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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.md8
-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-1.0.3_pre20200524.ebuild6
-rw-r--r--dev-cpp/blitz/blitz-9999.ebuild48
-rw-r--r--dev-java/flexdock/Manifest1
-rw-r--r--dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch12
-rw-r--r--dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch12
-rw-r--r--dev-java/flexdock/flexdock-1.2.4.ebuild46
-rw-r--r--dev-java/freehep-graphicsio-emf/Manifest1
-rw-r--r--dev-java/freehep-graphicsio-emf/files/github-30.patch34
-rw-r--r--dev-java/freehep-graphicsio-emf/freehep-graphicsio-emf-2.4-r1.ebuild61
-rw-r--r--dev-java/freehep-graphicsio-emf/metadata.xml11
-rw-r--r--dev-java/gluegen/Manifest2
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-copy-jars.patch17
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-strip.patch22
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-test-archive.patch16
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-copy-jars.patch17
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-strip.patch22
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-test-archive.patch16
-rw-r--r--dev-java/gluegen/gluegen-2.1.4.ebuild72
-rw-r--r--dev-java/gluegen/gluegen-2.2.4.ebuild72
-rw-r--r--dev-java/gluegen/metadata.xml22
-rw-r--r--dev-java/htsjdk/Manifest2
-rw-r--r--dev-java/htsjdk/htsjdk-2.19.0.ebuild53
-rw-r--r--dev-java/htsjdk/htsjdk-2.3.0.ebuild47
-rw-r--r--dev-java/htsjdk/htsjdk-9999.ebuild53
-rw-r--r--dev-java/htsjdk/metadata.xml15
-rw-r--r--dev-java/jcommon/Manifest1
-rw-r--r--dev-java/jcommon/jcommon-1.0.23.ebuild57
-rw-r--r--dev-java/jcommon/metadata.xml11
-rw-r--r--dev-java/jfreechart/Manifest1
-rw-r--r--dev-java/jfreechart/files/jfreechart-1.0.19-build.xml.patch25
-rw-r--r--dev-java/jfreechart/files/jfreechart-1.0.19-fix-TimeSeriesCollectionTest.patch24
-rw-r--r--dev-java/jfreechart/jfreechart-1.0.19-r2.ebuild71
-rw-r--r--dev-java/jfreechart/metadata.xml11
-rw-r--r--dev-java/jfreesvg/Manifest2
-rw-r--r--dev-java/jfreesvg/jfreesvg-2.1-r1.ebuild43
-rw-r--r--dev-java/jfreesvg/jfreesvg-3.0.ebuild40
-rw-r--r--dev-java/jfreesvg/metadata.xml16
-rw-r--r--dev-java/jgraphx/Manifest1
-rw-r--r--dev-java/jgraphx/jgraphx-4.2.2.ebuild40
-rw-r--r--dev-java/jgraphx/metadata.xml19
-rw-r--r--dev-java/jlatexmath-fop/Manifest1
-rw-r--r--dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch13
-rw-r--r--dev-java/jlatexmath-fop/files/version.xml5
-rw-r--r--dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild48
-rw-r--r--dev-java/jlatexmath-fop/metadata.xml13
-rw-r--r--dev-java/jlatexmath/Manifest1
-rw-r--r--dev-java/jlatexmath/jlatexmath-1.0.3.ebuild30
-rw-r--r--dev-java/jlatexmath/metadata.xml13
-rw-r--r--dev-java/jogl/Manifest1
-rw-r--r--dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch41
-rw-r--r--dev-java/jogl/files/1.1.0/uncouple-gluegen.patch32
-rw-r--r--dev-java/jogl/jogl-2.2.4.ebuild70
-rw-r--r--dev-java/jogl/metadata.xml18
-rw-r--r--dev-java/jrosetta/Manifest1
-rw-r--r--dev-java/jrosetta/files/api-build.xml262
-rw-r--r--dev-java/jrosetta/files/build.xml74
-rw-r--r--dev-java/jrosetta/files/engine-build.xml274
-rw-r--r--dev-java/jrosetta/jrosetta-1.0.4.ebuild39
-rw-r--r--dev-java/jrosetta/metadata.xml8
-rw-r--r--dev-java/lucene/Manifest3
-rw-r--r--dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch24
-rw-r--r--dev-java/lucene/files/lucene_contrib_icu4j_v50.patch20
-rw-r--r--dev-java/lucene/lucene-3.6.2-r2.ebuild162
-rw-r--r--dev-java/lucene/lucene-5.2.1.ebuild211
-rw-r--r--dev-java/lucene/lucene-8.4.0.ebuild223
-rw-r--r--dev-java/lucene/metadata.xml12
-rw-r--r--dev-java/skinlf/Manifest1
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-build.xml276
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-common.xml171
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch77
-rw-r--r--dev-java/skinlf/metadata.xml8
-rw-r--r--dev-java/skinlf/skinlf-6.7.10.ebuild56
-rw-r--r--dev-lang/terra/Manifest1
-rw-r--r--dev-lang/terra/metadata.xml14
-rw-r--r--dev-lang/terra/terra-1.0.0_beta2.ebuild46
-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-libs/optix/Manifest5
-rw-r--r--dev-libs/optix/optix-6.0.0.ebuild46
-rw-r--r--dev-libs/optix/optix-7.0.0.ebuild37
-rw-r--r--dev-libs/optix/optix-7.1.0.ebuild37
-rw-r--r--dev-libs/optix/optix-7.4.0.ebuild (renamed from dev-libs/optix/optix-7.2.0.ebuild)4
-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 dev-java/flexdock/metadata.xml)6
-rw-r--r--dev-python/asdf/Manifest2
-rw-r--r--dev-python/asdf/asdf-2.8.3.ebuild (renamed from dev-python/asdf/asdf-2.7.1.ebuild)10
-rw-r--r--dev-python/astropy-healpix/Manifest2
-rw-r--r--dev-python/astropy-healpix/astropy-healpix-0.6.ebuild (renamed from dev-python/astropy-healpix/astropy-healpix-0.5.ebuild)7
-rw-r--r--dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild6
-rw-r--r--dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild6
-rw-r--r--dev-python/astropy/Manifest2
-rw-r--r--dev-python/astropy/astropy-5.0.ebuild (renamed from dev-python/astropy/astropy-4.2.ebuild)13
-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/extension-helpers/extension-helpers-0.1.ebuild6
-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/fslpy/fslpy-3.8.1.ebuild10
-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/pyerfa/Manifest2
-rw-r--r--dev-python/pyerfa/pyerfa-2.0.0.1.ebuild (renamed from dev-python/pyerfa/pyerfa-1.7.1.1.ebuild)10
-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/pysolar/pysolar-0.8.ebuild6
-rw-r--r--dev-python/pytest-doctestplus/Manifest2
-rw-r--r--dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild (renamed from dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild)7
-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/sphinx-astropy/Manifest2
-rw-r--r--dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild (renamed from dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild)9
-rw-r--r--dev-python/sphinx-automodapi/Manifest2
-rw-r--r--dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild (renamed from dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild)8
-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/visvis/visvis-1.13.0.ebuild2
-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-util/bcm/Manifest1
-rw-r--r--dev-util/bcm/bcm-0.0.1_p20191110.ebuild19
-rw-r--r--dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch13
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-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-setup.patch14
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch14
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch13
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-setup.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch13
-rw-r--r--sci-libs/pytorch/files/pytorch-1.9.0-Change-library-directory-according-to-CMake-build.patch32
-rw-r--r--sci-libs/pytorch/files/pytorch-1.9.1-fix-wrong-hipify.patch13
-rw-r--r--sci-libs/pytorch/metadata.xml34
-rw-r--r--sci-libs/pytorch/pytorch-1.10.1-r1.ebuild339
-rw-r--r--sci-libs/rdkit/Manifest5
-rw-r--r--sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch59
-rw-r--r--sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch22
-rw-r--r--sci-libs/rdkit/rdkit-2020.03.6.ebuild57
-rw-r--r--sci-libs/rdkit/rdkit-2021.09.4.ebuild58
-rw-r--r--sci-libs/spyking-circus/Manifest2
-rw-r--r--sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild (renamed from sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild)11
-rw-r--r--sci-libs/superlu_dist/Manifest1
-rw-r--r--sci-libs/superlu_dist/metadata.xml26
-rw-r--r--sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild42
-rw-r--r--sci-libs/torchvision/torchvision-0.11.2.ebuild5
-rw-r--r--sci-mathematics/netgen/netgen-6.2.2105.ebuild2
-rw-r--r--sci-mathematics/open-axiom/Manifest1
-rw-r--r--sci-mathematics/open-axiom/metadata.xml17
-rw-r--r--sci-mathematics/open-axiom/open-axiom-1.4.2_p20180201.ebuild35
-rw-r--r--sci-mathematics/scilab/Manifest4
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch21
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-batik-1.9.patch104
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-bug15449.patch11
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch12
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch11
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch38
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-fortran-gcc8.patch57
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch12
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch11
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-hdf5-1.8.10.patch278
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch11
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-libxml-icu64.patch16
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch11
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-ocaml-4.0.4.patch12
-rw-r--r--sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch91
-rw-r--r--sci-mathematics/scilab/files/scilab-6.1.0-accessviolation.patch22
-rw-r--r--sci-mathematics/scilab/files/scilab-6.1.0-freehep.patch13
-rw-r--r--sci-mathematics/scilab/files/scilab-6.1.0-libxml.patch66
-rw-r--r--sci-mathematics/scilab/files/scilab-6.1.0-nogui.patch13
-rw-r--r--sci-mathematics/scilab/files/scilab.bash_completion54
-rw-r--r--sci-mathematics/scilab/files/scilab.xml13
-rw-r--r--sci-mathematics/scilab/metadata.xml24
-rw-r--r--sci-mathematics/scilab/scilab-5.5.2.ebuild311
-rw-r--r--sci-mathematics/scilab/scilab-6.0.2.ebuild306
-rw-r--r--sci-mathematics/scilab/scilab-6.1.0.ebuild305
-rw-r--r--sci-misc/europa-bin/Manifest1
-rw-r--r--sci-misc/europa-bin/europa-bin-1.1.0.ebuild57
-rw-r--r--sci-misc/europa-bin/metadata.xml12
-rw-r--r--sci-misc/opennlp-maxent/Manifest1
-rw-r--r--sci-misc/opennlp-maxent/metadata.xml10
-rw-r--r--sci-misc/opennlp-maxent/opennlp-maxent-3.0.0.ebuild53
-rw-r--r--sci-physics/openmx/Manifest1
-rw-r--r--sci-physics/openmx/openmx-3.9_p20211017.ebuild (renamed from sci-physics/openmx/openmx-3.9.ebuild)44
-rw-r--r--sci-physics/opticks-okconf/files/opticks-okconf-0.0.1_p20191110-no_lib_install.patch12
-rw-r--r--sci-physics/opticks-okconf/metadata.xml7
-rw-r--r--sci-physics/opticks-okconf/opticks-okconf-0.0.1_p20191110.ebuild46
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_cuda-helper.patch13
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_extG4-CLHEP.patch20
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_nvcc-flags.patch12
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_okconf.patch45
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_python-helper.patch48
-rw-r--r--sci-physics/opticks/files/opticks-0.0.1_split-cmake.patch29
-rw-r--r--sci-physics/opticks/metadata.xml7
-rw-r--r--sci-physics/opticks/opticks-0.0.1_p20191110.ebuild108
-rw-r--r--sci-visualization/clip/clip-0.7-r1.ebuild (renamed from sci-visualization/clip/clip-0.7.ebuild)14
-rw-r--r--sci-visualization/fsleyes-props/Manifest3
-rw-r--r--sci-visualization/fsleyes-props/fsleyes-props-1.6.7.ebuild46
-rw-r--r--sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild (renamed from sci-visualization/fsleyes-props/fsleyes-props-1.7.0.ebuild)26
-rw-r--r--sci-visualization/fsleyes-widgets/Manifest3
-rw-r--r--sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild (renamed from sci-visualization/fsleyes-widgets/fsleyes-widgets-0.9.0.ebuild)24
-rw-r--r--sci-visualization/fsleyes-widgets/fsleyes-widgets-0.8.4.ebuild47
-rw-r--r--sci-visualization/fsleyes/Manifest3
-rw-r--r--sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch13
-rw-r--r--sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch62
-rw-r--r--sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch61
-rw-r--r--sci-visualization/fsleyes/fsleyes-0.32.3.ebuild80
-rw-r--r--sci-visualization/fsleyes/fsleyes-0.34.2.ebuild88
-rw-r--r--sci-visualization/fsleyes/fsleyes-1.3.3.ebuild65
-rw-r--r--sci-visualization/surf-ice/surf-ice-9999.ebuild4
-rwxr-xr-xscripts/setup-and-run-repoman.sh30
629 files changed, 3741 insertions, 14296 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 99fcfe316..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)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
[![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
@@ -125,12 +124,7 @@ We welcome new contributors and are happy to include new packages.
### Areas to contribute
-- [Current open issues](https://github.com/gentoo/sci/issues)
- [Current open bugs](https://bugs.gentoo.org/buglist.cgi?no_redirect=1&quicksearch=[science+overlay])
-- EAPI 6 (or 5) ebuilds which need updating
-```
-find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done
-```
### Resources
@@ -144,4 +138,4 @@ Additionally, please make sure to add the Science Project as an additional maint
## Support
You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
-Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+Alternatively you can report bugs on the [Gentoo Bugzilla](https://bugs.gentoo.org/).
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)
- ${RDEPEND}
- )
-"
-
-python_test() {
- rm tests/golden/load-http.tsv || die "Could not remove network-dependent test."
- git init || die "Git init failed."
- git add tests/golden/ || die "Git add failed."
- dev/test.sh || die "Tests failed."
- rm .git -rf || die "Could not clean up git test directory."
-}
-
-pkg_postinst() {
- optfeature "integration with yaml" dev-python/pyyaml
- optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
- optfeature "integration with png" dev-python/pypng
- optfeature "integration with http" dev-python/requests
- optfeature "integration with postgres" dev-python/psycopg
- optfeature "integration with xlsx" dev-python/openpyxl
- optfeature "integration with xls" dev-python/xlrd
- optfeature "integration with hdf5" dev-python/h5py
- optfeature "integration with ttf/otf" dev-python/fonttools
- optfeature "integration with xml/htm/html" dev-python/lxml
- optfeature "integration with dta (Stata)" dev-python/pandas
- optfeature "integration with shapefiles" sci-libs/pyshp
- optfeature "integration with namestand" dev-python/graphviz
- #optfeature "integration with mbtiles" mapbox-vector-tile
- #optfeature "integration with xpt (SAS)" xport
- #optfeature "integration with sas7bdat (SAS)" sas7bdat
- #optfeature "integration with sav (SPSS)" savReaderWriter
-}
diff --git a/app-office/visidata/visidata-2.1.1.ebuild b/app-office/visidata/visidata-2.8.ebuild
index a214036d8..ab4d506ab 100644
--- a/app-office/visidata/visidata-2.1.1.ebuild
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 optfeature
@@ -20,6 +20,7 @@ RDEPEND="dev-python/python-dateutil[${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[${PYTHON_USEDEP}]
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 389e5430d..432004f11 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -1,14 +1,12 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..11} )
inherit cmake python-any-r1
COMMIT="39f885951a9b8b11f931f917935a16066a945056"
-
DESCRIPTION="Multi-dimensional array library for C++"
HOMEPAGE="https://github.com/blitzpp/blitz"
SRC_URI="https://github.com/blitzpp/blitz/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
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-java/flexdock/Manifest b/dev-java/flexdock/Manifest
deleted file mode 100644
index 19976b9ca..000000000
--- a/dev-java/flexdock/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST flexdock-1.2.4.tar.gz 5977054 BLAKE2B f0057d4a09fa994297c437c8ecd3e0f96c922bec5f95b142f19279e154fd352628a342a8dce9dcaab4b5997665b10fc98c8daf59c766a7b83cd7adda50f2b00c SHA512 f20c92d33b0567ed1e779d4c7c843ac9d72e5ae0f0a145d69adf5066bd1dcc426cd8acfe7d0587bd36fc09cab63dd7217f27cd8eee1d5d9b522bec860df9b44f
diff --git a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch b/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml 2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml 2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
- <src path="${java.src.drag}"/>
- <src path="${java.src.perspective}"/>
- </javac>
-- <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
-- <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
- </target>
-
-
diff --git a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch b/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml 2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml 2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
- <src path="${java.src.drag}"/>
- <src path="${java.src.perspective}"/>
- </javac>
-- <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
-- <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
- </target>
-
-
diff --git a/dev-java/flexdock/flexdock-1.2.4.ebuild b/dev-java/flexdock/flexdock-1.2.4.ebuild
deleted file mode 100644
index 64898244e..000000000
--- a/dev-java/flexdock/flexdock-1.2.4.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
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java docking framework for use in cross-platform Swing applications"
-HOMEPAGE="https://forge.scilab.org/index.php/p/flexdock/"
-SRC_URI="https://forge.scilab.org/index.php/p/flexdock/downloads/get/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=">=virtual/jre-1.5:=
- dev-java/skinlf:0"
-BDEPEND="app-arch/unzip"
-DEPEND="${RDEPEND}"
-
-EANT_BUILD_TARGET="jar"
-EANT_DOC_TARGET="doc"
-
-PATCHES=(
- "${FILESDIR}/${P}-nodemo.patch"
-)
-
-src_prepare() {
- default
-
- #some cleanups
- find . -name '*.so' -exec rm -v {} \;|| die
- find . -name '*.dll' -exec rm -v {} \;|| die
-
- #remove built-in jars and use the system ones
- cd lib || die
- rm -rvf *.jar jmf|| die
- java-pkg_jar-from skinlf
-}
-
-src_install() {
- java-pkg_newjar "build/${P}.jar" "${PN}.jar"
- use doc && java-pkg_dojavadoc build/docs/api
- use source && java-pkg_dosrc src
-}
diff --git a/dev-java/freehep-graphicsio-emf/Manifest b/dev-java/freehep-graphicsio-emf/Manifest
deleted file mode 100644
index 9ab19829d..000000000
--- a/dev-java/freehep-graphicsio-emf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST freehep-vectorgraphics-2.4.tar.gz 4118379 BLAKE2B c8a5840ebab43398a6f87f97855a38f843b0e05267f5446b5f22a0c0124c98717c00801fe93ef3b541b2c53d07176ab1319a27ad26ed177b6dded11e3fa2e7bb SHA512 b5cf083cc6951e7c4b438d5e648f61ca20b23e02163a8cfc4669beaaec2fa9e33338b0ba6875bfe4a3864ac48f9774acfedc2a3b2f59a7488ef99a4817e39382
diff --git a/dev-java/freehep-graphicsio-emf/files/github-30.patch b/dev-java/freehep-graphicsio-emf/files/github-30.patch
deleted file mode 100644
index c652ec6b8..000000000
--- a/dev-java/freehep-graphicsio-emf/files/github-30.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-https://github.com/freehep/freehep-vectorgraphics/issues/30
-
-diff -Naur freehep-vectorgraphics-freehep-vectorgraphics-2.4.orig/freehep-graphicsio-emf/src/main/java/org/freehep/graphicsio/emf/EMFConverter.java freehep-vectorgraphics-freehep-vectorgraphics-2.4/freehep-graphicsio-emf/src/main/java/org/freehep/graphicsio/emf/EMFConverter.java
---- freehep-vectorgraphics-freehep-vectorgraphics-2.4.orig/freehep-graphicsio-emf/src/main/java/org/freehep/graphicsio/emf/EMFConverter.java 2014-09-02 09:59:14.000000000 +0100
-+++ freehep-vectorgraphics-freehep-vectorgraphics-2.4/freehep-graphicsio-emf/src/main/java/org/freehep/graphicsio/emf/EMFConverter.java 2016-05-25 22:50:41.859734476 +0100
-@@ -4,6 +4,7 @@
- import org.freehep.graphicsbase.util.export.ExportFileType;
-
- import java.util.List;
-+import java.util.Properties;
- import java.io.FileInputStream;
- import java.io.File;
-
-@@ -64,9 +65,10 @@
- destFileName += type.toLowerCase();
- }
-
-+ Properties p = new Properties();
-+
- // TODO there is no possibility to use Constants of base class!
- /* create SVG properties
-- Properties p = new Properties();
- p.put(SVGGraphics2D.EMBED_FONTS, Boolean.toString(false));
- p.put(SVGGraphics2D.CLIP, Boolean.toString(true));
- p.put(SVGGraphics2D.COMPRESS, Boolean.toString(false));
-@@ -82,7 +84,7 @@
- new File(destFileName),
- emfPanel,
- emfPanel,
-- null,
-+ p,
- "Freehep EMF converter");
- } catch (Exception e) {
- e.printStackTrace();
diff --git a/dev-java/freehep-graphicsio-emf/freehep-graphicsio-emf-2.4-r1.ebuild b/dev-java/freehep-graphicsio-emf/freehep-graphicsio-emf-2.4-r1.ebuild
deleted file mode 100644
index 16fb74322..000000000
--- a/dev-java/freehep-graphicsio-emf/freehep-graphicsio-emf-2.4-r1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PN="freehep-vectorgraphics"
-MY_P="${MY_PN}-${PV}"
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-pkg-simple
-
-DESCRIPTION="High Energy Physics Java library - FreeHEP Enhanced Metafile Format Driver"
-HOMEPAGE="http://java.freehep.org/"
-SRC_URI="https://github.com/freehep/${MY_PN}/archive/${MY_P}.tar.gz"
-
-LICENSE="Apache-2.0 LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="~dev-java/freehep-graphics2d-${PV}:${SLOT}
- ~dev-java/freehep-graphicsbase-${PV}:${SLOT}
- ~dev-java/freehep-graphicsio-${PV}:${SLOT}
- dev-java/freehep-io:0"
-
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.7
- test? (
- ~dev-java/freehep-graphicsio-tests-${PV}:${SLOT}
- dev-java/junit:4
- )"
-
-RDEPEND="${CDEPEND}
- >=virtual/jre-1.7"
-
-S="${WORKDIR}/${MY_PN}-${MY_P}/${PN}"
-JAVA_SRC_DIR="src/main/java"
-JAVA_GENTOO_CLASSPATH="freehep-graphics2d,freehep-graphicsbase,freehep-graphicsio,freehep-io"
-
-PATCHES=( "${FILESDIR}/github-30.patch" )
-
-src_compile() {
- java-pkg-simple_src_compile
- java-pkg_addres ${PN}.jar src/main/resources
-}
-
-src_install() {
- java-pkg-simple_src_install
- java-pkg_register-optional-dependency freehep-graphicsio-svg
- java-pkg_dolauncher emf2svg --main org.freehep.graphicsio.emf.EMF2SVG
-}
-
-src_test() {
- local DIR=src/test/java
- local CP="${DIR}:${PN}.jar:$(java-pkg_getjars junit-4,freehep-graphicsio-tests,${JAVA_GENTOO_CLASSPATH})"
-
- ejavac -cp "${CP}" -d ${DIR} $(find ${DIR} -name "*.java")
- ejunit4 -classpath "${CP}" org.freehep.graphicsio.emf.test.EMFTestSuite
-}
diff --git a/dev-java/freehep-graphicsio-emf/metadata.xml b/dev-java/freehep-graphicsio-emf/metadata.xml
deleted file mode 100644
index 497d14c1c..000000000
--- a/dev-java/freehep-graphicsio-emf/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="github">freehep/freehep-vectorgraphics</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/gluegen/Manifest b/dev-java/gluegen/Manifest
deleted file mode 100644
index 4e44921ef..000000000
--- a/dev-java/gluegen/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gluegen-2.1.4.tar.gz 42235490 BLAKE2B 31e5a55c9cc983d0e1c7f53988b7cc0779e01d1c4c0df8a33ca817acd51d0d28e453e6a84e1be65ecfb62883e8900c62a2219f78035dc7a68c26412e7c2b5135 SHA512 196478de92686b168d6f35e2e7141a31f682d22a7f96b5bc84d46905c42eb5bf25bacd74ccc51975fc7894e2e0ba2e236a4a68c101bbabaaa5193e4bdc50f607
-DIST gluegen-2.2.4.tar.gz 43113191 BLAKE2B 8908cff19b4eeaac01eb91ecf51005433c60acbf35a2922e09f7bfe3d11dee46296b466ea22cf570cae5a1013ea6dd9b375fbaa5b0723509d0bad0926014b9fb SHA512 53e973ca8478f4513f9662d1375406af95f2181dae3fb3e3247e4752960e60e741f7eae36981967dba10ac7bc3dc0e85c159c193323c177ce733a9eb0540b98b
diff --git a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
deleted file mode 100644
index 6f51d6811..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/make/build.xml b/make/build.xml
-index 55ef270..bce6d12 100644
---- a/make/build.xml
-+++ b/make/build.xml
-@@ -806,12 +806,6 @@
- </fileset>
- </jar>
-
-- <!-- Copy antlr.jar into build directory for convenience so
-- gluegen.jar can be run via "java -jar". antlr.jar is
-- referenced via a Class-Path entry in the Manifest of
-- gluegen.jar. -->
-- <copy file="${antlr.jar}" todir="${build}" />
--
- <!-- copy a jnlp with empty codebase into build folder for local testing
- overwrite property in gluegen.proerpties if desired -->
- <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.1.4-dont-strip.patch b/dev-java/gluegen/files/2.1.4-dont-strip.patch
deleted file mode 100644
index d64c742cd..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/make/gluegen-cpptasks-base.xml b/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/make/gluegen-cpptasks-base.xml
-+++ b/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
- - Helper strip.libraries for stripping off debug information
- -->
- <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
-- <echo message="Strip symbols from libs in ${libdir}" />
-- <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false"
-- failonerror="true">
-- <arg line="${c.strip.args}"/>
-- <fileset dir="${libdir}">
-- <include name="**/*.so"/> <!-- unix -->
-- <include name="**/*.dll"/> <!-- windows -->
-- <include name="**/*.dylib"/> <!-- macosx -->
-- <include name="**/*.jnilib"/> <!-- macosx -->
-- </fileset>
-- </apply>
- </target>
-
- <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch b/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
deleted file mode 100644
index f03a28399..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/make/build-test.xml b/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/make/build-test.xml
-+++ b/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
-
- <!-- updates / create the test results zip file -->
- <target name="test-zip-archive" depends="init">
-+ <!--
- <archive.7z destfile="${build}/${test.archive.name}.7z"
- basedir="${project.root}"
- includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+ -->
- </target>
-
-
diff --git a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
deleted file mode 100644
index 6f51d6811..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/make/build.xml b/make/build.xml
-index 55ef270..bce6d12 100644
---- a/make/build.xml
-+++ b/make/build.xml
-@@ -806,12 +806,6 @@
- </fileset>
- </jar>
-
-- <!-- Copy antlr.jar into build directory for convenience so
-- gluegen.jar can be run via "java -jar". antlr.jar is
-- referenced via a Class-Path entry in the Manifest of
-- gluegen.jar. -->
-- <copy file="${antlr.jar}" todir="${build}" />
--
- <!-- copy a jnlp with empty codebase into build folder for local testing
- overwrite property in gluegen.proerpties if desired -->
- <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.2.4-dont-strip.patch b/dev-java/gluegen/files/2.2.4-dont-strip.patch
deleted file mode 100644
index d64c742cd..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/make/gluegen-cpptasks-base.xml b/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/make/gluegen-cpptasks-base.xml
-+++ b/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
- - Helper strip.libraries for stripping off debug information
- -->
- <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
-- <echo message="Strip symbols from libs in ${libdir}" />
-- <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false"
-- failonerror="true">
-- <arg line="${c.strip.args}"/>
-- <fileset dir="${libdir}">
-- <include name="**/*.so"/> <!-- unix -->
-- <include name="**/*.dll"/> <!-- windows -->
-- <include name="**/*.dylib"/> <!-- macosx -->
-- <include name="**/*.jnilib"/> <!-- macosx -->
-- </fileset>
-- </apply>
- </target>
-
- <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch b/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
deleted file mode 100644
index f03a28399..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/make/build-test.xml b/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/make/build-test.xml
-+++ b/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
-
- <!-- updates / create the test results zip file -->
- <target name="test-zip-archive" depends="init">
-+ <!--
- <archive.7z destfile="${build}/${test.archive.name}.7z"
- basedir="${project.root}"
- includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+ -->
- </target>
-
-
diff --git a/dev-java/gluegen/gluegen-2.1.4.ebuild b/dev-java/gluegen/gluegen-2.1.4.ebuild
deleted file mode 100644
index e98823dba..000000000
--- a/dev-java/gluegen/gluegen-2.1.4.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="https://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.1"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEP="
- dev-java/ant-core:0
- dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
- >=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
- >=virtual/jdk-1.5
- dev-java/cpptasks:0
- test? (
- dev-java/junit:4
- dev-java/ant-junit4
- )"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-PATCHES=(
- "${FILESDIR}/${PV}-dont-copy-jars.patch"
- "${FILESDIR}/${PV}-dont-strip.patch"
- "${FILESDIR}/${PV}-dont-test-archive.patch"
-)
-
-src_prepare() {
- rm -rf make/lib
- default
- java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
- EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
- java-pkg_dojar build/${PN}{,-rt}.jar
- java-pkg_doso build/obj/*.so
-
- use doc && dodoc -r doc/manual
- use source && java-pkg_dosrc src/java/*
-
- # for building jogl
- insinto /usr/share/${PN}-${SLOT}/make
- doins -r make/*
- insinto /usr/share/${PN}-${SLOT}/build
- doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/gluegen-2.2.4.ebuild b/dev-java/gluegen/gluegen-2.2.4.ebuild
deleted file mode 100644
index cd15a0c2a..000000000
--- a/dev-java/gluegen/gluegen-2.2.4.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="https://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEP="
- dev-java/ant-core:0
- dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
- >=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
- >=virtual/jdk-1.5
- dev-java/cpptasks:0
- test? (
- dev-java/junit:4
- dev-java/ant-junit4
- )"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-PATCHES=(
- "${FILESDIR}/${PV}-dont-copy-jars.patch"
- "${FILESDIR}/${PV}-dont-strip.patch"
- "${FILESDIR}/${PV}-dont-test-archive.patch"
-)
-
-src_prepare() {
- rm -rf make/lib
- default
- java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
- EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
- java-pkg_dojar build/${PN}{,-rt}.jar
- java-pkg_doso build/obj/*.so
-
- use doc && dodoc -r doc/manual
- use source && java-pkg_dosrc src/java/*
-
- # for building jogl
- insinto /usr/share/${PN}-${SLOT}/make
- doins -r make/*
- insinto /usr/share/${PN}-${SLOT}/build
- doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml
deleted file mode 100644
index b81144d5f..000000000
--- a/dev-java/gluegen/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="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-GlueGen is a tool which automatically generates the Java and JNI code necessary
-to call C libraries. It reads as input ANSI C header files and separate
-configuration files which provide control over many aspects of the glue code
-generation. GlueGen uses a complete ANSI C parser and an internal representation
-(IR) capable of representing all C types to represent the APIs for which it
-generates interfaces. It has the ability to perform significant transformations
-on the IR before glue code emission. GlueGen is currently powerful enough to
-bind even low-level APIs such as the Java Native Interface (JNI) and the AWT
-Native Interface (JAWT) back up to the Java programming language.
-</longdescription>
- <upstream>
- <remote-id type="github">sgothel/gluegen</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/htsjdk/Manifest b/dev-java/htsjdk/Manifest
deleted file mode 100644
index ee5ea5e79..000000000
--- a/dev-java/htsjdk/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST htsjdk-2.19.0.tar.gz 15602200 BLAKE2B eee9e4cbed27122020b7ec9de50c301c3078cc995a9aa6f89061518f9fab823054759dc17c16fb71da231b7e19876743146116ee7398af04a8e65b7781c62924 SHA512 07af3f5a592ab519349bd8a47dc336fe8673232daeb1d4c1a120dd4dde1c42db443998948185e2b18f27a5ac578b0afa0d7d09b36a66f69eba156ac0912d96b5
-DIST htsjdk-2.3.0.tar.gz 11466439 BLAKE2B 5bdfb89f99767335c3e3e45b43a237d8e050c68f02f4816d9cb23d2fce78ec133a1c29ea297eba0224ec11a162d2b40b3ea486d834488b4369d24931fbcb72b6 SHA512 43029b59c039accd5ae5d7631d72a11bfab80c38fcbfb3fa02e9bc9e9b795ca86f048a34a7182325c4d7123a82d2b6c5094e11f7118c09fca222b3b2327f6249
diff --git a/dev-java/htsjdk/htsjdk-2.19.0.ebuild b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
deleted file mode 100644
index 349e56673..000000000
--- a/dev-java/htsjdk/htsjdk-2.19.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0
- dev-java/gradle-bin:*"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
- default
-}
-
-src_compile(){
- # work around gradle writing $HOME/.gradle and $HOME/.git
- # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
- GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
-}
-
-src_install() {
- cd dist || die
-
- for i in *.jar; do
- java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- done
-
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-2.3.0.ebuild b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
deleted file mode 100644
index c94f79781..000000000
--- a/dev-java/htsjdk/htsjdk-2.3.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
- default
- rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
- cd dist || die
-
- for i in *.jar; do
- java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- done
-
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-9999.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
deleted file mode 100644
index 2123bbc55..000000000
--- a/dev-java/htsjdk/htsjdk-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit git-r3 java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0
- dev-java/gradle-bin:*"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
- default
-}
-
-src_compile(){
- # work around gradle writing $HOME/.gradle and $HOME/.git
- # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
- GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
-src_install() {
- cd build/libs || die
-
- #for i in *-SNAPSHOT.jar; do
- # java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- #done
- java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar
- use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar
- use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar
-}
diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml
deleted file mode 100644
index e18a4898a..000000000
--- a/dev-java/htsjdk/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>ercpe@gentoo.org</email>
- <name>Johann Schmitz (ercpe)</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">samtools/htsjdk</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jcommon/Manifest b/dev-java/jcommon/Manifest
deleted file mode 100644
index c7cdd4429..000000000
--- a/dev-java/jcommon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jcommon-1.0.23.zip 1373666 BLAKE2B 23c87cd18339ea8f5991933c1430464ca5a408d4d4afb42847ee8c3b941d8fd7ed9695af74ec9ff7fc5867758b826d49b5def73923e893910efc0a0d77f26f75 SHA512 c358239da8b1ddf53ce94bebb00b6518456aa921dd3aa84fc6a23144d499f14a85ba421cd71f3880e8d10153a6ab816f54c1fa872a4ab694ce3c7b8d69bc2a4b
diff --git a/dev-java/jcommon/jcommon-1.0.23.ebuild b/dev-java/jcommon/jcommon-1.0.23.ebuild
deleted file mode 100644
index 8005b903c..000000000
--- a/dev-java/jcommon/jcommon-1.0.23.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test"
-
-inherit java-pkg-2 java-ant-2
-
-MY_P=${PN}-$(ver_rs 3 -)
-DESCRIPTION="A collection of useful classes used by JFreeChart, JFreeReport and others"
-HOMEPAGE="http://www.jfree.org/jcommon"
-SRC_URI="mirror://sourceforge/jfreechart/${MY_P}.zip"
-
-LICENSE="LGPL-2"
-SLOT="1.0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-BDEPEND="
- >=virtual/jdk-1.6
- app-arch/unzip
- test? ( dev-java/junit:4 )"
-RDEPEND=">=virtual/jre-1.6"
-
-S="${WORKDIR}"/"${MY_P}"
-
-src_prepare() {
- default
- find "${WORKDIR}" -name '*.jar' -print -delete || die
-
- if ! use debug; then
- antflags="-Dbuild.debug=false -Dbuild.optimize=true"
- fi
-}
-
-src_compile() {
- if ! use debug; then
- antflags="-Dbuild.debug=false -Dbuild.optimize=true"
- fi
- eant -f ant/build.xml compile $(use_doc) $antflags
-}
-
-# No tests defined in build.xml. Let's turn them off.
-# src_test() {
-# java-pkg_jar-from --into lib junit-4
-# eant -f ant/build.xml compile-junit-tests
-# ejunit4 -cp "./lib/${P}-junit.jar:$(java-pkg_getjars junit-4)" \
-# org.jfree.junit.JCommonTestSuite
-# }
-
-src_install() {
- java-pkg_newjar ${P}.jar ${PN}.jar
- dodoc README.md
- use doc && java-pkg_dojavadoc javadoc
- use source && java-pkg_dosrc src/main/java/com src/main/java/org
-}
diff --git a/dev-java/jcommon/metadata.xml b/dev-java/jcommon/metadata.xml
deleted file mode 100644
index eae2d8963..000000000
--- a/dev-java/jcommon/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">jfreechart</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jfreechart/Manifest b/dev-java/jfreechart/Manifest
deleted file mode 100644
index b7458ca74..000000000
--- a/dev-java/jfreechart/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jfreechart-1.0.19.zip 8050676 BLAKE2B be5ac67befd6a16c9771f50bca59c3543251984b60e00e8aef350cadb1121caf391a8dddc383fa08ed89b0346e2a057a8da6a70b224d7f843f19535a4df873b2 SHA512 6345e6a6b4a82862f3908794efb70a6f5413f313ba5bcff1dfb713d21948034d80c743a0cea61be81921c62736b07209ed4b942fedca0c76226b1202a4596b31
diff --git a/dev-java/jfreechart/files/jfreechart-1.0.19-build.xml.patch b/dev-java/jfreechart/files/jfreechart-1.0.19-build.xml.patch
deleted file mode 100644
index ffe657b89..000000000
--- a/dev-java/jfreechart/files/jfreechart-1.0.19-build.xml.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/ant/build.xml 2011-11-20 22:40:13.000000000 +0100
-+++ b/ant/build.xml 2013-03-09 14:10:53.987970148 +0100
-@@ -40,10 +40,9 @@
- <available classname="java.lang.Annotation" property="src.version" value="1.5"/>
- <available classname="java.lang.Annotation" property="target.version" value="1.5"/>
- <path id="build.classpath">
-- <fileset dir="${basedir}/lib/">
-- <include name="${jcommon.name}-${jcommon.version}.jar"/>
-- <include name="servlet.jar"/>
-- </fileset>
-+ <pathelement location="${jcommon.jar}"/>
-+ <pathelement location="${servlet.jar}"/>
-+ <pathelement location="${gnujaxp.jar}"/>
- </path>
-
- </target>
-@@ -321,7 +320,7 @@
-
- <!-- COMPILE THE JUNIT TESTS. -->
- <target name="compile-tests"
-- depends="compile,compile-experimental"
-+ depends="initialise"
- description="Compile the test code">
-
- <mkdir dir="${basedir}/build-tests"/>
diff --git a/dev-java/jfreechart/files/jfreechart-1.0.19-fix-TimeSeriesCollectionTest.patch b/dev-java/jfreechart/files/jfreechart-1.0.19-fix-TimeSeriesCollectionTest.patch
deleted file mode 100644
index ebb6c4aef..000000000
--- a/dev-java/jfreechart/files/jfreechart-1.0.19-fix-TimeSeriesCollectionTest.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/tests/org/jfree/data/time/TimeSeriesCollectionTest.java 2011-11-20 22:40:13.000000000 +0100
-+++ b/tests/org/jfree/data/time/TimeSeriesCollectionTest.java 2013-05-21 00:18:03.840041846 +0200
-@@ -339,6 +339,10 @@
- * java.util.List, boolean)} method.
- */
- public void testFindDomainBounds() {
-+ // store the current time zone
-+ TimeZone saved = TimeZone.getDefault();
-+ TimeZone.setDefault(TimeZone.getTimeZone("Europe/Paris"));
-+
- TimeSeriesCollection dataset = new TimeSeriesCollection();
- List visibleSeriesKeys = new java.util.ArrayList();
- Range r = DatasetUtilities.findDomainBounds(dataset, visibleSeriesKeys,
-@@ -351,10 +355,6 @@
- r = DatasetUtilities.findDomainBounds(dataset, visibleSeriesKeys, true);
- assertNull(r);
-
-- // store the current time zone
-- TimeZone saved = TimeZone.getDefault();
-- TimeZone.setDefault(TimeZone.getTimeZone("Europe/Paris"));
--
- s1.add(new Year(2008), 8.0);
- r = DatasetUtilities.findDomainBounds(dataset, visibleSeriesKeys, true);
- assertEquals(1199142000000.0, r.getLowerBound(), EPSILON);
diff --git a/dev-java/jfreechart/jfreechart-1.0.19-r2.ebuild b/dev-java/jfreechart/jfreechart-1.0.19-r2.ebuild
deleted file mode 100644
index e83f79d4b..000000000
--- a/dev-java/jfreechart/jfreechart-1.0.19-r2.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
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="JFreeChart is a free Java class library for generating charts"
-HOMEPAGE="http://www.jfree.org/jfreechart"
-SRC_URI="mirror://sourceforge/${PN}/${P}.zip"
-
-LICENSE="LGPL-2.1"
-SLOT="1.0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-CDEPEND="
- dev-java/jfreesvg:2.1
- >=dev-java/jcommon-1.0.23:1.0
- java-virtuals/servlet-api:3.0"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.6"
-
-BDEPEND="
- ${CDEPEND}
- test? (
- dev-java/ant-junit:0
- dev-java/junit:4
- )
- app-arch/unzip
- >=virtual/jdk-1.6"
-
-RESTRICT="test"
-
-PATCHES=(
- "${FILESDIR}/${PN}-1.0.19-build.xml.patch"
- "${FILESDIR}/${PN}-1.0.19-fix-TimeSeriesCollectionTest.patch"
-)
-
-JAVA_ANT_ENCODING="ISO-8859-1"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-EANT_BUILD_XML="ant/build.xml"
-EANT_BUILD_TARGET="compile-experimental"
-EANT_GENTOO_CLASSPATH="
- jfreesvg-2.1
- jcommon-1.0
- servlet-api-3.0
-"
-
-EANT_DOC_TARGET="javadoc"
-
-src_prepare() {
- default
-
- java-pkg_clean
-}
-
-src_install() {
- java-pkg_newjar "lib/${P}.jar" "${PN}.jar"
- java-pkg_newjar "lib/${P}-experimental.jar" "${PN}-experimental.jar"
-
- dodoc README.txt ChangeLog NEWS
-
- use doc && java-pkg_dojavadoc javadoc
- use source && java-pkg_dosrc source/org
-}
diff --git a/dev-java/jfreechart/metadata.xml b/dev-java/jfreechart/metadata.xml
deleted file mode 100644
index eae2d8963..000000000
--- a/dev-java/jfreechart/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="sourceforge">jfreechart</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jfreesvg/Manifest b/dev-java/jfreesvg/Manifest
deleted file mode 100644
index e35008887..000000000
--- a/dev-java/jfreesvg/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST jfreesvg-2.1.zip 2042545 BLAKE2B 702ea55c6e51bca156a41c5e624452fdad8c1a5472c204cbf58f796134ed6027259abd0a48719bbb5f83f6891ab3aec5db58c8726b0275b894065148a07ec179 SHA512 6c1556c640e749778aeb969540db7724895fe2113a7ceea732793730301dd04a1beafef35249b27b75696271bcd67a59236a15c106f7717482561011a1a08bc4
-DIST jfreesvg-3.0.zip 1946062 BLAKE2B 58aa3c95db3a0472de1e2c184f1e8bc9aa72b86f508dd7d41f169f03c8f07380269a36d0a22a71378ab7c2d45427fb479994b907c4e25317794814da69f79d7c SHA512 7d0bdcbf56f0a7110058137d53e291c41e53040cbc19442989a0c6d28f5d6d3ed26ecedbfc947ce845b8a971729e2d784e8ce5a041f6f095ff626a3494a55715
diff --git a/dev-java/jfreesvg/jfreesvg-2.1-r1.ebuild b/dev-java/jfreesvg/jfreesvg-2.1-r1.ebuild
deleted file mode 100644
index 62b6965cd..000000000
--- a/dev-java/jfreesvg/jfreesvg-2.1-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="JFreeSVG is a fast, light-weight, vector graphics library for the Java platform"
-HOMEPAGE="http://www.jfree.org/jfreesvg/"
-SRC_URI="mirror://sourceforge/jfreegraphics2d/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-BDEPEND="
- app-arch/unzip
- >=virtual/jdk-1.6"
-
-RDEPEND="
- >=virtual/jre-1.6"
-
-src_prepare() {
- default
- java-pkg_clean
-}
-
-src_compile() {
- if ! use debug; then
- antflags="-Dbuild.debug=false -Dbuild.optimize=true"
- fi
- eant -f ant/build.xml compile $(use_doc) $antflags
-}
-
-src_install() {
- java-pkg_newjar "./lib/${P}.jar" ${PN}.jar
- dodoc README.md
- use doc && java-pkg_dojavadoc javadoc
- use source && java-pkg_dosrc src/main/java
-}
diff --git a/dev-java/jfreesvg/jfreesvg-3.0.ebuild b/dev-java/jfreesvg/jfreesvg-3.0.ebuild
deleted file mode 100644
index ec6f7ac34..000000000
--- a/dev-java/jfreesvg/jfreesvg-3.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="JFreeSVG is a fast, light-weight, vector graphics library for the Java platform"
-HOMEPAGE="http://www.jfree.org/jfreesvg/"
-SRC_URI="mirror://sourceforge/jfreegraphics2d/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="3.0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-BDEPEND=">=virtual/jdk-1.6
- app-arch/unzip"
-RDEPEND=">=virtual/jre-1.6"
-
-src_prepare() {
- default
- find "${WORKDIR}" -name '*.jar' -print -delete || die
-}
-
-src_compile() {
- if ! use debug; then
- antflags="-Dbuild.debug=false -Dbuild.optimize=true"
- fi
- eant -f ant/build.xml compile $(use_doc) $antflags
-}
-
-src_install() {
- java-pkg_newjar "./lib/${P}.jar" ${PN}.jar
- dodoc README.md
- use doc && java-pkg_dojavadoc javadoc
- use source && java-pkg_dosrc src/main/java
-}
diff --git a/dev-java/jfreesvg/metadata.xml b/dev-java/jfreesvg/metadata.xml
deleted file mode 100644
index bcad7a209..000000000
--- a/dev-java/jfreesvg/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <use>
- <flag name="debug">
- Enable debugging during compilation.
- </flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">jfreegraphics2d</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jgraphx/Manifest b/dev-java/jgraphx/Manifest
deleted file mode 100644
index 421fe6919..000000000
--- a/dev-java/jgraphx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jgraphx-4.2.2.tar.gz 3525225 BLAKE2B a716df6d843fdc3b0ef32ba9549701d658f1daa104fd90df00137753d837756a2008129cb449771ec8dac3731b3033b429a7758f7f2e3ca58f27b93c88732b5c SHA512 767c0972100c8ed41561304367cba4574d1ba1bcd5c5d57fa869dd0a1bc1b2d6d70253577a4d2a2f03641afec5bd0d4e81e52a13529681737de7918c0c24cee7
diff --git a/dev-java/jgraphx/jgraphx-4.2.2.ebuild b/dev-java/jgraphx/jgraphx-4.2.2.ebuild
deleted file mode 100644
index de4e6ab36..000000000
--- a/dev-java/jgraphx/jgraphx-4.2.2.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Open-source graph component for Java"
-HOMEPAGE="https://github.com/jgraph"
-SRC_URI="https://github.com/jgraph/jgraphx/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="doc examples source"
-
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
-
-src_prepare() {
- default
- # don't do javadoc always
- sed -i \
- -e 's/depends="doc"/depends="compile"/' \
- build.xml || die "sed failed"
- rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
- java-pkg_dojar lib/${PN}.jar
-
- use doc && java-pkg_dojavadoc docs/api
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/metadata.xml b/dev-java/jgraphx/metadata.xml
deleted file mode 100644
index 2a4062ae5..000000000
--- a/dev-java/jgraphx/metadata.xml
+++ /dev/null
@@ -1,19 +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>
- <longdescription lang="en">
-JGraph X is based on the mxGraph architecture, a re-designed core
-based on JGraph experience.
-Overall, JGraph X provides more features that JGraph, with a far
-smaller code size and complexity. Redesigning the codebase from
-scratch now means implementing common feature extensions are easier
-and require less coding. A number of new loosely coupled
-application-centric features have been added, making prototyping
-even faster, without their usage restricting application
-flexibility.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath-fop/Manifest b/dev-java/jlatexmath-fop/Manifest
deleted file mode 100644
index d92e07cb2..000000000
--- a/dev-java/jlatexmath-fop/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-fop-src-1.0.3.zip 115024 BLAKE2B c45d79c3b57c5439ab0f39fd17926e0cdb8bae4d5ef5bcec476c1daefefecbd197663beded3202dd53f25a3dee71c096f536b0c52b8d366c557c5ed89897abfe SHA512 92e81ab2c2a14cd9ac935028f6cd4370de5925f919e41fb94290a331660e2ea983ab3ca7a5fe7e5fd7c6a2caf34a4bae7ee45c0efc33b4ac0f154f16465c37f8
diff --git a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch b/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
deleted file mode 100644
index 1cd5b69eb..000000000
--- a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -urN a/build.xml b/build.xml
---- a/build.xml 2013-04-23 20:42:19.776644942 -0400
-+++ b/build.xml 2013-04-23 20:42:36.821646638 -0400
-@@ -1,7 +1,7 @@
- <?xml version="1.0" encoding="ISO-8859-1"?>
- <project name="jlatexmath-fop" basedir="." default="buildJar">
-- <import file="${basedir}/../../version.xml"/>
-- <property file="../../fop.properties"/>
-+ <import file="${basedir}/version.xml"/>
-+ <property file="fop.properties"/>
-
- <path id="libs-build-classpath">
- <pathelement location="${fop.jar}"/>
diff --git a/dev-java/jlatexmath-fop/files/version.xml b/dev-java/jlatexmath-fop/files/version.xml
deleted file mode 100644
index b538b79a3..000000000
--- a/dev-java/jlatexmath-fop/files/version.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project name="version_jlm">
- <property name="version" value="1.0.3" />
- <property name="java_version" value="5" />
-</project>
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
deleted file mode 100644
index 1782fb0b1..000000000
--- a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="jlatexmath plugin for dev-java/fop"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/jlatexmath:1
- dev-java/xmlgraphics-commons:2
- >=dev-java/fop-2.0-r1:0"
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.5"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="buildJar"
-
-S="${WORKDIR}"
-
-PATCHES=(
- "${FILESDIR}/${P}-fixpaths.patch"
-)
-
-src_prepare() {
- default
- cp "${FILESDIR}/version.xml" "${S}" || die
- echo "fop.jar=$(java-pkg_getjar fop fop.jar)
-xmlgraphics-commons.jar=$(java-pkg_getjar xmlgraphics-commons-2 xmlgraphics-commons.jar)
-jlatexmath.jar=$(java-pkg_getjar jlatexmath-1 jlatexmath.jar)" \
- >>fop.properties || die
-}
-
-src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath-fop/metadata.xml b/dev-java/jlatexmath-fop/metadata.xml
deleted file mode 100644
index 9ded36c47..000000000
--- a/dev-java/jlatexmath-fop/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style. This package installs the plugin for dev-java/fop.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath/Manifest b/dev-java/jlatexmath/Manifest
deleted file mode 100644
index 44a2a7205..000000000
--- a/dev-java/jlatexmath/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-src-1.0.3.zip 1086238 BLAKE2B 16e420326f5387bb6bae251032d6c3e262334adfa23083e38fc4d5e7552b415c03761172decc0c2a205d9fc3cd63190b949c44a32fa983f964d8a4557be82702 SHA512 85c71568b5bffd897338e7c3fd03be0c0f52fc0543b5d91f54453f20f3f4ec41225cb356667dbaca86df673db1b7ac8afc2b16e57db981ec8037143e26521e82
diff --git a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
deleted file mode 100644
index a9945c021..000000000
--- a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java API to render LaTeX"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=virtual/jdk-1.5"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-EANT_BUILD_TARGET="buildJar"
-EANT_DOC_TARGET="doc"
-
-src_install() {
- java-pkg_newjar dist/"${P}.jar" "${PN}.jar"
- use doc && java-pkg_dojavadoc doc
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath/metadata.xml b/dev-java/jlatexmath/metadata.xml
deleted file mode 100644
index 7ad985657..000000000
--- a/dev-java/jlatexmath/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>
- <longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jogl/Manifest b/dev-java/jogl/Manifest
deleted file mode 100644
index 09b10e415..000000000
--- a/dev-java/jogl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jogl-2.2.4.tar.gz 50214295 BLAKE2B 984d32e4bd43e33807dca1d0222aae9a9ca453d616002865d4a6b80ec9a8f3e8f833669067daa545103a391af8db6e5c75cfc45501053b3d850c5a28ac311a7e SHA512 79fb054d65e8aa532a75e8c8911f43987d877f7b71584ea24cc0f9152f8aaaddabd4afef7f7504b3df73c4d240bedc123bb8aeb8670d9ae2bd165bd0490e420e
diff --git a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch b/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
deleted file mode 100644
index 6d77bc3fe..000000000
--- a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff -Naur gluegen.orig/make/gluegen-cpptasks.xml gluegen/make/gluegen-cpptasks.xml
---- gluegen.orig/make/gluegen-cpptasks.xml 2007-03-14 23:09:20.000000000 +1300
-+++ gluegen/make/gluegen-cpptasks.xml 2007-03-14 23:09:40.000000000 +1300
-@@ -397,16 +397,16 @@
- <compilerarg value="-fPIC"/>
- </compiler>
-
-- <compiler id="compiler.cfg.solaris" name="suncc">
-+ <compiler id="compiler.cfg.solaris" name="gcc">
- </compiler>
-
-- <compiler id="compiler.cfg.solaris.sparcv9" name="suncc">
-+ <compiler id="compiler.cfg.solaris.sparcv9" name="gcc">
- <compilerarg value="-fast" />
- <compilerarg value="-xchip=ultra" />
- <compilerarg value="-xarch=v9a" />
- </compiler>
-
-- <compiler id="compiler.cfg.solaris.amd64" name="suncc">
-+ <compiler id="compiler.cfg.solaris.amd64" name="gcc">
- <compilerarg value="-fast" />
- <compilerarg value="-xchip=opteron" />
- <compilerarg value="-xarch=amd64" />
-@@ -492,14 +492,14 @@
- <linker id="linker.cfg.linux.amd64" name="gcc">
- </linker>
-
-- <linker id="linker.cfg.solaris" name="suncc">
-+ <linker id="linker.cfg.solaris" name="gcc">
- </linker>
-
-- <linker id="linker.cfg.solaris.sparcv9" name="suncc">
-+ <linker id="linker.cfg.solaris.sparcv9" name="gcc">
- <linkerarg value="-xarch=v9a" />
- </linker>
-
-- <linker id="linker.cfg.solaris.amd64" name="suncc">
-+ <linker id="linker.cfg.solaris.amd64" name="gcc">
- <linkerarg value="-xarch=amd64" />
- </linker>
-
diff --git a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch b/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
deleted file mode 100644
index a508c610f..000000000
--- a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-diff -Naur jogl.orig/make/build.xml jogl/make/build.xml
---- jogl.orig/make/build.xml 2007-02-13 17:45:16.000000000 +1300
-+++ jogl/make/build.xml 2007-03-14 22:55:50.000000000 +1300
-@@ -127,7 +127,18 @@
- <property name="gluegen.build.xml" value="${gluegen.make.dir}/build.xml" />
- <property name="gluegen.jar" value="../../gluegen/build/gluegen.jar" />
- <property name="gluegen-rt.jar" value="../../gluegen/build/gluegen-rt.jar" />
--
-+ <!-- This property is used to skip building gluegen if the jar files
-+ - are already available on the system and have been overridden
-+ - by the user. The purpose is to allow linux distro's to uncouple
-+ - gluegen from jogl.
-+ -->
-+ <condition property="gluegen.prebuilt" >
-+ <and>
-+ <available file="${gluegen.jar}" />
-+ <available file="${gluegen-rt.jar}" />
-+ </and>
-+ </condition>
-+
- <!-- Names of directories relative to the project root.
- Some of these are used in FileMappers later for dependence information
- and need exact string matching, which is why they use file.separator
-@@ -479,7 +490,7 @@
- <!--
- - Build GlueGen
- -->
-- <target name="build.gluegen" depends="init">
-+ <target name="build.gluegen" depends="init" unless="gluegen.prebuilt">
- <!-- Run the GlueGen build to ensure that the GlueGen ANT task
- - has been built. -->
- <!-- FIXME: remove passing down of antlr.jar when gluegen.properties is on all
diff --git a/dev-java/jogl/jogl-2.2.4.ebuild b/dev-java/jogl/jogl-2.2.4.ebuild
deleted file mode 100644
index 9d2345b53..000000000
--- a/dev-java/jogl/jogl-2.2.4.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
-
-JAVA_PKG_IUSE="doc source"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="https://jogamp.org/jogl/www/"
-SRC_URI="https://github.com/sgothel/jogl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cg"
-
-CDEPEND="
- ~dev-java/gluegen-${PV}:${SLOT}
- dev-java/antlr:0
- dev-java/ant-core:0
- x11-libs/libX11
- x11-libs/libXxf86vm
- dev-java/swt:3.7
- virtual/opengl
- cg? ( media-gfx/nvidia-cg-toolkit )"
-
-RDEPEND="${CDEPEND}
- >=virtual/jre-1.5"
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.5"
-
-# upstream has a crude way to call the junit tests, which cause a lot of trouble to pass
-# our test classpath...
-RESTRICT="test"
-
-JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="init build.nativewindow build.jogl build.newt build.oculusvr one.dir tag.build"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="gluegen-${SLOT},antlr,ant-core,swt-3.7"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}/*.jar:${S}/build/nativewindow/*.jar"
-EANT_NEEDS_TOOLS="yes"
-
-src_prepare() {
- default
- #we keep make/lib/plugin3/puglin3-public.jar
- find -name 'make/lib/swt/*.jar' -delete -print || die
-
- # Empty filesets are never out of date!
- sed -i -e 's/<outofdate>/<outofdate force="true">/' make/build*xml || die
-
- EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true"
- EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/"
- EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)"
- EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)"
-
- use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-}
-
-src_install() {
- java-pkg_dojar build/jar/*.jar
- java-pkg_doso build/lib/*.so
-
- use doc && dodoc -r doc
- use source && java-pkg_dosrc src/jogl/classes/*
-}
diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml
deleted file mode 100644
index 7751e096e..000000000
--- a/dev-java/jogl/metadata.xml
+++ /dev/null
@@ -1,18 +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>
- <longdescription lang="en">
-JOGL provides Java with a Binding for the OpenGL® API (JSR-231), and is designed
-to provide hardware-supported 3D graphics to applications written in Java.
-</longdescription>
- <use>
- <flag name="cg">Enable NVidia Cg binding.</flag>
- </use>
- <upstream>
- <remote-id type="github">sgothel/jogl</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jrosetta/Manifest b/dev-java/jrosetta/Manifest
deleted file mode 100644
index 3cb51fd1d..000000000
--- a/dev-java/jrosetta/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jrosetta-1.0.4-sources.jar 94931 BLAKE2B 205a3bf9c9be9f361902f59f7f1756161ba436a29cf5650bf7173f8e431818cab235754cbbc031eb69604bf8857150a17df069bc3f87fff8a1f5f75c2d136f4d SHA512 84b613a0dc6e3ca80414aba8f7c8cf044f013d27ed27c0f18fdbea056a6358c849ee193e3ab7320ffa7368fa17f255d4390fc306e8aa2c0ad70de51f36b6e878
diff --git a/dev-java/jrosetta/files/api-build.xml b/dev-java/jrosetta/files/api-build.xml
deleted file mode 100644
index 6627122ab..000000000
--- a/dev-java/jrosetta/files/api-build.xml
+++ /dev/null
@@ -1,262 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-api-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Build environment properties -->
- <!-- ====================================================================== -->
-
- <property file="${user.home}/.m2/maven.properties"/>
- <property file="maven-build.properties"/>
-
- <property name="maven.build.finalName" value="jrosetta-api-1.0.4"/>
- <property name="maven.build.dir" value="target"/>
- <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
- <property name="maven.build.srcDir.0" value="src/main/java"/>
- <property name="maven.build.resourceDir.0" value="src/main/resources"/>
- <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
- <property name="maven.build.testDir.0" value="src/test/java"/>
- <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
- <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
- <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
- <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
- <property name="maven.settings.offline" value="true"/>
- <property name="maven.settings.interactiveMode" value="true"/>
-
- <!-- ====================================================================== -->
- <!-- Defining classpaths -->
- <!-- ====================================================================== -->
-
- <path id="build.classpath"/>
- <path id="build.test.classpath">
- <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
- <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
- </path>
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <delete dir="${maven.build.dir}"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" depends="get-deps" description="Compile the code">
- <mkdir dir="${maven.build.outputDir}"/>
- <javac destdir="${maven.build.outputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.srcDir.0}"/>
- </src>
- <classpath refid="build.classpath"/>
- </javac>
- <copy todir="${maven.build.outputDir}">
- <fileset dir="${maven.build.resourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests"
- depends="compile"
- description="Compile the test code"
- unless="maven.test.skip">
- <mkdir dir="${maven.build.testOutputDir}"/>
- <javac destdir="${maven.build.testOutputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.testDir.0}"/>
- </src>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- </classpath>
- </javac>
- <copy todir="${maven.build.testOutputDir}">
- <fileset dir="${maven.build.testResourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test"
- depends="compile-tests, junit-missing"
- unless="junit.skipped"
- description="Run the test cases">
- <mkdir dir="${maven.test.reports}"/>
- <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
- <sysproperty key="basedir" value="."/>
- <formatter type="xml"/>
- <formatter type="plain" usefile="false"/>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- <pathelement location="${maven.build.testOutputDir}"/>
- </classpath>
- <batchtest todir="${maven.test.reports}" unless="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/Test*.java"/>
- <include name="**/*Test.java"/>
- <include name="**/*TestCase.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- <batchtest todir="${maven.test.reports}" if="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/${test}.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- </junit>
- </target>
-
- <target name="test-junit-present">
- <available classname="junit.framework.Test" property="junit.present"/>
- </target>
-
- <target name="test-junit-status"
- depends="test-junit-present">
- <condition property="junit.missing">
- <and>
- <isfalse value="${junit.present}"/>
- <isfalse value="${maven.test.skip}"/>
- </and>
- </condition>
- <condition property="junit.skipped">
- <or>
- <isfalse value="${junit.present}"/>
- <istrue value="${maven.test.skip}"/>
- </or>
- </condition>
- </target>
-
- <target name="junit-missing"
- depends="test-junit-status"
- if="junit.missing">
- <echo>=================================== WARNING ===================================</echo>
- <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
- <echo>===============================================================================</echo>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <javadoc sourcepath="${maven.build.srcDir.0}"
- packagenames="*"
- destdir="${maven.reporting.outputDirectory}/apidocs"
- access="protected"
- old="false"
- verbose="false"
- version="true"
- use="true"
- author="true"
- splitindex="false"
- nodeprecated="false"
- nodeprecatedlist="false"
- notree="false"
- noindex="false"
- nohelp="false"
- nonavbar="false"
- serialwarn="false"
- charset="ISO-8859-1"
- linksource="false"
- breakiterator="false"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" depends="compile,test" description="Package the application">
- <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar"
- compress="true"
- index="false"
- basedir="${maven.build.outputDir}"
- excludes="**/package.html">
- <manifest>
- </manifest>
- </jar>
- </target>
-
- <!-- ====================================================================== -->
- <!-- A dummy target for the package named after the type it creates -->
- <!-- ====================================================================== -->
-
- <target name="jar" depends="package" description="Builds the jar for the application"/>
-
- <!-- ====================================================================== -->
- <!-- Download dependencies target -->
- <!-- ====================================================================== -->
-
- <target name="test-offline">
- <condition property="maven.mode.offline">
- <equals arg1="${maven.settings.offline}" arg2="true"/>
- </condition>
- </target>
-
- <target name="get-deps"
- depends="test-offline"
- description="Download all dependencies"
- unless="maven.mode.offline">
- <mkdir dir="${maven.repo.local}"/>
- <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
- <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
- <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/build.xml b/dev-java/jrosetta/files/build.xml
deleted file mode 100644
index c6959deb0..000000000
--- a/dev-java/jrosetta/files/build.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="clean"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="clean"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" description="Compile the code">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests" description="Compile the test code">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile-tests"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile-tests"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test" description="Run the test cases">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="test"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="test"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="javadoc"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="javadoc"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" description="Package the application">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="package"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="package"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/engine-build.xml b/dev-java/jrosetta/files/engine-build.xml
deleted file mode 100644
index 9ee8429f4..000000000
--- a/dev-java/jrosetta/files/engine-build.xml
+++ /dev/null
@@ -1,274 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-engine-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Build environment properties -->
- <!-- ====================================================================== -->
-
- <property file="${user.home}/.m2/maven.properties"/>
- <property file="maven-build.properties"/>
-
- <property name="maven.build.finalName" value="jrosetta-engine-1.0.4"/>
- <property name="maven.build.dir" value="target"/>
- <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
- <property name="maven.build.srcDir.0" value="src/main/java"/>
- <property name="maven.build.resourceDir.0" value="src/main/resources"/>
- <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
- <property name="maven.build.testDir.0" value="src/test/java"/>
- <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
- <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
- <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
- <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
- <property name="maven.settings.offline" value="true"/>
- <property name="maven.settings.interactiveMode" value="true"/>
-
- <!-- ====================================================================== -->
- <!-- Defining classpaths -->
- <!-- ====================================================================== -->
-
- <path id="build.classpath">
- <pathelement location="../jrosetta-api/target/classes"/>
- </path>
- <path id="build.test.classpath">
- <pathelement location="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"/>
- <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
- <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
- </path>
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <delete dir="${maven.build.dir}"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" depends="get-deps" description="Compile the code">
- <mkdir dir="${maven.build.outputDir}"/>
- <javac destdir="${maven.build.outputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.srcDir.0}"/>
- </src>
- <classpath refid="build.classpath"/>
- </javac>
- <copy todir="${maven.build.outputDir}">
- <fileset dir="${maven.build.resourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests"
- depends="compile"
- description="Compile the test code"
- unless="maven.test.skip">
- <mkdir dir="${maven.build.testOutputDir}"/>
- <javac destdir="${maven.build.testOutputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.testDir.0}"/>
- </src>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- </classpath>
- </javac>
- <copy todir="${maven.build.testOutputDir}">
- <fileset dir="${maven.build.testResourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test"
- depends="compile-tests, junit-missing"
- unless="junit.skipped"
- description="Run the test cases">
- <mkdir dir="${maven.test.reports}"/>
- <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
- <sysproperty key="basedir" value="."/>
- <formatter type="xml"/>
- <formatter type="plain" usefile="false"/>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- <pathelement location="${maven.build.testOutputDir}"/>
- </classpath>
- <batchtest todir="${maven.test.reports}" unless="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/Test*.java"/>
- <include name="**/*Test.java"/>
- <include name="**/*TestCase.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- <batchtest todir="${maven.test.reports}" if="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/${test}.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- </junit>
- </target>
-
- <target name="test-junit-present">
- <available classname="junit.framework.Test" property="junit.present"/>
- </target>
-
- <target name="test-junit-status"
- depends="test-junit-present">
- <condition property="junit.missing">
- <and>
- <isfalse value="${junit.present}"/>
- <isfalse value="${maven.test.skip}"/>
- </and>
- </condition>
- <condition property="junit.skipped">
- <or>
- <isfalse value="${junit.present}"/>
- <istrue value="${maven.test.skip}"/>
- </or>
- </condition>
- </target>
-
- <target name="junit-missing"
- depends="test-junit-status"
- if="junit.missing">
- <echo>=================================== WARNING ===================================</echo>
- <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
- <echo>===============================================================================</echo>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <javadoc sourcepath="${maven.build.srcDir.0}"
- packagenames="*"
- destdir="${maven.reporting.outputDirectory}/apidocs"
- access="protected"
- old="false"
- verbose="false"
- version="true"
- use="true"
- author="true"
- splitindex="false"
- nodeprecated="false"
- nodeprecatedlist="false"
- notree="false"
- noindex="false"
- nohelp="false"
- nonavbar="false"
- serialwarn="false"
- charset="ISO-8859-1"
- linksource="false"
- breakiterator="false"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" depends="compile,test" description="Package the application">
- <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar"
- compress="true"
- index="false"
- basedir="${maven.build.outputDir}"
- excludes="**/package.html">
- <manifest>
- </manifest>
- </jar>
- </target>
-
- <!-- ====================================================================== -->
- <!-- A dummy target for the package named after the type it creates -->
- <!-- ====================================================================== -->
-
- <target name="jar" depends="package" description="Builds the jar for the application"/>
-
- <!-- ====================================================================== -->
- <!-- Download dependencies target -->
- <!-- ====================================================================== -->
-
- <target name="test-offline">
- <condition property="maven.mode.offline">
- <equals arg1="${maven.settings.offline}" arg2="true"/>
- </condition>
- </target>
-
- <target name="get-deps"
- depends="test-offline"
- description="Download all dependencies"
- unless="maven.mode.offline">
- <mkdir dir="${maven.repo.local}"/>
- <mkdir dir="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4"/>
- <get src="http://maven.artenum.com/content/groups/public/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
- <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
- <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/jrosetta-1.0.4.ebuild b/dev-java/jrosetta/jrosetta-1.0.4.ebuild
deleted file mode 100644
index bf0f72e79..000000000
--- a/dev-java/jrosetta/jrosetta-1.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Common base for graphical component to build a graphical console"
-HOMEPAGE="http://dev.artenum.com/projects/JRosetta"
-#currently down
-#SRC_URI="http://maven.artenum.com/content/groups/public/com/artenum/${PN}/${PV}/${P}-sources.jar"
-SRC_URI="http://pkgs.fedoraproject.org/repo/pkgs/${PN}/${P}-sources.jar/5c3589d4207f71bad6eeefd4857bce50/${P}-sources.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=virtual/jdk-1.5:*"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5:*"
-
-EANT_BUILD_TARGET="compile package"
-JAVA_ANT_BSFIX_EXTRA_ARGS="--maven-cleaning"
-
-src_prepare () {
- default
- cp "${FILESDIR}/api-build.xml" modules/jrosetta-api/build.xml || die
- cp "${FILESDIR}/engine-build.xml" modules/jrosetta-engine/build.xml || die
- cp "${FILESDIR}/build.xml" . || die
- echo "${PV}" > modules/jrosetta-engine/src/main/resources/version.txt || die
-}
-
-src_install () {
- java-pkg_newjar "modules/jrosetta-api/target/jrosetta-api-${PV}.jar" \
- jrosetta-api.jar
- java-pkg_newjar "modules/jrosetta-engine/target/jrosetta-engine-${PV}.jar" \
- jrosetta-engine.jar
-}
diff --git a/dev-java/jrosetta/metadata.xml b/dev-java/jrosetta/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-java/jrosetta/metadata.xml
+++ /dev/null
@@ -1,8 +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>
-</pkgmetadata>
diff --git a/dev-java/lucene/Manifest b/dev-java/lucene/Manifest
deleted file mode 100644
index 514721f91..000000000
--- a/dev-java/lucene/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST lucene-3.6.2-src.tgz 32139784 BLAKE2B 48fe88efeae8396e084f827aa66530480f40aee3a2e59c8524420059f004a73be4c1e50c98345ad0ad4808ff8a0a996f9406523bf5c124616657ec91f9797f70 SHA512 e9a08a1b5303c44e4feecc0bb6e7013e4a9420517ae4e98999bd318ec25b5b2ff3b6de8b51db8f68afc0fdc3149829297023a95b103d4f99e7db68deee4c3965
-DIST lucene-5.2.1-src.tgz 29669184 BLAKE2B ec69a85ddf7870c760aedf9e79d93dad623d3dd759b1b6d992f64a169a86ff5f7992c0af9bd1692b78bb2c9d2abd7ca57d7c43bd507dfd0a672d31db06a30514 SHA512 294f4a0b2d1d11a8da6db0b577b962037beb4331c1ddee3e65a54e9f3155e44c3aa945b8b8f04631eb42d9bee94c1bcc468d12278fd06f2740512b9375880a02
-DIST lucene-8.4.0-src.tgz 43420829 BLAKE2B df9f34ece8d6b477950ba22d3883d81652f0a6b43adcd55152d465fa99679520314edd61500dedc3ecab85ea8410948d91c37e27bfd774dce9b6281c782b5ff0 SHA512 3848372cc0ef914502bff8f139fdd3f3c2dda68ed69492b1b189ebdc734a9a14f2b1d9f00273f7794368ccc13be304c083029d2333cc2cf61e568f04d8e91936
diff --git a/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch b/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch
deleted file mode 100644
index 8d70c406f..000000000
--- a/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/lucene/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java b/lucene/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-index 5a9509c..beecebe 100644
---- a/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-+++ b/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-@@ -21,6 +21,7 @@ import java.io.File;
- import org.apache.tools.ant.BuildException;
- import org.apache.tools.ant.types.Parameter;
- import org.apache.tools.ant.types.selectors.BaseExtendSelector;
-+import org.apache.tools.ant.types.Resource;
-
- /** Divides filesets into equal groups */
- public class LuceneJUnitDividingSelector extends BaseExtendSelector {
-@@ -30,6 +31,11 @@ public class LuceneJUnitDividingSelector extends BaseExtendSelector {
- /** Current part to accept. */
- private int part;
-
-+ @Override
-+ public boolean isSelected(Resource r) {
-+ return false;
-+ }
-+
- @Override
- public void setParameters(Parameter[] pParameters) {
- super.setParameters(pParameters);
diff --git a/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch b/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch
deleted file mode 100644
index 8c3dd8a01..000000000
--- a/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/contrib/icu/src/java/org/apache/lucene/analysis/icu/segmentation/BreakIteratorWrapper.java
-+++ b/contrib/icu/src/java/org/apache/lucene/analysis/icu/segmentation/BreakIteratorWrapper.java
-@@ -21,7 +21,6 @@ import java.text.CharacterIterator;
-
- import com.ibm.icu.lang.UCharacter;
- import com.ibm.icu.text.BreakIterator;
--import com.ibm.icu.text.DictionaryBasedBreakIterator;
- import com.ibm.icu.text.RuleBasedBreakIterator;
- import com.ibm.icu.text.UTF16;
-
-@@ -67,8 +66,7 @@ abstract class BreakIteratorWrapper {
- * it like a generic BreakIterator.
- */
- static BreakIteratorWrapper wrap(BreakIterator breakIterator) {
-- if (breakIterator instanceof RuleBasedBreakIterator
-- && !(breakIterator instanceof DictionaryBasedBreakIterator))
-+ if (breakIterator instanceof RuleBasedBreakIterator)
- return new RBBIWrapper((RuleBasedBreakIterator) breakIterator);
- else
- return new BIWrapper(breakIterator);
diff --git a/dev-java/lucene/lucene-3.6.2-r2.ebuild b/dev-java/lucene/lucene-3.6.2-r2.ebuild
deleted file mode 100644
index bdec54f4c..000000000
--- a/dev-java/lucene/lucene-3.6.2-r2.ebuild
+++ /dev/null
@@ -1,162 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test contrib"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml contrib-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="mirror://apache/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="3.6"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- contrib? (
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:70
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.6"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.6"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-# [0]: Patch so that we can compile the package against ICU 50 and above
-PATCHES=(
- "${FILESDIR}"/lucene_contrib_icu4j_v50.patch
- "${FILESDIR}"/${P}-ant-1.10.patch
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- common-build.xml || die
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use contrib; then
- EANT_GENTOO_CLASSPATH+="
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-70
- "
- EANT_BUILD_TARGET+=" build-contrib"
- EANT_DOC_TARGET+=" javadocs-all"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use contrib; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-contrib"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- java-pkg_newjar build/core/${PN}-core-${PV}.jar ${PN}-core.jar
-
- if use contrib; then
- local i j
- for i in $(find build/contrib -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- fi
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs/api
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use contrib && java-pkg_dosrc contrib
- fi
-}
diff --git a/dev-java/lucene/lucene-5.2.1.ebuild b/dev-java/lucene/lucene-5.2.1.ebuild
deleted file mode 100644
index e6cea2888..000000000
--- a/dev-java/lucene/lucene-5.2.1.ebuild
+++ /dev/null
@@ -1,211 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test modules"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="https://archive.apache.org/dist/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="5.2"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- modules? (
- dev-java/ant-apache-log4j:0
- dev-java/antlr:3.5
- dev-java/asm:9
- dev-java/asm-commons:9
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:70
- dev-java/log4j:0
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.7"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.7"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-lucene-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- -e '/conf="${ivy.default.configuration}" sync="${ivy.sync}"/d' \
- -e '/<fail>Ivy is not available<\/fail>/d' \
- -e '/ivy:configure/d' \
- -e '/svnversion.exe/d' \
- common-build.xml || die
-
- # do not build tests if modules enabled, we are missing a dependency
- sed -i \
- -e 's/<target name="build-modules" depends="compile-test"/<target name="build-modules"/g' \
- build.xml
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- if use modules; then
- mkdir -p analysis/icu/lib
- java-pkg_jar-from --into analysis/icu/lib icu4j-70
- # disable morfologik, dependency does not build
- # disable uima, dependency does not build
- # disable phonetic, dependency does not exist
- sed -i \
- -e 's/morfologik,//g' \
- -e 's/,uima//g' \
- -e 's/phonetic,//g' \
- -e 's/,compile-test//g' \
- analysis/build.xml || die
- rm -r analysis/morfologik || die
- rm -r analysis/uima || die
- rm -r analysis/phonetic || die
- # do not compile all the tests just because we want the modules
- sed -i \
- -e 's/name="build-modules" depends="compile-test"/name="build-modules"/g' \
- build.xml || die
- sed -i \
- -e 's/, compile-test//g' \
- module-build.xml || die
- mkdir -p expressions/lib
- # facet requires hppc which does not compile
- sed -i \
- -e '/<ant dir="${common.dir}\/facet" target="jar-core" inheritall="false">/,+2d' \
- module-build.xml || die
- rm -r facet || die
- # requires spatial4j, which does not exist
- sed -i \
- -e '/<ant dir="${common.dir}\/spatial" target="jar-core" inheritAll="false">/,+2d' \
- module-build.xml || die
- rm -r spatial || die
- # these require modules which we have disabled
- rm -r benchmark || die
- rm -r demo || die
- # fails to build for unknown reasons
- rm -r replicator || die
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use modules; then
- EANT_GENTOO_CLASSPATH+="
- ant-apache-log4j
- antlr-3.5
- asm-9
- asm-commons-9
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-70
- log4j
- "
- EANT_BUILD_TARGET+=" build-modules"
- EANT_DOC_TARGET+=" javadocs-modules"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use modules; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-modules"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- local i j
- for i in $(find build -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use modules && java-pkg_dosrc */src */*/src
- fi
-}
diff --git a/dev-java/lucene/lucene-8.4.0.ebuild b/dev-java/lucene/lucene-8.4.0.ebuild
deleted file mode 100644
index 9d58ad6e6..000000000
--- a/dev-java/lucene/lucene-8.4.0.ebuild
+++ /dev/null
@@ -1,223 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test modules"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="https://archive.apache.org/dist/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="8.4"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- modules? (
- dev-java/ant-apache-log4j:0
- dev-java/antlr:4
- dev-java/asm:9
- dev-java/asm-commons:9
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:70
- dev-java/log4j:0
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.8"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.8"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-lucene-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- -e '/conf="${ivy.default.configuration}" sync="${ivy.sync}"/d' \
- -e '/<fail>Ivy is not available<\/fail>/d' \
- -e '/ivy:configure/d' \
- -e '/<groovy /d' \
- -e '/svnversion.exe/d' \
- -e 's/depends="ivy-availability-check,/depends="/g' \
- -e 's/ivy-availability-check,//g' \
- -e 's/resolve-groovy,//g' \
- -e 's/depends="resolve-groovy"//g' \
- -e '/<ivy:cachepath/,/\/>/d' \
- -e '/<ivy:cachepath/,/\/ivy:cachepath>/d' \
- -e '/<ivy:dependency/d' \
- -e '/<\/ivy:cachepath>/d' \
- -e '/<taskdef name="groovy"/,/\/>/d' \
- common-build.xml || die
-
- # do not build tests if modules enabled, we are missing a dependency
- sed -i \
- -e 's/<target name="build-modules" depends="compile-test"/<target name="build-modules"/g' \
- build.xml
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- if use modules; then
- mkdir -p analysis/icu/lib
- java-pkg_jar-from --into analysis/icu/lib icu4j-70
- # disable morfologik, dependency does not build
- # disable opennlp, dependency does not exist
- # disable phonetic, dependency does not exist
- sed -i \
- -e 's/morfologik,//g' \
- -e 's/opennlp,//g' \
- -e 's/phonetic,//g' \
- -e 's/,compile-test//g' \
- analysis/build.xml || die
- rm -r analysis/morfologik || die
- rm -r analysis/opennlp || die
- rm -r analysis/phonetic || die
- # do not compile all the tests just because we want the modules
- sed -i \
- -e 's/name="build-modules" depends="compile-test"/name="build-modules"/g' \
- build.xml || die
- sed -i \
- -e 's/, compile-test//g' \
- module-build.xml || die
- mkdir -p expressions/lib
- # facet requires hppc which does not compile
- sed -i \
- -e '/<ant dir="${common.dir}\/facet" target="jar-core" inheritall="false">/,+2d' \
- module-build.xml || die
- rm -r facet || die
- # requires spatial4j, which does not exist
- sed -i \
- -e '/<ant dir="${common.dir}\/spatial-extras" target="jar-core" inheritAll="false">/,+2d' \
- module-build.xml || die
- rm -r spatial-extras || die
- # these require modules which we have disabled
- rm -r benchmark || die
- rm -r demo || die
- # this fails due to missing log4j, even though it is included in classpath
- rm -r luke || die
- # fails to build for unknown reasons
- rm -r replicator || die
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use modules; then
- EANT_GENTOO_CLASSPATH+="
- ant-apache-log4j
- antlr-4
- asm-9
- asm-commons-9
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-70
- log4j
- "
- EANT_BUILD_TARGET+=" build-modules"
- EANT_DOC_TARGET+=" javadocs-modules"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use modules; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-modules"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- local i j
- for i in $(find build -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use modules && java-pkg_dosrc */src */*/src
- fi
-}
diff --git a/dev-java/lucene/metadata.xml b/dev-java/lucene/metadata.xml
deleted file mode 100644
index 8bfdfa59a..000000000
--- a/dev-java/lucene/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="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <use>
- <flag name="contrib">Include extra functionality from contrib/</flag>
- <flag name="modules">Also build optional modules</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-java/skinlf/Manifest b/dev-java/skinlf/Manifest
deleted file mode 100644
index 725284f44..000000000
--- a/dev-java/skinlf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST skinlf-6.7.10.tar.gz 185870 BLAKE2B 4534f4d463ad3c9604d21a7113c12b5bbe1aecd7cdd80610644ce668821cd2bd1e47d0b926550014301f84e20d52f63f16bee817c339fbdc1631f57f2d74a082 SHA512 24cb44f709c5202fff1a9ca58e8cdda4de0d5e9bad8c2a7579694eabcd590993ebd5d60e200a3ff67078627502c592da2e8a021faff8f95de4ab4f8bf4945899
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-build.xml b/dev-java/skinlf/files/skinlf-6.7.10-build.xml
deleted file mode 100644
index 42b4c1145..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-build.xml
+++ /dev/null
@@ -1,276 +0,0 @@
-<!DOCTYPE project [
- <!ENTITY build-COMMON SYSTEM "common.xml">
-]>
-
-<!--
- Skin Look And Feel Build
--->
-<project name="skinlf" default="compile.java" basedir=".">
-
- <!-- Allow user to override settings -->
- <property file="${user.home}/skinlf-ant.properties" />
- <property file="build.properties" />
-
- <!-- Project Identification -->
- <property name="project" value="skinlf"/>
- <property name="version" value="6.7"/>
- <property name="year" value="2000-2006"/>
- <property name="project.fullname" value="Skin Look And Feel"/>
- <property name="project.nativeskin" value="nativeskin"/>
-
- <property name="javadoc.packagenames" value="com.l2fprod.gui,com.l2fprod.gui.plaf.skin,com.l2fprod.gui.region,com.l2fprod.gui.nativeskin"/>
-
-
-
- <path id="classpath">
- <fileset dir="lib" includes="**/*.jar"/>
- </path>
-
- <property name="classpath.asprop" refid="classpath"/>
-
- &build-COMMON;
-
- <target name="compile.javacc" depends="init">
- <javacc target="src/com/l2fprod/gui/plaf/skin/impl/gtk/parser/GtkParser.jj"
- outputdirectory="src/com/l2fprod/gui/plaf/skin/impl/gtk/parser"
- javacchome="lib"
- static="false"
- javaunicodeescape="true" />
- </target>
-
- <target name="compile" depends="init">
- </target>
-
- <!--
- Utility targets to use the style converters
- -->
- <target name="convert.msstyles">
- <fail unless="msstyle" message="Specify path to msstyle xml -Dmsstyle=pathtoxml"/>
- <fail unless="skin" message="Specify themepack folder -Dskin=pathtothemepackdir"/>
- <java classname="com.l2fprod.tools.msstyles.MsStylesToSkinLF"
- classpath="${classpath.asprop}:${java.src.dir}:${build.classes}"
- fork="yes">
- <arg value="${msstyle}" />
- <arg value="${msstyle}.xml" />
- <arg value="${skin}" />
- </java>
- <copy todir="${skin}">
- <fileset dir="src/themepacks/skeletonthemepack" includes="**"/>
- </copy>
- </target>
-
- <!--
- Start Demos
- -->
- <target name="demo">
- <java classname="examples.demo"
- classpath="${classpath.asprop}:${java.src.dir}:${build.classes}"
- fork="yes">
- <arg value="${skin}" />
- </java>
- </target>
-
- <!-- Dist targets -->
- <target name="jar" depends="compile.java">
- <jar destfile="${build.dir}/${project}.jar">
- <fileset dir="${build.classes}" includes="*.class,com/**/*.class" excludes="**/region/**,**/nativeskin/**"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.properties"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.template"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.gif"/>
- <manifest>
- <attribute name="Built-by" value="${user.name}"/>
- <attribute name="Main-Class" value="com.l2fprod.gui.plaf.skin.Skinit"/>
- <attribute name="Class-Path" value="laf-plugin.jar"/>
- <section name="com/l2fprod/gui/plaf/skin">
- <attribute name="Specification-Title" value="${project.fullname}"/>
- <attribute name="Specification-Version" value="${version}"/>
- <attribute name="Specification-Vendor" value="L2FProd.com"/>
- <attribute name="Implementation-Title" value="${project.fullname}"/>
- <attribute name="Implementation-Version" value="${version}"/>
- <attribute name="Implementation-Vendor" value="L2FProd.com"/>
- </section>
- </manifest>
- </jar>
- </target>
-
- <target name="obfuscate" depends="jar">
- <taskdef name="proguard"
- classname="proguard.ant.ProGuardTask"
- classpath="lib/proguard.jar"/>
- <move file="${build.dir}/${project}.jar"
- tofile="${build.dir}/${project}-toobfuscate.jar"/>
- <proguard
- outjar="${build.dir}/${project}.jar"
- obfuscate="yes"
- usemixedclassnames="no"
- overloadaggressively="yes"
- printmapping="obfuscatemapping.txt"
- printusage="obfuscateusage.txt">
- <libraryjar name="${java.home}/lib/rt.jar"/>
- <injar name="${build.dir}/${project}-toobfuscate.jar"/>
- <keep access="public" type="class" name="Skinit">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.SkinApplet">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.SkinChooser">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.WindowSnapping">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.nativeskin.**">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.CompoundSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.IncorrectVersionException">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.LinuxLookAndFeel">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.Skin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinButton">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinFrame">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.Skinit">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinLookAndFeel">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinPersonality">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinPreviewWindow">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinProgress">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinScrollbar">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSeparator">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSlider">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSplitPane">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinTab">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.*">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.gtk.GtkSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.kde.KdeSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.region.*">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.tools.**">
- <method name="*"/>
- </keep>
- <keep type="class" name="com.l2fprod.util.**">
- <method name="*"/>
- </keep>
- </proguard>
- </target>
-
- <target name="dist.pre" depends="jar">
- <!-- examples.jar -->
- <jar destfile="${build.dist.lib}/examples.jar">
- <fileset dir="${build.classes}" includes="examples/**.class"/>
- <fileset dir="${java.src.dir}" includes="examples/**.properties,examples/**.gif,examples/**.jpg"/>
- </jar>
- <!-- nativeskin.jar -->
- <jar jarfile="${build.dist.lib}/nativeskin.jar">
- <fileset dir="${build.classes}"
- includes="com/l2fprod/gui/region/**,com/l2fprod/gui/nativeskin/**,com/l2fprod/util/OS**,,com/l2fprod/util/Access**"
- excludes="**/*.html"/>
- </jar>
- <!-- batch files -->
- <copy todir="${build.dist.bin}"
- flatten="yes"
- preservelastmodified="yes">
- <fileset dir="src" includes="**/*.bat"/>
- </copy>
- <!-- dlls -->
- <copy todir="${build.dist.lib}">
- <fileset dir="src/native/win32" includes="*.dll"/>
- </copy>
- <!-- default theme -->
- <zip destfile="${build.dist.lib}/themepack.zip">
- <zipfileset dir="src/themepacks/whistlerthemepack"/>
- </zip>
- </target>
-
- <!--
- Publish the new version of SKinLF
- -->
- <target name="publish" depends="init">
- <!-- copy zip to dist folder -->
- <copy todir="${publish.download.dir}"
- file="${project}-${version}-${build.version}.zip"/>
-
- <filter token="WEB" value="${publish.web.url}"/>
- <!-- update the jnlp website with the new release -->
- <!-- put skinlf.jar in jnlp folder -->
- <copy todir="${publish.skinlf.home}/jnlp/" filtering="on" overwrite="yes">
- <fileset dir="src/jnlp" includes="*.jnlp"/>
- </copy>
- <copy file="${build.dist.lib}/${project}.jar" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/examples.jar" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/themepack.zip" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/nativeskin.jar" todir="${publish.skinlf.home}/jnlp"/>
- <jar destfile="${publish.skinlf.home}/jnlp/nativeskinlibs.jar"
- basedir="${build.dist.lib}" includes="*.dll"/>
-
- <!-- copy the documentation
- <copy todir="${web.skinlf.home}/documentation">
- <fileset dir="${javadoc.destdir}"/>
- </copy>
- -->
- <!-- Sign all Jars -->
- <signjar keystore="../common/keystore" alias="L2FProd.com" storepass="L2FProd.com">
- <fileset dir="${publish.skinlf.home}/jnlp" includes="*.jar"/>
- </signjar>
-
- </target>
-
- <target name="themes">
- <zip destfile="${build.www.themedir}/cellshadedthemepack.zip"
- basedir="src/themepacks/cellshadedthemepack"/>
- <zip destfile="${build.www.themedir}/whistlerthemepack.zip"
- basedir="src/themepacks/whistlerthemepack"/>
- <zip destfile="${build.www.themedir}/xplunathemepack.zip"
- basedir="src/themepacks/xplunathemepack"/>
- <zip destfile="${build.www.themedir}/toxicthemepack.zip"
- basedir="src/themepacks/toxicthemepack"/>
- <zip destfile="${build.www.themedir}/beigeazulthemepack.zip"
- basedir="src/themepacks/beigeazulthemepack"/>
-
-
- <!-- png for these themepacks are not in cvs -->
- <zip destfile="${build.www.themedir}/aquathemepack.zip"
- basedir="src/themepacks/aquathemepack"/>
- <zip destfile="${build.www.themedir}/alloythemepack.zip"
- basedir="src/themepacks/alloythemepack"/>
- </target>
-
-</project>
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-common.xml b/dev-java/skinlf/files/skinlf-6.7.10-common.xml
deleted file mode 100644
index c2803acc5..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-common.xml
+++ /dev/null
@@ -1,171 +0,0 @@
-<!--
- Common Target which could be reused by other projects later.
--->
-
-<!-- COMMON PROPERTIES -->
-
- <property name="debug" value="true"/>
- <property name="optimize" value="false"/>
-
- <!-- Java Related -->
- <property name="java.src.dir" value="src"/>
- <property name="javac.compiler" value="modern"/>
-
- <!-- Destination Directory for the build -->
- <property name="build.dir" value="build"/>
- <property name="build.classes" value="${build.dir}/classes"/>
- <property name="build.src" value="${build.dir}/src"/>
- <property name="build.dist.dir" value="${project}-${version}"/>
- <property name="build.dist.src" value="${build.dist.dir}/src"/>
- <property name="build.dist.lib" value="${build.dist.dir}/lib"/>
- <property name="build.dist.bin" value="${build.dist.dir}/bin"/>
- <property name="build.www.dir" value="${build.dir}/www"/>
-
-<!-- COMMON TARGETS -->
-
- <target name="init.properties">
- <tstamp>
- <format property="build.time" pattern="MM/dd/yyyy hh:mm aa" locale="en"/>
- <format property="build.version" pattern="yyyyMMdd" locale="en"/>
- </tstamp>
- <filter token="VERSION" value="${version}"/>
- <filter token="PROJECT.FULLNAME" value="${project.fullname}"/>
- <filter token="DATE" value="${build.time}"/>
- <filter token="YEAR" value="${year}"/>
- </target>
-
- <target name="init.directories">
- <mkdir dir="${build.dir}"/>
- <mkdir dir="${build.classes}"/>
- <mkdir dir="${build.dist.dir}"/>
- <mkdir dir="${build.dist.src}"/>
- <mkdir dir="${build.dist.lib}"/>
- <mkdir dir="${build.dist.bin}"/>
- </target>
-
- <target name="init" depends="init.properties,init.directories">
- </target>
-
- <target name="clean">
- <delete dir="${build.dir}"/>
- <delete dir="${build.dist.dir}"/>
- </target>
-
- <target name="fixcrlf">
- <fixcrlf srcdir="${basedir}" eol="cr">
- <include name="AUTHORS,LICENSE*,README,THANKS" />
- <include name="**/*.java" />
- </fixcrlf>
- </target>
-
-<!-- Java Related Targets -->
-
- <target name="compile.java" depends="init">
- <depend srcdir="${java.src.dir}"
- destdir="${build.classes}"
- cache="${build.dir}/dependcache"
- closure="yes"/>
-
- <copy todir="${build.src}" filtering="yes">
- <fileset dir="${java.src.dir}">
- <include name="**/*.java"/>
- </fileset>
- </copy>
- <javac srcdir="${build.src}"
- destdir="${build.classes}"
- classpathref="classpath"
- compiler="${javac.compiler}"
- includeAntRuntime="false"
- includeJavaRuntime="false"
- debug="${debug}"
- optimize="${optimize}"
- target="1.3" source="1.3">
- </javac>
- </target>
-
-<!-- Distribution Target -->
-
- <target name="dist" depends="jar,dist.pre">
- <!-- project.jar -->
- <copy todir="${build.dist.lib}"
- file="${build.dir}/${project}.jar"
- preservelastmodified="yes"/>
- <!-- source code -->
- <copy todir="${build.dist.src}"
- preservelastmodified="yes">
- <fileset dir="${build.src}" includes="**/*.java"/>
- <fileset dir="${java.src.dir}" includes="**/*.properties"/>
- </copy>
- <!-- regular files -->
- <copy todir="${build.dist.dir}"
- filtering="yes"
- preservelastmodified="yes">
- <fileset dir="${basedir}">
- <include name="AUTHORS"/>
- <include name="INSTALL"/>
- <include name="README"/>
- <include name="THANKS"/>
- <include name="LICENSE"/>
- <include name="LICENSE_*"/>
- </fileset>
- </copy>
- <xslt in="xdocs/CHANGES.xml"
- out="${build.dist.dir}/CHANGES"
- style="xdocs/xsl/text.xsl"/>
- <!-- zip file -->
- <zip destfile="${project}-${version}-${build.version}.zip">
- <zipfileset dir="${build.dist.dir}"
- prefix="${project}-${version}" />
- </zip>
- </target>
-
-<!-- Source code formatting -->
-
- <target name="jalopy" depends="init">
- </target>
-
-<!-- Project Web Documentation -->
-
- <target name="www" depends="init">
- <mkdir dir="${build.www.dir}"/>
- <xslt in="xdocs/www.xml"
- out="${build.www.dir}/empty.html"
- style="xdocs/xsl/tohtml.xsl">
- <param name="output.dir" expression="${build.www.dir}"/>
- <param name="timestamp" expression="${build.time}"/>
- </xslt>
- <copy todir="${build.www.dir}">
- <fileset dir="xdocs">
- <include name="images/**"/>
- <include name="**.java"/>
- </fileset>
- </copy>
- <mkdir dir="${build.www.dir}/javadoc"/>
- <javadoc sourcepath="${java.src.dir}"
- classpath="${classpath}"
- destdir="${build.www.dir}/javadoc"
- packagenames="${javadoc.packagenames}"
- private="false" protected="true"
- windowtitle="${project.fullname} ${version} API"
- doctitle="${project.fullname} ${version}"
- version="false" author="false" use="false"
- stylesheetfile="xdocs/javadoc.css"
- splitindex="true"
- bottom="Copyright &#169; ${year} L2FProd.com. All Rights Reserved."/>
- <delete file="${build.www.dir}/empty.html"/>
- </target>
-
- <target name="www.sync" depends="init">
- <ftp server="${build.www.server}"
- userid="${build.www.userid}"
- password="${build.www.password}"
- remotedir="${build.www.remotedir}"
- action="put"
- verbose="yes"
- depends="yes">
- <fileset dir="${build.www.dir}">
- <include name="**/**"/>
- </fileset>
- </ftp>
- </target>
-
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch b/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch
deleted file mode 100644
index 123335241..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff -ru skinlf-1.2.12-orig/src/com/l2fprod/tools/ImageUtils.java skinlf-1.2.12/src/com/l2fprod/tools/ImageUtils.java
---- a/src/com/l2fprod/tools/ImageUtils.java 2006-01-24 20:09:36.000000000 +0100
-+++ b/src/com/l2fprod/tools/ImageUtils.java 2006-01-24 20:19:19.000000000 +0100
-@@ -6,15 +6,12 @@
-
- import javax.swing.ImageIcon;
-
--import com.ibm.imageconversion.*;
--import com.sun.jimi.core.*;
-+import javax.imageio.*;
-
- public class ImageUtils {
-
- public static Component bitmapCreator = new javax.swing.JLabel();
-
-- static BMPDecoder decoder = new BMPDecoder();
-- static BMPEncoder encoder = new BMPEncoder();
-
- public static Image loadPng(String pathToImage) throws Exception {
- ImageIcon icon = new ImageIcon(new File(pathToImage).toURL());
-@@ -22,29 +19,33 @@
- }
-
- public static void savePng(Image image, String pathToImage) throws Exception {
-- Jimi.putImage(image, pathToImage);
-+ ImageIO.write((RenderedImage)image, "png", new File(pathToImage));
- }
-
-+ private static String getFileFmt(String pathToImage) throws Exception {
-+ String fmt;
-+ if (pathToImage.toLowerCase().endsWith(".png")) {
-+ return "png";
-+ }
-+ if (pathToImage.toLowerCase().endsWith(".gif")) {
-+ return "gif";
-+ }
-+ if (pathToImage.toLowerCase().endsWith(".bmp")) {
-+ return "bmp";
-+ }
-+ return "";
-+ }
-+
- public static void createPicture(String pathToImage, int index, int maxParts,
- String filename, boolean horizontal) {
- try {
- System.out.println("working with " + pathToImage);
- Image image = null;
--
-- if (pathToImage.toLowerCase().endsWith(".png") ||
-- pathToImage.toLowerCase().endsWith(".gif")) {
-- image = loadPng(pathToImage);
-- } else if (pathToImage.toLowerCase().endsWith(".bmp")) {
-- decoder.setInputFilename(pathToImage);
-- decoder.triggerAction();
-- image = decoder.getResult();
-- } else {
-- throw new Error("do not know how to load " + pathToImage);
-- }
-+ image = Toolkit.getDefaultToolkit().getImage(pathToImage);
-
- // if only one image, dump it as it
-- if (index == 0 && maxParts == 1) {
-- Jimi.putImage(image, filename);
-+ if (index == 0 && maxParts == 1) {
-+ ImageIO.write((RenderedImage)image, getFileFmt(pathToImage), new File(pathToImage));
- } else {
- if (horizontal) {
- int partHeight = image.getHeight(bitmapCreator) / maxParts;
-@@ -55,7 +56,7 @@
- image = grab(image, partWidth * index, 0,
- partWidth, image.getHeight(bitmapCreator));
- }
-- Jimi.putImage(image, filename);
-+ ImageIO.write((RenderedImage)image, getFileFmt(pathToImage), new File(pathToImage));
- }
- } catch (Exception e) {
- System.out.println("error while working with " + pathToImage);
diff --git a/dev-java/skinlf/metadata.xml b/dev-java/skinlf/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-java/skinlf/metadata.xml
+++ /dev/null
@@ -1,8 +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>
-</pkgmetadata>
diff --git a/dev-java/skinlf/skinlf-6.7.10.ebuild b/dev-java/skinlf/skinlf-6.7.10.ebuild
deleted file mode 100644
index a63320a6d..000000000
--- a/dev-java/skinlf/skinlf-6.7.10.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Skin Look and Feel - Skinning Engine for the Swing toolkit"
-HOMEPAGE="http://skinlf.l2fprod.com/"
-# Upstream is gone, use this url from ubuntu/debian instead
-SRC_URI="https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/libskinlf-java/$(ver_rs 2 -)/libskinlf-java_$(ver_cut 1-2).orig.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/laf-plugin:0
- dev-java/xalan:0"
-
-RDEPEND=">=virtual/jre-1.4
- ${CDEPEND}"
-
-DEPEND=">=virtual/jdk-1.4
- ${CDEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-image-utils-without-jimi.patch"
-)
-
-S="${WORKDIR}/${PN}-$(ver_cut 1-2)"
-
-src_prepare() {
- default
-
- cp "${FILESDIR}/${P}-build.xml" build.xml || die
- cp "${FILESDIR}/${P}-common.xml" common.xml || die
-
- cd lib || die
-
- java-pkg_jar-from xalan,laf-plugin
-}
-
-src_install() {
- java-pkg_dojar build/${PN}.jar
-
- # laf-plugin.jar is referenced in manifest's Class-Path
- # doesn't work without it due to class loader trickery
- # upstream solved this by absorbing laf-plugin in own jar...
- java-pkg_dojar lib/laf-plugin.jar
-
- use examples && java-pkg_doexamples src/examples
- use source && java-pkg_dosrc src/com src/*.java
-
- dodoc CHANGES README
-}
diff --git a/dev-lang/terra/Manifest b/dev-lang/terra/Manifest
deleted file mode 100644
index 79c86caf5..000000000
--- a/dev-lang/terra/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST terra-1.0.0_beta2.tar.gz 1418736 BLAKE2B 6910e56afd863e2449902b17fa7b368458d75fce8c5f18b1424ed69e3fe563fdb910f682b8e0880d75d1ff2c6c49c54f063c2e226f01d8eb073693fd62f66c4d SHA512 0084cdd9d018f9b175a756587f122650c16af16195eef1271a5748f9bef6fcdcec4046bf9f753977eae5474212a7ba5abb62b2a19d6123170f90015a17df6a3c
diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml
deleted file mode 100644
index 5f4b89aee..000000000
--- a/dev-lang/terra/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>ottxor@gentoo.org</email>
- <name>Christoph Junghans</name>
- </maintainer>
- <upstream>
- <remote-id type="github">zdevito/terra</remote-id>
- </upstream>
- <use>
- <flag name="cuda">Enable CUDA</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-lang/terra/terra-1.0.0_beta2.ebuild b/dev-lang/terra/terra-1.0.0_beta2.ebuild
deleted file mode 100644
index d9b087cf9..000000000
--- a/dev-lang/terra/terra-1.0.0_beta2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV="${PV//_/-}"
-
-LUA_COMPAT=( lua5-{1..4} )
-
-inherit cmake llvm lua-single
-
-DESCRIPTION="A low-level counterpart to Lua"
-HOMEPAGE="http://terralang.org/"
-SRC_URI="https://github.com/zdevito/terra/archive/release-${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="cuda"
-
-REQUIRED_USE="${LUA_REQUIRED_USE}"
-
-DEPEND="${LUA_DEPS}
- cuda? ( dev-util/nvidia-cuda-toolkit )"
-RDEPEND="${DEPEND}"
-BDEPEND="
- sys-devel/clang:*
- sys-devel/llvm:=
- dev-lang/luajit:=
-"
-
-S="${WORKDIR}/${PN}-release-${MY_PV}"
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_PREFIX_PATH="$(get_llvm_prefix)"
- -DTERRA_ENABLE_CUDA="$(usex cuda ON OFF)"
- -DTERRA_STATIC_LINK_LLVM=OFF
- -DTERRA_SLIB_INCLUDE_LLVM=OFF
- -DTERRA_STATIC_LINK_LUAJIT=OFF
- -DTERRA_SLIB_INCLUDE_LUAJIT=OFF
- )
-
- cmake_src_configure
-}
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-libs/optix/Manifest b/dev-libs/optix/Manifest
index 11e08c79f..0a6859644 100644
--- a/dev-libs/optix/Manifest
+++ b/dev-libs/optix/Manifest
@@ -1,4 +1 @@
-DIST NVIDIA-OptiX-SDK-6.0.0-linux64-25650775.sh 642319364 BLAKE2B 5dc6e23d606ca9f947aff046d20592729e562c66c475d47aa0cda8d3e7361cabbe102b5b0e125744d27e25321d4ac8486a55bc145c54c96c719de6e821744ba9 SHA512 33fbb312c47174a9ddb26bd4b1a1e5089b70eaebdecd80561c91c1926fba2fb8c94ec39b4c2dc8f0ccbb5e27bbd38ad8fb08df1d605ed1ec5b3fd34ecca908b7
-DIST NVIDIA-OptiX-SDK-7.0.0-linux64.sh 28930132 BLAKE2B ae09bc862ccd39c25d5cc103d97b5587e21638079905e5811528b3d59deb7fd546034f24f73696c212274c0613f5b1dca7508bff696f5fec535dda7351166d7e SHA512 349baf367af7890afac87a879c8f7360cc9c93e984cf234216062af0a3cedce8fc6f3fd74240897d4b3854622ce1976a78433cbeadf6fa89c8e84d24e26eef89
-DIST NVIDIA-OptiX-SDK-7.1.0-linux64-x86_64.sh 45564234 BLAKE2B 374bdbe5045ff36b71da8200ad29189cc3afba9783a38a74515caafeb90176eec5bf7a7d5e2045e47c399aa226a61fd12e6e7dd6c034b8a0f260a5850f775e47 SHA512 808a45e2007d8081de21fe15cad4577ba9fe10fc3612486b1230e03b7f17de91902dc773d1f3fef2b89398f230448d9522a03e19d4e6fa12aa4ffd78f1a4f9dc
-DIST NVIDIA-OptiX-SDK-7.2.0-linux64-x86_64.sh 44573802 BLAKE2B 546f2f02336d7487e2aab3f348290aaf9bdac153a3fe161b48ad8a897f5d14f6126e06d3b8b4c301f8a6df5735d951dcf544795b2668bc42116bd909e032b18d SHA512 c37f36e2c0d5dbf151a03513e9dc82c21c46f1a88b123153647f44f4305367d1021e522236dda97ab9c641db006242507ae323d668cf2186cf04a83a54b5707f
+DIST NVIDIA-OptiX-SDK-7.4.0-linux64-x86_64.sh 57923655 BLAKE2B c3e159106ec6c8c446090ebd182fd3b0a75ec48b62e6984ae6559578688fd9a6cb29ea6065cb89aecdeb02247acbf3fb3bb0cbf69b10c29c222eb9fcbb0c6d90 SHA512 04f50c49d08c5e4e9be73ee322c4bff4f10a5e30445bc431e213c879a35cc5e36e0ceb8c864313f417628575a3c71593e65467ea13dd111b432fdf1db9383ae0
diff --git a/dev-libs/optix/optix-6.0.0.ebuild b/dev-libs/optix/optix-6.0.0.ebuild
deleted file mode 100644
index d0cb4c078..000000000
--- a/dev-libs/optix/optix-6.0.0.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
-
-inherit cmake cuda
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-25650775.sh"
-
-SLOT="0/6"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="dev-util/nvidia-cuda-toolkit
- virtual/opengl
- media-libs/freeglut"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-CMAKE_USE_DIR=${S}/SDK
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +218 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_prepare() {
- cmake_src_prepare
- rm -rf SDK-precompiled-samples
- export PATH=$(cuda_gccdir):${PATH}
-}
-
-src_install() {
- insinto /opt/${PN}
- doins -r doc include lib64
-}
diff --git a/dev-libs/optix/optix-7.0.0.ebuild b/dev-libs/optix/optix-7.0.0.ebuild
deleted file mode 100644
index c419a9cee..000000000
--- a/dev-libs/optix/optix-7.0.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64.sh"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit
- media-libs/freeglut
- virtual/opengl
-"
-S="${WORKDIR}"
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_install() {
- insinto /opt/${PN}
- dodoc -r doc
- doins -r include SDK
-}
diff --git a/dev-libs/optix/optix-7.1.0.ebuild b/dev-libs/optix/optix-7.1.0.ebuild
deleted file mode 100644
index afeda2b32..000000000
--- a/dev-libs/optix/optix-7.1.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit
- media-libs/freeglut
- virtual/opengl
-"
-S="${WORKDIR}"
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_install() {
- insinto /opt/${PN}
- dodoc -r doc
- doins -r include SDK
-}
diff --git a/dev-libs/optix/optix-7.2.0.ebuild b/dev-libs/optix/optix-7.4.0.ebuild
index 34dcf66c4..a3f61205e 100644
--- a/dev-libs/optix/optix-7.2.0.ebuild
+++ b/dev-libs/optix/optix-7.4.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2021 Gentoo Authors
+# Copyright 2021-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="NVIDIA Ray Tracing Engine"
HOMEPAGE="https://developer.nvidia.com/optix"
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/dev-java/flexdock/metadata.xml b/dev-python/asciitree/metadata.xml
index ae9640ffb..f6f63a810 100644
--- a/dev-java/flexdock/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/asdf/Manifest b/dev-python/asdf/Manifest
index ed535128d..3b2cf6ef8 100644
--- a/dev-python/asdf/Manifest
+++ b/dev-python/asdf/Manifest
@@ -1 +1 @@
-DIST asdf-2.7.1.tar.gz 494491 BLAKE2B 7ff36829626972e85362cb364bdf5ced4745a592c7229b70584ef36722935959a21c6cc11a37ea58c625c1aefdee96d72d5edfef67e5a7975c653f70ed9689c1 SHA512 dc807013d7dbf67c8cb269398d0b7ff56b1c5212d2cfbb768b7844979951c56b9263327cba3a3db32b65ac9de2ede94731823b4d7f120a4306efc203cfc75266
+DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df
diff --git a/dev-python/asdf/asdf-2.7.1.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild
index ddace4966..96663e49a 100644
--- a/dev-python/asdf/asdf-2.7.1.ebuild
+++ b/dev-python/asdf/asdf-2.8.3.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..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -27,8 +27,8 @@ BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]
"
RDEPEND="
+ >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}]
>=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}]
- <dev-python/jsonschema-4[${PYTHON_USEDEP}]
>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
>=dev-python/semantic_version-2.8[${PYTHON_USEDEP}]
@@ -40,5 +40,5 @@ distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-py
python_test() {
# discovers things in docs dir if we do not
# explicitly set it to run on the tests dir
- pytest -vv asdf/tests || die " Tests failed with ${EPYTHON}"
+ epytest asdf/tests
}
diff --git a/dev-python/astropy-healpix/Manifest b/dev-python/astropy-healpix/Manifest
index 50717914d..0845b8ed4 100644
--- a/dev-python/astropy-healpix/Manifest
+++ b/dev-python/astropy-healpix/Manifest
@@ -1 +1 @@
-DIST astropy-healpix-0.5.tar.gz 163123 BLAKE2B f82d7a7eba168353378eea56f9db4c8a3cae0c33fe504745ab53290ab049a7ebf5907b212b5fb35bfa9560ce0d7cba98b2ba81f75085a03bd2eed937fa6ebdda SHA512 8eb43da00b907de7763143153641117d57bd1ccdb50b57d721b5858fc33e5f4c63348134c2eaa044ee5619ae93cb6436d26565d42e9d9df6bfc515b388833576
+DIST astropy_healpix-0.6.tar.gz 104224 BLAKE2B a06474de29f2848d18dedb45202ea63ba5893d6993ef39ebb91e02b55c0f5e100522c267198a233c8771f3920c620f7eddb83f08c82c3cb4151432e1815b00d8 SHA512 c54a41e50c7eaa51126b20abc88e5fc8f7c02521baeb4a69a5a8eac42f59350273e8f30c17926daf628c7866550eec141980ce0349028ff72a4ac2786275f428
diff --git a/dev-python/astropy-healpix/astropy-healpix-0.5.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
index 06462034d..ce6ec0cd3 100644
--- a/dev-python/astropy-healpix/astropy-healpix-0.5.ebuild
+++ b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
@@ -1,15 +1,16 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="HEALPix for Astropy"
HOMEPAGE="https://github.com/astropy/astropy-healpix"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P/-/_}.tar.gz"
+S="${WORKDIR}/${P/-/_}"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
index 51514e535..393066583 100644
--- a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
+++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 xdg-utils
diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
index dae2f430f..844b614bd 100644
--- a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
+++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest
index 0bacc3982..c8278e21a 100644
--- a/dev-python/astropy/Manifest
+++ b/dev-python/astropy/Manifest
@@ -1 +1 @@
-DIST astropy-4.2.tar.gz 7462293 BLAKE2B 47a26cde10e99be3c2ea0e5f2e6fb90afc70a27c53bad63683c0cd6ca7a97ff45542d68c8326bbfcae23135594b1a2533eccdb54aec1e62ddc0ff11cb78aa263 SHA512 14bb90aac13f3fe668114ebe578aac401987e8e2cd2bb9fb0971e5b8e9f8df6a594d454bb53e330807c3854c44d295e2b4dc96b57ccb69e5f53ee11356869d9d
+DIST astropy-5.0.tar.gz 7823746 BLAKE2B e769f9ea26e156a2342dc75b307c16c2c38108adf0dfd931812b2eb3234941055c013378a492306f2247c16b4804fe569ba1cbfd8427df1aac2b808976082cf9 SHA512 3c0b0cdef434f27ee399fbfc3d55b95ce8395624caf8e73a205dba7742c39d8a2bcea9bf61c2c20235da7388d40c657c5474bfc7e3dc3c9e5911e39bab47cdb9
diff --git a/dev-python/astropy/astropy-4.2.ebuild b/dev-python/astropy/astropy-5.0.ebuild
index 9b17173a4..c650533d6 100644
--- a/dev-python/astropy/astropy-4.2.ebuild
+++ b/dev-python/astropy/astropy-5.0.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,7 +16,6 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
#TODO: Package all these pytest deps:
-# pytest-doctestplus>=0.2.0
# pytest-remotedata>=0.3.1
# pytest-openfiles>=0.3.1
# pytest-astropy-header>=0.1.2
@@ -26,8 +25,10 @@ RESTRICT="test"
RDEPEND="
dev-libs/expat:0=
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pyerfa[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+ >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}]
+ >=dev-python/packaging-19.0[${PYTHON_USEDEP}]
sci-astronomy/wcslib:0=
>=sci-libs/cfitsio-3.350:0=
sys-libs/zlib:0=
diff --git a/dev-python/astroscrappy/Manifest b/dev-python/astroscrappy/Manifest
index a4c5a9984..e18b6655d 100644
--- a/dev-python/astroscrappy/Manifest
+++ b/dev-python/astroscrappy/Manifest
@@ -1 +1 @@
-DIST astroscrappy-1.0.8.tar.gz 449193 BLAKE2B 0c4fda8055c5e50ff2fcc0adab17eb118b62f843cf5ca8c5d4c10bc7970efbfffd48a6c262a9bbc7bcda0c9e95237d3c3fe7121f56a7edfe26235ac351336466 SHA512 876ceb9596478930ebc9287657dcc6ff922a45daf56aa201255116247ca1a5029915292c189a5c740aed70093b050522c69186149ef721eda1669f7b5b3bd404
+DIST astroscrappy-1.1.0.tar.gz 368489 BLAKE2B d39caedd8a6b4346959c8af8546fee5fc69d41348f1743911af4c6d5755d5e8b6cdf603907d0962807d65a584422eb8c7355ada1b95c11221c735a1c94a24c5a SHA512 f6e8f7aa2eb930c5def05d33f8eb0788b15f53dda0cd583daae262e02d49b4d57e56b46562583aebf25c5e38295a62caf464b797f78deaf07962ebfca8862f8b
diff --git a/dev-python/astroscrappy/astroscrappy-1.0.8.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
index d71e7d1ac..f4ef741da 100644
--- a/dev-python/astroscrappy/astroscrappy-1.0.8.ebuild
+++ b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -24,6 +24,7 @@ RDEPEND="
>=dev-python/astropy-2.0[${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/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
index 714cb7123..8119b0206 100644
--- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild
+++ b/dev-python/extension-helpers/extension-helpers-0.1.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
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"
- "${FILESDIR}/fslpy-3-remove_dataclasses_req.patch"
-)
-
-distutils_enable_tests pytest
-
-python_test() {
- virtx pytest --niters=50 -m "not (dicomtest or longtest or fsltest)" --verbose || die
-}
diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.8.1.ebuild
index 092f36094..f28e7283e 100644
--- a/dev-python/fslpy/fslpy-3.8.1.ebuild
+++ b/dev-python/fslpy/fslpy-3.8.1.ebuild
@@ -3,13 +3,13 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 virtualx
DESCRIPTION="The FSL Python Library"
HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
-SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -34,6 +34,10 @@ PATCHES=(
distutils_enable_tests pytest
distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+src_test() {
+ virtx distutils-r1_src_test
+}
+
python_test() {
- virtx epytest --niters=50 -m "not (dicomtest or longtest or fsltest)"
+ epytest --niters=50 -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
}
diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.10.2.ebuild
index 6dde1c23f..e63aaa1bc 100644
--- a/dev-python/geopandas/geopandas-0.10.2.ebuild
+++ b/dev-python/geopandas/geopandas-0.10.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/pandas[${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/pyerfa/Manifest b/dev-python/pyerfa/Manifest
index 1f49a4621..29344f9fb 100644
--- a/dev-python/pyerfa/Manifest
+++ b/dev-python/pyerfa/Manifest
@@ -1 +1 @@
-DIST pyerfa-1.7.1.1.tar.gz 1322843 BLAKE2B 416c357faeb5316a692a214039e0e2792088fc93b26b6a006fc63b6b2fd9443c3399972ab8d12066b19640c8b97b5fdd24f3bd158a92dbf1224bf4a8f1eeb12b SHA512 59c2dceed6ef5b1ece618742dd0084b729cce8eb52f903dff2aad009fa0f495defb4511688da0a5203ed5900d041a552fbe50668ddac0c3a6bb3fd6d34d089bb
+DIST pyerfa-2.0.0.1.tar.gz 808497 BLAKE2B b9c6973330236f4a983fdbb6b0f3faefc3fd8ec8a2187b5cd37d3d4a97ab9aa7da4008c1d77f9b2465282b164cdf338f41e816344f5ba15af3fda48ccb71d3b8 SHA512 420e7bb2d00a9bd7d2290b6b0598b5963404ac021f713ae7bbf607135b9db6605f63dd89694d2cf406eb230b58b1028f2458f96ed834127ce9a398810cfea589
diff --git a/dev-python/pyerfa/pyerfa-1.7.1.1.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
index d8c73e666..2e5bdf3e0 100644
--- a/dev-python/pyerfa/pyerfa-1.7.1.1.ebuild
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,11 +16,11 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
# ImportError: cannot import name 'ufunc' from 'erfa'
-RESTRICT="test"
+#RESTRICT="test"
RDEPEND="
sci-astronomy/erfa:0=
- dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
"
BDEPEND="${RDEPEND}
dev-python/setuptools_scm[${PYTHON_USEDEP}]
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/pysolar/pysolar-0.8.ebuild b/dev-python/pysolar/pysolar-0.8.ebuild
index 88f0505ef..65027edb9 100644
--- a/dev-python/pysolar/pysolar-0.8.ebuild
+++ b/dev-python/pysolar/pysolar-0.8.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 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..10} )
AUTHOR=pingswept
@@ -23,6 +23,8 @@ RDEPEND="
dev-python/scipy[${PYTHON_USEDEP}]
"
+distutils_enable_tests nose
+
python_prepare_all() {
sed \
-e "s:'testsolar', ::" \
diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest
index 4f66e9882..4a1e50d88 100644
--- a/dev-python/pytest-doctestplus/Manifest
+++ b/dev-python/pytest-doctestplus/Manifest
@@ -1 +1 @@
-DIST pytest-doctestplus-0.8.0.tar.gz 27489 BLAKE2B 1377eeadc1c0558c0f0f497aec775f04fc111b7815468c87a48e1abedbb66f648128b10ba050a798232cc63cba1c79e794c4653e51f8ee5a27029a6ed10fb5a6 SHA512 108f6bf2d5d663bfc9c6c50e63633814baf248062b6e2d83ca6e83d1d8db9940251ebbb60cd57b04e8ede20b9511f4c86e4ac618618cb42ccaa68c6c38989f2e
+DIST pytest-doctestplus-0.11.2.tar.gz 34943 BLAKE2B a45779ff3d65e1b920282f400d67b618f620a9a905da69edff96db799f30e1b93562e69bd567a49629194b962a080b1f675619b0c6995227a1391c3d0e74be20 SHA512 fed49a551be78f51db60161ccfa592e461719cca76e2a48e3267e8a22dbec60d02d8fbb757a88cb5cf4dc22143e27d3d20f25b51855be835254c72fd8260abbd
diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
index 05b962262..17b19cbb0 100644
--- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild
+++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
# TODO: fix this
+# AttributeError: type object 'reprec' has no attribute 'assertoutcome'
RESTRICT="test"
RDEPEND="dev-python/pytest[${PYTHON_USEDEP}]"
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/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest
index fc19e0aa8..26a909677 100644
--- a/dev-python/sphinx-astropy/Manifest
+++ b/dev-python/sphinx-astropy/Manifest
@@ -1 +1 @@
-DIST sphinx-astropy-1.3.tar.gz 15797 BLAKE2B 737d7a4ae2f7ec6fb382cc8d6fa3de911d13000045e9691f21360b3938e4bebb9b4b70a804deb8bd4343f1bba8e297d8f39fd8ed7787946ba0cb859a4208c980 SHA512 c39df1df90d82e8f67546623fe334ca7d706020f1e00923fcfc41232289aff41d1e697f99ee9b6d43f35f31ef9566be4d9aa99404ee35e1ea85da4b8e30f2ae6
+DIST sphinx-astropy-1.7.0.tar.gz 18266 BLAKE2B 363733c5a3e5974cdf0f62f879babc9a28617ff61d15292649acd189798e24611c2d84e69af5dc05b89241f395cc997233f966bdf8e8a84ccfe235f873d533c2 SHA512 4b9af1528805c5017695be6ad9d0b789437da4ea01080190d5c0e44a76d927098864002cfd2a59529924a8d2844e26d2e7635fb3f0417ed90502e7e47d0239d3
diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
index 4fc2ef799..be4395414 100644
--- a/dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild
+++ b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -19,9 +19,10 @@ KEYWORDS="~amd64 ~x86"
RESTRICT="test"
RDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}]
dev-python/numpydoc[${PYTHON_USEDEP}]
- dev-python/sphinx[${PYTHON_USEDEP}]
+ >=dev-python/sphinx-1.7[${PYTHON_USEDEP}]
dev-python/sphinx-automodapi[${PYTHON_USEDEP}]
dev-python/sphinx-gallery[${PYTHON_USEDEP}]
dev-python/pillow[${PYTHON_USEDEP}]
diff --git a/dev-python/sphinx-automodapi/Manifest b/dev-python/sphinx-automodapi/Manifest
index 8856f8a59..31e6f3c8b 100644
--- a/dev-python/sphinx-automodapi/Manifest
+++ b/dev-python/sphinx-automodapi/Manifest
@@ -1 +1 @@
-DIST sphinx-automodapi-0.13.tar.gz 38240 BLAKE2B 51eaaebab92881563e0e9df03e2979dbf0d22bf61bd8a7c56198cfbbcf97a17447019296dcee25f3a5dce091efb0c8e0748fb83dd47e93976aa1b01e165cbce7 SHA512 394b45ddeb923248250989271e400586188df973c8b13d551345cd056322de1208a8d7a135c095b2daa7b5b491b77a4077bba2dc450ef718ea5dbe07f7f63d36
+DIST sphinx-automodapi-0.14.1.tar.gz 45504 BLAKE2B 1d6aa247c9991260c0d6421dbeb80adccec72f60e6e0035ef892d6582e62608dd526a77da6c4b5066c9c100228fd6aceb77a9965eab76c0b9117a96d76ee221a SHA512 fae2927f8f9ec29f5e8e945b2902a0fa94231446b514be884ddab1a8644b4e305408e986b74a4506447baf00c4941cf9e7585f0c8e82820935a3d831bcfa6374
diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
index 5c93e04fe..f98b972ae 100644
--- a/dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild
+++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.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_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -15,7 +15,7 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-# TODO: fix this
+# Requires network for some reason
RESTRICT="test"
RDEPEND="dev-python/sphinx[${PYTHON_USEDEP}]"
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/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild
index 80704b0c3..05eb0e162 100644
--- a/dev-python/visvis/visvis-1.13.0.ebuild
+++ b/dev-python/visvis/visvis-1.13.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_SETUPTOOLS=no
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
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-util/bcm/Manifest b/dev-util/bcm/Manifest
deleted file mode 100644
index 77dcd235c..000000000
--- a/dev-util/bcm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bcm-0.0.1_p20191110.tar.gz 28708 BLAKE2B 0c97f93607cb947ede7278f91cf64ddeb9ee06fafc19b8cf8df87ea1bcc49a47cba5276bea43cec3cc5fce390d463108561ba978a9ca5bd80a41a5f0ec114c6a SHA512 ce829791752eb7a2d1aa192173532c80a1d0bfc5ab451fdaf09ec926678653d38a4c6aa19c0fdf6c8aa921ce358bb87f367317c2cc54479c845c5741232b220d
diff --git a/dev-util/bcm/bcm-0.0.1_p20191110.ebuild b/dev-util/bcm/bcm-0.0.1_p20191110.ebuild
deleted file mode 100644
index 64611d6e9..000000000
--- a/dev-util/bcm/bcm-0.0.1_p20191110.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Boost cmake modules"
-HOMEPAGE="http://bcm.readthedocs.io"
-
-COMMIT="2045990a6ace40eb4c4a9f6e5cc1aeeaf7a05fc9"
-SRC_URI="https://github.com/simoncblyth/bcm/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${PN}-${COMMIT}
-
-KEYWORDS="~amd64"
-LICENSE="Boost-1.0"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}"/bcm-0.0.1_donot-send-error.patch )
diff --git a/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch b/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch
deleted file mode 100644
index 17c1c51ea..000000000
--- a/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: bcm-0.0.1_p20191110/share/bcm/cmake/BCMExport.cmake
-===================================================================
---- bcm-0.0.1_p20191110.orig/share/bcm/cmake/BCMExport.cmake
-+++ bcm-0.0.1_p20191110/share/bcm/cmake/BCMExport.cmake
-@@ -12,7 +12,7 @@ function(bcm_get_target_package_source O
- if(TARGET_IMPORTED OR TARGET_ALIAS)
- get_property(TARGET_FIND_PACKAGE_NAME TARGET ${TARGET} PROPERTY INTERFACE_FIND_PACKAGE_NAME)
- if(NOT TARGET_FIND_PACKAGE_NAME)
-- message(SEND_ERROR "The target ${TARGET_FIND_PACKAGE_NAME} does not have information about find_package() call.")
-+ message(AUTHOR_WARNING "The target ${TARGET_FIND_PACKAGE_NAME} does not have information about find_package() call.")
- endif()
- set(PKG_NAME ${TARGET_FIND_PACKAGE_NAME})
- get_property(TARGET_FIND_PACKAGE_VERSION TARGET ${TARGET} PROPERTY INTERFACE_FIND_PACKAGE_VERSION)
diff --git a/dev-util/bcm/metadata.xml b/dev-util/bcm/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/dev-util/bcm/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </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/CeCILL-2.1 b/licenses/CeCILL-2.1
deleted file mode 100644
index b705f37a2..000000000
--- a/licenses/CeCILL-2.1
+++ /dev/null
@@ -1,519 +0,0 @@
-
- CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-Version 2.1 dated 2013-06-21
-
-
- Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to users,
- * secondly, the election of a governing law, French law, with which it
- is conformant, both as regards the law of torts and intellectual
- property law, and the protection that it offers to both authors and
- holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are:
-
-Commissariat Ó l'Únergie atomique et aux Únergies alternatives - CEA, a
-public scientific, technical and industrial research establishment,
-having its principal place of business at 25 rue Leblanc, immeuble Le
-Ponant D, 75015 Paris, France.
-
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-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-Inria, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
- Preamble
-
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-the right to modify and redistribute the software governed by this
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-
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-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
- Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
- Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5 <#scope>).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 <#good-faith> and, in particular,
-without any warranty as to its commercial value, its secured, safe,
-innovative or relevant nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-expertise for its defense. Such technical and legal expertise shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
- Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
- Article 11 - MISCELLANEOUS
-
-
- 11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
- 11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
- Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4
-<#compatibility>.
-
-
- Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
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/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild b/media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild
deleted file mode 100644
index 00eece82f..000000000
--- a/media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild
+++ /dev/null
@@ -1,29 +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="A sample Dual Contouring implementation"
-HOMEPAGE="https://github.com/simoncblyth/DualContouringSample"
-
-EGIT_REPO_URI="https://github.com/simoncblyth/${PN}.git"
-EGIT_COMMIT="d5ed08c21228575f948292422cd8542cbdce255c"
-KEYWORDS="~amd64"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND="dev-util/bcm
- media-libs/glm"
-
-PATCHES=( "${FILESDIR}"/DualContouringSample-0_glm.patch )
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/${PN}
- )
-
- cmake_src_configure
-}
diff --git a/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch b/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch
deleted file mode 100644
index efa40b66e..000000000
--- a/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Index: DualContouringSample-0_p20191111/CMakeLists.txt
-===================================================================
---- DualContouringSample-0_p20191111.orig/CMakeLists.txt
-+++ DualContouringSample-0_p20191111/CMakeLists.txt
-@@ -3,18 +3,11 @@ set(name DualContouringSample)
- project(${name} VERSION 0.1.0)
-
- include(CTest)
--include(OpticksBuildOptions)
--
--include(GNUInstallDirs)
--set(CMAKE_INSTALL_INCLUDEDIR "externals/include/${name}")
--set(CMAKE_INSTALL_LIBDIR "externals/lib")
--set(CMAKE_INSTALL_BINDIR "lib")
--#set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
-
- find_package(BCM REQUIRED)
- include(BCMDeploy)
-
--find_package(GLM REQUIRED)
-+find_package(glm REQUIRED)
-
-
- set(SOURCES
-@@ -37,7 +30,7 @@ set(HEADERS
- )
-
- add_library(${name} SHARED ${SOURCES})
--target_link_libraries(${name} PUBLIC Opticks::GLM)
-+target_link_libraries(${name} PUBLIC glm)
-
- # needed for tests that use non-installed headers
- target_include_directories(${name} PUBLIC
diff --git a/media-libs/DualContouringSample/metadata.xml b/media-libs/DualContouringSample/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/DualContouringSample/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
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/media-libs/imgui/Manifest b/media-libs/imgui/Manifest
deleted file mode 100644
index 27a17860f..000000000
--- a/media-libs/imgui/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST imgui-1.80.tar.gz 1391496 BLAKE2B 34c66bc79396adef4f4ea32255be6a7572106a43eec14f9b3b02d3457924e25be6468580766132ef0876cb69cab7fd3e0289db7bff269bad258b945e41ab324e SHA512 760ba1e434d477677919766893681ff4f3c258f84875f5f9a8ba24f0a60f3dd2a386bc7d082aaf701639c6388eeb31ef571f6a61777f20fb6bb0e6d96ba32777
diff --git a/media-libs/imgui/files/imgui-1.48-pkgconfig.patch b/media-libs/imgui/files/imgui-1.48-pkgconfig.patch
deleted file mode 100644
index 14744138e..000000000
--- a/media-libs/imgui/files/imgui-1.48-pkgconfig.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-Index: imgui-1.73/CMakeLists.txt
-===================================================================
---- imgui-1.73.orig/CMakeLists.txt
-+++ imgui-1.73/CMakeLists.txt
-@@ -7,24 +7,18 @@ but has now been moved into my ImGui for
-
- set(name ImGui)
- project(${name} VERSION 0.1.0)
--include(OpticksBuildOptions)
-+include(FindPkgConfig)
-+pkg_check_modules(OpticksGLEW REQUIRED glew)
-+message(STATUS "ImGui.OpticksGLEW_INCLUDE_DIRS : ${OpticksGLEW_INCLUDE_DIRS}")
-+message(STATUS "ImGui.OpticksGLEW_LIBRARIES : ${OpticksGLEW_LIBRARIES}")
-
--set(OpticksGLEW_VERBOSE ON)
--find_package(OpticksGLEW REQUIRED MODULE)
--message(STATUS "ImGui.OpticksGLEW_INCLUDE_DIR : ${OpticksGLEW_INCLUDE_DIR}")
--message(STATUS "ImGui.OpticksGLEW_LIBRARY : ${OpticksGLEW_LIBRARY}")
-+find_package(glfw3 REQUIRED Config)
-
--find_package(OpticksGLFW REQUIRED MODULE)
--message(STATUS "ImGui.OpticksGLFW_INCLUDE_DIR : ${OpticksGLFW_INCLUDE_DIR}")
--message(STATUS "ImGui.OpticksGLFW_LIBRARY : ${OpticksGLFW_LIBRARY}")
--
--
--set(IMGUI_DEFINITIONS
--)
-+set(IMGUI_DEFINITIONS)
-
- set(LIBRARIES
-- ${OpticksGLEW_LIBRARY}
-- ${OpticksGLFW_LIBRARY}
-+ ${OpticksGLEW_LIBRARIES}
-+ glfw
- )
-
- if(APPLE)
-@@ -92,13 +86,13 @@ set(INCLUDE_DIRS
- ${CMAKE_CURRENT_BINARY_DIR}
-
- ${ImGui_SOURCE_DIR}/examples/opengl3_example
-- ${OpticksGLEW_INCLUDE_DIR}
-- ${OpticksGLFW_INCLUDE_DIR}
-+ ${OpticksGLEW_INCLUDE_DIRS}
-+ ${GLFW_INCLUDE_DIR}
- )
-
- set(DEFINITIONS
- ${OpticksGLEW_DEFINITIONS}
-- ${OpticksGLFW_DEFINITIONS}
-+ ${GLFW_DEFINITIONS}
- ${IMGUI_DEFINITIONS}
- )
-
-@@ -139,8 +133,8 @@ endif(WIN32)
-
- target_link_libraries(${name} ${LIBRARIES})
-
--install(TARGETS ${name} DESTINATION externals/lib)
--install(FILES ${HEADERS} DESTINATION externals/include/${name})
-+install(TARGETS ${name} DESTINATION ${LIBDIR})
-+install(FILES ${HEADERS} DESTINATION include/${name})
-
-
- #[=[
diff --git a/media-libs/imgui/imgui-1.80.ebuild b/media-libs/imgui/imgui-1.80.ebuild
deleted file mode 100644
index 239f915ed..000000000
--- a/media-libs/imgui/imgui-1.80.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Bloat-free graphical user interface library for C++"
-HOMEPAGE="https://github.com/simoncblyth/imgui"
-SRC_URI="https://github.com/ocornut/imgui/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="media-libs/glew:0"
-DEPEND="${RDEPEND}"
-
-src_install() {
- insinto "/usr/include/${PN}"
- doins *.h
- insinto "/usr/include/${PN}/backend"
- doins backends/*.h
-}
diff --git a/media-libs/imgui/metadata.xml b/media-libs/imgui/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/imgui/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/implicitmesher/Manifest b/media-libs/implicitmesher/Manifest
deleted file mode 100644
index 2feca3fdf..000000000
--- a/media-libs/implicitmesher/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST implicitmesher-0_p20200413.tar.gz 23224 BLAKE2B fd7d10406f56c88a42821b5aa9848d228317147e4a7d8283b13719ebd9a6e57fecc5b4fb140c1ae23da16e45f90332d9953d5daa1be80ec633c7c011342f00f5 SHA512 5641a44d8a02ef3868d23e92afb053556e775f5beeb5d618dabf7d3e3f19a0a597693134524be2d92387481306af89d8be54c1677fa61fa111dae72ed25b3ea4
diff --git a/media-libs/implicitmesher/files/implicitmesher-0_glm.patch b/media-libs/implicitmesher/files/implicitmesher-0_glm.patch
deleted file mode 100644
index 2f1841f4d..000000000
--- a/media-libs/implicitmesher/files/implicitmesher-0_glm.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index d1a0cf3..f9013cb 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,7 +1,6 @@
- cmake_minimum_required (VERSION 3.5)
- set(name ImplicitMesher)
- project(${name} VERSION 0.1.0)
--include(OpticksBuildOptions)
-
- #[=[
- Hmm OpticksBuildOptions sets CMAKE_INSTALL_INCLUDEDIR to "include/${name}"
-@@ -14,7 +13,7 @@ set(CMAKE_INSTALL_LIBDIR "externals/lib")
- set(CMAKE_INSTALL_BINDIR "lib")
-
-
--find_package(GLM REQUIRED)
-+find_package(glm REQUIRED)
-
- set(SOURCES
-
-@@ -44,7 +43,7 @@ set(HEADERS
- )
-
- add_library(${name} SHARED ${SOURCES})
--target_link_libraries(${name} PUBLIC Opticks::GLM)
-+target_link_libraries(${name} PUBLIC glm)
-
- if(UNIX AND NOT APPLE)
- message(STATUS "adding stdc++ m for UNIX AND NOT APPLE")
-@@ -74,7 +73,6 @@ if(PC_VERBOSE)
- endif()
-
-
--bcm_deploy(TARGETS ${name} NAMESPACE Opticks:: SKIP_HEADER_INSTALL)
- install(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
-
- add_subdirectory(tests)
diff --git a/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild b/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild
deleted file mode 100644
index e6fae861d..000000000
--- a/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-COMMIT="4b7a47056074"
-
-DESCRIPTION="Real-time implicit surface polygonization"
-HOMEPAGE="https://bitbucket.org/simoncblyth/implicitmesher"
-SRC_URI="https://bitbucket.org/simoncblyth/implicitmesher/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="media-libs/glm"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/simoncblyth-${PN}-${COMMIT}"
-
-PATCHES=( "${FILESDIR}"/implicitmesher-0_glm.patch )
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/ImplicitMesher
- )
-
- cmake_src_configure
-}
diff --git a/media-libs/implicitmesher/metadata.xml b/media-libs/implicitmesher/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/implicitmesher/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/yocto-gl/Manifest b/media-libs/yocto-gl/Manifest
deleted file mode 100644
index e1a26da8c..000000000
--- a/media-libs/yocto-gl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST yocto-gl-3.3.0.tar.gz 196860271 BLAKE2B a2b563a16d9b07a1e92fe5f05de56d1cc21abe2dd05b2d72700feba020989c60aa676072e70ebb83cd6cba0ea8dba521d6c8ee2d894a012a070773a715315171 SHA512 f6b824fe1b546a29a093ab7932fb2c5ca4e194813dfcc45e22f0f1532bf0693ef92ebe95eeeba6f02f8a46368925cea2275189ab2c4d022620e8ac4d8d2f4648
diff --git a/media-libs/yocto-gl/metadata.xml b/media-libs/yocto-gl/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/yocto-gl/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/yocto-gl/yocto-gl-3.3.0.ebuild b/media-libs/yocto-gl/yocto-gl-3.3.0.ebuild
deleted file mode 100644
index e6102dde1..000000000
--- a/media-libs/yocto-gl/yocto-gl-3.3.0.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
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DOCS_BUILDER="mkdocs"
-DOCS_DEPEND="dev-python/mkdocs-material"
-
-inherit cmake python-any-r1 docs
-
-DESCRIPTION="Single File Libraries for Physically-Based Graphics"
-HOMEPAGE="https://github.com/simoncblyth/yocto-gl"
-SRC_URI="https://github.com/xelatihy/yocto-gl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="dev-util/bcm"
-
-src_prepare() {
- sed -i -e 's/isnan/std::isnan/g' libs/yocto/yocto_mesh.cpp || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/YoctoGL
- )
-
- cmake_src_configure
-}
-
-src_compile() {
- docs_compile
- cmake_src_compile
-}
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index 5279c82e0..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-2.9.1.5500.tar.xz 5787048 BLAKE2B 6f7df0c1ca13e6074bbd75caaee838ddb822f9284a4f5cc95e1b2c1432adf2969e2413607bebc1542d4bc7790bd6e61edfba758d2205a23fbede6873b7e22316 SHA512 5c78cd0318b7cd35f32721cf364d6e807d32eb1f3651e7f22ff3f3c7737967193ad089062965b3dcee24c23c14cc0d7acdfc95094f4f90f8aaf718f45f22e18a
-DIST ownCloud-2.9.2.6206.tar.xz 5759996 BLAKE2B c328ea261a4fddecf93837dbcac01aab0971542d8dfb3f5b0a32a8432ca0e0904c3f4fc81c5c7811da8b3af64b58e929c055e7cec0649f00049e037372948eec SHA512 d075a11ee92aa9771c631a766feddfa1a70907d7d341b58043e1ba96ac52786a6a750b15c2f9b7a0992fe02a45586cc3445755dc9df4cd267e72f070d2222f0f
+DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2
+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-2.10.0.6519.ebuild
index 27080cd72..c4eeaa7be 100644
--- a/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.10.0.6519.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=$(usex test)
diff --git a/net-misc/cernbox-client/cernbox-client-2.9.1.5500.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
index d6961f8c5..c4eeaa7be 100644
--- a/net-misc/cernbox-client/cernbox-client-2.9.1.5500.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake rpm xdg
@@ -73,7 +73,6 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
- -DSYSCONF_INSTALL_DIR="${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 a1c408aaf..b338c8d20 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,63 +30,8 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Dec 2021)
-# cuda-10 is being removed from ::gentoo, mask revdeps in ::sci
-# for removal too. Removal in 90 days
-sci-physics/opticks
-sci-chemistry/MotionCor2
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
-# Last-rite scilab in favour of scilab-bin. Scilab's java dependencies make
-# a from-source ebuild very difficult since portage doesn't support gradle or
-# maven. In addition it requires old versions of libraries that have already
-# been removed.
-# Removal in 30 days
-sci-mathematics/scilab
->dev-java/lucene-4
-dev-java/flexdock
-dev-java/gluegen
-dev-java/jogl
-dev-java/jlatexmath
-dev-java/jlatexmath-fop
-dev-java/jfreechart
-dev-java/jfreesvg
-dev-java/jgraphx
-dev-java/jcommon
-dev-java/skinlf
-dev-java/jrosetta
-dev-java/freehep-graphicsio-emf
-# and also mask this which hasn't seen an upstream release since 2007!
-sci-biology/conrad
-# depends on dev-java/args4j which is being last-rited from ::gentoo
-sci-libs/jhdf5
-# ancient java, can't update due to gradle/maven limitation
-dev-java/htsjdk
-sci-biology/cramtools
-sci-biology/pilon-bin
-sci-misc/opennlp-maxent
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (13 Jan 2022)
-# Broken, no consumers
-# Removal in 30 days
-dev-lang/terra
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
-# Removal in 30 days, use jupyterlab-desktop instead.
-sci-misc/europa-bin
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (14 Jan 2022)
-# Does not compile, no upstream activity since 2016
-# https://github.com/gmarcais/Quorum/issues/2
-# https://github.com/gmarcais/Quorum/issues/1
-# Removal in 30 days
-sci-biology/quorum
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (15 Jan 2022)
-# No updates since 2009(!), no longer compiles
-# Removal in 30 days
-sci-biology/jigsaw
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org (21 Jan 2022)
-# Requires dev-java/nanoxml which is masked for removal in ::gentoo
-sci-biology/jtreeview
+# 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) sparse