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-rw-r--r--README.md1
-rw-r--r--app-arch/libdeflate/Manifest1
-rw-r--r--app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch54
-rw-r--r--app-arch/libdeflate/libdeflate-1.2.ebuild27
-rw-r--r--app-arch/libdeflate/metadata.xml5
-rw-r--r--dev-cpp/Fastor/metadata.xml3
-rw-r--r--dev-cpp/castxml/Manifest2
-rw-r--r--dev-cpp/castxml/castxml-0.3.6.ebuild35
-rw-r--r--dev-cpp/castxml/castxml-0.4.3.ebuild35
-rw-r--r--dev-cpp/castxml/castxml-9999.ebuild33
-rw-r--r--dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch12
-rw-r--r--dev-cpp/highwayhash/metadata.xml3
-rw-r--r--dev-cpp/xor_singleheader/metadata.xml3
-rw-r--r--dev-lang/icc/Manifest3
-rw-r--r--dev-lang/icc/icc-18.0.2.199-r1.ebuild41
-rw-r--r--dev-lang/icc/icc-19.0.4.243.ebuild40
-rw-r--r--dev-lang/icc/icc-19.1.1.217.ebuild41
-rw-r--r--dev-lang/icc/metadata.xml16
-rw-r--r--dev-lang/ifc/Manifest3
-rw-r--r--dev-lang/ifc/ifc-18.0.2.199-r1.ebuild40
-rw-r--r--dev-lang/ifc/ifc-19.0.4.243.ebuild39
-rw-r--r--dev-lang/ifc/ifc-19.1.1.217.ebuild43
-rw-r--r--dev-lang/ifc/metadata.xml17
-rw-r--r--dev-lang/vtune/Manifest3
-rw-r--r--dev-lang/vtune/metadata.xml15
-rw-r--r--dev-lang/vtune/vtune-18.0.2.0.551022.ebuild49
-rw-r--r--dev-lang/vtune/vtune-19.0.4.0.597835.ebuild48
-rw-r--r--dev-lang/vtune/vtune-2020.1.0.607630.ebuild52
-rw-r--r--dev-lang/yaggo/metadata.xml3
-rw-r--r--dev-libs/intel-common/Manifest4
-rw-r--r--dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild95
-rw-r--r--dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild101
-rw-r--r--dev-libs/intel-common/intel-common-19.0.4.243.ebuild101
-rw-r--r--dev-libs/intel-common/intel-common-19.1.1.217.ebuild102
-rw-r--r--dev-libs/intel-common/metadata.xml15
-rw-r--r--dev-libs/oneCCL/Manifest1
-rw-r--r--dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch102
-rw-r--r--dev-libs/oneCCL/metadata.xml (renamed from dev-libs/optix/metadata.xml)9
-rw-r--r--dev-libs/oneCCL/oneCCL-2021.7.1.ebuild54
-rw-r--r--dev-libs/optix/Manifest1
-rw-r--r--dev-libs/optix/optix-7.4.0.ebuild37
-rw-r--r--dev-libs/simclist/metadata.xml3
-rw-r--r--dev-libs/tut/metadata.xml5
-rw-r--r--dev-ml/lacaml/metadata.xml1
-rw-r--r--dev-python/asciitree/asciitree-0.3.3.ebuild2
-rw-r--r--dev-python/asciitree/metadata.xml5
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild2
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild2
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild2
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20210804.ebuild2
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild2
-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/fiat/metadata.xml1
-rw-r--r--dev-python/fslpy/Manifest2
-rw-r--r--dev-python/fslpy/fslpy-3.10.0.ebuild (renamed from dev-python/fslpy/fslpy-3.8.1.ebuild)16
-rw-r--r--dev-python/hopcroftkarp/metadata.xml19
-rw-r--r--dev-python/json_tricks/metadata.xml2
-rw-r--r--dev-python/keyrings_alt/Manifest1
-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.ebuild31
-rw-r--r--dev-python/keyrings_alt/metadata.xml24
-rw-r--r--dev-python/kmapper/metadata.xml3
-rw-r--r--dev-python/latexify_py/Manifest1
-rw-r--r--dev-python/latexify_py/latexify_py-0.2.0.ebuild34
-rw-r--r--dev-python/latexify_py/metadata.xml (renamed from sci-libs/ipp/metadata.xml)5
-rw-r--r--dev-python/llvmlite/Manifest2
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch (renamed from dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch)0
-rw-r--r--dev-python/llvmlite/llvmlite-0.39.1.ebuild (renamed from dev-python/llvmlite/llvmlite-0.39.0.ebuild)0
-rw-r--r--dev-python/meshpy/metadata.xml1
-rw-r--r--dev-python/numba/Manifest2
-rw-r--r--dev-python/numba/files/numba-0.51.2-skip_tests.patch46
-rw-r--r--dev-python/numba/metadata.xml3
-rw-r--r--dev-python/numba/numba-0.56.3.ebuild (renamed from dev-python/numba/numba-0.56.0.ebuild)8
-rw-r--r--dev-python/nwbinspector/Manifest5
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.3.9.ebuild2
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.12.ebuild39
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.14.ebuild39
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.19.ebuild31
-rw-r--r--dev-python/probeinterface/Manifest3
-rw-r--r--dev-python/probeinterface/metadata.xml (renamed from dev-cpp/castxml/metadata.xml)6
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.11.ebuild35
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.14.ebuild37
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.5.ebuild35
-rw-r--r--dev-python/pynwb/Manifest2
-rw-r--r--dev-python/pynwb/files/pynwb-2.2.0-versions.patch21
-rw-r--r--dev-python/pynwb/pynwb-2.0.0.ebuild46
-rw-r--r--dev-python/pynwb/pynwb-2.2.0.ebuild57
-rw-r--r--dev-python/pyparsing/Manifest1
-rw-r--r--dev-python/pyparsing/metadata.xml21
-rw-r--r--dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild29
-rw-r--r--dev-python/python-gantt/metadata.xml5
-rw-r--r--dev-python/pyvote/metadata.xml5
-rw-r--r--dev-python/pyzo/metadata.xml3
-rw-r--r--dev-python/repsep_utils/metadata.xml13
-rw-r--r--dev-python/snakemake/metadata.xml1
-rw-r--r--dev-python/sphinx-argparse/Manifest2
-rw-r--r--dev-python/sphinx-argparse/metadata.xml3
-rw-r--r--dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild (renamed from dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild)15
-rw-r--r--dev-python/ufl/metadata.xml1
-rw-r--r--dev-python/wraps/Manifest3
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch16
-rw-r--r--dev-python/wraps/wraps-0.1.0-r1.ebuild (renamed from dev-python/wraps/wraps-0.1.0.ebuild)3
-rw-r--r--dev-python/wraps/wraps-0.2.0.ebuild30
-rw-r--r--dev-python/xgboost/Manifest2
-rw-r--r--dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch31
-rw-r--r--dev-python/xgboost/xgboost-1.6.2.ebuild (renamed from dev-python/xgboost/xgboost-1.3.1.ebuild)10
-rw-r--r--dev-util/makefile2graph/metadata.xml3
-rw-r--r--dev-util/plog/metadata.xml3
-rw-r--r--dev-vcs/dandi-cli/Manifest6
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild6
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild6
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild4
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild)28
-rw-r--r--dev-vcs/datalad/Manifest3
-rw-r--r--dev-vcs/datalad/datalad-0.15.2.ebuild68
-rw-r--r--dev-vcs/datalad/datalad-0.16.1-r1.ebuild (renamed from dev-vcs/datalad/datalad-0.16.1.ebuild)9
-rw-r--r--dev-vcs/datalad/datalad-0.17.0-r1.ebuild (renamed from dev-vcs/datalad/datalad-0.17.0.ebuild)11
-rw-r--r--dev-vcs/datalad/datalad-0.17.2-r1.ebuild (renamed from dev-vcs/datalad/datalad-0.17.2.ebuild)9
-rw-r--r--dev-vcs/datalad/datalad-0.17.7.ebuild (renamed from dev-vcs/datalad/datalad-0.15.1.ebuild)41
-rw-r--r--dev-vcs/datalad/files/datalad-0.16.1-input.patch37
-rw-r--r--dev-vcs/datalad/files/datalad-0.16.1-tests.patch10
-rw-r--r--eclass/intel-sdp-r1.eclass571
-rw-r--r--licenses/estscan88
-rw-r--r--licenses/mRNAmarkup25
-rw-r--r--licenses/staden76
-rw-r--r--media-gfx/netgen/Manifest (renamed from sci-mathematics/netgen/Manifest)1
-rw-r--r--media-gfx/netgen/files/netgen-6.2.2105-find-tk.patch (renamed from sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch)0
-rw-r--r--media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch21
-rw-r--r--media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch34
-rw-r--r--media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch20
-rw-r--r--media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch30
-rw-r--r--media-gfx/netgen/files/netgen.desktop (renamed from sci-mathematics/netgen/files/netgen.desktop)0
-rw-r--r--media-gfx/netgen/files/netgen.png (renamed from sci-mathematics/netgen/files/netgen.png)bin4220 -> 4220 bytes
-rw-r--r--media-gfx/netgen/metadata.xml (renamed from sci-mathematics/netgen/metadata.xml)0
-rw-r--r--media-gfx/netgen/netgen-6.2.2105.ebuild (renamed from sci-mathematics/netgen/netgen-6.2.2105.ebuild)0
-rw-r--r--media-gfx/netgen/netgen-6.2.2204.ebuild137
-rw-r--r--media-libs/charls/Manifest1
-rw-r--r--media-libs/charls/charls-2.3.4.ebuild30
-rw-r--r--media-libs/charls/metadata.xml11
-rw-r--r--media-libs/libgfx/metadata.xml3
-rw-r--r--media-libs/mmg/metadata.xml3
-rw-r--r--metadata/pkgcheck.conf2
-rw-r--r--net-misc/cernbox-client/Manifest4
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild)18
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild80
-rw-r--r--profiles/package.use.mask16
-rw-r--r--profiles/updates/4Q-20221
-rw-r--r--sci-biology/BRAKER/metadata.xml3
-rw-r--r--sci-biology/GAL/metadata.xml3
-rw-r--r--sci-biology/RAILS/metadata.xml3
-rw-r--r--sci-biology/VelvetOptimiser/metadata.xml3
-rw-r--r--sci-biology/afni/metadata.xml3
-rw-r--r--sci-biology/angsd/metadata.xml3
-rw-r--r--sci-biology/ants/Manifest3
-rw-r--r--sci-biology/ants/ants-2.3.4.ebuild78
-rw-r--r--sci-biology/ants/ants-2.4.1-r1.ebuild60
-rw-r--r--sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch37
-rw-r--r--sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch40
-rw-r--r--sci-biology/ants/files/ants-2.3.4-libdir.patch117
-rw-r--r--sci-biology/ants/files/ants-2.3.4-version.patch17
-rw-r--r--sci-biology/ants/files/ants-2.4.1-fix-compile.patch13
-rw-r--r--sci-biology/ants/metadata.xml3
-rw-r--r--sci-biology/bamql/metadata.xml3
-rw-r--r--sci-biology/barrnap/metadata.xml3
-rw-r--r--sci-biology/bidsschematools/Manifest3
-rw-r--r--sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild37
-rw-r--r--sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild38
-rw-r--r--sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild38
-rw-r--r--sci-biology/bidsschematools/metadata.xml (renamed from dev-python/click-didyoumean/metadata.xml)9
-rw-r--r--sci-biology/bismark/metadata.xml3
-rw-r--r--sci-biology/btl_bloomfilter/metadata.xml3
-rw-r--r--sci-biology/bx-python/metadata.xml1
-rw-r--r--sci-biology/caftools/Manifest2
-rw-r--r--sci-biology/caftools/caftools-2.0.2.ebuild45
-rw-r--r--sci-biology/caftools/files/Makefile.in-2.0.2.patch43
-rw-r--r--sci-biology/caftools/files/Makefile.in.patch49
-rw-r--r--sci-biology/caftools/metadata.xml17
-rw-r--r--sci-biology/dcm2niix/metadata.xml3
-rw-r--r--sci-biology/dcmstack/metadata.xml3
-rw-r--r--sci-biology/diamond/metadata.xml3
-rw-r--r--sci-biology/estscan/Manifest9
-rw-r--r--sci-biology/estscan/estscan-3.0.3.ebuild124
-rw-r--r--sci-biology/estscan/metadata.xml19
-rw-r--r--sci-biology/fastqc/metadata.xml3
-rw-r--r--sci-biology/ffindex/metadata.xml3
-rw-r--r--sci-biology/longstitch/metadata.xml3
-rw-r--r--sci-biology/mRNAmarkup/Manifest1
-rw-r--r--sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild55
-rw-r--r--sci-biology/mreps/metadata.xml3
-rw-r--r--sci-biology/nextclip/metadata.xml3
-rw-r--r--sci-biology/ngs/metadata.xml3
-rw-r--r--sci-biology/ntCard/metadata.xml3
-rw-r--r--sci-biology/open-ephys-gui/Manifest1
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch15
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch12
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch12
-rw-r--r--sci-biology/open-ephys-gui/metadata.xml4
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild83
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild13
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild13
-rw-r--r--sci-biology/prokka/metadata.xml3
-rw-r--r--sci-biology/pyfaidx/metadata.xml1
-rw-r--r--sci-biology/quicktree/metadata.xml3
-rw-r--r--sci-biology/roche454ace2caf/Manifest1
-rw-r--r--sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild28
-rw-r--r--sci-biology/rtg-tools/metadata.xml3
-rw-r--r--sci-biology/salmon/Manifest10
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch18
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch11
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch22
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch10
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch12
-rw-r--r--sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch200
-rw-r--r--sci-biology/salmon/files/salmon-1.6.0-find-boost.patch116
-rw-r--r--sci-biology/salmon/metadata.xml15
-rw-r--r--sci-biology/salmon/salmon-0.10.2.ebuild73
-rw-r--r--sci-biology/salmon/salmon-1.6.0.ebuild70
-rw-r--r--sci-biology/seqtk/metadata.xml3
-rw-r--r--sci-biology/spm/metadata.xml3
-rw-r--r--sci-biology/staden/Manifest1
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch30
-rw-r--r--sci-biology/staden/metadata.xml15
-rw-r--r--sci-biology/staden/staden-2.0.0_beta11.ebuild76
-rw-r--r--sci-biology/staden_doc/Manifest1
-rw-r--r--sci-biology/staden_doc/metadata.xml15
-rw-r--r--sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild42
-rw-r--r--sci-biology/trans-abyss/metadata.xml3
-rw-r--r--sci-biology/trim_galore/metadata.xml3
-rw-r--r--sci-biology/ugene/metadata.xml3
-rw-r--r--sci-chemistry/erkale/metadata.xml3
-rw-r--r--sci-chemistry/relion/metadata.xml3
-rw-r--r--sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild (renamed from sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild)4
-rw-r--r--sci-libs/HDF5Plugin-Zstandard/metadata.xml3
-rw-r--r--sci-libs/fast5/metadata.xml3
-rw-r--r--sci-libs/gdcm/Manifest2
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-rw-r--r--sci-libs/vxl/metadata.xml1
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-rw-r--r--sci-mathematics/freefem++/Manifest1
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-rw-r--r--sci-mathematics/freefem++/metadata.xml3
-rw-r--r--sci-mathematics/pulp/metadata.xml1
-rw-r--r--sci-mathematics/ripser/metadata.xml27
-rw-r--r--sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild (renamed from sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild)2
-rw-r--r--sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch35
-rw-r--r--sci-misc/elmer-fem/files/elmer-fem-rpath.patch11
-rw-r--r--sci-misc/elmer-fem/metadata.xml1
-rw-r--r--sci-physics/feyncalc/metadata.xml3
-rw-r--r--sci-physics/formcalc/Manifest2
-rw-r--r--sci-physics/formcalc/formcalc-9.10-r1.ebuild (renamed from sci-physics/formcalc/formcalc-9.10.ebuild)4
-rw-r--r--sci-physics/formcalc/formcalc-9.9-r1.ebuild (renamed from sci-physics/formcalc/formcalc-9.9.ebuild)4
-rw-r--r--sci-physics/mcfm/Manifest1
-rw-r--r--sci-physics/mcfm/files/mcfm-10.2.1-rest.patch251
-rw-r--r--sci-physics/mcfm/mcfm-10.2.1.ebuild71
-rw-r--r--sci-physics/mcfm/metadata.xml15
-rw-r--r--sci-physics/oneloop/Manifest1
-rw-r--r--sci-physics/oneloop/files/oneloop-2020.07.31-config.patch11
-rw-r--r--sci-physics/oneloop/metadata.xml (renamed from sci-biology/mRNAmarkup/metadata.xml)8
-rw-r--r--sci-physics/oneloop/oneloop-2020.07.31.ebuild49
-rw-r--r--sci-physics/qcdloop/Manifest2
-rw-r--r--sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch11
-rw-r--r--sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch11
-rw-r--r--sci-physics/qcdloop/metadata.xml18
-rw-r--r--sci-physics/qcdloop/qcdloop-2.0.5.ebuild33
-rw-r--r--sci-physics/qcdloop/qcdloop-2.0.9.ebuild50
-rw-r--r--sci-physics/rivet/Manifest2
-rw-r--r--sci-physics/rivet/files/rivet-3.1.5-doc.patch38
-rw-r--r--sci-physics/rivet/files/rivet-3.1.5-test.patch11
-rw-r--r--sci-physics/rivet/files/rivet-3.1.6-binreloc.patch12
-rw-r--r--sci-physics/rivet/metadata.xml20
-rw-r--r--sci-physics/rivet/rivet-3.1.5.ebuild75
-rw-r--r--sci-physics/rivet/rivet-3.1.6.ebuild75
-rw-r--r--sci-visualization/clip/metadata.xml3
-rw-r--r--sci-visualization/fsleyes-props/Manifest2
-rw-r--r--sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild (renamed from sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild)2
-rw-r--r--sci-visualization/fsleyes-widgets/Manifest2
-rw-r--r--sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild (renamed from sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild)4
-rw-r--r--sci-visualization/fsleyes/Manifest2
-rw-r--r--sci-visualization/fsleyes/fsleyes-1.5.0.ebuild (renamed from sci-visualization/fsleyes/fsleyes-1.3.3.ebuild)14
-rw-r--r--sci-visualization/fsleyes/metadata.xml5
-rw-r--r--sys-devel/DPC++/DPC++-2022.09.ebuild176
-rw-r--r--sys-devel/DPC++/Manifest3
-rw-r--r--sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch217
-rw-r--r--sys-devel/DPC++/metadata.xml16
-rw-r--r--sys-devel/oneDPL/Manifest1
-rw-r--r--sys-devel/oneDPL/metadata.xml11
-rw-r--r--sys-devel/oneDPL/oneDPL-2021.7.1.ebuild57
328 files changed, 4254 insertions, 5005 deletions
diff --git a/README.md b/README.md
index 43484c14a..cd47d84a4 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,7 @@
### Contents
1. [Installation](#install)
+ - [Eselect](#install-eselect)
- [Manual](#install-manual)
- [Layman](#install-layman)
2. [Usage](#usage)
diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
index f26d506d5..b320be20c 100644
--- a/app-arch/libdeflate/Manifest
+++ b/app-arch/libdeflate/Manifest
@@ -1,5 +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
DIST libdeflate-1.8.tar.gz 145823 BLAKE2B 3597e41cbcae17b5b6b5bbb196af6ea52ac55b279f42e1ca3b12ba45638602e8a3f7520d84d7be637675c04fd82e096cb03d15f5fd742a31db5ba22cbd6e71f4 SHA512 b40caecdf783487488a5bd8213304175348b9db9bc1efdf6d5222fb912f61698b5e196522195a3640d7ff61ba953a93c0c8f75e07f548ac8b9d9c5dd5a787544
diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
deleted file mode 100644
index 790aa6de9..000000000
--- a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- libdeflate-1.2/Makefile 2019-01-15 06:37:48.000000000 +0100
-+++ libdeflate-1.2/Makefile 2019-01-22 14:06:13.427054892 +0100
-@@ -21,7 +21,7 @@
- 1>&2 2>/dev/null; then echo $(1); fi)
-
- override CFLAGS := \
-- $(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon \
-+ $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon \
- -Wall -Wundef \
- $(call cc-option,-Wpedantic) \
- $(call cc-option,-Wdeclaration-after-statement) \
-@@ -34,6 +34,9 @@
- ##############################################################################
-
- PREFIX ?= /usr
-+BINDIR ?= $(PREFIX)/bin
-+INCDIR ?= $(PREFIX)/include
-+LIBDIR ?= $(PREFIX)/lib
-
- SOVERSION := 0
- STATIC_LIB_SUFFIX := .a
-@@ -240,20 +243,20 @@
- all:$(DEFAULT_TARGETS)
-
- install:all
-- install -Dm644 -t $(DESTDIR)$(PREFIX)/lib $(STATIC_LIB)
-- install -Dm755 -t $(DESTDIR)$(PREFIX)/lib $(SHARED_LIB)
-- ln -sf $(SHARED_LIB) $(DESTDIR)$(PREFIX)/lib/libdeflate.so
-- install -Dm644 -t $(DESTDIR)$(PREFIX)/include libdeflate.h
-- install -Dm755 gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip
-- ln -f $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+ install -Dm644 -t $(DESTDIR)$(LIBDIR) $(STATIC_LIB)
-+ install -Dm755 -t $(DESTDIR)$(LIBDIR) $(SHARED_LIB)
-+ ln -sf $(SHARED_LIB) $(DESTDIR)$(LIBDIR)/libdeflate.so
-+ install -Dm644 -t $(DESTDIR)$(INCDIR) libdeflate.h
-+ install -Dm755 gzip $(DESTDIR)$(BINDIR)/libdeflate-gzip
-+ ln -f $(DESTDIR)$(BINDIR)/libdeflate-gzip $(DESTDIR)$(BINDIR)/libdeflate-gunzip
-
- uninstall:
-- rm -f $(DESTDIR)$(PREFIX)/lib/$(STATIC_LIB) \
-- $(DESTDIR)$(PREFIX)/lib/$(SHARED_LIB) \
-- $(DESTDIR)$(PREFIX)/lib/libdeflate.so \
-- $(DESTDIR)$(PREFIX)/include/libdeflate.h \
-- $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip \
-- $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+ rm -f $(DESTDIR)$(LIBDIR)/$(STATIC_LIB) \
-+ $(DESTDIR)$(LIBDIR)/$(SHARED_LIB) \
-+ $(DESTDIR)$(LIBDIR)/libdeflate.so \
-+ $(DESTDIR)$(INCDIR)/libdeflate.h \
-+ $(DESTDIR)$(BINDIR)/libdeflate-gzip \
-+ $(DESTDIR)$(BINDIR)/libdeflate-gunzip
-
- test_programs:$(TEST_PROGRAMS)
-
diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild b/app-arch/libdeflate/libdeflate-1.2.ebuild
deleted file mode 100644
index c5924c064..000000000
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate"
-SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-PATCHES=( "${FILESDIR}"/libdeflate-1.2-respect_EPREFIX.patch )
-
-src_install() {
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- emake install DESTDIR="${ED}" LIBDIR=/usr/"$(get_libdir)"
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml
index 6e347494a..fe240766f 100644
--- a/app-arch/libdeflate/metadata.xml
+++ b/app-arch/libdeflate/metadata.xml
@@ -8,9 +8,12 @@
<maintainer type="person">
<email>gentoo@aisha.cc</email>
<name>Aisha Tammy</name>
- </maintainer>
+ </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ebiggers/libdeflate</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-cpp/Fastor/metadata.xml b/dev-cpp/Fastor/metadata.xml
index e97c4322a..9937ac435 100644
--- a/dev-cpp/Fastor/metadata.xml
+++ b/dev-cpp/Fastor/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">romeric/Fastor</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-cpp/castxml/Manifest b/dev-cpp/castxml/Manifest
deleted file mode 100644
index a7d756e8b..000000000
--- a/dev-cpp/castxml/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST castxml-0.3.6.tar.gz 95844 BLAKE2B c0ab3c7ba29b2abb4755320d97c36ee850135fff6fd5bb7a9436d68f50e9c6a80108ac95958fe9b51afaf6b4ebdde7db825a9cdf047c5e8f47f4f57fba77dcc1 SHA512 c850ce9ce0ef716cf64139d4311955deb8373db691e3cb7348932bbd3945056366838187603e5850a088911a8be6b0e5b53e2c700c0b5c8fed71008de7ab2350
-DIST castxml-0.4.3.tar.gz 103188 BLAKE2B ceaeaa0e228865847fc9627e93366c9dc2d33f89c97621af25ce84746ffe79b0db7cf52a93aed3ac297ce116e1f63f4bcc636dc21419aabf3ba737f545b240c1 SHA512 af2c03e148d42615a9ad0366a224ebeb06ca0348c0b5fcc0a93cba4871710dd8901874e5e30968532cdb1254e63a7ab596403bf2f3c836eed57be287203ddbed
diff --git a/dev-cpp/castxml/castxml-0.3.6.ebuild b/dev-cpp/castxml/castxml-0.3.6.ebuild
deleted file mode 100644
index 6fb7ac720..000000000
--- a/dev-cpp/castxml/castxml-0.3.6.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/castxml-0.4.3.ebuild b/dev-cpp/castxml/castxml-0.4.3.ebuild
deleted file mode 100644
index 6fb7ac720..000000000
--- a/dev-cpp/castxml/castxml-0.4.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/castxml-9999.ebuild b/dev-cpp/castxml/castxml-9999.ebuild
deleted file mode 100644
index dbf7fff49..000000000
--- a/dev-cpp/castxml/castxml-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch b/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch
deleted file mode 100644
index 0b72085b4..000000000
--- a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 90feea4..4b058a8 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -194,5 +194,5 @@ install(DIRECTORY share/castxml/ DESTINATION "${CastXML_INSTALL_DATA_DIR}")
- install(FILES
- "LICENSE"
- "NOTICE"
-- DESTINATION "${CastXML_INSTALL_DOC_DIR}"
-+ DESTINATION "${CastXML_INSTALL_DATA_DIR}"
- )
-
diff --git a/dev-cpp/highwayhash/metadata.xml b/dev-cpp/highwayhash/metadata.xml
index ef6b5dcd5..ce99f4b00 100644
--- a/dev-cpp/highwayhash/metadata.xml
+++ b/dev-cpp/highwayhash/metadata.xml
@@ -5,4 +5,7 @@
<email>junghans@gentoo.org</email>
<name>Christoph Junghans</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">google/highwayhash</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-cpp/xor_singleheader/metadata.xml b/dev-cpp/xor_singleheader/metadata.xml
index e97c4322a..cebb00f2c 100644
--- a/dev-cpp/xor_singleheader/metadata.xml
+++ b/dev-cpp/xor_singleheader/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">FastFilter/xor_singleheader</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/icc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild
deleted file mode 100644
index 84641de62..000000000
--- a/dev-lang/icc/icc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# avoid file collision with ifc #476330
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "icc-common-ps-18.0.2-199-18.0.2-199.noarch.rpm"
- "icc-common-ps-ss-bec-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "icc-doc-18.0-18.0.2-199.noarch.rpm"
- "icc-doc-ps-18.0-18.0.2-199.noarch.rpm")
- fi
-}
diff --git a/dev-lang/icc/icc-19.0.4.243.ebuild b/dev-lang/icc/icc-19.0.4.243.ebuild
deleted file mode 100644
index 9a166f221..000000000
--- a/dev-lang/icc/icc-19.0.4.243.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# avoid file collision with ifc #476330
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-19.0.4-243-19.0.4-243.noarch.rpm"
- "icc-common-ps-19.0.4-243-19.0.4-243.noarch.rpm"
- "icc-common-ps-ss-bec-19.0.4-243-19.0.4-243.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-ss-bec-19.0.4-243-19.0.4-243.x86_64.rpm")
-
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-ss-bec-32bit-19.0.4-243-19.0.4-243.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "icc-doc-19.0-19.0.4-243.noarch.rpm"
- "icc-doc-ps-19.0-19.0.4-243.noarch.rpm")
- fi
-}
diff --git a/dev-lang/icc/icc-19.1.1.217.ebuild b/dev-lang/icc/icc-19.1.1.217.ebuild
deleted file mode 100644
index 226b9c784..000000000
--- a/dev-lang/icc/icc-19.1.1.217.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "icc-common-ps-${MY_PV}-${MY_PV}.noarch.rpm"
- "idesupport-icc-common-ps-19.1-${MY_PV}.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "icc-doc-19.1-${MY_PV}.noarch.rpm" )
- fi
-}
diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml
deleted file mode 100644
index 7c4d1a96d..000000000
--- a/dev-lang/icc/metadata.xml
+++ /dev/null
@@ -1,16 +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">
-The Intel® C++ Compiler is a full featured C/C++ compiler for Intel
-based architectures. The compiler supports multi-threading, automatic
-processor dispatch, vectorization, auto-parallelization, OpenMP, data
-prefetching, loop unrolling. The package comes with extensive
-documentation. The product can be installed as a non-commercial as
-well. License, terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/ifc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild b/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
deleted file mode 100644
index f37dd5491..000000000
--- a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-18.0.2-199-18.0.2-199.noarch.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-18.0-18.0.2-199.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/ifc-19.0.4.243.ebuild b/dev-lang/ifc/ifc-19.0.4.243.ebuild
deleted file mode 100644
index a45765a2f..000000000
--- a/dev-lang/ifc/ifc-19.0.4.243.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-19.0.4-243-19.0.4-243.noarch.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-19.0.4-243-19.0.4-243.x86_64.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.0-19.0.4-243.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/ifc-19.1.1.217.ebuild b/dev-lang/ifc/ifc-19.1.1.217.ebuild
deleted file mode 100644
index 4157a3eec..000000000
--- a/dev-lang/ifc/ifc-19.1.1.217.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-${MY_PV}-${MY_PV}.noarch.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-${MY_PV}-${MY_PV}.x86_64.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.1-${MY_PV}.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml
deleted file mode 100644
index 0cc12d890..000000000
--- a/dev-lang/ifc/metadata.xml
+++ /dev/null
@@ -1,17 +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">
-The Intel® Fortran Compiler is a full featured FORTRAN 77/95 and
-substantial FORTRAN 2003 compiler for Intel based architectures. The
-compiler supports multi-threading with automatic processor dispatch,
-vectorization, auto-parallelization, OpenMP, data prefetching, loop
-unrolling. The package comes with extensive documentation.
-The product can be installed as a non-commercial as well. License,
-terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/vtune/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml
deleted file mode 100644
index 718cc299c..000000000
--- a/dev-lang/vtune/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The Intel® VTune™ Profiler collects key profiling data and presents
-it with a powerful interface that simplifies its analysis and
-interpretation. The package comes with extensive documentation. The
-product can be installed as a non-commercial as well. License, terms
-of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild b/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
deleted file mode 100644
index 9ec0beef6..000000000
--- a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-INTEL_SUBDIR=vtune_amplifier
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-18.0.2.199[compiler]"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-amplifier-2018-cli-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-common-pset-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-gui-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-sep-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-target-2018.2-551022.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-amplifier-2018-cli-2018.2-551022.x86_64.rpm"
- "vtune-amplifier-2018-collector-64linux-2018.2-551022.x86_64.rpm"
- "vtune-amplifier-2018-gui-2018.2-551022.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-amplifier-2018-cli-32bit-2018.2-551022.i486.rpm"
- "vtune-amplifier-2018-collector-32linux-2018.2-551022.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2018-doc-2018.2-551022.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild b/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild
deleted file mode 100644
index e090c10b7..000000000
--- a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-INTEL_SUBDIR=vtune_amplifier
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-19.0.4.243[compiler]"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-amplifier-2019-cli-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-common-pset-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-gui-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-sep-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-target-2019.4-597835.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-amplifier-2019-cli-2019.4-597835.x86_64.rpm"
- "vtune-amplifier-2019-collector-64linux-2019.4-597835.x86_64.rpm"
- "vtune-amplifier-2019-gui-2019.4-597835.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-amplifier-2019-cli-32bit-2019.4-597835.i486.rpm"
- "vtune-amplifier-2019-collector-32linux-2019.4-597835.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2019-doc-2019.4-597835.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild b/dev-lang/vtune/vtune-2020.1.0.607630.ebuild
deleted file mode 100644
index e1ec58882..000000000
--- a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-INTEL_SUBDIR=vtune_profiler
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Profiler"
-HOMEPAGE="https://software.intel.com/en-us/vtune"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]"
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-profiler-2020-cli-common-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-common-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-common-pset-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-sep-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-target-${MY_PV}.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-profiler-2020-cli-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-collector-64linux-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-gui-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-vpp-server-${MY_PV}.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-profiler-2020-cli-32bit-${MY_PV}.i486.rpm"
- "vtune-profiler-2020-collector-32linux-${MY_PV}.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-profiler-2020-doc-${MY_PV}.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/yaggo/metadata.xml b/dev-lang/yaggo/metadata.xml
index 138cb7705..61d3a34e2 100644
--- a/dev-lang/yaggo/metadata.xml
+++ b/dev-lang/yaggo/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">gmarcais/yaggo</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest
deleted file mode 100644
index 21dea448d..000000000
--- a/dev-libs/intel-common/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update3_professional_edition.tgz 4777019188 BLAKE2B 1ebbc23d1370bb396b452dc73d4a79b4ea7be0e304e3d38b3cba77372df6af097ea1109535d166b56a6c50e28e3330a1ed49c6a9270411b14ccf48f32a9eaedd SHA512 622b1a8877f06247a0a93cb98d2cc6d5b359aa2c9cf7ff6f45a8e1dca34fecea10d603d632a7b3454d809d6e38cb860b40ae3f782e250279768937af6ceb015d
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild b/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
deleted file mode 100644
index 5397d76b6..000000000
--- a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-l-all-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-l-all-vars-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-nomcu-vars-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-18.0-18.0.2-199.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-2018.2-199-2018.2-199.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-2018-2018.2-199.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-18.0.2-199-18.0.2-199.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-18.0.2-199-18.0.2-199.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-18.0.2-199-18.0.2-199.noarch.rpm"
- "openmp-common-ifort-18.0.2-199-18.0.2-199.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-18.0.2-199-18.0.2-199.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild b/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild
deleted file mode 100644
index dc06e4551..000000000
--- a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update3_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV=$(ver_rs 3 '-') # 19.0.3-199
-MY_PV2=$(ver_cut 1-2) # 19.0
-MY_PV3='20'$(ver_cut 1) # 2019
-MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild b/dev-libs/intel-common/intel-common-19.0.4.243.ebuild
deleted file mode 100644
index df8f5574c..000000000
--- a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV=$(ver_rs 3 '-') # 19.0.3-199
-MY_PV2=$(ver_cut 1-2) # 19.0
-MY_PV3='20'$(ver_cut 1) # 2019
-MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild b/dev-libs/intel-common/intel-common-19.1.1.217.ebuild
deleted file mode 100644
index 4ba98edad..000000000
--- a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV="$(ver_rs 3 '-')" # 19.1.1-217
-MY_PV2="$(ver_cut 1-2)" # 19.1
-MY_PV3="2019" # 2019
-MY_PV4="${MY_PV3}.7-$(ver_cut 4)" # 2019.7-217 sic!
-
-CHECKREQS_DISK_BUILD=750M
-
-QA_PREBUILT="*"
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/metadata.xml b/dev-libs/intel-common/metadata.xml
deleted file mode 100644
index 026b5a33d..000000000
--- a/dev-libs/intel-common/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-This package contains the core files to be installed for the Intel
-compilers and libraries. Probably useless if installed standalone.
-</longdescription>
- <use>
- <flag name="compiler">Install the libraries needed for the icc and ifort compilers</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest
new file mode 100644
index 000000000..825fc0a11
--- /dev/null
+++ b/dev-libs/oneCCL/Manifest
@@ -0,0 +1 @@
+DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790
diff --git a/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
new file mode 100644
index 000000000..0f9a785b4
--- /dev/null
+++ b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
@@ -0,0 +1,102 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 74c4fc0..92c4d16 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -87,15 +87,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE
+ SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support")
+
+ set(CCL_COMMON_INSTALL_PREFIX "intel64")
+-set(CMAKE_INSTALL_LIBDIR "lib")
+ set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+ set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+ set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}")
+ set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}")
+-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env")
+-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc")
+-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing")
+-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles")
++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env")
++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}")
++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles")
+ set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples")
+ set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests")
+ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+@@ -103,23 +101,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+ # setup dependency directories
+ set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps")
+
+-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/")
+-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/")
++set(MPI_INCLUDE_DIR "/usr/include/")
++set(MPI_LIB_DIR "/usr/lib64/")
+ message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}")
+ message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}")
+
+ if ("${LIBFABRIC_DIR}" STREQUAL "")
+- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include")
+- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/")
++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/")
++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/")
+ else()
+ set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/")
+- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib")
++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/")
+ endif()
+ message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}")
+ message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}")
+
+-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/")
+-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/")
++set(HWLOC_INCLUDE_DIR "/usr/include/")
++set(HWLOC_LIB_DIR "/usr/lib64/")
+ message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}")
+ message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}")
+
+@@ -128,7 +126,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64")
+ message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}")
+ message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}")
+
+-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/")
++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero")
+ message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}")
+
+ set(CMAKE_SKIP_INSTALL_RPATH TRUE)
+@@ -241,8 +239,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party-
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE})
+-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE})
+-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE})
+
+ # copy kernels
+ if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 7b4cff9..7ef00f8 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -263,7 +263,7 @@ list(APPEND SRC_LINK_LIBS
+ pthread
+ ${EXTERNAL_LIBS}
+ fabric
+- ${HWLOC_LIB_DIR}/libhwloc.a
++ ${HWLOC_LIB_DIR}/libhwloc.so
+ ${ITT_LIB_DIR}/libittnotify.a)
+
+ if (ENABLE_MPI)
+@@ -335,16 +335,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "")
+ install(DIRECTORY ${DEPS_DIR}/ofi/lib/
+ DESTINATION ${CCL_INSTALL_LIB})
+ endif()
+-
+-if (ENABLE_MPI)
+- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*")
+- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN})
+- install(DIRECTORY ${DEPS_DIR}/mpi/include/
+- DESTINATION ${CCL_INSTALL_INCLUDE})
+- install(DIRECTORY ${DEPS_DIR}/mpi/lib/
+- DESTINATION ${CCL_INSTALL_LIB})
+- install(DIRECTORY ${DEPS_DIR}/mpi/etc/
+- DESTINATION ${CCL_INSTALL_ETC})
+- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/
+- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/)
+-endif()
diff --git a/dev-libs/optix/metadata.xml b/dev-libs/oneCCL/metadata.xml
index 43be4e4e4..ad55412d9 100644
--- a/dev-libs/optix/metadata.xml
+++ b/dev-libs/oneCCL/metadata.xml
@@ -2,9 +2,10 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>rich@warfaresdl.com</email>
+ <email>andrewammerlaan@gentoo.org</email>
+ <name>Andrew Ammerlaan</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">oneapi-src/oneCCL</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/oneCCL/oneCCL-2021.7.1.ebuild b/dev-libs/oneCCL/oneCCL-2021.7.1.ebuild
new file mode 100644
index 000000000..ae069bb2a
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.7.1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+DEPEND="
+ dev-libs/level-zero
+ sys-apps/hwloc
+ sys-block/libfabric
+ mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2021.7.1-use-system-libs.patch"
+)
+
+src_prepare() {
+ # No -Werror
+ find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+ # Use system libs instead
+ rm -r deps/hwloc deps/level_zero deps/mpi deps/ofi || die
+
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DBUILD_EXAMPLES=OFF
+ # BUILD_CONFIG causes sandbox violation
+ -DBUILD_CONFIG=OFF
+ -DCCL_ENABLE_ZE=ON
+ # TODO: Find out how to execute the tests
+ -DBUILD_FT=OFF
+ -DENABLE_MPI_TESTS=OFF
+ -DENABLE_MPI="$(usex mpi)"
+ # Use system fabric
+ -DLIBFABRIC_DIR="${ESYSROOT}/usr"
+ )
+ cmake_src_configure
+}
diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest
deleted file mode 100644
index 0a6859644..000000000
--- a/dev-libs/optix/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NVIDIA-OptiX-SDK-7.4.0-linux64-x86_64.sh 57923655 BLAKE2B c3e159106ec6c8c446090ebd182fd3b0a75ec48b62e6984ae6559578688fd9a6cb29ea6065cb89aecdeb02247acbf3fb3bb0cbf69b10c29c222eb9fcbb0c6d90 SHA512 04f50c49d08c5e4e9be73ee322c4bff4f10a5e30445bc431e213c879a35cc5e36e0ceb8c864313f417628575a3c71593e65467ea13dd111b432fdf1db9383ae0
diff --git a/dev-libs/optix/optix-7.4.0.ebuild b/dev-libs/optix/optix-7.4.0.ebuild
deleted file mode 100644
index a3f61205e..000000000
--- a/dev-libs/optix/optix-7.4.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2021-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
-S="${WORKDIR}"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch mirror"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit:=
- media-libs/freeglut
- virtual/opengl
-"
-
-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/simclist/metadata.xml b/dev-libs/simclist/metadata.xml
index 8426fdb21..62c13e1e4 100644
--- a/dev-libs/simclist/metadata.xml
+++ b/dev-libs/simclist/metadata.xml
@@ -15,4 +15,7 @@
<flag name="dump">Disable building of dump and restore functionalities</flag>
<flag name="hash">Allow list_hash() to work exclusively on memory locations</flag>
</use>
+ <upstream>
+ <remote-id type="github">mij/simclist</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/tut/metadata.xml b/dev-libs/tut/metadata.xml
index 026cdb22b..7a070008d 100644
--- a/dev-libs/tut/metadata.xml
+++ b/dev-libs/tut/metadata.xml
@@ -1,8 +1,11 @@
-<?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="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mrzechonek/tut-framework</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml
index 1094bf3da..24157e1f0 100644
--- a/dev-ml/lacaml/metadata.xml
+++ b/dev-ml/lacaml/metadata.xml
@@ -15,5 +15,6 @@
</longdescription>
<upstream>
<remote-id type="bitbucket">mmottl/lacaml</remote-id>
+ <remote-id type="github">mmottl/lacaml</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild
index 0ced423c8..57c0eb7a2 100644
--- a/dev-python/asciitree/asciitree-0.3.3.ebuild
+++ b/dev-python/asciitree/asciitree-0.3.3.ebuild
@@ -8,7 +8,7 @@ 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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/asciitree/metadata.xml b/dev-python/asciitree/metadata.xml
index f6f63a810..8b000b491 100644
--- a/dev-python/asciitree/metadata.xml
+++ b/dev-python/asciitree/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mbr/asciitree</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
index d6dfa1901..263546dbf 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -25,7 +25,7 @@ RDEPEND="
>=dev-python/pillow-7.1.0[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
>=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}]
- >=www-servers/tornado-5.1[${PYTHON_USEDEP}]
+ >=dev-python/tornado-5.1[${PYTHON_USEDEP}]
"
BDEPEND="
test? (
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
index 19494930c..3217b8774 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
@@ -29,7 +29,7 @@ SLOT="0"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
dev-python/clang-python[${PYTHON_USEDEP}]
dev-python/cymbal[${PYTHON_USEDEP}]
dev-python/toml[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
index b2213cef7..3197a52ea 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
@@ -29,7 +29,7 @@ SLOT="0"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
dev-python/clang-python[${PYTHON_USEDEP}]
dev-python/cymbal[${PYTHON_USEDEP}]
dev-python/toml[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
index 3eafde559..e31f8d37c 100644
--- a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
+++ b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
@@ -31,7 +31,7 @@ BDEPEND="
$(python_gen_cond_dep '
dev-python/pytest[${PYTHON_USEDEP}]
dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
')
)
"
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
index 26aa07b6d..a40a5c69a 100644
--- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
+++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
@@ -31,7 +31,7 @@ BDEPEND="
test? (
$(python_gen_cond_dep '
dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
')
)
"
diff --git a/dev-python/click-didyoumean/Manifest b/dev-python/click-didyoumean/Manifest
deleted file mode 100644
index 5c8198fe3..000000000
--- a/dev-python/click-didyoumean/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-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
deleted file mode 100644
index b9a65c5d8..000000000
--- a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# 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
deleted file mode 100644
index 9fe4373c8..000000000
--- a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# 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/fiat/metadata.xml b/dev-python/fiat/metadata.xml
index d08e0d509..23d9fd64c 100644
--- a/dev-python/fiat/metadata.xml
+++ b/dev-python/fiat/metadata.xml
@@ -17,5 +17,6 @@ support Hermite and nonconforming elements.
</longdescription>
<upstream>
<remote-id type="bitbucket">fenics-project/fiat</remote-id>
+ <remote-id type="github">FEniCS/fiat</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest
index 196e885ac..f2c52a88e 100644
--- a/dev-python/fslpy/Manifest
+++ b/dev-python/fslpy/Manifest
@@ -1 +1 @@
-DIST fslpy-3.8.1.tar.gz 4698603 BLAKE2B 33740081a065b6684b864eaf50910a38e26ce7aa10d18bf8faaeaf34ee87dfa22e8f2ee3cebc5681f2356cfb519a59ba07232a3cfb81526258ef92f3ced893ea SHA512 1b5d945f6aae6557e892e5700f228170bab8a235c77d06b162fc2afc16663f3bdbe18e54e4e20dad46ac873ccbf0cdc2649e5ac1c53e17b0d78c45e91e8a1896
+DIST fslpy-3.10.0.tar.gz 4695461 BLAKE2B 9ce74ed6175fb84fe0f123375273a9450c03b659c977b48e3fb874509d5b3f728c75aff850931e1af4fd398fb5eda80a6eef90b2a582e8db3f2135704b4124ed SHA512 b9b12350308d2aee5d10c16582abd96f17b56893287fc32ab3942e8edce8add1f96e1f5c83cca761707be9b2442262e28d961879d5d02e1001006805a74e1cda
diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild
index f28e7283e..7140be033 100644
--- a/dev-python/fslpy/fslpy-3.8.1.ebuild
+++ b/dev-python/fslpy/fslpy-3.10.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx
DESCRIPTION="The FSL Python Library"
@@ -16,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
+ dev-python/dill[${PYTHON_USEDEP}]
>=dev-python/h5py-2.9[${PYTHON_USEDEP}]
>=dev-python/indexed_gzip-0.7.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1[${PYTHON_USEDEP}]
@@ -27,17 +28,20 @@ RDEPEND="
>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
"
-PATCHES=(
- "${FILESDIR}/fslpy-2.7.0-coverage.patch"
-)
-
distutils_enable_tests pytest
distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+python_prepare_all() {
+ # Do not depend on coverage
+ sed -i -e 's/--cov=fsl//g' setup.cfg || die
+
+ distutils-r1_python_prepare_all
+}
+
src_test() {
virtx distutils-r1_src_test
}
python_test() {
- epytest --niters=50 -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
+ epytest -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
}
diff --git a/dev-python/hopcroftkarp/metadata.xml b/dev-python/hopcroftkarp/metadata.xml
index 2f2c0b51c..6959005e7 100644
--- a/dev-python/hopcroftkarp/metadata.xml
+++ b/dev-python/hopcroftkarp/metadata.xml
@@ -1,12 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <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>
+ <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>
+ <upstream>
+ <remote-id type="github">sofiatolaosebikan/hopcroftkarp</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/json_tricks/metadata.xml b/dev-python/json_tricks/metadata.xml
index f5804b4b0..2967a86bd 100644
--- a/dev-python/json_tricks/metadata.xml
+++ b/dev-python/json_tricks/metadata.xml
@@ -21,6 +21,6 @@
</longdescription>
<upstream>
<remote-id type="pypi">json-tricks</remote-id>
+ <remote-id type="github">mverleg/pyjson_tricks</remote-id>
</upstream>
</pkgmetadata>
-
diff --git a/dev-python/keyrings_alt/Manifest b/dev-python/keyrings_alt/Manifest
deleted file mode 100644
index ec1eff845..000000000
--- a/dev-python/keyrings_alt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST keyrings.alt-4.1.0.tar.gz 28581 BLAKE2B bb4c8c5faa130c4cfb377985ee8692bcce802f0e03d1121281a8d73ac1c4ced4c6f913e6ab9ff39b1b7d37ff41b37905910d3a02e91fa4160fbe109aa16c2ae0 SHA512 6c2a7637bc73971081b95851898dcc2fafe5fd155333cee7032983b16f668d8db941c972747c7c4a2e20b4d6a5fe52d8ad96448f8ae7d372cd1c32e2a0d344f9
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
deleted file mode 100644
index e0ca3a012..000000000
--- a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-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-r1.ebuild b/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
deleted file mode 100644
index 290c2f434..000000000
--- a/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Alternate keyring backend implementations used with dev-python/keyring"
-HOMEPAGE="https://github.com/jaraco/keyrings.alt/"
-SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~x86"
-
-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/keyrings_alt/metadata.xml b/dev-python/keyrings_alt/metadata.xml
deleted file mode 100644
index 59728c331..000000000
--- a/dev-python/keyrings_alt/metadata.xml
+++ /dev/null
@@ -1,24 +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">
- This package distributes backends extracted from the main Python keyring
- project to make them available for those who wish to employ them, but
- are discouraged for general production use. Include this module and use
- its backends at your own risk.
- For example, the PlaintextKeyring stores passwords in plain text on the
- file system, defeating the intended purpose of this library to encourage
- best practices for security.
- </longdescription>
- <upstream>
- <remote-id type="github">jaraco/keyrings.alt</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml
index e97c4322a..006b418f5 100644
--- a/dev-python/kmapper/metadata.xml
+++ b/dev-python/kmapper/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">scikit-tda/kepler-mapper</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/latexify_py/Manifest b/dev-python/latexify_py/Manifest
new file mode 100644
index 000000000..7a500fe7d
--- /dev/null
+++ b/dev-python/latexify_py/Manifest
@@ -0,0 +1 @@
+DIST latexify_py-0.2.0.tar.gz 30995 BLAKE2B 2b55c83ea073b221096b4e44fad362d421f5d526bdff79a825b67a5fb419ff6185cd9f18a49727b988409f257318845a90f78223cf6eb9dd264ce6d1c0b71b82 SHA512 17250784d7a009705854d3f6118b3c854c4e86e007a45740c2b6d314ff25503b3561327b610b17e49652fa59ff6612bae8e74ea4caedeaa4f6a0b1e446fe086c
diff --git a/dev-python/latexify_py/latexify_py-0.2.0.ebuild b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
new file mode 100644
index 000000000..5079c5ef3
--- /dev/null
+++ b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1
+
+DESCRIPTION="Generate LaTeX expression from Python code"
+HOMEPAGE="https://github.com/google/latexify_py"
+SRC_URI="https://github.com/google/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/dill[${PYTHON_USEDEP}]
+"
+
+BDEPEND="test? (
+ dev-python/notebook[${PYTHON_USEDEP}]
+ dev-python/twine[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_tests pytest
+
+DOCS=( README.md docs )
+
+python_test() {
+ PYTHONPATH="${S}/src" epytest
+}
diff --git a/sci-libs/ipp/metadata.xml b/dev-python/latexify_py/metadata.xml
index 7bd17909e..ae9640ffb 100644
--- a/sci-libs/ipp/metadata.xml
+++ b/dev-python/latexify_py/metadata.xml
@@ -5,9 +5,4 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
- <longdescription lang="en">
-Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a
-library of multi-core-ready, optimized software functions for
-multimedia data processing, and communications applications.
-</longdescription>
</pkgmetadata>
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
index 1749985b0..86f967801 100644
--- a/dev-python/llvmlite/Manifest
+++ b/dev-python/llvmlite/Manifest
@@ -1 +1 @@
-DIST llvmlite-0.39.0.gh.tar.gz 237009 BLAKE2B 41e485c636d285d039cd559c6386f79d05d51c266b31e24c68a30a921e9131d422e5782befdbdac7407b61fd44cab4b14863fdefa1c76ced235dd89eb0328110 SHA512 3493afc14c08b06bfb26230409d678b9a72d3957e412a4a6a6367aea0bc743fc46191ba050aa70e403424567038ab9fc2721c839df8035e4511dbf9ee4caddfa
+DIST llvmlite-0.39.1.gh.tar.gz 237119 BLAKE2B c2538994a6b9116d9a124ad8b8fff9c06d654bcdd345fb25251505b7577c6dffdfa56c9226250dbc2de6253cf6154523ec0d3cd849697a66cabf5b522c5e76ca SHA512 16b341300e4034aff4ce9553fec6b5923b9f4cb261c1ec0ee2cef6d87addcbebe8f4805dbc2fb30f357800fa029c3b6fc8ed62a5fdaad7c262e723c3b9c4ad32
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
index 17eb80e87..17eb80e87 100644
--- a/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch
+++ b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
diff --git a/dev-python/llvmlite/llvmlite-0.39.0.ebuild b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
index a2c3a6750..a2c3a6750 100644
--- a/dev-python/llvmlite/llvmlite-0.39.0.ebuild
+++ b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml
index fff86775c..77991f7a8 100644
--- a/dev-python/meshpy/metadata.xml
+++ b/dev-python/meshpy/metadata.xml
@@ -15,5 +15,6 @@ Hang Si. Both are included in the package in slightly modified versions.
</longdescription>
<upstream>
<remote-id type="pypi">MeshPy</remote-id>
+ <remote-id type="github">inducer/meshpy</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index 6282580a9..ded0ae03c 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1 +1 @@
-DIST numba-0.56.0.tar.gz 2488023 BLAKE2B ebfc00e2f131de54cf97db0f7bb6034a650c76db1b001fc68adec7800f4890b598d83cbcf8e5beb7f8023b770b310a2d837bfc0a43d5b901f2e09a40908ec307 SHA512 cedeb683120505a02ce2911efc46c0137cc03a25b1a6864b1ff68fe69655abfbe1d9880785ea718cd14577c985e1baa8b2cb3ecaf5c591c843b9021fa182c284
+DIST numba-0.56.3.tar.gz 2492552 BLAKE2B a8a3070ef6ca709594f308c751700a8c2cae1077c15b12291632a2022ca47460af245f02253555f4dfd4a93ef179c262baa36127b135158e48d60783f2ee0bb4 SHA512 42a1d9007ff89a58a79a80743e883e013a7a53b5035e1754b4c9f1ec715834a036eee32bff42ab0aa89132a7b6cb15decd9e918a9e49c42ce5a024e10ece3169
diff --git a/dev-python/numba/files/numba-0.51.2-skip_tests.patch b/dev-python/numba/files/numba-0.51.2-skip_tests.patch
deleted file mode 100644
index 327271a04..000000000
--- a/dev-python/numba/files/numba-0.51.2-skip_tests.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-diff --git a/numba/tests/test_jitclasses.py b/numba/tests/test_jitclasses.py
-index 87f1165..c1c5f35 100644
---- a/numba/tests/test_jitclasses.py
-+++ b/numba/tests/test_jitclasses.py
-@@ -909,6 +909,7 @@ class TestJitClass(TestCase, MemoryLeakMixin):
- self.assertEqual(t[2:2:1], 2)
- self.assertEqual(t[6:6:1], 3)
-
-+ @unittest.skip("Gentoo has not reverted the LLVM 'truncate longlabel' patch")
- def test_jitclass_longlabel_not_truncated(self):
- # See issue #3872, llvm 7 introduced a max label length of 1024 chars
- # Numba ships patched llvm 7.1 (ppc64le) and patched llvm 8 to undo this
-diff --git a/numba/tests/test_np_functions.py b/numba/tests/test_np_functions.py
-index 01c15fd..3d9e228 100644
---- a/numba/tests/test_np_functions.py
-+++ b/numba/tests/test_np_functions.py
-@@ -2028,6 +2028,7 @@ class TestNPFunctions(MemoryLeakMixin, TestCase):
- params = {'ary': ary, 'to_begin': a, 'to_end': b}
- _check(params)
-
-+ @unittest.skip("unhandled type error")
- def test_ediff1d_edge_cases(self):
- # NOTE: NumPy 1.16 has a variety of behaviours for type conversion, see
- # https://github.com/numpy/numpy/issues/13103, as this is not resolved
-diff --git a/numba/tests/test_record_dtype.py b/numba/tests/test_record_dtype.py
-index 6d479c4..2357206 100644
---- a/numba/tests/test_record_dtype.py
-+++ b/numba/tests/test_record_dtype.py
-@@ -796,7 +796,7 @@ class TestRecordDtype(unittest.TestCase):
- # len(transformed) is generally 10, but could be longer if a large
- # number of typecodes are in use. Checking <20 should provide enough
- # tolerance.
-- self.assertLess(len(transformed), 20)
-+ self.assertLessEqual(len(transformed), 20)
-
- struct_arr = types.Array(rec, 1, 'C')
- transformed = mangle_type(struct_arr)
-@@ -804,7 +804,7 @@ class TestRecordDtype(unittest.TestCase):
- self.assertNotIn('first', transformed)
- self.assertNotIn('second', transformed)
- # Length is usually 50 - 5 chars tolerance as above.
-- self.assertLess(len(transformed), 50)
-+ self.assertLessEqual(len(transformed), 50)
-
- def test_record_two_arrays(self):
- """
diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml
index e97c4322a..43b02aeec 100644
--- a/dev-python/numba/metadata.xml
+++ b/dev-python/numba/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">numba/numba</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/numba/numba-0.56.0.ebuild b/dev-python/numba/numba-0.56.3.ebuild
index 15eae53a7..9644fdf54 100644
--- a/dev-python/numba/numba-0.56.0.ebuild
+++ b/dev-python/numba/numba-0.56.3.ebuild
@@ -5,7 +5,7 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=setuptools
inherit optfeature multiprocessing distutils-r1
DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
@@ -22,15 +22,14 @@ RDEPEND="
>=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
<=dev-python/llvmlite-0.40.0
>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.23[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.1 )
+ <dev-python/numpy-1.24[${PYTHON_USEDEP}]
+ threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 )
"
BDEPEND="
dev-python/pip[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
"
-DISTUTILS_IN_SOURCE_BUILD=1
distutils_enable_tests unittest
distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
@@ -73,7 +72,6 @@ python_compile() {
# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
python_test() {
- distutils_install_for_testing
${EPYTHON} setup.py build_ext --inplace || die \
"${EPYTHON} failed to build_ext"
${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
index f5e2c79b7..9c121302b 100644
--- a/dev-python/nwbinspector/Manifest
+++ b/dev-python/nwbinspector/Manifest
@@ -1 +1,4 @@
-DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e
+DIST nwbinspector-0.3.9.gh.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e
+DIST nwbinspector-0.4.12.gh.tar.gz 455926 BLAKE2B 4bb8b493367593fdd575535e574b8494980a60a6ed1983a08f895c106e03e25ad6cd76b6c72cfcc42a34778d5059c90940bc9907dc9d87569df79aeae1698135 SHA512 60bb799beaff61612e7993069a34f62e0b6053dc3e820474f33c020c02f8c7b11bed0bca7e2bb335edfd60b06159be90b1a50dfcd497f6a3fb0916dc49cf17b7
+DIST nwbinspector-0.4.14.gh.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa
+DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c
diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
index e248266d4..b25a071ff 100644
--- a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
@@ -9,7 +9,7 @@ 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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
new file mode 100644
index 000000000..2fd918bd9
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/test_inspector.py
+ tests/unit_tests/test_time_series.py
+ )
+ epytest
+}
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
new file mode 100644
index 000000000..2fd918bd9
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/test_inspector.py
+ tests/unit_tests/test_time_series.py
+ )
+ epytest
+}
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
new file mode 100644
index 000000000..f18fc135f
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
@@ -0,0 +1,31 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest
new file mode 100644
index 000000000..b2c8e3956
--- /dev/null
+++ b/dev-python/probeinterface/Manifest
@@ -0,0 +1,3 @@
+DIST probeinterface-0.2.11.gh.tar.gz 194474 BLAKE2B 806d1d83a47fdd3a3196386d08ac5cee7f8561547be819fe814f67265e5b1e31e35107a047ed5c5ae533123b318ab6dca4b37ec8ddb6d30431644402b499b5d2 SHA512 a7e12fba55b952dea3b062dde37178b02259424ec82f788bb210a94cf7fb48d325045f2451c3e764b68563948fe81b60d1d378827a15ae5470931b120b2bc10d
+DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
+DIST probeinterface-0.2.5.gh.tar.gz 154572 BLAKE2B fdd339fdeec0c71f404fb96665b7d92db29d15f84163924d4508cbe17bf88b4a95e0296c48cf8f878034ed0ce3b249e750363ad32385b2e9d3e83900a760bebe SHA512 fdf170e1e4057445b0c8701105c7e6283258b460b1250e992f9896d6d3a0feacf3eb7dc6f8b35b77f591e1654930bd20d548758ea01b5d4cdb15a57dac24c4f9
diff --git a/dev-cpp/castxml/metadata.xml b/dev-python/probeinterface/metadata.xml
index 3cef409d1..58f800ce0 100644
--- a/dev-cpp/castxml/metadata.xml
+++ b/dev-python/probeinterface/metadata.xml
@@ -2,9 +2,6 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>gw.fossdev@gmail.com</email>
- </maintainer>
- <maintainer type="person">
<email>gentoo@chymera.eu</email>
<name>Horea Christian</name>
</maintainer>
@@ -12,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">SpikeInterface/probeinterface</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/probeinterface/probeinterface-0.2.11.ebuild b/dev-python/probeinterface/probeinterface-0.2.11.ebuild
new file mode 100644
index 000000000..d7751fe0d
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.11.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2021-2022 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="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
new file mode 100644
index 000000000..ac66253b4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.5.ebuild b/dev-python/probeinterface/probeinterface-0.2.5.ebuild
new file mode 100644
index 000000000..d7751fe0d
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.5.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2021-2022 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="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index ddb67415a..3a1d1f7a9 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,3 +1,3 @@
-DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a
DIST pynwb-2.0.1.tar.gz 452718 BLAKE2B d29347d748bd37bdf9326e0f9cc88b84742714ba78e6b0c56a923a4dd723c94e69ab3f325b5a5c66aef3ef819228abd64704268240fbdd369dac41b25e226b43 SHA512 897fa3bce93e733222a94bf9f043ed39c606c29f392f932a21c1004eebc1866d4caf50905a8e59baca87744af04d93e9957a7efb7e775422af5022787c4d086e
DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025
+DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57
diff --git a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
new file mode 100644
index 000000000..6141f629a
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.2.0-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>=2.10,<4',
+- 'hdmf>=3.4.2,<4',
+- 'numpy>=1.16,<1.24',
+- 'pandas>=1.1.5,<2',
+- 'python-dateutil>=2.7.3,<3',
++ 'h5py',
++ 'hdmf',
++ 'numpy',
++ 'pandas',
++ 'python-dateutil',
+ 'setuptools'
+ ]
+
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild
deleted file mode 100644
index e133d027b..000000000
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# 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}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- sci-libs/hdf5[ros3(-)]
- <dev-python/hdmf-3.3.2[${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/NeurodataWithoutBorders/pynwb/issues/1425
- 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-2.2.0.ebuild b/dev-python/pynwb/pynwb-2.2.0.ebuild
new file mode 100644
index 000000000..6ea595a8f
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.2.0.ebuild
@@ -0,0 +1,57 @@
+# 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="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3(-)]
+ >=dev-python/hdmf-3.3.2[${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/NeurodataWithoutBorders/pynwb/issues/1580
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_non_external_format
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_nonmatch_starting_frame
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data_construct_mode
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format_construct_mode
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_starting_frame
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pyparsing/Manifest b/dev-python/pyparsing/Manifest
deleted file mode 100644
index 736d09882..000000000
--- a/dev-python/pyparsing/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 2692e21d7..000000000
--- a/dev-python/pyparsing/metadata.xml
+++ /dev/null
@@ -1,21 +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>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
deleted file mode 100644
index 55da214a2..000000000
--- a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2004-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# please keep this ebuild at EAPI 7 -- sys-apps/portage dep
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..10} pypy3 )
-inherit distutils-r1
-
-MY_P=${P/-/_}
-DESCRIPTION="Easy-to-use Python module for text parsing"
-HOMEPAGE="https://github.com/pyparsing/pyparsing https://pypi.org/project/pyparsing/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz"
-S=${WORKDIR}/${PN}-${MY_P}
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~x64-cygwin ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
-IUSE="examples"
-
-distutils_enable_tests setup.py
-
-python_install_all() {
- if use examples; then
- docompress -x /usr/share/doc/${PF}/examples
- dodoc -r examples
- fi
- distutils-r1_python_install_all
-}
diff --git a/dev-python/python-gantt/metadata.xml b/dev-python/python-gantt/metadata.xml
index 3febd988f..18071f943 100644
--- a/dev-python/python-gantt/metadata.xml
+++ b/dev-python/python-gantt/metadata.xml
@@ -1,4 +1,4 @@
-<?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">
@@ -13,4 +13,7 @@
Python-Gantt makes it possible to easily draw gantt charts from Python
and export outputs as scalable vector graphics (SVG).
</longdescription>
+ <upstream>
+ <remote-id type="github">stefanSchinkel/gantt</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml
index d208f0f55..5fbf687f3 100644
--- a/dev-python/pyvote/metadata.xml
+++ b/dev-python/pyvote/metadata.xml
@@ -1,4 +1,4 @@
-<?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">
@@ -16,4 +16,7 @@
(or normal) probability density function for outcomes, or a fixed
outcome probability.
</longdescription>
+ <upstream>
+ <remote-id type="github">TheChymera/pyvote</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml
index ae9640ffb..8019eb9d1 100644
--- a/dev-python/pyzo/metadata.xml
+++ b/dev-python/pyzo/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">pyzo/pyzo</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml
index aa31ba351..9656580bb 100644
--- a/dev-python/repsep_utils/metadata.xml
+++ b/dev-python/repsep_utils/metadata.xml
@@ -1,15 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>chr@chymera.eu</email>
- <name>Horea Christian</name>
- </maintainer>
- <longdescription lang="en">
+ <maintainer type="person">
+ <email>chr@chymera.eu</email>
+ <name>Horea Christian</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
PythonTeX-interaction, as used by all RepSeP-style articles, as well as an
executable file allowing single-script execution for development and
debugging purposes.
</longdescription>
+ <upstream>
+ <remote-id type="github">TheChymera/repsep_utils</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index 440b5758f..d9550c50f 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/metadata.xml
@@ -8,5 +8,6 @@
<upstream>
<remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
<remote-id type="pypi">snakemake</remote-id>
+ <remote-id type="github">snakemake/snakemake</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/sphinx-argparse/Manifest b/dev-python/sphinx-argparse/Manifest
index cc6a6ba19..db92db585 100644
--- a/dev-python/sphinx-argparse/Manifest
+++ b/dev-python/sphinx-argparse/Manifest
@@ -1 +1 @@
-DIST sphinx-argparse-0.3.1.tar.gz 42953 BLAKE2B 76c74a270a638b1b894548bc898918fbfa5fde6bcf1ccbf5e69a3daaada829bc1ae27ad8befd18e834646dc2fc3b025f36807c2be894911cc0c6d65294174898 SHA512 3d289c90165eb6a3d7a94dff8e6a429a49eb404ce373e80e007a0cd9abaae1e1236f5393df2fbf11701c349dade9d199640dc398064da4fd50a58a90eb3f8f12
+DIST sphinx-argparse-0.3.2.tar.gz 45841 BLAKE2B 7f8a7159974bca803705736c848973d605594732983462d7636d82125e195d8ab87b76c247c9081e626cfe17d0f8d12a66d79076c643b0fe780c4f3eb5bbdc23 SHA512 fcc179d85ac9d30e327f75b02086c8f831856b099d9a26bc10adc4f20b57781a117a5dac2d6882e1f7c07604157dda2c2344c29ae3c475022ce252cde96646bb
diff --git a/dev-python/sphinx-argparse/metadata.xml b/dev-python/sphinx-argparse/metadata.xml
index ae9640ffb..3b119bca0 100644
--- a/dev-python/sphinx-argparse/metadata.xml
+++ b/dev-python/sphinx-argparse/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ashb/sphinx-argparse</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
index 5b380202e..4210a094b 100644
--- a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild
+++ b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
@@ -3,25 +3,24 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+PYTHON_COMPAT=( python3_{8..11} )
+DISTUTILS_USE_PEP517=poetry
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"
+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}
+RDEPEND="
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/ufl/metadata.xml b/dev-python/ufl/metadata.xml
index 142da2a70..3dff10f36 100644
--- a/dev-python/ufl/metadata.xml
+++ b/dev-python/ufl/metadata.xml
@@ -14,5 +14,6 @@ mathematical notation.
</longdescription>
<upstream>
<remote-id type="bitbucket">fenics-project/ufl</remote-id>
+ <remote-id type="github">FEniCS/ufl</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest
index 84f3a1b37..94118dae2 100644
--- a/dev-python/wraps/Manifest
+++ b/dev-python/wraps/Manifest
@@ -1 +1,2 @@
-DIST wraps-0.1.0.tar.gz 11126 BLAKE2B 6db25f60750fedcc44896e7d30f90400994a5c8c8fbb8bcad33696dfa4b3eb53f41c6a4e29a69c11610c6d32084019e9dbbdcdc6d7e462a0fda7f3cc3459c0fc SHA512 597afa975c0cc434ab861699d9de59c3815d240c59364c064346ab267f1f3c1177163db7c3fff20c6e2e68bed9eb9eff7eb068488d1bf427eca84925ba8e2e9f
+DIST wraps-0.1.0.tar.gz 25356 BLAKE2B 844293a5f7dfd84aa17f636d4863182118d40aa6ae53e044e77b77207be5b744cc78ef5235b889a963332fedb6922ce8ad829075099d9428be335366fe22cc56 SHA512 0e34d811869be2b22ec61638acb21342693e0fa44cf3d152dde179903c26771a9e26c673d2f37107122ba4bc92fe944b18ed16ebece7df0c07178845fc72bebb
+DIST wraps-0.2.0.tar.gz 25308 BLAKE2B b68359d34995f7bc39535e97458807a5d55e3547124ccb8b34f9cd34fe1d3b38921a3a0c16df031410022f74d414aba97af9e9f60a20fb635428030bc400b130 SHA512 daf72785c3215db06f4bf06704f02c7ecfd1ef5c58dbf5c50b2dee14755d73b519f8a13be9658bf825c296689d9b3effd08aec4254779812583c1024522751f0
diff --git a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
index 8a6de2917..c1b2ccd3e 100644
--- a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
+++ b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
@@ -1,14 +1,14 @@
--- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
+++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
-@@ -37,29 +37,6 @@
+@@ -36,31 +36,6 @@
- typing-extensions = ">= 4.2.0"
+ typing-extensions = ">= 4.3.0"
-[tool.poetry.group.format]
-optional = true
-
-[tool.poetry.group.format.dependencies]
--black = "22.6.0"
+-black = "22.8.0"
-
-[tool.poetry.group.format.dependencies.isort]
-version = "5.10.1"
@@ -18,17 +18,19 @@
-optional = true
-
-[tool.poetry.group.check.dependencies]
--mypy = "0.961"
+-mypy = "0.971"
-
-[tool.poetry.group.test]
-optional = true
-
-[tool.poetry.group.test.dependencies]
--pytest = "7.1.2"
+-pytest = "7.1.3"
-pytest-cov = "3.0.0"
+-anyio = "3.6.1"
+-trio = "0.21.0"
-
- [tool.black]
- line_length = 100
+ [tool.poetry.group.docs]
+ optional = true
@@ -67,29 +44,6 @@
line_length = 100
diff --git a/dev-python/wraps/wraps-0.1.0.ebuild b/dev-python/wraps/wraps-0.1.0-r1.ebuild
index 79df009b5..8474019e7 100644
--- a/dev-python/wraps/wraps-0.1.0.ebuild
+++ b/dev-python/wraps/wraps-0.1.0-r1.ebuild
@@ -10,7 +10,7 @@ inherit distutils-r1
DESCRIPTION=" Meaningful and safe wrapping types. "
HOMEPAGE="https://github.com/nekitdev/wraps"
-SRC_URI="https://github.com/nekitdev/wraps/releases/download/v${PV}/${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
@@ -24,7 +24,6 @@ RDEPEND="
"
PATCHES=(
- "${FILESDIR}/${P}-includes.patch"
"${FILESDIR}/${P}-poetry_groups.patch"
)
diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild
new file mode 100644
index 000000000..f3b37bb5c
--- /dev/null
+++ b/dev-python/wraps/wraps-0.2.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit distutils-r1
+
+DESCRIPTION=" Meaningful and safe wrapping types. "
+HOMEPAGE="https://github.com/nekitdev/wraps"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+# package does not have test suite (yet)
+
+RDEPEND="
+ >=dev-python/attrs-21.4.0[${PYTHON_USEDEP}]
+ >=dev-python/typing-extensions-4.2.0[${PYTHON_USEDEP}]
+ "
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.1.0-poetry_groups.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest
index 1bcc6ae18..7c74e59be 100644
--- a/dev-python/xgboost/Manifest
+++ b/dev-python/xgboost/Manifest
@@ -1 +1 @@
-DIST xgboost-1.3.1.tar.gz 764139 BLAKE2B cde5e36b07fd4e2dba4961921bc169b730c775a12d8ec98a80d3f442a894f4bcc946094122df8d9fc5e76c8f505d4c57416e2deb13fe88751a9f51d8e4e09cad SHA512 ffe5851bd600d3a2f9b92850df6a028ec2c7d5f40ce4bad8e21b24e128a251e577e4344d8ce5cc50d6c17accf23bf283ff605d93fe6e12b9bfea6b544c57f428
+DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b
diff --git a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch b/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch
deleted file mode 100644
index 8c2d3d180..000000000
--- a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-The BUILD_TEMP_DIR variable is set in the build phase but is no
-longer available in the install phase. We write the variable to
-a tmp file and read it later in the install phase as a workaround
-diff --git a/setup.py b/setup.py
-index 6244066..934e7cf 100644
---- a/setup.py
-+++ b/setup.py
-@@ -137,6 +137,11 @@ class BuildExt(build_ext.build_ext): # pylint: disable=too-many-ancestors
- build_dir = self.build_temp
- global BUILD_TEMP_DIR # pylint: disable=global-statement
- BUILD_TEMP_DIR = build_dir
-+ tmp_workdir = os.environ["WORKDIR"]
-+ py_vers = os.environ["EPYTHON"]
-+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "w")
-+ f.write(BUILD_TEMP_DIR)
-+ f.close()
- libxgboost = os.path.abspath(
- os.path.join(CURRENT_DIR, os.path.pardir, 'lib', lib_name()))
-
-@@ -229,6 +234,11 @@ class InstallLib(install_lib.install_lib):
- dst = os.path.join(self.install_dir, 'xgboost', 'lib', lib_name())
-
- global BUILD_TEMP_DIR # pylint: disable=global-statement
-+ tmp_workdir = os.environ["WORKDIR"]
-+ py_vers = os.environ["EPYTHON"]
-+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "r")
-+ BUILD_TEMP_DIR = f.read()
-+ f.close()
- libxgboost_path = lib_name()
-
- dft_lib_dir = os.path.join(CURRENT_DIR, os.path.pardir, 'lib')
diff --git a/dev-python/xgboost/xgboost-1.3.1.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild
index 25145f93d..e429f5741 100644
--- a/dev-python/xgboost/xgboost-1.3.1.ebuild
+++ b/dev-python/xgboost/xgboost-1.6.2.ebuild
@@ -1,10 +1,10 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="XGBoost Python Package"
@@ -15,11 +15,7 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-PATCHES=( "${FILESDIR}/${P}-fix-install.patch" )
-
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
-
-PATCHES=( "${FILESDIR}/${P}-fix-install.patch" )
diff --git a/dev-util/makefile2graph/metadata.xml b/dev-util/makefile2graph/metadata.xml
index 138cb7705..41bb35aa0 100644
--- a/dev-util/makefile2graph/metadata.xml
+++ b/dev-util/makefile2graph/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">lindenb/makefile2graph</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-util/plog/metadata.xml b/dev-util/plog/metadata.xml
index 7203fb853..40a8e36c6 100644
--- a/dev-util/plog/metadata.xml
+++ b/dev-util/plog/metadata.xml
@@ -4,4 +4,7 @@
<maintainer type="person">
<email>heroxbd@gentoo.org</email>
</maintainer>
+ <upstream>
+ <remote-id type="github">SergiusTheBest/plog</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index 9cc6d0a63..d58fa0e76 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,4 +1,4 @@
DIST dandi-0.45.1.tar.gz 321362 BLAKE2B d07296be6bd4237fea4aa83c0b087de45234157aa6aa457f8d44f56b514a4deca11226831182b84c19a72b398183b3b181beb3946c7f8cce2d842ac80f0b57e2 SHA512 07d97420651bbd82d8d4146322ff80873489bd49869834ace9986f1ddc1880be5ff6bd1d625d8b4607a90de8007aeba152e8161af05c25a804cb18c7a0c78e29
-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
+DIST dandi-0.46.6.tar.gz 218868 BLAKE2B 7900c153172aa9669d0eae6bc2293ef51d1640b2fdd4e40eb887b1aba555d61617f95fb76601f1e81aeb9e0a54901c711bfb3c95eb478853490b29a0c1ee20e7 SHA512 db04e261205be716d6a098fbb63760411d3869c692df78954b50b649228747e0c18a9a32d3a9b0a5f21f55432e6a6cadad2142ee99168d02f02cfe51bf7eef93
+DIST dandi-cli-0.38.0.gh.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054
+DIST dandi-cli-0.39.4.gh.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
index 08d652de9..1842cbb5e 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
@@ -10,11 +10,11 @@ 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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
@@ -28,7 +28,7 @@ RDEPEND="
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
index 0c8ba225e..a83a0b219 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
@@ -10,11 +10,11 @@ inherit distutils-r1
DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
@@ -28,7 +28,7 @@ RDEPEND="
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
index dcdb13e85..0453e2f00 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
@@ -18,7 +18,7 @@ SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
@@ -32,7 +32,7 @@ RDEPEND="
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
index 08d652de9..581257bdb 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
@@ -8,27 +8,31 @@ PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
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 -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
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/dandi-schema-0.7*[${PYTHON_USEDEP}]
dev-python/fasteners[${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/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[${PYTHON_USEDEP}]
@@ -43,7 +47,7 @@ RDEPEND="
dev-python/zarr[${PYTHON_USEDEP}]
"
-DEPEND="
+BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
dev-python/responses[${PYTHON_USEDEP}]
@@ -55,22 +59,10 @@ DEPEND="
# 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"
-)
+S="${WORKDIR}/${MY_P}"
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
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
index 5ad5852a2..521f7a0be 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,5 +1,4 @@
-DIST datalad-0.15.1.tar.gz 1357778 BLAKE2B 7c12c3ff1bd8d260e8e7cfd9e477a1f0798f6fc0fbdbc335229bcf88362ebc7280eeb92bb59c45e0f66677297680e4d8d7bc8f56c7ac171f921bc389c1ceef7c SHA512 d5ae7859486748cbf40bd27f3351fa5620b8342c6a4347b8e3e0cb331de5fa33b9384071adbb899fd7878641a210a11b360a9ea68d0c7437eae709244fa08fd1
-DIST datalad-0.15.2.tar.gz 1361038 BLAKE2B c515b374f0781693ed0f1d0d2c260a0bdb1c9e998b782a2232c501b4ab7c022adc38f00a79d0aed04ffde4ade5c696705d53bf16dbaec2378c74ef4ab35a7a15 SHA512 f0206855439c2d376172218ec6bf1ffa3277508256a5a49a2ec65a57bb5720e039481329c16459ed62eb1c9ed0126dc178ca34fa2c3b8dfdf8b8a0706a2b8658
DIST datalad-0.16.1.tar.gz 1472447 BLAKE2B b62f2fb37d0bc5cdaa8fd36f1bdea1beab4b4c071ba32c45b1ba5f2036788e4dc4767b406b20c0e0ccf3a5e02fbcb77b73ac9d8f254d02d6004ce909a94bffb5 SHA512 7236e635f8c9b9fbc9f82776d325dce1585d9a99d767b66f2877fb935d788c36335562ae8679821dea1b433f5d122f687e0c6b2098d8e388b8f8f6134751cc5b
DIST datalad-0.17.0.tar.gz 1510529 BLAKE2B 797a4d15139a88d20f03d1b81cf8b19088cf91925852a0a0d2079b3a64debfaa4945c31f21cc701ac507b00c1eabe10eb57653d8cbef1914d2c7babc48324458 SHA512 fea35a574f13b4957149f87553c80eceaebde064921e5fa28960b088e6d8f38a2eb2cbf797c9e031bd696bdca1400c2baa4c3e94c2b78bf8c1349a752928b09c
DIST datalad-0.17.2.tar.gz 1512123 BLAKE2B 83f1d437f6a2d300c169710fd12c8e126e5ab89aee9f0ccda48325c13c26a7e895fc11d33e61a266d7e4f5ac976244950851080055639b679819f659286c3c57 SHA512 7eceaea6bd0f0e251f194d8c1846e5abfff46174c536a42c1c0f891ca06f9688f8d291dec706f4ca51128d6588ceaf28039d80e63ebc5a15417bca3c74f0d866
+DIST datalad-0.17.7.tar.gz 1534265 BLAKE2B daeee7a6ca66ac632b085ce1fed2a702f3189da195d50b3fe5bc63c568c2f6633dbcc6da91883f64dd8d2391d8cfdef9bdbcd28091b098fc9edde6ca743767c1 SHA512 b01442bdd672e6ab0ebfe7fc71721437e117df0ddbe68558b8c21d4f5d387de807870250eac83630e52d2bb5ecf69686b5679c2a1458edb13b7e2a940c4e1330
diff --git a/dev-vcs/datalad/datalad-0.15.2.ebuild b/dev-vcs/datalad/datalad-0.15.2.ebuild
deleted file mode 100644
index 1142cad18..000000000
--- a/dev-vcs/datalad/datalad-0.15.2.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# 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="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-arch/p7zip
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wrapt[${PYTHON_USEDEP}]
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/whoosh[${PYTHON_USEDEP}]
- )
- misc? (
- dev-python/argcomplete[${PYTHON_USEDEP}]
- dev-python/pyperclip[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- )
- publish? (
- dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- dev-python/PyGithub[${PYTHON_USEDEP}]
- )
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests nose
-
-python_test() {
- export DATALAD_TESTS_NONETWORK=1
- ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
-}
diff --git a/dev-vcs/datalad/datalad-0.16.1.ebuild b/dev-vcs/datalad/datalad-0.16.1-r1.ebuild
index 50e29f19d..d1592fbf6 100644
--- a/dev-vcs/datalad/datalad-0.16.1.ebuild
+++ b/dev-vcs/datalad/datalad-0.16.1-r1.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -19,6 +20,7 @@ RESTRICT="!test? ( test )"
RDEPEND="
app-arch/p7zip
dev-python/annexremote[${PYTHON_USEDEP}]
+ dev-vcs/git-annex
dev-python/appdirs[${PYTHON_USEDEP}]
>=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${PYTHON_USEDEP}]
@@ -31,7 +33,7 @@ RDEPEND="
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
@@ -49,9 +51,10 @@ RDEPEND="
dev-python/PyGithub[${PYTHON_USEDEP}]
)
"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
+ ${RDEPEND}
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
diff --git a/dev-vcs/datalad/datalad-0.17.0.ebuild b/dev-vcs/datalad/datalad-0.17.0-r1.ebuild
index 4fb1d3de1..8e2de55bb 100644
--- a/dev-vcs/datalad/datalad-0.17.0.ebuild
+++ b/dev-vcs/datalad/datalad-0.17.0-r1.ebuild
@@ -20,6 +20,7 @@ RESTRICT="!test? ( test )"
RDEPEND="
app-arch/p7zip
app-arch/patool[${PYTHON_USEDEP}]
+ dev-vcs/git-annex
dev-python/annexremote[${PYTHON_USEDEP}]
>=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${PYTHON_USEDEP}]
@@ -32,7 +33,7 @@ RDEPEND="
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
@@ -50,10 +51,12 @@ RDEPEND="
)
"
DEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]
test? (
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/nose[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
)
"
@@ -62,6 +65,12 @@ DEPEND="
# https://github.com/datalad/datalad/issues/6623
PATCHES=( "${FILESDIR}/${PN}-0.17.0-skip.patch" )
+EPYTEST_DESELECT=(
+ # Reported upstream: https://github.com/datalad/datalad/issues/6870
+ datalad/tests/test_misc.py::test_test
+ datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper
+)
+
distutils_enable_tests pytest
python_test() {
diff --git a/dev-vcs/datalad/datalad-0.17.2.ebuild b/dev-vcs/datalad/datalad-0.17.2-r1.ebuild
index 753985ef6..c06056657 100644
--- a/dev-vcs/datalad/datalad-0.17.2.ebuild
+++ b/dev-vcs/datalad/datalad-0.17.2-r1.ebuild
@@ -20,6 +20,7 @@ RESTRICT="!test? ( test )"
RDEPEND="
app-arch/p7zip
app-arch/patool[${PYTHON_USEDEP}]
+ dev-vcs/git-annex
dev-python/annexremote[${PYTHON_USEDEP}]
>=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${PYTHON_USEDEP}]
@@ -32,7 +33,7 @@ RDEPEND="
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
@@ -49,11 +50,13 @@ RDEPEND="
dev-vcs/python-gitlab[${PYTHON_USEDEP}]
)
"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
+ ${RDEPEND}
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/nose[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
)
"
diff --git a/dev-vcs/datalad/datalad-0.15.1.ebuild b/dev-vcs/datalad/datalad-0.17.7.ebuild
index 1142cad18..fc8276b00 100644
--- a/dev-vcs/datalad/datalad-0.15.1.ebuild
+++ b/dev-vcs/datalad/datalad-0.17.7.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -18,20 +19,21 @@ RESTRICT="!test? ( test )"
RDEPEND="
app-arch/p7zip
+ app-arch/patool[${PYTHON_USEDEP}]
+ dev-vcs/git-annex
dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
>=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
- app-arch/patool[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/iso8601[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wrapt[${PYTHON_USEDEP}]
+ dev-python/wraps[${PYTHON_USEDEP}]
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
@@ -46,23 +48,34 @@ RDEPEND="
)
publish? (
dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- dev-python/PyGithub[${PYTHON_USEDEP}]
)
"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
+BEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
+ ${RDEPEND}
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/mypy[${PYTHON_USEDEP}]
+ dev-python/nose[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
)
"
+# also wants base RDEPEND:
+# looseversion
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
+
+EPYTEST_DESELECT=(
+ # Reported upstream: https://github.com/datalad/datalad/issues/6870
+ datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper
+)
-distutils_enable_tests nose
+distutils_enable_tests pytest
python_test() {
- export DATALAD_TESTS_NONETWORK=1
- ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
+ local -x DATALAD_TESTS_NONETWORK=1
+ # see test groups in "tox.ini"
+ epytest -k "not turtle and not slow and not usecase"
}
diff --git a/dev-vcs/datalad/files/datalad-0.16.1-input.patch b/dev-vcs/datalad/files/datalad-0.16.1-input.patch
index beb539b5d..97d16e70a 100644
--- a/dev-vcs/datalad/files/datalad-0.16.1-input.patch
+++ b/dev-vcs/datalad/files/datalad-0.16.1-input.patch
@@ -92,3 +92,40 @@ index 09387a70d..6dc0e0be4 100644
@with_tempfile
def test_credential_cycle(path):
+--- a/datalad/distribution/tests/test_siblings.py 2022-10-24 16:06:18.740935265 -0400
++++ b/datalad/distribution/tests/test_siblings.py 2022-10-24 16:08:43.054322297 -0400
+@@ -9,6 +9,8 @@
+
+ """
+
++from nose import SkipTest
++
+ from datalad.support.path import (
+ basename,
+ join as opj,
+@@ -504,6 +504,7 @@
+ @with_tempfile(mkdir=True)
+ @serve_path_via_http
+ def test_as_common_datasource(testbed, viapath, viaurl, remotepath, url):
++ raise SkipTest("Known to fail in Portage environment.")
+ ds = Dataset(remotepath).create()
+ (ds.pathobj / 'testfile').write_text('likemagic')
+ (ds.pathobj / 'testfile2').write_text('likemagic2')
+--- a/datalad/local/tests/test_add_archive_content.py
++++ b/datalad/local/tests/test_add_archive_content.py
+@@ -13,6 +13,7 @@
+ __docformat__ = 'restructuredtext'
+
+ import os
++from nose import SkipTest
+ from glob import glob
+ from os import unlink
+ from os.path import (
+@@ -514,6 +515,7 @@
+ assert_false(lexists(self.ds.pathobj / '1.tar'))
+
+ def test_add_archive_leading_dir(self):
++ raise SkipTest("Known to fail in Portage environment.")
+ import os
+ os.mkdir(self.ds.pathobj / 'sub')
+ f123 = Path('sub') / '123.tar'
diff --git a/dev-vcs/datalad/files/datalad-0.16.1-tests.patch b/dev-vcs/datalad/files/datalad-0.16.1-tests.patch
new file mode 100644
index 000000000..e6231b7f1
--- /dev/null
+++ b/dev-vcs/datalad/files/datalad-0.16.1-tests.patch
@@ -0,0 +1,10 @@
+--- a/datalad-0.16.1/datalad/distribution/tests/test_siblings.py 2022-10-24 16:06:18.740935265 -0400
++++ b/datalad-0.16.1/datalad/distribution/tests/test_siblings.py 2022-10-24 16:08:43.054322297 -0400
+@@ -504,6 +504,7 @@
+ @with_tempfile(mkdir=True)
+ @serve_path_via_http
+ def test_as_common_datasource(testbed, viapath, viaurl, remotepath, url):
++ raise SkipTest("Known to fail in Portage environment.")
+ ds = Dataset(remotepath).create()
+ (ds.pathobj / 'testfile').write_text('likemagic')
+ (ds.pathobj / 'testfile2').write_text('likemagic2')
diff --git a/eclass/intel-sdp-r1.eclass b/eclass/intel-sdp-r1.eclass
deleted file mode 100644
index 9d902395f..000000000
--- a/eclass/intel-sdp-r1.eclass
+++ /dev/null
@@ -1,571 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: intel-sdp-r1.eclass
-# @MAINTAINER:
-# Justin Lecher <jlec@gentoo.org>
-# David Seifert <soap@gentoo.org>
-# Sci Team <sci@gentoo.org>
-# @BLURB: Handling of Intel's Software Development Products package management
-
-MULTILIB_COMPAT=( abi_x86_{32,64} )
-
-inherit check-reqs eutils multilib-build
-
-EXPORT_FUNCTIONS src_unpack src_install pkg_postinst pkg_postrm pkg_pretend
-
-if [[ ! ${_INTEL_SDP_R1_ECLASS_} ]]; then
-
-case "${EAPI}" in
- 7) ;;
- *) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-# @ECLASS-VARIABLE: INTEL_DIST_NAME
-# @DESCRIPTION:
-# The package name to download from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. parallel_studio_xe
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_NAME:=parallel_studio_xe}
-
-# @ECLASS-VARIABLE: INTEL_DIST_PV
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# The package download version from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. 2016_update1
-#
-# Must be defined before inheriting the eclass.
-
-# @ECLASS-VARIABLE: INTEL_DIST_TARX
-# @DESCRIPTION:
-# The package distfile suffix.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. tgz
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_TARX:=tgz}
-
-# @ECLASS-VARIABLE: INTEL_SUBDIR
-# @DESCRIPTION:
-# The package sub-directory (without version numbers) where it will end-up in /opt/intel
-#
-# e.g. compilers_and_libraries
-#
-# To determine its value, you have to do a raw install from the Intel tarball.
-: ${INTEL_SUBDIR:=compilers_and_libraries}
-
-# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# Possibility to skip the mandatory check for licenses. Only set this if there
-# is really no fix.
-
-# @ECLASS-VARIABLE: INTEL_RPMS_DIR
-# @DESCRIPTION:
-# Main subdirectory which contains the rpms to extract.
-: ${INTEL_RPMS_DIR:=rpm}
-
-# @ECLASS-VARIABLE: INTEL_DIST_BIN_RPMS
-# @DESCRIPTION:
-# Functional name of rpm without any version/arch tag.
-# Has to be a bash array
-#
-# e.g. ("icc-l-all-devel")
-#
-# if the rpm is located in a directory other than INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli")
-[[ ${INTEL_DIST_BIN_RPMS[@]} ]] || INTEL_DIST_BIN_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_AMD64_RPMS
-# @DESCRIPTION:
-# AMD64 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_AMD64_RPMS[@]} ]] || INTEL_DIST_AMD64_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_X86_RPMS
-# @DESCRIPTION:
-# X86 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_X86_RPMS[@]} ]] || INTEL_DIST_X86_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_DAT_RPMS
-# @DESCRIPTION:
-# Functional name of rpm of common data which are arch free
-# without any version tag. Has to be a bash array.
-#
-# e.g. ("openmp-l-all-devel")
-#
-# if the rpm is located in a directory different to INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli-common")
-[[ ${INTEL_DIST_DAT_RPMS[@]} ]] || INTEL_DIST_DAT_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_SPLIT_ARCH
-# @DESCRIPTION:
-# Set to "true" if arches are to be fetched separately, instead of using
-# the combined tarball.
-: ${INTEL_DIST_SPLIT_ARCH:=false}
-
-# @FUNCTION: _isdp_path_exists
-# @INTERNAL
-# @USAGE: [-a|-o] <paths>
-# @DESCRIPTION:
-# Check if the specified paths exist. Works for all types of paths
-# (files/dirs/etc...). The -a and -o flags control the requirements
-# of the paths. They correspond to "and" and "or" logic. So the -a
-# flag means all the paths must exist while the -o flag means at least
-# one of the paths must exist. The default behavior is "and". If no
-# paths are specified, then the return value is "false".
-_isdp_path_exists() {
- local opt=$1
- [[ ${opt} == -[ao] ]] && shift || opt="-a"
-
- # no paths -> return false
- # same behavior as: [[ -e "" ]]
- [[ $# -eq 0 ]] && return 1
-
- local p r=0
- for p in "$@" ; do
- [[ -e ${p} ]]
- : $(( r += $? ))
- done
-
- case ${opt} in
- -a) return $(( r != 0 )) ;;
- -o) return $(( r == $# )) ;;
- esac
- eerror "path_exists has been removed. Please see the following post"
- eerror "for a replacement snippet:"
- eerror "https://blogs.gentoo.org/mgorny/2018/08/09/inlining-path_exists/"
- die "path_exists is banned"
-}
-
-# @FUNCTION: _isdp_get-sdp-year
-# @INTERNAL
-# @DESCRIPTION:
-# Gets the year component from INTEL_DIST_PV
-_isdp_get-sdp-year() {
- local _intel_sdp_year
- _intel_sdp_year=${INTEL_DIST_PV}
- _intel_sdp_year=${_intel_sdp_year%_sp*}
- _intel_sdp_year=${_intel_sdp_year%_update*}
- echo "${_intel_sdp_year}"
-}
-
-# @FUNCTION: isdp_get-sdp-dir
-# @DESCRIPTION:
-# Gets the full rootless path to the installation directory
-#
-# e.g. opt/intel/compilers_and_libraries_2016.1.150
-# opt/intel/vtune_amplifier_2018.2.0.551022
-isdp_get-sdp-dir() {
- local _intel_sdp_dir="opt/intel/${INTEL_SUBDIR}_$(_isdp_get-sdp-year).$(ver_cut 3-)"
- echo "${_intel_sdp_dir}"
-}
-
-# @FUNCTION: isdp_get-sdp-edir
-# @DESCRIPTION:
-# Gets the full rooted/prefixed path to the installation directory
-#
-# e.g. /opt/intel/compilers_and_libraries_2016.1.150
-isdp_get-sdp-edir() {
- local _intel_sdp_edir="${EPREFIX%/}/$(isdp_get-sdp-dir)"
- echo "${_intel_sdp_edir}"
-}
-
-SRC_URI="${INTEL_DIST_NAME}_${INTEL_DIST_PV}.${INTEL_DIST_TARX}"
-LICENSE="Intel-SDP"
-# TODO: Proper slotting
-# Future work, #394411
-SLOT="0"
-
-RESTRICT="bindist mirror fetch"
-
-RDEPEND=""
-DEPEND="app-arch/rpm2targz"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="$(isdp_get-sdp-dir)/*"
-
-# @FUNCTION: isdp_convert2intel-arch
-# @USAGE: <arch>
-# @DESCRIPTION:
-# Convert between portage arch (e.g. amd64, x86) and intel installed arch
-# nomenclature (e.g. intel64, ia32)
-isdp_convert2intel-arch() {
- debug-print-function ${FUNCNAME} "${@}"
-
- case $1 in
- *amd64*|abi_x86_64)
- echo "intel64"
- ;;
- *x86*)
- echo "ia32"
- ;;
- *)
- die "Abi \'$1\' is unsupported"
- ;;
- esac
-}
-
-# @FUNCTION: isdp_get-native-abi-arch
-# @DESCRIPTION:
-# Determine the the intel arch string of the native ABI
-isdp_get-native-abi-arch() {
- debug-print-function ${FUNCNAME} "${@}"
-
- use amd64 && echo "$(isdp_convert2intel-arch abi_x86_64)"
- use x86 && echo "$(isdp_convert2intel-arch abi_x86_32)"
-}
-
-# @FUNCTION: isdp_get-sdp-installed-arches
-# @DESCRIPTION:
-# Returns a space separated list of the arch suffixes used in directory
-# names for enabled ABIs. Intel uses "ia32" for x86 and "intel64" for
-# amd64. The result would be "ia32 intel64" if both ABIs were enabled.
-isdp_get-sdp-installed-arches() {
- local arch=()
- use abi_x86_64 && arch+=($(isdp_convert2intel-arch abi_x86_64))
- use abi_x86_32 && arch+=($(isdp_convert2intel-arch abi_x86_32))
- echo "${arch[*]}"
-}
-
-# @FUNCTION: _isdp_generate-list-install-rpms
-# @INTERNAL
-# @DESCRIPTION:
-# Generates the list of fully expanded RPMs to be extracted.
-_isdp_generate-list-install-rpms() {
- debug-print-function ${FUNCNAME} "${@}"
-
- # Expand components into full RPM filenames
- expand_component_into_full_rpm() {
- local deref_var="${1}[@]"
- local p rpm_prefix expanded_full_rpms=()
-
- for p in "${!deref_var}"; do
- # check if a directory is prefixed
- if [[ "${p}" == "${p##*/}" ]]; then
- rpm_prefix="${INTEL_RPMS_DIR}/intel-"
- else
- rpm_prefix=""
- fi
- expanded_full_rpms+=( "${rpm_prefix}${p}" )
- done
- echo ${expanded_full_rpms[*]}
- }
-
- local vars_to_expand=("INTEL_DIST_BIN_RPMS" "INTEL_DIST_DAT_RPMS")
- if use abi_x86_32; then
- vars_to_expand+=("INTEL_DIST_X86_RPMS")
- fi
- if use abi_x86_64; then
- vars_to_expand+=("INTEL_DIST_AMD64_RPMS")
- fi
-
- local i fully_expanded_intel_rpms=()
- for ((i=0; i<${#vars_to_expand[@]}; i++)); do
- fully_expanded_intel_rpms+=($(expand_component_into_full_rpm "${vars_to_expand[i]}"))
- done
- echo ${fully_expanded_intel_rpms[*]}
-}
-
-# @FUNCTION: _isdp_big-warning
-# @USAGE: [pre-check | test-failed]
-# @INTERNAL
-# @DESCRIPTION:
-# warn user that we really require a license
-_isdp_big-warning() {
- debug-print-function ${FUNCNAME} "${@}"
-
- case ${1} in
- pre-check )
- ewarn "License file not found!"
- ;;
-
- test-failed )
- ewarn "Function test failed. Most probably due to an invalid license."
- ewarn "This means you already tried to bypass the license check once."
- ;;
- esac
-
- ewarn
- ewarn "Make sure you have received an Intel license."
- ewarn "To receive a non-commercial license, you need to register at:"
- ewarn "https://software.intel.com/en-us/qualify-for-free-software"
- ewarn "Install the license file into ${EPREFIX}/opt/intel/licenses"
-
- case ${1} in
- pre-check )
- ewarn "before proceeding with installation of ${P}"
- ;;
- * )
- ;;
- esac
-}
-
-# @FUNCTION: _isdp_version_test
-# @INTERNAL
-# @DESCRIPTION:
-# Testing for valid license by asking for version information of the compiler.
-_isdp_version_test() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local comp
- case ${PN} in
- ifc )
- debug-print "Testing ifort"
- comp=ifort
- ;;
- icc )
- debug-print "Testing icc"
- comp=icc
- ;;
- *)
- die "${PN} is not supported for testing"
- ;;
- esac
-
- local comp_full arch warn
- for arch in $(isdp_get-sdp-installed-arches); do
- case ${EBUILD_PHASE} in
- install )
- comp_full="${ED%/}/$(isdp_get-sdp-dir)/linux/bin/${arch}/${comp}"
- ;;
- postinst )
- comp_full="$(isdp_get-sdp-edir)/linux/bin/${arch}/${comp}"
- ;;
- * )
- die "Compile test not supported in ${EBUILD_PHASE}"
- ;;
- esac
-
- debug-print "LD_LIBRARY_PATH=\"$(isdp_get-sdp-edir)/linux/bin/${arch}/\" \"${comp_full}\" -V"
-
- LD_LIBRARY_PATH="$(isdp_get-sdp-edir)/linux/bin/${arch}/" "${comp_full}" -V &>/dev/null || warn=yes
- done
- [[ ${warn} == yes ]] && _isdp_big-warning test-failed
-}
-
-# @FUNCTION: _isdp_run-test
-# @INTERNAL
-# @DESCRIPTION:
-# Test if installed compiler is working.
-_isdp_run-test() {
- debug-print-function ${FUNCNAME} "${@}"
-
- if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
- case ${PN} in
- ifc | icc )
- _isdp_version_test
- ;;
- * )
- debug-print "No test available for ${PN}"
- ;;
- esac
- fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_pretend
-# @DESCRIPTION:
-#
-# * Check for a (valid) license before proceeding.
-#
-# * Check for space requirements being fulfilled.
-#
-intel-sdp-r1_pkg_pretend() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local warn=1 dir dirs ret arch a p
-
- : ${CHECKREQS_DISK_BUILD:=256M}
- check-reqs_pkg_pretend
-
- if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
- if [[ ${INTEL_LICENSE_FILE} == *@* ]]; then
- einfo "Looks like you are using following license server:"
- einfo " ${INTEL_LICENSE_FILE}"
- return 0
- fi
-
- dirs=(
- "${EPREFIX}/opt/intel/licenses"
- "$(isdp_get-sdp-edir)/licenses"
- "$(isdp_get-sdp-edir)/Licenses"
- )
- for dir in "${dirs[@]}" ; do
- ebegin "Checking for a license in: ${dir}"
- _isdp_path_exists "${dir}"/*lic && warn=0
- eend ${warn} && break
- done
- if [[ ${warn} == 1 ]]; then
- _isdp_big-warning pre-check
- die "Could not find license file"
- fi
- else
- eqawarn "The ebuild doesn't check for presence of a proper intel license!"
- eqawarn "This shouldn't be done unless there is a very good reason."
- fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_nofetch
-# @DESCRIPTION:
-# Advice user to download the parallel studio tarball
-pkg_nofetch() {
- einfo "Please download"
- einfo " ${SRC_URI}"
- einfo "from"
- einfo " https://registrationcenter.intel.com/RegCenter/MyProducts.aspx"
- einfo "and place the tarball in your DISTDIR directory."
-}
-
-# @FUNCTION: intel-sdp-r1_src_unpack
-# @DESCRIPTION:
-# Unpacking necessary rpms from tarball, extract them and rearrange the output.
-intel-sdp-r1_src_unpack() {
- local t
- for t in ${A}; do
- local r list=() source_rpms=($(_isdp_generate-list-install-rpms))
- for r in "${source_rpms[@]}"; do
- list+=( ${t%%.*}/${r} )
- done
-
- local debug_list
- debug_list="$(IFS=$'\n'; echo ${list[@]} )"
-
- debug-print "Adding to decompression list:"
- debug-print ${debug_list}
-
- tar -xvf "${DISTDIR}"/${t} ${list[@]} &> "${T}"/rpm-extraction.log
-
- for r in ${list[@]}; do
- einfo "Unpacking ${r}"
- printf "\nUnpacking %s\n" "${r}" >> "${T}"/rpm-extraction.log
- rpm2tar -O ${r} | tar -xvf - &>> "${T}"/rpm-extraction.log; assert "Unpacking ${r} failed"
- done
- done
-}
-
-# @FUNCTION: intel-sdp-r1_src_install
-# @DESCRIPTION:
-# Install everything
-intel-sdp-r1_src_install() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local i
- # remove uninstall information
- ebegin "Cleaning out uninstall"
- while IFS='\n' read -r -d '' i; do
- rm -r "${i}" || die
- done < <(find opt -regextype posix-extended -regex '.*(uninstall|uninstall.sh)$' -print0)
- eend
-
- # handle documentation
- if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)"; then
- # normal man pages
- if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)/en/man/common/man1"; then
- doman opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man/common/man1/*
- rm -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man || die
- fi
-
- use doc && dodoc -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/*
-
- ebegin "Cleaning out documentation"
- rm -r "opt/intel/documentation_$(_isdp_get-sdp-year)" || die
- rm -rf "$(isdp_get-sdp-dir)"/linux/{documentation,man} || die
- eend
- fi
-
- # MPI man pages
- if _isdp_path_exists "$(isdp_get-sdp-dir)/linux/mpi/man/man3"; then
- doman "$(isdp_get-sdp-dir)"/linux/mpi/man/man3/*
- rm -r "$(isdp_get-sdp-dir)"/linux/mpi/man || die
- fi
-
- # licensing docs
- if _isdp_path_exists "$(isdp_get-sdp-dir)/licensing/documentation"; then
- dodoc -r "$(isdp_get-sdp-dir)/licensing/documentation"/*
- rm -rf "$(isdp_get-sdp-dir)/licensing/documentation" || die
- fi
-
- if _isdp_path_exists opt/intel/"${INTEL_DIST_NAME}"*/licensing; then
- dodoc -r opt/intel/"${INTEL_DIST_NAME}"*/licensing
- rm -rf opt/intel/"${INTEL_DIST_NAME}"* || die
- fi
-
- # handle examples
- if _isdp_path_exists "opt/intel/samples_$(_isdp_get-sdp-year)"; then
- use examples && dodoc -r opt/intel/samples_"$(_isdp_get-sdp-year)"/*
-
- ebegin "Cleaning out examples"
- rm -r "opt/intel/samples_$(_isdp_get-sdp-year)" || die
- eend
- fi
-
- # remove eclipse unconditionally
- ebegin "Cleaning out eclipse files"
- rm -rf opt/intel/ide_support_* || die
- eend
-
- # repair shell scripts used for sourcing PATH (iccvars.sh and such)
- ebegin "Tagging ${PN}"
- find opt -name \*sh -type f -exec sed -i \
- -e "s:<.*DIR>:$(isdp_get-sdp-edir)/linux:g" \
- '{}' + || die
- eend
-
- ebegin "Removing broken symlinks"
- while IFS='\n' read -r -d '' i; do
- rm "${i}" || die
- done < <(find opt -xtype l -print0)
- eend
-
- mv opt "${ED%/}"/ || die "moving files failed"
-
- keepdir "$(isdp_get-sdp-dir)"/licenses /opt/intel/ism/rm
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postinst
-# @DESCRIPTION:
-# Test for all things working
-intel-sdp-r1_pkg_postinst() {
- debug-print-function ${FUNCNAME} "${@}"
-
- _isdp_run-test
-
- if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" ; then
- #add ccache links as icc might get installed after ccache
- "${EROOT}"/usr/bin/ccache-config --install-links
- fi
-
- elog "Beginning with the 2016 suite of Intel tools, Gentoo has removed"
- elog "support for the eclipse plugin. If you require the IDE support,"
- elog "you will have to install the suite on your own, outside portage."
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postrm
-# @DESCRIPTION:
-# Sanitize cache links
-intel-sdp-r1_pkg_postrm() {
- debug-print-function ${FUNCNAME} "${@}"
-
- if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" && [[ -z ${REPLACED_BY_VERSION} ]]; then
- # --remove-links would remove all links, --install-links updates them
- "${EROOT}"/usr/bin/ccache-config --install-links
- fi
-}
-
-_INTEL_SDP_R1_ECLASS_=1
-fi
diff --git a/licenses/estscan b/licenses/estscan
deleted file mode 100644
index 46089aab6..000000000
--- a/licenses/estscan
+++ /dev/null
@@ -1,88 +0,0 @@
- ESTScan license
- ---------------
-
-Copyright (c) Swiss Institute of Bioinformatics, Ludwig Institute for
-Cancer Research (LICR), and Swiss Institute for Experimental Cancer
-Research (ISREC), 1999, 2004. For the purposes of this copyright, the
-Swiss Institute of Bioinformatics acts on behalf of its partners, LICR
-and ISREC.
-
-The ESTScan software is the exclusive property of the copyright
-owners, at UNIL - BEP, CH-1015 LAUSANNE, Switzerland. The Swiss
-Institute of Bioinformatics provides the ESTScan program WITHOUT ANY
-WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR
-ANY OTHER WARRANTY, EXPRESS OR IMPLIED.
-
-
-License Terms:
-
-Use, Modification and Redistribution (including distribution of any
-modified or derived work) in source and binary forms is permitted only
-if each of the following conditions is met:
-
-1. Redistributions qualify as "freeware" or "Open Source Software" under
- one of the following terms:
-
- (a) Redistributions are made at no charge beyond the reasonable cost of
- materials and delivery.
-
- (b) Redistributions are accompanied by a copy of the Source Code or by an
- irrevocable offer to provide a copy of the Source Code for up to three
- years at the cost of materials and delivery. Such redistributions
- must allow further use, modification, and redistribution of the Source
- Code under substantially the same terms as this license. For the
- purposes of redistribution "Source Code" means the complete source
- code of ESTScan including all modifications.
-
- Other forms of redistribution are allowed only under a separate royalty-
- free agreement permitting such redistribution subject to standard
- commercial terms and conditions. A copy of such agreement may be
- obtained from the Swiss Institute of Bioinformatics at the above address.
-
-2. Redistributions of source code must retain the copyright notices as they
- appear in each source code file, these license terms, and the
- disclaimer/limitation of liability set forth in the introductory paragraph.
-
-3. Redistributions in binary form must reproduce the Copyright Notice,
- these license terms, and the disclaimer/limitation of liability set
- forth as above, in the documentation and/or other materials
- provided with the distribution. For the purposes of binary distribution
- the "Copyright Notice" refers to the following language:
- "Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
- All rights reserved."
-
-4. Neither the name of the Swiss Institute of Bioinformatics nor
- the names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written
- permission.
-
-5. All redistributions must comply with the conditions imposed by the
- Swiss Institute of Bioinformatics on certain embedded code, whose copyright
- notice and conditions for redistribution are as follows:
-
- (a) Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
- All rights reserved.
-
- (b) Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- (i) Redistributions of source code must retain the above copyright
- notice, this list of conditions and the above disclaimer.
-
- (ii) Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- (iii) All advertising materials mentioning features or use of this
- software must display the following acknowledgement: "This
- product includes software developed by the Swiss Institute of
- Bioinformatics and its contributors."
-
- (iv) Neither the name of the Institute nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
-($Id: COPYRIGHT,v 1.1.1.1 2004/12/16 12:44:29 c4chris Exp $
-Version 1.1, last updated 9 December 2004)
diff --git a/licenses/mRNAmarkup b/licenses/mRNAmarkup
deleted file mode 100644
index 884ed1bd3..000000000
--- a/licenses/mRNAmarkup
+++ /dev/null
@@ -1,25 +0,0 @@
-Copyright (c) 2000 Volker Brendel
-All Rights Reserved. E-mail: vbrendel@iastate.edu
-
-Permission to use, copy, modify, and distribute this software and its
-documentation for educational, research and non-profit purposes, without fee,
-and without a written agreement is hereby granted, provided that the above
-copyright notice, this paragraph and the following three paragraphs appear in
-all copies. If you modify this file or included files you must cause the
-modified files to carry prominent notices stating that you changed the files.
-
-Inqueries for permission to incorporate this software into commercial products
-should be directed to the Office of Intellectual Property and Technology
-Transfer, 310 Lab of Mechanics, Iowa State University, Ames, IA 50011, phone:
-(515) 294-4740, E-mail: Licensing@iastate.edu.
-
-IN NO EVENT SHALL THE AUTHOR OR IOWA STATE UNIVERSITY BE LIABLE TO ANY PARTY FOR
-DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST
-PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
-IOWA STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-IOWA STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
-AND IOWA STATE UNIVERSITY HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
diff --git a/licenses/staden b/licenses/staden
deleted file mode 100644
index f2e77291a..000000000
--- a/licenses/staden
+++ /dev/null
@@ -1,76 +0,0 @@
-=============================================================================
-
-The Staden Package
-
-Copyright (c) 2003 MEDICAL RESEARCH COUNCIL
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- . Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
- . Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-
- . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
-MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
-
-Portions of this code have been modified by the Wellcome Trust Sanger
-Institute (Genome Research Limited). In some cases entirely new
-programs and/or source files have been created. These are licenced
-under essentially the same conditions as the MRC code (with just name
-changes).
-
-The following licence only applies to files bearing the Genome
-Research Limited copyright notice:
-
-
-
-Copyright (c) 2004 GENOME RESEARCH LIMITED
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- . Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
- . Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-
- . Neither the name of the GENOME RESEARCH LIMITED, the WELLCOME TRUST
-SANGER INSTITUTE nor the names of its contributors may be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
diff --git a/sci-mathematics/netgen/Manifest b/media-gfx/netgen/Manifest
index 32cbc28b8..5a2cfb72a 100644
--- a/sci-mathematics/netgen/Manifest
+++ b/media-gfx/netgen/Manifest
@@ -1 +1,2 @@
DIST netgen-6.2.2105.tar.gz 3372181 BLAKE2B 73ce8aff6e73a6a0ab79b0511c6c32c41240b9b6a743b8132cf27565b3c9f68820ad8337a9e761a37b74ffd7623a0321495a31dd868986ab4b90ff0dde66e9a8 SHA512 ed2727b7779af1ba564b0a7d9cc52fad5d3dccd478dcb71a4a77c7b9768a17eedfb6bfc2555f839cf592a7fc4ded5057f0e649239582e3d366d37ccfd030f4e9
+DIST netgen-6.2.2204.tar.gz 3394806 BLAKE2B 2b99854cab0890662f1ab7ffee6fb444b60a28ba0bfe9970a89c80c0e4c930c40b8034f9c600ddd61c9b60f542d1cae758a8c220a1ba76949bf9f97fb2fe9020 SHA512 964c40753613c111b0372b0e403b19734cc0c559d1e7e45bbe6b452f4daba10c6bde8abaa5c9541c92b4bccff02d32ea6ba8e8e06ba64f11fec1733f2e374cbf
diff --git a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch b/media-gfx/netgen/files/netgen-6.2.2105-find-tk.patch
index c638d83a7..c638d83a7 100644
--- a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch
+++ b/media-gfx/netgen/files/netgen-6.2.2105-find-tk.patch
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch b/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch
new file mode 100644
index 000000000..cf7b9d31e
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch
@@ -0,0 +1,21 @@
+From 53c45343f5a26841be10d930467e215da4a779f2 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 15:17:55 +0100
+Subject: [PATCH] find Tk include directories
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -270,6 +270,9 @@ if (USE_GUI)
+ endif(APPLE)
+ find_package(OpenGL REQUIRED)
+
++ include_directories(${TK_INCLUDE_PATH}/generic)
++ include_directories(${TK_INCLUDE_PATH}/unix)
++
+ target_compile_definitions(netgen_gui INTERFACE -DTCL -DOPENGL -DUSE_TOGL_2 -DUSE_TCL_STUBS -DUSE_TK_STUBS)
+ target_include_directories(netgen_gui INTERFACE ${TCL_INCLUDE_PATH} ${TK_INCLUDE_PATH})
+ target_link_libraries(netgen_gui INTERFACE ${TCL_STUB_LIBRARY} ${TK_STUB_LIBRARY})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch b/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch
new file mode 100644
index 000000000..c45f5a4e4
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch
@@ -0,0 +1,34 @@
+From 39160b692fd051f2638f1a6e1df38eb616b6d6cb Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 16:09:43 +0100
+Subject: [PATCH] find libjpeg-turbo library
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/libsrc/visualization/CMakeLists.txt
++++ b/libsrc/visualization/CMakeLists.txt
+@@ -7,7 +7,7 @@ target_sources(nggui PRIVATE
+ vssolution.cpp
+ visualpkg.cpp
+ )
+-target_link_libraries( nggui PUBLIC "$<BUILD_INTERFACE:netgen_python>" ${MPI_CXX_LIBRARIES} ${OPENGL_LIBRARIES} )
++target_link_libraries( nggui PUBLIC "$<BUILD_INTERFACE:netgen_python>" ${MPI_CXX_LIBRARIES} ${OPENGL_LIBRARIES} ${JPEG_LIBRARIES} )
+
+ install(FILES
+ meshdoc.hpp mvdraw.hpp visual_api.hpp
+--- a/nglib/CMakeLists.txt
++++ b/nglib/CMakeLists.txt
+@@ -7,6 +7,11 @@ endif(USE_OCC)
+
+ target_link_libraries(nglib PUBLIC ngcore)
+
++if(TARGET JPEG::JPEG)
++ get_target_property(JPEG_LIBRARIES JPEG::JPEG IMPORTED_LOCATION_RELEASE)
++else()
++ set(JPEG_LIBRARIES ${JPEG_LIBRARY_RELEASE})
++endif()
+ target_link_libraries( nglib PRIVATE ${MPI_CXX_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${JPEG_LIBRARIES} ${MKL_LIBRARIES} ${ZLIB_LIBRARIES} ${OCC_LIBRARIES} netgen_cgns )
+
+ install(TARGETS nglib netgen_cgns ${NG_INSTALL_DIR})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch b/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch
new file mode 100644
index 000000000..6f7a8bc3c
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch
@@ -0,0 +1,20 @@
+From 69d9c2da29adc9b7a209e78aae950d9834683f58 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Mon, 31 Oct 2022 13:07:05 +0100
+Subject: [PATCH] link against ffmpeg
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/ng/CMakeLists.txt
++++ b/ng/CMakeLists.txt
+@@ -28,7 +28,7 @@ if(USE_GUI)
+ if(APPLE)
+ set_target_properties(netgen PROPERTIES OUTPUT_NAME netgen)
+ endif(APPLE)
+- target_link_libraries( netgen ${PYTHON_LIBRARIES} ${TCL_LIBRARY} ${TK_LIBRARY})
++ target_link_libraries( netgen ${PYTHON_LIBRARIES} ${TCL_LIBRARY} ${TK_LIBRARY} ${FFMPEG_LIBRARIES})
+ endif(NOT BUILD_FOR_CONDA)
+
+ install(TARGETS nggui ${NG_INSTALL_DIR})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch b/media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch
new file mode 100644
index 000000000..ef11c8b08
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch
@@ -0,0 +1,30 @@
+From c3c55fe646ad6934e429edd080aceae54260551c Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 14:50:48 +0100
+Subject: [PATCH] use external pybind11
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -302,7 +302,7 @@ else()
+ endif()
+
+ if (USE_PYTHON)
+- add_subdirectory(external_dependencies/pybind11)
++ find_package(pybind11)
+ find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h HINTS ${PYTHON_INCLUDE_DIR})
+ if( PYBIND_INCLUDE_DIR )
+ message(STATUS "Found Pybind11: ${PYBIND_INCLUDE_DIR}")
+--- a/cmake/SuperBuild.cmake
++++ b/cmake/SuperBuild.cmake
+@@ -154,7 +154,6 @@ endif()
+ #######################################################################
+ if (USE_PYTHON)
+ find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h PATHS ${CMAKE_CURRENT_SOURCE_DIR}/external_dependencies/pybind11/include NO_DEFAULT_PATH)
+- set(NG_INSTALL_PYBIND ON)
+ if( NOT PYBIND_INCLUDE_DIR )
+ # if the pybind submodule is missing, try to initialize and update all submodules
+ execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+--
+2.38.1
+
diff --git a/sci-mathematics/netgen/files/netgen.desktop b/media-gfx/netgen/files/netgen.desktop
index 714ba53c4..714ba53c4 100644
--- a/sci-mathematics/netgen/files/netgen.desktop
+++ b/media-gfx/netgen/files/netgen.desktop
diff --git a/sci-mathematics/netgen/files/netgen.png b/media-gfx/netgen/files/netgen.png
index cb2fd8466..cb2fd8466 100644
--- a/sci-mathematics/netgen/files/netgen.png
+++ b/media-gfx/netgen/files/netgen.png
Binary files differ
diff --git a/sci-mathematics/netgen/metadata.xml b/media-gfx/netgen/metadata.xml
index cb94caeca..cb94caeca 100644
--- a/sci-mathematics/netgen/metadata.xml
+++ b/media-gfx/netgen/metadata.xml
diff --git a/sci-mathematics/netgen/netgen-6.2.2105.ebuild b/media-gfx/netgen/netgen-6.2.2105.ebuild
index ed85bcb69..ed85bcb69 100644
--- a/sci-mathematics/netgen/netgen-6.2.2105.ebuild
+++ b/media-gfx/netgen/netgen-6.2.2105.ebuild
diff --git a/media-gfx/netgen/netgen-6.2.2204.ebuild b/media-gfx/netgen/netgen-6.2.2204.ebuild
new file mode 100644
index 000000000..06a2bf53f
--- /dev/null
+++ b/media-gfx/netgen/netgen-6.2.2204.ebuild
@@ -0,0 +1,137 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit cmake desktop python-single-r1 xdg
+
+DESCRIPTION="Automatic 3d tetrahedral mesh generator"
+HOMEPAGE="https://ngsolve.org/ https://github.com/NGSolve/netgen"
+SRC_URI="https://github.com/NGSolve/netgen/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="ffmpeg jpeg mpi opencascade python gui"
+REQUIRED_USE="
+ ${PYTHON_REQUIRED_USE}
+ ffmpeg? ( gui )
+ jpeg? ( gui )
+ python? ( gui )
+"
+
+DEPEND="
+ sys-libs/zlib
+ ffmpeg? ( media-video/ffmpeg:= )
+ gui? (
+ dev-lang/tcl:0/8.6
+ dev-lang/tk:0/8.6
+ media-libs/glu
+ virtual/opengl
+ x11-libs/libX11
+ x11-libs/libXmu
+ x11-libs/libxcb:=
+ )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
+ mpi? (
+ sci-libs/metis
+ virtual/mpi
+ )
+ opencascade? ( sci-libs/opencascade:= )
+ python? (
+ ${PYTHON_DEPS}
+ $(python_gen_cond_dep '
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ '
+ )
+ mpi? (
+ $(python_gen_cond_dep 'dev-python/mpi4py[${PYTHON_USEDEP}]' )
+ )
+ )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ sys-apps/lsb-release
+ virtual/pkgconfig
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-use-external-pybind11.patch"
+ "${FILESDIR}/${P}-find-Tk-include-directories.patch"
+ "${FILESDIR}/${P}-find-libjpeg-turbo-library.patch"
+ "${FILESDIR}/${P}-link-against-ffmpeg.patch"
+)
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ # NOTE: need to manually check and update this string on version bumps!
+ cat <<- EOF > "${S}/version.txt" || die
+ v${PV}-0-gde0d706e
+ EOF
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ # currently not working in a sandbox, expects netgen to be installed
+ # see https://github.com/NGSolve/netgen/issues/132
+ -DBUILD_STUB_FILES=OFF
+ -DINSTALL_PROFILES=OFF
+ -DNG_INSTALL_DIR_CMAKE="$(get_libdir)/cmake/${PN}"
+ -DNG_INSTALL_DIR_INCLUDE="include/${PN}"
+ -DNG_INSTALL_DIR_LIB="$(get_libdir)"
+ -DUSE_CCACHE=OFF
+ # doesn't build with this version
+ -DUSE_CGNS=OFF
+ -DUSE_GUI="$(usex gui)"
+ -DUSE_INTERNAL_TCL=OFF
+ -DUSE_JPEG="$(usex jpeg)"
+ -DUSE_MPEG="$(usex ffmpeg)"
+ # respect users -march= choice
+ -DUSE_NATIVE_ARCH=OFF
+ -DUSE_MPI="$(usex mpi)"
+ -DUSE_OCC="$(usex opencascade)"
+ -DUSE_PYTHON="$(usex python)"
+ -DUSE_SUPERBUILD=OFF
+ )
+ # no need to set this, if we only build the library
+ if use gui; then
+ mycmakeargs+=( -DTK_INCLUDE_PATH="/usr/$(get_libdir)/tk8.6/include" )
+ fi
+ if use python; then
+ mycmakeargs+=(
+ -DPYBIND_INCLUDE_DIR="/usr/lib/${EPYTHON}/site-packages/pybind11/include/"
+ -DNG_INSTALL_PYBIND=OFF
+ )
+ fi
+ if use mpi && use python; then
+ mycmakeargs+=( -DUSE_MPI4PY=ON )
+ else
+ mycmakeargs+=( -DUSE_MPI4PY=OFF )
+ fi
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ use python && python_optimize
+
+ local NETGENDIR="/usr/share/${PN}"
+ echo -e "NETGENDIR=${NETGENDIR}" > ./99netgen || die
+ doenvd 99netgen
+
+ if use gui; then
+ mv "${ED}"/usr/bin/{*.tcl,*.ocf} "${ED}${NETGENDIR}" || die
+
+ doicon "${FILESDIR}"/${PN}.png
+ domenu "${FILESDIR}"/${PN}.desktop
+ fi
+
+ mv "${ED}"/usr/share/${PN}/doc/ng4.pdf "${ED}"/usr/share/doc/${PF} || die
+ dosym -r /usr/share/doc/${PF}/ng4.pdf /usr/share/${PN}/doc/ng4.pdf
+}
diff --git a/media-libs/charls/Manifest b/media-libs/charls/Manifest
new file mode 100644
index 000000000..5275ba74f
--- /dev/null
+++ b/media-libs/charls/Manifest
@@ -0,0 +1 @@
+DIST charls-2.3.4.tar.gz 9483782 BLAKE2B 655bbe2f143df1c3b86f2bbb033217c9fa30f39cf9b449cb84ffd56ef2e3eb0ceb7088c8757cc1a59d6d9462363e59e62acee7dabcbe5a16fb68be0d5036b3eb SHA512 3f6e1a054d5f7cfa5309e3d1b280d0dbaaeac7f06b08619cefe15677367631d9f6eb96e54b3e5ec921ac50793a570c39178c3e4b52ce9837b731bbccd6a3d0ad
diff --git a/media-libs/charls/charls-2.3.4.ebuild b/media-libs/charls/charls-2.3.4.ebuild
new file mode 100644
index 000000000..155e910a8
--- /dev/null
+++ b/media-libs/charls/charls-2.3.4.ebuild
@@ -0,0 +1,30 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="C++ JPEG-LS library implementation"
+HOMEPAGE="https://github.com/team-charls/charls"
+SRC_URI="https://github.com/team-charls/charls/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_configure() {
+ # It doesn't seem like there is an automated way to run the test programs
+ # The samples option builds them, but do not install the resulting binaries
+ local mycmakeargs=(
+ -DCHARLS_BUILD_TESTS=OFF
+ -DCHARLS_BUILD_FUZZ_TEST=OFF
+ -DCHARLS_BUILD_SAMPLES=OFF
+ -DBUILD_SHARED_LIBS=ON
+ )
+ cmake_src_configure
+}
diff --git a/media-libs/charls/metadata.xml b/media-libs/charls/metadata.xml
new file mode 100644
index 000000000..3eef65eb8
--- /dev/null
+++ b/media-libs/charls/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>fx.carton91@gmail.com</email>
+ <name>François-Xavier Carton</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">team-charls/charls</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml
index ae9640ffb..2103548da 100644
--- a/media-libs/libgfx/metadata.xml
+++ b/media-libs/libgfx/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mjgarland/libgfx</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/media-libs/mmg/metadata.xml b/media-libs/mmg/metadata.xml
index 2b9123050..bd7221f19 100644
--- a/media-libs/mmg/metadata.xml
+++ b/media-libs/mmg/metadata.xml
@@ -13,4 +13,7 @@
<flag name="scotch">Use SCOTCH TOOL for renumbering</flag>
<flag name="vtk">Use VTK I/O</flag>
</use>
+ <upstream>
+ <remote-id type="github">MmgTools/mmg</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/metadata/pkgcheck.conf b/metadata/pkgcheck.conf
new file mode 100644
index 000000000..979ee255d
--- /dev/null
+++ b/metadata/pkgcheck.conf
@@ -0,0 +1,2 @@
+[DEFAULT]
+profiles = stable,dev,-default/linux/amd64/17.0/musl
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index ad8668437..d117605d1 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,5 @@
DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
-DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2
+DIST cernbox-client-2.9.2-6339.src.rpm 6243132 BLAKE2B c73c3c338f9d3fb7fa7b22efe9b6ff1380d80f3804e2e732873f5804ed31d98fb04f9dbcdc0f614136c08081bea825d70948f94a6c0c9dddfe20eca66e41c4c1 SHA512 ec0edff177a5b77144eef173e4e3f5d549762faa6682618124f5c64e37f657c3aa00f639723cf2c48b6c4d1049373cd24b41d347cd9bf3c7bb291ab3340d6b2a
DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
+DIST ownCloud-2.11.1.8438.tar.xz 5655380 BLAKE2B da34adafabfc8c2b0bbfdff99a81b56f2d2639b5168b2165a847a6d5a4efe4e86578984c0f0c20564d0978aab18bb1a62330539bdd137f608a5cfc3ff8d84cf0 SHA512 fe38471f62e7233a7ba04f7fd2c7c7231957e6927c39d0bcf3f6f77fd6cbb1223618bbf6a8cc5fa15de10a35c7f07f2f5df0e49acbc2af5fe9333cda2eb41c92
+DIST ownCloud-2.11.1.8946.tar.xz 5654496 BLAKE2B 6b5b82730460071ae590b35d653824f4e56d506d87929c5d4ebb31eef921d0cb0141a44d7f0c996b8d1afffa5874d3e4dda75feaba740e652df2939633475fcd SHA512 b44f72e22c539a731901d9c146f00edbf0a4dabb992d6cde06be1b50506d5bc4a8aa861c6ea0207eed72aaea8c8af8651ce07f9e9154e6e44ccdecdd27e35b75
diff --git a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild b/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild
index c4eeaa7be..c698f7562 100644
--- a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild
@@ -10,8 +10,8 @@ DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
# Origin is classic owncloud-client, branded for CERN during compilation.
ORIGIN_PN="ownCloud"
BRANDED_P="cernbox"
-BRANDED_PV="2.7.1"
-BRANDED_REL="2596"
+BRANDED_PV="2.9.2"
+BRANDED_REL="6339"
HOMEPAGE="https://cernbox.cern.ch/"
SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
@@ -21,8 +21,9 @@ LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="dolphin gnome-keyring nautilus test"
+RESTRICT="!test? ( test )"
-COMMON_DEPEND=">=dev-db/sqlite-3.4:3
+RDEPEND=">=dev-db/sqlite-3.4:3
dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
dev-qt/qtconcurrent:5
dev-qt/qtcore:5
@@ -39,21 +40,18 @@ COMMON_DEPEND=">=dev-db/sqlite-3.4:3
)
nautilus? ( dev-python/nautilus-python )"
-RDEPEND="${COMMON_DEPEND}"
-DEPEND="${COMMON_DEPEND}
- dev-qt/linguist-tools:5
- kde-frameworks/extra-cmake-modules
+DEPEND="${RDEPEND}
test? (
dev-util/cmocka
dev-qt/qttest:5
)"
-RESTRICT="!test? ( test )"
+BDEPEND="
+ dev-qt/linguist-tools:5
+ kde-frameworks/extra-cmake-modules"
S=${WORKDIR}/${ORIGIN_PN}-${PV}
-PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch )
-
src_unpack() {
rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
diff --git a/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild b/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild
new file mode 100644
index 000000000..c698f7562
--- /dev/null
+++ b/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake rpm xdg
+
+DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
+
+# Origin is classic owncloud-client, branded for CERN during compilation.
+ORIGIN_PN="ownCloud"
+BRANDED_P="cernbox"
+BRANDED_PV="2.9.2"
+BRANDED_REL="6339"
+HOMEPAGE="https://cernbox.cern.ch/"
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+ https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
+
+LICENSE="CC-BY-3.0 GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dolphin gnome-keyring nautilus test"
+RESTRICT="!test? ( test )"
+
+RDEPEND=">=dev-db/sqlite-3.4:3
+ dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
+ dev-qt/qtconcurrent:5
+ dev-qt/qtcore:5
+ dev-qt/qtdbus:5
+ dev-qt/qtgui:5
+ dev-qt/qtnetwork:5[ssl]
+ dev-qt/qtsql:5
+ dev-qt/qtwidgets:5
+ dev-qt/qtxml:5
+ sys-fs/inotify-tools
+ dolphin? (
+ kde-frameworks/kcoreaddons:5
+ kde-frameworks/kio:5
+ )
+ nautilus? ( dev-python/nautilus-python )"
+
+DEPEND="${RDEPEND}
+ test? (
+ dev-util/cmocka
+ dev-qt/qttest:5
+ )"
+
+BDEPEND="
+ dev-qt/linguist-tools:5
+ kde-frameworks/extra-cmake-modules"
+
+S=${WORKDIR}/${ORIGIN_PN}-${PV}
+
+src_unpack() {
+ rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
+ mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
+}
+
+src_prepare() {
+ # Keep tests in ${T}
+ sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
+
+ if ! use nautilus; then
+ pushd shell_integration > /dev/null || die
+ cmake_comment_add_subdirectory nautilus
+ popd > /dev/null || die
+ fi
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+ -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
+ -DBUILD_TESTING=$(usex test)
+ )
+
+ cmake_src_configure
+}
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 92d1d843a..79c0fcb5c 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,20 +15,10 @@
## =media-video/mplayer-0.90_pre5-r1 foo
#
-# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
-# doesn't link with plotutils-2.6
-sci-physics/qcl plotutils
-
-# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
+# vtk<9 no longer available in ::gentoo
+sci-libs/gdcm python
# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Jan 2022)
-# dependencies not available
-# https://github.com/gentoo/sci/issues/1085
-# https://github.com/gentoo/sci/issues/1084
-sci-libs/mlpack go R
diff --git a/profiles/updates/4Q-2022 b/profiles/updates/4Q-2022
new file mode 100644
index 000000000..b80d5a910
--- /dev/null
+++ b/profiles/updates/4Q-2022
@@ -0,0 +1 @@
+move sci-mathematics/netgen media-gfx/netgen
diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml
index 138cb7705..aa4766e73 100644
--- a/sci-biology/BRAKER/metadata.xml
+++ b/sci-biology/BRAKER/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">Gaius-Augustus/BRAKER</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml
index 138cb7705..480ba370b 100644
--- a/sci-biology/GAL/metadata.xml
+++ b/sci-biology/GAL/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">The-Sequence-Ontology/GAL</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml
index 138cb7705..a3f152e56 100644
--- a/sci-biology/RAILS/metadata.xml
+++ b/sci-biology/RAILS/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/RAILS</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml
index 138cb7705..cc34f33b5 100644
--- a/sci-biology/VelvetOptimiser/metadata.xml
+++ b/sci-biology/VelvetOptimiser/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/VelvetOptimiser</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
index acf637dca..cbb8a4299 100644
--- a/sci-biology/afni/metadata.xml
+++ b/sci-biology/afni/metadata.xml
@@ -13,4 +13,7 @@
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
functional MRI data—a technique for mapping human brain activity.
</longdescription>
+ <upstream>
+ <remote-id type="github">afni/afni</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
index 138cb7705..ed9e5b12d 100644
--- a/sci-biology/angsd/metadata.xml
+++ b/sci-biology/angsd/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ANGSD/angsd</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest
index 867a142eb..c00c77f25 100644
--- a/sci-biology/ants/Manifest
+++ b/sci-biology/ants/Manifest
@@ -1,2 +1 @@
-DIST ants-2.3.4.tar.gz 2455843 BLAKE2B c00a2d3edebc0a121fa3b6618982c64fd986db9ea6aed1a1b2c7ced2f77ab154837a47e5bcb01f432b937160de2248b30a2bb7b526952852946e686858334e12 SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575
-DIST ants_testdata-2.3.4.tar.xz 25056552 BLAKE2B 6478ffe0c98fd3700a6de201f1271339276b45b461b02d4753acdcd1335c83196aa2ed89a89b5b4b0b3df33026f77b231ba1418c9eb7a2380356d4e224f9b310 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d
+DIST ants-2.4.1.tar.gz 2473738 BLAKE2B 9abe2ade15bd8348452a23e15d8c862771ca2c8f971c44f185febfb1ee725b1ceb7e89359c8dfee31bd9c4087f10104831fe56bd1528ea7f5a81d52c1a4a4709 SHA512 533ca8adb934e8fe4e24425b3f8a9a8f0b67999d9593f8c8842e0298087d5bc58f65d1fcbfe78ac7dc17d0e786badc4a65bbde80d82d21c277ee6c1b3af7eae4
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
deleted file mode 100644
index 95eb6355b..000000000
--- a/sci-biology/ants/ants-2.3.4.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-CMAKE_MAKEFILE_GENERATOR="emake"
-
-inherit cmake
-
-MY_PN="ANTs"
-
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
-SRC_URI="
- https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
- test? (
- http://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
- )
-"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="test vtk"
-RESTRICT="!test? ( test )"
-
-DEPEND="
- vtk? (
- ~sci-libs/itk-5.1.0[vtkglue]
- sci-libs/vtk
- )
- !vtk? ( ~sci-libs/itk-5.1.0 )
-"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-version.patch"
- "${FILESDIR}/${P}-libdir.patch"
-)
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-src_unpack() {
- default
- if use test; then
- mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory."
- tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data."
- fi
-}
-
-src_configure() {
- local mycmakeargs=(
- -DUSE_SYSTEM_ITK=ON
- -DITK_DIR="${EPREFIX}/usr/include/ITK-5.1/"
- -DBUILD_TESTING="$(usex test ON OFF)"
- -DUSE_VTK=$(usex vtk ON OFF)
- -DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
- -DANTS_SNAPSHOT_VERSION:STRING=${PV}
- )
- use vtk && mycmakeargs+=(
- -DVTK_DIR="${EPREFIX}/usr/include/vtk-8.1/"
- )
- use test && mycmakeargs+=(
- -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
- )
- cmake_src_configure
-}
-
-src_install() {
- BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
- cmake_src_install
- cd "${S}/Scripts" || die "scripts dir not found"
- dobin *.sh
- dodir /usr/$(get_libdir)/ants
- insinto "/usr/$(get_libdir)/ants"
- doins *
- doenvd "${FILESDIR}"/99ants
-}
diff --git a/sci-biology/ants/ants-2.4.1-r1.ebuild b/sci-biology/ants/ants-2.4.1-r1.ebuild
new file mode 100644
index 000000000..70d5d8873
--- /dev/null
+++ b/sci-biology/ants/ants-2.4.1-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake
+
+MY_PN="ANTs"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="https://stnava.github.io/ANTs/"
+SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="test vtk"
+RESTRICT="test"
+
+DEPEND="
+ !vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] )
+ vtk? (
+ =sci-libs/itk-5.2*[fftw,vtkglue]
+ =sci-libs/vtk-9.1*
+ )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-fix-compile.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DBUILD_EXAMPLES=OFF
+ -DUSE_SYSTEM_ITK=ON
+ -DITK_USE_SYSTEM_FFTW=ON
+ -DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/"
+ -DBUILD_TESTING="$(usex test ON OFF)"
+ -DUSE_VTK=$(usex vtk ON OFF)
+ -DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
+ )
+ use vtk && mycmakeargs+=(
+ -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/"
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build"
+ cmake_src_install
+ cd "${S}/Scripts" || die "scripts dir not found"
+ dobin *.sh
+ dodir /usr/$(get_libdir)/ants
+ insinto "/usr/$(get_libdir)/ants"
+ doins *
+ doenvd "${FILESDIR}"/99ants
+}
diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
deleted file mode 100644
index 932da9954..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001
-From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
-Date: Mon, 7 Oct 2019 22:01:51 -0400
-Subject: [PATCH] Fix install logic
-
----
- ANTS.cmake | 3 ++-
- SuperBuild.cmake | 2 ++
- 2 files changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/ANTS.cmake b/ANTS.cmake
-index a1baf845..95ffdc74 100644
---- a/ANTS.cmake
-+++ b/ANTS.cmake
-@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh
- COMPONENT SCRIPTS
- )
-
--if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK))
-+#Only install ITK/VTK libraries if shared build and superbuild is used
-+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK)))
- install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/
- DESTINATION lib)
- endif()
-diff --git a/SuperBuild.cmake b/SuperBuild.cmake
-index f4630e64..32b930c2 100644
---- a/SuperBuild.cmake
-+++ b/SuperBuild.cmake
-@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS
- CMAKE_C_COMPILER_LAUNCHER:STRING
- CMAKE_CXX_COMPILER_LAUNCHER:STRING
- CMAKE_CUDA_COMPILER_LAUNCHER:STRING
-+ USE_SYSTEM_ITK:BOOL
-+ USE_SYSTEM_VTK:BOOL
- )
-
- _expand_external_project_vars()
diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
deleted file mode 100644
index aaea92808..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -16,8 +16,9 @@
-+include(GNUInstallDirs)
- install(TARGETS antsUtilities
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_antsUtilities
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_antsUtilities
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_antsUtilities
- )
-@@ -38,8 +38,8 @@
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
-@@ -61,8 +61,8 @@
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch
deleted file mode 100644
index b593c2778..000000000
--- a/sci-biology/ants/files/ants-2.3.4-libdir.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
-From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
-Date: Fri, 26 Jun 2020 18:23:08 +0000
-Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
-
-Trying to enable installation to the correct lib dir for each platform
----
- Common.cmake | 7 +++++--
- Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
- 2 files changed, 21 insertions(+), 18 deletions(-)
-
-diff --git a/Common.cmake b/Common.cmake
-index 5e52d7f1..1e604113 100644
---- a/Common.cmake
-+++ b/Common.cmake
-@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
- endif()
- endif()
-
--
--
- #-------------------------------------------------------------------------
- # Augment compiler flags
- #-------------------------------------------------------------------------
-@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
- set(CMAKE_POSITION_INDEPENDENT_CODE ON)
- endif()
- endif()
-+
-+#-------------------------------------------------------------------------
-+# Define install dirs for different platforms
-+#-------------------------------------------------------------------------
-+include(GNUInstallDirs)
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
-index 61781f56..cb352748 100644
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -1,4 +1,4 @@
--SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
- ## Note that the antsUtilities can always be built static. It will then be linked
- ## Directly into the other libraries.
- add_library(antsUtilities antsUtilities.cxx
-@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx
- )
- target_link_libraries(antsUtilities ${ITK_LIBRARIES} )
- install(TARGETS antsUtilities
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_antsUtilities
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_antsUtilities
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_antsUtilities
- )
-
-@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
-
- if (ANTS_INSTALL_LIBS_ONLY)
- install(TARGETS l_${ANTS_FUNCTION_NAME}
-- # RUNTIME DESTINATION bin
-+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- else()
- add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx )
- target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- endif()
-@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
-
- if (ANTS_INSTALL_LIBS_ONLY)
- install(TARGETS l_${ANTS_FUNCTION_NAME}
-- # RUNTIME DESTINATION bin
-+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- else()
-@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
- target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
-
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- endif()
diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch
deleted file mode 100644
index 487151d69..000000000
--- a/sci-biology/ants/files/ants-2.3.4-version.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400
-+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400
-@@ -37,7 +37,6 @@
- set(${PROJECT_NAME}_VERSION_MAJOR 0)
- set(${PROJECT_NAME}_VERSION_MINOR 0)
- set(${PROJECT_NAME}_VERSION_PATCH 0)
-- set(${PROJECT_NAME}_VERSION_TWEAK 0)
- set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}")
- endif()
-
-@@ -46,7 +45,6 @@
- set(${PROJECT_NAME}_VERSION_MAJOR 0)
- set(${PROJECT_NAME}_VERSION_MINOR 0)
- set(${PROJECT_NAME}_VERSION_PATCH 0)
-- set(${PROJECT_NAME}_VERSION_TWEAK 0)
- set(${PROJECT_NAME}_VERSION "0.0.0.0")
- endif()
diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
new file mode 100644
index 000000000..bd7eecbcf
--- /dev/null
+++ b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
@@ -0,0 +1,13 @@
+diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx
+index d1e7586..048d934 100644
+--- a/Examples/PrintHeader.cxx
++++ b/Examples/PrintHeader.cxx
+@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[])
+ // Get the metadata as a generic object
+ string key = itMeta->first, v_string;
+ itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags =
+- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID;
++ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID;
+
+ if (itk::ExposeMetaData<string>(mdd, key, v_string))
+ {
diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml
index 9f969ddf9..e8372d21b 100644
--- a/sci-biology/ants/metadata.xml
+++ b/sci-biology/ants/metadata.xml
@@ -21,4 +21,7 @@
<use>
<flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag>
</use>
+ <upstream>
+ <remote-id type="github">ANTsX/ANTs</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml
index 138cb7705..927a160ba 100644
--- a/sci-biology/bamql/metadata.xml
+++ b/sci-biology/bamql/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">BoutrosLaboratory/bamql</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml
index 138cb7705..9183ef1ec 100644
--- a/sci-biology/barrnap/metadata.xml
+++ b/sci-biology/barrnap/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/barrnap</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest
new file mode 100644
index 000000000..ab53258d3
--- /dev/null
+++ b/sci-biology/bidsschematools/Manifest
@@ -0,0 +1,3 @@
+DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd
+DIST bidsschematools-0.5.1.tar.gz 1159308 BLAKE2B a53355b24e87ea7008fa64ca4f7e71c7bf29effc52f4aa3f855af633ce83817d5551eead4224d39f8cd46693dc48a7d9325a7ad8698e159b468e902982c5a940 SHA512 f1d9ab6b37c8fd4fd6a6aa821ef718c1af7f3d453d44c2c76c104f5601d40e5a328b0332255a591d8431e8c0ca3406dccd852c6c1fc8d832657b27a6b0076adc
+DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1
diff --git a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
new file mode 100644
index 000000000..41b71e7a5
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
@@ -0,0 +1,37 @@
+# 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..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild
new file mode 100644
index 000000000..3a6e51898
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/markdown-it-py[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
new file mode 100644
index 000000000..3a6e51898
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
@@ -0,0 +1,38 @@
+# 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..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/markdown-it-py[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/dev-python/click-didyoumean/metadata.xml b/sci-biology/bidsschematools/metadata.xml
index d206a1b1c..3fac5f14b 100644
--- a/dev-python/click-didyoumean/metadata.xml
+++ b/sci-biology/bidsschematools/metadata.xml
@@ -1,4 +1,4 @@
-<?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">
@@ -10,7 +10,10 @@
<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>
+ <remote-id type="github">bids-standard/bids-specification</remote-id>
+ <remote-id type="pypi">bidsschematools</remote-id>
</upstream>
+ <use>
+ <flag name="render">Support for schema table rendering</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml
index 4c433a8ca..4ee13c559 100644
--- a/sci-biology/bismark/metadata.xml
+++ b/sci-biology/bismark/metadata.xml
@@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
and CHH context.
</longdescription>
+ <upstream>
+ <remote-id type="github">FelixKrueger/Bismark</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml
index 138cb7705..1e02bb596 100644
--- a/sci-biology/btl_bloomfilter/metadata.xml
+++ b/sci-biology/btl_bloomfilter/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/btl_bloomfilter</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index 3e13342e3..80a22b44a 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -12,5 +12,6 @@
<upstream>
<remote-id type="bitbucket">james_taylor/bx-python</remote-id>
<remote-id type="pypi">bx-python</remote-id>
+ <remote-id type="github">bxlab/bx-python</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
deleted file mode 100644
index 761665281..000000000
--- a/sci-biology/caftools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d
-DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
deleted file mode 100644
index 7d58f3375..000000000
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/"
-SRC_URI="
- ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
- ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- sci-libs/io_lib
- dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/Makefile.in-"${PV}".patch
-)
-
-src_prepare(){
- default
- mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
-}
-
-src_configure(){
- default
- sed \
- -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
- -i Makefile src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
- default
- doman man/*.[1-5] || die
- elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
- elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
-}
diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch
deleted file mode 100644
index 1e5160487..000000000
--- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- src/Makefile.in.ori 2010-12-05 22:59:40.000000000 +0100
-+++ src/Makefile.in 2010-12-05 23:01:19.000000000 +0100
-@@ -32,8 +32,6 @@
- includedir = @includedir@
- oldincludedir = /usr/include
-
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
- pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
-@@ -323,18 +321,18 @@
-
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- if test -f $$p; then \
-- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+ echo " $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-+ $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- else :; fi; \
- done
-
- uninstall-binPROGRAMS:
- @$(NORMAL_UNINSTALL)
- list='$(bin_PROGRAMS)'; for p in $$list; do \
-- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+ rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- done
-
- .c.o:
-@@ -579,7 +577,7 @@
- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
- installdirs: installdirs-recursive
- installdirs-am:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
-
-
- mostlyclean-generic:
diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch
deleted file mode 100644
index 4ddd9f628..000000000
--- a/sci-biology/caftools/files/Makefile.in.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100
-+++ src/Makefile.in 2010-12-05 22:10:07.000000000 +0100
-@@ -18,7 +18,7 @@
- srcdir = @srcdir@
- top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
-+prefix = $(DESTDIR)/@prefix@
- exec_prefix = @exec_prefix@
-
- bindir = @bindir@
-@@ -394,14 +394,14 @@
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- if test -f $$p \
- ; then \
- f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
-- echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
-- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
-+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \
-+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \
- else :; fi; \
- done
-
-@@ -409,8 +409,8 @@
- @$(NORMAL_UNINSTALL)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
-- echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
-- rm -f $(DESTDIR)$(bindir)/$$f; \
-+ echo " rm -f $(bindir)/$$f"; \
-+ rm -f $(bindir)/$$f; \
- done
-
- clean-binPROGRAMS:
-@@ -663,7 +663,7 @@
- all-am: Makefile $(PROGRAMS) config.h
- installdirs: installdirs-recursive
- installdirs-am:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
-
- install: install-recursive
- install-exec: install-exec-recursive
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
deleted file mode 100644
index 224641279..000000000
--- a/sci-biology/caftools/metadata.xml
+++ /dev/null
@@ -1,17 +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>
- <longdescription>
-CAF is a text format for describing sequence assemblies. It is acedb-compliant
-and is an extension of the ace-file format used earlier, but with support for
-base quality measures and a more extensive description of the Sequence data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
index 9c9e19081..773e706a6 100644
--- a/sci-biology/dcm2niix/metadata.xml
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -19,4 +19,7 @@
format to the NIfTI format. ICOM provides many ways to store/compress
image data, known as transfer syntaxes.
</longdescription>
+ <upstream>
+ <remote-id type="github">rordenlab/dcm2niix</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml
index ae9640ffb..0272cf14e 100644
--- a/sci-biology/dcmstack/metadata.xml
+++ b/sci-biology/dcmstack/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">moloney/dcmstack</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml
index 138cb7705..ac7dfc24a 100644
--- a/sci-biology/diamond/metadata.xml
+++ b/sci-biology/diamond/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bbuchfink/diamond</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest
deleted file mode 100644
index 79281bc74..000000000
--- a/sci-biology/estscan/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09
-DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2
-DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4
-DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de
-DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447
-DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5
-DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43
-DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c
-DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1
diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild
deleted file mode 100644
index a0992b76b..000000000
--- a/sci-biology/estscan/estscan-3.0.3.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2 perl-module toolchain-funcs
-
-DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
-HOMEPAGE="https://sourceforge.net/projects/estscan/"
-SRC_URI="
- https://downloads.sourceforge.net/${PN}/${P}.tar.gz
- https://downloads.sourceforge.net/${PN}/At.smat.gz
- https://downloads.sourceforge.net/${PN}/Dm.smat.gz
- https://downloads.sourceforge.net/${PN}/Dr.smat.gz
- https://downloads.sourceforge.net/${PN}/Hs.smat.gz
- https://downloads.sourceforge.net/${PN}/Mm.smat.gz
- https://downloads.sourceforge.net/${PN}/Rn.smat.gz
- https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
- https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"
-
-SLOT="0"
-LICENSE="estscan"
-KEYWORDS="~amd64 ~x86"
-IUSE="icc ifc"
-
-DEPEND="
- dev-perl/BTLib
- icc? ( dev-lang/icc )
- ifc? ( dev-lang/ifc )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
- default
- sed \
- -e 's/\\rm -f/rm -rf/' \
- -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
- -i "${P}"/Makefile || die "failed to edit Makefile"
-
- # fix hard-coded paths
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die
-
- if ! use icc; then
- sed \
- -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die
- fi
-
- if ! use ifc; then
- sed \
- -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
- -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \
- || die
- fi
-
- if use icc; then
- # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives
- # me gcc instead, same for $(tc-getF77)
- # Moreover, the if/else logic here should separate users having only icc
- # while not ifort (and vice-versa) from those having only
- # gcc/gfortran/g77
- #
- # FIXME: below as a dirty hack I force gfortran instead of ifort for
- # my testing purposes. Didn't ebuild contain "PROVIDES" line?
- # Same for FFLAGS.
- sed \
- -e "s:^# CC = icc:CC = icc:" \
- -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \
- -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
- -e "s/^ CC = gcc/# CC = gcc/" \
- -i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC"
-
- fi
-
- if use ifc; then
- sed \
- -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \
- -e "s/^# F77 = ifort/F77 = gfortran/" \
- -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
- -e "s/^ F77 = g77/# F77 = g77/" \
- -i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77"
- fi
-}
-
-src_compile() {
- emake -C ${P}
-}
-
-src_install() {
- # FIXME: Some kind of documentation is in {P}/${PN}.spec
- cd ${P} || die "Failed to chdir to ${P}"
- dobin \
- build_model ${PN} evaluate_model extract_EST extract_UG_EST \
- extract_mRNA makesmat maskred prepare_data winsegshuffle
- # the file build_model_utils.pl should go into some PERL site-packages dir
- # see {P}/${PN}.spec
-
- # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension
- insinto /usr/share/doc/${PN}
- # grab the file directly from ../distdir/
- doins "${DISTDIR}"/user_guide_fev_07.pdf
-
- # install the default precomputed matrices
- cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}"
- insinto /usr/share/${PN}
- doins *.smat
-
- # install BTlib (in perl)
- # dobin fetch indexer netfetch
- insinto /usr/share/${PN}/
- # install the config file which is packed inside the BTLib tarball while is not
- # being installed by dev-perl/BTLib
- doins "${WORKDIR}"/BTLib-0.19/fetch.conf
-
- # FIXME: install the *.pm files from BTLib-0.19
- # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19
- # myinst="DESTDIR=${D}"
- # perl-module_src_install
-
- einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout."
- einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/."
- einfo "You may follow the hints from http://${PN}.sourceforge.net/"
-}
diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml
deleted file mode 100644
index c79c2d1b5..000000000
--- a/sci-biology/estscan/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="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>
- <use>
- <flag name="icc">Undocumented USE</flag>
- <flag name="ifc">Undocumented USE</flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml
index 7c86089a2..f13c6ccba 100644
--- a/sci-biology/fastqc/metadata.xml
+++ b/sci-biology/fastqc/metadata.xml
@@ -13,4 +13,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">s-andrews/FastQC</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml
index 138cb7705..a9577a9c3 100644
--- a/sci-biology/ffindex/metadata.xml
+++ b/sci-biology/ffindex/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ahcm/ffindex</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml
index 138cb7705..b25087121 100644
--- a/sci-biology/longstitch/metadata.xml
+++ b/sci-biology/longstitch/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/LongStitch</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest
deleted file mode 100644
index fb61347b3..000000000
--- a/sci-biology/mRNAmarkup/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
deleted file mode 100644
index fb37b69f9..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Transcript annotation workflow"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB
-
-LICENSE="mRNAmarkup"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- sci-biology/ncbi-tools++
- sci-biology/estscan"
-# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
-# but, mRNAmarkup/INSTALL says:
-# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
-#
-# has a slightly modified estscan copy in src/contributed
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare(){
- default
- sed -e \
- "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
- -i bin/mRNAmarkup.orig || die
- sed -e \
- "s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
- -i bin/mRNAmarkup.orig
-}
-
-src_compile(){
- cd src
- emake
-}
-
-src_install(){
- mv bin/mRNAmarkup.orig bin/mRNAmarkup
- sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
- dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
- # TODO: there are some more files in bin/ , sigh!
- insinto /usr/share/mRNAmarkup/etc
- mv mRNAmarkup.conf.orig mRNAmarkup.conf
- doins mRNAmarkup.conf
- doins bin/ESTScan.conf
- dodoc 0README INSTALL
-}
-
-pkg_postinst(){
- einfo "Please obtain a local copy of NCBI CDD dastabase"
-}
diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml
index 8417d1580..a60e8c1b5 100644
--- a/sci-biology/mreps/metadata.xml
+++ b/sci-biology/mreps/metadata.xml
@@ -5,4 +5,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">gregorykucherov/mreps</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml
index 138cb7705..b0874714e 100644
--- a/sci-biology/nextclip/metadata.xml
+++ b/sci-biology/nextclip/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">richardmleggett/nextclip</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
index 138cb7705..f165e6cbc 100644
--- a/sci-biology/ngs/metadata.xml
+++ b/sci-biology/ngs/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ncbi/ngs</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml
index 138cb7705..fb03df79c 100644
--- a/sci-biology/ntCard/metadata.xml
+++ b/sci-biology/ntCard/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/ntCard</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
index a2611bd74..53d2e5925 100644
--- a/sci-biology/open-ephys-gui/Manifest
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -1 +1,2 @@
DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
+DIST open-ephys-gui-0.6.1.tar.gz 44674639 BLAKE2B 10113418c41ccc62064bd8b993aab5402691259702c53c580e39371bd5034bc3b65babfa0adcaa7e2aadb8a86758e52cc4a86fee83db05614c849ed4c2b76ff4 SHA512 00ef7e5fd1242c84948e8eaf0479337365de21a28cb77252bf2baf806b186b9c8b7a424d756a4b6a883ecac48aefd6d2a532a8cadaa910e295b474d38056547e
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
new file mode 100644
index 000000000..0992f2241
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
@@ -0,0 +1,15 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300
++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300
+@@ -171,8 +171,8 @@
+ target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug
+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
+ target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release
+- else()
+- message(FATAL_ERROR "Invalid build type")
++ # else()
++ # message(FATAL_ERROR "Invalid build type")
+ endif()
+ find_package(CURL REQUIRED)
+ find_package(PkgConfig REQUIRED)
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/metadata.xml b/sci-biology/open-ephys-gui/metadata.xml
index ed9bf87e3..2c9af77a9 100644
--- a/sci-biology/open-ephys-gui/metadata.xml
+++ b/sci-biology/open-ephys-gui/metadata.xml
@@ -5,6 +5,10 @@
<email>malfatti@disroot.org</email>
<name>T Malfatti</name>
</maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
<upstream>
<remote-id type="github">open-ephys/plugin-GUI</remote-id>
</upstream>
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
new file mode 100644
index 000000000..fe6791a2d
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="main"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="development"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+else
+ SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ Suffix=${PV}
+ SubDir="plugin-GUI-${PV}"
+ S="${WORKDIR}/${SubDir}"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+ dev-libs/openssl
+ media-libs/alsa-lib
+ media-libs/freeglut
+ media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
+ x11-libs/libXrandr
+ x11-libs/libXcursor
+ x11-libs/libXinerama
+ jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+ opt/open-ephys-*/plugins/*.so
+ opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+ cmake_src_prepare
+
+ if use jack; then
+ sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+ cmake_src_configure
+}
+
+src_install() {
+ dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+ udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+ dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
index 1c2b20e24..446972aeb 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2019-2021 Gentoo Authors
+# Copyright 2019-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
@@ -11,7 +11,7 @@ LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
+ EGIT_BRANCH="main"
Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
@@ -32,9 +32,12 @@ SLOT="${PV}"
IUSE="jack"
DEPEND="
+ dev-libs/openssl
media-libs/alsa-lib
media-libs/freeglut
media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
@@ -43,7 +46,7 @@ DEPEND="
RDEPEND="${DEPEND}"
BUILD_DIR="${S}/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch )
QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
@@ -66,7 +69,7 @@ src_configure() {
src_install() {
dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
index 1c2b20e24..446972aeb 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2019-2021 Gentoo Authors
+# Copyright 2019-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
@@ -11,7 +11,7 @@ LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
+ EGIT_BRANCH="main"
Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
@@ -32,9 +32,12 @@ SLOT="${PV}"
IUSE="jack"
DEPEND="
+ dev-libs/openssl
media-libs/alsa-lib
media-libs/freeglut
media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
@@ -43,7 +46,7 @@ DEPEND="
RDEPEND="${DEPEND}"
BUILD_DIR="${S}/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch )
QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
@@ -66,7 +69,7 @@ src_configure() {
src_install() {
dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml
index 138cb7705..9272f0d9c 100644
--- a/sci-biology/prokka/metadata.xml
+++ b/sci-biology/prokka/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/prokka</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml
index fd0f24633..47cc39d79 100644
--- a/sci-biology/pyfaidx/metadata.xml
+++ b/sci-biology/pyfaidx/metadata.xml
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">pyfaidx</remote-id>
+ <remote-id type="github">mdshw5/pyfaidx</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml
index 8417d1580..e3ce321ed 100644
--- a/sci-biology/quicktree/metadata.xml
+++ b/sci-biology/quicktree/metadata.xml
@@ -5,4 +5,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">khowe/quicktree</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest
deleted file mode 100644
index 6711cecd3..000000000
--- a/sci-biology/roche454ace2caf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732
diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
deleted file mode 100644
index a3c4eee39..000000000
--- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.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
-
-DESCRIPTION="ace to gap4 converter"
-HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/"
-SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"
-
-LICENSE="FLI-Jena"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/align_to_scf
- sci-biology/sff_dump
- sci-biology/caftools
- sci-biology/staden
- dev-lang/perl
- app-shells/ksh"
-
-S="${WORKDIR}/roche2gap"
-
-src_install(){
- dobin bin/*.pl bin/roche454ace2gap
- einstalldocs
-}
diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml
index 138cb7705..026053b60 100644
--- a/sci-biology/rtg-tools/metadata.xml
+++ b/sci-biology/rtg-tools/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">RealTimeGenomics/rtg-tools</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
deleted file mode 100644
index 37410d297..000000000
--- a/sci-biology/salmon/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
-DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
-DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
-DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2
-DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d
-DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
-DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6
-DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
-DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
deleted file mode 100644
index ac561d793..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200
-+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200
-@@ -213,15 +213,6 @@
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--if(CONDA_BUILD)
-- set (Boost_USE_STATIC_LIBS OFF)
--else ()
-- set (Boost_USE_STATIC_LIBS ON)
--endif(CONDA_BUILD)
--
- set (Boost_USE_MULTITHREADED ON)
- #set (Boost_USE_STATIC_RUNTIME OFF)
-
diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
deleted file mode 100644
index 81edf96f5..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200
-+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200
-@@ -5,7 +5,7 @@
- )
-
- if (SALMON_QUASI_INDEX_RESULT)
-- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}")
-+ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}")
- endif()
-
- set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant)
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
deleted file mode 100644
index eb606c00c..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200
-@@ -296,6 +296,8 @@
- )
- ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-
-+include(GNUInstallDirs)
-+
- set(INSTALL_LIB_DIR lib )
- set(INSTALL_BIN_DIR bin )
- set(INSTALL_INCLUDE_DIR include )
-@@ -311,8 +313,8 @@
-
- install(TARGETS salmon salmon_core
- RUNTIME DESTINATION bin
-- LIBRARY DESTINATION lib
-- ARCHIVE DESTINATION lib
-+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
- )
-
- add_custom_command(TARGET unitTests POST_BUILD
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
deleted file mode 100644
index 0a95757a8..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200
-@@ -335,6 +335,6 @@
- )
-
- include(InstallRequiredSystemLibraries)
--add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
-+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
- add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake )
- add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake )
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
deleted file mode 100644
index 8eddc6e3a..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200
-+++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200
-@@ -29,7 +29,8 @@
- EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
-
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
-
- hashcheck=""
- if exists sha256sum; then
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
deleted file mode 100644
index 438763960..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
+++ /dev/null
@@ -1,200 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200
-+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200
-@@ -235,31 +235,7 @@
-
- find_package (LibLZMA)
- if (NOT LIBLZMA_FOUND)
-- message ("Will attempt to fetch and build liblzma")
-- message ("=======================================")
--ExternalProject_Add(liblzma
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- ##
-- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
-- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
-- tar -xzvf xz-5.2.2.tar.gz
-- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
-- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
-- ##
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- BUILD_IN_SOURCE TRUE
-- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
-- BUILD_COMMAND make ${QUIET_MAKE}
-- INSTALL_COMMAND make ${QUIET_MAKE} install
--)
--
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBLZMA TRUE)
-+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
- else()
- message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
- message("===========================================")
-@@ -267,28 +243,7 @@
-
- find_package (BZip2)
- if (NOT BZIP2_FOUND)
-- message ("Will attempt to fetch and build libbz2")
-- message ("=======================================")
--ExternalProject_Add(libbz2
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
-- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
-- tar -xzvf bzip2-1.0.6.tar.gz
-- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
-- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- BUILD_IN_SOURCE TRUE
-- CONFIGURE_COMMAND ""
-- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
--)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBBZ2 TRUE)
-+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
- else()
- message("Found libbz2 library: ${BZIP2_LIBRARIES}")
- message("===========================================")
-@@ -333,61 +288,15 @@
- # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
- # option, go and grab it for them.
- ##
--if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
-+if (NOT Boost_FOUND)
- message(FATAL_ERROR
- "Salmon cannot be compiled without Boost.\n"
- "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
- "This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
- "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
- )
--elseif(FETCH_BOOST)
-- ## Let the rest of the build process know we're going to be fetching boost
-- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
-- --with-filesystem --with-graph --with-graph_parallel --with-math
-- --with-program_options --with-system --with-thread
-- --with-timer)
-- set (BOOST_WILL_RECONFIGURE TRUE)
-- set (FETCH_BOOST FALSE)
-- message("Build system will fetch and build Boost")
-- message("==================================================================")
-- ExternalProject_Add(libboost
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
-- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
-- tar xzf boost_1_66_0.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
-- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
-- BUILD_IN_SOURCE 1
-- INSTALL_COMMAND ""
-- )
--
-- ##
-- # After we've installed boost,
-- ##
-- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
-- ExternalProject_Add_Step(libboost reconfigure
-- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
-- DEPENDEES install
-- )
-- set (FETCHED_BOOST TRUE)
- endif()
-
--##
--# If we're fetching boost and we need to have dummy paths for these variables
--# so that CMake won't complain
--##
--if (BOOST_WILL_RECONFIGURE)
-- message("Setting Temporary Boost paths")
-- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
-- set(Boost_FOUND TRUE)
--endif()
--
--
- message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
- message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
- message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
-@@ -422,9 +331,9 @@
- include(ExternalProject)
- ExternalProject_Add(libcereal
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&
-- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz &&
-- tar -xzvf cereal-v1.2.2.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&
-+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz &&
-+ tar -xzvf cereal-1.2.2.tar.gz
-
- ##
- #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
-@@ -455,12 +364,12 @@
- ExternalProject_Add(libbwa
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
-- #DOWNLOAD_NAME bwa-master.tar.gz
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
-- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
-- mkdir -p bwa-master &&
-- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
-+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
-+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
-+ mkdir -p bwa-0.7.12.5 &&
-+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
-+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
- BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
-@@ -562,9 +471,9 @@
- message("==================================================================")
- ExternalProject_Add(libgff
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
-- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz &&
-- tar -xzvf libgff.tgz
-+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
-+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
-+ tar -xzvf libgff-1.1.tgz
- ##
- #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
- #DOWNLOAD_NAME libff.tgz
-@@ -600,10 +509,10 @@
- message("==================================================================")
- ExternalProject_Add(libstadenio
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
-- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
-+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
-+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
- mkdir -p staden-io_lib-1.14.8 &&
-- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
- rm -fr staden-io_lib &&
- mv -f staden-io_lib-1.14.8 staden-io_lib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
-@@ -620,9 +529,9 @@
- message("==================================================================")
- ExternalProject_Add(libspdlog
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
-- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
-- tar -xzf spdlog-v0.16.1.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
-+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
-+ tar -xzf spdlog-0.16.1.tar.gz
- ##
- #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
- #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
deleted file mode 100644
index 76ef25547..000000000
--- a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be02ab..48ffda2 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -428,9 +428,9 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
-+set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
- if (NOT BOOST_RECONFIGURE)
--find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
-+find_package(Boost 1.59.0 COMPONENTS ALL)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
-@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
- endif()
-
- ## Try and find TBB first
--find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
-+find_package(TBB)
-
- ## NOTE: we actually require at least 2019 U4 or greater
- ## since we are using tbb::global_control. However, they
-@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
- ## source. Check before release if we can bump to the 2020
- ## version (requires having tbb 2020 for OSX).
- if (${TBB_FOUND})
-- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
- message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
- set(TBB_TARGET_EXISTED TRUE)
-- else()
-- set(TBB_TARGET_EXISTED FALSE)
-- endif()
- else()
- set(TBB_TARGET_EXISTED FALSE)
- endif()
-@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
- message("Build system will compile libgff")
- message("==================================================================")
- externalproject_add(libgff
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
-- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
-- tar -xzvf libgff.tgz
- ##
- #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
- #DOWNLOAD_NAME libff.tgz
-diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
-index c8b3eb5..b4c23da 100644
---- a/cmake/Modules/FindTBB.cmake
-+++ b/cmake/Modules/FindTBB.cmake
-@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
- ##################################
-
- if(TBB_INCLUDE_DIRS)
-- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
- string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
- TBB_VERSION_MAJOR "${_tbb_version_file}")
- string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
-diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
-index d32e131..1b5cbf2 100755
---- a/scripts/fetchPufferfish.sh
-+++ b/scripts/fetchPufferfish.sh
-@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
- EXTERNAL_DIR=${CURR_DIR}/../external
- INSTALL_DIR=${CURR_DIR}/../external/install
-
--if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
-- rm -fr ${EXTERNAL_DIR}/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
-- rm -fr ${INSTALL_DIR}/include/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
-- rm -fr ${INSTALL_DIR}/src/pufferfish
--fi
--
- SVER=salmon-v1.6.0
- #SVER=develop
- #SVER=sketch-mode
-@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
- EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
-
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
--
--hashcheck=""
--if exists sha256sum; then
-- hashcheck="sha256sum"
--elif exists shasum; then
-- hashcheck="shasum -a256"
--else
-- unset hashcheck
--fi
--
--if [ -z "${hashcheck-}" ]; then
-- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
--else
-- if [[ $SVER != develop ]]; then
-- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
-- else
-- echo "not testing sha since pulling from develop"
-- fi
--fi
--
--
--rm -fr ${EXTERNAL_DIR}/pufferfish
--unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
-
- mkdir -p ${INSTALL_DIR}/include/pufferfish
-
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
deleted file mode 100644
index 1907254d6..000000000
--- a/sci-biology/salmon/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
- <upstream>
- <remote-id type="github">COMBINE-lab/salmon</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
deleted file mode 100644
index c3ef9e50a..000000000
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
- https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
- https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
- https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
- https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
- https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
- "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
- "${FILESDIR}"/salmon-0.10.2_fix_tests.patch
- "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-RDEPEND="${DEPEND}"
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-# https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
-#
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- app-arch/xz-utils
- dev-libs/boost:0=
- dev-libs/libdivsufsort
- sci-biology/bwa
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
-"
-RDEPEND="${DEPEND}"
-BDEPEND="
- net-misc/curl
- app-arch/unzip
-"
-
-src_prepare() {
- # use system libs
- sed -i \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \
- src/CMakeLists.txt || die
-
- cmake_src_prepare
-}
diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
deleted file mode 100644
index 6c19ff58f..000000000
--- a/sci-biology/salmon/salmon-1.6.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="
- https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
- https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
-"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-libs/boost:=
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- dev-libs/cereal
- sci-libs/io_lib[static-libs]
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
-
-PATCHES=(
- "${FILESDIR}/${P}-find-boost.patch"
-)
-
-src_unpack() {
- default
- mkdir -p "${S}/external/install/lib" || die
- mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
- mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
- ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
- ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
- ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
- -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
- -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DFETCH_BOOST=FALSE
- -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
- -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
- -DBoost_ALL_FOUND=TRUE
- -Dboost_headers_FOUND=TRUE
- -DBoost_FOUND=TRUE
- )
- cmake_src_configure
-}
diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml
index 138cb7705..a2d91d1c4 100644
--- a/sci-biology/seqtk/metadata.xml
+++ b/sci-biology/seqtk/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">lh3/seqtk</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml
index ae9640ffb..d888971d1 100644
--- a/sci-biology/spm/metadata.xml
+++ b/sci-biology/spm/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">spm/spm12</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
deleted file mode 100644
index 13f7d3536..000000000
--- a/sci-biology/staden/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a
diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
-
- getABIdate: $(OBJSD)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-
- getABIcomment: $(OBJSC)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
-
- alfsplit: $(ALFOBJ)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-
- RSOBJ = $(ALFBIN)/2rs.o
-
diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">staden</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
deleted file mode 100644
index a0f91720b..000000000
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
- app-arch/xz-utils
- dev-lang/tk:0=
- dev-tcltk/tklib
- media-libs/libpng:0
- sci-biology/samtools:0
- >=sci-libs/io_lib-1.13.8
- sys-libs/zlib"
-RDEPEND="${DEPEND}
- >=dev-tcltk/iwidgets-4.0
- tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )
- net-misc/curl
- doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
-
-PATCHES=(
- "${FILESDIR}/${P}-ldflags.patch"
-)
-
-src_prepare() {
- default
- sed \
- -e 's:svnversion:false:' \
- -i configure.in || die
-}
-
-src_configure(){
- use debug && append-cflags "-DCACHE_REF_DEBUG"
- econf \
- $(use_enable X x) \
- $(use_enable amd64 64bit) \
- --with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-src_install() {
- default
- # install the LDPATH so that it appears in /etc/ld.so.conf after env-update
- # subsequently, apps linked against /usr/lib/staden can be run because
- # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
- # somehow for gap2caf, for example
- cat >> "${T}"/99staden <<- EOF
- STADENROOT="${EPREFIX}"/usr/share/staden
- LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
- EOF
- doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
- einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest
deleted file mode 100644
index 108aad2fe..000000000
--- a/sci-biology/staden_doc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden_doc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">staden</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
deleted file mode 100644
index 5a70701b0..000000000
--- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Documentation files for the staden package"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- dev-lang/perl
- app-text/texlive
- app-text/texi2html"
-BDEPEND="app-editors/emacs"
-RDEPEND="${DEPEND} ${BDEPEND}"
-
-S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
-
-# do not use texi2html-5 because it fails with:
-# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
-# Unknown option: index_char
-# src_prepare(){
-# default
-# # avoid running bundled texi2html code
-# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
-# }
-
-src_compile(){
- cd manual || die
- emake -j1 spotless || die
- cd .. || die
- emake -j1 unix PAPER=A4
-}
-
-src_install(){
- emake -j1 install prefix="${D}"/usr
- dodoc gkb547_gml.pdf
-}
diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml
index 138cb7705..079fb5aae 100644
--- a/sci-biology/trans-abyss/metadata.xml
+++ b/sci-biology/trans-abyss/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/transabyss</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml
index 138cb7705..ac0e44aa7 100644
--- a/sci-biology/trim_galore/metadata.xml
+++ b/sci-biology/trim_galore/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">FelixKrueger/TrimGalore</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml
index a3daeebd2..36e8936e5 100644
--- a/sci-biology/ugene/metadata.xml
+++ b/sci-biology/ugene/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ugeneunipro/ugene</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml
index eea62e858..996e48735 100644
--- a/sci-chemistry/erkale/metadata.xml
+++ b/sci-chemistry/erkale/metadata.xml
@@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core
(x-ray absorption and x-ray Raman scattering) and valence electron
excitation spectra of atoms and molecules.
</longdescription>
+ <upstream>
+ <remote-id type="github">susilehtola/erkale</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
index cdabe7f2c..33e6e7e5d 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -12,4 +12,7 @@
<use>
<flag name="gui">Enable relion gui</flag>
</use>
+ <upstream>
+ <remote-id type="github">3dem/relion</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
index a74996b46..d1257f0ee 100644
--- a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild
+++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2020 Gentoo Authors
+# Copyright 2020-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -14,7 +14,7 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r2"
+DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5"
RDEPEND="${DEPEND}"
S=${WORKDIR}/${PN}-${COMMIT}
diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
index 753464ee5..a171606a6 100644
--- a/sci-libs/HDF5Plugin-Zstandard/metadata.xml
+++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
@@ -5,4 +5,7 @@
<email>xgreenlandforwyy@gmail.com</email>
<name>Yiyang Wu</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml
index 138cb7705..6f7127e91 100644
--- a/sci-libs/fast5/metadata.xml
+++ b/sci-libs/fast5/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mateidavid/fast5</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest
new file mode 100644
index 000000000..64b9caefd
--- /dev/null
+++ b/sci-libs/gdcm/Manifest
@@ -0,0 +1,2 @@
+DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220
+DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee
diff --git a/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
new file mode 100644
index 000000000..ba99c3547
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
@@ -0,0 +1,15 @@
+https://cgit.freebsd.org/ports/plain/devel/gdcm/files/patch-Utilities_VTK_vtkImageMapToWindowLevelColors2.cxx?id=8f5541298099b722e34632ca9ed388bda91064e7
+
+- workaround for https://sourceforge.net/p/gdcm/bugs/536/
+
+--- a/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx 2022-06-26 20:39:45 UTC
++++ b/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx
+@@ -37,6 +37,8 @@
+ #include "vtkScalarsToColors.h"
+ #include "vtkPointData.h"
+
++#include <math.h>
++
+ //vtkCxxRevisionMacro(vtkImageMapToWindowLevelColors2, "$Revision: 1.3 $")
+ vtkStandardNewMacro(vtkImageMapToWindowLevelColors2)
+
diff --git a/sci-libs/gdcm/files/gdcm_support_vtk9.patch b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
new file mode 100644
index 000000000..3818a82b5
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
@@ -0,0 +1,70 @@
+--- a/Utilities/VTK/CMakeLists.txt
++++ b/Utilities/VTK/CMakeLists.txt
+@@ -26,6 +26,11 @@
+ )
+ endif()
+
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ set(VTK_INCLUDE_DIRS "${VTK_PREFIX_PATH}/include/vtk-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}")
++ include_directories(AFTER ${VTK_INCLUDE_DIRS})
++endif()
++
+ include(CheckCXXSourceCompiles)
+ set(CMAKE_REQUIRED_INCLUDES ${VTK_INCLUDE_DIRS})
+ CHECK_CXX_SOURCE_COMPILES(
+@@ -94,6 +99,10 @@
+ endforeach()
+ endif()
+
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ string(REGEX REPLACE "vtk([^;]+)" "VTK::\\1" vtkgdcm_LIBS "${vtkgdcm_LIBS}")
++endif()
++
+ # Use wrapping hints for this project.
+ #set(VTK_WRAP_HINTS "${PROJECT_SOURCE_DIR}/hints")
+
+--- a/Utilities/VTK/Applications/CMakeLists.txt
++++ b/Utilities/VTK/Applications/CMakeLists.txt
+@@ -25,6 +25,11 @@
+ )
+ endif()
+
++set(vtk_ioxml vtkIOXML)
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ set(vtk_ioxml VTK::IOXML)
++endif()
++
+ foreach(app ${GDCM_VTK_APPS})
+ add_executable(${app} ${app}.cxx)
+ if(GDCM_EXECUTABLE_PROPERTIES)
+@@ -42,7 +47,7 @@
+ endif()
+ else()
+ # >= 6.0
+- target_link_libraries(${app} ${VTK_LIBRARIES} vtkIOXML)
++ target_link_libraries(${app} ${VTK_LIBRARIES} ${vtk_ioxml})
+ endif()
+ if(WIN32 AND NOT CYGWIN)
+ target_link_libraries(${app} gdcmgetopt)
+--- a/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
++++ b/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
+@@ -496,6 +496,9 @@
+ sqi = new SequenceOfItems;
+
+ vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++ const
++#endif
+ vtkIdType *indx = 0;
+ double v[3];
+ unsigned int cellnum = 0;
+@@ -759,6 +762,9 @@
+ vtkPoints *pts;
+ vtkCellArray *polys;
+ vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++ const
++#endif
+ vtkIdType *indx = 0;
+ pts = theData->GetPoints();
+ polys = theData->GetPolys();
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
new file mode 100644
index 000000000..5249e81b7
--- /dev/null
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -0,0 +1,121 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..10} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Cross-platform DICOM implementation"
+HOMEPAGE="http://gdcm.sourceforge.net/"
+SRC_URI="mirror://sourceforge/gdcm/${P}.tar.bz2
+ test? ( mirror://sourceforge/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc python test vtk"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+ app-text/poppler:0=[cxx]
+ dev-libs/expat:0=
+ dev-libs/json-c:0=
+ dev-libs/libxml2:2=
+ dev-libs/openssl:0=
+ >=media-libs/charls-2.0.0:0=
+ >=media-libs/openjpeg-2.0.0:2=
+ sys-apps/util-linux:0=
+ sys-libs/zlib:0=
+ python? ( ${PYTHON_DEPS} )
+ vtk? (
+ sci-libs/vtk[rendering]
+ python? (
+ sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}]
+ )
+ )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ dev-libs/libxslt
+ app-text/docbook-xsl-ns-stylesheets
+ doc? ( app-doc/doxygen[dot] )
+ python? (
+ ${PYTHON_DEPS}
+ >=dev-lang/swig-3.0.7
+ )"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+PATCHES=(
+ "${FILESDIR}/gdcm_support_vtk9.patch"
+ "${FILESDIR}/gdcm-3.0.14-include-math-h.patch"
+)
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ # drop unbundled libs
+ local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release )
+ local x
+ for x in "${DROPS[@]}"; do
+ ebegin "Dropping bundled ${x#gdcm}"
+ rm -r "Utilities/${x}" || die
+ sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die
+ eend $?
+ done
+ find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \
+ -exec ewarn "Using bundled" {} ';' || die
+
+ # fix charls include case
+ sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die
+ sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die
+
+ # Use prefixed socket++ (to avoid potential conflicts)
+ sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \
+ Source/MessageExchangeDefinition/CMakeLists.txt \
+ Applications/Cxx/CMakeLists.txt \
+ || die
+
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_SKIP_RPATH=ON
+ -DGDCM_BUILD_SHARED_LIBS=ON
+ -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData"
+ -DGDCM_INSTALL_LIB_DIR="$(get_libdir)"
+ -DGDCM_INSTALL_DOC_DIR="share/doc/${P}"
+ -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages"
+ -DGDCM_USE_SYSTEM_ZLIB=ON
+ -DGDCM_USE_SYSTEM_OPENSSL=ON
+ -DGDCM_USE_SYSTEM_UUID=ON
+ -DGDCM_USE_SYSTEM_EXPAT=ON
+ -DGDCM_USE_SYSTEM_JSON=ON
+ -DGDCM_USE_SYSTEM_PAPYRUS3=OFF
+ -DGDCM_USE_SYSTEM_SOCKETXX=OFF
+ -DSOCKETXX_NAMESPACE=GDCMSOCKETXX
+ -DGDCM_USE_SYSTEM_LJPEG=OFF
+ -DGDCM_USE_SYSTEM_OPENJPEG=ON
+ -DGDCM_USE_SYSTEM_CHARLS=ON
+ -DGDCM_USE_SYSTEM_POPPLER=ON
+ -DGDCM_USE_SYSTEM_LIBXML2=ON
+ -DGDCM_BUILD_TESTING=$(usex test)
+ -DGDCM_WRAP_PYTHON=$(usex python)
+ $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "")
+ -DGDCM_WRAP_PERL=OFF
+ -DGDCM_WRAP_PHP=OFF
+ -DGDCM_WRAP_JAVA=OFF
+ -DGDCM_WRAP_CSHARP=OFF
+ -DGDCM_DOCUMENTATION=$(usex doc)
+ $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "")
+ -DGDCM_BUILD_EXAMPLES=OFF
+ -DGDCM_BUILD_APPLICATIONS=ON
+ -DGDCM_USE_VTK=$(usex vtk)
+ )
+ cmake_src_configure
+}
diff --git a/sci-libs/gdcm/metadata.xml b/sci-libs/gdcm/metadata.xml
new file mode 100644
index 000000000..1845bf1bd
--- /dev/null
+++ b/sci-libs/gdcm/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>fx.carton91@gmail.com</email>
+ <name>François-Xavier Carton</name>
+ </maintainer>
+ <use>
+ <flag name="vtk">Build <pkg>sci-libs/vtk</pkg> bridge</flag>
+ </use>
+ <upstream>
+ <remote-id type="sourceforge">gdcm</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/handyg/Manifest b/sci-libs/handyg/Manifest
new file mode 100644
index 000000000..3487702bd
--- /dev/null
+++ b/sci-libs/handyg/Manifest
@@ -0,0 +1 @@
+DIST handyg-v0.1.5.tar.gz 107946 BLAKE2B 338b0027f51fd8b329c1af4e6a0e76dda7b9a3d29a12cffcf60948c5800ee8e280ff97726359df483b60dc3d76a26c40bf21804113d318d83539828e54c4a1ff SHA512 f6f068e05c80c6dccf1c4c8a284da752d04d4fd3f15a78eee933227c6a93906fe794ef3ada359831a4098c00b0a7684af91e2f9cca2a06dd8d0381c1c20c59be
diff --git a/sci-libs/handyg/files/handyg-0.1.5-ld.patch b/sci-libs/handyg/files/handyg-0.1.5-ld.patch
new file mode 100644
index 000000000..f3f06cd91
--- /dev/null
+++ b/sci-libs/handyg/files/handyg-0.1.5-ld.patch
@@ -0,0 +1,22 @@
+--- a/configure 2022-09-19 01:59:40.382091704 +0200
++++ b/configure 2022-09-19 02:00:00.734380534 +0200
+@@ -358,7 +358,7 @@
+ FLDFLAGS+=" $1" ;;
+ -Bstatic | -Bdynamic | *.ld)
+ echo "Found linker flag $1" 1>&2
+- FLDFLAGS+=" -Wl,$1" ;;
++ FLDFLAGS+=" $1" ;;
+ /*)
+ echo "Found linker flag $1" 1>&2
+ FLDFLAGS+=" -L$1" ;;
+--- a/configure 2022-09-19 02:02:18.064324729 +0200
++++ b/configure 2022-09-19 02:02:22.935393539 +0200
+@@ -364,7 +364,7 @@
+ FLDFLAGS+=" -L$1" ;;
+ -rpath*)
+ echo "Found linker flag $1" 1>&2
+- FLDFLAGS+=" -Wl,$1,$2"
++ FLDFLAGS+=" $1,$2"
+ shift ;;
+ -dynamic-linker)
+ shift ;;
diff --git a/sci-libs/handyg/files/handyg-0.1.5-so.patch b/sci-libs/handyg/files/handyg-0.1.5-so.patch
new file mode 100644
index 000000000..48815780e
--- /dev/null
+++ b/sci-libs/handyg/files/handyg-0.1.5-so.patch
@@ -0,0 +1,23 @@
+--- a/configure 2022-09-19 22:54:12.742507414 +0200
++++ b/configure 2022-09-19 23:00:13.452378883 +0200
+@@ -839,7 +839,7 @@
+ objects = \$(addprefix build/,\$(files))
+
+
+-all: libhandyg.a handyg.mod ${CONF_MPREP:+handyG} geval test
++all: libhandyg.a libhandyg.so handyg.mod ${CONF_MPREP:+handyG} geval test
+
+ EOF
+
+@@ -868,6 +868,11 @@
+ @echo "AR \$@"
+ @\$(AR) \$@ \$^
+
++libhandyg.so:\$(objects)
++ @echo "\$(FC) \$@"
++ \$(FC) \$(LFLAGS) -Wl,-soname,libhandyg.so -shared -o \$@ \$^
++
++
+ handyg.mod: build/handyg.mod
+ cp \$< \$@
+
diff --git a/sci-libs/handyg/handyg-0.1.5.ebuild b/sci-libs/handyg/handyg-0.1.5.ebuild
new file mode 100644
index 000000000..97a18c08e
--- /dev/null
+++ b/sci-libs/handyg/handyg-0.1.5.ebuild
@@ -0,0 +1,44 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+MY_P=${PN}-v${PV}
+
+DESCRIPTION="Rapid numerical evaluation of generalised polylogarithms"
+HOMEPAGE="https://gitlab.com/mule-tools/handyg"
+SRC_URI="https://gitlab.com/mule-tools/${PN}/-/archive/v${PV}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND="
+ virtual/fortran
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-so.patch"
+)
+
+src_configure() {
+ tc-export CC CXX FC AR
+ FFLAGS="${FFLAGS} -fPIC" LD="${FC}" ./configure --prefix="${EPREFIX}/usr" LDFLAGS="${LDFLAGS}"
+}
+
+src_compile() {
+ # single thread force needed since fortan mods depend on each other
+ export MAKEOPTS=-j1
+ emake all
+}
+
+src_install() {
+ dolib.a libhandyg.a
+ dolib.so libhandyg.so
+ doheader handyg.mod
+ dobin geval
+}
diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-libs/handyg/metadata.xml
index 138cb7705..bdee6992b 100644
--- a/sci-biology/roche454ace2caf/metadata.xml
+++ b/sci-libs/handyg/metadata.xml
@@ -2,11 +2,11 @@
<!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>
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
</maintainer>
<maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
</maintainer>
</pkgmetadata>
diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/sci-libs/ipp/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/sci-libs/ipp/ipp-18.0.2.199.ebuild b/sci-libs/ipp/ipp-18.0.2.199.ebuild
deleted file mode 100644
index 5253840b9..000000000
--- a/sci-libs/ipp/ipp-18.0.2.199.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel Integrated Performance Primitive library"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND=""
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=6500M
-
-INTEL_DIST_DAT_RPMS=(
- "ipp-common-2018.2-199-2018.2-199.noarch.rpm"
- "ipp-common-ps-2018.2-199-2018.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "ipp-mt-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-mt-devel-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-devel-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-devel-ps-2018.2-199-2018.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "ipp-mt-32bit-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-mt-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-32bit-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm"
- "ipp-st-devel-ps-32bit-2018.2-199-2018.2-199.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "ipp-doc-2018-2018.2-199.noarch.rpm")
- fi
-}
diff --git a/sci-libs/ipp/ipp-19.0.4.243.ebuild b/sci-libs/ipp/ipp-19.0.4.243.ebuild
deleted file mode 100644
index e42583e20..000000000
--- a/sci-libs/ipp/ipp-19.0.4.243.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel Integrated Performance Primitive library"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND=""
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=6500M
-
-INTEL_DIST_DAT_RPMS=(
- "ipp-common-2019.4-243-2019.4-243.noarch.rpm"
- "ipp-common-ps-2019.4-243-2019.4-243.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "ipp-mt-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-mt-devel-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-devel-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-devel-ps-2019.4-243-2019.4-243.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "ipp-mt-32bit-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-mt-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-32bit-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm"
- "ipp-st-devel-ps-32bit-2019.4-243-2019.4-243.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "ipp-doc-2019-2019.4-243.noarch.rpm")
- fi
-}
diff --git a/sci-libs/ipp/ipp-2020.1.217.ebuild b/sci-libs/ipp/ipp-2020.1.217.ebuild
deleted file mode 100644
index 2c0be6abf..000000000
--- a/sci-libs/ipp/ipp-2020.1.217.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel Integrated Performance Primitive library"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND=""
-RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]"
-
-CHECKREQS_DISK_BUILD=6500M
-
-MY_PV="$(ver_rs 2 '-')" # 2020.1-217
-
-QA_PREBUILT="*"
-
-INTEL_DIST_DAT_RPMS=(
- "ipp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "ipp-common-ps-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "ipp-mt-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-mt-devel-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-st-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-st-devel-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "ipp-mt-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-mt-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-st-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "ipp-st-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "ipp-doc-2020-${MY_PV}.noarch.rpm")
- fi
-}
diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest
index 31310f8b1..b346829c9 100644
--- a/sci-libs/itk/Manifest
+++ b/sci-libs/itk/Manifest
@@ -1,10 +1,7 @@
-DIST ITKGenericLabelInterpolator-5.0.1.tar.gz 136432 BLAKE2B c367d5f29b3b3250f73d3b03b80b50a99607d895ebb83c3613b40ed665bce87b2731b2ecf471a5b77983db1f8894e486404662bb5787056f23de24c8ee897704 SHA512 6044aab4893d6c68c6190c5d81f460ea0dfc4683d33a03a5d56a8a0ae3b767edde530cdc8976e6777237cb1d172f66df044afe11c4cfc9148e5712cf9f3a11fc
-DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 BLAKE2B 1c8efa033586368931d78fe4620ddd1449fcd15153b1585c716bce580df74a6fc990b3714677a81cdcedcd0e4626e4f155c522f6e7306e5be399d521213891b4 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489
-DIST ITKGenericLabelInterpolator_test-5.0.1.zip 430662 BLAKE2B f46683bd1b3479ae6fc9ae63752810a1dda7940c67d4be8524edcb8b40ed384b331ac785ab752c3ed1570cce8d79af7de873820fdb76a11f2e4241ad7fd2d2c2 SHA512 435200a70ee8de30cc02b30d805697ebc61fb2792e6e7d8f5da923d2773ccd6adfdcec2ab953a6a043d624ebb01b9f7f30e2aad83a6442272f28104d357a7bde
-DIST InsightData-5.0.1.tar.gz 290801718 BLAKE2B dcb7657cb1f8555365b2ec94e7f95c4feab13ba4d585fd70ec240e63e7a55cf48aadf091a63ba2263f1f8c10ce3935812655449bea275af3d2eeff3f2689ef46 SHA512 eb766c115049949937d6527937f1f49ef84304a71dc4924581a53173f45c4e5a0c5a0e180550e75ecd840314609580b9d1fe9b2358c5a87c82a2c6aff8e9f50e
-DIST InsightData-5.1.0.tar.gz 292322103 BLAKE2B e55eddf06d72e87e68e7654c634f545923202467b710c75aa929cd040f37a9caa48ee262ca6465631961816af1cd854b9a046ff7e7ffed7731e428e092bc6020 SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa
-DIST InsightToolkit-5.0.1.tar.gz 20627889 BLAKE2B 2bd53f64f18746a7d0226d4d97bc02529a1dd2c05fc2294b0c2a5adb3783a8e766b1d20e051a17f20b4e5855e7c5b4a18d5f177f239113bc64f1a0400ce6f04b SHA512 f36613ff72c513ded3d32504f71308a94fe75555cf9fd22b77485d1375601f6e1f1539cc5ac82a9e1e229bcf514a88ccb55122a7dfc74a6ae1b6604aa70bd814
-DIST InsightToolkit-5.1.0.tar.gz 20694338 BLAKE2B 6a14e2e00f6d68a1420cdeebabdef254d23c6ba6610828bb860cf4e27a87f0e1448cd222bf3bc02f6d32b4eb262d7ba032f4459ed05f59f8c95d80907e03571c SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c
-DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1017 BLAKE2B e6a3b734c3f4a23238dbb921c46297b491436e6c4b0b6d8992fe8fa3c813374f354495ca575d5d371ef49b7bcdc8b63d89a5e8d1ae608bce50fea0efc95ec60d SHA512 e69c77894cab5b295ec5edbecdf693525ec9a4673810b87cbc28646ea40888b7792b5707840069e277905c8b0014bd84ecea036836f87c3b16f388f544e34341
-DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1018 BLAKE2B 50cad64ac0b674fe4dce36c732f8fababe13ec2893e22caa0b22274320fb4f6d70aec1e8b4f6ee5878ebc20b02c7300c877db911b77f82ac0cf2d6e3284f4ffa SHA512 27952af5d6243aa31c187280ea9ba82c434db3614b3db3b406fe8e5c7e4b7e333bc179d5d9956d5a17aa670a7aa7cfce037d37c4225125e703602e322d8ec68b
-DIST itk-5.1.0-testingdata.tar.gz 2409232372 BLAKE2B 7eb1c3ca21558603d3aa915c2a17e9bb656867331dc48e7b514ece50a7eac3d24bdf01c8b0acc703566b598959780d6736b27d1516d932f949e3a5cfe6acd9e0 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f
+DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4
+DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6
+DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704
+DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7
+DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398
+DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a
+DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f
diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
deleted file mode 100644
index 094ee3229..000000000
--- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001
-From: Matt McCormick <matt.mccormick@kitware.com>
-Date: Wed, 5 Feb 2014 15:52:34 -0500
-Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter.
-
-Missing CMakeLists.txt in the wrapping directory. Need to explicitly include
-the headers after "Template" was appended to the class name.
-
-Suggested-by: Sami Koho <sami.koho@gmail.com>
-
-Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7
----
- Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++
- Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++
- Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++
- 3 files changed, 7 insertions(+)
- create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt
-
-diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-new file mode 100644
-index 0000000..6072567
---- /dev/null
-+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-@@ -0,0 +1,3 @@
-+itk_wrap_module(ITKIOTransformBase)
-+itk_auto_load_submodules()
-+itk_end_wrap_module()
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-index 9b52fbc..662df9e 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileReader.h")
- itk_wrap_class("itk::TransformFileReaderTemplate" POINTER)
- foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-index 4f1ac4a..356aaf3 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileWriter.h")
- itk_wrap_class("itk::TransformFileWriterTemplate" POINTER)
- foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
deleted file mode 100644
index 4c74d5451..000000000
--- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Fri, 7 Feb 2014 19:24:49 +0100
-Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
-
-The warning :
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef]
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double >
----
- .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-index 4a43dd4..7eed11c 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkQuasiNewtonOptimizerv4.h")
-+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
deleted file mode 100644
index d77345edf..000000000
--- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Mon, 10 Feb 2014 09:41:42 +0100
-Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping
- warnings
-
-I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping.
-
-The warnings :
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double >
-
-Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/)
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored.
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template.
-
-Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364
----
- .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++
- .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++---
- .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++
- 3 files changed, 21 insertions(+), 3 deletions(-)
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-new file mode 100644
-index 0000000..74f5a6c
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerBasev4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-index d53a176..3236448 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-@@ -1,3 +1,7 @@
--itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerv4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-new file mode 100644
-index 0000000..61b2c44
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkObjectToObjectOptimizerBase.h")
-+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
deleted file mode 100644
index 83b395626..000000000
--- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Author: Matt McCormick <matt.mccormick@kitware.com>
-Date: Thu Feb 6 10:26:49 2014 -0500
-
- COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
-
- The class name changed and it became templated. Fixes:
-
- /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
- warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator
- [typedef]
- /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
- warning(4): ITK type not wrapped, or currently not known:
- itk::OptimizerParameterScalesEstimatorTemplate< double >
-
- Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim
-index efd6a8c..a647ee4 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkOptimizerParameterScalesEstimator.h")
-+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-
diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
deleted file mode 100644
index d760ac7ba..000000000
--- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-index e98077c..70f4286 100644
---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-@@ -1,5 +1,5 @@
- if(ITK_USE_SYSTEM_GDCM)
-- add_library(ITKGDCM ITK-GDCM.cxx)
-+ add_library(ITKGDCM STATIC ITK-GDCM.cxx)
- target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF)
- itk_module_target(ITKGDCM)
- return()
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch
deleted file mode 100644
index eb130159a..000000000
--- a/sci-libs/itk/files/ITKModuleRemote.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Disable automatic git clone attempt for modules:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1157
-
---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200
-+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200
-@@ -165,39 +165,4 @@
- set(Module_${_name} ON CACHE FORCE "${_description}")
- endif()
-
-- if(Module_${_name})
-- itk_download_attempt_check(Module_${_name})
-- include(CMakeParseArguments)
-- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
-- find_package(Git)
-- if(NOT GIT_EXECUTABLE)
-- message(FATAL_ERROR "error: could not find git for clone of ${_name}")
-- endif()
-- execute_process(
-- COMMAND "${GIT_EXECUTABLE}" --version
-- OUTPUT_VARIABLE ov
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- )
-- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
-- if("${_version}" VERSION_LESS 1.6.6)
-- message(FATAL_ERROR "Git version 1.6.6 or later is required.")
-- endif()
--
-- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
--
-- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}")
-- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
-- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
-- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
-- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
-- endif()
-- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}")
-- mark_as_advanced(REMOTE_GIT_TAG_${_name})
--
-- _fetch_with_git("${GIT_EXECUTABLE}"
-- "${_fetch_options_GIT_REPOSITORY}"
-- "${REMOTE_GIT_TAG}"
-- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
-- )
-- endif()
- endfunction()
diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch
deleted file mode 100644
index 34fdb76d1..000000000
--- a/sci-libs/itk/files/itk-5.1.0-downloads.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-@@ -11,7 +11,7 @@
-
- macro(itk_download_attempt_check _name)
- if(ITK_FORBID_DOWNLOADS)
-- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
-+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
- endif()
- endmacro()
-
---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
- "A generic interpolator for multi-label images."
- MODULE_COMPLIANCE_LEVEL 2
-- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
-- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
- )
diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..000000000
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include <limits>
-
- namespace gdcm
- {
diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
new file mode 100644
index 000000000..05c9d5635
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
@@ -0,0 +1,25 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Thu, 9 Jun 2022 14:56:22 +0200
+Subject: [PATCH] fix attr malloc error with recent glibc/gcc
+
+Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang
+does not. castxml uses clang internally. And recent glibc/gcc uses the attribute
+with arguments. Mix all this, and you get:
+
+error: '__malloc__' attribute takes no arguments
+
+when compiling itk with python wrapping.
+
+To fix this, we add a define to castxml flags to remove the extra arguments.
+
+--- a/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:53:15.582352715 +0200
++++ b/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:54:38.182351433 +0200
+@@ -237,7 +237,7 @@
+ set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0")
+ endif()
+ else()
+- set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} ))
++ set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ ))
+ endif()
+ set(_target)
+ if(CMAKE_CROSSCOMPILING)
diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
new file mode 100644
index 000000000..ad717f677
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
@@ -0,0 +1,558 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+
+-set(ITKOpenJPEG_INCLUDE_DIRS
+- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+- )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++ find_package(OpenJPEG REQUIRED)
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src
++ )
++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++ ${OPENJPEG_INCLUDE_DIRS}
++ )
++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++ set(ITKOpenJPEG_NO_SRC 1)
++else()
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ )
++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+ DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+ COMPONENT Development
+ )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+
+-#include <itkopenjpeg/openjpeg.h>
++/* Use the openjpeg library configured for ITK. */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include <openjpeg.h>
++#else
++# include <itkopenjpeg/openjpeg.h>
++#endif
+
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+
+
+@@ -139,11 +137,11 @@
+ {
+ itkDebugMacro(<< "ReadImageInformation()");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- /* decompression parameters */
++ /* set decoding parameters to default values */
++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+
+- if (!l_file)
++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++ if (!cio)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -151,10 +149,5 @@
+ }
+
+- /* set decoding parameters to default values */
+- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+ this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+
+ opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -230,7 +220,6 @@
+ }
+ default:
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -248,26 +237,8 @@
+ }
+
+- // Image parameters - first tile
+- OPJ_INT32 l_tile_x0;
+- OPJ_INT32 l_tile_y0;
+-
+- // Image parameters - tile width, height and number of tiles
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+ itkDebugMacro(<< "Trying to read header now...");
+
+- bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- cio);
++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+@@ -284,13 +255,21 @@
+ }
+
+- this->m_Internal->m_TileStartX = l_tile_x0;
+- this->m_Internal->m_TileStartY = l_tile_y0;
++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo);
++ if (!cp)
++ {
++ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
++ << "Reason: Error while reading image header");
++ }
++ this->m_Internal->m_TileStartX = cp->tx0;
++ this->m_Internal->m_TileStartY = cp->ty0;
+
+- this->m_Internal->m_TileWidth = l_tile_width;
+- this->m_Internal->m_TileHeight = l_tile_height;
++ this->m_Internal->m_TileWidth = cp->tdx;
++ this->m_Internal->m_TileHeight = cp->tdy;
+
+- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++ this->m_Internal->m_NumberOfTilesInX = cp->tw;
++ this->m_Internal->m_NumberOfTilesInY = cp->th;
+
+
+ itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -307,6 +286,7 @@
+ else
+ {
+ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: "
+ << "Unknown precision in file: "
+@@ -320,6 +300,6 @@
+ break;
+ case 3:
+- if (l_image->color_space != CLRSPC_SRGB)
++ if (l_image->color_space != OPJ_CLRSPC_SRGB)
+ {
+ itkWarningMacro(<< "file does not specify color space, assuming sRGB");
+ }
+@@ -349,7 +329,6 @@
+
+ /* close the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -368,16 +347,7 @@
+ {
+ itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true);
++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+ if (!l_stream)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,9 +367,10 @@
+ {
+ /* JPEG-2000 codestream */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
+@@ -410,9 +381,10 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
+@@ -423,9 +395,10 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
+@@ -433,7 +406,7 @@
+ break;
+ }
+ default:
+- fclose(l_file);
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -445,32 +418,17 @@
+ if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters)))
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_setup_decoder returns false");
+ }
+
+- OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+- bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- l_stream);
++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_read_header returns false");
+ }
+@@ -499,7 +457,7 @@
+ itkDebugMacro(<< "p_end_x = " << p_end_x);
+ itkDebugMacro(<< "p_end_y = " << p_end_y);
+
+- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y);
++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y);
+
+ itkDebugMacro(<< "opj_set_decode_area() after");
+
+@@ -509,6 +467,5 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_set_decode_area returns false");
+ }
+@@ -525,13 +482,14 @@
+
+ OPJ_UINT32 l_max_data_size = 1000;
+
+- bool l_go_on = true;
++ OPJ_BOOL l_go_on = true;
+
+ auto * l_data = (OPJ_BYTE *)malloc(1000);
+
+ while (l_go_on)
+ {
+ bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++ l_stream,
+ &l_tile_index,
+ &l_data_size,
+ &l_current_tile_x0,
+@@ -540,13 +498,11 @@
+ &l_current_tile_y1,
+ &l_nb_comps,
+- &l_go_on,
+- l_stream);
++ &l_go_on);
+
+ if (!tileHeaderRead)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@
+ if (!l_data)
+ {
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -667,13 +620,11 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: error whle reading image");
+ }
+
+ /* close the byte stream */
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -775,6 +726,6 @@
+ }
+
+- for (int i = 0; i < parameters.numpocs; i++)
++ for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++)
+ {
+ if (parameters.POC[i].prg == -1)
+ {
+@@ -840,13 +791,13 @@
+
+ parameters.numresolution = numberOfResolutions;
+
+- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY;
++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY;
+ opj_image_cmptparm_t cmptparms[3];
+
+ if (this->GetNumberOfComponents() == 3)
+ {
+
+- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED;
++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@
+
+ if (this->GetNumberOfComponents() == 1)
+ {
+- color_space = CLRSPC_GRAY;
++ color_space = OPJ_CLRSPC_GRAY;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -941,8 +892,9 @@
+ if (extension == ".j2k")
+ {
+- cinfo = opj_create_compress(CODEC_J2K);
++ cinfo = opj_create_compress(OPJ_CODEC_J2K);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_J2K) returns nullptr");
+@@ -950,9 +902,10 @@
+ }
+ else if (extension == ".jp2")
+ {
+- cinfo = opj_create_compress(CODEC_JP2);
++ cinfo = opj_create_compress(OPJ_CODEC_JP2);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JP2) returns nullptr");
+@@ -960,9 +913,10 @@
+ }
+ else if (extension == ".jpt")
+ {
+- cinfo = opj_create_compress(CODEC_JPT);
++ cinfo = opj_create_compress(OPJ_CODEC_JPT);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JPT) returns nullptr");
+@@ -970,6 +924,7 @@
+ }
+ else
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: unknown encode format: " << extension);
+ }
+@@ -985,23 +940,19 @@
+
+ if (!opj_setup_encoder(cinfo, &parameters, l_image))
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_setup_encoder returns false");
+ }
+
+- FILE * l_file = fopen(parameters.outfile, "wb");
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+ /* open a byte stream for writing */
+ /* allocate memory for all tiles */
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false);
+ if (!cio)
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -1017,7 +968,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_start_compress returns false");
+ }
+@@ -1026,7 +978,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_encode returns false");
+ }
+@@ -1035,14 +988,14 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_end_compress returns false");
+ }
+
+ /* close and free the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ /* free remaining compression structures */
+ opj_destroy_codec(cinfo);
+--- a/Modules/Nonunit/Review/src/CMakeLists.txt
++++ b/Modules/Nonunit/Review/src/CMakeLists.txt
+@@ -5,7 +5,7 @@
+
+ add_library(ITKReview ${ITKReview_SRC})
+ itk_module_link_dependencies()
+-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg)
++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+
+
diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
new file mode 100644
index 000000000..25c44db2c
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
@@ -0,0 +1,18 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Wed, 8 Jun 2022 19:36:48 +0200
+Subject: [PATCH] system libtiff has INT64
+
+Enabling this, otherwise using system libtiff leads to errors. In particular
+tests fail because there is some IFD8 data but the itkTIFFDataSize function
+returns 0 instead of 8, resulting in invalid mem access.
+
+--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig 2022-06-08 19:34:04.412431969 +0200
++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in 2022-06-08 19:34:26.240431631 +0200
+@@ -34,6 +34,7 @@
+ #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount
+ #cmakedefine ITK_TIFF_HAS_TIFFField
+ #ifdef ITK_USE_SYSTEM_TIFF
++# define TIFF_INT64_T int64_t
+ # include <tiffio.h>
+ #else
+ # include "itktiff/tiffio.h"
diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
new file mode 100644
index 000000000..2af8c4998
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -0,0 +1,309 @@
+https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch
+
+From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001
+From: Niels Dekker <N.Dekker@lumc.nl>
+Date: Thu, 24 Jun 2021 18:00:01 +0200
+Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module
+ test
+
+Fixed a Visual C++ 2019 error, saying:
+
+> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std'
+---
+ .../Deprecated/test/itkSimpleFastMutexLockTest.cxx | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+index 11ad0c52700..60aa1c065b4 100644
+--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+@@ -19,6 +19,8 @@
+
+ #include "itkSimpleFastMutexLock.h"
+
++#include <iostream> // For cout.
++
+
+ int
+ itkSimpleFastMutexLockTest(int, char *[])
+From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001
+From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com>
+Date: Tue, 20 Apr 2021 17:21:21 +0200
+Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists
+
+Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES
+
+```bash
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+ Found relative path while evaluating include directories of
+ "ITKVtkGluePython":
+
+ "_vtk_lib_include_dirs-NOTFOUND"
+```
+
+Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON`
+aka `ITK_WRAP_PYTHON:BOOL=ON`.
+
+Full error log with extra printing:
+
+```bash
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message):
+ ITKVtkGlue_VTK_LIBRARIES:
+ VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs:
+ build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs:
+ build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+-- ITKVtkGlue: Creating module.
+-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule.
+-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule.
+-- ITKVtkGlue: Creating itkViewImage submodule.
+-- MGHIO: Creating module.
+-- MGHIO: Creating itkMGHImageIO submodule.
+-- MorphologicalContourInterpolation: Creating module.
+-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule.
+-- ITKPyUtils: Creating module.
+-- ITKPyUtils: Creating itkPyCommand submodule.
+-- ITKPyUtils: Creating itkPyImageFilter submodule.
+-- Configuring done
+CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
+Please set them or make sure they are set and tested correctly in the CMake files:
+_vtk_lib_include_dirs
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+ Found relative path while evaluating include directories of
+ "ITKVtkGluePython":
+
+ "_vtk_lib_include_dirs-NOTFOUND"
+
+```
+---
+ Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+index 3f3322957e1..2fd6a5af8f6 100644
+--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+@@ -2,7 +2,9 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+ foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES)
+ get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES)
+- include_directories(${_vtk_lib_include_dirs})
++ if(_vtk_lib_include_dirs)
++ include_directories(${_vtk_lib_include_dirs})
++ endif()
+ endforeach()
+ endif()
+
+From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001
+From: Butui Hu <hot123tea123@gmail.com>
+Date: Mon, 1 Aug 2022 14:26:39 +0800
+Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils
+ module
+
+---
+ Wrapping/Generators/Python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt
+index fca3d999b87..3b7a1d37334 100644
+--- a/Wrapping/Generators/Python/CMakeLists.txt
++++ b/Wrapping/Generators/Python/CMakeLists.txt
+@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python)
+ ###############################################################################
+ # Configure Python wrapping installation
+ if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH)
+- set(python_check "try:\n import distutils.sysconfig\n print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n pass")
++ set(python_check "try:\n import sysconfig\n print(sysconfig.get_path('platlib'))\nexcept:\n pass")
+ file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check})
+ execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
+ OUTPUT_VARIABLE py_spp
+From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001
+From: Hans Johnson <hans-johnson@uiowa.edu>
+Date: Wed, 15 Dec 2021 08:10:58 -0600
+Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers
+
+The ability to include either .h or .hxx files as
+header files required recursively reading the
+.h files twice. The added complexity is
+unnecessary, costly, and can confuse static
+analysis tools that monitor header guardes (due
+to reaching the maximum depth of recursion
+limits for nested #ifdefs in checking).
+
+Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr>
+---
+ CMake/ITKModuleHeaderTest.cmake | 3 +--
+ Utilities/Maintenance/BuildHeaderTest.py | 4 ----
+ 2 files changed, 1 insertion(+), 6 deletions(-)
+
+diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake
+index eb809d7e93d..82ad192a6f8 100644
+--- a/CMake/ITKModuleHeaderTest.cmake
++++ b/CMake/ITKModuleHeaderTest.cmake
+@@ -36,8 +36,7 @@ macro( itk_module_headertest _name )
+ # effected.
+ set( _include ${${_name}_SOURCE_DIR}/include )
+ file( GLOB _h_files ${_include}/*.h )
+- file( GLOB _hxx_files ${_include}/*.hxx )
+- set( _header_files ${_h_files} ${_hxx_files} )
++ set( _header_files ${_h_files} )
+ list( LENGTH _h_files _num_headers )
+ set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx )
+ set( _test_num 1 )
+diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py
+index 26a4b6ccb3f..f8ed9f7901e 100755
+--- a/Utilities/Maintenance/BuildHeaderTest.py
++++ b/Utilities/Maintenance/BuildHeaderTest.py
+@@ -130,15 +130,11 @@ def main():
+ else:
+ max_idx = added_header_idx + maximum_number_of_headers
+ for i in range(added_header_idx, max_idx):
+- # Use the .hxx if possible.
+- hxx_file = h_files[i][:-1] + "hxx"
+ # Files that include VTK headers need to link to VTK.
+ if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1:
+ to_include = (
+ '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n'
+ )
+- elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)):
+- to_include = '#include "' + hxx_file + '"\n'
+ else:
+ to_include = '#include "' + h_files[i] + '"\n'
+
diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch
deleted file mode 100644
index a549650d2..000000000
--- a/sci-libs/itk/files/nrrdio-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: Link libITKNrrdIO with -lm (needed for sqrt)
-Author: Steve Robbins <smr@debian.org>
-Forwarded: no
-
---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-@@ -64,7 +64,7 @@
- ADD_DEFINITIONS(-DTEEM_ZLIB=1)
-
- ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} )
--TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES})
-+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm)
-
- IF(ITK_LIBRARY_PROPERTIES)
- SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES})
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..000000000
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
- list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
-- itkVtkConnectedComponentImageFilterTest.cxx
-- QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
- NAME itkVTKImageToImageFilterTest
- COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-- itk_add_test(
-- NAME itkVtkMedianImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
-- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME QuickViewTest
-- COMMAND ITKVtkGlueTestDriver
-- --compare DATA{Baseline/QuickViewTest.png,:}
-- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
-- --compareNumberOfPixelsTolerance 1500
-- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
-- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME itkVtkConnectedComponentImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
-- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--endif()
diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
deleted file mode 100644
index 4580c659a..000000000
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ /dev/null
@@ -1,178 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake python-single-r1
-
-MY_PN="InsightToolkit"
-MY_P="${MY_PN}-${PV}"
-GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1"
-GLI_TEST_HASH="57b5d5de8d777f10f269445a"
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="
- https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
- https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz
- test? (
- https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
- https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
- )
- "
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples fftw python review test vtkglue"
-RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
-
-RDEPEND="
- dev-libs/double-conversion:0=
- media-libs/openjpeg:2
- media-libs/libpng:0=
- media-libs/tiff:0=
- sci-libs/dcmtk:0=
- sci-libs/hdf5:0=[cxx]
- sys-libs/zlib:0=
- media-libs/libjpeg-turbo:0=
- fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
- python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
- sys-apps/coreutils
- python? (
- >=dev-lang/swig-2.0:0
- dev-cpp/castxml
- )
- doc? ( app-doc/doxygen )
-"
-BDEPEND="app-arch/unzip"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}"/ITKModuleRemote.patch
- "${FILESDIR}"/tests.patch
-)
-
-pkg_pretend() {
- if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
- elog "To tune ITK to make the best use of working memory you can set"
- elog " ITK_COMPUTER_MEMORY_SIZE=XX"
- elog "in make.conf, default is 1 (unit is GB)"
- fi
- if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
- elog "For Python language bindings, you can define the dimensions"
- elog "you want to create bindings for by setting"
- elog " ITK_WRAP_DIMS=X;Y;Z..."
- elog "in make.conf, default is 2;3 for 2D and 3D data"
- fi
-}
-
-src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die
- if use test; then
- for filename in ../GenericLabelInterpolator/test/*/*mha; do
- MD5=$(md5sum $filename) || die
- MD5=${MD5% *} || die
- cp "$filename" ".ExternalData/MD5/${MD5}" || die
- done
- fi
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
- -DGDCM_USE_SYSTEM_OPENJPEG=ON
- -DITK_FORBID_DOWNLOADS:BOOL=OFF
- -DITK_USE_SYSTEM_DCMTK=ON
- -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
- -DITK_USE_SYSTEM_CASTXML=ON
- -DITK_USE_SYSTEM_HDF5=ON
- -DITK_USE_SYSTEM_JPEG=ON
- -DITK_USE_SYSTEM_PNG=ON
- -DITK_USE_SYSTEM_SWIG=ON
- -DITK_USE_SYSTEM_TIFF=ON
- -DITK_USE_SYSTEM_ZLIB=ON
- -DITK_USE_KWSTYLE=OFF
- -DITK_BUILD_DEFAULT_MODULES=ON
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
- -DWRAP_ITK_JAVA=OFF
- -DWRAP_ITK_TCL=OFF
- -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
- -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
- -DModule_GenericLabelInterpolator:BOOL=ON
- -DModule_ITKReview:BOOL=ON
- -DBUILD_TESTING="$(usex test ON OFF)"
- -DBUILD_EXAMPLES="$(usex examples ON OFF)"
- -DITK_USE_REVIEW="$(usex review ON OFF)"
- -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
- -DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
- )
- if use fftw; then
- mycmakeargs+=(
- -DUSE_FFTWD=ON
- -DUSE_FFTWF=ON
- -DUSE_SYSTEM_FFTW=ON
- -DITK_WRAP_double=ON
- -DITK_WRAP_vector_double=ON
- -DITK_WRAP_covariant_vector_double=ON
- -DITK_WRAP_complex_double=ON
- )
- fi
- if use vtkglue; then
- mycmakeargs+=(
- -DModule_ITKVtkGlue=ON
- )
- fi
- if use python; then
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=ON
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
- )
- else
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=OFF
- )
- fi
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- if use examples; then
- docinto examples
- docompress -x /usr/share/doc/${PF}/examples
- dodoc -r "${S}"/Examples/*
- fi
-
- echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
- local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
- if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
- ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
- fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
- doenvd "${T}"/40${PN}
-
- if use doc; then
- cd "${WORKDIR}"/html || die
- rm *.md5 || die "Failed to remove superfluous hashes"
- einfo "Installing API docs. This may take some time."
- docinto api-docs
- dodoc -r *
- fi
-}
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index e6e0b25f9..98e39935e 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -1,16 +1,18 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{9..10} )
+VIRTUALX_REQUIRED="manual"
-inherit cmake python-single-r1
+inherit cmake python-single-r1 virtualx
MY_PN="InsightToolkit"
MY_P="${MY_PN}-${PV}"
-GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
-TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
+GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
+TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0"
declare -a GLI_TEST_HASHES=(
"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
@@ -18,14 +20,15 @@ declare -a GLI_TEST_HASHES=(
GLI_TEST_SRC=""
for i in "${GLI_TEST_HASHES[@]}"; do
- GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} "
+ GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} "
done
DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
+HOMEPAGE="https://itk.org"
SRC_URI="
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz
+ https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz
test? (
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz
@@ -37,42 +40,55 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
RDEPEND="
+ dev-cpp/eigen:3
dev-libs/double-conversion:0=
+ dev-libs/expat:0=
media-libs/openjpeg:2
media-libs/libpng:0=
media-libs/tiff:0=[jpeg]
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
+ sci-libs/gdcm:0=
sys-libs/zlib:0=
media-libs/libjpeg-turbo:0=
fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+ vtkglue? (
+ sci-libs/vtk:0=[rendering]
+ python? (
+ sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}]
+ )
+ )
python? ( ${PYTHON_DEPS} )
"
DEPEND="${RDEPEND}
sys-apps/coreutils
python? (
>=dev-lang/swig-2.0:0
- dev-cpp/castxml
+ dev-libs/castxml
)
doc? ( app-doc/doxygen )
"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+BDEPEND="
+ test? (
+ vtkglue? ( ${VIRTUALX_DEPEND} )
+ python? (
+ $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]')
+ )
+ )
+"
S="${WORKDIR}/${MY_P}"
PATCHES=(
- "${FILESDIR}"/tests.patch
- "${FILESDIR}"/${P}-downloads.patch
- "${FILESDIR}"/${P}-include_limits.patch
+ "${FILESDIR}/${P}-upstream-fixes.patch"
+ "${FILESDIR}/${P}-system-tiff-has-64.patch"
+ "${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch"
+ "${FILESDIR}/${P}-system-openjpeg.patch"
)
pkg_pretend() {
@@ -90,16 +106,42 @@ pkg_pretend() {
}
src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
+ # drop bundled libs
+ local -a DROPS=(
+ DoubleConversion/src/double-conversion
+ Eigen3/src/itkeigen
+ Expat/src/expat
+ GDCM/src/gdcm
+ JPEG/src/itkjpeg
+ HDF5/src/itkhdf5
+ OpenJPEG/src/openjpeg
+ PNG/src/itkpng
+ TIFF/src/itktiff
+ ZLIB/src/itkzlib
+ )
+ local x
+ for x in "${DROPS[@]}"; do
+ ebegin "Dropping bundled ${x%%/*}"
+ rm -r "Modules/ThirdParty/${x}" || die
+ eend $?
+ done
+ {
+ find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n'
+ printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,'
+ } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
+
+ # Remote modules
+ ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die
+ ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die
+
cmake_src_prepare
+
if use test; then
cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
for i in "${GLI_TEST_HASHES[@]}"; do
- cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die
- cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die
+ cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die
+ cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die
done
fi
}
@@ -107,6 +149,7 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
-DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
+ -DITK_INSTALL_DOC_DIR="share/doc/${P}"
-DBUILD_EXAMPLES="$(usex examples ON OFF)"
-DBUILD_SHARED_LIBS=ON
-DBUILD_TESTING="$(usex test ON OFF)"
@@ -119,8 +162,12 @@ src_configure() {
-DITK_USE_SYSTEM_DCMTK=ON
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-DITK_USE_SYSTEM_CASTXML=ON
+ -DITK_USE_SYSTEM_EIGEN=ON
+ -DITK_USE_SYSTEM_EXPAT=ON
+ -DITK_USE_SYSTEM_GDCM=ON
-DITK_USE_SYSTEM_HDF5=ON
-DITK_USE_SYSTEM_JPEG=ON
+ -DITK_USE_SYSTEM_OPENJPEG=ON
-DITK_USE_SYSTEM_PNG=ON
-DITK_USE_SYSTEM_SWIG=ON
-DITK_USE_SYSTEM_TIFF=ON
@@ -128,6 +175,7 @@ src_configure() {
-DITK_USE_KWSTYLE=OFF
-DITK_BUILD_DEFAULT_MODULES=ON
-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+ -DModule_AdaptiveDenoising:BOOL=ON
-DModule_GenericLabelInterpolator:BOOL=ON
-DModule_ITKReview:BOOL=ON
-DWRAP_ITK_JAVA=OFF
@@ -153,6 +201,7 @@ src_configure() {
if use python; then
mycmakeargs+=(
-DITK_WRAP_PYTHON=ON
+ -DPython3_EXECUTABLE="${PYTHON}"
-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
)
else
@@ -172,13 +221,13 @@ src_install() {
dodoc -r "${S}"/Examples/*
fi
- echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
+ echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die
local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
+ echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die
ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
+ echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die
doenvd "${T}"/40${PN}
if use doc; then
@@ -188,4 +237,14 @@ src_install() {
docinto api-docs
dodoc -r *
fi
+
+ use python && python_optimize
+}
+
+src_test() {
+ if use vtkglue; then
+ virtx cmake_src_test
+ else
+ cmake_src_test
+ fi
}
diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest
deleted file mode 100644
index 827319a78..000000000
--- a/sci-libs/mlpack/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mlpack-3.4.1.tar.gz 5782241 BLAKE2B d5a1050489c61a934330a0f3d1142e7949f7fdd9c31f679d7963208fc8aaea8fd8c0eb7e45920c3799712cb059808c75098e31b913557ec3c2af2f1d32e561f0 SHA512 53de83c2ca36829a0ae952357b25bee44bf85d01c2414848fe2c5f09ebe4732bd0a1d3c72de202646345fa66964fbc3247ddeb6a327e87459c036a215fe55fc2
-DIST mlpack-3.4.2.tar.gz 5782921 BLAKE2B d775124462357b489f91f6ef75f5f908d9a9234082c48223f19a728ab9e41cb6576fca9b4b59415d3096471f4ab2d2970296387954977652169a447b8e036263 SHA512 05a66b73cba8d83f630b0999023913e7a4a3214632930ff3c598d964d52bcae4eab113018eecf385130c0e7e9c16c25380b31dd62a2e0ecf419b4bf3856b34b0
diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml
deleted file mode 100644
index f587c48a7..000000000
--- a/sci-libs/mlpack/metadata.xml
+++ /dev/null
@@ -1,27 +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@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">
- mlpack is a C++ machine learning library with emphasis on
- scalability, speed, and ease-of-use. Its aim is to make machine
- learning possible for novice users by means of a simple, consistent
- API, while simultaneously exploiting C++ language features to
- provide maximum performance and maximum flexibility for expert
- users.
- </longdescription>
- <use>
- <flag name="arma-debug">build with armadillo dbug symbols</flag>
- <flag name="go">build go bindings</flag>
- <flag name="julia">build julia bindings</flag>
- <flag name="matlab">build matlab bindings</flag>
- <flag name="R">build R bindings</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild b/sci-libs/mlpack/mlpack-3.4.1.ebuild
deleted file mode 100644
index d03dd9ab1..000000000
--- a/sci-libs/mlpack/mlpack-3.4.1.ebuild
+++ /dev/null
@@ -1,112 +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 python-single-r1
-
-DESCRIPTION="scalable C++ machine learning library"
-HOMEPAGE="https://www.mlpack.org/"
-SRC_URI="https://www.mlpack.org/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE+="arma-debug debug doc go julia matlab openmp profile R test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
- ${PYTHON_DEPS}
- julia? ( || (
- dev-lang/julia
- dev-lang/julia-bin:*
- )
- )
- go? ( dev-lang/go )
- R? ( dev-lang/R )
-"
-
-RDEPEND="
- ${CDEPEND}
- $(python_gen_cond_dep '
- dev-libs/boost[${PYTHON_USEDEP}]
- dev-libs/libxml2[${PYTHON_USEDEP}]
- ')
- dev-python/pandas
- dev-python/cython
- dev-python/numpy
- dev-libs/stb
- >=sci-libs/armadillo-8.4.0[arpack,blas,lapack]
- sci-libs/ensmallen
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${CDEPEND}
- app-text/txt2man
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-libs/mathjax
- )
- test? ( $( python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- ')
- )
-"
-
-pkg_setup() {
- elog "If you want to build matlab bindings then you"
- elog "need to make sure that matlab has been installed"
- elog "prior to building this package and it is available"
- elog "in the standard locations to be found by"
- elog "CMake, library finders, header includes and other"
- elog "trinkets that are used while compiling."
- elog "Matlab will not be entertained as a first class"
- elog "citizen until we have enough personnel"
-
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- sed -i \
- -e "s:share/doc/mlpack:share/doc/${PF}:" \
- -e 's/-O3//g' \
- CMakeLists.txt || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDISABLE_DOWNLOADS=ON
- -DDOWNLOAD_ENSMALLEN=OFF
- -DDOWNLOAD_STB_IMAGE=OFF
- -DBUILD_WITH_COVERAGE=OFF
- -DBUILD_PYTHON_BINDINGS=ON
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_CLI_EXECUTABLES=ON
- -DTEST_VERBOSE=$(usex test)
- -DBUILD_TESTS=$(usex test)
- -DDEBUG=$(usex debug)
- -DPROFILE=$(usex profile)
- -DARMA_EXTRA_DEBUG=$(usex arma-debug)
- -DUSE_OPENMP=$(usex openmp)
- -DMATLAB_BINDINGS=$(usex matlab)
- -DBUILD_GO_SHLIB=$(usex go)
- -DBUILD_JULIA_BINDINGS=$(usex julia)
- -DBUILD_GO_BINDINGS=$(usex go)
- -DBUILD_R_BINDINGS=$(usex R)
- -DBUILD_MARKDOWN_BINDINGS=$(usex doc)
- -DMATHJAX=$(usex doc)
- ${EXTRA_ECONF[@]}
- )
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- python_optimize
-}
diff --git a/sci-libs/mlpack/mlpack-3.4.2.ebuild b/sci-libs/mlpack/mlpack-3.4.2.ebuild
deleted file mode 100644
index bfc7231e1..000000000
--- a/sci-libs/mlpack/mlpack-3.4.2.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake python-single-r1
-
-DESCRIPTION="scalable C++ machine learning library"
-HOMEPAGE="https://www.mlpack.org/"
-SRC_URI="https://www.mlpack.org/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE+="arma-debug debug doc go julia matlab openmp profile R test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
- ${PYTHON_DEPS}
- julia? ( || (
- dev-lang/julia
- dev-lang/julia-bin:*
- )
- )
- go? ( dev-lang/go )
- R? ( dev-lang/R )
-"
-
-RDEPEND="
- ${CDEPEND}
- $(python_gen_cond_dep '
- dev-libs/boost[${PYTHON_USEDEP}]
- dev-libs/libxml2[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- ')
- dev-libs/stb
- >=sci-libs/armadillo-8.4.0[arpack,blas,lapack]
- sci-libs/ensmallen
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${CDEPEND}
- app-text/txt2man
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-libs/mathjax
- )
- $(python_gen_cond_dep '
- dev-python/cython[${PYTHON_USEDEP}]
- ')
- test? ( $( python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- ')
- )
-"
-
-pkg_setup() {
- elog "If you want to build matlab bindings then you"
- elog "need to make sure that matlab has been installed"
- elog "prior to building this package and it is available"
- elog "in the standard locations to be found by"
- elog "CMake, library finders, header includes and other"
- elog "trinkets that are used while compiling."
- elog "Matlab will not be entertained as a first class"
- elog "citizen until we have enough personnel"
-
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- sed -i \
- -e "s:share/doc/mlpack:share/doc/${PF}:" \
- -e 's/-O3//g' \
- CMakeLists.txt || die
- # drop dep on pytest-runner
- sed -i -e "/setup_requires/d" \
- src/mlpack/bindings/python/setup.py.in || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDISABLE_DOWNLOADS=ON
- -DDOWNLOAD_ENSMALLEN=OFF
- -DDOWNLOAD_STB_IMAGE=OFF
- -DBUILD_WITH_COVERAGE=OFF
- -DBUILD_PYTHON_BINDINGS=ON
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_CLI_EXECUTABLES=ON
- -DTEST_VERBOSE=$(usex test)
- -DBUILD_TESTS=$(usex test)
- -DDEBUG=$(usex debug)
- -DPROFILE=$(usex profile)
- -DARMA_EXTRA_DEBUG=$(usex arma-debug)
- -DUSE_OPENMP=$(usex openmp)
- -DMATLAB_BINDINGS=$(usex matlab)
- -DBUILD_GO_SHLIB=$(usex go)
- -DBUILD_JULIA_BINDINGS=$(usex julia)
- -DBUILD_GO_BINDINGS=$(usex go)
- -DBUILD_R_BINDINGS=$(usex R)
- -DBUILD_MARKDOWN_BINDINGS=$(usex doc)
- -DMATHJAX=$(usex doc)
- ${EXTRA_ECONF[@]}
- )
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- python_optimize
-}
diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml
index 327dd23d3..30440d9a2 100644
--- a/sci-libs/nipy/metadata.xml
+++ b/sci-libs/nipy/metadata.xml
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">nipy</remote-id>
+ <remote-id type="github">nipy/nipy</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.5.0.ebuild
index 757ff5cdb..f2a0815dc 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.5.0.ebuild
@@ -52,7 +52,7 @@ PATCHES=(
src_prepare() {
# Remove etelemetry
- sed -i '/"etelemetry/d' nipype/info.py || die
+ sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
sed -i \
diff --git a/sci-libs/scikits_video/metadata.xml b/sci-libs/scikits_video/metadata.xml
index 186bb5c9c..bdfe14284 100644
--- a/sci-libs/scikits_video/metadata.xml
+++ b/sci-libs/scikits_video/metadata.xml
@@ -14,5 +14,6 @@
</longdescription>
<upstream>
<remote-id type="pypi">scikit-video</remote-id>
+ <remote-id type="github">scikit-video/scikit-video</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-libs/spyking-circus/metadata.xml b/sci-libs/spyking-circus/metadata.xml
index 844f386de..89a208f6f 100644
--- a/sci-libs/spyking-circus/metadata.xml
+++ b/sci-libs/spyking-circus/metadata.xml
@@ -16,4 +16,7 @@
on datasets coming from in vitro retina with 252 electrodes MEA, from in
vivo hippocampus with tetrodes, and in vivo and in vitro cortex data.
</longdescription>
+ <upstream>
+ <remote-id type="github">spyking-circus/spyking-circus</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml
index ad3ef354b..9c4ddaefd 100644
--- a/sci-libs/torchvision/metadata.xml
+++ b/sci-libs/torchvision/metadata.xml
@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>jpizarrocallejas@gmail.com</email>
- <name>Jorge Pizarro Callejas</name>
- </maintainer>
- <use>
- <flag name="cuda">Enable CUDA support if enabled in PyTorch</flag>
- </use>
+ <maintainer type="person">
+ <email>jpizarrocallejas@gmail.com</email>
+ <name>Jorge Pizarro Callejas</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">pytorch/vision</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/torchvision/torchvision-0.11.2.ebuild b/sci-libs/torchvision/torchvision-0.11.2.ebuild
index b17ac9007..765fd05b7 100644
--- a/sci-libs/torchvision/torchvision-0.11.2.ebuild
+++ b/sci-libs/torchvision/torchvision-0.11.2.ebuild
@@ -14,7 +14,6 @@ SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="cuda"
RDEPEND="
dev-python/av[${PYTHON_USEDEP}]
@@ -23,7 +22,7 @@ RDEPEND="
dev-python/six[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/pytorch[cuda(-)?,${PYTHON_USEDEP}]
+ sci-libs/pytorch[${PYTHON_USEDEP}]
media-video/ffmpeg
dev-qt/qtcore:5
"
@@ -38,10 +37,3 @@ BDEPEND="
S="${WORKDIR}/vision-${PV}"
distutils_enable_tests pytest
-
-pkg_setup() {
- if use cuda; then
- export FORCE_CUDA=1
- export TORCH_CUDA_ARCH_LIST="3.5;3.7;5.0;5.2;5.3;6.0;6.0+PTX;6.1;6.1+PTX;6.2;6.2+PTX;7.0;7.0+PTX;7.2;7.2+PTX;7.5;7.5+PTX"
- fi
-}
diff --git a/sci-libs/vxl/metadata.xml b/sci-libs/vxl/metadata.xml
index 22feba67c..f7d43af09 100644
--- a/sci-libs/vxl/metadata.xml
+++ b/sci-libs/vxl/metadata.xml
@@ -13,5 +13,6 @@ written in ANSI/ISO C++ and is designed to be portable over many platforms.
</longdescription>
<upstream>
<remote-id type="sourceforge">vxl</remote-id>
+ <remote-id type="github">vxl/vxl</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml
index a7ac8e977..273952673 100644
--- a/sci-libs/wannier90/metadata.xml
+++ b/sci-libs/wannier90/metadata.xml
@@ -18,5 +18,6 @@
<upstream>
<doc>http://www.wannier.org/</doc>
<remote-id type="launchpad">wannier90</remote-id>
+ <remote-id type="github">wannier-developers/wannier90</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest
index da96d35bc..cde77c554 100644
--- a/sci-mathematics/freefem++/Manifest
+++ b/sci-mathematics/freefem++/Manifest
@@ -1,2 +1 @@
DIST freefem++-4.10.tar.gz 12607380 BLAKE2B 2adcbcb48555c218bdec087b52b955fef7d2b8c0b17045be64d8acf9cde0910dd9c1a1856c046582e3d3e3024848db284cf8262f2e7c9a2e46024768f0dbad7a SHA512 768e8657884e92cd32f08ea82b3f384ed1522d1a693c6de95281fe1bf49e61d084d7d4d5c6c31f70a05ed95ba7cc0af75979242225466d06c2173176e862995e
-DIST freefem++-4.7.1.tar.gz 12522562 BLAKE2B a94cc91406486cf4acbd9d544ecdb3f9744d8e4172d84ee6c5bbad4aa8db04bd958e574f98537ec652deb2b1d74adb8d125138f6092030363cdf74c86c6f8a07 SHA512 e42b29f9aa4edf1e4a170425a304996d291b0c3127d75267d421d0f2ff757cdc64fb9b177e38f4e183edc6f256430c39880fea307698417721605b72f6d3c2d0
diff --git a/sci-mathematics/freefem++/freefem++-4.7.1.ebuild b/sci-mathematics/freefem++/freefem++-4.7.1.ebuild
deleted file mode 100644
index 6d55116fd..000000000
--- a/sci-mathematics/freefem++/freefem++-4.7.1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-MY_PV="$(ver_rs 2 -)"
-
-DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains"
-HOMEPAGE="https://freefem.org/"
-SRC_URI="https://github.com/FreeFem/FreeFem-sources/archive/v4.7-1.tar.gz -> ${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples mpi opengl X"
-
-RDEPEND="
- sci-libs/fftw:3.0
- virtual/cblas
- virtual/lapack
- sci-libs/umfpack
- sci-libs/arpack
- sci-libs/hdf5[cxx]
- mpi? ( virtual/mpi )
- opengl? (
- media-libs/freeglut
- virtual/opengl
- )
- X? (
- media-fonts/font-misc-misc
- x11-libs/libX11
- x11-libs/libXext
- x11-libs/libXpm
- x11-libs/libXxf86vm
- )"
-
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-S="${WORKDIR}/FreeFem-sources-${MY_PV}"
-
-src_prepare() {
- default
-
- eautoreconf
-}
-
-src_configure() {
- local myconf
-
- if use mpi; then
- myconf="${myconf} --with-mpi=/usr/bin/mpi"
- else
- myconf="--without-mpi"
- fi
-
- econf \
- --disable-download \
- --disable-optim \
- --enable-generic \
- --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
- --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \
- $(use_enable opengl) \
- ${myconf}
-}
-
-src_test() {
- if use mpi; then
- # This may depend on the used MPI implementation. It is needed
- # with mpich2, but should not be needed with lam-mpi or mpich
- # (if the system is configured correctly).
- ewarn "Please check that your MPI root ring is on before running"
- ewarn "the test phase. Failing to start it before that phase may"
- ewarn "result in a failing emerge."
- epause
- fi
- emake -j1 check
-}
-
-src_install() {
- default
-
- if use examples; then
- einfo "Installing examples..."
-
- # Remove compiled examples:
- emake clean
-
- einfo "Some of the installed examples assumes that the user has write"
- einfo "permissions in the working directory and other will look for"
- einfo "data files in the working directory. For this reason in order to"
- einfo "run the examples it's better to temporary copy them somewhere"
- einfo "in the user folder. For example to run the tutorial examples"
- einfo "it's better to copy the entire examples++-tutorial folder into"
- einfo "the user directory."
-
- rm -f examples*/Makefile* || die
- doins -r examples*
- fi
-}
diff --git a/sci-mathematics/freefem++/metadata.xml b/sci-mathematics/freefem++/metadata.xml
index a605d78d7..5cee338ce 100644
--- a/sci-mathematics/freefem++/metadata.xml
+++ b/sci-mathematics/freefem++/metadata.xml
@@ -10,4 +10,7 @@ FreeFem++ is an implementation of a language dedicated to the finite
element method. It enables you to solve Partial Differential Equations
(PDE) easily.
</longdescription>
+ <upstream>
+ <remote-id type="github">FreeFem/FreeFem-sources</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml
index ce584d233..c86c3b501 100644
--- a/sci-mathematics/pulp/metadata.xml
+++ b/sci-mathematics/pulp/metadata.xml
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">PuLP</remote-id>
+ <remote-id type="github">coin-or/pulp</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-mathematics/ripser/metadata.xml b/sci-mathematics/ripser/metadata.xml
index fbef5ab11..05f38b851 100644
--- a/sci-mathematics/ripser/metadata.xml
+++ b/sci-mathematics/ripser/metadata.xml
@@ -1,16 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <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>
- <use>
- <flag name="progress">print progress of calculations in console</flag>
- <flag name="sparsehash">use google sparsehash for storage</flag>
- </use>
+ <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>
+ <use>
+ <flag name="progress">print progress of calculations in console</flag>
+ <flag name="sparsehash">use google sparsehash for storage</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">Ripser/ripser</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
index 6d810ed14..82e1c796f 100644
--- a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild
+++ b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
@@ -40,6 +40,8 @@ DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}/${PN}-DCRComplexSolve-compile-error.patch"
"${FILESDIR}/${PN}-ElmerIce-compile.patch"
+ "${FILESDIR}/${PN}-rpath.patch"
+ "${FILESDIR}/${P}-qwt-6.2.patch"
)
S="${WORKDIR}/elmerfem-release-${PV}"
diff --git a/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
new file mode 100644
index 000000000..13eaf1c5f
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
@@ -0,0 +1,35 @@
+From 48e9430ccb858ca5bda28b967a0c84b51e2404b2 Mon Sep 17 00:00:00 2001
+From: "E. Albiter" <ealbiter@gmail.com>
+Date: Fri, 15 Oct 2021 13:12:48 -0500
+Subject: [PATCH] Compatibility with Qwt 6.2. Fix for #293
+
+---
+ ElmerGUI/Application/src/convergenceview.h | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/ElmerGUI/Application/src/convergenceview.h b/ElmerGUI/Application/src/convergenceview.h
+index 377b644b99..4259eb730e 100755
+--- a/ElmerGUI/Application/src/convergenceview.h
++++ b/ElmerGUI/Application/src/convergenceview.h
+@@ -51,8 +51,8 @@
+ #include <qwt_plot_curve.h>
+ #include <qwt_plot_grid.h>
+ #include <qwt_legend.h>
+-/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead*/
+-#include <qwt_compat.h>
++/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead
++#include <qwt_compat.h> <-- Removed in Qwt 6.2 */
+ #include <qwt_text.h>
+ #include <qwt_scale_engine.h>
+
+@@ -76,8 +76,8 @@ class CurveData
+
+ private:
+ int d_count;
+- QwtArray<double> d_x;
+- QwtArray<double> d_y;
++ QVector<double> d_x;
++ QVector<double> d_y;
+ };
+
+ class Curve
diff --git a/sci-misc/elmer-fem/files/elmer-fem-rpath.patch b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
new file mode 100644
index 000000000..27249fef9
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt.orig 2022-08-24 21:50:59.940905698 -0500
++++ b/CMakeLists.txt 2022-08-24 21:51:08.610804464 -0500
+@@ -479,7 +479,7 @@
+
+ # Set up rpaths to point ELMER_INSTALL_LIB_DIR
+ IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+- SET(ELMERSOLVER_RPATH_STRING "\$ORIGIN/../${ELMER_INSTALL_LIB_DIR}")
++ SET(ELMERSOLVER_RPATH_STRING "${ELMER_INSTALL_LIB_DIR}")
+ SET(ELMERLIB_RPATH_STRING "\$ORIGIN/")
+ ELSEIF(APPLE)
+ SET(ELMERSOLVER_RPATH_STRING "@loader_path/../${ELMER_INSTALL_LIB_DIR}")
diff --git a/sci-misc/elmer-fem/metadata.xml b/sci-misc/elmer-fem/metadata.xml
index feab34b47..37464c70a 100644
--- a/sci-misc/elmer-fem/metadata.xml
+++ b/sci-misc/elmer-fem/metadata.xml
@@ -7,6 +7,7 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">svn</remote-id>
+ <remote-id type="github">ElmerCSC/elmerfem</remote-id>
</upstream>
<use>
<flag name="gui">Build the ElmerGUI</flag>
diff --git a/sci-physics/feyncalc/metadata.xml b/sci-physics/feyncalc/metadata.xml
index 9e87f772e..826061ef4 100644
--- a/sci-physics/feyncalc/metadata.xml
+++ b/sci-physics/feyncalc/metadata.xml
@@ -19,4 +19,7 @@
<use>
<flag name="FCtraditionalFormOutput">Use TraditionalForm typesetting.</flag>
</use>
+ <upstream>
+ <remote-id type="github">FeynCalc/feyncalc</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-physics/formcalc/Manifest b/sci-physics/formcalc/Manifest
index de9e1e708..6ac4c74b1 100644
--- a/sci-physics/formcalc/Manifest
+++ b/sci-physics/formcalc/Manifest
@@ -1,2 +1,2 @@
-DIST FormCalc-9.10.tar.gz 32069351 BLAKE2B e46b9cbce5c797b8d4f09d03f617668df799edcdfec8f55631e6a626c4f06bf317f5d3b546b7e335babf734e5919d7c5900e1959a6f46f1343e758b7bdec045b SHA512 4a8c620fecbe07ce0fbdef459645a44b4f2abfe2d92085d7891e980ee162bf559556ba8dfea68cdc9bf71e36223f88683fb7f76bbf1f1969fdbc761e68ba2c42
+DIST FormCalc-9.10.tar.gz 32070519 BLAKE2B e789d7eea0cc92f27033373fd6516e94ec66d1780ae7bb1254537fa508640436a4595dbf09594a2cad8b4178d1e950806089ae4584bff0f2848674325a734212 SHA512 30519fcd6a9e616f6bfa23825056afdc27111605ca66e35f6baebac5bcb7ff43e07c7d40ed90157c584be82392fc85a32b769e637a793817377a8ffc5601af6d
DIST FormCalc-9.9.tar.gz 32059045 BLAKE2B 69e3d063bf746d86d02f63d3a1fdce314582b190bafc66d063a6f25575476fcb6b60121b9133f850ffd5d173e437b160a2661072051083b3f4affc48fcb4bda7 SHA512 9661a07fac13348de13ec09dc8f043df02ef9a5391be64217d432e04d4d82ad3dea94f43951f839fbe8947338bc0ab721a9a9ebdc0900979e16ea89d857c87c7
diff --git a/sci-physics/formcalc/formcalc-9.10.ebuild b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
index 81f69f294..9a3734d2a 100644
--- a/sci-physics/formcalc/formcalc-9.10.ebuild
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
RDEPEND="
sci-mathematics/mathematica
- sci-mathematics/form
+ sci-mathematics/form[threads]
"
DEPEND="${RDEPEND}"
BDEPEND="
@@ -46,7 +46,7 @@ src_install() {
done
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
- dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+ dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
dodoc manual/*.pdf
}
diff --git a/sci-physics/formcalc/formcalc-9.9.ebuild b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
index 6e031ef5c..c73a3e804 100644
--- a/sci-physics/formcalc/formcalc-9.9.ebuild
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64"
RDEPEND="
sci-mathematics/mathematica
- sci-mathematics/form
+ sci-mathematics/form[threads]
"
DEPEND="${RDEPEND}"
BDEPEND="
@@ -48,7 +48,7 @@ src_install() {
done
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
- dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+ dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
dodoc manual/*.pdf
}
diff --git a/sci-physics/mcfm/Manifest b/sci-physics/mcfm/Manifest
new file mode 100644
index 000000000..9163b57a5
--- /dev/null
+++ b/sci-physics/mcfm/Manifest
@@ -0,0 +1 @@
+DIST MCFM-10.2.1.tar.gz 39365160 BLAKE2B 59b6fc55e4a21d4dea979d973cac0378763585088b7b5f032d671a30358e6bd8b6332fd3fa0eeca573177e46f642b3ba8b0c78c503bf37ac4ee0d6c0b962e4df SHA512 994f243b5460784eb5d62f81adf6c08d7ffd03df0d2fa8ac8e4522ab5127f54c3218cd4fe9984adff505c02804613c570d228f88c9343804e20d08f7187575c1
diff --git a/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch
new file mode 100644
index 000000000..f43a1cb48
--- /dev/null
+++ b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch
@@ -0,0 +1,251 @@
+--- a/CMakeLists.txt 2022-09-19 02:30:49.215050000 +0200
++++ b/CMakeLists.txt 2022-09-19 21:03:05.409746266 +0200
+@@ -41,48 +41,48 @@
+
+ include(ExternalProject)
+
+-ExternalProject_Add(qd
+- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/
+- PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
+- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
+- BUILD_IN_SOURCE ON
+- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib
+- BUILD_COMMAND ${MAKE}
+- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
+-
+-ExternalProject_Add(qcdloop
+- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib
+- PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
+- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
+- BUILD_IN_SOURCE ON
+- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+- CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib
+- BUILD_COMMAND ${MAKE}
+- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
+-
+-ExternalProject_Add(liboneloop
+- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/
+- PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop
+- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop
+- BUILD_IN_SOURCE ON
+- CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
+- BUILD_COMMAND ${MAKE}
+- INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include
+-)
+-
+-ExternalProject_Add(handyg
+- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/
+- PREFIX ${CMAKE_BINARY_DIR}/lib/handyG
+- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG
+- BUILD_IN_SOURCE ON
+- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include
+- BUILD_COMMAND ${MAKE}
+- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
++#ExternalProject_Add(qd
++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/
++# PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
++# BUILD_IN_SOURCE ON
++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++# CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib
++# BUILD_COMMAND ${MAKE}
++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
++#
++#ExternalProject_Add(qcdloop
++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib
++# PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
++# BUILD_IN_SOURCE ON
++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++# CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib
++# BUILD_COMMAND ${MAKE}
++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
++#
++#ExternalProject_Add(liboneloop
++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/
++# PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop
++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop
++# BUILD_IN_SOURCE ON
++# CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
++# BUILD_COMMAND ${MAKE}
++# INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include
++#)
++#
++#ExternalProject_Add(handyg
++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/
++# PREFIX ${CMAKE_BINARY_DIR}/lib/handyG
++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG
++# BUILD_IN_SOURCE ON
++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++# CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include
++# BUILD_COMMAND ${MAKE}
++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
+
+ ## Configuration options
+
+@@ -169,7 +169,7 @@
+ add_subdirectory(lib/SpecialFunctions)
+ add_subdirectory(lib/AMOS)
+
+-add_dependencies(objlib qd qcdloop liboneloop handyg)
++#add_dependencies(objlib qd qcdloop liboneloop handyg)
+
+ if(${with_vvamp})
+ add_compile_definitions(WITH_VVAMP=1)
+@@ -182,7 +182,7 @@
+ PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+ CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
+ BUILD_COMMAND ${MAKE}
+- INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include
++ INSTALL_COMMAND mv ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include
+ )
+ add_library(vvamp STATIC IMPORTED)
+ set_property(TARGET vvamp PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/VVamp/libvvamp.a")
+@@ -192,7 +192,6 @@
+ else()
+ set(linkvvamp "")
+ endif()
+-
+ set_target_properties(objlib PROPERTIES
+ CXX_STANDARD 11
+ Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/include"
+@@ -222,48 +221,51 @@
+ target_link_libraries(mcfm ${OpenMP_Fortran_LIBRARIES})
+ endif()
+
+-add_library(oneloop STATIC IMPORTED)
+-set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a")
++find_library(qcdloop qcdloop)
+
+-add_library(qcdloop_lib_static STATIC IMPORTED)
+-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a")
+-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qcdloop_lib_static qcdloop)
+-
+-add_library(qcdloop_lib_shared SHARED IMPORTED)
+-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qcdloop_lib_shared qcdloop)
+-
+-add_library(qd_lib_static STATIC IMPORTED)
+-set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a")
+-set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qd_lib_static qd)
+-
+-add_library(qd_lib_shared SHARED IMPORTED)
+-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qd_lib_shared qd)
+-
+-add_library(qdmod_lib_static STATIC IMPORTED)
+-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a")
+-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qdmod_lib_static qd)
+-
+-add_library(qdmod_lib_shared SHARED IMPORTED)
+-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qdmod_lib_shared qd)
+-
+-add_library(handyg_lib_static STATIC IMPORTED)
+-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a")
+-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(handyg_lib_static handyg)
+-
+-add_dependencies(objlib qdmod_lib_static)
+-add_dependencies(objlib qd_lib_static)
+-add_dependencies(objlib qcdloop_lib_static)
+-add_dependencies(objlib handyg_lib_static)
++#add_library(oneloop STATIC IMPORTED)
++#set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a")
++#
++#add_library(qcdloop_lib_static STATIC IMPORTED)
++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a")
++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qcdloop_lib_static qcdloop)
++
++#add_library(qcdloop_lib_shared SHARED IMPORTED)
++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qcdloop_lib_shared qcdloop)
++#
++#add_library(qd_lib_static STATIC IMPORTED)
++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a")
++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qd_lib_static qd)
++#
++#add_library(qd_lib_shared SHARED IMPORTED)
++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qd_lib_shared qd)
++#
++#add_library(qdmod_lib_static STATIC IMPORTED)
++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a")
++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qdmod_lib_static qd)
++#
++#add_library(qdmod_lib_shared SHARED IMPORTED)
++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qdmod_lib_shared qd)
++#
++#add_library(handyg_lib_static STATIC IMPORTED)
++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a")
++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(handyg_lib_static handyg)
++
++#add_dependencies(objlib qdmod_lib_static)
++#add_dependencies(objlib qd_lib_static)
++#add_dependencies(objlib qcdloop_lib_static)
++#add_dependencies(objlib handyg_lib_static)
++target_link_libraries(objlib qdmod qd qcdloop handyg)
+
+ if(use_internal_lhapdf)
+ ExternalProject_Add(lhapdf
+@@ -285,13 +287,15 @@
+
+ add_dependencies(lhapdf_lib_static lhapdf)
+ target_link_libraries(mcfm lhapdf_lib_static)
+- target_include_directories(objlib PRIVATE "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd")
++ target_include_directories(objlib PRIVATE
++ "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd")
+ add_dependencies(objlib lhapdf)
+ elseif(use_external_lhapdf)
+ find_library(lhapdf_lib NAMES LHAPDF REQUIRED)
+ target_link_libraries(mcfm ${lhapdf_lib})
+ if (${lhapdf_include_path})
+- target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}" "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd")
++ target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}"
++ "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd")
+ endif()
+ endif()
+
+@@ -299,9 +303,9 @@
+
+ if(${with_library})
+ if(use_internal_lhapdf)
+- target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ lhapdf_lib_static)
++ target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ lhapdf_lib_static)
+ else()
+- target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ ${lhapdf_lib})
++ target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ ${lhapdf_lib})
+ endif()
+ if (DEFINED OLDIR)
+ target_link_libraries(oltest libmcfm ${openloops_lib})
+@@ -320,7 +324,7 @@
+ endif()
+ endif()
+
+-target_link_libraries(mcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++)
++target_link_libraries(mcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++)
+
+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+ set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/local/lib")
diff --git a/sci-physics/mcfm/mcfm-10.2.1.ebuild b/sci-physics/mcfm/mcfm-10.2.1.ebuild
new file mode 100644
index 000000000..9a928e4c9
--- /dev/null
+++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake
+
+MY_PN=MCFM
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="Monte Carlo for FeMtobarn processes"
+HOMEPAGE="https://mcfm.fnal.gov"
+SRC_URI="https://mcfm.fnal.gov/downloads/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# Manual states multithreading bug in lhapdf-6.3.0 ?!
+# MCFM has been tested against lhapdf-6.2.0 which ::gentoo already dropped
+DEPEND="
+ sci-physics/lhapdf
+ >=sci-libs/qd-2.3.22
+ >=sci-physics/qcdloop-2.0.5
+ >=sci-physics/oneloop-2020.07.31
+ >=sci-libs/handyg-0.1.5
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ virtual/fortran
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-rest.patch
+)
+src_prepare() {
+ sed -i -e 's/\(name=".*\)"/\1_"/g' src/Mods/mod_qcdloop_c.f || die
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -Duse_external_lhapdf=ON
+ -Duse_internal_lhapdf=OFF
+ -Dlhapdf_include_path=ON
+ -Dwith_library=ON
+ -Dwith_vvamp=OFF
+ )
+ cmake_src_configure
+ # Fix relative path in working dir to something absolute
+ sed -i "s/process\.DAT/${EPREFIX}\/usr\/share\/${MY_PN}\/process\.DAT/g" src/Procdep/chooser.f || die
+}
+
+src_compile() {
+ # Single thread force needed since fortan mods depend on each other
+ # This problem only happend very rarely
+ export MAKEOPTS=-j1
+ cmake_src_compile
+}
+
+src_install() {
+ # this did not work
+ #cmake_src_install
+ dobin "${BUILD_DIR}"/mcfm
+ dolib.so "${BUILD_DIR}"/libmcfm.so
+ insinto "/usr/share/${MY_PN}/"
+ doins "Bin/process.DAT"
+}
diff --git a/sci-physics/mcfm/metadata.xml b/sci-physics/mcfm/metadata.xml
new file mode 100644
index 000000000..a8720d7dd
--- /dev/null
+++ b/sci-physics/mcfm/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>APN-Pucky@users.noreply.github.com</email>
+ <name>APN-Pucky</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The program calculates cross-sections for various femtobarn-level processes at hadron-hadron colliders. A number of processes can be calculated at NLO order in QCD, while most other processes are included at NNLO order in QCD. The calculation of some processes can also account for next-to-leading order weak effects.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/oneloop/Manifest b/sci-physics/oneloop/Manifest
new file mode 100644
index 000000000..f698d0a23
--- /dev/null
+++ b/sci-physics/oneloop/Manifest
@@ -0,0 +1 @@
+DIST oneloop-2020.07.31.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220
diff --git a/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch
new file mode 100644
index 000000000..4af47e066
--- /dev/null
+++ b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch
@@ -0,0 +1,11 @@
+--- a/Config 2022-05-19 17:34:51.000000000 +0200
++++ b/Config 2022-05-19 17:34:51.000000000 +0200
+@@ -3,7 +3,7 @@
+ #FFLAGS = -Wall
+
+ DPKIND = kind(1d0)
+-QPKIND = kind(1q0)
++#QPKIND = kind(1q0)
+ #DPKIND = selected_real_kind(15)
+ #QPKIND = 16
+ #DDTYPE = ddfun90
diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-physics/oneloop/metadata.xml
index 138cb7705..bdee6992b 100644
--- a/sci-biology/mRNAmarkup/metadata.xml
+++ b/sci-physics/oneloop/metadata.xml
@@ -2,11 +2,11 @@
<!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>
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
</maintainer>
<maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
</maintainer>
</pkgmetadata>
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
new file mode 100644
index 000000000..49b30f07e
--- /dev/null
+++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
@@ -0,0 +1,49 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# python only needed for create.py to get binaries
+PYTHON_COMPAT=( python3_{8..11} )
+inherit toolchain-funcs python-any-r1
+
+DESCRIPTION="Library of one-loop scalar functions"
+HOMEPAGE="https://bitbucket.org/hameren/oneloop"
+SRC_URI="https://bitbucket.org/hameren/oneloop/get/3762b8bad6ad.zip -> ${P}.zip"
+S="${WORKDIR}/hameren-oneloop-3762b8bad6ad"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND="
+ ${PYTHON_DEPS}
+ app-arch/unzip
+ virtual/fortran
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-config.patch
+)
+
+src_configure() {
+ tc-export FC
+ sed -i "/FC = /s/gfortran/${FC}/g" Config || die
+ sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die
+}
+
+src_compile() {
+ tc-export FC
+ emake -f make_cuttools
+ ${EPYTHON} ./create.py || die "Failed to compile"
+ #./create.py dynamic || die
+ ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so avh_olo.o || die "Failed to link"
+}
+
+src_install() {
+ dolib.a libavh_olo.a
+ dolib.so libavh_olo.so
+ doheader avh_olo.mod
+}
diff --git a/sci-physics/qcdloop/Manifest b/sci-physics/qcdloop/Manifest
new file mode 100644
index 000000000..84ca31226
--- /dev/null
+++ b/sci-physics/qcdloop/Manifest
@@ -0,0 +1,2 @@
+DIST qcdloop-2.0.5.tar.gz 199141 BLAKE2B b16c193bd267b838535a572dd3b1cf50ac9af03b65347877b550bcbdcc9cfdd42f08e198732c513cff8298632ea65be82f2986701de75cee80cec2f9c30e3368 SHA512 9bfa3bad7a8c808b2db5eda32a755da4dadf67eba10845eb798d447fd47062bd40aa877929b60d95ec6b4e3b4a2cbba6384a3d1b13f92cfdec06e76177532c0f
+DIST qcdloop-2.0.9.tar.gz 214697 BLAKE2B 19d426cc61b8a8f08fc56522b5a2d48c7fea7027225e1317c2e2908b8a87367ff69077bfe5508ee50ee585d8d0f68ae4c1fdad312b4cbc73ca4f3fd735fa94c9 SHA512 c8031dbee1c83d2bd0fcca0b1d94f18e7d07b77c247ca7a15cfec9bc402391e89036a64507c48e743eeecb3a19fe25d4e766ff13ede9f042d4d723adc8adb238
diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch
new file mode 100644
index 000000000..56a665de2
--- /dev/null
+++ b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt 2022-09-19 11:13:08.777453946 +0200
++++ b/CMakeLists.txt 2022-09-19 11:13:27.315507011 +0200
+@@ -20,7 +20,7 @@
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ set(CMAKE_CXX_EXTENSIONS OFF)
+ set(VERSION "\"2.0.5\"")
+-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE)
+ set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE)
+ set(prefix ${CMAKE_INSTALL_PREFIX})
diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch
new file mode 100644
index 000000000..b3babf764
--- /dev/null
+++ b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt 2022-09-19 11:13:08.777453946 +0200
++++ b/CMakeLists.txt 2022-09-19 11:13:27.315507011 +0200
+@@ -20,7 +20,7 @@
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ set(CMAKE_CXX_EXTENSIONS OFF)
+ set(VERSION "\"2.0.9\"")
+-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE)
+ set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE)
+ set(prefix ${CMAKE_INSTALL_PREFIX})
diff --git a/sci-physics/qcdloop/metadata.xml b/sci-physics/qcdloop/metadata.xml
new file mode 100644
index 000000000..84c79dc3b
--- /dev/null
+++ b/sci-physics/qcdloop/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ QCDLoop is a library of one-loop scalar Feynman integrals, evaluated close to four dimensions. First documented in arXiv:0712.1851 and recently in arXiv:1605.03181.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">scarrazza/qcdloop</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
new file mode 100644
index 000000000..19a247ba2
--- /dev/null
+++ b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
@@ -0,0 +1,33 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake
+
+DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
+HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
+SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND="
+ virtual/fortran
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-cxx.patch
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_PREFIX="${ESYSROOT}/usr/$(get_libdir)"
+ )
+ cmake_src_configure
+}
diff --git a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
new file mode 100644
index 000000000..ccea20aa5
--- /dev/null
+++ b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
@@ -0,0 +1,50 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake
+
+DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
+HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
+SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND="
+ virtual/fortran
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-cxx.patch
+)
+
+src_prepare() {
+ cmake_src_prepare
+
+ # gentoo libdir love
+ sed -i \
+ -e '/DESTINATION/s/lib/lib${LIB_SUFFIX}/g' \
+ CMakeLists.txt || die
+ sed -i \
+ -e '/libdir.*/s/lib/lib${LIB_SUFFIX}/g' \
+ CMakeLists.txt || die
+
+ #sed -i \
+ # -e '/qcdloop/s/SHARED/STATIC/g' \
+ # CMakeLists.txt || die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_PREFIX="${ESYSROOT}"/usr
+ -DENABLE_FORTRAN_WRAPPER=ON
+ )
+ cmake_src_configure
+}
diff --git a/sci-physics/rivet/Manifest b/sci-physics/rivet/Manifest
new file mode 100644
index 000000000..5950a9997
--- /dev/null
+++ b/sci-physics/rivet/Manifest
@@ -0,0 +1,2 @@
+DIST Rivet-3.1.5.tar.gz 30576082 BLAKE2B 2fcf0f03219832d48546235f25d844837c37aa20e3972c35184741d1e14d70224bd7db597cd01e946dde4768b941ce9cf1dee3b3c385cb8a81e7b291c7edb1d3 SHA512 8dea32ef1ec7596904f1209a89343ed767e57b67e5fb85a230fd52a05231c901ea9f4663e6cea145e72d5d1beaf94dd642afaa1d5814843672b33073bb359c3f
+DIST Rivet-3.1.6.tar.gz 28804847 BLAKE2B b4e5a35285a4abdedaefbeaa06e5a703e5bf3b1ef4721db3d664dac5197b63845d228ab0dc0370b7b5095dccc3c9b5f3456ef59aabdcfb6c2f65cfbccd322635 SHA512 dd57d40db15fd55bae06a0faffbea80a15558763caf1f6f1defdde69d3abda709bdf806a1d9703f5e5796743af0482643c577332f69892de858aa5802e26279e
diff --git a/sci-physics/rivet/files/rivet-3.1.5-doc.patch b/sci-physics/rivet/files/rivet-3.1.5-doc.patch
new file mode 100644
index 000000000..ae01b1812
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.5-doc.patch
@@ -0,0 +1,38 @@
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -11,7 +11,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-html || true
+
+@@ -21,7 +21,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-json || true
+
+@@ -31,7 +31,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-txt || true
+
+@@ -46,7 +46,7 @@
+ $(mkdir_p) coverage && cd coverage && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(LD_LIBRARY_PATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(DYLD_LIBRARY_PATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(abs_srcdir)/coverage/mk-coverage-htmls || true
+
diff --git a/sci-physics/rivet/files/rivet-3.1.5-test.patch b/sci-physics/rivet/files/rivet-3.1.5-test.patch
new file mode 100644
index 000000000..915473eb1
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.5-test.patch
@@ -0,0 +1,11 @@
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -26,7 +26,7 @@
+ LIBLOCATION=$(top_builddir)/src/.libs \
+ LD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \
+ DYLD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \
+- PYTHONPATH=$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(top_builddir)/pyext/build/lib*):$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \
+ PATH=$(top_builddir)/bin:$(top_srcdir)/bin:$(PATH) \
+ PYTHON=$(PYTHON) \
+ RIVET_TESTS_SRC=$(srcdir)
diff --git a/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch b/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
new file mode 100644
index 000000000..68fd4436c
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
@@ -0,0 +1,12 @@
+diff -Naru Rivet-3.1.6.orig/src/Tools/binreloc.c Rivet-3.1.6/src/Tools/binreloc.c
+--- Rivet-3.1.6.orig/src/Tools/binreloc.c 2022-06-26 23:23:44.359890803 +0200
++++ Rivet-3.1.6/src/Tools/binreloc.c 2022-06-26 23:24:36.962045655 +0200
+@@ -215,7 +215,7 @@
+ break;
+
+ /* Sanity check. */
+- if (strchr (line, '/') == NULL)
++ if (strstr (line, " r-xp ") == NULL || strchr (line, '/') == NULL)
+ /* With binutils > 2.30 (const void *) "" is placed in "r--p" area of memory
+ In general, for the mechanism of detection it doesn't really matter where your symbol is,
+ therefore, check for strstr (line, " r-xp ") == NULL is removed */
diff --git a/sci-physics/rivet/metadata.xml b/sci-physics/rivet/metadata.xml
new file mode 100644
index 000000000..7f9434874
--- /dev/null
+++ b/sci-physics/rivet/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>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Rivet is a system for preservation of particle-collider analysis logic, analysis reinterpretation via MC simulations, and the validation and improvement of Monte Carlo event generator codes.
+ It covers all aspects of collider physics, from unfolded precision measurements to reconstruction-level searches, and physics from the Standard Model to BSM theories, and from perturbative jet, boson and top-quarks to hadron decays, inclusive QCD, and Heavy Ion physics.
+ </longdescription>
+ <use>
+ <flag name="hepmc3">Build with HepMC3</flag>
+ <flag name="hepmc2">Build with HepMC2</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/rivet/rivet-3.1.5.ebuild b/sci-physics/rivet/rivet-3.1.5.ebuild
new file mode 100644
index 000000000..4cc7c6018
--- /dev/null
+++ b/sci-physics/rivet/rivet-3.1.5.ebuild
@@ -0,0 +1,75 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 flag-o-matic autotools
+
+MY_PN="Rivet"
+MY_PF=${MY_PN}-${PV}
+
+DESCRIPTION="Rivet toolkit (Robust Independent Validation of Experiment and Theory)"
+HOMEPAGE="https://gitlab.com/hepcedar/rivet"
+SRC_URI="https://www.hepforge.org/archive/rivet/${MY_PF}.tar.gz"
+S=${WORKDIR}/${MY_PF}
+
+LICENSE="GPL-3+"
+SLOT="3"
+KEYWORDS="~amd64"
+IUSE="+hepmc3 hepmc2"
+REQUIRED_USE="
+ ^^ ( hepmc3 hepmc2 )
+ ${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+ >=sci-physics/yoda-1.9.4[python(-),${PYTHON_SINGLE_USEDEP}]
+ >=sci-physics/fastjet-3.4.0[plugins]
+ >=sci-physics/fastjet-contrib-1.046
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+
+ sci-libs/gsl
+
+ virtual/latex-base
+ media-gfx/imagemagick
+ app-text/ghostscript-gpl
+
+ ${PYTHON_DEPS}
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/fortran
+ >=dev-python/cython-0.29.24
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-doc.patch
+ "${FILESDIR}"/${P}-test.patch
+)
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ # Eigen complains about alignment (see https://gitlab.com/libeigen/eigen/-/issues/2523).
+ # does this affect more cpus?
+ replace-cpu-flags znver1 x86-64
+ PREFIX_YODA=$(yoda-config --prefix) || die
+ PREFIX_FJ=$(fastjet-config --prefix) || die
+ econf \
+ $(usex hepmc2 "--with-hepmc=${ESYSROOT}/usr" "") \
+ $(usex hepmc3 "--with-hepmc3=${ESYSROOT}/usr" "") \
+ --with-yoda=${PREFIX_YODA} \
+ --with-fastjet=${PREFIX_FJ}
+}
+
+src_install() {
+ default
+ python_optimize
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/rivet/rivet-3.1.6.ebuild b/sci-physics/rivet/rivet-3.1.6.ebuild
new file mode 100644
index 000000000..3a83f7136
--- /dev/null
+++ b/sci-physics/rivet/rivet-3.1.6.ebuild
@@ -0,0 +1,75 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 flag-o-matic autotools
+
+MY_PN="Rivet"
+MY_PF=${MY_PN}-${PV}
+
+DESCRIPTION="Rivet toolkit (Robust Independent Validation of Experiment and Theory)"
+HOMEPAGE="https://gitlab.com/hepcedar/rivet"
+SRC_URI="https://www.hepforge.org/archive/rivet/${MY_PF}.tar.gz"
+S=${WORKDIR}/${MY_PF}
+
+LICENSE="GPL-3+"
+SLOT="3"
+KEYWORDS="~amd64"
+IUSE="+hepmc3 hepmc2"
+REQUIRED_USE="
+ ^^ ( hepmc3 hepmc2 )
+ ${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+ >=sci-physics/yoda-1.9.5[python(-),${PYTHON_SINGLE_USEDEP}]
+ >=sci-physics/fastjet-3.4.0[plugins]
+ >=sci-physics/fastjet-contrib-1.048
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+
+ sci-libs/gsl
+
+ virtual/latex-base
+ media-gfx/imagemagick
+ app-text/ghostscript-gpl
+
+ ${PYTHON_DEPS}
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/fortran
+ >=dev-python/cython-0.29.24
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-binreloc.patch
+ "${FILESDIR}"/${PN}-3.1.5-test.patch
+)
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ # Eigen complains about alignment (see https://gitlab.com/libeigen/eigen/-/issues/2523).
+ # does this affect more cpus?
+ replace-cpu-flags znver1 x86-64
+ PREFIX_YODA=$(yoda-config --prefix) || die
+ PREFIX_FJ=$(fastjet-config --prefix) || die
+ econf \
+ $(usex hepmc2 "--with-hepmc=${ESYSROOT}/usr" "") \
+ $(usex hepmc3 "--with-hepmc3=${ESYSROOT}/usr" "") \
+ --with-yoda=${PREFIX_YODA} \
+ --with-fastjet=${PREFIX_FJ}
+}
+
+src_install() {
+ default
+ python_optimize
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-visualization/clip/metadata.xml b/sci-visualization/clip/metadata.xml
index e97c4322a..8f000a818 100644
--- a/sci-visualization/clip/metadata.xml
+++ b/sci-visualization/clip/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">asmuth/clip</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-visualization/fsleyes-props/Manifest b/sci-visualization/fsleyes-props/Manifest
index 51fcf1b3c..6cafd64da 100644
--- a/sci-visualization/fsleyes-props/Manifest
+++ b/sci-visualization/fsleyes-props/Manifest
@@ -1 +1 @@
-DIST props-1.7.3.tar.gz 122655 BLAKE2B 158d1fe055ed977455888af6daa2f07d12cc98156ada67e3ffb78336423b18ecb321c8be0b3265e98a3352fd9f2dd6b1520b5bf6c3cae7ed9ca84053e4ad4f22 SHA512 9ae299ad67e9a0da8c09235e911679254df1331deb6f1ef1c3eff42a67877eff7766d91917c2c72103e2e0c247912b6e7f11c2f3abe5d91ccd0507854adda9a7
+DIST props-1.8.2.tar.gz 124579 BLAKE2B 5a4a399c18b3a8299fa62d378713988c42f25fba7baa90f52b81aad6786dafeda1dc3fb273f159e88d17b5319977ca007854253eba781b579fd771a84d812bba SHA512 66c6e6d47ecd17e7bde245a6b8c94b3710dbec01e16d1829a257c3315d2f013dcce878f972eb65d0642a0231445f1cc1b0b16987676f5c2ea19e62fe19a9432f
diff --git a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild
index 3fd2a3e01..eff42e1bb 100644
--- a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild
+++ b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx
MY_PN="props"
diff --git a/sci-visualization/fsleyes-widgets/Manifest b/sci-visualization/fsleyes-widgets/Manifest
index f81be256c..b88ec6d0e 100644
--- a/sci-visualization/fsleyes-widgets/Manifest
+++ b/sci-visualization/fsleyes-widgets/Manifest
@@ -1 +1 @@
-DIST fsleyes-widgets-0.12.2.tar.gz 1068565 BLAKE2B db322e7cadfef8d7ba5a63ed089a6979337837418afeb8e0cd10418a119f7e359a360b16dc2dc3756d1f353033d60b4387bff69b9dc864b515fab16daa939e6f SHA512 6c6da4bb2d61a1fe4cff8a7db887595de2df9b3e76984a0ab7492f859f8a47d14b4999e2a3e31c6f6e13f31b7557e55e6b04378dd970d227aa02920c250de088
+DIST fsleyes-widgets-0.12.3.tar.gz 1138692 BLAKE2B beb4125760b4aff463bc3f9ccb03ae3aa0c88a35af4d992a1f2cb728cb607e846e616a0c91bc3c725db613ef82d3d5acefd47195342aa7bfce2d9bfbcb90428c SHA512 93ebf267eee345ce57bc0096b294f399be9815848d5d2b3c8644a4d177ce37b77a37036bc7825541a7e3a8b364701ab5f6a24532a156b258787e0a0961657aed
diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild
index 4153ca1b8..ad56317e4 100644
--- a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild
+++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx
MY_P="widgets-${PV}"
@@ -57,5 +57,5 @@ python_test() {
# If this could be set for the eclass, it might fix some of the tests:
# https://github.com/pauldmccarthy/fsleyes-widgets/issues/1#issuecomment-575387724
#xvfbargs="-screen 0 1920x1200x24 +extension RANDR"
- epytest || die "Tests failed with ${EPYTHON}"
+ epytest
}
diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest
index 776a7e0ee..a22884a06 100644
--- a/sci-visualization/fsleyes/Manifest
+++ b/sci-visualization/fsleyes/Manifest
@@ -1 +1 @@
-DIST fsleyes-1.3.3.tar.gz 91819897 BLAKE2B dde5d4f4831b1fe856c3f6a5eae438cab6570954ab3b11ba6d654fc1ffcbd44bca012c53f4b36bc7fa05a090144b249dea541f5b22147c105c35f01bf14517cf SHA512 a1ce870d88442be3f168e84c3cdc8d468b8a9751a20e2bee33755ef5712f82538e420e94b65ab0a9db3fa2bf91b8630a9868d550c7ee0dad9ff6a8a6c390a122
+DIST fsleyes-1.5.0.tar.gz 98895209 BLAKE2B 1f8b7545a894c281fb596b94d38330662fd5e6fa92e6bf88e480b214b925355e6f660e9312c7b82da41a1217edf1b7026d95832f31a08cbb0a3106e5bd3123e6 SHA512 cc74244ff56b66fca6ffeb10ae21dc69a0a771a1fb0fbaa6b95837cf8a25e674e7b0f81e96ce7583c22844e217f5b258ec0bd3639559de4e74e85847afdd70b7
diff --git a/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild
index ac86c16fd..83fe78c68 100644
--- a/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild
+++ b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild
@@ -3,8 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
-
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517=setuptools
inherit xdg distutils-r1 desktop virtualx
DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
@@ -19,19 +19,19 @@ SLOT="0"
KEYWORDS="~amd64"
RDEPEND="
- >=dev-python/fslpy-3.6[${PYTHON_USEDEP}]
+ >=dev-python/fslpy-3.9[${PYTHON_USEDEP}]
>=dev-python/jinja-2[${PYTHON_USEDEP}]
>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.14[${PYTHON_USEDEP}]
>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
- =dev-python/pyparsing-2*[${PYTHON_USEDEP}]
+ >=dev-python/pyparsing-2[${PYTHON_USEDEP}]
>=dev-python/wxpython-4[${PYTHON_USEDEP}]
>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
>=sci-libs/nibabel-2.3[${PYTHON_USEDEP}]
- >=sci-visualization/fsleyes-widgets-0.12[${PYTHON_USEDEP}]
- >=sci-visualization/fsleyes-props-1.7.2[${PYTHON_USEDEP}]
+ >=sci-visualization/fsleyes-widgets-0.12.3[${PYTHON_USEDEP}]
+ >=sci-visualization/fsleyes-props-1.8[${PYTHON_USEDEP}]
"
PATCHES=(
diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml
index 805623e43..d38edeff2 100644
--- a/sci-visualization/fsleyes/metadata.xml
+++ b/sci-visualization/fsleyes/metadata.xml
@@ -1,4 +1,4 @@
-<?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">
@@ -15,4 +15,7 @@
to FSLView, and aims to improve and expand upon this functionality in many
ways.
</longdescription>
+ <upstream>
+ <remote-id type="github">pauldmccarthy/fsleyes</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sys-devel/DPC++/DPC++-2022.09.ebuild b/sys-devel/DPC++/DPC++-2022.09.ebuild
new file mode 100644
index 000000000..fc7ebb76d
--- /dev/null
+++ b/sys-devel/DPC++/DPC++-2022.09.ebuild
@@ -0,0 +1,176 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+inherit cmake python-any-r1
+DOCS_BUILDER="doxygen"
+DOCS_DIR="build/docs"
+DOCS_CONFIG_NAME="doxygen.cfg"
+DOCS_DEPEND="
+ media-gfx/graphviz
+ virtual/latex-base
+ $(python_gen_any_dep '
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ dev-python/recommonmark[${PYTHON_USEDEP}]
+ dev-python/myst_parser[${PYTHON_USEDEP}]
+ ')
+"
+inherit docs
+
+# We cannot unbundle this because it has to be compiled with the clang/llvm
+# that we are building here. Otherwise we run into problems running the compiler.
+CPU_EMUL_PV="2022-08-22"
+VC_INTR_PV="0.8.1" # Newer versions cause compile failure
+
+DESCRIPTION="oneAPI Data Parallel C++ compiler"
+HOMEPAGE="https://github.com/intel/llvm"
+SRC_URI="
+ https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz
+ https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz
+ esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz )
+"
+S="${WORKDIR}/llvm-${PV//./-}"
+CMAKE_USE_DIR="${S}/llvm"
+BUILD_DIR="${S}/build"
+
+LICENSE="Apache-2.0 MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430
+ NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore )
+ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" )
+LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?}
+
+IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}"
+REQUIRED_USE="
+ ?? ( cuda hip )
+ cuda? ( llvm_targets_NVPTX )
+ hip? ( llvm_targets_AMDGPU )
+"
+RESTRICT="!test? ( test )"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+ dev-libs/boost:=
+ dev-libs/level-zero:=
+ dev-libs/opencl-icd-loader
+ dev-util/opencl-headers
+ dev-util/spirv-headers
+ dev-util/spirv-tools
+ media-libs/libva
+ sys-devel/libtool
+ esimd_emulator? ( dev-libs/libffi:= )
+ cuda? ( dev-util/nvidia-cuda-toolkit:= )
+ hip? ( dev-util/hip:= )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-system-libs.patch"
+)
+
+src_configure() {
+ # Extracted from buildbot/configure.py
+ local mycmakeargs=(
+ -DLLVM_ENABLE_ASSERTIONS=ON
+ -DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}"
+ -DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+ -DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl"
+ -DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv"
+ -DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti"
+ -DXPTI_SOURCE_DIR="${S}/xpti"
+ -DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw"
+ -DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice"
+ -DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+ -DLLVM_BUILD_TOOLS=ON
+ -DSYCL_ENABLE_WERROR=OFF
+ -DSYCL_INCLUDE_TESTS="$(usex test)"
+ -DCLANG_INCLUDE_TESTS="$(usex test)"
+ -DLLVM_INCLUDE_TESTS="$(usex test)"
+ -DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)"
+ -DLLVM_ENABLE_DOXYGEN="$(usex doc)"
+ -DLLVM_ENABLE_SPHINX="$(usex doc)"
+ -DLLVM_BUILD_DOCS="$(usex doc)"
+ -DSYCL_ENABLE_XPTI_TRACING=ON
+ -DLLVM_ENABLE_LLD=OFF
+ -DXPTI_ENABLE_WERROR=OFF
+ -DSYCL_ENABLE_PLUGINS="level_zero;opencl;$(usev esimd_emulator);$(usev hip);$(usev cuda)"
+ -DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr"
+ -DBOOST_MP11_SOURCE_DIR="${ESYSROOT}/usr "
+ -DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so"
+ -DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include"
+ -DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}"
+ -DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}"
+ # The sycl part of the build system insists on installing during compiling
+ # Install it to some temporary directory
+ -DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install"
+ -DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man"
+ -DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info"
+ -DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}"
+ )
+
+ if use hip; then
+ mycmakeargs+=(
+ -DSYCL_BUILD_PI_HIP_PLATFORM=AMD
+ -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+ -DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa"
+ )
+ fi
+
+ if use cuda; then
+ mycmakeargs+=(
+ -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+ -DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl"
+ )
+ fi
+
+ if use esimd_emulator; then
+ mycmakeargs+=(
+ -DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include"
+ -DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}"
+ )
+ fi
+
+ if use doc; then
+ mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF )
+ fi
+
+ cmake_src_configure
+}
+
+src_compile() {
+ # Build sycl (this also installs some stuff already)
+ cmake_build deploy-sycl-toolchain
+
+ use doc && cmake_build doxygen-sycl
+
+ # Install all other files into the same temporary directory
+ cmake_build install
+}
+
+src_test() {
+ cmake_build check
+}
+
+src_install() {
+ einstalldocs
+
+ local LLVM_INTEL_DIR="/usr/lib/llvm/intel"
+ dodir "${LLVM_INTEL_DIR}"
+
+ # Copy our temporary directory to the image directory
+ mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die
+
+ # Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang
+ newenvd - "60llvm-intel" <<-_EOF_
+ PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+ # we need to duplicate it in ROOTPATH for Portage to respect...
+ ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+ MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man"
+ LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64"
+ _EOF_
+}
diff --git a/sys-devel/DPC++/Manifest b/sys-devel/DPC++/Manifest
new file mode 100644
index 000000000..9527a6642
--- /dev/null
+++ b/sys-devel/DPC++/Manifest
@@ -0,0 +1,3 @@
+DIST DPC++-2022.09-cm-cpu-emulation-2022-08-22.tar.gz 328563 BLAKE2B 86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc
+DIST DPC++-2022.09-vc-intrinsics-0.8.1.tar.gz 138462 BLAKE2B 0f86f5fbeb7931a564eb598d527fd67e96489d0f2e7dba7166ffa468470022eff05e150877c3dd380ad003beb8651a0ac9ffe9c3dceeae6552c46b5f3e00aa64 SHA512 9763f1b624121694d6880ca3ffdf2e344ce3ed1a39c1c1e7dc06195b79acccce5e3d86032bba5c0de440376821c383f8ff59fdd57b0ae93fede17595b0fe0b42
+DIST DPC++-2022.09.tar.gz 171848301 BLAKE2B 48f57fee53370135b25a4e5f27926375fe9e4b707909f5841afa4c0d27a53932404f066db6384b8e8c327f1328cd00339e1c055935eb38fca2a8ce34f3556727 SHA512 f17ac91d4ec03c067595abd8355a54484c2cd8b79bb8b1ed8c90fabd8d83b73cce0271a8b3aa26e2c92e8083a2b3cf145c7e78b68e568c3cb036c80b8a4f9e12
diff --git a/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch
new file mode 100644
index 000000000..7d2cdc823
--- /dev/null
+++ b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch
@@ -0,0 +1,217 @@
+diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt
+index 954317fe2..ba3bf19d3 100644
+--- a/opencl/CMakeLists.txt
++++ b/opencl/CMakeLists.txt
+@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO
+ set(OCL_HEADERS_TAG dcd5bede6859d26833cd85f0d6bbcee7382dc9b3)
+ set(OCL_LOADER_TAG 792682ad3d877ab38573b997808bab3b43902b70)
+
+-# OpenCL Headers
+-if(NOT OpenCL_HEADERS)
+- message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}")
+-
+- FetchContent_Declare(ocl-headers
+- GIT_REPOSITORY ${OCL_HEADERS_REPO}
+- GIT_TAG ${OCL_HEADERS_TAG}
+- )
+-else()
+- message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}")
+-
+- FetchContent_Declare(ocl-headers
+- URL ${OpenCL_HEADERS}
+- )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-headers)
+-FetchContent_GetProperties(ocl-headers)
+ set(OpenCL_INCLUDE_DIR
+- ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers")
+-
+-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220)
+-add_library(OpenCL-Headers ALIAS Headers)
++ /usr/include CACHE PATH "Path to OpenCL Headers")
+
+ # OpenCL Library (ICD Loader)
+
+@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR
+ # library.
+ set(BUILD_SHARED_LIBS ON)
+
+-if(NOT OpenCL_LIBRARY_SRC)
+- message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}")
+-
+- FetchContent_Declare(ocl-icd
+- GIT_REPOSITORY ${OCL_LOADER_REPO}
+- GIT_TAG ${OCL_LOADER_TAG}
+- )
+-else()
+- # TODO: add possibility to use prebuilt OpenCL library rather than building
+- # together with llvm.
+- message(STATUS
+- "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}")
+-
+- FetchContent_Declare(ocl-icd
+- URL ${OpenCL_LIBRARY_SRC}
+- )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-icd)
+-add_library(OpenCL-ICD ALIAS OpenCL)
+-
+ add_subdirectory(opencl-aot)
+diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt
+index ff905fd88..b673f79a4 100644
+--- a/opencl/opencl-aot/CMakeLists.txt
++++ b/opencl/opencl-aot/CMakeLists.txt
+@@ -19,5 +19,5 @@ endif()
+
+ target_link_libraries(${OPENCL_AOT_PROJECT_NAME}
+ PRIVATE
+- OpenCL-Headers
+- OpenCL-ICD)
++ OpenCL
++)
+diff --git a/sycl/cmake/modules/AddSYCL.cmake b/sycl/cmake/modules/AddSYCL.cmake
+index aa0cfcadd..9cfa5aadd 100644
+--- a/sycl/cmake/modules/AddSYCL.cmake
++++ b/sycl/cmake/modules/AddSYCL.cmake
+@@ -47,7 +47,7 @@ function(add_sycl_plugin PLUGIN_NAME)
+ ${sycl_inc_dir}
+ LIBRARIES
+ ${ARG_LIBRARIES}
+- OpenCL-Headers
++ OpenCL
+ )
+
+ install(TARGETS pi_${PLUGIN_NAME}
+diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+index 9f5e6dc30..fe0e18b2f 100644
+--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake
++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+@@ -53,7 +53,7 @@ macro(add_sycl_unittest test_dirname link_variant)
+ target_link_libraries(${test_dirname}
+ PRIVATE
+ LLVMTestingSupport
+- OpenCL-Headers
++ OpenCL
+ ${SYCL_LINK_LIBS}
+ )
+ target_include_directories(${test_dirname}
+diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt
+index 0b32c3925..e8b8616bc 100755
+--- a/sycl/plugins/esimd_emulator/CMakeLists.txt
++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt
+@@ -58,6 +58,7 @@ if ((DEFINED USE_DEFAULT_CM_EMU_SOURCE) OR (DEFINED USE_LOCAL_CM_EMU_SOURCE))
+ INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install
+ CMAKE_ARGS -DLIBVA_INSTALL_PATH=/usr
+ -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true
++ -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR}
+ -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+ BUILD_BYPRODUCTS ${LIBCM} ${LIBIGFXCMRT_EMU}
+ )
+diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt
+index 9391ff1e5..aa823e8fa 100755
+--- a/sycl/plugins/level_zero/CMakeLists.txt
++++ b/sycl/plugins/level_zero/CMakeLists.txt
+@@ -82,7 +82,7 @@ else()
+ COMMAND
+ ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR}
+ COMMAND
+- ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl
++ ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero
+ DEPENDS
+ ${LEVEL_ZERO_LIBRARY}
+ ${LEVEL_ZERO_INCLUDE_DIR}
+diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt
+index 9943827e4..29fae166e 100644
+--- a/sycl/plugins/opencl/CMakeLists.txt
++++ b/sycl/plugins/opencl/CMakeLists.txt
+@@ -15,7 +15,7 @@ add_sycl_plugin(opencl
+ "${sycl_inc_dir}/sycl/detail/pi.h"
+ "pi_opencl.cpp"
+ LIBRARIES
+- OpenCL-ICD
++ OpenCL
+ )
+
+ set_target_properties(pi_opencl PROPERTIES LINKER_LANGUAGE CXX)
+diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt
+index 23b161480..4a5c48625 100644
+--- a/sycl/source/CMakeLists.txt
++++ b/sycl/source/CMakeLists.txt
+@@ -82,7 +82,7 @@ function(add_sycl_rt_library LIB_NAME LIB_OBJ_NAME)
+ )
+ #TODO: Remove dependency on opencl headers.
+ target_link_libraries(${LIB_OBJ_NAME}
+- PRIVATE OpenCL-Headers
++ PRIVATE OpenCL
+ )
+
+ find_package(Threads REQUIRED)
+diff --git a/sycl/tools/CMakeLists.txt b/sycl/tools/CMakeLists.txt
+index eb62c48e1..6a7ff9aef 100644
+--- a/sycl/tools/CMakeLists.txt
++++ b/sycl/tools/CMakeLists.txt
+@@ -38,9 +38,8 @@ endif()
+
+ target_link_libraries(get_device_count_by_type
+ PRIVATE
+- OpenCL-Headers
++ OpenCL
+ LevelZeroLoader::Headers
+- OpenCL-ICD
+ ${LEVEL_ZERO_LIBRARY}
+ # The CUDA and HIP for NVIDA plugins need cudadrv
+ $<$<OR:$<BOOL:${SYCL_BUILD_PI_CUDA}>,$<AND:$<BOOL:${SYCL_BUILD_PI_HIP}>,$<STREQUAL:${SYCL_BUILD_PI_HIP_PLATFORM},NVIDIA>>>:cudadrv>
+diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt
+index f5909cf49..f9c52e3a3 100644
+--- a/sycl/tools/sycl-ls/CMakeLists.txt
++++ b/sycl/tools/sycl-ls/CMakeLists.txt
+@@ -11,7 +11,7 @@ endif()
+ target_link_libraries(sycl-ls
+ PRIVATE
+ ${sycl_lib}
+- OpenCL-Headers
++ OpenCL
+ )
+ install(TARGETS sycl-ls
+ RUNTIME DESTINATION "bin" COMPONENT sycl-ls)
+diff --git a/sycl/tools/sycl-prof/CMakeLists.txt b/sycl/tools/sycl-prof/CMakeLists.txt
+index 09586c1b8..ff708db67 100644
+--- a/sycl/tools/sycl-prof/CMakeLists.txt
++++ b/sycl/tools/sycl-prof/CMakeLists.txt
+@@ -16,7 +16,7 @@ add_library(sycl_profiler_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_profiler_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_profiler_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+- target_link_libraries(sycl_profiler_collector PRIVATE OpenCL-Headers)
++ target_link_libraries(sycl_profiler_collector PRIVATE OpenCL)
+ endif()
+ target_include_directories(sycl_profiler_collector PRIVATE
+ "${sycl_inc_dir}"
+diff --git a/sycl/tools/sycl-sanitize/CMakeLists.txt b/sycl/tools/sycl-sanitize/CMakeLists.txt
+index 16e7a1a49..e27b2cb21 100644
+--- a/sycl/tools/sycl-sanitize/CMakeLists.txt
++++ b/sycl/tools/sycl-sanitize/CMakeLists.txt
+@@ -14,7 +14,7 @@ add_library(sycl_sanitizer_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_sanitizer_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_sanitizer_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+- target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL-Headers)
++ target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL)
+ endif()
+
+ target_include_directories(sycl_sanitizer_collector PRIVATE
+diff --git a/sycl/tools/sycl-trace/CMakeLists.txt b/sycl/tools/sycl-trace/CMakeLists.txt
+index 385a348f6..721e29125 100644
+--- a/sycl/tools/sycl-trace/CMakeLists.txt
++++ b/sycl/tools/sycl-trace/CMakeLists.txt
+@@ -46,7 +46,7 @@ add_custom_target(ze-pretty-printers
+ target_compile_definitions(sycl_pi_trace_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_pi_trace_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+- target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL-Headers)
++ target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL)
+ endif()
+
+ target_include_directories(sycl_pi_trace_collector PRIVATE
diff --git a/sys-devel/DPC++/metadata.xml b/sys-devel/DPC++/metadata.xml
new file mode 100644
index 000000000..771c45a25
--- /dev/null
+++ b/sys-devel/DPC++/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="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">intel/llvm</remote-id>
+ </upstream>
+ <use>
+ <flag name="cuda">use the cuda backend</flag>
+ <flag name="esimd_emulator">enable ESIMD CPU emulation</flag>
+ <flag name="hip">use the HIP backend</flag>
+ </use>
+</pkgmetadata>
diff --git a/sys-devel/oneDPL/Manifest b/sys-devel/oneDPL/Manifest
new file mode 100644
index 000000000..14df20ed9
--- /dev/null
+++ b/sys-devel/oneDPL/Manifest
@@ -0,0 +1 @@
+DIST oneDPL-2021.7.1-release.tar.gz 3704195 BLAKE2B 32b47a8ed27a59487b030af8a1cb5f521fb9c03c25bebeb682d601a92594fd2e7c0437b209fead1e3a2b7ad0ad9b6afe736fcef97266619f19cac32d965fb5fa SHA512 264b5e866985e23c28e411d89a5e2e4bb306ac70976c4b3d40991d53dc70a211ab67821f7ea94ff57f093205b1e9f0bb41308e394b4dc0d439b771a6316c1709
diff --git a/sys-devel/oneDPL/metadata.xml b/sys-devel/oneDPL/metadata.xml
new file mode 100644
index 000000000..5fbeb1b05
--- /dev/null
+++ b/sys-devel/oneDPL/metadata.xml
@@ -0,0 +1,11 @@
+<?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>
+ <upstream>
+ <remote-id type="github">oneapi-src/oneDPL</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild
new file mode 100644
index 000000000..e9f773726
--- /dev/null
+++ b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+DOCS_BUILDER="sphinx"
+DOCS_DIR="documentation/library_guide"
+DOCS_AUTODOC=0
+inherit cmake python-any-r1 docs
+
+DESCRIPTION="oneAPI Data Parallel C++ Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDPL"
+SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-release.tar.gz"
+S="${WORKDIR}/${PN}-${P}-release"
+
+LICENSE="Apache-2.0-with-LLVM-exceptions"
+SLOT="0"
+KEYWORDS="~amd64"
+
+#TODO: Figure out how to use the test
+RESTRICT="test"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+ sys-devel/DPC++
+ dev-libs/level-zero:=
+ dev-cpp/tbb:=
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ cmake_src_prepare
+ # Not using the DPC++ compiler doesn't really make sense here
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DONEDPL_DEVICE_BACKEND="level_zero"
+ -DONEDPL_BACKEND="dpcpp"
+ )
+
+ cmake_src_configure
+}
+
+src_compile() {
+ # Nothing to compile, header only
+ docs_compile
+}
+
+src_install() {
+ einstalldocs
+ dodir /usr/include
+ mv "${S}/include/oneapi" "${ED}/usr/include/" || die
+}