrinsics=$(usex cpu_flags_x86_sse3 sse none)
- $(use_enable static-libs static-build)
$(use_enable scc)
$(use_enable supermatrix)
)
econf "${myconf[@]}"
}
-src_compile() {
- default
-}
-
src_install() {
- emake -j1 DESTDIR="${D}" install
+ # -j1 because otherwise cannot create file that already exists
+ DESTDIR="${ED}" emake -j1 install
+ einstalldocs
}
diff --git a/sci-libs/libsufr/Manifest b/sci-libs/libsufr/Manifest
index 7faa3abc0..2ba7a16c9 100644
--- a/sci-libs/libsufr/Manifest
+++ b/sci-libs/libsufr/Manifest
@@ -1 +1 @@
-DIST libsufr-0.7.5.tar.gz 200473 BLAKE2B b1835af6acea211623cf545aef8f224648c12059f155d17e632432eb328ea977f2c028a246bb16d97911c9dfd33520e3e69bebe3cc9af0d4bacb01e925db2260 SHA512 5b6ee5b166f7e306ec4ce0df8542ca5439a8113e53a6fa6e27e52ca9b9e7e7793b1a839f4c734df7b9e5bec37c073ee409c42038d360c5a1036ff2b7047693cc
+DIST libsufr-0.7.7.tar.gz 207409 BLAKE2B ba366ee8ce19c6b4fed0d45cf8bde39bc9589f46e4e428cc0346966f76e8a185edec6947fb14a5ff63414b3c08b8df56c2367b4f47fe53ed96ae0d26e1d67951 SHA512 c24cb69361f8db31396e554a48eb864b7cc2c8ac437b2c0d3113e02adf9a53017973e2ff49cc9a7a6debeaaea5d9f20c8aa8d505b23e1974f19b3560fded9ca4
diff --git a/sci-libs/libsufr/libsufr-0.7.5-r1.ebuild b/sci-libs/libsufr/libsufr-0.7.7.ebuild
index 0f0cc83fe..3515005bc 100644
--- a/sci-libs/libsufr/libsufr-0.7.5-r1.ebuild
+++ b/sci-libs/libsufr/libsufr-0.7.7.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
CMAKE_BUILD_TYPE=Release
-inherit cmake fortran-2
CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
DESCRIPTION="LIBrary of Some Useful Fortran Routines"
HOMEPAGE="http://libsufr.sourceforge.net/"
@@ -23,7 +23,6 @@ DOCS=( "CHANGELOG" "README" "VERSION" )
src_unpack() {
default
-
gunzip -r "${S}"/man || die
}
diff --git a/sci-libs/pg2plplot/Manifest b/sci-libs/pg2plplot/Manifest
index 762415606..7a4b1af78 100644
--- a/sci-libs/pg2plplot/Manifest
+++ b/sci-libs/pg2plplot/Manifest
@@ -1 +1 @@
-DIST pg2plplot-5.13.0.tar.gz 39330 BLAKE2B 45221573132f4d4556612e7d6ae280ed225a8c3e08c860a269c39c566cd36513a51ad1c9108d8bf053bf71725f72bb990e88b60f8a5792ef06191581cbdc13bb SHA512 38261e2bed8b2700c2b797a6d220a9ede0f18ddfb00260ef1eccfcdf3c7f8bef23918d659927650644e10976a4a7cb7855a01aa6da0b033dace8bb356b141345
+DIST pg2plplot-5.13.1.tar.gz 39935 BLAKE2B c233e68548652145dd845640ec54de6d7f64dc89b52b2f6794b1eb2ee3d02af6333c192c3754d69cd2655474b7fd14f03e7e8e827493e91eae03c4f6374bee2d SHA512 d594630b1154b56009ed9b8f97b2d4e9d401ce06387954eda05e04de230586965b3868fd7a257a8628e53ac1624092850bfa4ccf0e8238daecfc40c3bc6af03c
diff --git a/sci-libs/pg2plplot/pg2plplot-5.13.0.ebuild b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild
index 5b5373e58..de2fa76c1 100644
--- a/sci-libs/pg2plplot/pg2plplot-5.13.0.ebuild
+++ b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
CMAKE_BUILD_TYPE=Release
-inherit cmake fortran-2
CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs"
HOMEPAGE="http://pg2plplot.sourceforge.net"
@@ -16,14 +16,17 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="X png postscript static-libs"
-DEPEND="virtual/fortran
- sci-libs/plplot[fortran]"
+DEPEND="
+ virtual/fortran
+ sci-libs/plplot[fortran]
+"
# If USE="png" or "postscript", ensure PLplot has USE="cairo":
RDEPEND="${DEPEND}
- sci-libs/plplot[fortran,X?]
- png? ( sci-libs/plplot[cairo] )
- postscript? ( sci-libs/plplot[cairo] )"
+ sci-libs/plplot[fortran,X?]
+ png? ( sci-libs/plplot[cairo] )
+ postscript? ( sci-libs/plplot[cairo] )
+"
src_configure() {
local mycmakeargs=(
@@ -31,5 +34,3 @@ src_configure() {
)
cmake_src_configure
}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-libs/pytorch/Manifest b/sci-libs/pytorch/Manifest
deleted file mode 100644
index c0bf8daef..000000000
--- a/sci-libs/pytorch/Manifest
+++ /dev/null
@@ -1,38 +0,0 @@
-DIST FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
-DIST FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
-DIST NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz 219318 BLAKE2B 6b6619c8a706ef9630f20fda1e276314b2ef7f6c9aed26836a48bdaa0ae198a86383e68b04c651f37c07d34e400bc54b5daa75b06fc18cdb0a9c55e2cb33bbe1 SHA512 f0b261e8698b412d12dd739e5d0cf71c284965ae28da735ae22814a004358ba3ecaea6cd26fa17b594c0245966b7dd2561c1e05c6cbf0592fd7b85ea0f21eb37
-DIST PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
-DIST QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
-DIST XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz 3955905 BLAKE2B d787d4a965c53c8d65887f3b111da950f3b5558cd28ce468764c5bf8efbaddeea567803cfcd89a1aab4a0bc781816871dcca2901e762257aaf96a1d8f868ffd2 SHA512 72c3e53b00d77cfd94db93c60276ca7fd419554dadddf74286e85e0500dbdad0bf65694e451e832de89ea17e7731a9ec9e9f1d831b03c1b81946e0dacb96197d
-DIST asmjit-d0d14ac774977d0060a351f66e35cb57ba0bf59c.tar.gz 717277 BLAKE2B 1e743a3293f780aadd413efe896d75851dfde03a60604f09f2230a6bb3923e57a12a5b124531dddb8ca3d226b4abf7c3906c007da47e9326250a5864d5241f9d SHA512 2822763fcb3c18f6699119c1773404667d81f8afb86f8f2e8dbe627526a2877b049d16505557e680e4e310f0e0667263dc4ac442f682e95f2568bf0bf8b61b4b
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-DIST kineto-879a203d9bf554e95541679ddad6e0326f272dc1.tar.gz 7478317 BLAKE2B 0e73fdb99d2f8b4fb0ed53ef6d3f0360a313c5ed26418a705bcaf6fdd0e73ad578cc0793da4015eb43be007aec6420f46f1b3678da5687a42fe87d522fabe7eb SHA512 1d530eceb5d2e1d69e50951983c6b3d1e5b7a07552b7e7ffe7d776a3034566b7176ed5eb124c25d838e1d7b381fffa64a98ce5cbeeaa5f77fd94f186e61eafcb
-DIST libnop-aa95422e.tar.gz 124202 BLAKE2B 5a74ecbf473dba09db1a11172a4aa432d81b14adb3826bef9aa8bae1bf1e2d0d5a7bf775fd4343fa9d7b235b17cafe949e47c903e92fd5eae9cc0717a552ea45 SHA512 62b21be874d2117294925c2497394d166da43d534776764c9c124699b5799d99790a2c6420804f8e143e1a18a536106852082f3a9d0052a726abc624fc19f937
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-DIST lss-e1e7b0ad8ee99a875b272c8e33e308472e897660.tar.gz 38399 BLAKE2B 6646858cde85b62664d157c9af9697f41c432fc97e4492b8159718c15c00de2b6441341648c5925d6d1a987cc6dee942382abaeebbae3b850a683dd42b5d648e SHA512 79b0deb923d69b34cbb239bfda9c36635b27f67eca0e2112967fa72a4d8235e0232dae3782eebf8a61e109503eac50e962bcbdd10b32e8ad8ddaf87ea953f66b
-DIST mkl-dnn-5ef631a0.tar.gz 5799312 BLAKE2B ea2aafcf45adadb0546781b00b44a0e9712c28e4937ef4daeef8b910e76bbb152e5434e45bec2aae0f6cb86fd7b5098e61842d7e99258db6fa846a79996d2e23 SHA512 66df9ea574010616df46d85ef25d23bd9ed31f9719cdbec4c727de58728fe095cd412d7663c2d456dba2f26848e45c1d67e34bffe4e25beeef9c1d40f187e8d6
-DIST nccl-c5790b36722d5b41ee2a9b2bad69e364180ffd22.tar.gz 240451 BLAKE2B 8f66d009f2f236f2341c782ca668a3f736581a8329ab3aee3cbcf2874f6fb771bd40e18050c47f08e91917b69dfa693c39007ee9eb038e638fa151b6aa4a23df SHA512 b3e95c56215bbb74ab703f0b08fa828e0afea322763148eb499438eefd2f4935fc39f07a483f77dbb7517077e9cfb732733f2349893f759165dcd767caf63a7d
-DIST onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz 9332964 BLAKE2B 20858ed93a7e2064624f13bb345ad7ad699ddc8c5e9ce9af27ae49d14bd7db9a0d9ff463919dd0c840595916ac7a720344608c586e87b522d5e2b78fde42eb6a SHA512 bcc1edbc4ce29b1c3c9f1ac4854f13d547d9efa6b712ddb5afb3d84637687aba1dbb2224ac4278a2b2e677ee485397c432554e7f02d51333c57a1ed7e0909d32
-DIST onnx-a82c6a70.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
-DIST onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
-DIST psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
-DIST pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz 49011 BLAKE2B 7bfbca81321243e64aa53c668dfe380ce4f7b88477a1c794a4dea9062c9b0969ca745dbfe0abbb95fffbf44080763506609c387ed085d89f6c612be6804b5cc2 SHA512 5f5a1275bbcef13cea88e381010bf2654c9646d30c5fb061f1d6e9e9a0ae6398e137c5e4f7da69f7d8d8b58fb5a7e79f7a4c0c1c3bbaad8f3d0c896d21bc7691
-DIST pytorch-1.10.1.tar.gz 18475578 BLAKE2B db951d029dfa227376c0f551f04c618730042e868d1b33feadee804fd56cbb2b2a581ee9034ea7f3101a77400db26dd2109050b064ccec564b72c355065704e8 SHA512 55e443ed1c5c709a33824003caa08c1d24712965cb9bdbe22b94b80fb9d94ecbd76d6ff30449fcc0c060ac08a7b54eefdec1c16484328e215c957aa42012c22b
-DIST sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz 1642070 BLAKE2B 366fa96e35f429199e8462c63bc9cfbd1888aa65170d3203a5b0391fb855c29241eb225f847e416650e6ed5544f17a745c5a43a622a2847416ad7bd207572840 SHA512 13ea28745e796f8b77a40c99f679e0955e213128fb05d17b61cdcef102b7a758cbda04def3544767a81ddf170b7800f168d25fb1b55093614c7126456765cbea
-DIST tensorpipe-d2aa3485e8229c98891dfd604b514a39d45a5c99.tar.gz 259599 BLAKE2B 89a948430a4a662a475417b60c8a962e5f89eadabe72f303275d113bcd768ad4d86308cceb902c9c65b1c6f23eeef6fe0e5e5329d270d37ae87632ca34406de8 SHA512 fbefc18792458ac2234045df8e3cce8dbb17a5e719258f020c2c1d388092358bd2562e53a0377ca18f40bcfbeae4367c277a74c31c5e45296b891453a962e460
diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch
deleted file mode 100644
index de9fe9a0d..000000000
--- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From e5003b88ad3a504eb04c0ba66c2f439149de2ee3 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Tue, 5 Nov 2019 00:58:17 +0300
-Subject: [PATCH 2/7] Don't build `libtorch` again for PyTorch
-
-If starting with building of `libtorch` using CMake,
-don't build it again for the sake of running `setup.py`
-to build Python version (PyTorch).
----
- setup.py | 7 -------
- 1 file changed, 7 deletions(-)
-
-Index: pytorch-1.4.0_p0/setup.py
-===================================================================
---- pytorch-1.4.0_p0.orig/setup.py
-+++ pytorch-1.4.0_p0/setup.py
-@@ -303,13 +303,6 @@ def build_deps():
- check_pydep('yaml', 'pyyaml')
- check_pydep('typing', 'typing')
-
-- build_caffe2(version=version,
-- cmake_python_library=cmake_python_library,
-- build_python=True,
-- rerun_cmake=RERUN_CMAKE,
-- cmake_only=CMAKE_ONLY,
-- cmake=cmake)
--
- version_path = os.path.join(cwd, 'torch', 'version.py')
- with open(version_path, 'w') as f:
- f.write("__version__ = '{}'\n".format(version))
diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
deleted file mode 100644
index 16d2c1f2e..000000000
--- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 2db381644c..2241a33015 100644
---- a/setup.py
-+++ b/setup.py
-@@ -307,13 +307,6 @@ def build_deps():
- check_pydep('yaml', 'pyyaml')
- check_pydep('typing', 'typing')
-
-- build_caffe2(version=version,
-- cmake_python_library=cmake_python_library,
-- build_python=True,
-- rerun_cmake=RERUN_CMAKE,
-- cmake_only=CMAKE_ONLY,
-- cmake=cmake)
--
- if CMAKE_ONLY:
- report('Finished running cmake. Run "ccmake build" or '
- '"cmake-gui build" to adjust build options and '
diff --git a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch b/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch
deleted file mode 100644
index f71ba17bc..000000000
--- a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-From dbb0bac77986016217cdfe779499a2ccd0e10570 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Wed, 6 Nov 2019 00:16:24 +0300
-Subject: [PATCH 3/4] Change path to `caffe2` build dir made by `libtorch`
-
-Setup and use properly `caffe2` build dir made while
-`libtorch` building with CMake, so that it was used
-by the Python installation.
----
- setup.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index f4bfdc99cd..60502b6add 100644
---- a/setup.py
-+++ b/setup.py
-@@ -236,7 +236,7 @@ else:
- cwd = os.path.dirname(os.path.abspath(__file__))
- lib_path = os.path.join(cwd, "torch", "lib")
- third_party_path = os.path.join(cwd, "third_party")
--caffe2_build_dir = os.path.join(cwd, "build")
-+caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
- # lib/pythonx.x/site-packages
- rel_site_packages = distutils.sysconfig.get_python_lib(prefix='')
- # full absolute path to the dir above
-@@ -279,7 +279,7 @@ elif sha != 'Unknown':
- version += '+' + sha[:7]
- report("Building wheel {}-{}".format(package_name, version))
-
--cmake = CMake()
-+cmake = CMake(caffe2_build_dir)
-
- # all the work we need to do _before_ setup runs
- def build_deps():
-@@ -445,7 +445,7 @@ class build_ext(setuptools.command.build_ext.build_ext):
- filename = self.get_ext_filename(fullname)
- report("\nCopying extension {}".format(ext.name))
-
-- src = os.path.join("torch", rel_site_packages, filename)
-+ src = os.path.join(caffe2_build_dir, filename)
- if not os.path.exists(src):
- report("{} does not exist".format(src))
- del self.extensions[i]
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch b/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch
deleted file mode 100644
index c8f57d9e6..000000000
--- a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch
+++ /dev/null
@@ -1,104 +0,0 @@
-From a0ace7295b6895954d2a0f8d6fe311a34a7c4e85 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Tue, 12 Nov 2019 02:01:36 +0300
-Subject: [PATCH 4/4] Don't fill rpath of Caffe2 library for system-wide
- install
-
-Don't fill in runtime path of Caffe2 library for the case of
-building for system-wide installation.
----
- CMakeLists.txt | 3 +++
- caffe2/CMakeLists.txt | 18 +++++++++++++++---
- cmake/Dependencies.cmake | 19 +++++++++++--------
- 3 files changed, 29 insertions(+), 11 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 20923c0544..45a882ae0e 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -193,6 +193,9 @@ option(USE_TBB "Use TBB" OFF)
- # Used when building Caffe2 through setup.py
- option(BUILDING_WITH_TORCH_LIBS "Tell cmake if Caffe2 is being built alongside torch libs" ON)
-
-+# Used when building Caffe2 for further system-wide installation
-+option(BUILDING_SYSTEM_WIDE "Tell cmake if Caffe2 is being built for system-wide installation" OFF)
-+
- # /Z7 override option
- # When generating debug symbols, CMake default to use the flag /Zi.
- # However, it is not compatible with sccache. So we rewrite it off.
-diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt
-index 1f7d037243..30d5615cdb 100644
---- a/caffe2/CMakeLists.txt
-+++ b/caffe2/CMakeLists.txt
-@@ -1235,7 +1235,11 @@ if (BUILD_PYTHON)
- if (MSVC AND BUILD_SHARED_LIBS)
- install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL)
- endif()
-- set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+else()
-+ set_target_properties(caffe2_pybind11_state PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
-
- if(USE_CUDA)
- add_library(caffe2_pybind11_state_gpu MODULE ${Caffe2_GPU_PYTHON_SRCS})
-@@ -1261,7 +1265,11 @@ if (BUILD_PYTHON)
- if (MSVC AND BUILD_SHARED_LIBS)
- install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state_gpu> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL)
- endif()
-- set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ else()
-+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
- endif()
-
- if(USE_ROCM)
-@@ -1284,7 +1292,11 @@ if (BUILD_PYTHON)
- caffe2_pybind11_state_hip PROPERTIES LIBRARY_OUTPUT_DIRECTORY
- ${CMAKE_BINARY_DIR}/caffe2/python)
- install(TARGETS caffe2_pybind11_state_hip DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python")
-- set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ else()
-+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
- endif()
-
- if (MSVC AND CMAKE_GENERATOR MATCHES "Visual Studio")
-diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
-index a8e9769536..6ef9d7b0e2 100644
---- a/cmake/Dependencies.cmake
-+++ b/cmake/Dependencies.cmake
-@@ -6,14 +6,17 @@ if (APPLE)
- else()
- set(_rpath_portable_origin $ORIGIN)
- endif(APPLE)
--# Use separate rpaths during build and install phases
--set(CMAKE_SKIP_BUILD_RPATH FALSE)
--# Don't use the install-rpath during the build phase
--set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
--set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}")
--# Automatically add all linked folders that are NOT in the build directory to
--# the rpath (per library?)
--set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-+
-+if (NOT BUILDING_SYSTEM_WIDE)
-+ # Use separate rpaths during build and install phases
-+ set(CMAKE_SKIP_BUILD_RPATH FALSE)
-+ # Don't use the install-rpath during the build phase
-+ set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-+ set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}")
-+ # Automatically add all linked folders that are NOT in the build directory to
-+ # the rpath (per library?)
-+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-+endif()
-
- # UBSAN triggers when compiling protobuf, so we need to disable it.
- set(UBSAN_FLAG "-fsanitize=undefined")
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch b/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch
deleted file mode 100644
index 324b8f682..000000000
--- a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From 52019a3f395e5fa97b26d424152d91f73b400f8e Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Wed, 13 Nov 2019 23:44:12 +0300
-Subject: [PATCH 5/5] Change library directory according to CMake build
-
-Change `lib_path` in favour of out-of-tree CMake build
-directory, so that all the C++ libraries be found.
----
- setup.py | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 60502b6add..cbced52192 100644
---- a/setup.py
-+++ b/setup.py
-@@ -234,9 +234,10 @@ else:
-
- # Constant known variables used throughout this file
- cwd = os.path.dirname(os.path.abspath(__file__))
--lib_path = os.path.join(cwd, "torch", "lib")
-+cmake_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
-+lib_path = os.path.join(cmake_build_dir, "lib")
- third_party_path = os.path.join(cwd, "third_party")
--caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
-+caffe2_build_dir = cmake_build_dir
- # lib/pythonx.x/site-packages
- rel_site_packages = distutils.sysconfig.get_python_lib(prefix='')
- # full absolute path to the dir above
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch b/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch
deleted file mode 100644
index 49835d201..000000000
--- a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From 0f3a0d9a948fdd8481a5f7751a255ecd9ed4d37a Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Mon, 20 Jan 2020 01:21:22 +0300
-Subject: [PATCH 3/3] Remove conversion ambiguity in ternary operators
-
-It fails to compile with recent versions of Clang
-(namely, version 10 used behind HCC compiler when
-being built with ROCm support) with the
-`conditional expression is ambiguous` error.
----
- caffe2/operators/relu_op.cu | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/caffe2/operators/relu_op.cu b/caffe2/operators/relu_op.cu
-index f6edf7105e..ab49540fc9 100644
---- a/caffe2/operators/relu_op.cu
-+++ b/caffe2/operators/relu_op.cu
-@@ -51,7 +51,7 @@ __global__ void ReluCUDAKernel<half2>(const int N, const half2* X, half2* Y) {
- #else
- const float2 xx = __half22float2(X[i]);
- Y[i] =
-- __floats2half2_rn(xx.x > 0.0f ? xx.x : 0.0f, xx.y > 0.0f ? xx.y : 0.0f);
-+ __floats2half2_rn(xx.x > 0.0f ? float(xx.x) : 0.0f, xx.y > 0.0f ? float(xx.y) : 0.0f);
- #endif
- }
- }
-@@ -101,7 +101,7 @@ __global__ void ReluGradientCUDAKernel<half2>(
- const float2 dy = __half22float2(dY[i]);
- const float2 yy = __half22float2(Y[i]);
- dX[i] =
-- __floats2half2_rn(yy.x > 0.0f ? dy.x : 0.0f, yy.y > 0.0f ? dy.y : 0.0f);
-+ __floats2half2_rn(yy.x > 0.0f ? float(dy.x) : 0.0f, yy.y > 0.0f ? float(dy.y) : 0.0f);
- #endif
- }
- }
---
-2.24.1
-
diff --git a/sci-libs/pytorch/files/get_third_parties b/sci-libs/pytorch/files/get_third_parties
deleted file mode 100644
index 8c38a9b73..000000000
--- a/sci-libs/pytorch/files/get_third_parties
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-path_url() {
- local dir=$(dirname $1)/
- git config --file $1 --get-regexp '(path|url)' | sed -r -e "N;s,[^ ]* ([^ ]*)\n[^ ]* ([^ ]*),${dir#./}\1 \2,"
-}
-
-join \
- <(for gm in $(find . -name '.gitmodules' | sort -r); do path_url $gm; done | sort -u) \
- <(git submodule status --recursive | awk '{print $2 " " $1}' | sort -u) | \
-while read path url hash; do
- [[ ${path} =~ (eigen|six|ios|neon2sse|protobuf|pybind11|python-enum|tbb|zstd|fbjni) ]] && continue
- u=${url%.git}
- hfull=${hash#-}
- h=${hfull:0:8}
- p=$(basename $u)
- echo "${u}/archive/${h}.tar.gz -> ${p}-${h}.tar.gz" >> SRC_URI
- [[ $p = fbgemm ]] && p=${p^^}
- echo "rmdir ${path} && ln -sv \"\${WORKDIR}\"/${p}-${hfull} ${path}" >> src_prepare
-done
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch b/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch
deleted file mode 100644
index 9c267dc6e..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-diff --git a/caffe2/contrib/opencl/OpenCL/cl.hpp b/caffe2/contrib/opencl/OpenCL/cl.hpp
-index 87cc4a1..7c27e33 100644
---- a/caffe2/contrib/opencl/OpenCL/cl.hpp
-+++ b/caffe2/contrib/opencl/OpenCL/cl.hpp
-@@ -76,7 +76,7 @@
- * #if defined(__APPLE__) || defined(__MACOSX)
- * #include <OpenCL/cl.hpp>
- * #else
-- * #include <CL/cl.hpp>
-+ * #include <CL/cl2.hpp>
- * #endif
- * #include <cstdio>
- * #include <cstdlib>
-diff --git a/caffe2/contrib/opencl/context.h b/caffe2/contrib/opencl/context.h
-index b1e61c2..968d3c7 100644
---- a/caffe2/contrib/opencl/context.h
-+++ b/caffe2/contrib/opencl/context.h
-@@ -11,7 +11,7 @@
- #if defined(__APPLE__) || defined(__MACOSX)
- #include <OpenCL/cl.hpp>
- #else
--#include <CL/cl.hpp>
-+#include <CL/cl2.hpp>
- #endif
-
- #define OPENCL_CHECK(expr) (void)expr
-diff --git a/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp b/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-index f3badf7..928c9f0 100644
---- a/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-+++ b/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-@@ -76,7 +76,7 @@
- * #if defined(__APPLE__) || defined(__MACOSX)
- * #include <OpenCL/cl.hpp>
- * #else
-- * #include <CL/cl.hpp>
-+ * #include <CL/cl2.hpp>
- * #endif
- * #include <cstdio>
- * #include <cstdlib>
-diff --git a/third_party/tensorflow_cuda_bazel_build/cuda/BUILD b/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-index f7271af..334f4ec 100755
---- a/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-+++ b/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-@@ -188,7 +188,7 @@ CUDA_INCLUDES_FILES = [
- "include/CL/cl_gl_ext.h",
- "include/CL/cl_gl.h",
- "include/CL/cl.h",
-- "include/CL/cl.hpp",
-+ "include/CL/cl2.hpp",
- "include/CL/cl_platform.h",
- "include/CL/opencl.h",
- "include/common_functions.h",
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch b/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch
deleted file mode 100644
index 334bcda6f..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch
+++ /dev/null
@@ -1,93 +0,0 @@
-This fix distutils-r1_src_install failure with setuptools-59
-
-From 9af2edb158b3603c44eff6e12896f1d215e8b898 Mon Sep 17 00:00:00 2001
-From: Nikita Shulga <nshulga@fb.com>
-Date: Tue, 14 Dec 2021 07:15:34 -0800
-Subject: [PATCH] Properly import LooseVersion
-
-This fixes regression introduced by https://github.com/pytorch/pytorch/pull/57040
-
-Somehow importing `distutils` from `setuptool` caused import of
-`distutils.versions`, which is not a documented dependency and got
-change with the release of
-[setuptools-59.6.0](https://github.com/pypa/setuptools/tree/v59.6.0)
-We should not rely on that, as
-`import distutils` never re-imports `distutils.version`, which one can
-see by observing
-https://github.com/python/cpython/blob/3.9/Lib/distutils/__init__.py
-or by running:
-```
-% python3 -c "import distutils;print(distutils.__version__, dir(distutils))"
-3.7.5 ['__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'sys']
-% python3 -c "from setuptools import distutils;print(distutils.__version__, dir(distutils))"
-3.7.5 ['__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'archive_util', 'ccompiler', 'cmd', 'config', 'core', 'debug', 'dep_util', 'dir_util', 'dist', 'errors', 'extension', 'fancy_getopt', 'file_util', 'filelist', 'log', 'spawn', 'sys', 'sysconfig', 'util', 'version']
-```
----
- test/run_test.py | 4 ++--
- tools/setup_helpers/cmake.py | 8 ++++----
- torch/testing/_internal/common_methods_invocations.py | 8 ++++----
- 3 files changed, 10 insertions(+), 10 deletions(-)
-
-diff --git a/tools/setup_helpers/cmake.py b/tools/setup_helpers/cmake.py
-index 01e87b4bca879..686b5c4a34f4c 100644
---- a/tools/setup_helpers/cmake.py
-+++ b/tools/setup_helpers/cmake.py
-@@ -8,7 +8,7 @@
- from subprocess import check_call, check_output, CalledProcessError
- import sys
- import sysconfig
--from setuptools import distutils # type: ignore[import]
-+from distutils.version import LooseVersion
- from typing import IO, Any, Dict, List, Optional, Union, cast
-
- from . import which
-@@ -120,10 +120,10 @@ def _get_cmake_command() -> str:
- return cmake_command
- cmake3 = which('cmake3')
- cmake = which('cmake')
-- if cmake3 is not None and CMake._get_version(cmake3) >= distutils.version.LooseVersion("3.10.0"):
-+ if cmake3 is not None and CMake._get_version(cmake3) >= LooseVersion("3.10.0"):
- cmake_command = 'cmake3'
- return cmake_command
-- elif cmake is not None and CMake._get_version(cmake) >= distutils.version.LooseVersion("3.10.0"):
-+ elif cmake is not None and CMake._get_version(cmake) >= LooseVersion("3.10.0"):
- return cmake_command
- else:
- raise RuntimeError('no cmake or cmake3 with version >= 3.10.0 found')
-@@ -134,7 +134,7 @@ def _get_version(cmd: str) -> Any:
-
- for line in check_output([cmd, '--version']).decode('utf-8').split('\n'):
- if 'version' in line:
-- return distutils.version.LooseVersion(line.strip().split(' ')[2])
-+ return LooseVersion(line.strip().split(' ')[2])
- raise RuntimeError('no version found')
-
- def run(self, args: List[str], env: Dict[str, str]) -> None:
-diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py
-index b66e6470b590c..6ec77c2b0ce2e 100644
---- a/torch/testing/_internal/common_methods_invocations.py
-+++ b/torch/testing/_internal/common_methods_invocations.py
-@@ -40,7 +40,7 @@
- freeze_rng_state)
- import torch.testing._internal.opinfo_helper as opinfo_helper
-
--from setuptools import distutils
-+from distutils.version import LooseVersion
-
- has_scipy_fft = False
- if TEST_SCIPY:
-@@ -14008,11 +14008,11 @@ def ref_pairwise_distance(input1, input2):
- skips=(
- # Reference: https://github.com/pytorch/pytorch/pull/49155#issuecomment-742664611
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_extremal',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_hard',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_normal',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- )),
- UnaryUfuncInfo('lgamma',
- ref=reference_lgamma if TEST_SCIPY else _NOTHING,
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch b/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch
deleted file mode 100644
index adc258556..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- a/torch/csrc/jit/frontend/ir_emitter.cpp 2021-10-15 05:35:23.000000000 +0400
-+++ b/torch/csrc/jit/frontend/ir_emitter.cpp 2021-10-15 05:35:23.000000000 +0400
-@@ -1678,7 +1678,7 @@
- << "Union type annotation `" << type_hint->repr_str()
- << "` can hold " << vector_repr.str() << ", but none of "
- << "those list types can hold the types of the given dict"
-- << " elements, which were unified to " << candidate->repr_str();
-+ << " elements, which were unified";
- } else {
- refined_type_hint = candidate;
- }
-
diff --git a/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch
deleted file mode 100644
index 0ac12a1e7..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From 7b04cd503fa1a6265893e0320ee246bcc0bd98cf Mon Sep 17 00:00:00 2001
-From: Miezhiko <Miezhiko@gmail.com>
-Date: Mon, 27 Dec 2021 14:48:12 +0400
-Subject: [PATCH] neutral flags
-
----
- makefiles/common.mk | 10 +---------
- 1 file changed, 1 insertion(+), 9 deletions(-)
-
-diff --git a/makefiles/common.mk b/makefiles/common.mk
-index 64f8d2dc6..7a979c90f 100644
---- a/makefiles/common.mk
-+++ b/makefiles/common.mk
-@@ -55,7 +55,7 @@ CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) -DCUDA_MINOR=$(CUDA_MINOR) -fPIC -fvisi
- # Maxrregcount needs to be set accordingly to NCCL_MAX_NTHREADS (otherwise it will cause kernel launch errors)
- # 512 : 120, 640 : 96, 768 : 80, 1024 : 60
- # We would not have to set this if we used __launch_bounds__, but this only works on kernels, not on functions.
--NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -std=c++11 --expt-extended-lambda -Xptxas -maxrregcount=96 -Xfatbin -compress-all
-+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -std=c++11 --expt-extended-lambda -Xptxas -maxrregcount=96 -Xfatbin -compress-all
- # Use addprefix so that we can specify more than one path
- NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt
-
-@@ -69,14 +69,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler %}
- # $(warning GCOV_FLAGS=${GCOV_FLAGS})
- ########## GCOV ##########
-
--ifeq ($(DEBUG), 0)
--NVCUFLAGS += -O3
--CXXFLAGS += -O3 -g
--else
--NVCUFLAGS += -O0 -G -g
--CXXFLAGS += -O0 -g -ggdb3
--endif
--
- ifneq ($(VERBOSE), 0)
- NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter
- CXXFLAGS += -Wall -Wextra
diff --git a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch b/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch
deleted file mode 100644
index 85e796a60..000000000
--- a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Index: pytorch-1.4.0_p0/setup.py
-===================================================================
---- pytorch-1.4.0_p0.orig/setup.py
-+++ pytorch-1.4.0_p0/setup.py
-@@ -288,9 +288,7 @@ def build_deps():
- sys.exit(1)
-
- check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt"))
-- check_file(os.path.join(third_party_path, "pybind11", "CMakeLists.txt"))
- check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt'))
-- check_file(os.path.join(third_party_path, 'tbb', 'Makefile'))
- check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt'))
-@@ -341,9 +339,6 @@ def build_deps():
- if not same:
- shutil.copyfile(orig_file, sym_file)
-
-- dir_util.copy_tree('third_party/pybind11/include/pybind11/',
-- 'torch/include/pybind11')
--
- ################################################################################
- # Building dependent libraries
- ################################################################################
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch
deleted file mode 100644
index 165e79dd4..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Index: nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk
-===================================================================
---- nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf.orig/makefiles/common.mk
-+++ nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk
-@@ -46,7 +46,7 @@ endif
- CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) -DCUDA_MINOR=$(CUDA_MINOR) -fPIC -fvisibility=hidden
- CXXFLAGS += -Wall -Wno-unused-function -Wno-sign-compare -std=c++11 -Wvla
- CXXFLAGS += -I $(CUDA_INC)
--NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
-+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
- # Use addprefix so that we can specify more than one path
- NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt
-
-@@ -60,14 +60,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler
- # $(warning GCOV_FLAGS=${GCOV_FLAGS})
- ########## GCOV ##########
-
--ifeq ($(DEBUG), 0)
--NVCUFLAGS += -O3
--CXXFLAGS += -O3 -g
--else
--NVCUFLAGS += -O0 -G -g
--CXXFLAGS += -O0 -g -ggdb3
--endif
--
- ifneq ($(VERBOSE), 0)
- NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter
- CXXFLAGS += -Wall -Wextra
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch b/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch
deleted file mode 100644
index 3682469d7..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Disable expected test failures.
-
-TCPStoreTest is too slow to run.
-
-Reference: https://github.com/pytorch/pytorch/issues/13746
-Reference: https://github.com/pytorch/pytorch/issues/21873
-
-Index: pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0_p0.orig/torch/lib/c10d/test/CMakeLists.txt
-+++ pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt
-@@ -14,7 +14,6 @@ function(c10d_add_test test_src)
- endfunction()
-
- c10d_add_test(FileStoreTest.cpp c10d)
--c10d_add_test(TCPStoreTest.cpp c10d)
-
- if(USE_CUDA)
- if(USE_C10D_GLOO)
-Index: pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0_p0.orig/caffe2/share/contrib/depthwise/CMakeLists.txt
-+++ pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-@@ -6,4 +6,3 @@ set(Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU
- )
-
- set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_CPU_SRC} PARENT_SCOPE)
--set(Caffe2_CPU_TEST_SRCS ${Caffe2_CPU_TEST_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU_SRC} PARENT_SCOPE)
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch b/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch
deleted file mode 100644
index 222a0f73e..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Give the location of sleef.h.
-
-Reference: https://github.com/pytorch/pytorch/issues/26555
-Index: pytorch-1.4.0/caffe2/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0.orig/caffe2/CMakeLists.txt
-+++ pytorch-1.4.0/caffe2/CMakeLists.txt
-@@ -1062,6 +1062,7 @@ if (BUILD_TEST)
- add_executable(${test_name} "${test_src}")
- target_link_libraries(${test_name} ${Caffe2_MAIN_LIBS} gtest_main)
- target_include_directories(${test_name} PRIVATE $<INSTALL_INTERFACE:include>)
-+ target_include_directories(${test_name} PRIVATE $<BUILD_INTERFACE:${C