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-rw-r--r--app-arch/libdeflate/Manifest5
-rw-r--r--app-arch/libdeflate/libdeflate-1.11.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.6.ebuild21
-rw-r--r--app-arch/libdeflate/libdeflate-1.7.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.8.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.9.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-9999.ebuild28
-rw-r--r--app-arch/libdeflate/metadata.xml19
-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild2
-rw-r--r--dev-java/scijava-common/Manifest2
-rw-r--r--dev-java/scijava-common/scijava-common-2.97.1.ebuild (renamed from dev-java/scijava-common/scijava-common-2.94.2.ebuild)17
-rw-r--r--dev-java/scijava-common/scijava-common-9999.ebuild17
-rw-r--r--dev-libs/oneDNN/Manifest3
-rw-r--r--dev-libs/oneDNN/metadata.xml11
-rw-r--r--dev-libs/oneDNN/oneDNN-2.7.2.ebuild60
-rw-r--r--dev-libs/oneDNN/oneDNN-3.0.1.ebuild60
-rw-r--r--dev-libs/oneDNN/oneDNN-3.2.1.ebuild60
-rw-r--r--dev-libs/simclist/simclist-1.6_p1.ebuild2
-rw-r--r--dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild2
-rw-r--r--dev-python/archspec/Manifest1
-rw-r--r--dev-python/archspec/archspec-0.1.4.ebuild2
-rw-r--r--dev-python/archspec/archspec-0.2.2.ebuild13
-rw-r--r--dev-python/astropy/astropy-5.2.1.ebuild3
-rw-r--r--dev-python/awkward-cpp/Manifest1
-rw-r--r--dev-python/awkward-cpp/awkward-cpp-28.ebuild26
-rw-r--r--dev-python/awkward-cpp/metadata.xml19
-rw-r--r--dev-python/awkward/Manifest1
-rw-r--r--dev-python/awkward/awkward-2.5.2.ebuild38
-rw-r--r--dev-python/awkward/metadata.xml19
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild5
-rw-r--r--dev-python/boost-histogram/Manifest1
-rw-r--r--dev-python/boost-histogram/boost-histogram-1.4.0.ebuild39
-rw-r--r--dev-python/boost-histogram/metadata.xml19
-rw-r--r--dev-python/cadquery-ocp/Manifest1
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild197
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild63
-rw-r--r--dev-python/cadquery-pywrap/metadata.xml12
-rw-r--r--dev-python/cadquery/Manifest1
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild60
-rw-r--r--dev-python/cadquery/metadata.xml12
-rw-r--r--dev-python/ccdproc/ccdproc-2.3.0.ebuild2
-rw-r--r--dev-python/colormath/Manifest1
-rw-r--r--dev-python/colormath/colormath-3.0.0.ebuild23
-rw-r--r--dev-python/colormath/metadata.xml12
-rw-r--r--dev-python/dandi-schema/Manifest4
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.2.ebuild42
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.3.ebuild42
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.9.1.ebuild (renamed from dev-python/dandi-schema/dandi-schema-0.7.1.ebuild)19
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch10
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch13
-rw-r--r--dev-python/docstring-parser/Manifest1
-rw-r--r--dev-python/docstring-parser/docstring-parser-0.16.ebuild18
-rw-r--r--dev-python/docstring-parser/metadata.xml (renamed from dev-python/tridesclous/metadata.xml)4
-rw-r--r--dev-python/dpctl/dpctl-0.14.1_rc2.ebuild4
-rw-r--r--dev-python/dpctl/dpctl-0.14.5.ebuild4
-rw-r--r--dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch82
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch47
-rw-r--r--dev-python/dpnp/dpnp-0.11.1_rc1.ebuild4
-rw-r--r--dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch97
-rw-r--r--dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch80
-rw-r--r--dev-python/fslpy/files/fslpy-2.7.0-coverage.patch16
-rw-r--r--dev-python/gammapy/gammapy-1.0.ebuild2
-rw-r--r--dev-python/hdmf-zarr/Manifest1
-rw-r--r--dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch28
-rw-r--r--dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild32
-rw-r--r--dev-python/hdmf-zarr/metadata.xml (renamed from dev-python/numba/metadata.xml)8
-rw-r--r--dev-python/hdmf/Manifest5
-rw-r--r--dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch10
-rw-r--r--dev-python/hdmf/files/hdmf-3.3.2-versions.patch20
-rw-r--r--dev-python/hdmf/files/hdmf-3.5.0-open_links.patch170
-rw-r--r--dev-python/hdmf/hdmf-3.13.0.ebuild (renamed from dev-python/hdmf/hdmf-3.5.2.ebuild)10
-rw-r--r--dev-python/hdmf/hdmf-3.4.7.ebuild28
-rw-r--r--dev-python/hdmf/hdmf-3.5.0_p1.ebuild37
-rw-r--r--dev-python/hdmf/hdmf-3.5.1.ebuild28
-rw-r--r--dev-python/heudiconv/Manifest2
-rw-r--r--dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch24
-rw-r--r--dev-python/heudiconv/heudiconv-1.0.0.ebuild (renamed from dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild)6
-rw-r--r--dev-python/holoviews/holoviews-1.15.3.ebuild4
-rw-r--r--dev-python/jacobi/Manifest2
-rw-r--r--dev-python/jacobi/jacobi-0.8.1.ebuild24
-rw-r--r--dev-python/jacobi/jacobi-0.9.2.ebuild26
-rw-r--r--dev-python/jacobi/metadata.xml21
-rw-r--r--dev-python/kmapper/kmapper-2.0.1-r1.ebuild2
-rw-r--r--dev-python/llvmlite/Manifest3
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch13
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch97
-rw-r--r--dev-python/llvmlite/llvmlite-0.39.1.ebuild66
-rw-r--r--dev-python/llvmlite/llvmlite-0.40.1.ebuild63
-rw-r--r--dev-python/llvmlite/llvmlite-0.41.0.ebuild57
-rw-r--r--dev-python/llvmlite/metadata.xml18
-rw-r--r--dev-python/lzstring/Manifest1
-rw-r--r--dev-python/lzstring/lzstring-1.0.4.ebuild16
-rw-r--r--dev-python/lzstring/metadata.xml12
-rw-r--r--dev-python/neo/Manifest1
-rw-r--r--dev-python/neo/neo-0.12.0.ebuild57
-rw-r--r--dev-python/nptyping/Manifest1
-rw-r--r--dev-python/nptyping/metadata.xml16
-rw-r--r--dev-python/nptyping/nptyping-2.5.0.ebuild66
-rw-r--r--dev-python/numba-dpex/Manifest1
-rw-r--r--dev-python/numba-dpex/metadata.xml12
-rw-r--r--dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild41
-rw-r--r--dev-python/numba/Manifest2
-rw-r--r--dev-python/numba/files/numba-0.52.0-skip_tests.patch34
-rw-r--r--dev-python/numba/files/numba-0.56.4-allow-py3.11.patch13
-rw-r--r--dev-python/numba/numba-0.56.4.ebuild85
-rw-r--r--dev-python/numba/numba-0.57.1.ebuild83
-rw-r--r--dev-python/numcodecs/Manifest1
-rw-r--r--dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild43
-rw-r--r--dev-python/numpy/Manifest4
-rw-r--r--dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch50
-rw-r--r--dev-python/numpy/metadata.xml24
-rw-r--r--dev-python/numpy/numpy-1.23.5.ebuild184
-rw-r--r--dev-python/pandas-stubs/Manifest1
-rw-r--r--dev-python/pandas-stubs/metadata.xml16
-rw-r--r--dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild52
-rw-r--r--dev-python/panel/panel-0.14.2-r1.ebuild (renamed from dev-python/panel/panel-0.14.2.ebuild)6
-rw-r--r--dev-python/persim/persim-0.3.1.ebuild2
-rw-r--r--dev-python/photutils/photutils-1.6.0.ebuild2
-rw-r--r--dev-python/plac/Manifest2
-rw-r--r--dev-python/plac/plac-1.4.2.ebuild (renamed from dev-python/plac/plac-1.3.5.ebuild)7
-rw-r--r--dev-python/probeinterface/Manifest1
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.20.ebuild37
-rw-r--r--dev-python/pyaml-env/Manifest1
-rw-r--r--dev-python/pyaml-env/metadata.xml12
-rw-r--r--dev-python/pyaml-env/pyaml-env-1.2.1.ebuild22
-rw-r--r--dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild3
-rw-r--r--dev-python/pynndescent/Manifest1
-rw-r--r--dev-python/pynndescent/metadata.xml16
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.6.ebuild27
-rw-r--r--dev-python/pynwb/Manifest5
-rw-r--r--dev-python/pynwb/files/pynwb-2.0.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.1.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.2.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch54
-rw-r--r--dev-python/pynwb/files/pynwb-2.3.1-typing.patch13
-rw-r--r--dev-python/pynwb/pynwb-2.2.0-r1.ebuild56
-rw-r--r--dev-python/pynwb/pynwb-2.5.0.ebuild (renamed from dev-python/pynwb/pynwb-2.3.2.ebuild)10
-rw-r--r--dev-python/pynwb/pynwb-2.6.0.ebuild (renamed from dev-python/pynwb/pynwb-2.3.1-r1.ebuild)17
-rw-r--r--dev-python/pyout/Manifest2
-rw-r--r--dev-python/pyout/pyout-0.7.3.ebuild (renamed from dev-python/pyout/pyout-0.7.1-r1.ebuild)12
-rw-r--r--dev-python/python-igraph/python-igraph-0.10.4.ebuild2
-rw-r--r--dev-python/pytorch-lightning/Manifest1
-rw-r--r--dev-python/pytorch-lightning/metadata.xml12
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild31
-rw-r--r--dev-python/rich-click/Manifest1
-rw-r--r--dev-python/rich-click/metadata.xml12
-rw-r--r--dev-python/rich-click/rich-click-1.7.2.ebuild25
-rw-r--r--dev-python/ripser/ripser-0.6.4.ebuild2
-rw-r--r--dev-python/schema/Manifest1
-rw-r--r--dev-python/schema/metadata.xml13
-rw-r--r--dev-python/schema/schema-0.7.4.ebuild26
-rw-r--r--dev-python/snakemake/Manifest2
-rw-r--r--dev-python/snakemake/snakemake-7.32.4.ebuild (renamed from dev-python/snakemake/snakemake-7.32.3.ebuild)1
-rw-r--r--dev-python/spectra/Manifest1
-rw-r--r--dev-python/spectra/metadata.xml12
-rw-r--r--dev-python/spectra/spectra-0.0.11.ebuild22
-rw-r--r--dev-python/spikeinterface/Manifest1
-rw-r--r--dev-python/spikeinterface/spikeinterface-0.99.1.ebuild53
-rw-r--r--dev-python/tridesclous/Manifest2
-rw-r--r--dev-python/tridesclous/tridesclous-1.6.4.ebuild100
-rw-r--r--dev-python/tridesclous/tridesclous-1.6.6.ebuild101
-rw-r--r--dev-python/typish/typish-1.9.3.ebuild2
-rw-r--r--dev-python/uhi/Manifest1
-rw-r--r--dev-python/uhi/metadata.xml19
-rw-r--r--dev-python/uhi/uhi-0.4.0.ebuild27
-rw-r--r--dev-python/umap-learn/Manifest1
-rw-r--r--dev-python/umap-learn/metadata.xml15
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.2.ebuild25
-rw-r--r--dev-python/vector/Manifest2
-rw-r--r--dev-python/vector/metadata.xml19
-rw-r--r--dev-python/vector/vector-1.1.1.ebuild22
-rw-r--r--dev-python/vector/vector-1.3.1.ebuild22
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-includes.patch16
-rw-r--r--dev-python/xgboost/Manifest1
-rw-r--r--dev-python/xgboost/xgboost-2.0.3.ebuild27
-rw-r--r--dev-python/yte/Manifest2
-rw-r--r--dev-python/yte/yte-1.5.4.ebuild (renamed from dev-python/yte/yte-1.5.1.ebuild)4
-rw-r--r--dev-python/zarr/Manifest3
-rw-r--r--dev-python/zarr/zarr-2.14.2.ebuild (renamed from dev-python/zarr/zarr-2.11.3.ebuild)0
-rw-r--r--dev-python/zarr/zarr-2.16.1.ebuild61
-rw-r--r--dev-python/zarr_checksum/Manifest1
-rw-r--r--dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild26
-rw-r--r--dev-vcs/dandi-cli/Manifest5
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild81
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild)27
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild)34
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch46
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch13
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch40
-rw-r--r--dev-vcs/datalad/Manifest4
-rw-r--r--dev-vcs/datalad/datalad-0.18.0.ebuild74
-rw-r--r--dev-vcs/datalad/datalad-0.18.3.ebuild74
-rw-r--r--dev-vcs/datalad/datalad-0.19.6-r1.ebuild (renamed from dev-vcs/datalad/datalad-0.18.1.ebuild)5
-rw-r--r--dev-vcs/datalad/metadata.xml1
-rw-r--r--media-gfx/brlcad/brlcad-7.32.4.ebuild2
-rw-r--r--media-gfx/brlcad/brlcad-9999.ebuild2
-rw-r--r--media-libs/imglib2/Manifest2
-rw-r--r--media-libs/imglib2/imglib2-6.3.0.ebuild (renamed from media-libs/imglib2/imglib2-6.2.0.ebuild)2
-rw-r--r--media-libs/imglib2/imglib2-9999.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.0.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.1.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.2.ebuild2
-rw-r--r--profiles/desc/lhapdf_sets.desc4
-rw-r--r--profiles/package.mask12
-rw-r--r--sci-biology/SPAdes/Manifest8
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.5.ebuild (renamed from sci-biology/SPAdes/SPAdes-3.15.3.ebuild)10
-rw-r--r--sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch49
-rw-r--r--sci-biology/SPAdes/metadata.xml11
-rw-r--r--sci-biology/afni/Manifest7
-rw-r--r--sci-biology/afni/afni-20.1.16.ebuild73
-rw-r--r--sci-biology/afni/afni-20.3.03.ebuild73
-rw-r--r--sci-biology/afni/afni-22.0.21.ebuild75
-rw-r--r--sci-biology/afni/afni-24.0.04-r1.ebuild110
-rw-r--r--sci-biology/afni/afni-24.0.08-r1.ebuild114
-rw-r--r--sci-biology/afni/files/afni-20.1.16-python.patch11
-rw-r--r--sci-biology/afni/files/afni-24.0.04-whirlgif.patch39
-rw-r--r--sci-biology/afni/metadata.xml3
-rw-r--r--sci-biology/ants/files/ants-2.4.1-fix-compile.patch13
-rw-r--r--sci-biology/behaviopy/Manifest1
-rw-r--r--sci-biology/behaviopy/behaviopy-0.2.ebuild42
-rw-r--r--sci-biology/behaviopy/metadata.xml26
-rw-r--r--sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch30
-rw-r--r--sci-biology/clview/Manifest2
-rw-r--r--sci-biology/clview/clview-0.1.ebuild108
-rw-r--r--sci-biology/clview/metadata.xml15
-rw-r--r--sci-biology/deeptools/deeptools-3.5.0.ebuild5
-rw-r--r--sci-biology/deeptools/deeptools-3.5.1.ebuild5
-rw-r--r--sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild5
-rw-r--r--sci-biology/fastp/Manifest1
-rw-r--r--sci-biology/fastp/fastp-0.23.4.ebuild20
-rw-r--r--sci-biology/fastp/metadata.xml (renamed from dev-python/cadquery-ocp/metadata.xml)8
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch12
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch21
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch10
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-setup.patch198
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild4
-rw-r--r--sci-biology/gffcompare/files/Makefile.patch79
-rw-r--r--sci-biology/imagej/Manifest5
-rw-r--r--sci-biology/imagej/imagej-1.53t.ebuild122
-rw-r--r--sci-biology/imagej/imagej-1.54h-r1.ebuild (renamed from sci-biology/imagej/imagej-1.54f.ebuild)4
-rw-r--r--sci-biology/imagej/imagej-9999.ebuild4
-rw-r--r--sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild2
-rw-r--r--sci-biology/libBigWig/Manifest1
-rw-r--r--sci-biology/libBigWig/libBigWig-0.4.7.ebuild31
-rw-r--r--sci-biology/multiqc/Manifest1
-rw-r--r--sci-biology/multiqc/metadata.xml12
-rw-r--r--sci-biology/multiqc/multiqc-1.19.ebuild40
-rw-r--r--sci-biology/neuroconv/Manifest2
-rw-r--r--sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild (renamed from sci-biology/neuroconv/neuroconv-0.2.4.ebuild)12
-rw-r--r--sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch39
-rw-r--r--sci-biology/nitime/Manifest1
-rw-r--r--sci-biology/nitime/metadata.xml6
-rw-r--r--sci-biology/nitime/nitime-0.10.2.ebuild33
-rw-r--r--sci-biology/nitime/nitime-9999.ebuild10
-rw-r--r--sci-biology/samri/samri-0.5.3.ebuild2
-rw-r--r--sci-biology/samri/samri-0.5.4.ebuild2
-rw-r--r--sci-biology/samri/samri-9999.ebuild2
-rw-r--r--sci-biology/sra-tools/files/libs_sra_Makefile.patch77
-rw-r--r--sci-biology/sra-tools/files/sra_sdk-destdir.patch76
-rw-r--r--sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch12
-rw-r--r--sci-electronics/mpremote/Manifest1
-rw-r--r--sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch12
-rw-r--r--sci-electronics/mpremote/mpremote-1.22.0.ebuild29
-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.2.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.3.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.8.0.ebuild2
-rw-r--r--sci-libs/asl/asl-0.1.7.ebuild2
-rw-r--r--sci-libs/asl/asl-9999.ebuild2
-rw-r--r--sci-libs/daal4py/daal4py-2023.0.2.ebuild2
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch69
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch72
-rw-r--r--sci-libs/gdcm/gdcm-3.0.14.ebuild2
-rw-r--r--sci-libs/gvar/Manifest1
-rw-r--r--sci-libs/gvar/gvar-13.0.2.ebuild22
-rw-r--r--sci-libs/gvar/metadata.xml19
-rw-r--r--sci-libs/handyg/files/handyg-0.1.5-ld.patch22
-rw-r--r--sci-libs/itk/itk-5.2.1-r2.ebuild2
-rw-r--r--sci-libs/itk/itk-5.3.0-r1.ebuild2
-rw-r--r--sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch11
-rw-r--r--sci-libs/mpfun90/Manifest1
-rw-r--r--sci-libs/mpfun90/metadata.xml18
-rw-r--r--sci-libs/mpfun90/mpfun90-2023.02.26.ebuild29
-rw-r--r--sci-libs/nexus/nexus-4.4.3_p20200126.ebuild2
-rw-r--r--sci-libs/nibabel/Manifest2
-rw-r--r--sci-libs/nibabel/nibabel-5.1.0.ebuild (renamed from sci-libs/nibabel/nibabel-4.0.0.ebuild)10
-rw-r--r--sci-libs/nipy/Manifest2
-rw-r--r--sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild52
-rw-r--r--sci-libs/nipy/nipy-0.6.0.ebuild37
-rw-r--r--sci-libs/nipype/Manifest2
-rw-r--r--sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch50
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r1.ebuild1
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r2.ebuild (renamed from sci-libs/nipype/nipype-1.5.0.ebuild)22
-rw-r--r--sci-libs/nipype/nipype-1.8.6.ebuild97
-rw-r--r--sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild4
-rw-r--r--sci-libs/torchvision/Manifest1
-rw-r--r--sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch36
-rw-r--r--sci-libs/torchvision/torchvision-0.17.1.ebuild45
-rw-r--r--sci-libs/vegas/Manifest1
-rw-r--r--sci-libs/vegas/metadata.xml19
-rw-r--r--sci-libs/vegas/vegas-6.0.1.ebuild24
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0001.patch16
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0002.patch105
-rw-r--r--sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch12
-rw-r--r--sci-mathematics/cipi/cipi-1.0-r1.ebuild51
-rw-r--r--sci-mathematics/cipi/files/cipi-1.0-boost.patch11
-rw-r--r--sci-mathematics/frama-c/files/ocamlgraph185_compat.patch254
-rw-r--r--sci-mathematics/lie/lie-2.2.2.ebuild2
-rw-r--r--sci-mathematics/ltl2ba/Manifest2
-rw-r--r--sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild31
-rw-r--r--sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild31
-rw-r--r--sci-physics/apfelxx/Manifest1
-rw-r--r--sci-physics/apfelxx/apfelxx-4.8.0.ebuild39
-rw-r--r--sci-physics/apfelxx/metadata.xml18
-rw-r--r--sci-physics/cernlib/Manifest2
-rw-r--r--sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild72
-rw-r--r--sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch21
-rw-r--r--sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch31
-rw-r--r--sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch22
-rw-r--r--sci-physics/cernlib/metadata.xml24
-rw-r--r--sci-physics/collier/Manifest1
-rw-r--r--sci-physics/collier/collier-1.2.8.ebuild34
-rw-r--r--sci-physics/collier/files/collier-1.2.7-mod.patch40
-rw-r--r--sci-physics/collier/metadata.xml19
-rw-r--r--sci-physics/formcalc/formcalc-9.10-r1.ebuild11
-rw-r--r--sci-physics/formcalc/formcalc-9.9-r1.ebuild11
-rw-r--r--sci-physics/hepunits/Manifest1
-rw-r--r--sci-physics/hepunits/hepunits-2.3.2.ebuild2
-rw-r--r--sci-physics/hepunits/hepunits-2.3.3.ebuild25
-rw-r--r--sci-physics/hepunits/hepunits-9999.ebuild6
-rw-r--r--sci-physics/hoppet/Manifest1
-rw-r--r--sci-physics/hoppet/hoppet-1.2.0.ebuild35
-rw-r--r--sci-physics/hoppet/metadata.xml19
-rw-r--r--sci-physics/lhapdf-sets/Manifest2
-rw-r--r--sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild6
-rw-r--r--sci-physics/mcfm/mcfm-10.2.1.ebuild5
-rw-r--r--sci-physics/oneloop/metadata.xml3
-rw-r--r--sci-physics/oneloop/oneloop-2020.07.31.ebuild5
-rw-r--r--sci-physics/particle/Manifest2
-rw-r--r--sci-physics/particle/particle-0.23.0.ebuild4
-rw-r--r--sci-physics/particle/particle-0.23.1.ebuild44
-rw-r--r--sci-physics/particle/particle-0.24.0.ebuild44
-rw-r--r--sci-physics/particle/particle-9999.ebuild6
-rw-r--r--sci-physics/pyhepmc/Manifest1
-rw-r--r--sci-physics/pyhepmc/metadata.xml19
-rw-r--r--sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild20
-rw-r--r--sci-physics/pyhf/pyhf-0.7.3.ebuild2
-rw-r--r--sci-physics/pylhe/Manifest2
-rw-r--r--sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch8
-rw-r--r--sci-physics/pylhe/metadata.xml19
-rw-r--r--sci-physics/pylhe/pylhe-0.7.0.ebuild35
-rw-r--r--sci-physics/pylhe/pylhe-0.8.0.ebuild35
-rw-r--r--sci-physics/qcdloop/qcdloop-2.0.5.ebuild8
-rw-r--r--sci-physics/qcdloop/qcdloop-2.0.9.ebuild8
-rw-r--r--sci-physics/qgraf/Manifest4
-rw-r--r--sci-physics/qgraf/qgraf-3.4.2.ebuild (renamed from sci-physics/qgraf/qgraf-3.6.5.ebuild)8
-rw-r--r--sci-physics/qgraf/qgraf-3.5.2.ebuild32
-rw-r--r--sci-physics/qgraf/qgraf-3.6.7.ebuild32
-rw-r--r--sci-physics/rivet/Manifest3
-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-physics/rivet/rivet-3.1.7.ebuild78
-rw-r--r--sci-physics/scikit-hep-testdata/Manifest1
-rw-r--r--sci-physics/scikit-hep-testdata/metadata.xml19
-rw-r--r--sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild30
-rw-r--r--sci-physics/spheno/Manifest3
-rw-r--r--sci-physics/spheno/files/spheno-4.0.5-gfortran.patch29
-rw-r--r--sci-physics/spheno/spheno-3.3.8-r1.ebuild (renamed from sci-physics/spheno/spheno-3.3.8.ebuild)14
-rw-r--r--sci-physics/spheno/spheno-4.0.5.ebuild39
-rw-r--r--sci-physics/tauola/tauola-1.1.8.ebuild2
-rw-r--r--sci-physics/uproot/Manifest1
-rw-r--r--sci-physics/uproot/metadata.xml21
-rw-r--r--sci-physics/uproot/uproot-5.3.1.ebuild28
-rw-r--r--sci-visualization/forge/forge-1.0.5.ebuild2
-rw-r--r--sci-visualization/forge/forge-1.0.7.ebuild2
-rw-r--r--sci-visualization/forge/forge-9999.ebuild2
-rw-r--r--sys-cluster/easybuild-easyblocks/Manifest1
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild2
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild36
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild37
-rw-r--r--sys-cluster/easybuild-easyconfigs/Manifest1
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild2
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild34
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild34
-rw-r--r--sys-cluster/easybuild-framework/Manifest1
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild2
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild40
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild40
-rw-r--r--sys-cluster/easybuild/Manifest1
-rw-r--r--sys-cluster/easybuild/easybuild-4.6.2.ebuild2
-rw-r--r--sys-cluster/easybuild/easybuild-4.9.0.ebuild40
-rw-r--r--sys-cluster/easybuild/easybuild-9999.ebuild40
-rw-r--r--sys-devel/DPC++/DPC++-2021.12.ebuild4
-rw-r--r--sys-devel/DPC++/DPC++-2022.09.ebuild4
-rw-r--r--sys-devel/DPC++/DPC++-2022.12.ebuild4
401 files changed, 3643 insertions, 5575 deletions
diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
deleted file mode 100644
index b320be20c..000000000
--- a/app-arch/libdeflate/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST libdeflate-1.11.tar.gz 162862 BLAKE2B 70ee15bdbe697083f84eef4bfce069b3bff8499a8daf53037a52fd247a47cd04867c1d93265e1b88232da52919ad15333e90d787dff05f7d8e5abe7a9613a07a SHA512 71badc0d934dde5fa79c0d8661b3a38a45d7189fba6f1c77986b2fb6baa03233b8474f0a83f004242410421c2063d2f98f02ca4f8a7a7a14cc7bcd3a9be4fbbc
-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
-DIST libdeflate-1.9.tar.gz 157565 BLAKE2B a8762bb1c2e73d9f7bf26121ac194362be61fd14a8e2a2a0ca72ffc7c512f5c96b19f3f0c563495e25e849342de26f89260af5e67aa5ec2b37b30da596ec3cdf SHA512 aecfa2414a4d22f5233cbe58385e1637b5cbe252e1d4dc55e20e7769908158190a22af11af175e5dfb376f3b4a90fcee58e25468ccb47a5d5b02ae2b248c58f3
diff --git a/app-arch/libdeflate/libdeflate-1.11.ebuild b/app-arch/libdeflate/libdeflate-1.11.ebuild
deleted file mode 100644
index 9e7344b22..000000000
--- a/app-arch/libdeflate/libdeflate-1.11.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS.md README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.6.ebuild b/app-arch/libdeflate/libdeflate-1.6.ebuild
deleted file mode 100644
index 666506943..000000000
--- a/app-arch/libdeflate/libdeflate-1.6.ebuild
+++ /dev/null
@@ -1,21 +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/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-src_install() {
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- emake install DESTDIR="${ED}" PREFIX=/usr LIBDIR=/usr/"$(get_libdir)"
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.7.ebuild b/app-arch/libdeflate/libdeflate-1.7.ebuild
deleted file mode 100644
index bfafcfecd..000000000
--- a/app-arch/libdeflate/libdeflate-1.7.ebuild
+++ /dev/null
@@ -1,28 +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"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.8.ebuild b/app-arch/libdeflate/libdeflate-1.8.ebuild
deleted file mode 100644
index bfafcfecd..000000000
--- a/app-arch/libdeflate/libdeflate-1.8.ebuild
+++ /dev/null
@@ -1,28 +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"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild b/app-arch/libdeflate/libdeflate-1.9.ebuild
deleted file mode 100644
index ef7ead774..000000000
--- a/app-arch/libdeflate/libdeflate-1.9.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2022 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"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS,d README.md
-}
diff --git a/app-arch/libdeflate/libdeflate-9999.ebuild b/app-arch/libdeflate/libdeflate-9999.ebuild
deleted file mode 100644
index 35aff28c3..000000000
--- a/app-arch/libdeflate/libdeflate-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
-else
- SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="static-libs test"
-RESTRICT="!test? ( test )"
-
-src_install() {
- emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- dodoc NEWS.md README.md
-}
diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml
deleted file mode 100644
index fe240766f..000000000
--- a/app-arch/libdeflate/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="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </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/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 38e0dfbd0..e331bc6c9 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -20,7 +20,7 @@ RESTRICT="!test? ( test )"
BDEPEND="
${PYTHON_DEPS}
- doc? ( app-doc/doxygen[dot] )
+ doc? ( app-text/doxygen[dot] )
"
DEPEND="
boost? ( dev-libs/boost:= )
diff --git a/dev-java/scijava-common/Manifest b/dev-java/scijava-common/Manifest
index 093710215..51c68561b 100644
--- a/dev-java/scijava-common/Manifest
+++ b/dev-java/scijava-common/Manifest
@@ -1 +1 @@
-DIST scijava-common-2.94.2-sources.tar.gz 558014 BLAKE2B eb045006f96ee9eddd6413049162c8f99d90cf8c44b0c2bce916423eba6234241b6e8324b8ffc4300e228eb7e337d9b89e8f570bc744078c8e7859c0965dd46a SHA512 a56c0d957307ecd610b3b72dd98481118ca7a380f44662a6d1bae93d5dcd5d1bb55a630d9724403e6d16430d84a7e5452962d9dca06ddd97c30a4414672b2a86
+DIST scijava-common-2.97.1-sources.tar.gz 559336 BLAKE2B 4511202aaa7947a57a8fff6420397c05d5768571045519b9d02aa67a5b3ecefd738418d8412f447678d5133e089fa73bd335543979a58ae55b0e31e53eedc8ae SHA512 cf8e47097f608480c59b24d7487dbf1e138c16a63660aa3b5f5de4c600913e509b64e2d9360f7fdb6e5558a1320fb7d6f09bd3184e5e99da2c5265a91050002b
diff --git a/dev-java/scijava-common/scijava-common-2.94.2.ebuild b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
index f384bf8bd..37a9bca8d 100644
--- a/dev-java/scijava-common/scijava-common-2.94.2.ebuild
+++ b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
@@ -25,7 +25,7 @@ else
https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ MAVEN_ID="org.scijava:scijava-common:2.97.1"
KEYWORDS="~amd64"
fi
@@ -38,20 +38,19 @@ CDEPEND="
dev-java/jaxb-api:2
"
-BDEPEND="
+BDEPEND="${CDEPEND}
>=virtual/jdk-1.8:*
- ${CDEPEND}
+"
+
+DEPEND="${CDEPEND}
test? (
>=dev-java/junit-4.13.2
- >=dev-java/mockito-2.19.0:2
+ >=dev-java/mockito-4.11.0:4
)
"
-DEPEND="${CDEPEND}"
-
-RDEPEND="
+RDEPEND="${CDEPEND}
>=virtual/jre-1.8:*
- ${CDEPEND}
"
JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
@@ -61,7 +60,7 @@ JAVA_RESOURCE_DIRS=(
"src/main/resources"
)
-JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
JAVA_TEST_SRC_DIR="src/test/java"
JAVA_TEST_RESOURCE_DIRS=(
"src/test/resources"
diff --git a/dev-java/scijava-common/scijava-common-9999.ebuild b/dev-java/scijava-common/scijava-common-9999.ebuild
index f384bf8bd..37a9bca8d 100644
--- a/dev-java/scijava-common/scijava-common-9999.ebuild
+++ b/dev-java/scijava-common/scijava-common-9999.ebuild
@@ -25,7 +25,7 @@ else
https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ MAVEN_ID="org.scijava:scijava-common:2.97.1"
KEYWORDS="~amd64"
fi
@@ -38,20 +38,19 @@ CDEPEND="
dev-java/jaxb-api:2
"
-BDEPEND="
+BDEPEND="${CDEPEND}
>=virtual/jdk-1.8:*
- ${CDEPEND}
+"
+
+DEPEND="${CDEPEND}
test? (
>=dev-java/junit-4.13.2
- >=dev-java/mockito-2.19.0:2
+ >=dev-java/mockito-4.11.0:4
)
"
-DEPEND="${CDEPEND}"
-
-RDEPEND="
+RDEPEND="${CDEPEND}
>=virtual/jre-1.8:*
- ${CDEPEND}
"
JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
@@ -61,7 +60,7 @@ JAVA_RESOURCE_DIRS=(
"src/main/resources"
)
-JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
JAVA_TEST_SRC_DIR="src/test/java"
JAVA_TEST_RESOURCE_DIRS=(
"src/test/resources"
diff --git a/dev-libs/oneDNN/Manifest b/dev-libs/oneDNN/Manifest
deleted file mode 100644
index 80f52571c..000000000
--- a/dev-libs/oneDNN/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST oneDNN-2.7.2.tar.gz 6409290 BLAKE2B 8e6fb262a77469cfaddd633bf11334d04ffb641fa798f0de23e458086c66c9b7e932d45d52baf8a93453495df9280f6a97dc3f220d7674850d1ca6c525ce2a7f SHA512 faf8ea953f552afaafcc597f647a98187c8c6dabd8a532fc1b8037626fa77a8a6543dce3247d953a470391d39189ba421ab7de589a8bb7c4c38e22327ab1c401
-DIST oneDNN-3.0.1.tar.gz 7189577 BLAKE2B e55798bb3ab921945873040876514c0b22a77edce34d4bba249537cc56bbcd846eecb461dc22d2ea3bf4b1c47f9079a9c876307f3044e059f71e69b5669886aa SHA512 ca7d7d97469c878953507ddd7c4e3a09bb9955f160ce57529b5a943afd08db0ff82755ffded857518193fcab0e0be2b4ebe45f5e8bfba1a53006b0f161ac15b5
-DIST oneDNN-3.2.1.tar.gz 9186820 BLAKE2B f85cb1b410c3f57e098106ca13939c8c93c396e012b15a63c4f728ba75138a6f371db5fd182a54711479beca8f215578ea52d9c3d07be36647f6befb6c16746a SHA512 115819dc47fce5ef8fc7403f88e141743b360bc33243c90740d1b3871849ac379930d23e3e1d62d0abaaa3af5d2cdbd4218b80aa1be1edb09d0d949f7532a559
diff --git a/dev-libs/oneDNN/metadata.xml b/dev-libs/oneDNN/metadata.xml
deleted file mode 100644
index 0d6dc84a7..000000000
--- a/dev-libs/oneDNN/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">oneapi-src/oneDNN</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild b/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
deleted file mode 100644
index 1c66ec72c..000000000
--- a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep Neural Network Library"
-HOMEPAGE="https://github.com/oneapi-src/oneDNN"
-SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="test"
-# TODO: get the tests up and running
-#RESTRICT="!test? ( test )"
-RESTRICT="test"
-
-BDEPEND="sys-devel/DPC++"
-
-DEPEND="
- dev-cpp/tbb:=
- dev-libs/level-zero:=
- virtual/opencl
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDNNL_CPU_RUNTIME=DPCPP
- -DDNNL_GPU_RUNTIME=DPCPP
- -DDNNL_BUILD_TESTS="$(usex test)"
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- # Correct docdir
- mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die
- rm -r "${ED}/usr/share/doc/dnnl" || die
-}
diff --git a/dev-libs/oneDNN/oneDNN-3.0.1.ebuild b/dev-libs/oneDNN/oneDNN-3.0.1.ebuild
deleted file mode 100644
index 1c66ec72c..000000000
--- a/dev-libs/oneDNN/oneDNN-3.0.1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep Neural Network Library"
-HOMEPAGE="https://github.com/oneapi-src/oneDNN"
-SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="test"
-# TODO: get the tests up and running
-#RESTRICT="!test? ( test )"
-RESTRICT="test"
-
-BDEPEND="sys-devel/DPC++"
-
-DEPEND="
- dev-cpp/tbb:=
- dev-libs/level-zero:=
- virtual/opencl
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDNNL_CPU_RUNTIME=DPCPP
- -DDNNL_GPU_RUNTIME=DPCPP
- -DDNNL_BUILD_TESTS="$(usex test)"
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- # Correct docdir
- mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die
- rm -r "${ED}/usr/share/doc/dnnl" || die
-}
diff --git a/dev-libs/oneDNN/oneDNN-3.2.1.ebuild b/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
deleted file mode 100644
index 1c66ec72c..000000000
--- a/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}_build"
-# There is additional sphinx documentation but we are missing dependency doxyrest.
-inherit cmake docs
-
-DESCRIPTION="oneAPI Deep Neural Network Library"
-HOMEPAGE="https://github.com/oneapi-src/oneDNN"
-SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="test"
-# TODO: get the tests up and running
-#RESTRICT="!test? ( test )"
-RESTRICT="test"
-
-BDEPEND="sys-devel/DPC++"
-
-DEPEND="
- dev-cpp/tbb:=
- dev-libs/level-zero:=
- virtual/opencl
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDNNL_CPU_RUNTIME=DPCPP
- -DDNNL_GPU_RUNTIME=DPCPP
- -DDNNL_BUILD_TESTS="$(usex test)"
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- # Correct docdir
- mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die
- rm -r "${ED}/usr/share/doc/dnnl" || die
-}
diff --git a/dev-libs/simclist/simclist-1.6_p1.ebuild b/dev-libs/simclist/simclist-1.6_p1.ebuild
index 2b7eb84f1..41c9151c5 100644
--- a/dev-libs/simclist/simclist-1.6_p1.ebuild
+++ b/dev-libs/simclist/simclist-1.6_p1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug doc dump hash threads"
-BDEPEND="doc? ( app-doc/doxygen )"
+BDEPEND="doc? ( app-text/doxygen )"
CMAKE_IN_SOURCE_BUILD=1
diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
index cb24f5d19..23e03adcf 100644
--- a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
+++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1
inherit distutils-r1 pypi
diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest
index 5351b4321..8ad1830fc 100644
--- a/dev-python/archspec/Manifest
+++ b/dev-python/archspec/Manifest
@@ -1 +1,2 @@
DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286
+DIST archspec-0.2.2.tar.gz 38306 BLAKE2B c8f8011e122d31a603120231b5f4f034316e06412d64e0bb0fe38886508470d264f7a20da5ef79634fa5ba2f3d3b176b08151f9b5d72d64dbc5c90ce9bd6ff42 SHA512 e2310ca041064109358c918abbdfb581a1494d51d4c0f41e6172fdb9defcefd60f1b80ae2187c8143e37569c815fdc29508d52c048fe88c8c198e85997cef34d
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild
index f1b1cb0f1..35500e00d 100644
--- a/dev-python/archspec/archspec-0.1.4.ebuild
+++ b/dev-python/archspec/archspec-0.1.4.ebuild
@@ -16,4 +16,4 @@ RDEPEND="
<=dev-python/six-2.0.0[${PYTHON_USEDEP}]
>=dev-python/click-7.1.2[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/archspec/archspec-0.2.2.ebuild b/dev-python/archspec/archspec-0.2.2.ebuild
new file mode 100644
index 000000000..a7287fc72
--- /dev/null
+++ b/dev-python/archspec/archspec-0.2.2.ebuild
@@ -0,0 +1,13 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=poetry
+inherit distutils-r1 pypi
+
+DESCRIPTION="Labels for various aspects of a system architecture like CPU, etc."
+HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
diff --git a/dev-python/astropy/astropy-5.2.1.ebuild b/dev-python/astropy/astropy-5.2.1.ebuild
index ac5c388b0..b52d1e6f5 100644
--- a/dev-python/astropy/astropy-5.2.1.ebuild
+++ b/dev-python/astropy/astropy-5.2.1.ebuild
@@ -33,7 +33,8 @@ RDEPEND="
>=sci-libs/cfitsio-3.350:0=
sys-libs/zlib:0=
"
-BDEPEND="${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
dev-python/astropy-helpers[${PYTHON_USEDEP}]
dev-python/extension-helpers[${PYTHON_USEDEP}]
dev-python/cython[${PYTHON_USEDEP}]
diff --git a/dev-python/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest
new file mode 100644
index 000000000..8d27c5f19
--- /dev/null
+++ b/dev-python/awkward-cpp/Manifest
@@ -0,0 +1 @@
+DIST awkward-cpp-28.tar.gz 1422514 BLAKE2B ec87c37a37e3aceb0a35b580122a8c632070dc9fd284e34de66db2611cf1024dbd7ec8a355f52349783258cdaa91e0f966156689c82427f72574230c8b6ae6e1 SHA512 bbe0df527a7863b192c3c85a90c1295d2eb788eb7670a04a001838294dcdd434b49bdc2b4c3f71e34f5f160b4b9cafdea1cf290206fdcb14c0555005797a666d
diff --git a/dev-python/awkward-cpp/awkward-cpp-28.ebuild b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
new file mode 100644
index 000000000..57634d120
--- /dev/null
+++ b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+DISTUTILS_USE_PEP517=scikit-build-core
+PYPI_NO_NORMALIZE=1
+
+inherit pypi distutils-r1
+
+DESCRIPTION="awkward-cpp bindings for Python"
+HOMEPAGE="https://github.com/scikit-hep/awkward/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ >=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward-cpp/metadata.xml b/dev-python/awkward-cpp/metadata.xml
new file mode 100644
index 000000000..a94e99f4b
--- /dev/null
+++ b/dev-python/awkward-cpp/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ awkward-cpp provides precompiled routines for the awkward package. It is not useful on its own, only as a dependency for awkward .
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">awkward</remote-id>
+ <remote-id type="github">scikit-hep/awkward</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/awkward/Manifest b/dev-python/awkward/Manifest
new file mode 100644
index 000000000..d3422fc99
--- /dev/null
+++ b/dev-python/awkward/Manifest
@@ -0,0 +1 @@
+DIST awkward-2.5.2.tar.gz 5561040 BLAKE2B 4799eeb25fa7433b4889328f9f147b435024c3f507ce66b5cbfcfc5b9c50e63f77131a43b8acd3d9f22d20915eaeb129162e26ffa83fd2071b9a393fbc441e7e SHA512 b6f4f2841e642bfc17aaf40779030d125e9737ef0ded20cc8a898c4b8c15c2932f12c8a0bda3e8c48bb8d13729cf97e181866f15913317bd2dba13b0dad6b929
diff --git a/dev-python/awkward/awkward-2.5.2.ebuild b/dev-python/awkward/awkward-2.5.2.ebuild
new file mode 100644
index 000000000..c11095214
--- /dev/null
+++ b/dev-python/awkward/awkward-2.5.2.ebuild
@@ -0,0 +1,38 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms."
+HOMEPAGE="https://github.com/scikit-hep/awkward"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+ ~dev-python/awkward-cpp-28[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+ dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}]
+ test? (
+ dev-libs/apache-arrow[zstd]
+ dev-python/pyarrow[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ dev-python/numexpr[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_IGNORE=(
+ tests-cuda/
+ tests-cuda-kernels/
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward/metadata.xml b/dev-python/awkward/metadata.xml
new file mode 100644
index 000000000..b3ac679d3
--- /dev/null
+++ b/dev-python/awkward/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Awkward Array is a library for nested, variable-sized data, including arbitrary-length lists, records, mixed types, and missing data, using NumPy-like idioms.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">awkward</remote-id>
+ <remote-id type="github">scikit-hep/awkward</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 0a0c64b4b..7347e5110 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -3,9 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 optfeature pypi
DESCRIPTION="Statistical and interactive HTML plots for Python"
diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest
new file mode 100644
index 000000000..1fb711744
--- /dev/null
+++ b/dev-python/boost-histogram/Manifest
@@ -0,0 +1 @@
+DIST boost_histogram-1.4.0.tar.gz 1329002 BLAKE2B 1636ed04c5df2f6c156468ffc0fed7b82469bb903c316b1b9fd209b7072ebb5b0de9969f4f8b50da69db7ee40009df534959db7734f1161da2c6216bddce858b SHA512 e7f61cc2d013a0664646d9edf1f713eb5f06f000ad2105e90229ef9b01b25a08c8e717a2ac241ed990fa2c082a1bb84af18e17b238640de5679d0ab76ff08af6
diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
new file mode 100644
index 000000000..96950ebe5
--- /dev/null
+++ b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
@@ -0,0 +1,39 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python bindings for the C++14 Boost::Histogram library"
+HOMEPAGE="https://github.com/scikit-hep/boost-histogram"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-libs/boost:=[python,${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ dev-python/cloudpickle[${PYTHON_USEDEP}]
+ dev-python/hypothesis[${PYTHON_USEDEP}]
+ )
+"
+
+src_prepare() {
+ default
+ sed -i 's/"pytest-benchmark"//g' pyproject.toml || die
+}
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ tests/test_benchmark_1d.py
+ tests/test_benchmark_2d.py
+ tests/test_benchmark_category_axis.py
+ tests/test_pickle.py
+ tests/test_threaded_fill.py
+)
diff --git a/dev-python/boost-histogram/metadata.xml b/dev-python/boost-histogram/metadata.xml
new file mode 100644
index 000000000..345502cba
--- /dev/null
+++ b/dev-python/boost-histogram/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Python bindings for Boost::Histogram (source), a C++14 library. This is one of the fastest libraries for histogramming, while still providing the power of a full histogram object. See what's new.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">boost-histogram</remote-id>
+ <remote-id type="github">scikit-hep/boost-histogram</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest
deleted file mode 100644
index 9b34bca41..000000000
--- a/dev-python/cadquery-ocp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
deleted file mode 100644
index 8a97782bd..000000000
--- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
+++ /dev/null
@@ -1,197 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
-inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
-
-MY_PN=OCP
-MY_PV="${PV//_/-}"
-MY_P="${MY_PN}-${MY_PV}"
-OCCT_PV=$(ver_cut 1-3)
-
-DESCRIPTION="Python wrapper for OCCT generated using pywrap"
-HOMEPAGE="https://github.com/CadQuery/OCP"
-SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-# Hard masking due to opencascade slot 0/7.5 having been removed from ::gentoo in ff9032e688571dde15e9d36cebedf5a247ded1b8
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-SLOT="0"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file
-# generated by the src_prepare() phase. OCP currently requires opencascade
-# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also:
-# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994
-BDEPEND="
- >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}]
- >=dev-util/cmake-3.16
-"
-RDEPEND="
- ${PYTHON_DEPS}
- sci-libs/opencascade:0/7.5[json,tbb,vtk]
- >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
-"
-DEPEND="${RDEPEND}
- $(python_gen_cond_dep '
- >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]')
-"
-
-S="${WORKDIR}/${MY_P}"
-
-# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare().
-CMAKE_IN_SOURCE_BUILD=True
-
-# Ensure the path returned by get_llvm_prefix() contains clang.
-llvm_check_deps() {
- has_version -r "sys-devel/clang:${LLVM_SLOT}"
-}
-
-cadquery-ocp_check_reqs() {
- CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE}
-}
-
-pkg_pretend() {
- cadquery-ocp_check_reqs
-}
-
-pkg_setup() {
- cadquery-ocp_check_reqs
- llvm_pkg_setup
- python-single-r1_pkg_setup
-}
-
-# OCP currently requires manual configuration, compilation, and installation
-# loosely inspired by the conda-specific "build-bindings-job.yml" file.
-#
-# Note that the cmake_src_prepare() function called below handles user patches.
-src_prepare() {
- # Most recently installed version of Clang.
- local _CLANG_VERSION="$(CPP=clang clang-fullversion)"
-
- # Most recently installed version (excluding trailing patch) of VTK.
- local _VTK_VERSION="$(best_version -r sci-libs/vtk)"
- _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")"
-
- # Absolute dirname of the most recently installed Clang include directory,
- # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also:
- # https://bugs.gentoo.org/619490
- local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include"
-
- # Absolute filename of the most recently installed Clang shared library.
- local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so"
-
- # Absolute dirname of OCCT's include and shared library directories.
- local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade"
- local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade"
-
- # Absolute dirname of a temporary directory to store symbol tables for this
- # OCCT version dumped below by the "dump_symbols.py" script.
- local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols"
- local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux"
-
- # Absolute dirname of VTK's include directory,
- local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}"
-
- # Ensure the above paths exist as a crude sanity test.
- test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found."
- test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found."
- test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found."
- test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found."
- test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found."
-
- # "dev-python/clang-python" atom targeting this Clang version.
- local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}"
-
- # Ensure "dev-python/clang-python" targets this Clang version.
- has_version -r "=${_CLANG_PYTHON_ATOM}" ||
- die "${_CLANG_PYTHON_ATOM} not installed."
-
- # Remove all vendored paths.
- rm -r conda opencascade pywrap *.dat || die
-
- # Inject a symlink to OCCT's include directory.
- ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die
-
- # Inject a symlink from OCCT's shared library directory into this temporary
- # directory as required by the "dump_symbols.py" script.
- mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die
- ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die
-
- # Update all hardcoded OCCT shared library versions in "dump_symbols.py".
- sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \
- dump_symbols.py || die
-
- # Dump (i.e., generate) symbol tables for this OCCT version.
- einfo 'Dumping OCCT symbol tables...'
- ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die
-
- # Generate OCCT bindings in the "OCP/" subdirectory.
- einfo 'Building OCP CMake binary tree...'
- ${EPYTHON} -m bindgen \
- --verbose \
- --njobs $(makeopts_jobs) \
- --libclang "${_CLANG_LIB_FILE}" \
- --include "${_CLANG_INCLUDE_DIR}" \
- --include "${_VTK_INCLUDE_DIR}" \
- all ocp.toml || die
-
- # Remove the source "FindOpenCascade.cmake" after generating bindings,
- # which copied that file to the target "OCP/FindOpenCascade.cmake".
- rm FindOpenCascade.cmake || die
-
- #FIXME: Submit an issue recommending upstream replace their
- #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level
- #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl
- # find_package(vtk 9 CONFIG REQUIRED)
- # if(TARGET VTK::VTK)
- # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES)
- # endif()
-
- # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with
- # standard OCCT paths derived above. That file is both fundamentally
- # broken and useless, as the ${CASROOT} environment variable and
- # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file
- # already reliably identify all requisite OpenCASCADE paths. Failure to
- # patch this file results in src_configure() failures resembling:
- # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES)
- sed -i \
- -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \
- -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \
- -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \
- OCP/FindOpenCascade.cmake || die
-
- # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed
- # as an absolute path both here and below to minimize eclass issues.
- CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -B "${S}/OCP.build"
- -DPYTHON_EXECUTABLE="${PYTHON}"
- -Wno-dev
- )
-
- CMAKE_USE_DIR="${S}/OCP" cmake_src_configure
-}
-
-src_compile() {
- CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile
-}
-
-# OCP currently ships no test suite, so we synthesize a crude import unit test.
-src_test() {
- PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \
- 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ'
-}
-
-src_install() {
- python_moduleinto .
- python_domodule "${S}/OCP.build/"OCP*.so
-}
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
deleted file mode 100644
index 4bccc9e86..000000000
--- a/dev-python/cadquery-pywrap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
deleted file mode 100644
index 7a3b772f3..000000000
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit llvm distutils-r1
-
-DESCRIPTION="C++ binding generator based on libclang and pybind11"
-HOMEPAGE="https://github.com/CadQuery/pywrap"
-
-#FIXME: Uncomment on bumping to the next stable release.
-# MY_PN=occt
-# MY_PV=$(ver_cut 1-2)
-# MY_P="${MY_PN}${MY_PV}"
-# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz"
-
-# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.3 has yet to be
-# officially released. We instead package a commit known to work as expected.
-MY_COMMIT="66e7376d3a27444393fc99acbdbef40bbc7031ae"
-SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-# Dependencies are intentionally listed in "setup.py" order.
-RDEPEND="
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path[${PYTHON_USEDEP}]
- dev-python/clang-python[${PYTHON_USEDEP}]
- dev-python/cymbal[${PYTHON_USEDEP}]
- dev-python/toml[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/toposort[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/pybind11[${PYTHON_USEDEP}]
- dev-python/schema[${PYTHON_USEDEP}]
- sci-libs/vtk
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/pywrap-${MY_COMMIT}"
-
-src_prepare() {
- #FIXME: Submit an upstream issue. This violates PEP 440 standards.
- # Sanitize the "bindgen" version to avoid Gentoo QA notices.
- sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die
-
- # Replace conda- with Gentoo-specific prefix dirnames.
- sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py ||
- die
-
- # Reduce all hardcoded header includes to noops.
- sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die
-
- distutils-r1_src_prepare
-}
diff --git a/dev-python/cadquery-pywrap/metadata.xml b/dev-python/cadquery-pywrap/metadata.xml
deleted file mode 100644
index aef989a0c..000000000
--- a/dev-python/cadquery-pywrap/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="github">CadQuery/pywrap</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest
deleted file mode 100644
index 2b4ddbec1..000000000
--- a/dev-python/cadquery/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
deleted file mode 100644
index 29edf6601..000000000
--- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_SINGLE_IMPL=1
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python parametric CAD scripting framework based on OCCT"
-HOMEPAGE="https://cadquery.readthedocs.io"
-
-# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but
-# CadQuery 2.2 has yet to be officially released. We instead package a commit
-# known to work as expected with OCCT 7.5.2.
-MY_COMMIT="803a05e78c233fdb537a8604c3f2b56a52179bbe"
-
-#FIXME: Uncomment on bumping to the next stable release.
-# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz"
-SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-# Hard masking since package depends on dev-python/cadquery-ocp, which depends on sci-libs/opencascade, which is no longer available from ::gentoo in the required slot.
-KEYWORDS=""
-#KEYWORDS="~amd64 ~x86"
-
-# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its
-# Anaconda focus, "setup.py" currently fails to list dependencies.
-BDEPEND="
- test? (
- $(python_gen_cond_dep '
- dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path[${PYTHON_USEDEP}]
- ')
- )
-"
-RDEPEND="
- >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
- >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}]
- dev-python/ezdxf[${PYTHON_USEDEP}]
- dev-python/ipython[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/nptyping[${PYTHON_USEDEP}]
- sci-libs/nlopt[python,${PYTHON_USEDEP}]
- dev-python/multimethod[${PYTHON_USEDEP}]
- dev-python/typish[${PYTHON_USEDEP}]
- ')
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-${MY_COMMIT}"
-
-distutils_enable_tests pytest
-
-#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints".
-# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints
diff --git a/dev-python/cadquery/metadata.xml b/dev-python/cadquery/metadata.xml
deleted file mode 100644
index 86166e277..000000000
--- a/dev-python/cadquery/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="github">CadQuery/cadquery</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
index 481ce2e7b..cdbe1c92c 100644
--- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild
+++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
@@ -28,7 +28,7 @@ RDEPEND="
>=dev-python/astropy-4.0.6[${PYTHON_USEDEP}]
>=dev-python/astroscrappy-1.0.8[${PYTHON_USEDEP}]
>=dev-python/reproject-0.7[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
diff --git a/dev-python/colormath/Manifest b/dev-python/colormath/Manifest
new file mode 100644
index 000000000..82abf9e32
--- /dev/null
+++ b/dev-python/colormath/Manifest
@@ -0,0 +1 @@
+DIST colormath-3.0.0.tar.gz 39761 BLAKE2B 3c7cdd08336a3ab35618a79ad31717433c08b23d8ee4fc5484da7305395fce61fa442fc9ff979ff107808c56e809deca9d176677f17106651047be14edc27e9e SHA512 12d1ab931000dadb087fdf7e56280690ff51a299e976347026703eac83373edcacd3310255fd52e05d842aab54d4f7d3ed19deda8db4b78574a7273f1c8cc058
diff --git a/dev-python/colormath/colormath-3.0.0.ebuild b/dev-python/colormath/colormath-3.0.0.ebuild
new file mode 100644
index 000000000..8bd5a2b02
--- /dev/null
+++ b/dev-python/colormath/colormath-3.0.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/colormath/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]"
+
+# Nose test no longer supported
+RESTRICT="test"
+#distutils_enable_tests nose
diff --git a/dev-python/colormath/metadata.xml b/dev-python/colormath/metadata.xml
new file mode 100644
index 000000000..a633acfa0
--- /dev/null
+++ b/dev-python/colormath/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">gtaylor/python-colormath</remote-id>
+ <remote-id type="pypi">colormath</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
index c33eb24f9..acdfa9d63 100644
--- a/dev-python/dandi-schema/Manifest
+++ b/dev-python/dandi-schema/Manifest
@@ -1,3 +1 @@
-DIST dandi-schema-0.7.1.gh.tar.gz 57312 BLAKE2B 5aa77c4c98633f82511a964f0b202b44acdb63e162cff62785f44fab64fdf97c04f10b10b3c1329ea7176d7ee1b12eeabd64d467d9646550b1db14b2fcc36a2b SHA512 04e0bf6caa9183cdac021430869be884ba8db207e7056a145ecac11858e9ecf051212cee10f5b4d501ca513838edc112dde014e256ab2256729c810d0c2c6cdf
-DIST dandi-schema-0.8.2.gh.tar.gz 57936 BLAKE2B 2ba355137196b805214e6c9321dd0b8dd9f5f1a39cf732aa3733b51a90f043d39a003e46620e1ec4bf77654cf21a7a45e9d888321b2ceb59f33a52c75db11597 SHA512 b792b5bdc6c51dc63ab796997e3b61cbb3ae3b0dbc5d1c55c51e1c879d1a694e3fc6a89640ac26909399bc63a2a3480c7ef630952cac44a3bb5a27d7fe11d09e
-DIST dandi-schema-0.8.3.gh.tar.gz 58040 BLAKE2B 03313fa126eb8805b72de6431e7cb1489aeb54f7415c4ee0899f012881147dd612d2736f27df4c4e314951b589d4167bda17a5144d7346b6371ed3e7160aa50f SHA512 4e9ed27a773e8609a16d841c5c3876026fa1ab6fccb688f6477e1c95f3da72bc99f7bb987799da69948036f0922ed33ed7c096bdc5be6c59b9a74a266ffd47b2
+DIST dandi-schema-0.9.1.gh.tar.gz 61794 BLAKE2B f18dda919dad9a685793d075e54c798fd9a0d68926b776f1f5617d414554fed7609684dab3311d35056f385443037f03ab16f7edfb7b57c33f9da1aed9c8016c SHA512 c6ed9763a5a77b8741063ef5f311a889e7e0ba2ef02ab97e2912e1a129da503453d9ccb1b9ed13726f071594af42e564986ef9298b21c07cff6ef48eb3f58fc1
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
deleted file mode 100644
index 6f026c947..000000000
--- a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="Schemata for DANDI archive project"
-HOMEPAGE="https://github.com/dandi/dandi-schema"
-SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
- dev-python/email-validator[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.3.4-coverage.patch"
-)
-
-src_configure() {
- echo "__version__ = '${PV}'" >> dandischema/_version.py
-}
-
-distutils_enable_tests pytest
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
-}
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild
deleted file mode 100644
index 6f026c947..000000000
--- a/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="Schemata for DANDI archive project"
-HOMEPAGE="https://github.com/dandi/dandi-schema"
-SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
- dev-python/email-validator[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.3.4-coverage.patch"
-)
-
-src_configure() {
- echo "__version__ = '${PV}'" >> dandischema/_version.py
-}
-
-distutils_enable_tests pytest
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
-}
diff --git a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
index 6f026c947..0e7986806 100644
--- a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1
@@ -16,27 +16,34 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+# Package has pydantic version restriction (2.4*), which, however, breaks the test suite:
+# https://github.com/dandi/dandi-schema/issues/228
+# Commented failing tests with upstream version restriction listed below.
RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-2.5[${PYTHON_USEDEP}]
dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+ "${FILESDIR}/${P}-coverage.patch"
)
src_configure() {
echo "__version__ = '${PV}'" >> dandischema/_version.py
}
+#EPYTEST_DESELECT=(
+# "dandischema/tests/test_metadata.py::test_asset"
+# "dandischema/tests/test_metadata.py::test_aggregate[files1-summary1]"
+# "dandischema/tests/test_metadata.py::test_aggregate[files2-summary2]"
+#)
+
distutils_enable_tests pytest
python_test() {
export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
+ epytest dandischema
}
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
deleted file mode 100644
index 589091756..000000000
--- a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/setup.py 2021-09-22 19:31:20.533576086 -0400
-+++ b/setup.py 2021-09-23 07:42:02.856983656 -0400
-@@ -21,7 +21,7 @@
-
- # Give setuptools a hint to complain if it's too old a version
- # Should match pyproject.toml
--SETUP_REQUIRES = ["setuptools >= 42.0.0", "versioningit ~= 0.1.0"]
-+SETUP_REQUIRES = ["setuptools >= 42.0.0"]
- # This enables setuptools to install wheel on-the-fly
- SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
new file mode 100644
index 000000000..7f9b7dba0
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
@@ -0,0 +1,13 @@
+diff --git a/tox.ini b/tox.ini
+index c32f3b9..d552c6c 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -30,7 +30,7 @@ commands =
+ mypy dandischema
+
+ [pytest]
+-addopts = --cov=dandischema --tb=short --durations=10
++addopts = --tb=short --durations=10
+ filterwarnings =
+ error
+ # <https://github.com/dateutil/dateutil/issues/1284>
diff --git a/dev-python/docstring-parser/Manifest b/dev-python/docstring-parser/Manifest
new file mode 100644
index 000000000..9f508a4f7
--- /dev/null
+++ b/dev-python/docstring-parser/Manifest
@@ -0,0 +1 @@
+DIST docstring_parser-0.16.tar.gz 26565 BLAKE2B 3785bc9176bc06624a43c50a147c3143e344b8093b9c2db90ab49baed807d598a3538344f79a3da7515c16fc2afc90813e26a3a8f3aa5deb6bc2bf1554303d2e SHA512 6bda195f0e60173c9e78f300a05f8ab2d51ec37848c6f3eddccf889f01abc7dd00b1987028bc59058056e2ab4a50e4631d4d0ec10e54180178372001d65c431f
diff --git a/dev-python/docstring-parser/docstring-parser-0.16.ebuild b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
new file mode 100644
index 000000000..1d82de77c
--- /dev/null
+++ b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Parse Python docstrings in various flavors"
+HOMEPAGE="https://github.com/rr-/docstring_parser"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/tridesclous/metadata.xml b/dev-python/docstring-parser/metadata.xml
index 819340cd1..140ee785a 100644
--- a/dev-python/tridesclous/metadata.xml
+++ b/dev-python/docstring-parser/metadata.xml
@@ -10,7 +10,7 @@
<name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="github">tridesclous/tridesclous</remote-id>
- <remote-id type="pypi">tridesclous</remote-id>
+ <remote-id type="pypi">docstring-parser</remote-id>
+ <remote-id type="github">rr-/docstring_parser</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
index 65526b110..4ef429b97 100644
--- a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
+++ b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -21,7 +21,7 @@ BDEPEND="
dev-python/scikit-build[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
dev-vcs/git
sys-devel/DPC++
"
diff --git a/dev-python/dpctl/dpctl-0.14.5.ebuild b/dev-python/dpctl/dpctl-0.14.5.ebuild
index 65526b110..4ef429b97 100644
--- a/dev-python/dpctl/dpctl-0.14.5.ebuild
+++ b/dev-python/dpctl/dpctl-0.14.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -21,7 +21,7 @@ BDEPEND="
dev-python/scikit-build[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
dev-vcs/git
sys-devel/DPC++
"
diff --git a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
deleted file mode 100644
index b7dab5c75..000000000
--- a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 23ae1dd..e144e90 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -26,15 +26,7 @@ install(FILES ${_dpctl_capi_headers}
- # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
- include(GNUInstallDirs)
-
--# Fetch pybind11
--include(FetchContent)
--
--FetchContent_Declare(
-- pybind11
-- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.9.2.tar.gz
-- URL_HASH SHA256=6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1
--)
--FetchContent_MakeAvailable(pybind11)
-+include(/usr/share/cmake/pybind11/pybind11Config.cmake)
-
- add_subdirectory(dpctl)
-
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
deleted file mode 100644
index ac0301886..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-index 2929c33..731f054 100644
---- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-+++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-@@ -26,76 +26,10 @@
-
- function(get_level_zero_headers)
-
-- if(EXISTS level-zero)
-- # Update the checkout
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} fetch
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not update Level Zero sources."
-- )
-- endif()
-- else()
-- # Clone the Level Zero git repo
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero."
-- )
-- endif()
-- endif()
--
-- # Use git describe to get latest tag name
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0
-- RESULT_VARIABLE result
-- OUTPUT_VARIABLE latest_tag
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not get the name for the latest release."
-- )
-- endif()
--
-- # Use git describe to get latest tag name
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag}
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not checkout the latest release."
-- )
-- endif()
--
- # Populate the path to the headers
- find_path(LEVEL_ZERO_INCLUDE_DIR
- NAMES zet_api.h
-- PATHS ${CMAKE_BINARY_DIR}/level-zero/include
-+ PATHS /usr/include/level_zero
- NO_DEFAULT_PATH
- NO_CMAKE_ENVIRONMENT_PATH
- NO_CMAKE_PATH
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
deleted file mode 100644
index b2b8c5d81..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index da138c1..ecab139 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -28,15 +28,7 @@ install(FILES ${_dpctl_capi_headers}
- # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
- include(GNUInstallDirs)
-
--# Fetch pybind11
--include(FetchContent)
--
--FetchContent_Declare(
-- pybind11
-- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.1.tar.gz
-- URL_HASH SHA256=111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad
--)
--FetchContent_MakeAvailable(pybind11)
-+include(/usr/share/cmake/pybind11/pybind11Config.cmake)
-
- add_subdirectory(dpctl)
-
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
deleted file mode 100644
index 44b950cb6..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From d0d3e6f1a9ffbac91f24cc06abce6dcad6509a6b Mon Sep 17 00:00:00 2001
-From: Julien Jerphanion <git@jjerphan.xyz>
-Date: Tue, 6 Dec 2022 10:24:26 +0100
-Subject: [PATCH 1/2] MAINT Include tuple in 'utils/strided_iters.hpp'
-
-This include directive seems to have been forgotten and it is impossible
-for me to compile dpctl without it.
----
- dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-index c24ed54941..595ad3f4a7 100644
---- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-+++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-@@ -30,6 +30,7 @@
- #include <array>
- #include <numeric> // std::iota
- #include <vector>
-+#include <tuple>
-
- /* An N-dimensional array can be stored in a single
- * contiguous chunk of memory by contiguously laying
-
-From f75ccd8c8aeaae92f0cb03874f93be5e7a63a6a7 Mon Sep 17 00:00:00 2001
-From: Julien Jerphanion <git@jjerphan.xyz>
-Date: Tue, 6 Dec 2022 14:45:40 +0100
-Subject: [PATCH 2/2] Make clang-format happy
-
----
- dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-index 595ad3f4a7..0abd7f4f2a 100644
---- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-+++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-@@ -29,8 +29,8 @@
- #include <algorithm> // sort
- #include <array>
- #include <numeric> // std::iota
--#include <vector>
- #include <tuple>
-+#include <vector>
-
- /* An N-dimensional array can be stored in a single
- * contiguous chunk of memory by contiguously laying
diff --git a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
index 5443b2dfd..5d25d62d1 100644
--- a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
+++ b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
# Breaks library installation
#DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -19,7 +19,7 @@ KEYWORDS="~amd64"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
sys-devel/DPC++
"
diff --git a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
deleted file mode 100644
index deaa95d0b..000000000
--- a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-diff --git a/0.build.sh b/0.build.sh
-index c089b1d..3bb0739 100755
---- a/0.build.sh
-+++ b/0.build.sh
-@@ -10,14 +10,14 @@ python setup.py clean
- DPLROOT=/opt/intel/oneapi/dpl/latest python setup.py build_clib
-
- # inplace build
--CC=dpcpp python setup.py build_ext --inplace
-+CC=${CC} python setup.py build_ext --inplace
-
- # development build. Root privileges needed
- # python setup.py develop
-
- echo
- echo =========example3==============
--dpcpp -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
-+${CXX} -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
- # LD_DEBUG=libs,bindings,symbols ./example3
- ./example3
-
-diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
-index 81f073c..bcc4ecc 100644
---- a/dpnp/backend/CMakeLists.txt
-+++ b/dpnp/backend/CMakeLists.txt
-@@ -88,24 +88,6 @@ if (CMAKE_VERSION VERSION_EQUAL 3.19.1)
- )
- endif()
-
--if(UNIX)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # add_compile_options(-fPIC)
--elseif(WIN32)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
-- # set(CMAKE_LINKER "lld-link")
-- # include (Platform/Windows-Clang)
-- # set(CMAKE_LINKER "dpcpp")
-- # set(CMAKE_AR "llvm-ar")
-- # set(CMAKE_RANLIB "llvm-ranlib")
-- # set(CMAKE_CXX_FLAGS "/EHsc")
--
-- add_compile_options(/EHsc) # /Ox /W3 /GL /DNDEBUG /MD /EHsc
--else()
-- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
--endif()
--
- # set language version
- set(CMAKE_CXX_STANDARD 17)
- set(CMAKE_CXX_STANDARD_REQUIRED ON)
-@@ -280,6 +262,7 @@ endif()
- # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
-
- install(TARGETS dpnp_backend_c
-+ DESTINATION ${DPNP_INSTALL_PREFIX}
- PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
- )
-
-diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
-index dc9f322..35432fa 100644
---- a/utils/command_build_clib.py
-+++ b/utils/command_build_clib.py
-@@ -60,8 +60,8 @@ else:
- Set compiler for the project
- """
- # default variables (for Linux)
--_project_compiler = "dpcpp"
--_project_linker = "dpcpp"
-+_project_compiler = os.environ.get("CXX")
-+_project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel"]
- _project_cmplr_flag_sycl = ["-fsycl"]
- _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
-@@ -113,8 +113,8 @@ except ImportError:
-
- # other OS specific
- if IS_WIN:
-- _project_compiler = "dpcpp"
-- _project_linker = "lld-link"
-+ _project_compiler = os.environ.get("CXX")
-+ _project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl = []
- _project_cmplr_flag_stdcpp_static = []
- _project_cmplr_flag_compatibility = []
-diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
-index 0ef0e24..84f2469 100644
---- a/utils/command_build_cmake_clib.py
-+++ b/utils/command_build_cmake_clib.py
-@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
- "-S" + backend_directory,
- "-B" + abs_build_temp_path,
- "-DCMAKE_BUILD_TYPE=" + config,
-- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
-+ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
- "-DDPNP_INSTALL_STRUCTURED=OFF",
- # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
- "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
deleted file mode 100644
index 2ccc0a6b8..000000000
--- a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
-index 409a29f..11d21f1 100644
---- a/dpnp/backend/CMakeLists.txt
-+++ b/dpnp/backend/CMakeLists.txt
-@@ -98,30 +98,7 @@ string(CONCAT COMMON_LINK_FLAGS
- "-fsycl "
- "-fsycl-device-code-split=per_kernel "
- )
--if(UNIX)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # add_compile_options(-fPIC)
--elseif(WIN32)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
-- # set(CMAKE_LINKER "lld-link")
-- # include (Platform/Windows-Clang)
-- # set(CMAKE_LINKER "dpcpp")
-- # set(CMAKE_AR "llvm-ar")
-- # set(CMAKE_RANLIB "llvm-ranlib")
-- # set(CMAKE_CXX_FLAGS "/EHsc")
-
-- string(APPEND COMMON_COMPILER_FLAGS
-- "/EHsc "
--# "/Ox "
--# "/W3 "
--# "/GL "
--# "/DNDEBUG "
--# "/MD "
-- )
--else()
-- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
--endif()
-
- # set language version
- set(CMAKE_CXX_STANDARD 17)
-@@ -327,6 +304,7 @@ endif()
- # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
-
- install(TARGETS dpnp_backend_c
-+ DESTINATION ${DPNP_INSTALL_PREFIX}
- PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
- )
-
-diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
-index 3d1177b..d8fbdac 100644
---- a/utils/command_build_clib.py
-+++ b/utils/command_build_clib.py
-@@ -61,8 +61,8 @@ else:
- Set compiler for the project
- """
- # default variables (for Linux)
--_project_compiler = "dpcpp"
--_project_linker = "dpcpp"
-+_project_compiler = os.environ.get("CXX")
-+_project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func"]
- _project_cmplr_flag_sycl = ["-fsycl"]
- _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
-@@ -114,7 +114,7 @@ except ImportError:
-
- # other OS specific
- if IS_WIN:
-- _project_compiler = "dpcpp"
-+ _project_compiler = os.environ.get("CXX")
- _project_linker = "lld-link"
- _project_cmplr_flag_sycl = []
- _project_cmplr_flag_stdcpp_static = []
-diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
-index 0ef0e24..84f2469 100644
---- a/utils/command_build_cmake_clib.py
-+++ b/utils/command_build_cmake_clib.py
-@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
- "-S" + backend_directory,
- "-B" + abs_build_temp_path,
- "-DCMAKE_BUILD_TYPE=" + config,
-- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
-+ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
- "-DDPNP_INSTALL_STRUCTURED=OFF",
- # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
- "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch b/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch
deleted file mode 100644
index 3de6d92f1..000000000
--- a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/setup.cfg b/setup.cfg
-index 9ea1ddb..00eb59b 100644
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -18,8 +18,8 @@ markers =
-
-
- testpaths = tests
--addopts = -v --niters=50 --cov=fsl -m "not longtest"
-+addopts = -v --niters=50 -m "not longtest"
-
-
- [flake8]
--ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
-\ No newline at end of file
-+ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
diff --git a/dev-python/gammapy/gammapy-1.0.ebuild b/dev-python/gammapy/gammapy-1.0.ebuild
index ab50e7a85..6357014ed 100644
--- a/dev-python/gammapy/gammapy-1.0.ebuild
+++ b/dev-python/gammapy/gammapy-1.0.ebuild
@@ -47,7 +47,7 @@ pkg_postinst() {
optfeature "Plotting" dev-python/matplotlib
optfeature "Plotting Astronomical Images" dev-python/aplpy
optfeature "Read/write CVS files" dev-python/pandas
- optfeature "Image Processing" sci-libs/scikit-image
+ optfeature "Image Processing" dev-python/scikit-image
optfeature "Conversion helper functions" dev-python/rootpy
# In science overlay:
diff --git a/dev-python/hdmf-zarr/Manifest b/dev-python/hdmf-zarr/Manifest
new file mode 100644
index 000000000..6b7d2418b
--- /dev/null
+++ b/dev-python/hdmf-zarr/Manifest
@@ -0,0 +1 @@
+DIST hdmf_zarr-0.5.0.tar.gz 3095566 BLAKE2B f824b480bb99ffbf495b18505d561a3511af60f654df66f89c2c5c081ba49889512e29cb31b6eb617ef7abac58472fa4b6d9f23cd9c33be436a77ceb2d54130a SHA512 205dd5b2de1a403fc7098e7ba26e4bbba1949b8f50641173ea614011e821a77a461ab255f19afefddcd5fa019ed0e7c047fd7c940a2d09a1f63c5de5f1ac50cb
diff --git a/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
new file mode 100644
index 000000000..d82c30960
--- /dev/null
+++ b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
@@ -0,0 +1,28 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 4008b3b..40e281a 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -62,9 +62,6 @@ exclude = [".git_archival.txt"]
+ [tool.hatch.build.targets.wheel]
+ packages = ["src/hdmf_zarr"]
+
+-[tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+-
+ [tool.codespell]
+ skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
+ ignore-words-list = "datas"
+diff --git a/tox.ini b/tox.ini
+index 720a97f..66d0df3 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -28,8 +28,7 @@ commands =
+ [testenv:localcoverage]
+ basepython = python3.11
+ commands =
+- pytest --cov=hdmf_zarr
+- coverage html -d tests/coverage/htmlcov
++ pytest
+
+ # Test with python 3.11; pinned dev and optional reqs
+ [testenv:py311-optional]
diff --git a/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
new file mode 100644
index 000000000..692197867
--- /dev/null
+++ b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Zarr I/O backend for HDMF"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf-zarr"
+#SRC_URI="https://github.com/hdmf-dev/hdmf-zarr/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/numcodecs[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/numba/metadata.xml b/dev-python/hdmf-zarr/metadata.xml
index 63bc398e0..1ced471a1 100644
--- a/dev-python/numba/metadata.xml
+++ b/dev-python/hdmf-zarr/metadata.xml
@@ -2,15 +2,15 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
</maintainer>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="github">numba/numba</remote-id>
- <remote-id type="pypi">numba</remote-id>
+ <remote-id type="github">hdmf-dev/hdmf-zarr</remote-id>
+ <remote-id type="pypi">hdmf-zarr</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest
index a8bb51f14..204753b4e 100644
--- a/dev-python/hdmf/Manifest
+++ b/dev-python/hdmf/Manifest
@@ -1,4 +1 @@
-DIST hdmf-3.4.7.tar.gz 319714 BLAKE2B 189b7629b818371bea002f4c340149e5807a5da9e2b27301574b74c50eda575b711ffbffac997ee2c2d25c30c926ada13d84319e054bf796e5bd74516d84be21 SHA512 c5b6b9dfeace0ea140bcd2cf822f9b45007ea7acefd6eca950b4b023731e31b8ebc592da0e3633e41a41e377a33565f6f5c04a88852a190816c95e89b49efa02
-DIST hdmf-3.5.0.tar.gz 324330 BLAKE2B 256fd974230fb750c5329fbf2cece0f151b6d7366aea26ffd08bafff0601ba6fde789dc906f4de5dbb1a02e9a0d21965a17eda76083df03d3a3afdacf9a7ba70 SHA512 8e1244f70c75f01d18d2d09b6c481efcab59bd02e69392f3da46d2e4541073fccaa9606907cee1ca0873221011e9ce8040668f2affd2ef4ee98fd35bd6356ff4
-DIST hdmf-3.5.1.tar.gz 324778 BLAKE2B b82d2389466be8e8b4acd843beaafe69b731a38045abab0a741fb7a6143e8ed8f60d570603629c7485f7f7a261047bcc9e21ebeb61802e6d81b35aa276d09af0 SHA512 1545f0c1c6b2bac66437941e631adaa45a42c18436ed68d5ee21a7cafe950a85e2843a4b2258b3f5c0ece5fd6d3ef6f0fd596a83bacd208750bfb5b78a1d5815
-DIST hdmf-3.5.2.tar.gz 567466 BLAKE2B 99872885aec1b0aff30dfde17cc3c2f5f30e9da7f3ac5aa77dad203fe795ad6c207bdafd6d19548bf8c3f901a1ec8655b048d9ba41be11eaca3a7c55e6de2825 SHA512 47f8de397fe3defe814db3da7f2bf7ec3814bf3a1d9389c6fe823e229ddea441c97122e41a11883f1c7b5968a841d8fdd0c7314e9d82d4e5ea43a713a40afbfa
+DIST hdmf-3.13.0.tar.gz 15855926 BLAKE2B 8eb386540768a83954745c02f7142d2a0b466ef670baaf13a1dfee0ce02261f0f89a9b173dfb8d2673d1f538c35e800117f6f0fe2ca77e5ca6a94b01e9908917 SHA512 5d6f97abb28b46136b3a62f915f8c14cc48e49c1ec3d44e3d863b1c3e7aebb1cfea428b77311ca51dbf5ef9a1e529e73cdb477d863e3d0cd6641fbf79a043f20
diff --git a/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
new file mode 100644
index 000000000..e44a68902
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
@@ -0,0 +1,10 @@
+--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml 2023-12-11 12:00:19.368474488 -0500
+@@ -76,7 +76,6 @@
+ # verbose = 1
+
+ [tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+ norecursedirs = "tests/unit/helpers"
+
+ [tool.codespell]
diff --git a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
deleted file mode 100644
index aaf62e115..000000000
--- a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/setup.py 2022-01-31 02:48:24.645837186 -0500
-+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
-@@ -18,12 +18,12 @@
- schema_dir = 'common/hdmf-common-schema/common'
-
- reqs = [
-- 'h5py>=2.10,<4',
-- 'jsonschema>=2.6.0,<5',
-- 'numpy>=1.16,<1.23',
-- 'pandas>=1.0.5,<2',
-- 'ruamel.yaml>=0.16,<1',
-- 'scipy>=1.1,<2',
-+ 'h5py',
-+ 'jsonschema',
-+ 'numpy',
-+ 'pandas',
-+ 'ruamel.yaml',
-+ 'scipy',
- 'setuptools',
- ]
diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
deleted file mode 100644
index 544bf8f4b..000000000
--- a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
+++ /dev/null
@@ -1,170 +0,0 @@
-From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 16:05:57 -0800
-Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to
- clsoe links
-
----
- src/hdmf/backends/hdf5/h5tools.py | 13 +++++++++----
- 1 file changed, 9 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index ba8946c60..acf2061ad 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -746,10 +746,15 @@ def close_linked_files(self):
- not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened,
- linked-to files.
- """
-- for obj in self.__open_links:
-- if obj:
-- obj.file.close()
-- self.__open_links = []
-+ # Make sure
-+ try:
-+ for obj in self.__open_links:
-+ if obj:
-+ obj.file.close()
-+ except AttributeError: # In case that self.__open_links does not exist on delete
-+ pass
-+ finally:
-+ self.__open_links = []
-
- @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the HDF5 file'},
- {'name': 'link_data', 'type': bool,
-
-From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 17:32:20 -0800
-Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error
-
----
- src/hdmf/backends/hdf5/h5tools.py | 19 +++++++++++++++----
- 1 file changed, 15 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index acf2061ad..75044a64a 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -736,8 +736,15 @@ def close(self, close_links=True):
- """
- if close_links:
- self.close_linked_files()
-- if self.__file is not None:
-- self.__file.close()
-+ try:
-+ if self.__file is not None:
-+ self.__file.close()
-+ except AttributeError:
-+ # Do not do anything in case that self._file does not exist. This
-+ # may happen in case that an error occurs before HDF5IO has been fully
-+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
-+ # and error before self.__file has been created
-+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__file")
-
- def close_linked_files(self):
- """Close all opened, linked-to files.
-@@ -751,8 +758,12 @@ def close_linked_files(self):
- for obj in self.__open_links:
- if obj:
- obj.file.close()
-- except AttributeError: # In case that self.__open_links does not exist on delete
-- pass
-+ except AttributeError:
-+ # Do not do anything in case that self.__open_links does not exist. This
-+ # may happen in case that an error occurs before HDF5IO has been fully
-+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
-+ # and error before self.__open_links has been created.
-+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__open_links.")
- finally:
- self.__open_links = []
-
-
-From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 17:32:55 -0800
-Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called
- before HDF5IO.__init__ is complete
-
----
- tests/unit/test_io_hdf5_h5tools.py | 34 ++++++++++++++++++++++++++++++
- 1 file changed, 34 insertions(+)
-
-diff --git a/tests/unit/test_io_hdf5_h5tools.py b/tests/unit/test_io_hdf5_h5tools.py
-index 8c03e72f8..0f2f81e31 100644
---- a/tests/unit/test_io_hdf5_h5tools.py
-+++ b/tests/unit/test_io_hdf5_h5tools.py
-@@ -826,6 +826,40 @@ def test_constructor(self):
- self.assertEqual(io.manager, self.manager)
- self.assertEqual(io.source, self.path)
-
-+ def test_delete_with_incomplete_construction_missing_file(self):
-+ """
-+ Here we test what happens when close is called before HDF5IO.__init__ has
-+ bee completed. In this case self.__file is missing
-+ """
-+ class MyHDF5IO(HDF5IO):
-+ def __init__(self):
-+ raise ValueError("test error")
-+ with self.assertWarnsWith(warn_type=UserWarning,
-+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__file"):
-+ try:
-+ with MyHDF5IO() as _:
-+ pass
-+ except ValueError:
-+ pass
-+
-+ def test_delete_with_incomplete_construction_missing_open_files(self):
-+ """
-+ Here we test what happens when close is called before HDF5IO.__init__ has
-+ bee completed. In this case self.__open_file is missing
-+ """
-+
-+ class MyHDF5IO(HDF5IO):
-+ def __init__(self):
-+ raise ValueError("test error")
-+
-+ with self.assertWarnsWith(warn_type=UserWarning,
-+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__open_links."):
-+ try:
-+ with MyHDF5IO() as _:
-+ pass
-+ except ValueError:
-+ pass
-+
- def test_set_file_mismatch(self):
- self.file_obj = File(get_temp_filepath(), 'w')
- err_msg = ("You argued %s as this object's path, but supplied a file with filename: %s"
-
-From f79b3a26bdfaee22b8d24bd3094c93be77e5595f Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Thu, 19 Jan 2023 13:54:33 -0800
-Subject: [PATCH 5/5] Move init of __file and __openlink up to prevent warning
- during close
-
----
- src/hdmf/backends/hdf5/h5tools.py | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index 75044a64a..44b9c612c 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -55,6 +55,9 @@ def __init__(self, **kwargs):
- path, manager, mode, comm, file_obj, driver = popargs('path', 'manager', 'mode', 'comm', 'file', 'driver',
- kwargs)
-
-+ self.__open_links = [] # keep track of other files opened from links in this file
-+ self.__file = None # This will be set below, but set to None first in case an error occurs and we need to close
-+
- if path is None and file_obj is None:
- raise ValueError("You must supply either a path or a file.")
-
-@@ -89,7 +92,6 @@ def __init__(self, **kwargs):
- self.__dci_queue = HDF5IODataChunkIteratorQueue() # a queue of DataChunkIterators that need to be exhausted
- ObjectMapper.no_convert(Dataset)
- self._written_builders = WriteStatusTracker() # track which builders were written (or read) by this IO object
-- self.__open_links = [] # keep track of other files opened from links in this file
-
- @property
- def comm(self):
diff --git a/dev-python/hdmf/hdmf-3.5.2.ebuild b/dev-python/hdmf/hdmf-3.13.0.ebuild
index ee978516e..7068afb01 100644
--- a/dev-python/hdmf/hdmf-3.5.2.ebuild
+++ b/dev-python/hdmf/hdmf-3.13.0.ebuild
@@ -3,14 +3,13 @@
EAPI=8
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1 pypi
DESCRIPTION="The Hierarchical Data Modeling Framework"
HOMEPAGE="https://github.com/hdmf-dev/hdmf"
SRC_URI="$(pypi_sdist_url hdmf)"
-#SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
@@ -24,6 +23,9 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
-BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${PN}-3.11.0-no_test_coverage.patch"
+ )
distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild b/dev-python/hdmf/hdmf-3.4.7.ebuild
deleted file mode 100644
index 883b5b95b..000000000
--- a/dev-python/hdmf/hdmf-3.4.7.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf"
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
deleted file mode 100644
index 053831f8d..000000000
--- a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-MY_PV="${PV//_p*/}"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf"
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${MY_PV}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${MY_P}-open_links.patch"
-)
-
-distutils_enable_tests pytest
-
-S="${WORKDIR}/${MY_P}"
diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild b/dev-python/hdmf/hdmf-3.5.1.ebuild
deleted file mode 100644
index 883b5b95b..000000000
--- a/dev-python/hdmf/hdmf-3.5.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf"
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest
index e3afb5ed5..fe38a3307 100644
--- a/dev-python/heudiconv/Manifest
+++ b/dev-python/heudiconv/Manifest
@@ -1,2 +1,2 @@
-DIST heudiconv-0.11.6.tar.gz 9070519 BLAKE2B df6c66080bbaa89f74490f136674eabd64e9b2844ae7daef82ef4b4ef8c42ed16d3ae3b790534cc13ec121e63de8486838eb7e7becbcdbffff2df6e8bd2bd54c SHA512 c4d1f0caaed9713360ad2614bc276f2cc0e356c54b1b37c8912d762db429313c75d0f081886cb6ea0b8fd171bc5fc5a338fd3b670a8b10a3fbed0c6f9dfb7477
DIST heudiconv-0.13.0.tar.gz 9158053 BLAKE2B 9f87fbcd5ea8ccca39cc029f1bdd84906412a22e5d18e2afe280d19737f0dda4c03248ba93f58c06aae4b15366477e8a5d1c41d09d1b1d3a10ff673aaa050e26 SHA512 b867ee0a60ad98099a3802e290ebb24b858befbd45e93772fafe437a87ea867c5076680ea3ed7856272397267c740ef2eade9f64ffc0d4216d4a37be39add158
+DIST heudiconv-1.0.0.tar.gz 9158631 BLAKE2B af5b3dee2448a025a231fad0ac9692b13d431288ea0ca19b4919d9ae83c86a7c72cf11f9bd3a0ec6b18259d2f8e8cecf9372a0fae605ecb5e9cac0bd4975693a SHA512 165bd814e3c7f25b51ed8884bddde45b82dc226ee93af5984b822aa53ad5e7504aae57088cd1f777c62835669e8816d95dbf84de7fb379038308dca7871d8739
diff --git a/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch b/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch
deleted file mode 100644
index 23be6d000..000000000
--- a/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From 0c30781248e0c1f2d437e0dfd923a74d7e647411 Mon Sep 17 00:00:00 2001
-From: Horea Christian <chr@chymera.eu>
-Date: Wed, 1 Feb 2023 21:34:58 -0500
-Subject: [PATCH] Setting git author and email in test environment
-
----
- heudiconv/tests/conftest.py | 3 +++
- 1 file changed, 3 insertions(+)
- create mode 100644 heudiconv/tests/conftest.py
-
-diff --git /dev/null b/heudiconv/tests/conftest.py
-new file mode 100644
-index 00000000..f4f47d16
---- /dev/null
-+++ b/heudiconv/tests/conftest.py
-@@ -0,0 +1,8 @@
-+import os
-+import pytest
-+@pytest.fixture(autouse=True, scope="session")
-+def git_env():
-+ os.environ["GIT_AUTHOR_EMAIL"] = "maxm@example.com"
-+ os.environ["GIT_AUTHOR_NAME"] = "Max Mustermann"
-+ os.environ["GIT_COMMITTER_EMAIL"] = "maxm@example.com"
-+ os.environ["GIT_COMMITTER_NAME"] = "Max Mustermann"
diff --git a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
index 8dbfcfa0f..7f7db0b0e 100644
--- a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild
+++ b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
@@ -33,12 +33,6 @@ BDEPEND="
)
"
-# Patch sumbitted upstream, check if removal possible in next release:
-# https://github.com/nipy/heudiconv/pull/631
-PATCHES=(
- "${FILESDIR}/${P}-gitenv.patch"
-)
-
# Reported upstream:
# https://github.com/nipy/heudiconv/issues/679
EPYTEST_DESELECT=(
diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild
index 783d9b1cb..154b7195d 100644
--- a/dev-python/holoviews/holoviews-1.15.3.ebuild
+++ b/dev-python/holoviews/holoviews-1.15.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
@@ -15,7 +15,7 @@ HOMEPAGE="https://holoviews.org"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Reported upstream:
# https://github.com/holoviz/holoviews/issues/5592
RESTRICT="test"
diff --git a/dev-python/jacobi/Manifest b/dev-python/jacobi/Manifest
new file mode 100644
index 000000000..be04d75f2
--- /dev/null
+++ b/dev-python/jacobi/Manifest
@@ -0,0 +1,2 @@
+DIST jacobi-0.8.1.tar.gz 997020 BLAKE2B ba54654e8a202976242674afa79de06d486d03c6d78b5566711df7df4ddcf5bbaa0e536eb9feeb0b0d6aaa9a444f677dfbbfa9928e38431aa9377c97132d4a26 SHA512 4a9a280cfae81926563c9736bf1805a3fe379809fe51421bdd0659651008d07d9f772df5006a1b796959311956822839791289eacb03af39823dd5a671b3845a
+DIST jacobi-0.9.2.tar.gz 998268 BLAKE2B 93ed0a03e8984143229929d04dd7b166c71bf10e98b98d396c58a5cea556b2b8da7977538a419cfbff26a5f681885df2f952a7aef98822dea885b408e12033a7 SHA512 ef91d8aceab8823913820c46e33db43a3daba90bfacf640167987cd92006c4b253ec17166fc1750902afec69385d35559fede17a8ed227dab582f1490711bff1
diff --git a/dev-python/jacobi/jacobi-0.8.1.ebuild b/dev-python/jacobi/jacobi-0.8.1.ebuild
new file mode 100644
index 000000000..93afcbf16
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.8.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ tests/bench.py
+)
+
diff --git a/dev-python/jacobi/jacobi-0.9.2.ebuild b/dev-python/jacobi/jacobi-0.9.2.ebuild
new file mode 100644
index 000000000..806967a38
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.9.2.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/bench.py
+ )
+ epytest
+}
diff --git a/dev-python/jacobi/metadata.xml b/dev-python/jacobi/metadata.xml
new file mode 100644
index 000000000..ebbabb06c
--- /dev/null
+++ b/dev-python/jacobi/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Robustly compute the generalised Jacobi matrix for an arbitrary real analytic mapping ℝⁿ → ℝⁱ¹ × ... × ℝⁱⁿ
+ Returns error estimates for derivatives
+ Perform statistical error propagation based on numerically computed jacobian
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">jacobi</remote-id>
+ <remote-id type="github">HDembinski/jacobi</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
index c8bdf2b00..22f35fbda 100644
--- a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
+++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
@@ -15,7 +15,7 @@ S="${WORKDIR}"/kepler-mapper-${PV}
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="${PYTHON_DEPS}
dev-python/jinja[${PYTHON_USEDEP}]
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
deleted file mode 100644
index ee0fc458a..000000000
--- a/dev-python/llvmlite/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST llvmlite-0.39.1.gh.tar.gz 237119 BLAKE2B c2538994a6b9116d9a124ad8b8fff9c06d654bcdd345fb25251505b7577c6dffdfa56c9226250dbc2de6253cf6154523ec0d3cd849697a66cabf5b522c5e76ca SHA512 16b341300e4034aff4ce9553fec6b5923b9f4cb261c1ec0ee2cef6d87addcbebe8f4805dbc2fb30f357800fa029c3b6fc8ed62a5fdaad7c262e723c3b9c4ad32
-DIST llvmlite-0.40.1.gh.tar.gz 261765 BLAKE2B f795fc7e0256333a6f6172788fb839b0b3fd304b654baaa58cae53d5e5e145f6e937fcb83ed096a3885c060a03fbf1d8546007ea7fafaa4028cd21b5aee19bd1 SHA512 b88d931cf252169a9246d8c935fe28ad509fe7da1f8b1842c4b4c40808c64b68d47a2387ed4664c0c0812b39cfbfc30ea4f9e702a7cd893c4c61a3596bc2e697
-DIST llvmlite-0.41.0.gh.tar.gz 248547 BLAKE2B 3b5aa6b19e08d300384cedd123024d6c73368db255f2010cfbe4fa04e1e1f2d81e644db8b1c8540a5c1134d36c0fce333940c92f3ec984c239dc8c47537e8dca SHA512 bd84b754f07bfc82f9800e1e0a2bc965cfee0f726b4f06b21b8ca04a46c388bc4c423c4ed5f6e6b14562f5ff97e3f356022ad770ea1d351f0330277a4f350966
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
deleted file mode 100644
index d35979ebc..000000000
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 02b1604..a45c9b8 100644
---- a/setup.py
-+++ b/setup.py
-@@ -33,7 +33,7 @@ except ImportError:
-
-
- min_python_version = "3.7"
--max_python_version = "3.11" # exclusive
-+max_python_version = "3.12" # exclusive
-
-
- def _guard_py_ver():
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
deleted file mode 100644
index 17eb80e87..000000000
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
-From: Richard Barnes <rbarnes@umn.edu>
-Date: Wed, 1 Dec 2021 10:29:08 -0700
-Subject: [PATCH] Enable LLVM-12 and LLVM-13
-
----
- ffi/build.py | 5 ++---
- ffi/targets.cpp | 2 ++
- llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
- 3 files changed, 20 insertions(+), 6 deletions(-)
-
-Index: llvmlite-0.39.0/ffi/build.py
-===================================================================
---- llvmlite-0.39.0.orig/ffi/build.py
-+++ llvmlite-0.39.0/ffi/build.py
-@@ -163,9 +163,8 @@ def main_posix(kind, library_ext):
- print(msg)
- print(warning + '\n')
- else:
--
-- if not out.startswith('11'):
-- msg = ("Building llvmlite requires LLVM 11.x.x, got "
-+ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')):
-+ msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
- "{!r}. Be sure to set LLVM_CONFIG to the right executable "
- "path.\nRead the documentation at "
- "http://llvmlite.pydata.org/ for more information about "
-Index: llvmlite-0.39.0/ffi/targets.cpp
-===================================================================
---- llvmlite-0.39.0.orig/ffi/targets.cpp
-+++ llvmlite-0.39.0/ffi/targets.cpp
-@@ -204,7 +204,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef
- rm = Reloc::DynamicNoPIC;
-
- TargetOptions opt;
-+#if LLVM_VERSION_MAJOR < 12
- opt.PrintMachineCode = PrintMC;
-+#endif
- opt.MCOptions.ABIName = ABIName;
-
- bool jit = JIT;
-Index: llvmlite-0.39.0/llvmlite/tests/test_binding.py
-===================================================================
---- llvmlite-0.39.0.orig/llvmlite/tests/test_binding.py
-+++ llvmlite-0.39.0/llvmlite/tests/test_binding.py
-@@ -18,6 +18,16 @@ from llvmlite.binding import ffi
- from llvmlite.tests import TestCase
-
-
-+def clean_string_whitespace(x: str) -> str:
-+ # Remove trailing whitespace from the end of each line
-+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
-+ # Remove intermediate blank lines
-+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
-+ # Remove extraneous whitespace from the beginning and end of the string
-+ x = x.strip()
-+ return x
-+
-+
- # arvm7l needs extra ABI symbols to link successfully
- if platform.machine() == 'armv7l':
- llvm.load_library_permanently('libgcc_s.so.1')
-@@ -555,7 +565,10 @@ class TestMisc(BaseTest):
- bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
- bd.ret(ir.Constant(ir.IntType(32), 12345))
- asm = str(mod)
-- self.assertEqual(asm, asm_nonalphanum_blocklabel)
-+ self.assertEqual(
-+ clean_string_whitespace(asm),
-+ clean_string_whitespace(asm_nonalphanum_blocklabel)
-+ )
-
- def test_global_context(self):
- gcontext1 = llvm.context.get_global_context()
-@@ -640,7 +653,7 @@ class TestMisc(BaseTest):
- def test_version(self):
- major, minor, patch = llvm.llvm_version_info
- # one of these can be valid
-- valid = [(11,)]
-+ valid = [(11,), (12,), (13,)]
- self.assertIn((major,), valid)
- self.assertIn(patch, range(10))
-
-Index: llvmlite-0.39.0/ffi/passmanagers.cpp
-===================================================================
---- llvmlite-0.39.0.orig/ffi/passmanagers.cpp
-+++ llvmlite-0.39.0/ffi/passmanagers.cpp
-@@ -17,9 +17,6 @@
- #include "llvm-c/Transforms/IPO.h"
- #include "llvm-c/Transforms/Scalar.h"
- #include "llvm/IR/LegacyPassManager.h"
--#if LLVM_VERSION_MAJOR > 11
--#include "llvm/IR/RemarkStreamer.h"
--#endif
- #include "llvm/IR/LLVMRemarkStreamer.h"
- #include "llvm/Remarks/RemarkStreamer.h"
- #include "llvm/Transforms/IPO.h"
diff --git a/dev-python/llvmlite/llvmlite-0.39.1.ebuild b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
deleted file mode 100644
index 7302c93dd..000000000
--- a/dev-python/llvmlite/llvmlite-0.39.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/"
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=15
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-llvm12.patch"
- "${FILESDIR}/${P}-allow-py3.11.patch"
-)
-
-src_prepare() {
- sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
- distutils-r1_src_prepare
-}
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/llvmlite-0.40.1.ebuild b/dev-python/llvmlite/llvmlite-0.40.1.ebuild
deleted file mode 100644
index bacb0358b..000000000
--- a/dev-python/llvmlite/llvmlite-0.40.1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/"
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=14
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=()
-
-src_prepare() {
- sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
- distutils-r1_src_prepare
-}
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/llvmlite-0.41.0.ebuild b/dev-python/llvmlite/llvmlite-0.41.0.ebuild
deleted file mode 100644
index 595218e7c..000000000
--- a/dev-python/llvmlite/llvmlite-0.41.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_EXT=1
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/"
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=14
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/metadata.xml b/dev-python/llvmlite/metadata.xml
deleted file mode 100644
index 0983f7a41..000000000
--- a/dev-python/llvmlite/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
- llvmlite uses the LLVM library for JIT (just-in-time) compilation of
- Python code into native machine instructions during runtime. Instead
- of exposing large parts of the LLVM C++ API for direct calls into the
- LLVM library, llvmlite follows a lightweight multi-layered approach.
- </longdescription>
- <upstream>
- <remote-id type="pypi">llvmlite</remote-id>
- <remote-id type="github">numba/llvmlite</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/lzstring/Manifest b/dev-python/lzstring/Manifest
new file mode 100644
index 000000000..f44e5e773
--- /dev/null
+++ b/dev-python/lzstring/Manifest
@@ -0,0 +1 @@
+DIST lzstring-1.0.4.tar.gz 4256 BLAKE2B e1a205f980de050635114e26a86d7251e0822a4459c44042291e80d55129d815f0753ff2b45a179fb468e9020a0a6255748566bc4e62fc98e7e041b07ae073f3 SHA512 0d61fe04402aaa5325d3ab555b9b83132048124a2ff11ae3a947a188d5507f1043b0522fcb7024009d75cf3efd3afbb64d24c238c4c2181346a823c77cb4ea02
diff --git a/dev-python/lzstring/lzstring-1.0.4.ebuild b/dev-python/lzstring/lzstring-1.0.4.ebuild
new file mode 100644
index 000000000..bfdb76a67
--- /dev/null
+++ b/dev-python/lzstring/lzstring-1.0.4.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="String encoding/decoding of binary data"
+HOMEPAGE="https://pypi.org/project/lzstring/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
diff --git a/dev-python/lzstring/metadata.xml b/dev-python/lzstring/metadata.xml
new file mode 100644
index 000000000..4dde9fdd9
--- /dev/null
+++ b/dev-python/lzstring/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">gkovacs/lz-string-python</remote-id>
+ <remote-id type="pypi">lzstring</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/neo/Manifest b/dev-python/neo/Manifest
index e3b133b9e..346e022b8 100644
--- a/dev-python/neo/Manifest
+++ b/dev-python/neo/Manifest
@@ -1,2 +1,3 @@
DIST neo-0.11.0.tar.gz 9411608 BLAKE2B 9257fd8ff9eea8ec80b0a4eb701b63a9db10d51e6f145b704eb5e9a394dd13a5c6e567cb3469fa4d86f538637f80e9c660823d358bb7ddfd651291dc5df73450 SHA512 dab4832317c8dc6a794ffc9fb118124734fa2428c0527eb9c86bc3d35195a34bdb162bc0a44a3604cb8067fff7263ab5b106c0f9871007a093e7185df5ba9993
DIST neo-0.11.1.tar.gz 3906151 BLAKE2B 26b60c715d6f3ec017cdb909c1f54b1509db4862f0630ab6d60b4b07153d5cb8512fbf16dd9039d1998b08e0f9e828bb271d4f482cc2d34a5d17a010ef4d203b SHA512 1f93a9eea020ee40f792f038bef76e053ff4f6e05951f78afa70bf4009bac3da8222be57c2cee88ae5e7539c5c8978cf50bf52cce787dbacafe6d5450d5e1aa7
+DIST neo-0.12.0.tar.gz 28377158 BLAKE2B efc6ae96d8cf8325355367af482d4e6dcc0dc3e3c5f3d449076a1c3ef32f530f777a2b125c946360b05a070cd75ae3f04b31a9e63d9bee7fecf437c3a19fc284 SHA512 1849c5074afb71cba7e90a78fa51b9967b27cb3f0b6242cfbadc3c29faf7a4a13da0a15a1c43cf43df810a5c0ed0b45cf60b42f3ed83520689acc27d3bde07b9
diff --git a/dev-python/neo/neo-0.12.0.ebuild b/dev-python/neo/neo-0.12.0.ebuild
new file mode 100644
index 000000000..6e058728e
--- /dev/null
+++ b/dev-python/neo/neo-0.12.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
+HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/quantities[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/probeinterface[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-vcs/datalad[${PYTHON_USEDEP}]
+ )
+"
+# Testing deps also need:
+# igor
+# pyedflib https://github.com/holgern/pyedflib
+# klusta
+# nixio
+# sonpy
+# ipython
+
+distutils_enable_tests pytest
+
+python_test() {
+ # Reported upstream
+ # https://github.com/NeuralEnsemble/python-neo/issues/1037
+ local EPYTEST_IGNORE=(
+ neo/test/iotest/*
+ neo/test/rawiotest/*
+ )
+ # Requires dynamic data download
+ local EPYTEST_DESELECT=(
+ neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset
+ )
+ epytest
+}
diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest
new file mode 100644
index 000000000..8a541f60d
--- /dev/null
+++ b/dev-python/nptyping/Manifest
@@ -0,0 +1 @@
+DIST nptyping-2.5.0.gh.tar.gz 72870 BLAKE2B 16c6cb90c36bbf0b97da5ff74cee7030c641ef76d055cc5691b9d83adab2714d6e3515fd4e8616fece74606e109e6b115348964614b408df06b4f5c3cbccce37 SHA512 2cde9c5f7694d4f916b85c93b86df7f72709a70b2ffa91b7bbc98c5884236f5b36bb545a89c37e8c02a9b460065c97151d77c64f8d93b92fd93bcff406f039d9
diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml
new file mode 100644
index 000000000..45345f0dc
--- /dev/null
+++ b/dev-python/nptyping/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">nptyping</remote-id>
+ <remote-id type="github">ramonhagenaars/nptyping</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/nptyping/nptyping-2.5.0.ebuild b/dev-python/nptyping/nptyping-2.5.0.ebuild
new file mode 100644
index 000000000..f6e8864df
--- /dev/null
+++ b/dev-python/nptyping/nptyping-2.5.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Type hints for Numpy"
+HOMEPAGE="
+ https://pypi.org/project/nptyping/
+ https://github.com/ramonhagenaars/nptyping/
+"
+SRC_URI="
+ https://github.com/ramonhagenaars/nptyping/archive/v${PV}.tar.gz
+ -> ${P}.gh.tar.gz
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/mypy[${PYTHON_USEDEP}]
+ dev-python/pandas-stubs[${PYTHON_USEDEP}]
+ dev-python/typeguard[${PYTHON_USEDEP}]
+ dev-python/beartype[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_IGNORE=(
+ # requires pyright, which is not yet packaged
+ tests/test_pyright.py
+ # requires Internet + feedparser, meaningless for users
+ tests/test_package_info.py
+ # relying on Internet access to fetch packages for pip
+ tests/test_wheel.py
+ tests/pandas_/test_fork_sync.py
+)
+
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/ramonhagenaars/nptyping/issues/113
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_any
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_shape
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_structure
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_function_arguments
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_variable_hints
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_nptyping_types
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_numpy_types
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_recarray_with_structure
+ tests/test_mypy.py::MyPyTest::test_mypy_disapproves_ndarray_with_wrong_function_arguments
+ tests/test_mypy.py::MyPyTest::test_mypy_knows_of_ndarray_methods
+ tests/test_typeguard.py::TypeguardTest::test_success
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_accepts_dataframe
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_disapproves_dataframe_with_wrong_function_arguments
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_knows_of_dataframe_methods
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/numba-dpex/Manifest b/dev-python/numba-dpex/Manifest
deleted file mode 100644
index 5286ff524..000000000
--- a/dev-python/numba-dpex/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST numba-dpex-0.20.0_rc3.gh.tar.gz 237831 BLAKE2B 69e1f133f6f015139d37258eac039380a14b139acaee010f66af233e34702f9f5d8a27070c34a917c0c3f40950070c948c609f6d8e40d429e55e1d83c9569f8c SHA512 3f381c0719ca6fad380b1f3729ec77caa47bb3e097d842e8fab1b82627e1f9b5d6905b3eb9682d80977ac745335a7bab20849b883f12fdc77f1ffb3ab9a706e8
diff --git a/dev-python/numba-dpex/metadata.xml b/dev-python/numba-dpex/metadata.xml
deleted file mode 100644
index c98aa52a0..000000000
--- a/dev-python/numba-dpex/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">IntelPython/numba-dpex</remote-id>
- <remote-id type="pypi">numba-dpex</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild b/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild
deleted file mode 100644
index a3b63bf1f..000000000
--- a/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="Data Parallel Extension for Numba"
-HOMEPAGE="https://github.com/IntelPython/numba-dpex"
-SRC_URI="https://github.com/IntelPython/numba-dpex/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz"
-S="${WORKDIR}/${PN}-${PV//_rc/dev}"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- sys-devel/DPC++
-"
-
-RDEPEND="
- dev-python/dpctl[${PYTHON_USEDEP}]
- dev-python/dpnp[${PYTHON_USEDEP}]
- dev-python/numba[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
- export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
deleted file mode 100644
index d77998df2..000000000
--- a/dev-python/numba/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST numba-0.56.4.gh.tar.gz 2492671 BLAKE2B c4669d15861bfea3d0fd187df9d2d4264a4b0c440fd5d46203f0494f3282ec89116fa31763550ce9593694bf2b264d6b086d206ced4aacb653d0910d2baa15d3 SHA512 15ed581cb34be30711e64e54289a29d845ceb841f8341bbbdac4d4cb7fa7cebfd4409cac7f0e0f5b1164c9bd142897b90761529ef3ad1c198a00d16ada38942e
-DIST numba-0.57.1.gh.tar.gz 2616955 BLAKE2B 58e3e5903aa1f82ae91b9b96c088630c45e816001a8e246503de527f2d6e8caf85887f0f39213aa2b054edb03e9a0553c9f494648b6d816a0cb862819ef4bbcb SHA512 d1e3b205b2b2289e92375cbe85b2cd3d5b92a301458a056d7ba19c7522ef75b0a36020848cb69cae1f34da3b90019aac02b43d22466e3f9d62e8cec4ae5d666d
diff --git a/dev-python/numba/files/numba-0.52.0-skip_tests.patch b/dev-python/numba/files/numba-0.52.0-skip_tests.patch
deleted file mode 100644
index f31af4bfb..000000000
--- a/dev-python/numba/files/numba-0.52.0-skip_tests.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Index: numba-0.52.0/numba/tests/test_jitclasses.py
-===================================================================
---- numba-0.52.0.orig/numba/tests/test_jitclasses.py
-+++ numba-0.52.0/numba/tests/test_jitclasses.py
-@@ -929,6 +929,7 @@ class TestJitClass(TestCase, MemoryLeakM
- 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
-Index: numba-0.52.0/numba/tests/test_record_dtype.py
-===================================================================
---- numba-0.52.0.orig/numba/tests/test_record_dtype.py
-+++ numba-0.52.0/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/files/numba-0.56.4-allow-py3.11.patch b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
deleted file mode 100644
index 07c1b5d88..000000000
--- a/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 68feca4..1d254ec 100644
---- a/setup.py
-+++ b/setup.py
-@@ -20,7 +20,7 @@ except ImportError:
-
-
- min_python_version = "3.7"
--max_python_version = "3.11" # exclusive
-+max_python_version = "3.12" # exclusive
- min_numpy_build_version = "1.11"
- min_numpy_run_version = "1.18"
- max_numpy_run_version = "1.24"
diff --git a/dev-python/numba/numba-0.56.4.ebuild b/dev-python/numba/numba-0.56.4.ebuild
deleted file mode 100644
index 3fcfd4a94..000000000
--- a/dev-python/numba/numba-0.56.4.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-# py3.11 fails to compile:
-# error: ‘CFrame’ does not name a type; did you mean ‘_frame’?
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit optfeature multiprocessing distutils-r1
-
-DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
-HOMEPAGE="https://numba.pydata.org/
- https://github.com/numba"
-SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="openmp threads"
-
-RDEPEND="
- >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.40.0
- >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.24[${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_enable_tests unittest
-distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx-rtd-theme
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
- "${FILESDIR}/${PN}-0.56.4-allow-py3.11.patch"
-)
-
-pkg_setup() {
- if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1 || die
- else
- unset NUMBA_DISABLE_OPENMP || die
- fi
- if ! use threads; then
- export NUMBA_DISABLE_TBB=1 || die
- else
- unset NUMBA_DISABLE_TBB || die
- export TBBROOT="${EPREFIX}/usr" || die
- fi
-}
-
-python_prepare_all() {
- # This conf.py only works in a git repo
- if use doc; then
- git init -q || die
- git config user.email "larry@gentoo.org" || die
- git config user.name "Larry the Cow" || die
- git add . || die
- git commit -m "init" || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # FIXME: parallel python building fails. See Portage bug #614464 and
- # gentoo/sci issue #1080.
- export MAKEOPTS=-j1 || die
- distutils-r1_python_compile
-}
-
-# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
-python_test() {
- ${EPYTHON} setup.py build_ext --inplace || die \
- "${EPYTHON} failed to build_ext"
- ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
- "${EPYTHON} failed unittests"
-}
-
-pkg_postinst() {
- optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
-}
diff --git a/dev-python/numba/numba-0.57.1.ebuild b/dev-python/numba/numba-0.57.1.ebuild
deleted file mode 100644
index 814dc36f9..000000000
--- a/dev-python/numba/numba-0.57.1.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_EXT=1
-inherit optfeature multiprocessing distutils-r1
-
-DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
-HOMEPAGE="https://numba.pydata.org/
- https://github.com/numba"
-SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="openmp threads"
-
-RDEPEND="
- >=dev-python/llvmlite-0.40.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.41.0
- >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.25[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.6 )
-"
-BDEPEND="
- dev-python/pip[${PYTHON_USEDEP}]
- dev-python/versioneer[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests unittest
-distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx-rtd-theme
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
-)
-
-pkg_setup() {
- if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1 || die
- else
- unset NUMBA_DISABLE_OPENMP || die
- fi
- if ! use threads; then
- export NUMBA_DISABLE_TBB=1 || die
- else
- unset NUMBA_DISABLE_TBB || die
- export TBBROOT="${EPREFIX}/usr" || die
- fi
-}
-
-python_prepare_all() {
- # This conf.py only works in a git repo
- if use doc; then
- git init -q || die
- git config user.email "larry@gentoo.org" || die
- git config user.name "Larry the Cow" || die
- git add . || die
- git commit -m "init" || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # FIXME: parallel python building fails. See Portage bug #614464 and
- # gentoo/sci issue #1080.
- export MAKEOPTS=-j1 || die
- distutils-r1_python_compile
-}
-
-# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
-python_test() {
- ${EPYTHON} setup.py build_ext --inplace || die \
- "${EPYTHON} failed to build_ext"
- ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
- "${EPYTHON} failed unittests"
-}
-
-pkg_postinst() {
- optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
-}
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
index d256ba401..b14e3311b 100644
--- a/dev-python/numcodecs/Manifest
+++ b/dev-python/numcodecs/Manifest
@@ -1 +1,2 @@
DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2
+DIST numcodecs-0.12.1.tar.gz 4091415 BLAKE2B d7fa8cc549495c7c54130898f2047eb409559541b299640fb34a2332d874049afa64d5c14151426b24a1ab04c0e0444245477aa26f9336ce3ba7aefc8043abcf SHA512 716a1144c17b08cc1737bd429517b5434a7e5dbc9626ed613ca9ab4f9cda356ed97cb4ef0e2bba747a7681dc5b43818cb07c6db7f5537b4910790f6ea23c696c
diff --git a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
new file mode 100644
index 000000000..3d20684ba
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_compile() {
+ local -x DISABLE_NUMCODECS_AVX2=1
+ local -x DISABLE_NUMCODECS_SSE2=1
+ distutils-r1_python_compile
+}
+
+python_test() {
+ cd "${T}" || die
+ epytest --pyargs numcodecs
+}
diff --git a/dev-python/numpy/Manifest b/dev-python/numpy/Manifest
deleted file mode 100644
index fdd711d83..000000000
--- a/dev-python/numpy/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST numpy-1.23.5.tar.gz 10731755 BLAKE2B d2ed6d359a51343a1618f64604e4d5c030115caa63f2aadf2fc150775630e40fbebaad28f5657faae1365264fd45bc9efb00854bf9cd393b7628c96d6fc87db9 SHA512 8f3ece76dbe79bc887275332d25f851ade2087de3026de5fb7ed793590b3e7d274f590357296e152373b4e9a245d4d563393ba7198bca6d44631b941acb89c2c
-DIST numpy-html-1.23.5.zip 27964271 BLAKE2B 0aa26d7c39f2d6b119e404dfb9642967770881ee0d640157a9ed11d16f21cd43109bed3c08f89fda457ec470292d945e2bf8b2dab56e4b36192d5e8eb3757b44 SHA512 218a2e893816af767c7cedd1f2256e05f68e59491c29277c95de653a206aaff35c5fe3bc6afd6d6d5ea7957748ec565593eb30d004e36e94c894ea4a6884902a
-DIST numpy-ref-1.23.5.pdf 7715485 BLAKE2B 7fbb0ce29e86fc7cd4932a6a9f0221b579b6cae695231edfebf863e5b4c2920796d802ccf9ae3e05b331964ac7c4f51099578d91b6b7fb357c6de2110a5f7cba SHA512 6036c6a36f332b83f371c7530a6ba6f354b1334d667d2a52993a1e52aa9d94d524e216f768928a006c717ed4b4131879f6e491a294ecfd3a0d1b0f9f937a887a
-DIST numpy-user-1.23.5.pdf 4123384 BLAKE2B d4587c9f979e1ef4734768598d6e106f2b4b0c8222f901a6c4caf0920e41622201252c5bd172b16346e0357138b5ff27c59e56c851be5ae3b7712624bd9cc5b4 SHA512 58e1ab96d2cfbd96df205c86f0a1a09e204349f70d21df7f8481c21ded8b46f4b9ede3216d5cce6c2b9bfc0aacbecdfa198bdb2d4c258a0dd4acb6e3ba421f9c
diff --git a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
deleted file mode 100644
index d87a16a4b..000000000
--- a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-Originally added in: https://gitweb.gentoo.org/repo/gentoo.git/commit/dev-python/numpy/files?id=e5ce90a04e79f6413604e96e4803cb95ada7c859
-https://bugs.gentoo.org/567938
---- a/numpy/distutils/system_info.py
-+++ b/numpy/distutils/system_info.py
-@@ -505,33 +505,7 @@ def get_info(name, notfound_action=0):
- 'blas_armpl': blas_armpl_info,
- 'lapack_armpl': lapack_armpl_info,
- 'fftw3_armpl': fftw3_armpl_info,
-- 'atlas': atlas_info, # use lapack_opt or blas_opt instead
-- 'atlas_threads': atlas_threads_info, # ditto
-- 'atlas_blas': atlas_blas_info,
-- 'atlas_blas_threads': atlas_blas_threads_info,
-- 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead
-- 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto
-- 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead
-- 'atlas_3_10_threads': atlas_3_10_threads_info, # ditto
-- 'atlas_3_10_blas': atlas_3_10_blas_info,
-- 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info,
-- 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt instead
-- 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, # ditto
-- 'flame': flame_info, # use lapack_opt instead
-- 'mkl': mkl_info,
-- # openblas which may or may not have embedded lapack
-- 'openblas': openblas_info, # use blas_opt instead
-- # openblas with embedded lapack
-- 'openblas_lapack': openblas_lapack_info, # use blas_opt instead
-- 'openblas_clapack': openblas_clapack_info, # use blas_opt instead
-- 'blis': blis_info, # use blas_opt instead
-- 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead
-- 'blas_mkl': blas_mkl_info, # use blas_opt instead
- 'accelerate': accelerate_info, # use blas_opt instead
-- 'openblas64_': openblas64__info,
-- 'openblas64__lapack': openblas64__lapack_info,
-- 'openblas_ilp64': openblas_ilp64_info,
-- 'openblas_ilp64_lapack': openblas_ilp64_lapack_info,
- 'x11': x11_info,
- 'fft_opt': fft_opt_info,
- 'fftw': fftw_info,
-@@ -951,10 +925,7 @@ class system_info:
- return [b for b in [a.strip() for a in libs.split(',')] if b]
-
- def get_libraries(self, key='libraries'):
-- if hasattr(self, '_lib_names'):
-- return self.get_libs(key, default=self._lib_names)
-- else:
-- return self.get_libs(key, '')
-+ return self.get_libs(key, '')
-
- def library_extensions(self):
- c = customized_ccompiler()
diff --git a/dev-python/numpy/metadata.xml b/dev-python/numpy/metadata.xml
deleted file mode 100644
index 26b229a9c..000000000
--- a/dev-python/numpy/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <maintainer type="project">
- <email>python@gentoo.org</email>
- <name>Python</name>
- </maintainer>
- <longdescription lang="en">
- NumPy is a general-purpose array-processing Python package designed to
- efficiently manipulate large multi-dimensional arrays of arbitrary
- records without sacrificing too much speed for small multi-dimensional
- arrays. There are also basic facilities for discrete fourier transform,
- basic linear algebra and random number generation.
- It is the successor of Numeric and numarray.
- </longdescription>
- <upstream>
- <remote-id type="github">numpy/numpy</remote-id>
- <remote-id type="pypi">numpy</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/numpy/numpy-1.23.5.ebuild b/dev-python/numpy/numpy-1.23.5.ebuild
deleted file mode 100644
index 5a9224e54..000000000
--- a/dev-python/numpy/numpy-1.23.5.ebuild
+++ /dev/null
@@ -1,184 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-PYTHON_REQ_USE="threads(+)"
-FORTRAN_NEEDED=lapack
-inherit distutils-r1 flag-o-matic fortran-2 pypi toolchain-funcs
-
-DOC_PV=${PV}
-# For when docs aren't ready yet, set to last version
-#DOC_PV=1.23.0
-DESCRIPTION="Fast array and numerical python library"
-HOMEPAGE="
- https://numpy.org/
- https://github.com/numpy/numpy/
- https://pypi.org/project/numpy/
-"
-SRC_URI+="
- doc? (
- https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-html.zip -> numpy-html-${DOC_PV}.zip
- https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-ref.pdf -> numpy-ref-${DOC_PV}.pdf
- https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-user.pdf -> numpy-user-${DOC_PV}.pdf
- )
-"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~x64-solaris ~x86-solaris"
-IUSE="doc lapack"
-
-RDEPEND="
- lapack? (
- >=virtual/cblas-3.8
- >=virtual/lapack-3.8
- )
-"
-BDEPEND="
- ${RDEPEND}
- >=dev-python/cython-0.29.30[${PYTHON_USEDEP}]
- lapack? (
- virtual/pkgconfig
- )
- doc? (
- app-arch/unzip
- )
- test? (
- >=dev-python/hypothesis-5.8.0[${PYTHON_USEDEP}]
- >=dev-python/pytz-2019.3[${PYTHON_USEDEP}]
- >=dev-python/cffi-1.14.0[${PYTHON_USEDEP}]
- )
-"
-
-PATCHES=(
- "${FILESDIR}"/numpy-1.22.0-no-hardcode-blasv2.patch
-)
-
-distutils_enable_tests pytest
-
-src_unpack() {
- default
- if use doc; then
- unzip -qo "${DISTDIR}"/numpy-html-${DOC_PV}.zip -d html || die
- fi
-}
-
-python_prepare_all() {
- # Allow use with setuptools 60.x
- # See numpy-1.22.1-revert-setuptools-upper-bound.patch for details
- export SETUPTOOLS_USE_DISTUTILS=stdlib
-
- if use lapack; then
- local incdir="${EPREFIX}"/usr/include
- local libdir="${EPREFIX}"/usr/$(get_libdir)
- cat >> site.cfg <<-EOF || die
- [blas]
- include_dirs = ${incdir}
- library_dirs = ${libdir}
- blas_libs = cblas,blas
- [lapack]
- library_dirs = ${libdir}
- lapack_libs = lapack
- EOF
- else
- export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None
- fi
-
- export CC="$(tc-getCC) ${CFLAGS}"
-
- append-flags -fno-strict-aliasing
-
- # See progress in http://projects.scipy.org/scipy/numpy/ticket/573
- # with the subtle difference that we don't want to break Darwin where
- # -shared is not a valid linker argument
- if [[ ${CHOST} != *-darwin* ]]; then
- append-ldflags -shared
- fi
-
- # only one fortran to link with:
- # linking with cblas and lapack library will force
- # autodetecting and linking to all available fortran compilers
- append-fflags -fPIC
- if use lapack; then
- NUMPY_FCONFIG="config_fc --noopt --noarch"
- # workaround bug 335908
- [[ $(tc-getFC) == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95"
- fi
-
- # don't version f2py, we will handle it.
- sed -i -e '/f2py_exe/s: + os\.path.*$::' numpy/f2py/setup.py || die
-
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- export MAKEOPTS=-j1 #660754
-
- distutils-r1_python_compile ${NUMPY_FCONFIG}
-}
-
-python_test() {
- local EPYTEST_DESELECT=(
- # very disk- and memory-hungry
- numpy/lib/tests/test_io.py::test_large_zip
-
- # precision problems
- numpy/core/tests/test_umath_accuracy.py::TestAccuracy::test_validate_transcendentals
-
- # runs the whole test suite recursively, that's just crazy
- numpy/core/tests/test_mem_policy.py::test_new_policy
-
- # very slow, unlikely to be practically useful
- numpy/typing/tests/test_typing.py
- )
-
- if use arm && [[ $(uname -m || echo "unknown") == "armv8l" ]] ; then
- # Degenerate case. arm32 chroot on arm64.
- # bug #774108
- EPYTEST_DESELECT+=(
- numpy/core/tests/test_cpu_features.py::Test_ARM_Features::test_features
- )
- fi
-
- if use x86 ; then
- EPYTEST_DESELECT+=(
- # https://github.com/numpy/numpy/issues/18388
- numpy/core/tests/test_umath.py::TestRemainder::test_float_remainder_overflow
- # https://github.com/numpy/numpy/issues/18387
- numpy/random/tests/test_generator_mt19937.py::TestRandomDist::test_pareto
- # more precision problems
- numpy/core/tests/test_einsum.py::TestEinsum::test_einsum_sums_int16
- )
- fi
- if use arm || use x86 ; then
- EPYTEST_DESELECT+=(
- # too large for 32-bit platforms
- numpy/core/tests/test_ufunc.py::TestUfunc::test_identityless_reduction_huge_array
- )
- fi
-
- distutils_install_for_testing --single-version-externally-managed \
- --record "${TMPDIR}/record.txt" ${NUMPY_FCONFIG}
-
- cd "${TEST_DIR}/lib" || die
- epytest -k "not _fuzz"
-}
-
-python_install() {
- # https://github.com/numpy/numpy/issues/16005
- local mydistutilsargs=( build_src )
- distutils-r1_python_install ${NUMPY_FCONFIG}
- python_optimize
-}
-
-python_install_all() {
- local DOCS=( LICENSE.txt README.md THANKS.txt )
-
- if use doc; then
- local HTML_DOCS=( "${WORKDIR}"/html/. )
- DOCS+=( "${DISTDIR}"/${PN}-{user,ref}-${DOC_PV}.pdf )
- fi
-
- distutils-r1_python_install_all
-}
diff --git a/dev-python/pandas-stubs/Manifest b/dev-python/pandas-stubs/Manifest
new file mode 100644
index 000000000..856ff2fe2
--- /dev/null
+++ b/dev-python/pandas-stubs/Manifest
@@ -0,0 +1 @@
+DIST pandas-stubs-2.1.1.230928.gh.tar.gz 192865 BLAKE2B f3604def27a3ba7444969473c5800f7cc72fd4487f2363f326de6d637f1b6b60d2a8707f6cbb2647389691fbd856a2e7e5cf3710c0ad014ae106472c76dfb1c8 SHA512 5f9e71f187d1532388a98e0139852098c00d44d3ddf32fc3bad1c5199291c7dd4af82b2d73605b1e16b09a79f3b9df02752b37cf87fcb222faee9e704f52dd47
diff --git a/dev-python/pandas-stubs/metadata.xml b/dev-python/pandas-stubs/metadata.xml
new file mode 100644
index 000000000..8cbc804ad
--- /dev/null
+++ b/dev-python/pandas-stubs/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>python@gentoo.org</email>
+ <name>Gentoo Python Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">pandas-dev/pandas-stubs</remote-id>
+ <remote-id type="pypi">pandas-stubs</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
new file mode 100644
index 000000000..e10fd1aca
--- /dev/null
+++ b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
@@ -0,0 +1,52 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Public type stubs for pandas"
+HOMEPAGE="https://github.com/pandas-dev/pandas-stubs"
+SRC_URI="https://github.com/pandas-dev/pandas-stubs/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# Allegedly also needs dev-python/types-pytz (available in ::guru), but somehow works without it...
+# https://github.com/pandas-dev/pandas-stubs/blob/3c2affdaeb1cb03777cc59832dcdd4b030add27d/pyproject.toml#L34
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/xarray[${PYTHON_USEDEP}]
+ dev-python/pyarrow[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Package has a bunch of test deps missing from ::gentoo and ::science
+ tests/test_frame.py::test_to_markdown
+ tests/test_frame.py::test_types_to_feather
+ tests/test_io.py::test_orc
+ tests/test_io.py::test_orc_path
+ tests/test_io.py::test_orc_buffer
+ tests/test_io.py::test_orc_columns
+ tests/test_io.py::test_orc_bytes
+ tests/test_io.py::test_hdf
+ tests/test_io.py::test_hdfstore
+ tests/test_io.py::test_read_hdf_iterator
+ tests/test_io.py::test_hdf_context_manager
+ tests/test_io.py::test_hdf_series
+ tests/test_io.py::test_spss
+ tests/test_io.py::test_parquet
+ tests/test_io.py::test_parquet_options
+ tests/test_io.py::test_excel_writer_engine
+ tests/test_io.py::test_all_read_without_lxml_dtype_backend
+ tests/test_series.py::test_types_agg
+ tests/test_series.py::test_types_aggregate
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/panel/panel-0.14.2.ebuild b/dev-python/panel/panel-0.14.2-r1.ebuild
index bf4df1861..4674f8161 100644
--- a/dev-python/panel/panel-0.14.2.ebuild
+++ b/dev-python/panel/panel-0.14.2-r1.ebuild
@@ -3,9 +3,10 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
# Panel imports from "distutils" at runtime.
-DISTUTILS_USE_SETUPTOOLS=rdepend
+#DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 pypi
DESCRIPTION="High-level app and dashboarding solution for Python"
@@ -20,6 +21,7 @@ KEYWORDS="~amd64 ~x86"
DEPEND="
>=dev-python/param-1.10.0[${PYTHON_USEDEP}]
>=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+ dev-python/bleach[${PYTHON_USEDEP}]
"
RDEPEND="${DEPEND}
dev-python/markdown[${PYTHON_USEDEP}]
diff --git a/dev-python/persim/persim-0.3.1.ebuild b/dev-python/persim/persim-0.3.1.ebuild
index 78b86d6ea..994dca206 100644
--- a/dev-python/persim/persim-0.3.1.ebuild
+++ b/dev-python/persim/persim-0.3.1.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="https://persim.scikit-tda.org/"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
dev-python/hopcroftkarp[${PYTHON_USEDEP}]
diff --git a/dev-python/photutils/photutils-1.6.0.ebuild b/dev-python/photutils/photutils-1.6.0.ebuild
index b2ea8d831..a1fa5f2d2 100644
--- a/dev-python/photutils/photutils-1.6.0.ebuild
+++ b/dev-python/photutils/photutils-1.6.0.ebuild
@@ -37,4 +37,4 @@ distutils_enable_tests pytest
# dev-python/scipy \
# dev-python/matplotlib \
# sci-libs/scikit-learn \
-# sci-libs/scikit-image \
+# dev-python/scikit-image \
diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest
index e50aa7618..f50e462dc 100644
--- a/dev-python/plac/Manifest
+++ b/dev-python/plac/Manifest
@@ -1 +1 @@
-DIST plac-1.3.5.tar.gz 38074 BLAKE2B 8c770ea43d94a5fa80fa22f0e1fb6433e7901769315e0ecd9d6889d773e454b428265c3cd43792867dd56757cc6e31dcbda76052b46266878f07e493cf899c14 SHA512 9de705fbcc7585f9be8bb648ca3136cf0f031702e3def3ae069be6cff0e71969fe193e1420bd4018392f4a323cfe9131f86a10a2a2ecd0001fd1e82ad63a0d4a
+DIST plac-1.4.2.tar.gz 37595 BLAKE2B 5205e9d8a5a775eb2e23ea7ad30e576417a8ba944cb196ccb7a16b514b6c4902856a7191b1bbf71ab0176910b5d8dc163ab36fe3fb0c5bb5765c02d16ae347b1 SHA512 c8c320cabda42f33071d7675b64befab8344bde746d0befe661a9bb26f658559435d2895dad0a27dc1d7c2dc59f07a359b529880e115d900b4fca8f245186742
diff --git a/dev-python/plac/plac-1.3.5.ebuild b/dev-python/plac/plac-1.4.2.ebuild
index dcc47aa3d..50b269f42 100644
--- a/dev-python/plac/plac-1.3.5.ebuild
+++ b/dev-python/plac/plac-1.4.2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( pypy3 python3_{10..12} )
inherit pypi distutils-r1
@@ -15,4 +15,9 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+EPYTEST_DESELECT=(
+ # Missing index.rst
+ doc/test_plac.py::test_doctest
+)
+
distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest
index 53fb37ba4..189bbfcaf 100644
--- a/dev-python/probeinterface/Manifest
+++ b/dev-python/probeinterface/Manifest
@@ -1,2 +1,3 @@
DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84
+DIST probeinterface-0.2.20.gh.tar.gz 1930434 BLAKE2B 0087f82f8cea3e1eb225ba188487eb3862de8444cadb0cf76ebba1046f194eb1f369bab7b3ff35eb6b99c054409b902c1907037d42aa84d0d4253a47fa6009ce SHA512 16cee1845d4cd40f1bfdea654fff99ea5949fbd8606ffc038ea0ca27d6a4f3faa65e2dd448bcda1066c0d2984ce7e3995a0ead028ef57ae59743c34c6c5a4c39
diff --git a/dev-python/probeinterface/probeinterface-0.2.20.ebuild b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
new file mode 100644
index 000000000..75dd43bd4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+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/pyaml-env/Manifest b/dev-python/pyaml-env/Manifest
new file mode 100644
index 000000000..06b54d70e
--- /dev/null
+++ b/dev-python/pyaml-env/Manifest
@@ -0,0 +1 @@
+DIST pyaml_env-1.2.1.tar.gz 12759 BLAKE2B 5a037ccefaaa3c60ce393dae5847777eb43745549a31b763ef2f50feb3a6e216ef793f9501df9e80cb381f78782e54b888ee4b043736dc05bcd01619d839ff86 SHA512 1ef873fa66660e4949dc1064260405244c8b3a2ee4391831a0a52be30e503e99d0b80b087c78db78683e9fe2fc1fd73f2e30c1eacc4c94a1394000d8526c9d68
diff --git a/dev-python/pyaml-env/metadata.xml b/dev-python/pyaml-env/metadata.xml
new file mode 100644
index 000000000..44769bf23
--- /dev/null
+++ b/dev-python/pyaml-env/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mkaranasou/pyaml_env</remote-id>
+ <remote-id type="pypi">pyaml-env</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
new file mode 100644
index 000000000..a5169040a
--- /dev/null
+++ b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Parse YAML configuration with environment variables in Python"
+HOMEPAGE="https://pypi.org/project/pyaml-env/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]"
+
+# tests not included in pypi tarball
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
index b52026473..11a68c169 100644
--- a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
@@ -22,7 +22,8 @@ RDEPEND="
sci-astronomy/erfa:0=
>=dev-python/numpy-1.17[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
dev-python/setuptools-scm[${PYTHON_USEDEP}]
test? (
dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
diff --git a/dev-python/pynndescent/Manifest b/dev-python/pynndescent/Manifest
deleted file mode 100644
index a92be64b7..000000000
--- a/dev-python/pynndescent/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pynndescent-0.5.6.tar.gz 1135907 BLAKE2B 53f09045b14b3026ff1a2fa1ed27a4ce75f23e9c25ca0469c5ce207a51a25c778a7c2d3af51c3a724e1c0cd4eb148b3a8e73b6d39e819fc9c4cb0549240623be SHA512 9556754d4edbdfe442abf6b95b1970b8c606616a0012fc7a6875e1dfbe9a98b21b317eee84836c2b521dffb0db4e19ba6c8f1f9009498d43153ffda0f0a3b820
diff --git a/dev-python/pynndescent/metadata.xml b/dev-python/pynndescent/metadata.xml
deleted file mode 100644
index 7930c1730..000000000
--- a/dev-python/pynndescent/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="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">lmcinnes/pynndescent</remote-id>
- <remote-id type="pypi">pynndescent</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/pynndescent/pynndescent-0.5.6.ebuild b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
deleted file mode 100644
index 770630cac..000000000
--- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index d80f44e8e..0dffbb9ab 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,3 +1,2 @@
-DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57
-DIST pynwb-2.3.1.tar.gz 617910 BLAKE2B 6f8a965ff077523d043dd20b34ab1c69387b434a2a489a2a9dab718270fe7484cd88df4acce17da2aa513c56afbc75022fed132d157a0c804c6ced84a0bd627b SHA512 795a20b52d7734d2b1d4ba7da0df75d0e8cdbac4f8911a0a8977fd8890751d8c10b58858f2740a73557dc0d8ffa95530437544b71f4bf14ec0cc9e99213afda0
-DIST pynwb-2.3.2.tar.gz 618295 BLAKE2B 5a7e96437e0fe6dae2067e11ae4e927dcaa9574ca1d85594ebd2915d166281751808470f97ea8ba5a6df5f0023ed5f316396fe11da768f6197485a36fc497396 SHA512 bf8633275080735b864e28d792672ebda38ed5dd27c8f5eeb714f848447688c2be2d15cca809b97ee545b29833047d2db26a31272c2e9b4e24cef4ac5fe95c00
+DIST pynwb-2.5.0.tar.gz 620770 BLAKE2B 470f5127560bf79f112061e9e8af208051d76833e449a66b03e31bb0828ffbfd6aa0b9efc136ecc0b7efba758334c3f15525a41ec4540c6f55d02f8afbd55ab2 SHA512 cad84e3ac6c3c67c3c28e3c3ec44402bfc94c4cf988fbe64ddfa461a67115398b24bb9bcac1bd00933e1b63d73048d9b20ec6cd736a51d9f2c7bf4d294edb261
+DIST pynwb-2.6.0.tar.gz 625188 BLAKE2B ac179af7e3c9de6ec4fb841dfd6279a1c3ba191b9d786553af02397a49c511f4a257a0e62f3b57a217ebb08588ad8ca64219fd435b3ec25776775d05e6a9ab9b SHA512 5c830cb37e8c6fe0643bd5bfee947565ddb1d0eff16dadadd3ebec7ec14a6e1ebcf34c3909ad05c3eedd8dd5f9e3669348216d695123f2013de0e969a403ec1c
diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
deleted file mode 100644
index d09c50594..000000000
--- a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/setup.py b/tmp/setup.py
-index 39e75824..f7948f64 100755
---- a/setup.py
-+++ b/setup.py
-@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
- schema_dir = 'nwb-schema/core'
-
- reqs = [
-- 'h5py>=2.9,<4',
-- 'hdmf>=3.1.1,<4',
-- 'numpy>=1.16,<1.22',
-- 'pandas>=1.0.5,<2',
-- 'python-dateutil>=2.7,<3',
-+ 'h5py',
-+ 'hdmf',
-+ 'numpy',
-+ 'pandas',
-+ 'python-dateutil',
- 'setuptools'
- ]
-
diff --git a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch b/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
deleted file mode 100644
index 8c816d226..000000000
--- a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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>=3.3.2,<4',
-- 'numpy>=1.16,<1.23',
-- 'pandas>=1.0.5,<2',
-- 'python-dateutil>=2.7,<3',
-+ 'h5py',
-+ 'hdmf',
-+ 'numpy',
-+ 'pandas',
-+ 'python-dateutil',
- 'setuptools'
- ]
-
diff --git a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
deleted file mode 100644
index 6141f629a..000000000
--- a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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/files/pynwb-2.3.1-pkg_resources.patch b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
deleted file mode 100644
index bf496b900..000000000
--- a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
-From: rly <rly@lbl.gov>
-Date: Fri, 24 Mar 2023 10:17:13 -0700
-Subject: [PATCH] Fix deprecation warning with pkg_resources
-
----
- src/pynwb/__init__.py | 14 +++++++++++---
- tests/back_compat/test_import_structure.py | 1 -
- 2 files changed, 11 insertions(+), 4 deletions(-)
-
-diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py
-index 2df273d43..023cda237 100644
---- a/src/pynwb/__init__.py
-+++ b/src/pynwb/__init__.py
-@@ -15,16 +15,24 @@
- import hdmf.common
-
- CORE_NAMESPACE = 'core'
--__core_ns_file_name = 'nwb.namespace.yaml'
-
- from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402
- from .validate import validate # noqa: F401, E402
-
-
- def __get_resources():
-- from pkg_resources import resource_filename
-+ try:
-+ from importlib.resources import files
-+ except ImportError:
-+ # TODO: Remove when python 3.9 becomes the new minimum
-+ from importlib_resources import files
-+
-+ __location_of_this_file = files(__name__)
-+ __core_ns_file_name = 'nwb.namespace.yaml'
-+ __schema_dir = 'nwb-schema/core'
-+
- ret = dict()
-- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)
-+ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name)
- return ret
-
-
-diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py
-index dba11a48a..e5f931f5d 100644
---- a/tests/back_compat/test_import_structure.py
-+++ b/tests/back_compat/test_import_structure.py
-@@ -34,7 +34,6 @@ def test_outer_import_structure(self):
- "__TYPE_MAP",
- "__builtins__",
- "__cached__",
-- "__core_ns_file_name",
- "__doc__",
- "__file__",
- "__get_resources",
diff --git a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
deleted file mode 100644
index e672f243b..000000000
--- a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/pynwb/ophys.py b/src/pynwb/ophys.py
-index b09267ff6..e3d9f8f6d 100644
---- a/src/pynwb/ophys.py
-+++ b/src/pynwb/ophys.py
-@@ -192,7 +192,7 @@ def __init__(self, **kwargs):
- args_to_set = popargs_to_dict(keys_to_set, kwargs)
- super().__init__(**kwargs)
-
-- if args_to_set["binning"] < 0:
-+ if args_to_set["binning"] is not None and args_to_set["binning"] < 0:
- raise ValueError(f"Binning value must be >= 0: {args_to_set['binning']}")
- if isinstance(args_to_set["binning"], int):
- args_to_set["binning"] = np.uint(args_to_set["binning"])
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
deleted file mode 100644
index 5a286c3b6..000000000
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 pypi
-
-DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=sci-libs/hdf5-1.12.2
- >=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/pynwb/pynwb-2.3.2.ebuild b/dev-python/pynwb/pynwb-2.5.0.ebuild
index 6599fbf8f..ca11c3dbe 100644
--- a/dev-python/pynwb/pynwb-2.3.2.ebuild
+++ b/dev-python/pynwb/pynwb-2.5.0.ebuild
@@ -15,14 +15,14 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
"
-BDEPEND=""
EPYTEST_DESELECT=(
# Reported upsream:
@@ -39,6 +39,12 @@ EPYTEST_DESELECT=(
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
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
)
distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild b/dev-python/pynwb/pynwb-2.6.0.ebuild
index 382bfdb60..2f403981c 100644
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.6.0.ebuild
@@ -15,20 +15,14 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
"
-BDEPEND=""
-
-# Remove both in next release
-PATCHES=(
- "${FILESDIR}/${P}-typing.patch"
- "${FILESDIR}/${P}-pkg_resources.patch"
- )
EPYTEST_DESELECT=(
# Reported upsream:
@@ -45,6 +39,13 @@ EPYTEST_DESELECT=(
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
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+ tests/unit/test_base.py::TestTimeSeries::test_repr_html
)
distutils_enable_tests pytest
diff --git a/dev-python/pyout/Manifest b/dev-python/pyout/Manifest
index 551424495..5878b2e20 100644
--- a/dev-python/pyout/Manifest
+++ b/dev-python/pyout/Manifest
@@ -1,2 +1,2 @@
-DIST pyout-0.7.1.tar.gz 180439 BLAKE2B b64808edfa013c8460961afacbe70caad4f3c0520d8b87656e909e278534bf111154fd31a186f95246d3084671c841ea421ed52118ddeee3f08f21106f2f80b1 SHA512 66338ce6dbf1e4ee6a187993609f762fcd2f8dddd981bc976b3240b6ecd461ba1fd47b9f08b91fc29853ce88e26158c7047de0adfcf28a0dd66869adfad5ab71
DIST pyout-0.7.2.tar.gz 181753 BLAKE2B 780e536921151f81097e5dee7c74cfa086153f916fc9b9fd684f01008ada34102ba33ee7bdd3dd8cc4ccf89a8d9821ec0aecdbd87bc356abf25c6e4fe32d4c5a SHA512 e7be6f7829f6b09ead64c596cfdecfa45073af0a1da15401702327e141bbfae10e7968ee5e332358aa04bfc7ddf71b7b6caf2d5877aca8514e4ba544d3b1670a
+DIST pyout-0.7.3.tar.gz 45726 BLAKE2B 4c5bc42b835fefd3db5d97db46c086ec2a7ca488a339813937f6e795a5fef699451dd67cd5078737f4f2bc47a36c96e2cb9f0010645fa45ebd288d24b5e0c3ba SHA512 784a7dd5b1eb811073466828f81783f89e3a251e05bc49edf124cdfc916c2447982299c83b087942845b61791481850f8c89379eea920e91d35c8abc2cbeb8ef
diff --git a/dev-python/pyout/pyout-0.7.1-r1.ebuild b/dev-python/pyout/pyout-0.7.3.ebuild
index 9cd796883..7246139ee 100644
--- a/dev-python/pyout/pyout-0.7.1-r1.ebuild
+++ b/dev-python/pyout/pyout-0.7.3.ebuild
@@ -3,17 +3,17 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
DESCRIPTION="Terminal styling for structured data"
HOMEPAGE="https://github.com/pyout/pyout"
-SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
SLOT="0"
LICENSE="MIT"
KEYWORDS="~amd64 ~x86"
-RESTRICT="test"
RDEPEND="
dev-python/jsonschema[${PYTHON_USEDEP}]
@@ -27,9 +27,7 @@ DEPEND="
distutils_enable_tests pytest
-
-PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" )
-
+#PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" )
python_prepare_all() {
sed -i -e '/pytest-runner/d' setup.py || die
diff --git a/dev-python/python-igraph/python-igraph-0.10.4.ebuild b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
index 5ef24cedf..3ee6e1eb4 100644
--- a/dev-python/python-igraph/python-igraph-0.10.4.ebuild
+++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
@@ -14,7 +14,7 @@ S="${WORKDIR}/igraph-${PV}"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
>=dev-libs/igraph-$(ver_cut 1-2)
diff --git a/dev-python/pytorch-lightning/Manifest b/dev-python/pytorch-lightning/Manifest
deleted file mode 100644
index 2876dd7d6..000000000
--- a/dev-python/pytorch-lightning/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pytorch-lightning-1.8.6.tar.gz 576205 BLAKE2B a8a2d0a14d331303f45319f3aa840f4bc0a21e6c6ac3bac8e7d72f92947126f64e06da36a62eed6ff0c33caae935905348ccb1379b53ee73cd35e569973d6551 SHA512 85e6474637f5d237c22cf0775ee8d6f56c000c3c0376af2087b68d0c4311608d35d02e856ef1dddca1c481e531ee0fb246357b91f5c185637a740c80a0152510
diff --git a/dev-python/pytorch-lightning/metadata.xml b/dev-python/pytorch-lightning/metadata.xml
deleted file mode 100644
index df24db4ac..000000000
--- a/dev-python/pytorch-lightning/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">Lightning-AI/lightning</remote-id>
- <remote-id type="pypi">pytorch-lightning</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
deleted file mode 100644
index a775be3bf..000000000
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_SINGLE_IMPL=1
-PYPI_NO_NORMALIZE=1
-inherit distutils-r1 pypi
-
-DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
-HOMEPAGE="https://github.com/Lightning-AI/lightning"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/fsspec[${PYTHON_USEDEP}]
- sci-visualization/tensorboard[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/ratelimit[${PYTHON_USEDEP}]
- ')
-"
diff --git a/dev-python/rich-click/Manifest b/dev-python/rich-click/Manifest
new file mode 100644
index 000000000..ae8d92c2f
--- /dev/null
+++ b/dev-python/rich-click/Manifest
@@ -0,0 +1 @@
+DIST rich-click-1.7.2.tar.gz 39362 BLAKE2B c4ad70d449ce9ceb3d9bbbccf7c7d3cd43386c35061d60c6395ff7845f606558af36a7c465a3393484008ece244f8e684ca9d71cea14463f04cac21803108543 SHA512 f4046e54874c4f3cc4f77651fdeb1f888d9435ff282f54d320c16c7c42f57c48018c0159230e780684336d29edff6e654454b8940b5b8df5a19139d2219c671b
diff --git a/dev-python/rich-click/metadata.xml b/dev-python/rich-click/metadata.xml
new file mode 100644
index 000000000..79a5238bd
--- /dev/null
+++ b/dev-python/rich-click/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">ewels/rich-click</remote-id>
+ <remote-id type="pypi">rich-click</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/rich-click/rich-click-1.7.2.ebuild b/dev-python/rich-click/rich-click-1.7.2.ebuild
new file mode 100644
index 000000000..e642303e2
--- /dev/null
+++ b/dev-python/rich-click/rich-click-1.7.2.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+PYPI_NO_NORMALIZE=1
+inherit pypi distutils-r1
+
+DESCRIPTION="Format click help output nicely with rich"
+HOMEPAGE="https://pypi.org/project/rich-click/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]"
+
+RESTRICT="test"
+# ModuleNotFoundError: No module named 'tests.conftest'
+#distutils_enable_tests pytest
diff --git a/dev-python/ripser/ripser-0.6.4.ebuild b/dev-python/ripser/ripser-0.6.4.ebuild
index e0ea6f24b..21d6b6ccd 100644
--- a/dev-python/ripser/ripser-0.6.4.ebuild
+++ b/dev-python/ripser/ripser-0.6.4.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="https://ripser.scikit-tda.org/"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
RDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
diff --git a/dev-python/schema/Manifest b/dev-python/schema/Manifest
deleted file mode 100644
index e69b4b33b..000000000
--- a/dev-python/schema/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST schema-0.7.4.tar.gz 41340 BLAKE2B 3f897e7443da2a227e58e4f8655d75d2dfc9da95faca9f1737488ea7d95eefabf55c0606864164a7146d89fdb22cfb522e7e89bd648b001ac1cfe2e8e8ba4020 SHA512 6dd0ee8348fde4c6a9a39baf2b0fafff851f10ea581b16f438717d5435481f34829176bb4b82ecdd092da26332fd114fab856691b755ecf8e5648fb2233a0daf
diff --git a/dev-python/schema/metadata.xml b/dev-python/schema/metadata.xml
deleted file mode 100644
index 440ea4da1..000000000
--- a/dev-python/schema/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="pypi">schema</remote-id>
- <remote-id type="github">keleshev/schema</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild
deleted file mode 100644
index faa082e58..000000000
--- a/dev-python/schema/schema-0.7.4.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 pypy3 )
-inherit distutils-r1 pypi
-
-DESCRIPTION="Schema validation just got Pythonic"
-HOMEPAGE="https://pypi.org/project/schema/"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )"
-
-distutils_enable_tests pytest
-
-src_prepare() {
- distutils-r1_src_prepare
-
- # Prevent schema from unconditionally requiring the last-rited contextlib2,
- # which schema actually conditionally requires only under EOL Python 2.x.
- sed -i -e '/\binstall_requires=/d' setup.py || die
-}
diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest
index 9beeb00c6..eca03bc0e 100644
--- a/dev-python/snakemake/Manifest
+++ b/dev-python/snakemake/Manifest
@@ -1 +1 @@
-DIST snakemake-7.32.3.gh.tar.gz 8886818 BLAKE2B d407e8bf65bacb5a1d3decaa54caee602f6588239c6c42062897bfaee3a13d6afd6d4afcab85a3b1de0994e2d46fcd4851e9dfd500b164a5c05a73aeba38f92a SHA512 675d1206bda44309f38b4cde441584f4c6243c1c63fb3ab07a781e3538c604e66ef013f75a27dd3b11f620611cf583e4e2fca5531a5492cef5cbd85f44f0b77e
+DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
diff --git a/dev-python/snakemake/snakemake-7.32.3.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild
index 94dd9e925..711aac286 100644
--- a/dev-python/snakemake/snakemake-7.32.3.ebuild
+++ b/dev-python/snakemake/snakemake-7.32.4.ebuild
@@ -42,6 +42,7 @@ RDEPEND="
dev-python/jinja[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/nbformat[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
dev-python/psutil[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
diff --git a/dev-python/spectra/Manifest b/dev-python/spectra/Manifest
new file mode 100644
index 000000000..97bcfc93a
--- /dev/null
+++ b/dev-python/spectra/Manifest
@@ -0,0 +1 @@
+DIST spectra-0.0.11.tar.gz 18819 BLAKE2B 45ceefa8d2bab051a8fa8ee687f9fa25f6436e66987bb84c6982f64a522fb0b04120e068ef890f4b04f6626a130c5df1e81090913c143df1e82bda5ca3a01d4d SHA512 7b4e244ba200df8c6d7cff19ddf36a5af6cfe8cf6f89283f8dbb64345a3eb85b4f62456e3c75b7c8ce2d24e01c8a123a5763605b1e702903fe16839966e47b32
diff --git a/dev-python/spectra/metadata.xml b/dev-python/spectra/metadata.xml
new file mode 100644
index 000000000..9332eceee
--- /dev/null
+++ b/dev-python/spectra/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">jsvine/spectra</remote-id>
+ <remote-id type="pypi">spectra</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/spectra/spectra-0.0.11.ebuild b/dev-python/spectra/spectra-0.0.11.ebuild
new file mode 100644
index 000000000..d0df23724
--- /dev/null
+++ b/dev-python/spectra/spectra-0.0.11.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/spectra/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/colormath[${PYTHON_USEDEP}]"
+
+# requires nose
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest
index 28ed71b4c..bdf3e4b60 100644
--- a/dev-python/spikeinterface/Manifest
+++ b/dev-python/spikeinterface/Manifest
@@ -1,2 +1,3 @@
DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef
DIST spikeinterface-0.97.0.tar.gz 6735715 BLAKE2B c11bee4306f8d96ae5cd09cf1b852e267c1db6caa13565f6364cd65ee36fe62c04589e8e0657517003ed1dd6d76d25f60bef226820403111db4ed7717e8a20cd SHA512 befdf3382de6aad2ef2c72e3bbdf64fbee1c1f72f83610ca8bba2f8693992c84b515f8c000dc6b3609825347b0bcd85b026747633e90777d7fdd30dc0ae0ef13
+DIST spikeinterface-0.99.1.tar.gz 11475537 BLAKE2B 9427079f70020b882c7bdbaadb9b60508827f1131f3aeb4fa8fdaaada73f2aa2cb3ec018f87467cd2a7505bea435d6bcf04d9784d921829533ebf41d686d72bb SHA512 4dd513aa6eb8af58fa9d1a80671973b01cb81643588c4522f3f87cfd0ccebcfb7a1f2926e554bc7dadbb2201fc0b2f2873b0003483dd5ca578b5a76d4cce05a2
diff --git a/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
new file mode 100644
index 000000000..a428775eb
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines."
+HOMEPAGE="https://github.com/SpikeInterface/spikeinterface"
+SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+# Reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/2339
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/neo[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ extractors? (
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+ full? (
+ dev-python/distinctipy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/xarray[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+ )
+"
+# Also wants:
+# # Extractors:
+# MEArec
+# pyedflib
+# sonpy
+# dev-python/hdf5storage (in ::science, masked)
+
+distutils_enable_tests pytest
diff --git a/dev-python/tridesclous/Manifest b/dev-python/tridesclous/Manifest
deleted file mode 100644
index 4bcef3213..000000000
--- a/dev-python/tridesclous/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST tridesclous-1.6.4.tar.gz 571689 BLAKE2B c941c159a0aed2f69dd098b5a7073898f305aa04c4db4753fc7de135cf87866fe8857a89b2d1248e3a2dada09229195f2dad557c0c110ac2f061dfe39c8aa257 SHA512 29182af03dc9219c422e37000ceb40787db89408f66b94201bbb2226f97ef251140eafa28a77554aaa1539978c46eece0156d2941c8156212499f544cf42740c
-DIST tridesclous-1.6.6.gh.tar.gz 11798502 BLAKE2B af9eb4d4e899f2a065d37e6daaae9ad04209b3d10c250957985ef3603e5d5727947dafff75adf5bb892a4ccbbf2f575f682bd601afcf36bda48f5f7a2af6ab26 SHA512 b101a8a8c2e95b7eb51b7d24d2708a30421be63d48d5a7047dfa2be3ce0f15ce02ce518d5516d5fae3d040cb0d2037a49afd34fdbd03bc641dc42014d8861d0d
diff --git a/dev-python/tridesclous/tridesclous-1.6.4.ebuild b/dev-python/tridesclous/tridesclous-1.6.4.ebuild
deleted file mode 100644
index 131156160..000000000
--- a/dev-python/tridesclous/tridesclous-1.6.4.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 pypi
-
-DESCRIPTION="offline/online spike sorting"
-HOMEPAGE="https://github.com/tridesclous/tridesclous"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="gui test"
-
-RDEPEND="
- <dev-python/numpy-1.24.0[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/hdbscan[${PYTHON_USEDEP}]
- dev-python/loky[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/neo[${PYTHON_USEDEP}]
- dev-python/numba
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- gui? (
- dev-python/PyQt5[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-# Network sandboxing, this is sadly more than half the test suite :(
-EPYTEST_DESELECT=(
- tridesclous/tests/test_cleancluster.py::test_auto_split
- tridesclous/tests/test_cleancluster.py::test_trash_not_aligned
- tridesclous/tests/test_cleancluster.py::test_auto_merge
- tridesclous/tests/test_cleancluster.py::test_trash_low_extremum
- tridesclous/tests/test_cleancluster.py::test_trash_small_cluster
- tridesclous/tests/test_cluster.py::test_sawchaincut
- tridesclous/tests/test_cluster.py::test_pruningshears
- tridesclous/tests/test_decomposition.py::test_all_decomposition
- tridesclous/tests/test_export.py::test_export
- tridesclous/tests/test_export.py::test_export_catalogue_spikes
- tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor
- tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_signals
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms
- tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d
- tridesclous/tests/test_metrics.py::test_all_metrics
- tridesclous/tests/test_metrics.py::test_cluster_ratio
- tridesclous/tests/test_peeler.py::test_peeler_geometry
- tridesclous/tests/test_peeler.py::test_peeler_geometry_cl
- tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue
- tridesclous/tests/test_peeler.py::test_peeler_several_chunksize
- tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor
- tridesclous/tests/test_peeler.py::test_export_spikes
- tridesclous/tests/test_report.py::test_summary_catalogue_clusters
- tridesclous/tests/test_report.py::test_summary_noise
- tridesclous/tests/test_report.py::test_summary_after_peeler_clusters
- tridesclous/tests/test_report.py::test_generate_report
- tridesclous/tests/test_autoparams.py::test_get_auto_params
- tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue
- tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude
- tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection
- tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps
- tridesclous/tests/test_dataio.py::test_DataIO
- tridesclous/tests/test_dataio.py::test_DataIO_probes
- tridesclous/tests/test_datasets.py::test_download_dataset
- tridesclous/tests/test_datasets.py::test_get_dataset
- tridesclous/tests/test_datasource.py::test_RawDataSource
- tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator
- tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines
- tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks
- tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry
- tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines
- tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width
- tridesclous/tests/test_tools.py::test_fix_prb_file_py2
-)
-
-python_test() {
- local EPYTEST_IGNORE=(
- tridesclous/online/tests/*
- )
- if use !gui ; then
- local EPYTEST_IGNORE+=(
- tridesclous/gui/*
- )
- fi
- epytest
-}
diff --git a/dev-python/tridesclous/tridesclous-1.6.6.ebuild b/dev-python/tridesclous/tridesclous-1.6.6.ebuild
deleted file mode 100644
index fb401397f..000000000
--- a/dev-python/tridesclous/tridesclous-1.6.6.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="offline/online spike sorting"
-HOMEPAGE="https://github.com/tridesclous/tridesclous"
-SRC_URI="https://github.com/tridesclous/tridesclous/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="gui test"
-
-RDEPEND="
- <dev-python/numpy-1.24.0[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/hdbscan[${PYTHON_USEDEP}]
- dev-python/loky[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/neo[${PYTHON_USEDEP}]
- dev-python/numba
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- gui? (
- dev-python/PyQt5[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-# Network sandboxing, this is sadly more than half the test suite :(
-EPYTEST_DESELECT=(
- tridesclous/tests/test_cleancluster.py::test_auto_split
- tridesclous/tests/test_cleancluster.py::test_trash_not_aligned
- tridesclous/tests/test_cleancluster.py::test_auto_merge
- tridesclous/tests/test_cleancluster.py::test_trash_low_extremum
- tridesclous/tests/test_cleancluster.py::test_trash_small_cluster
- tridesclous/tests/test_cluster.py::test_sawchaincut
- tridesclous/tests/test_cluster.py::test_pruningshears
- tridesclous/tests/test_decomposition.py::test_all_decomposition
- tridesclous/tests/test_export.py::test_export
- tridesclous/tests/test_export.py::test_export_catalogue_spikes
- tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor
- tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_signals
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms
- tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d
- tridesclous/tests/test_metrics.py::test_all_metrics
- tridesclous/tests/test_metrics.py::test_cluster_ratio
- tridesclous/tests/test_peeler.py::test_peeler_geometry
- tridesclous/tests/test_peeler.py::test_peeler_geometry_cl
- tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue
- tridesclous/tests/test_peeler.py::test_peeler_several_chunksize
- tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor
- tridesclous/tests/test_peeler.py::test_export_spikes
- tridesclous/tests/test_report.py::test_summary_catalogue_clusters
- tridesclous/tests/test_report.py::test_summary_noise
- tridesclous/tests/test_report.py::test_summary_after_peeler_clusters
- tridesclous/tests/test_report.py::test_generate_report
- tridesclous/tests/test_autoparams.py::test_get_auto_params
- tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue
- tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude
- tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection
- tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps
- tridesclous/tests/test_dataio.py::test_DataIO
- tridesclous/tests/test_dataio.py::test_DataIO_probes
- tridesclous/tests/test_datasets.py::test_download_dataset
- tridesclous/tests/test_datasets.py::test_get_dataset
- tridesclous/tests/test_datasource.py::test_RawDataSource
- tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator
- tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines
- tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks
- tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry
- tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines
- tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width
- tridesclous/tests/test_tools.py::test_fix_prb_file_py2
-)
-
-python_test() {
- local EPYTEST_IGNORE=(
- tridesclous/online/tests/*
- )
- if use !gui ; then
- local EPYTEST_IGNORE+=(
- tridesclous/gui/*
- )
- fi
- epytest
-}
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
index f597d0175..a4ecbb65f 100644
--- a/dev-python/typish/typish-1.9.3.ebuild
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -17,7 +17,7 @@ SRC_URI="
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+KEYWORDS="~amd64"
BDEPEND="
test? (
diff --git a/dev-python/uhi/Manifest b/dev-python/uhi/Manifest
new file mode 100644
index 000000000..199ee2a62
--- /dev/null
+++ b/dev-python/uhi/Manifest
@@ -0,0 +1 @@
+DIST uhi-0.4.0.tar.gz 52953 BLAKE2B b0c16c58c676f405d7b46398507968e92e4c3939a53224b49cbd935c3473800341903a9e9c5e3c598d68f171a9ec098feedaa774b2bbfe780581a663e99b2592 SHA512 4f7f0bdce3fef14c8789e0860956d6d4d2ab91e48eb95b6bceb67aef47b23a260f0f33a565c052fe48933f108adfe32f4c28c8cf874cc908929d407687bbc385
diff --git a/dev-python/uhi/metadata.xml b/dev-python/uhi/metadata.xml
new file mode 100644
index 000000000..c1ee047a1
--- /dev/null
+++ b/dev-python/uhi/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ This is a package meant primarily for documenting histogram indexing and the PlottableHistogram Protocol and any future cross-library standards. It also contains the code for the PlottableHistogram Protocol, to be used in type checking libraries wanting to conform to the protocol. Eventually, it might gain a set of tools for testing conformance to UHI indexing, as well. It is not usually a runtime dependency, but only a type checking, testing, and/or docs dependency in support of other libraries (such as boost-histogram 0.13+, hist 2.1+, mplhep 0.2.15+, uproot 4+, and histoprint 2+). There are a few useful runtime usable components (listed below). It requires Python 3.6+. See what's new.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">uhi</remote-id>
+ <remote-id type="github">scikit-hep/uhi</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/uhi/uhi-0.4.0.ebuild b/dev-python/uhi/uhi-0.4.0.ebuild
new file mode 100644
index 000000000..380e3bdbd
--- /dev/null
+++ b/dev-python/uhi/uhi-0.4.0.ebuild
@@ -0,0 +1,27 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Universal Histogram Interface"
+HOMEPAGE="https://github.com/scikit-hep/uhi"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+ test? (
+ dev-python/pytest[${PYTHON_USEDEP}]
+ dev-python/boost-histogram[${PYTHON_USEDEP}]
+ )
+"
+BDEPEND="
+ ${RDEPEND}
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/umap-learn/Manifest b/dev-python/umap-learn/Manifest
deleted file mode 100644
index 911c8ce27..000000000
--- a/dev-python/umap-learn/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST umap-learn-0.5.2.tar.gz 86805 BLAKE2B b1381647c947472a10472475477d3f4c91446606b1ee7235dd91c65606e4c54119a706864364845ad34d74db33760013f93fd6f2a3b7e75a5161bbbc216a2c5a SHA512 89d7e7680554c63429eee1c0702f6b0b03f5a29d7770af0630a15bd50aeeaa3c272d87f2380ec71a60accea96fe9936c7c807bfe4143c6afa1444741c865eef5
diff --git a/dev-python/umap-learn/metadata.xml b/dev-python/umap-learn/metadata.xml
deleted file mode 100644
index 36f603448..000000000
--- a/dev-python/umap-learn/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>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="pypi">umap-learn</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
deleted file mode 100644
index ea2769294..000000000
--- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-PYPI_NO_NORMALIZE=1
-inherit distutils-r1 pypi
-
-DESCRIPTION="Uniform Manifold Approximation and Projection"
-HOMEPAGE="https://umap-learn.readthedocs.io/"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=dev-python/numba-0.49[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
- >=dev-python/pynndescent-0.5[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest
new file mode 100644
index 000000000..541d150c6
--- /dev/null
+++ b/dev-python/vector/Manifest
@@ -0,0 +1,2 @@
+DIST vector-1.1.1.tar.gz 289916 BLAKE2B 35281c498f244b0307d744a20d0364c4cf664d0bd08a4f17d8d3110aa4eae6d7f66e3b51b4e9847f31d3a6ab943248115221dee4dcd3c3f2f8c47842001b553a SHA512 b1e195751de35ca2c67749b6b2b330db8a29e023f42e9b454adc8fc2408c29b5926b39e9ed6dc6a93f97006fbfb286a2217be8b14cb0eb2b96c9538f6c3943e6
+DIST vector-1.3.1.tar.gz 299581 BLAKE2B 36e99e814b5e8afc7a0179acce74f399db8f76e3c3c59ebbb5a2616bfa8f34ca2cfabe9e42752226dbabbdcd77fc15a4725c4e296f5329533a85cade8fcfae0c SHA512 524752789f6ea0201e1bb3dc09e7396a8bc64a1ee78ccab383bbe968134783bbf7499948784b141353612649f8188d0cb93147b53afdf37ba26f812d8ebd84b0
diff --git a/dev-python/vector/metadata.xml b/dev-python/vector/metadata.xml
new file mode 100644
index 000000000..b6aaa9af7
--- /dev/null
+++ b/dev-python/vector/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Vector is a Python 3.8+ library (Python 3.6 and 3.7 supported till v0.9.0 and v1.0.0, respectively) for 2D, 3D, and Lorentz vectors, especially arrays of vectors, to solve common physics problems in a NumPy-like way.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">vector</remote-id>
+ <remote-id type="github">scikit-hep/vector</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/vector/vector-1.1.1.ebuild b/dev-python/vector/vector-1.1.1.ebuild
new file mode 100644
index 000000000..8b5a45c3d
--- /dev/null
+++ b/dev-python/vector/vector-1.1.1.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
diff --git a/dev-python/vector/vector-1.3.1.ebuild b/dev-python/vector/vector-1.3.1.ebuild
new file mode 100644
index 000000000..8b5a45c3d
--- /dev/null
+++ b/dev-python/vector/vector-1.3.1.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
diff --git a/dev-python/wraps/files/wraps-0.1.0-includes.patch b/dev-python/wraps/files/wraps-0.1.0-includes.patch
deleted file mode 100644
index a5184e52e..000000000
--- a/dev-python/wraps/files/wraps-0.1.0-includes.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
-+++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
-@@ -20,8 +20,11 @@
- "Topic :: Utilities",
- "Typing :: Typed",
- ]
--
--include = ["CHANGELOG.md", "tests"]
-+include = [
-+ { path = "LICENSE", format = "sdist" },
-+ { path = "README.md", format = "sdist" },
-+ { path = "CHANGELOG.md", format = "sdist" },
-+]
-
- [tool.poetry.urls]
- Discord = "https://nekit.dev/discord"
diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest
index 7c74e59be..b76de8dcc 100644
--- a/dev-python/xgboost/Manifest
+++ b/dev-python/xgboost/Manifest
@@ -1 +1,2 @@
DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b
+DIST xgboost-2.0.3.tar.gz 1048322 BLAKE2B 2140b805aaed441da956e47cbfe08d84db1b0af96844771f4912480b05346b18632051886b237bef3e2b55a80f09c1db996be4dfeff48c942220079c4a4a149c SHA512 93614a9ad9d0a256cc31586b701c46eef4353df76c3eac26f39df23c8c02fa9ec95e72a0cea0b51bc3e416b81b3ac557ed361afeda246376a7b561bb6f7da579
diff --git a/dev-python/xgboost/xgboost-2.0.3.ebuild b/dev-python/xgboost/xgboost-2.0.3.ebuild
new file mode 100644
index 000000000..60302a1cb
--- /dev/null
+++ b/dev-python/xgboost/xgboost-2.0.3.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517="standalone"
+inherit distutils-r1 pypi
+
+DESCRIPTION="XGBoost Python Package"
+HOMEPAGE="
+ https://xgboost.readthedocs.io
+ https://github.com/dmlc/xgboost/
+"
+
+REQUIRED_USE="
+ ${PYTHON_REQUIRED_USE}
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/yte/Manifest b/dev-python/yte/Manifest
index e0bd09674..2ad6d3366 100644
--- a/dev-python/yte/Manifest
+++ b/dev-python/yte/Manifest
@@ -1 +1 @@
-DIST yte-1.5.1.tar.gz 6764 BLAKE2B ebe65bf961e028cb87ec0c7f8e552bcd5890329c0e66b9227becc21480a3b3ce5734090acc3fe32d44efcf2ecc7a2456f7056e75eccf7def75781910bef7dbc5 SHA512 5012e47d1ad8c20cb755b9c605d866d56850f0d16381f74c8d405232de95f43a6ea9ab65eb07cf23a14eeaa18e9105e0f0642a54f2847584bfffe432ce909267
+DIST yte-1.5.4.tar.gz 6352 BLAKE2B f304d1846c0f54949397570564f6bf9d048cd26a99a87feb62f8944403fd0f619546ed0989a2f9fda381c0f39adaa4d987ff66eb4e3bcbce107a460091c1b775 SHA512 eb61553d4c17f6d39f954ea5ab1a09a83009ab8f6f653afbf780b7a30f355e149b4508f8e3755a804f245246e0a1184c74be995f1477e1d2d27bc536bc1ff1f7
diff --git a/dev-python/yte/yte-1.5.1.ebuild b/dev-python/yte/yte-1.5.4.ebuild
index bb3b6354a..ad7b669b1 100644
--- a/dev-python/yte/yte-1.5.1.ebuild
+++ b/dev-python/yte/yte-1.5.4.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=poetry
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit pypi distutils-r1
@@ -20,5 +20,3 @@ RDEPEND="
dev-python/plac[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
"
-
-distutils_enable_tests pytest
diff --git a/dev-python/zarr/Manifest b/dev-python/zarr/Manifest
index 87617bcb1..bb2213da1 100644
--- a/dev-python/zarr/Manifest
+++ b/dev-python/zarr/Manifest
@@ -1,2 +1,3 @@
-DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65
DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
+DIST zarr-2.14.2.tar.gz 3589944 BLAKE2B 5e7de6c3a2bd9bd970b07bdfe1d51f14ad0e50bac37f2fbad91d98066d5239d237fa5af8cfef2f0a1ab4461dba4eeaed1db9fa0a4a1bfcd1757d54da4bbb15f7 SHA512 cc1eb40cd3723e87916e84f958d26df6353fc1e767e33a986068e182ad2a83c2dd7eb4939bf12ff45d4de49d822a0e6cb0afb5a5f1292d4c196f812d48939191
+DIST zarr-2.16.1.tar.gz 3597771 BLAKE2B 459f8022b3a4e3298b0f9650738713f6c13bb474ae50005b9387fefc87360f6358e4899037b26b9893d87298b14606d7b29bc1539fc8fa1479a08b30f2c8323b SHA512 e3b7c234c6376bea535d47304d83ee5b4d8b4bfc6952dde5e0bf1276833c1f427c98a7af0867f351e0139404d3729024b591a1f9b2242e219846a994e0762ee5
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.14.2.ebuild
index f18e92d44..f18e92d44 100644
--- a/dev-python/zarr/zarr-2.11.3.ebuild
+++ b/dev-python/zarr/zarr-2.14.2.ebuild
diff --git a/dev-python/zarr/zarr-2.16.1.ebuild b/dev-python/zarr/zarr-2.16.1.ebuild
new file mode 100644
index 000000000..f18e92d44
--- /dev/null
+++ b/dev-python/zarr/zarr-2.16.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/asciitree[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+ zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme
diff --git a/dev-python/zarr_checksum/Manifest b/dev-python/zarr_checksum/Manifest
index ec799eebf..5ca7cc376 100644
--- a/dev-python/zarr_checksum/Manifest
+++ b/dev-python/zarr_checksum/Manifest
@@ -1 +1,2 @@
DIST zarr_checksum-0.2.8.tar.gz 11824 BLAKE2B b26b6e1b9559e6572c95fb3700afada3c9040dfa1d26f736dcf6edfe4272c2e513f209286e24d7690de9fa2789297075469258f65edc8a2999fa2c4eee58f3ee SHA512 5c79611568decc8b9a353002e96c6ca73ec2c378debcba11f89feecb62089a78a4c3a8f4948971dd1a120a476dba7f357b23ba0b6edcf93d3f44dbb7c531feb5
+DIST zarr_checksum-0.4.0.tar.gz 11618 BLAKE2B 90c963f6540fd9a7a667f0a683b6c3d4a70230b4d71eb08f62a1cfecb20b7eb46b515b4cafc12b90fbc6c80fb83d5c5779682c6313bc56a819a4a8a5ff1843dc SHA512 e903bbc04847767dd14a0e0ad7e2fae47e97b18b813911b3bdb835e75454f573e8e1021c68f79cbf44fa21af64a4833f41ecb754a5b263e5d46dc0c7dc83447f
diff --git a/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
new file mode 100644
index 000000000..58cb87329
--- /dev/null
+++ b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=poetry
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Calculatine zarr checksums from local or cloud storage"
+HOMEPAGE="https://github.com/dandi/zarr_checksum"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/boto3[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index d249e7c33..f84e21730 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,3 +1,2 @@
-DIST dandi-0.51.0.tar.gz 233955 BLAKE2B 500a6290cba32f413610879357c0ee525d877575c4ad520818a556ae7f58f90c2aec88387dbb0ca78e7906b48673c2c2d3c9c457833727fb312e5ca6d75ce088 SHA512 e77fa803dd2707df8cab2318377a71c28abb8bdc6e2d086cb43daf24512f361e533d249dabd88bfc6c0de06e6332606ac2f3c57482ae9717fedb66da4e2e8d89
-DIST dandi-0.55.0.tar.gz 292471 BLAKE2B 2ccdba123c61025894a327d56163fd71cd0294b315b83396688903d969ba243fe2bb3ad9d2db5cf24d36254395a7de452d6e4ff4a65cf264f001a0cda527cd08 SHA512 e41f699a55cd75161048dd0e0334b84527ae0f4e02c81eedf7c8811b8bc50229488599f9601263e65a97fd815ce1d2cb41c94968fcc9ffde7726b72fe4e0180c
-DIST dandi-0.55.1.tar.gz 296372 BLAKE2B 06d1b020bc3362f64779da8a4d229c9919c1edee83b530bf248c7dfa591f97c10b08eb1e9cb2f54ec30d8e7a1bcc0ffe9ee8f925e0a51fb0ba3882699a605a33 SHA512 341f82b8b59ececf8addbb0a9087e2a5ace3b0c452d4da1d94c413daef594590d8350ba4421a077865a4eafbcefe4189478f385e8cfe0dd53a9e46c7782b3ce5
+DIST dandi-0.61.0.tar.gz 306755 BLAKE2B 8d279fddf4a9c390c91d09915d978f5709c297bb4284e8c8f3026ef9c94a9b2bab4b24409ff1d915550ab2564f8398a1afb236b226a41303264898de51deed42 SHA512 3cbd5c81c024cfca01c94fd2f9c794b22170f830a39c283f5cde1dfd998447287559457e324f81f46154fa38bf065720736da3be13a5668bc7453d091dd51869
+DIST dandi-0.61.2.tar.gz 306867 BLAKE2B 9a51c26f36d462e518241d40604726973727f17c70855136b6ea8e8402fb2c30ecc3adbbf7db6ed967bdb8c63a11da0809c09ae61f3a4996784b0b2083c1ec3a SHA512 9f4f3a02e62a3c4af3496a29faa18c696263e71dd2baf56c2925696c09e4c633a3a28a1fe30329764b98cba3006e4ccfe0884f5bae3d580f643f4cf946b2d291
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild
deleted file mode 100644
index c626dbe8b..000000000
--- a/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1 pypi
-
-MY_PN="dandi"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="DANDI command line client to facilitate common operations"
-HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="$(pypi_sdist_url dandi)"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test etelemetry"
-
-RDEPEND="
- <sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
- =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/click-didyoumean[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/fscacher[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/interleave[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/nwbinspector[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pycryptodome[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyout[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/semantic-version[${PYTHON_USEDEP}]
- dev-python/tenacity[${PYTHON_USEDEP}]
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/zarr[${PYTHON_USEDEP}]
- dev-python/zarr_checksum[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
- test? (
- dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
- dev-python/pyfakefs[${PYTHON_USEDEP}]
- dev-python/pytest-mock[${PYTHON_USEDEP}]
- media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
- )
-"
-# Upstream might be amenable to dropping opencv:
-# https://github.com/dandi/dandi-cli/issues/944
-
-S="${WORKDIR}/${MY_P}"
-
-distutils_enable_tests pytest
-
-src_prepare() {
- if use etelemetry; then
- default
- else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
- default
- sed -i "/etelemetry/d" setup.cfg
- fi
-}
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- epytest
-}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild
index beb2ffcc7..35ac320f5 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -21,10 +21,9 @@ KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ >=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}]
>=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
@@ -36,6 +35,7 @@ RDEPEND="
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyout[${PYTHON_USEDEP}]
@@ -44,9 +44,10 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
- dev-python/zarr_checksum[${PYTHON_USEDEP}]
+ >=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}]
"
BDEPEND="
@@ -65,22 +66,14 @@ BDEPEND="
S="${WORKDIR}/${MY_P}"
-PATCHES=(
- "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/dandi/dandi-cli/issues/1394
+ dandi/cli/tests/test_command.py::test_no_heavy_imports
)
distutils_enable_tests pytest
-src_prepare() {
- if use etelemetry; then
- default
- else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
- default
- sed -i "/etelemetry/d" setup.cfg
- fi
-}
-
python_test() {
export DANDI_TESTS_NONETWORK=1
epytest
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
index 060424cdb..760fb32b4 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -15,16 +15,18 @@ DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
SRC_URI="$(pypi_sdist_url dandi)"
+S="${WORKDIR}/${MY_P}"
+
LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- <sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
- =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
+ >=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}]
+ >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
+ >=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
@@ -36,6 +38,7 @@ RDEPEND="
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyout[${PYTHON_USEDEP}]
@@ -44,9 +47,10 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/yarl[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
- dev-python/zarr_checksum[${PYTHON_USEDEP}]
"
BDEPEND="
@@ -63,24 +67,14 @@ BDEPEND="
# Upstream might be amenable to dropping opencv:
# https://github.com/dandi/dandi-cli/issues/944
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/dandi/dandi-cli/issues/1394
+ dandi/cli/tests/test_command.py::test_no_heavy_imports
)
distutils_enable_tests pytest
-src_prepare() {
- if use etelemetry; then
- default
- else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
- default
- sed -i "/etelemetry/d" setup.cfg
- fi
-}
-
python_test() {
export DANDI_TESTS_NONETWORK=1
epytest
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
deleted file mode 100644
index 4d4715f95..000000000
--- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-From a363b68b79b3dd2004912640c90958882a918537 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
-Date: Wed, 4 May 2022 19:49:37 +0200
-Subject: [PATCH] Prepend to sys.path to fix versioneer in PEP517 mode
-
-Prepend the current directory to sys.path rather than appending it
-in order to fix the build in PEP517 mode properly. If the path
-is appended and versioneer is installed on the system, the system
-versioneer.py (i.e. the module used to install versioneer into projects)
-is imported rather than the local file, and the build fails:
-
-```
-Traceback (most recent call last):
- File "/usr/lib/python-exec/python3.10/gpep517", line 4, in <module>
- sys.exit(main())
- File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 136, in main
- return func(args)
- File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 44, in build_wheel
- wheel_name = backend.build_wheel(args.wheel_dir, args.config_json)
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel
- return self._build_with_temp_dir(['bdist_wheel'], '.whl',
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir
- self.run_setup()
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
- exec(compile(code, __file__, 'exec'), locals())
- File "setup.py", line 32, in <module>
- "version": versioneer.get_version(),
-AttributeError: module 'versioneer' has no attribute 'get_version'
-```
----
- setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index e8dddc985..05765009c 100755
---- a/setup.py
-+++ b/setup.py
-@@ -23,7 +23,7 @@
- # This is needed for versioneer to be importable when building with PEP 517.
- # See <https://github.com/warner/python-versioneer/issues/193> and links
- # therein for more information.
--sys.path.append(os.path.dirname(__file__))
-+sys.path.insert(0, os.path.dirname(__file__))
-
- try:
- import versioneer
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
deleted file mode 100644
index bcc3853d3..000000000
--- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/setup.cfg 2021-10-06 11:44:40.549337707 -0400
-+++ b/dsetup.cfg 2021-10-06 11:45:10.236935245 -0400
-@@ -30,8 +30,8 @@
- appdirs
- click
- click-didyoumean
-- dandischema ~= 0.6.0
-- etelemetry >= 0.2.2
-+ dandischema
-+ etelemetry
- fasteners
- fscacher
- # Specifying != might be what causes pip 19.3.1 first to install hdmf 1.5.1
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
new file mode 100644
index 000000000..4d4f42a03
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
@@ -0,0 +1,40 @@
+diff --git a/dandi/files/bases.py b/dandi/files/bases.py
+index 45f5929f..38bde34f 100644
+--- a/dandi/files/bases.py
++++ b/dandi/files/bases.py
+@@ -18,7 +18,6 @@ from dandischema.digests.dandietag import DandiETag
+ from dandischema.models import BareAsset, CommonModel
+ from dandischema.models import Dandiset as DandisetMeta
+ from dandischema.models import get_schema_version
+-from etelemetry import get_project
+ from packaging.version import Version
+ from pydantic import ValidationError
+ import requests
+@@ -737,6 +736,7 @@ def _get_nwb_inspector_version():
+ _current_nwbinspector_version = get_package_version(name="nwbinspector")
+ # Ensure latest version of NWB Inspector is installed and used client-side
+ try:
++ from etelemetry import get_project
+ max_version = Version(
+ get_project(repo="NeurodataWithoutBorders/nwbinspector")["version"]
+ )
+diff --git a/setup.cfg b/setup.cfg
+--- a/setup.cfg 2024-01-09 14:08:33.952653200 -0500
++++ b/setup.cfg 2024-01-25 01:45:34.594335960 -0500
+@@ -34,7 +34,6 @@
+ click >= 7.1
+ click-didyoumean
+ dandischema ~= 0.8.0
+- etelemetry >= 0.2.2
+ fasteners
+ fscacher >= 0.3.0
+ hdmf != 3.5.0
+@@ -147,9 +146,6 @@
+ [mypy-click_didyoumean.*]
+ ignore_missing_imports = True
+
+-[mypy-etelemetry.*]
+-ignore_missing_imports = True
+-
+ [mypy-fasteners.*]
+ ignore_missing_imports = True
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
index 78bcf187d..7875ed2b6 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,3 +1 @@
-DIST datalad-0.18.0.tar.gz 1425155 BLAKE2B 8d7cbf7f56b1de82c74fa823b2d4512112f1b4c4be106cac433c8db696b2e7f77da758c0bb62b7cb9fe0fbb08d49431dda2818d08d5c60b5052154895c335b33 SHA512 0df8276edc3872c73fee7286ea4e578648a6fb2a630fa49a4f8945e0d6ff88353d9b11d29d942c0ce22ed17a8223e71f99d8b519a6a8afbc2ac9e6da89d95ee5
-DIST datalad-0.18.1.tar.gz 1425820 BLAKE2B 574e864feb500062f829dfea3f9c8c51f9ad2e0e68e70966c2a5ea315fafffb259de9a0f57427c0aae1ee93c24ec9a3a91ef42637d109d912cf5b6c41ac07b11 SHA512 19f011428fe66d9f21410ae33276133f26cf2b1a367c23a83c56ab48a0e038837ba18163e12ab2d74eba7d0ec9ce2e660a21494ddba0da3a2df6da2c043c4aad
-DIST datalad-0.18.3.tar.gz 1435282 BLAKE2B 8077c0a639920e914b30598ded435ad74564f3947a187f5d57752cd22e0d435838db9bdd797a6d8d8cc54282e1303f5ca5d673d3674da09c678a47f35e8ef3f6 SHA512 06f5a73caaacffb35f11852f69ee48c485ebd1cce55e1440eb8686d8614a29809b01de2d129a48591fd66c02a59af9dcd064b0e7ead698842cc7f79d12af729c
+DIST datalad-0.19.6.tar.gz 1420979 BLAKE2B 49d8e19449652f284f89f99e6696c6d1abf7ddcc58a8eb00004c657be38ce2532ed9c11855dca4a0a8f82c55fbf1633f53ff2bdea063fd18ad946145d27a3404 SHA512 db7cd807a8106727f0b6f587be8c0ce3abcf0dc7cf72b4757e6b44650adca05482e6b0a6c1719050fba37660dcd5de2a6f27df044a8db180ac6855ee7ff8cbda
diff --git a/dev-vcs/datalad/datalad-0.18.0.ebuild b/dev-vcs/datalad/datalad-0.18.0.ebuild
deleted file mode 100644
index cd90c1db2..000000000
--- a/dev-vcs/datalad/datalad-0.18.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-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 -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- app-arch/p7zip
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/looseversion[${PYTHON_USEDEP}]
- dev-python/platformdirs[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wraps[${PYTHON_USEDEP}]
- dev-vcs/git-annex
- 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[${PYTHON_USEDEP}]
- )
-"
-BDEPEND="
- dev-python/packaging[${PYTHON_USEDEP}]
- test? (
- ${RDEPEND}
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/mypy[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-# Also wants test dep:
-# dev-python/types-requests
-# dev-python/types-python-dateutil
-
-distutils_enable_tests pytest
-
-python_test() {
- local -x DATALAD_TESTS_NONETWORK=1
- # see test groups in "tox.ini"
- epytest -k "not turtle and not slow and not usecase"
-}
diff --git a/dev-vcs/datalad/datalad-0.18.3.ebuild b/dev-vcs/datalad/datalad-0.18.3.ebuild
deleted file mode 100644
index cd90c1db2..000000000
--- a/dev-vcs/datalad/datalad-0.18.3.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- app-arch/p7zip
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/looseversion[${PYTHON_USEDEP}]
- dev-python/platformdirs[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wraps[${PYTHON_USEDEP}]
- dev-vcs/git-annex
- 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[${PYTHON_USEDEP}]
- )
-"
-BDEPEND="
- dev-python/packaging[${PYTHON_USEDEP}]
- test? (
- ${RDEPEND}
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/mypy[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-# Also wants test dep:
-# dev-python/types-requests
-# dev-python/types-python-dateutil
-
-distutils_enable_tests pytest
-
-python_test() {
- local -x DATALAD_TESTS_NONETWORK=1
- # see test groups in "tox.ini"
- epytest -k "not turtle and not slow and not usecase"
-}
diff --git a/dev-vcs/datalad/datalad-0.18.1.ebuild b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
index cd90c1db2..c95bc935f 100644
--- a/dev-vcs/datalad/datalad-0.18.1.ebuild
+++ b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
@@ -5,11 +5,11 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
@@ -32,7 +32,6 @@ RDEPEND="
dev-python/wraps[${PYTHON_USEDEP}]
dev-vcs/git-annex
downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
diff --git a/dev-vcs/datalad/metadata.xml b/dev-vcs/datalad/metadata.xml
index 8a6c00a2d..9c40d4f36 100644
--- a/dev-vcs/datalad/metadata.xml
+++ b/dev-vcs/datalad/metadata.xml
@@ -26,5 +26,6 @@
</use>
<upstream>
<remote-id type="github">datalad/datalad</remote-id>
+ <remote-id type="pypi">datalad</remote-id>
</upstream>
</pkgmetadata>
diff --git a/media-gfx/brlcad/brlcad-7.32.4.ebuild b/media-gfx/brlcad/brlcad-7.32.4.ebuild
index aa70351e9..180542cac 100644
--- a/media-gfx/brlcad/brlcad-7.32.4.ebuild
+++ b/media-gfx/brlcad/brlcad-7.32.4.ebuild
@@ -43,7 +43,7 @@ DEPEND="${RDEPEND}
)
doc? (
dev-libs/libxslt
- app-doc/doxygen
+ app-text/doxygen
)"
# Install into /usr/ not recommended by upstream due to possible file conflicts
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index 5d6a345ce..5f7c0ad4c 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -41,7 +41,7 @@ DEPEND="${RDEPEND}
)
doc? (
dev-libs/libxslt
- app-doc/doxygen
+ app-text/doxygen
)"
# Install into /usr/ not recommended by upstream due to possible file conflicts
diff --git a/media-libs/imglib2/Manifest b/media-libs/imglib2/Manifest
index 3ce824e00..eaae671d4 100644
--- a/media-libs/imglib2/Manifest
+++ b/media-libs/imglib2/Manifest
@@ -1 +1 @@
-DIST imglib2-6.2.0-sources.tar.gz 1088844 BLAKE2B 919b4261199415e0e575bba297900e5dc177785b70511d797a7f962675adaa61f19467d37d664c12a4dc91df3f1f6cd575309c7f508c4792706942670c6946c0 SHA512 e3381979884dac13d051f1754be0837049e430b71c382666d036fa1d3403bc233a7b39c3b0c587852b08d7d12851043111a1ab206e4049d117dedf847da687e9
+DIST imglib2-6.3.0-sources.tar.gz 1100228 BLAKE2B 65aba1c43980e98018154972bc143093d25e000148805d8ee75459f43dbe301cb0ae10463585fccc51dab28c926900e7c43df13696d408e79d2b4cb55ffadfc6 SHA512 9f6159379d1be6478a9cd53ee88241277761a5e569cd2042e26363f43394abc85d3ea2f72e592a57cff6f8b5f8f4cd46821a4168bf76939f7f77680844231748
diff --git a/media-libs/imglib2/imglib2-6.2.0.ebuild b/media-libs/imglib2/imglib2-6.3.0.ebuild
index d024676c7..4233e6795 100644
--- a/media-libs/imglib2/imglib2-6.2.0.ebuild
+++ b/media-libs/imglib2/imglib2-6.3.0.ebuild
@@ -24,7 +24,7 @@ else
https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ MAVEN_ID="net.imglib2:imglib2:6.3.0"
KEYWORDS="~amd64"
fi
diff --git a/media-libs/imglib2/imglib2-9999.ebuild b/media-libs/imglib2/imglib2-9999.ebuild
index d024676c7..4233e6795 100644
--- a/media-libs/imglib2/imglib2-9999.ebuild
+++ b/media-libs/imglib2/imglib2-9999.ebuild
@@ -24,7 +24,7 @@ else
https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ MAVEN_ID="net.imglib2:imglib2:6.3.0"
KEYWORDS="~amd64"
fi
diff --git a/media-libs/mmg/mmg-5.5.0.ebuild b/media-libs/mmg/mmg-5.5.0.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.0.ebuild
+++ b/media-libs/mmg/mmg-5.5.0.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/media-libs/mmg/mmg-5.5.1.ebuild b/media-libs/mmg/mmg-5.5.1.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.1.ebuild
+++ b/media-libs/mmg/mmg-5.5.1.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/media-libs/mmg/mmg-5.5.2.ebuild b/media-libs/mmg/mmg-5.5.2.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.2.ebuild
+++ b/media-libs/mmg/mmg-5.5.2.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
index 7270fbee7..66da0763c 100644
--- a/profiles/desc/lhapdf_sets.desc
+++ b/profiles/desc/lhapdf_sets.desc
@@ -14,4 +14,6 @@ nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid
nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
cteq66 - CTEQ66 LHAPDF grid
cteq6l1 - CTEQ6L1 LHAPDF grid
-mrst2004qed - MRST2004qed LHAPDF grid \ No newline at end of file
+mrst2004qed - MRST2004qed LHAPDF grid
+nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid
+nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid \ No newline at end of file
diff --git a/profiles/package.mask b/profiles/package.mask
index 3aac93f31..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,15 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (24 Oct 2023)
-# Depends on removed dev-python/nptyping
-dev-python/pynrrd
-dev-python/typish
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
-# Depends on removed dev-python/toml.
-# Alternatives are tomli or tomlkit
-dev-python/cadquery
-dev-python/cadquery-ocp
-dev-python/cadquery-pywrap
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index 57f4fc569..cf724a82a 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,4 +1,4 @@
-DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4
-DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b
-DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
-DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
+DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd
+DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa
+DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
index 002004bca..026dd0476 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..12} )
inherit python-single-r1
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
@@ -27,7 +27,13 @@ DEPEND="
${PYTHON_DEPS}
"
RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
+BDEPEND="dev-build/cmake"
+
+# Remove for next release:
+# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831
+PATCHES=(
+ "${FILESDIR}/${P}-gcc13.patch"
+)
src_install(){
einstalldocs
diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
new file mode 100644
index 000000000..3dd3f8c02
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
@@ -0,0 +1,49 @@
+From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001
+From: Bo YU <tsu.yubo@gmail.com>
+Date: Wed, 19 Jul 2023 18:42:04 +0800
+Subject: [PATCH] fix build issues due to gcc-13
+
+Signed-off-by: Bo YU <tsu.yubo@gmail.com>
+---
+ ext/include/llvm/Support/Signals.h | 1 +
+ src/common/pipeline/library_data.hpp | 1 +
+ src/common/sequence/nucl.hpp | 2 ++
+ 3 files changed, 4 insertions(+)
+
+diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h
+index e0a18e72f..148216b8f 100644
+--- a/ext/include/llvm/Support/Signals.h
++++ b/ext/include/llvm/Support/Signals.h
+@@ -14,6 +14,7 @@
+ #ifndef LLVM_SUPPORT_SIGNALS_H
+ #define LLVM_SUPPORT_SIGNALS_H
+
++#include <cstdint>
+ #include <string>
+
+ namespace llvm {
+diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp
+index 3cbaf0adb..1ffaa7b37 100644
+--- a/src/common/pipeline/library_data.hpp
++++ b/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+
+ #include <map>
+ #include <string>
++#include <cstdint>
+
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } }
+diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp
+index 9c7d6de13..e10e7f583 100755
+--- a/src/common/sequence/nucl.hpp
++++ b/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+
++#include <cstdint>
++
+ #include "utils/verify.hpp"
+
+ /**
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 0845ad7a4..5f573393e 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -10,8 +10,11 @@
<name>Gentoo Biology Project</name>
</maintainer>
<longdescription>
-truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
-hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
-dipspades is assembly module for highly polymorphic diploid genomes
-</longdescription>
+ truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+ hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+ dipspades is assembly module for highly polymorphic diploid genomes
+ </longdescription>
+ <upstream>
+ <remote-id type="github">ablab/spades</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index e8caa43d1..d1e783ff1 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,3 +1,4 @@
-DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6
-DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65
-DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b
+DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8
+DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6
+DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2
+DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
deleted file mode 100644
index e3e16f834..000000000
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${P}-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
deleted file mode 100644
index 1d9043ebb..000000000
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
deleted file mode 100644
index 149deede8..000000000
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-
-LICENSE="GPL-3+"
-SLOT="0"
-# SUMA error: https://ppb.chymera.eu/4223de.log
-KEYWORDS=""
-
-RDEPEND="
- dev-libs/libf2c
- dev-libs/expat
- media-libs/freeglut
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif
-"
-
-DEPEND="${RDEPEND}
- app-shells/tcsh
-"
-
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
-
-src_prepare() {
- # more easily applied here than via PATCHES at phase end.
- eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} + || die
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}" || die
- done
-}
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
new file mode 100644
index 000000000..557fbd579
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -0,0 +1,110 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+ https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+ https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${P}-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+ -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
new file mode 100644
index 000000000..20293877f
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+ https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+ https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+ -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
deleted file mode 100644
index 8c3e859f5..000000000
--- a/sci-biology/afni/files/afni-20.1.16-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration
diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
new file mode 100644
index 000000000..a357799e6
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
@@ -0,0 +1,39 @@
+diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt
+index 127193338..ba8825a7b 100644
+--- a/packaging/installation_components.txt
++++ b/packaging/installation_components.txt
+@@ -347,7 +347,6 @@ uniq_images, corebinaries
+ unu, corebinaries
+ waver, corebinaries
+ whereami, corebinaries
+-whirlgif, corebinaries
+ 3dMax, tcsh
+ 3dPAR2AFNI.pl, tcsh
+ @1dDiffMag, tcsh
+diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt
+index d53368390..8c8e9e1fb 100644
+--- a/src/CMakeLists_binaries.txt
++++ b/src/CMakeLists_binaries.txt
+@@ -209,7 +209,6 @@ foreach(
+ uniq_images
+ unu
+ whereami
+- whirlgif
+ )
+
+ add_afni_executable(${target} ${target}.c)
+diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE
+index f44103def..7ac08a87d 100644
+--- a/src/Makefile.INCLUDE
++++ b/src/Makefile.INCLUDE
+@@ -3495,11 +3495,6 @@ help_format:help_format.o
+ ibinom:ibinom.o
+ $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS)
+
+-## GIF animation
+-
+-whirlgif:whirlgif.h whirlgif.c
+- $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+-
+ extor.o:extor.c
+ $(CCFAST) -c extor.c $(INFLAGS)
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
index cbb8a4299..39ec69d08 100644
--- a/sci-biology/afni/metadata.xml
+++ b/sci-biology/afni/metadata.xml
@@ -13,6 +13,9 @@
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>
+ <use>
+ <flag name="whirlgif">Build optional whirlgif binary</flag>
+ </use>
<upstream>
<remote-id type="github">afni/afni</remote-id>
</upstream>
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
deleted file mode 100644
index bd7eecbcf..000000000
--- a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-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/behaviopy/Manifest b/sci-biology/behaviopy/Manifest
deleted file mode 100644
index 916b93320..000000000
--- a/sci-biology/behaviopy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc
diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild
deleted file mode 100644
index dc875e7a5..000000000
--- a/sci-biology/behaviopy/behaviopy-0.2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://github.com/TheChymera/behaviopy"
-SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="evaluation"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-
-python_prepare_all() {
- if ! use evaluation; then
- rm behaviopy/evaluation.py || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- cd behaviopy/examples || die
- echo "backend : Agg" > matplotlibrc || die
- for i in *py; do
- echo "Executing $i"
- ${EPYTHON} $i || die
- done
-}
diff --git a/sci-biology/behaviopy/metadata.xml b/sci-biology/behaviopy/metadata.xml
deleted file mode 100644
index a33886a68..000000000
--- a/sci-biology/behaviopy/metadata.xml
+++ /dev/null
@@ -1,26 +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">
- BehavioPy is a Python toolkit providing evaluation (e.g. event
- tracking) and plotting functions for behavioural data. Manual event
- tracking is done via a simple and configurable PsychoPy-based
- interface. Plotting functions are designed to work with preformatted
- data in CSV format (e.g. as exported by pandas), and use Seaborn and
- custom BehavioPy styles for maximum beautification.
- </longdescription>
- <upstream>
- <remote-id type="github">TheChymera/behaviopy</remote-id>
- </upstream>
- <use>
- <flag name="evaluation">Installs evaluation submodule.</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
deleted file mode 100644
index 69f3a963e..000000000
--- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500
-+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500
-@@ -1786,15 +1786,15 @@
- { int item_no = (int) client_data;
- switch (item_no)
- { case CMD_HELP_HTMLHELP:
-- { system("netscape "PREFIX"/cluster/html/index.html &");
-+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &");
- break;
- }
- case CMD_HELP_MANUAL:
-- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &");
-+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &");
- break;
- }
- case CMD_HELP_DOWNLOAD:
-- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
-+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
- break;
- }
- case CMD_HELP_FILEFORMAT:
-@@ -1852,7 +1852,7 @@
- XtManageChild(widget);
- free(helptext);
- n = 0;
-- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0);
-+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0);
- XtSetArg(args[n], XmNx, 10); n++;
- XtSetArg(args[n], XmNy, 410); n++;
- XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++;
diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest
deleted file mode 100644
index 271e4eb76..000000000
--- a/sci-biology/clview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1
-DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9
diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
deleted file mode 100644
index 2f200426d..000000000
--- a/sci-biology/clview/clview-0.1.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools"
-HOMEPAGE="https://sourceforge.net/projects/clview"
-SRC_URI="
- https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz"
-
-# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz
-# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/
-# contents. clview compiles against both versions with same warning messages from g++.
-#
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/
-# total 188
-# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Dec 2 22:23 .
-# drwx------ 5 mmokrejs portage 4096 Dec 2 22:23 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17 2008 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 906 Sep 14 2008 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec 2 22:23 AceParser.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22 2009 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 9200 Dec 16 2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 8844 Dec 2 22:23 GBase.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29 2008 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10 2008 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22 2009 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6246 Sep 14 2008 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec 2 22:23 LayoutParser.o
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/
-# total 268
-# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Nov 18 2008 .
-# drwxr-xr-x 3 mmokrejs mmokrejs 4096 Oct 18 2006 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs 9515 Nov 7 2005 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 886 Nov 7 2005 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov 7 2005 BitHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 7250 Nov 7 2005 GArgs.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 2507 Nov 7 2005 GArgs.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18 2008 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 8142 Nov 18 2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov 7 2005 GCdbYank.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 1831 Nov 7 2005 GCdbYank.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov 7 2005 GFastaFile.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov 7 2005 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov 7 2005 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 28 Nov 7 2005 GReadBuf.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 4022 Nov 7 2005 GReadBuf.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 48 Nov 7 2005 GShMem.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 4012 Nov 7 2005 GShMem.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov 7 2005 GString.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 8453 Nov 7 2005 GString.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov 7 2005 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6063 Nov 7 2005 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov 7 2005 gcdb.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6941 Nov 7 2005 gcdb.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 8998 Nov 7 2005 gcompress.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 3670 Nov 7 2005 gcompress.h
-#
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="=x11-libs/fox-1.6*"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_unpack() {
- unpack clview_src.tar.gz
-}
-
-src_prepare() {
- default
- # FIXME: we have to run `/usr/bin/fox-config --cflags' to yield
- # `-I/usr/include/fox-1.6'
- # similarly `fox-config --libs' to yield e.g.
- # `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11
- # -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm
- # -lcups -lnsl -lGLU -lGL'
- FOXVERSION=`WANT_FOX="1.6" fox-config --version`
- FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix`
- FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags`
- FOXLIBS=`WANT_FOX="1.6" fox-config --libs`
- einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}"
-
- sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile"
- sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile"
- sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile"
- sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile"
- sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile"
- sed -i "s#-I-#-I #" clview/Makefile || die
-
- # see tgi_cl/gcl/
- sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die
-}
-
-src_compile(){
- cd "${S}"/clview || die
- default
-}
-
-src_install() {
- # install at least the binaries for clview when we cannot compile it
- dobin clview/clview
-}
diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml
deleted file mode 100644
index 7adf609cd..000000000
--- a/sci-biology/clview/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">clview</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.1.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
index 86304f4f3..8ddd4007e 100644
--- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
+++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit check-reqs
DESCRIPTION="BIDS data files released with the DRLFOM publication"
-HOMEPAGE="http://chymera.eu/docs/focus/open-science/"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
SRC_URI="
https://zenodo.org/record/3598424/files/${P}.tar.xz
"
@@ -15,9 +15,6 @@ LICENSE="CC-BY-SA-4.0"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-RDEPEND=""
-DEPEND=""
-
pkg_pretend() {
CHECKREQS_DISK_BUILD="21G"
check-reqs_pkg_pretend
diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest
new file mode 100644
index 000000000..c158050fa
--- /dev/null
+++ b/sci-biology/fastp/Manifest
@@ -0,0 +1 @@
+DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76
diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild
new file mode 100644
index 000000000..70d5ce330
--- /dev/null
+++ b/sci-biology/fastp/fastp-0.23.4.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor"
+HOMEPAGE="https://github.com/OpenGene/fastp"
+SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="app-arch/libdeflate
+ dev-libs/isa-l"
+
+src_install() {
+ dodir /usr/bin
+ emake PREFIX="${ED}"/usr install
+}
diff --git a/dev-python/cadquery-ocp/metadata.xml b/sci-biology/fastp/metadata.xml
index a8bf5ee04..d51d87c5a 100644
--- a/dev-python/cadquery-ocp/metadata.xml
+++ b/sci-biology/fastp/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="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
</maintainer>
<upstream>
- <remote-id type="github">CadQuery/OCP</remote-id>
+ <remote-id type="github">OpenGene/fastp</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
deleted file mode 100644
index a3872acf0..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400
-+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400
-@@ -141,7 +141,7 @@
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
- #$(info $$CUDAVER is [${CUDAVER}])
--CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
-+CUDA_INSTALLATION = /opt/cuda
- GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION})
- LIB_CUDA = ${CUDA_INSTALLATION}/lib64
- INC_CUDA = ${CUDA_INSTALLATION}/include
diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
deleted file mode 100644
index 40409ec08..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400
-+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400
-@@ -29,6 +29,8 @@
- TMPCXXFLAGS_2=
- TMPNAME_1=
- TMPNAME_2=
-+cuda=1
-+cpu=1
-
- ifndef cuda
- ifndef cpu #Default single cpu, no threading
-@@ -74,7 +75,7 @@
- ifdef NVCC11
- NVCC=${NVCC11}
- endif
--NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
-+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
- ifeq ($(CLOBBER_CLANG),1)
- NVCCFLAGS+= -DCLOBBER_CLANG
- endif
diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
deleted file mode 100644
index 9ddb11a2b..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400
-+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400
-@@ -75,6 +75,7 @@
- #include <iostream>
- #include <fstream>
- #include <sstream>
-+#include <stdexcept>
- #include "NewNifti/NewNifti.h"
- #include "newmatio.h"
- #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
deleted file mode 100644
index 39737fd85..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch
+++ /dev/null
@@ -1,198 +0,0 @@
-From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:54:37 +1300
-Subject: [PATCH] Adjust the build system so it doesnt build packages
- externally provided by portage. Make the compilation flags more generic and
- easily adjustable. Make the build system stop at the first fault.
-
----
- build | 6 +++---
- config/buildSettings.mk | 20 ++++++++++----------
- config/common/buildproj | 8 +++++---
- config/common/vars.mk | 10 +++++-----
- extras/build | 8 ++++----
- src/mist-clean/Makefile | 2 +-
- 6 files changed, 28 insertions(+), 26 deletions(-)
-
-diff --git a/build b/build
-index 05dac06c..d90e407b 100755
---- a/build
-+++ b/build
-@@ -3,7 +3,7 @@
- if [ $# -ge 1 ] ; then
- PROJECTS="$@";
- else
-- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
-+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
- meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
- DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
- asl_mfree \
-@@ -80,8 +80,8 @@ xtract";
- done
- fi
-
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
- finalStatus=$?
- if [ $finalStatus -eq 0 ]; then
- echo "Build completed successfully.";
-diff --git a/config/buildSettings.mk b/config/buildSettings.mk
-index b2e1f150..04532fc2 100644
---- a/config/buildSettings.mk
-+++ b/config/buildSettings.mk
-@@ -18,7 +18,7 @@ MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
- INSTALL = install -p
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- DEPENDFLAGS = -MM
- MACHDBGFLAGS = -g
- #####################################################################
-@@ -124,19 +124,19 @@ endif # if Darwin
- #####################################################################
- ifeq ($(SYSTYPE), Linux)
- ############### System Vars #####################################
--CC = gcc
--CXX = c++
--CXX11 = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
-+CXX11 = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
--ARCHFLAGS = -m64
--ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
-+ARCHFLAGS =
-+ARCHLDFLAGS =
- PARALLELFLAGS = -fopenmp
--OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
- SGI_ANSI_FLAGS = -ansi -fullwarn
- ANSI_FLAGS = ${GNU_ANSI_FLAGS}
--RANLIB = echo
-+RANLIB = @@GENTOO_RANLIB@@
- FSLML = ${FSLDIR}/bin/fslml
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
-@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
- NVCC = ${CUDA_INSTALLATION}/bin/nvcc
- ############### External Libs #####################################
- # ZLIB library
--LIB_ZLIB = /lib64
--INC_ZLIB = /usr/include
-+#LIB_ZLIB = /lib64
-+#INC_ZLIB = /usr/include
- # QT library
- QTDIR = /usr/lib/qt3
- LIB_QT = ${QTDIR}/lib
-diff --git a/config/common/buildproj b/config/common/buildproj
-index 2f0f2b8f..48624a1f 100755
---- a/config/common/buildproj
-+++ b/config/common/buildproj
-@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
- fi
- PROJECTS="$@" ; export PROJECTS ;
-
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- FSLMASTERBUILD=1
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
-
-@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
- if [ -x ./fslconfig ] ; then
- . ./fslconfig ;
- fi
-- if ${MAKE} -k ${MAKEOPTIONS} ; then
-+ if ${MAKE} ${MAKEOPTIONS} ; then
- if ${MAKE} ${MAKEOPTIONS} install ; then
- installok=true;
- # Clean up after ourselves
-@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
- if [ $installok = false ] ; then
- echo " "
- echo "ERROR::Could not install $projname successfully" ;
-+ exit 1
- fi
- else
- echo " "
-@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
- echo " "
- echo " "
- errorprojs="$errorprojs $projname" ; export errorprojs ;
-+ exit 1
- fi
- fi
- done
-diff --git a/config/common/vars.mk b/config/common/vars.mk
-index b027b010..aeeae67c 100755
---- a/config/common/vars.mk
-+++ b/config/common/vars.mk
-@@ -24,15 +24,15 @@ USRINCFLAGS =
- USRCFLAGS =
- USRCXXFLAGS =
-
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
-
--AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
-
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCFLAGS}
-
--CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
-
- HFILES = *.h
- AFILES = *.a
-diff --git a/extras/build b/extras/build
-index 59e7a2ed..0d68232e 100755
---- a/extras/build
-+++ b/extras/build
-@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
- BUILDICONV=1
- fi
- fi
--PROJECTS="tcl tk"
-+#PROJECTS="tcl tk"
- if [ ${BUILDZLIB} -eq 1 ]; then
- PROJECTS="${PROJECTS} zlib"
- fi
--PROJECTS="${PROJECTS} libpng"
-+#PROJECTS="${PROJECTS} libpng"
- if [ ${BUILDICONV} -eq 1 ]; then
- PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
--PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
-+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
- for projname in $PROJECTS; do
- if [ -d $FSLESRCDIR/$projname ] ; then
- buildIt $FSLESRCDIR $projname 1
-diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
-index 20402cca..6918bee4 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,6 +52,6 @@ installpython:
- cp -r python/* ${DESTDIR}/python/mist
-
- clean:
-- rm -f ${OBJS} mist/mist.o mist/mist
-+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
-
- .PHONY: all clean installdata
---
-2.24.1
-
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index cd91cf192..6e5d6e779 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -151,8 +151,8 @@ src_compile() {
# define the default build system to match upstream official standard
# -> individual projects may overwrite the '-std=' flag
- export ANSI_CFLAGS="-std=c99"
- export ANSI_CXXFLAGS="-std=c++98"
+ export ANSI_CFLAGS="-std=c11"
+ export ANSI_CXXFLAGS="-std=c++11"
export USERLDFLAGS="${LDFLAGS}"
export USERCFLAGS="${CFLAGS}"
diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch
deleted file mode 100644
index afb52b2e1..000000000
--- a/sci-biology/gffcompare/files/Makefile.patch
+++ /dev/null
@@ -1,79 +0,0 @@
---- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200
-+++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200
-@@ -16,7 +16,7 @@
- endif
-
- # CVS checked in
--CC := g++
-+CXX ?= g++
- BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \
- -fno-exceptions -fno-rtti -D_REENTRANT
-
-@@ -24,7 +24,8 @@
-
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
- # -- release build
-- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS)
-+ CXXFLAGS ?= -O3 -g
-+ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- LDFLAGS =
- LIBS =
- ifneq (,$(findstring static,$(MAKECMDGOALS)))
-@@ -37,16 +38,16 @@
- ifeq "$(GCCVER49)" "0"
- $(error gcc version 4.9 or greater is required for this build target)
- endif
-- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
-+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
- GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
- ifeq "$(GCCVER5)" "1"
-- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-- #CFLAGS += -fcheck-pointer-bounds -mmpx
-+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx
- endif
-- CFLAGS += $(BASEFLAGS)
-- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS)
-- LDFLAGS := -g
-+ CXXFLAGS += $(BASEFLAGS)
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
-+ LDFLAGS ?= -g
- #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
- LIBS := -lasan -lubsan -ldl $(LIBS)
- else
-@@ -55,26 +56,26 @@
- # GMEMTRACE=1
- #endif
- #--- just plain debug build ---
-- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-- LDFLAGS = -g
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-+ LDFLAGS += -g
- LIBS =
- endif
- endif
-
- %.o : %.c
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest
index bd58b4117..4c5068f0a 100644
--- a/sci-biology/imagej/Manifest
+++ b/sci-biology/imagej/Manifest
@@ -1,4 +1,3 @@
DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
-DIST ij153.zip 6503763 BLAKE2B 7b3b30b55fe844e110f3e85eab7790376fc2d62300312c0b9037726758fcbfd5c4a6072842aa09e6ed08a2d593c2b1966d985de5972d801cf01638b41134325e SHA512 788003b35f7c3dd6f9bcda298637a3de78d745de8dd685cf88d8cc6ae22e142b07620c1e47a182d1e87178d68d591e381813f40cedc59f08d21af317065d7de0
-DIST ij153t-src.zip 1549329 BLAKE2B 7e43b759b96c8683be2175348a88080cdd4f038153a937717ebb0f480f9c8fb83d15184f8bf25060dc395ac3b13fd57f905621e680e481ad7dfdc090bbefb323 SHA512 861ecba6a20835566ec4038ffa30211308d37c41cecdfb97ea33d963c0ac2f1dbec0679c014335f89df24317334aeb30350dd09ee5f0fa33990f5355dd2fd06f
-DIST imagej-1.54f.gh.tar.gz 5768851 BLAKE2B a3c04ec949937e01ccf9b2a3a8432206c30833fc1f26a8ff0f487dece26c35a315b3c72cf88fec63ba090c5da6db51795c471b85d43f017f676c9f557f802cfc SHA512 a46deeec0e43c56598a0950393e6d72f866c9026434fb87fd5e4a604efcd13f3e50332b3893ba9cf443dd73fdfab9ddbcbf90604d7acfba7d1a1b72d7d1c916b
+DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9
+DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615
diff --git a/sci-biology/imagej/imagej-1.53t.ebuild b/sci-biology/imagej/imagej-1.53t.ebuild
deleted file mode 100644
index 952eff08b..000000000
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit java-pkg-2 java-ant-2 desktop
-
-MY_PN="ij"
-MY_PV=${PV//.}
-IJ_PV=${MY_PV::-1}
-
-DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="https://imagej.nih.gov/ij/"
-
-SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
- https://imagej.nih.gov/ij/images/ImageJ.png
- plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
-# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
-# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
-
-LICENSE="public-domain" # http://imagej.net/disclaimer.html
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-IUSE="doc plugins debug"
-
-RDEPEND="
- >=virtual/jre-1.7:*
- dev-java/java-config
-"
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.7:*
-"
-BDEPEND="
- dev-java/ant-core
- app-arch/unzip
-"
-
-S="${WORKDIR}/source"
-IJ_S=${WORKDIR}/ImageJ
-
-src_prepare() {
- cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
-
- if ! use debug ; then
- sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
- fi
- default
-}
-
-src_compile() {
- local antflags="build"
- use doc && antflags="${antflags} javadocs"
-
- ant ${antflags} || die "ant build failed"
-
- # Max memory usage depends on available memory and CPU type
- MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
- IJ_MAX_MEM=$(expr ${MEM} / 1024)
- if use x86 && $IJ_MAX_MEM -gt 2048 ; then
- IJ_MAX_MEM=2048
- fi
- # build finished, generate startup wrapper
- cat <<EOF > "${T}/${PN}"
-#!${EPREFIX}/bin/bash
-IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
-if !([ "\${IJ_HOME}" ]) ; then
- IJ_HOME=\${HOME}/.imagej
-fi
-if [ -d \${IJ_HOME}/plugins ] ; then
- IJ_PLG=\${IJ_HOME}
-else
- IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
-fi
-if !([ "\$IJ_MEM" ]) ; then
- IJ_MEM=${IJ_MAX_MEM}
-fi
-if !([ "\$IJ_CP" ]) ; then
- IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
-else
- IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
-fi
-\$(java-config --java) \\
- -Xmx\${IJ_MEM}m -Dswing.aatext=true \\
- -Dawt.useSystemAAFontSettings=on\\
- -cp \${IJ_CP} \\
- -Duser.home=\${IJ_HOME} \\
- -Dplugins.dir=\${IJ_PLG} \\
- ij.ImageJ "\$@"
-EOF
-}
-
-src_install() {
- java-pkg_dojar *.jar
- dobin "${T}/${PN}"
-
- if use plugins ; then
- cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
- cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
- fi
-
- use doc && java-pkg_dohtml -r "${WORKDIR}"/api
-
- insinto /usr/share/pixmaps
- doins "${WORKDIR}/${PN}".png
- make_desktop_entry "${PN}" ImageJ "${PN}" Graphics
-}
-
-pkg_postinst() {
- einfo ""
- einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
- einfo "by setting the environmental variable, \$IJ_HOME."
- einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
- einfo ""
- einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
- einfo "and the class path by setting the environmental variable, \$IJ_CP."
- einfo ""
- einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
- einfo "and add *.class files to \$IJ_HOME/plugins folder"
- einfo ""
-}
diff --git a/sci-biology/imagej/imagej-1.54f.ebuild b/sci-biology/imagej/imagej-1.54h-r1.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-1.54f.ebuild
+++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit java-pkg-2 java-ant-2 desktop
MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
@@ -59,7 +59,7 @@ src_prepare() {
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
fi
fi
diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit java-pkg-2 java-ant-2 desktop
MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
@@ -59,7 +59,7 @@ src_prepare() {
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
fi
fi
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
index 3faf27a11..021929bad 100644
--- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
+++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit check-reqs
DESCRIPTION="BIDS data files released with the IRSABI publication"
-HOMEPAGE="http://chymera.eu/docs/focus/open-science/"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
SRC_URI="
https://zenodo.org/record/3601531/files/${P}.tar.xz
"
diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest
index 4a1880c5f..249395f6f 100644
--- a/sci-biology/libBigWig/Manifest
+++ b/sci-biology/libBigWig/Manifest
@@ -1 +1,2 @@
DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71
+DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40
diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
new file mode 100644
index 000000000..7dc83ceed
--- /dev/null
+++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
+HOMEPAGE="https://github.com/dpryan79/libBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/dpryan79/libBigWig"
+else
+ SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="net-misc/curl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ default
+ sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
+ sed -e "s:/lib:/$(get_libdir):" -i Makefile || die
+}
+
+src_install(){
+ emake install DESTDIR="${ED}"
+}
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
new file mode 100644
index 000000000..3585038a3
--- /dev/null
+++ b/sci-biology/multiqc/Manifest
@@ -0,0 +1 @@
+DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml
new file mode 100644
index 000000000..09bd2b6e6
--- /dev/null
+++ b/sci-biology/multiqc/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">ewels/MultiQC</remote-id>
+ <remote-id type="pypi">multiqc</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
new file mode 100644
index 000000000..187f06c22
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.19.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
+HOMEPAGE="https://multiqc.info/"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/coloredlogs[${PYTHON_USEDEP}]
+ dev-python/future[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/lzstring[${PYTHON_USEDEP}]
+ dev-python/markdown[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+ dev-python/rich-click[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/spectra[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[$PYTHON_USEDEP]
+ dev-python/humanize[$PYTHON_USEDEP]
+ dev-python/pyaml-env[$PYTHON_USEDEP]"
+
+# pypi tarball does not include tests
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest
index 54770b3ae..35c461b92 100644
--- a/sci-biology/neuroconv/Manifest
+++ b/sci-biology/neuroconv/Manifest
@@ -1 +1 @@
-DIST neuroconv-0.2.4.gh.tar.gz 757136 BLAKE2B a3a21b3a00667bde4461d91ade514891c8710f309413b100e1cccfd2684dfcbf9b21feaf4f58b3c5ff845aa08e69bf47467b411926eeb7d3b2862753302b1d9b SHA512 293038feae2704442b81ba0f012d775ba96d7bdffb6aaacaaebd09ca2f8b39e91ef4ea69c972abf060f0f9ab8cb76fedb77dda67455fa992edd52f0e6e504b0d
+DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d
diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
index c554ce791..b21c2fd8e 100644
--- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
+++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
@@ -17,17 +17,21 @@ KEYWORDS="~amd64"
IUSE="+ecephys +icephys +ophys"
RDEPEND="
+ dev-python/docstring-parser[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/hdmf-zarr[${PYTHON_USEDEP}]
dev-python/hdmf[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/parse[${PYTHON_USEDEP}]
dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
- dev-vcs/dandi-cli[${PYTHON_USEDEP}]
ecephys? (
dev-python/spikeinterface[${PYTHON_USEDEP}]
)
@@ -46,6 +50,12 @@ BDEPEND="
distutils_enable_tests pytest
+# Reported upstream:
+# https://github.com/catalystneuro/neuroconv/issues/785
+EPYTEST_DESELECT=(
+ tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface
+)
+
python_test() {
# Additional tests require complex data getting infrastructure, ophys tests still have issues:
# https://github.com/catalystneuro/neuroconv/issues/305
diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
deleted file mode 100644
index e229d25fb..000000000
--- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- a/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:07.700111595 +0200
-+++ b/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:29.453556439 +0200
-@@ -219,36 +219,6 @@
- assert_raises(ValueError, masker.fit_transform, data_img)
-
-
--def test_joblib_cache():
-- from sklearn.externals.joblib import hash, Memory
-- mask = np.zeros((40, 40, 40))
-- mask[20, 20, 20] = 1
-- mask_img = Nifti1Image(mask, np.eye(4))
--
-- with testing.write_tmp_imgs(mask_img, create_files=True) as filename:
-- masker = NiftiMasker(mask_img=filename)
-- masker.fit()
-- mask_hash = hash(masker.mask_img_)
-- masker.mask_img_.get_data()
-- assert_true(mask_hash == hash(masker.mask_img_))
--
-- # Test a tricky issue with memmapped joblib.memory that makes
-- # imgs return by inverse_transform impossible to save
-- cachedir = mkdtemp()
-- try:
-- masker.memory = Memory(cachedir=cachedir, mmap_mode='r',
-- verbose=0)
-- X = masker.transform(mask_img)
-- # inverse_transform a first time, so that the result is cached
-- out_img = masker.inverse_transform(X)
-- out_img = masker.inverse_transform(X)
-- out_img.to_filename(os.path.join(cachedir, 'test.nii'))
-- finally:
-- # enables to delete "filename" on windows
-- del masker
-- shutil.rmtree(cachedir, ignore_errors=True)
--
--
- def test_mask_init_errors():
- # Errors that are caught in init
- mask = NiftiMasker(mask_strategy='oops')
diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest
index 2ba87b1bb..4a9a85cc0 100644
--- a/sci-biology/nitime/Manifest
+++ b/sci-biology/nitime/Manifest
@@ -1 +1,2 @@
+DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21
DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406
diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml
index 041507ac7..606822ddb 100644
--- a/sci-biology/nitime/metadata.xml
+++ b/sci-biology/nitime/metadata.xml
@@ -10,9 +10,9 @@
<name>Gentoo Science Project</name>
</maintainer>
<longdescription lang="en">
-Nitime is a library for time-series analysis of data from neuroscience experiments
-in both the time and spectral domains.
-</longdescription>
+ Nitime is a library for time-series analysis of data from neuroscience experiments
+ in both the time and spectral domains.
+ </longdescription>
<upstream>
<remote-id type="github">nipy/nitime</remote-id>
<remote-id type="pypi">nitime</remote-id>
diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild
new file mode 100644
index 000000000..7e47d7288
--- /dev/null
+++ b/sci-biology/nitime/nitime-0.10.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Time-series analysis of neuroscience data"
+HOMEPAGE="http://nipy.org/nitime/index.html"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND="${COMMON_DEPEND}
+ dev-python/cython[${PYTHON_USEDEP}]
+ "
+RDEPEND="
+ ${COMMON_DEPEND}
+ dev-python/networkx[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ "
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild
index f297c85f0..ee81c01dc 100644
--- a/sci-biology/nitime/nitime-9999.ebuild
+++ b/sci-biology/nitime/nitime-9999.ebuild
@@ -3,9 +3,10 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 git-r3 virtualx
+inherit distutils-r1 git-r3
DESCRIPTION="Time-series analysis of neuroscience data"
HOMEPAGE="http://nipy.org/nitime/index.html"
@@ -16,9 +17,6 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS=""
-# import file mismatch:
-RESTRICT="test"
-
COMMON_DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
@@ -35,7 +33,3 @@ RDEPEND="
distutils_enable_tests pytest
distutils_enable_sphinx doc
-
-python_test() {
- virtx pytest -v || die
-}
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.4.ebuild
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch
deleted file mode 100644
index 44acc42b0..000000000
--- a/sci-biology/sra-tools/files/libs_sra_Makefile.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100
-@@ -100,7 +100,7 @@
- $(addsuffix .$(LOBX),$(SRAPATH_SRC))
-
- $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ)
-- $(LD) --slib -o $@ $^
-+ $(LD) --slib -o $(DESTDIR)$@ $^
-
- libsrapath.vers.h:
- @ true
-@@ -138,10 +138,10 @@
- -dklib
-
- $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB)
-
- $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB)
-
- SRASCHEMA_SRC = \
- sraschema-stub
-@@ -168,10 +168,10 @@
- $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC))
-
- $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS)
-- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
-+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
-
- $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS)
-- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
-+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
-
- libsraschema_tag:
- @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ)
-@@ -205,10 +205,10 @@
- -dklib
-
- $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
-
- $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
-
- libsradb_tag: $(SRADB_TAGS)
- @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ)
-@@ -236,10 +236,10 @@
- -dklib
-
- $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
-
- $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
-
- libwsradb_tag: $(WSRADB_TAGS)
- @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ)
-@@ -266,10 +266,10 @@
- -dklib
-
- $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
-
- $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
-
- libsrareader_tag:
- @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ)
diff --git a/sci-biology/sra-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch
deleted file mode 100644
index bf66c6e46..000000000
--- a/sci-biology/sra-tools/files/sra_sdk-destdir.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100
-@@ -141,7 +141,7 @@
-
- # create all required output directories
- makedirs:
-- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
-+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR)
-
- ifeq (win,$(OS))
-
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100
-@@ -38,10 +38,10 @@
- # versioned output
- if [ "$VERS" = "" ]
- then
-- DLIB_CMD="$DLIB_CMD -o $TARG"
-- EXE_CMD="$EXE_CMD -o $TARG"
-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG"
-+ EXE_CMD="$EXE_CMD -o $TARG"
- else
- set-vers $(echo $VERS | tr '.' ' ')
-- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS"
- fi
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100
-@@ -52,12 +52,12 @@
-
- set-vers $(echo $VERS | tr '.' ' ')
-
--cd "$OUTDIR" || exit 5
-+cd $DESTDIR$OUTDIR || exit 5
-
- # create link
- create-link ()
- {
-- rm -f "$2"
-+ rm -f $DESTDIR"$2"
- local CMD="ln -s $1 $2"
- echo $CMD
- $CMD
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100
-@@ -77,7 +77,7 @@
- CMD="$CMD $TARG"
- else
- set-vers $(echo $VERS | tr '.' ' ')
-- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
-+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS"
- fi
-
- # tack on object files
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100
-@@ -36,12 +36,12 @@
- LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
-
- LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
-
- # tool options
- WARN = -Wall -Wno-variadic-macros # -Wconversion
diff --git a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
deleted file mode 100644
index 738d67cbd..000000000
--- a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100
-@@ -89,7 +89,7 @@
- $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg
-
- $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg
-- cp $^ $@
-+ cp $^ $(DESTDIR)$@
-
- VDB_COPY_SRC = \
- num-gen \
diff --git a/sci-electronics/mpremote/Manifest b/sci-electronics/mpremote/Manifest
index a23fad530..1e55b52d3 100644
--- a/sci-electronics/mpremote/Manifest
+++ b/sci-electronics/mpremote/Manifest
@@ -1 +1,2 @@
DIST mpremote-0.4.0.tar.gz 27266 BLAKE2B b31b6184d0f4fc5c525ea7d5d8d2722404e9ce82ce143ea9a14b8bdef28af3260514dd25ec756a0ac2507d5b206fa9d07ce67bd2228b1568d9495c9082bdace8 SHA512 580f0286d8973a93105a04c681428f798e0d72b4b75debbc43f8e49ea7a81da849987aeab795baff66c9cf40607fde27fb54b7b32ab311ae5e9fb3b8f8f976fc
+DIST mpremote-1.22.0.tar.gz 24042 BLAKE2B 8bd6df4b9a46c10a93d42974a569adb42577d2783cb78b5b76ac6a6750f8219611ca49106ed91cb7f69910e3dfb28bb07a4522dbd721af0baac94d3e793c0576 SHA512 a3135e3be347370c967b7dc936f112e1ed5898288fa2dda4c485d216ebf432cb9706e539299d6769c1982ac02e456e9594ed2a7a86cbac2a1c7d08f2ff8a980b
diff --git a/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
new file mode 100644
index 000000000..4d06c25aa
--- /dev/null
+++ b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
@@ -0,0 +1,12 @@
+--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml 2024-01-22 03:59:19.414593373 -0500
+@@ -33,9 +33,6 @@
+ [project.scripts]
+ mpremote = "mpremote.main:main"
+
+-[tool.hatch.metadata.hooks.requirements_txt]
+-files = ["requirements.txt"]
+-
+ # This will be PEP-440 normalised into either:
+ # mpremote-X.Y.Z (on vX.Y.Z release tag)
+ # mpremote-X.Y.Zrc0 (on vX.Y.Z-preview tag, i.e. first commit in the cycle)
diff --git a/sci-electronics/mpremote/mpremote-1.22.0.ebuild b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
new file mode 100644
index 000000000..741478265
--- /dev/null
+++ b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="MicroPython remote control"
+HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/pyserial[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-requirements_txt.patch"
+)
+
+# The package might not have a test suite:
+# https://github.com/orgs/micropython/discussions/11308
+#distutils_enable_tests pytest
diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild
index 50eaeea5d..cbfbde5c6 100644
--- a/sci-libs/asl/asl-0.1.7.ebuild
+++ b/sci-libs/asl/asl-0.1.7.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
S="${WORKDIR}/${MY_PN}-${PV}"
diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild
index 82b464f7f..905c8813a 100644
--- a/sci-libs/asl/asl-9999.ebuild
+++ b/sci-libs/asl/asl-9999.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
src_prepare() {
cmake_src_prepare
diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
index 09fc690fd..f23e1c738 100644
--- a/sci-libs/daal4py/daal4py-2023.0.2.ebuild
+++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
@@ -19,7 +19,7 @@ KEYWORDS="~amd64"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
sys-devel/DPC++
test? (
sci-libs/scikit-learn[${PYTHON_USEDEP}]
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
deleted file mode 100644
index 5d3754d56..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index a252a1d..c36a312 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -116,10 +116,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- cxx = 'dpcpp'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 864ab5d..7eaa52f 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -306,8 +306,8 @@ def build_oneapi_backend():
- eca, ela, includes = get_build_options()
-
- return build_backend.build_cpp(
-- cc='dpcpp',
-- cxx='dpcpp',
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
deleted file mode 100644
index 9ccf0f156..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index bb38056..7216983 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -115,13 +115,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- if IS_WIN:
-- cxx = 'icx'
-- else:
-- cxx = 'icpx'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 00b4f43..76857a2 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -313,8 +313,8 @@ def build_oneapi_backend():
- eca += ['-fsycl']
-
- return build_backend.build_cpp(
-- cc=cc,
-- cxx=cxx,
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
index 10f1d3b50..c1000fea9 100644
--- a/sci-libs/gdcm/gdcm-3.0.14.ebuild
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -40,7 +40,7 @@ RDEPEND="${DEPEND}"
BDEPEND="
dev-libs/libxslt
app-text/docbook-xsl-ns-stylesheets
- doc? ( app-doc/doxygen[dot] )
+ doc? ( app-text/doxygen[dot] )
python? (
${PYTHON_DEPS}
>=dev-lang/swig-3.0.7
diff --git a/sci-libs/gvar/Manifest b/sci-libs/gvar/Manifest
new file mode 100644
index 000000000..16bdf1de2
--- /dev/null
+++ b/sci-libs/gvar/Manifest
@@ -0,0 +1 @@
+DIST gvar-13.0.2.tar.gz 1001282 BLAKE2B 5c4032406e3d514351bac6f21b5353c8db4e2081efd26b758cce126cce4a3df350ac8086e89895c73ffc27367773a43354138e8598490cbe8f7bacdde216f0bd SHA512 541cb5cc44909cf44e9f808a08a959aa5e3e91c49356fb8865879a9dbb5fe6f3c4b46d88bc4f9346d9b83163c938dfd697e73b7b9a00815ed6dc383630795cb4
diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild
new file mode 100644
index 000000000..b9d9121e4
--- /dev/null
+++ b/sci-libs/gvar/gvar-13.0.2.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Gaussian random variables."
+HOMEPAGE="https://github.com/gplepage/gvar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml
new file mode 100644
index 000000000..31346f0dd
--- /dev/null
+++ b/sci-libs/gvar/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ This package facilitates the creation and manipulation of arbitrarily complicated (correlated) multi-dimensional Gaussian random variables. The random variables are represented by a new data type (gvar.GVar) that can be used in arithmetic expressions and pure Python functions. Such expressions/functions create new Gaussian random variables while automatically tracking statistical correlations between the new and old variables. This data type is useful for simple error propagation, but also is heavily used by the Bayesian least-squares fitting module lsqfit.py to define priors and specify fit results, while accounting for correlations between all variables.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">gvar</remote-id>
+ <remote-id type="github">gplepage/gvar</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/handyg/files/handyg-0.1.5-ld.patch b/sci-libs/handyg/files/handyg-0.1.5-ld.patch
deleted file mode 100644
index f3f06cd91..000000000
--- a/sci-libs/handyg/files/handyg-0.1.5-ld.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- 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,$2"
- shift ;;
- -dynamic-linker)
- shift ;;
diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 1aa0dc43a..0b1f25860 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -71,7 +71,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 29a3da5d0..b2c3af801 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -79,7 +79,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
deleted file mode 100644
index 0f64b325f..000000000
--- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib2bit-0.2.1/Makefile.ori 2017-03-31 22:09:48.387098439 +0200
-+++ lib2bit-0.2.1/Makefile 2017-03-31 22:10:29.889020564 +0200
-@@ -8,7 +8,7 @@
- LDLIBS =
- INCLUDES =
-
--prefix = /usr/local
-+prefix = $(DESTDIR)/usr/local
- includedir = $(prefix)/include
- libdir = $(exec_prefix)/lib
-
diff --git a/sci-libs/mpfun90/Manifest b/sci-libs/mpfun90/Manifest
new file mode 100644
index 000000000..56d64f14c
--- /dev/null
+++ b/sci-libs/mpfun90/Manifest
@@ -0,0 +1 @@
+DIST 2023-02-26.tar.gz 66883 BLAKE2B 3b93099977b614e0d9a16df76f7f3c1eda9b76905664db3f0dc0ad0bd00b503105649aeb4c960d7293e7d536e3a902dbe8cb62f89be3bce655e9bae963097f35 SHA512 7280ecba6cb95f15cea91ea95f5cf21b69f76a490a3c92bef40cf8a1dfadd651cb93480bddddd684d0f18144db65cdb1590964df11d37a9f35eaeeb94f369d63
diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml
new file mode 100644
index 000000000..e3eb0d9c1
--- /dev/null
+++ b/sci-libs/mpfun90/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ This package permits one to perform floating-point computations (real and complex) to arbitrarily high numeric precision
+ </longdescription>
+ <upstream>
+ <remote-id type="github">APN-Pucky/mpfun90</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
new file mode 100644
index 000000000..4f885fa2c
--- /dev/null
+++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="High-Precision Software"
+HOMEPAGE="
+ https://www.davidhbailey.com/dhbsoftware/
+ https://github.com/APN-Pucky/mpfun90
+"
+MY_PV=$(ver_rs 1- '-')
+SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz"
+S="${WORKDIR}/mpfun90-${MY_PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_compile() {
+ emake -j1 dynamic
+}
+
+src_install() {
+ doheader *.mod
+ dolib.so libmpfun90.so
+ dolib.a libmpfun90.a
+}
diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
index b19a65fbe..58d8264cf 100644
--- a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
+++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
@@ -29,7 +29,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- app-doc/doxygen[dot]
+ app-text/doxygen[dot]
"
pkg_setup() {
diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest
index 4bc4a8fd6..d50b1b3b7 100644
--- a/sci-libs/nibabel/Manifest
+++ b/sci-libs/nibabel/Manifest
@@ -1,2 +1,2 @@
-DIST nibabel-4.0.0.tar.gz 4505565 BLAKE2B 5efee05adbb0ff9204218060f75acdf6b5b77a1a7cc9b884d122f4a95805f6110a0d9433946d4a53d3aa615932012effe35b4ffa9773fb992da8ff273bf3cfd7 SHA512 1b34901e69ff7aaabfb94e49199de761eb7e397a0a7360c2077935d250368cd061cf1fa9c6ef561fa7707e4853c421b039818bfa4b32fc4792555f3d6235eeb7
DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4
+DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e
diff --git a/sci-libs/nibabel/nibabel-4.0.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild
index 4a24fb940..0fec805b1 100644
--- a/sci-libs/nibabel/nibabel-4.0.0.ebuild
+++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -27,11 +27,9 @@ RDEPEND="
)
"
-EPYTEST_DESELECT=(
- # Rported upstream:
- # https://github.com/nipy/nibabel/issues/1191
- nibabel/tests/test_volumeutils.py::test_a2f_nan2zero_range
-)
+BDEPEND="test? (
+ dev-python/pytest-httpserver[${PYTHON_USEDEP}]
+)"
distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
distutils_enable_tests pytest
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
index 362628814..9444a9dd3 100644
--- a/sci-libs/nipy/Manifest
+++ b/sci-libs/nipy/Manifest
@@ -1 +1 @@
-DIST nipy-0.5.1_pre20230103.gh.tar.gz 2462662 BLAKE2B 0e6aa24875e514bf16280e20bb3059027ad30c3d510db62b0ed80b33724aacb0a20260f7cf9d87858a9da5d07fab58535cee1306fe2b7be7a72364156197aeab SHA512 7ed89b5e637159c90893a02dd9481a662f7e589fc6fe76c3e7919231144a56668815edc0f57a77728a9c95c7640e474563e922609c56cd0ad0fcfbd3c5bdb6bd
+DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f
diff --git a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild b/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
deleted file mode 100644
index 25bdee0b8..000000000
--- a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-MY_HASH="35a5f5205ba2aa54f1f0524564a6f1f8dafb237f"
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://nipy.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- "
-DEPEND=""
-
-S="${WORKDIR}/${PN}-${MY_HASH}"
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # bug #397605
- [[ ${CHOST} == *-darwin* ]] \
- && append-ldflags -bundle "-undefined dynamic_lookup" \
- || append-ldflags -shared
-
- # nipy uses the horrible numpy.distutils automagic
-}
-
-#python_test() {
-# distutils-r1_install_for_testing
-# cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
-# cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
-# cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
-# cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
-# mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cd "${BUILD_DIR}" || die
-# echo "backend : agg" > matplotlibrc
-# nosetests || die
-#}
diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild
new file mode 100644
index 000000000..8f8ea83e8
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.6.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=meson-python
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_EXT=1
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="https://nipy.org/"
+SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Test data unavailable:
+# https://github.com/nipy/nipy/issues/561#event-11866547632
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/sympy[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ "
+DEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ rm -rf nipy || die
+ epytest
+}
diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest
index a2ffd1d7a..6c9059e1c 100644
--- a/sci-libs/nipype/Manifest
+++ b/sci-libs/nipype/Manifest
@@ -1,2 +1,2 @@
-DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85
DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b
+DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec
diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
new file mode 100644
index 000000000..b5c223422
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
@@ -0,0 +1,50 @@
+diff --git a/nipype/__init__.py b/nipype/__init__.py
+index 06084e823..2e42dcbce 100644
+--- a/nipype/__init__.py
++++ b/nipype/__init__.py
+@@ -73,23 +73,6 @@ from .interfaces import (
+ )
+
+
+-def check_latest_version(raise_exception=False):
+- """
+- Check for the latest version of the library.
+-
+- Parameters
+- ----------
+- raise_exception: bool
+- Raise a RuntimeError if a bad version is being used
+- """
+- import etelemetry
+-
+- logger = logging.getLogger("nipype.utils")
+- return etelemetry.check_available_version(
+- "nipy/nipype", __version__, logger, raise_exception
+- )
+-
+-
+ # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
+ if config.getboolean("execution", "check_version"):
+ import __main__
+@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"):
+ from .interfaces.base import BaseInterface
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index c8099be63..f7770dbfc 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -183,10 +183,9 @@ class BaseInterface(Interface):
+ config.getboolean("execution", "check_version")
+ and "NIPYPE_NO_ET" not in os.environ
+ ):
+- from ... import check_latest_version
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+
+ if not self.input_spec:
+ raise Exception("No input_spec in class: %s" % self.__class__.__name__)
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
index 8214ccff4..7c2e801ff 100644
--- a/sci-libs/nipype/nipype-1.8.4-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
index 750c3ba05..4c3da70b3 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
@@ -28,30 +29,29 @@ DEPEND="
${RDEPEND}
)
"
-# Dependency disabled as upstream test configuration which requires it fails
-#dev-python/pytest-xdist[${PYTHON_USEDEP}]
RDEPEND="
- >=dev-python/click-6.6[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pydotplus[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
- >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/traits[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${P}"-version_check.patch
- "${FILESDIR}/${P}"-collections.patch
+ "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
)
src_prepare() {
# Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
@@ -69,12 +69,10 @@ python_install_all() {
doenvd "${FILESDIR}/98nipype"
}
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
EPYTEST_DESELECT=(
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor_variance_threshold_and_metadata
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor
nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
- nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help
)
python_test() {
diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild
new file mode 100644
index 000000000..88bc23395
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.6.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Tests fail with numpy import error:
+# https://github.com/nipy/nipype/issues/3626
+RESTRICT="test"
+
+DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/prov[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ test? (
+ dev-python/mock[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ ${RDEPEND}
+ )
+"
+
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pydot[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+ # Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
+ sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+ # Mark failing tests
+ sed -i \
+ -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+ nipype/tests/test_nipype.py || die
+ sed -i \
+ -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+ nipype/interfaces/fsl/tests/test_base.py || die
+ default
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+ nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+ # Setting environment variable to disable etelemetry version check:
+ # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+ NIPYPE_NO_ET=1 epytest
+ # Upstream test configuration fails
+ #-c nipype/pytest.ini\
+ #--doctest-modules nipype\
+ #--cov nipype\
+ #--cov-config .coveragerc\
+ #--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use nipype from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 976a8535b..9b9233020 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz -
LICENSE="CeCILL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Wants to run mpirun (and fails)
RESTRICT="test"
@@ -27,7 +27,7 @@ RDEPEND="
>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
- >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
"
diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest
index 2167de395..7cf5fa956 100644
--- a/sci-libs/torchvision/Manifest
+++ b/sci-libs/torchvision/Manifest
@@ -1 +1,2 @@
DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f
+DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be
diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
new file mode 100644
index 000000000..7a3637f3a
--- /dev/null
+++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
@@ -0,0 +1,36 @@
+From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?=
+ <zboszor@gmail.com>
+Date: Tue, 7 Nov 2023 10:43:11 +0100
+Subject: [PATCH] Fix build with ffmpeg 6.0
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com>
+---
+ torchvision/csrc/io/decoder/stream.cpp | 11 ++---------
+ 1 file changed, 2 insertions(+), 9 deletions(-)
+
+diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp
+index 0d625ef211c..8c914050587 100644
+--- a/torchvision/csrc/io/decoder/stream.cpp
++++ b/torchvision/csrc/io/decoder/stream.cpp
+@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) {
+ codecCtx_->thread_count = num_threads;
+ } else {
+ // otherwise set sensible defaults
+- // with the special case for the different MPEG4 codecs
+- // that don't have threading context functions
+- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) {
+- codecCtx_->thread_type = FF_THREAD_FRAME;
+- codecCtx_->thread_count = 2;
+- } else {
+- codecCtx_->thread_count = 8;
+- codecCtx_->thread_type = FF_THREAD_SLICE;
+- }
++ codecCtx_->thread_count = 8;
++ codecCtx_->thread_type = FF_THREAD_SLICE;
+ }
+
+ int ret;
diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.17.1.ebuild
new file mode 100644
index 000000000..e0c72684c
--- /dev/null
+++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2020-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+inherit distutils-r1 multiprocessing
+
+DESCRIPTION="Datasets, transforms and models to specific to computer vision"
+HOMEPAGE="https://github.com/pytorch/vision"
+SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/vision-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="test"
+
+RDEPEND="
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ ')
+ sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+ media-video/ffmpeg:=
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" )
+
+src_compile()
+{
+ export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS
+
+ # Ensure some ext_module sources are compiled before linking
+ export MAKEOPTS="-j1"
+
+ distutils-r1_src_compile
+}
diff --git a/sci-libs/vegas/Manifest b/sci-libs/vegas/Manifest
new file mode 100644
index 000000000..c636ac4c2
--- /dev/null
+++ b/sci-libs/vegas/Manifest
@@ -0,0 +1 @@
+DIST vegas-6.0.1.tar.gz 1535565 BLAKE2B 3cd30387e9369ce7efe62e1f5838f87c73bb93e1690c131602a8e0b77a6671e9d9cadb6b909e1f9ba548cd4a32cb09bd6d1d50bfaf536b7c3fbd269c4595ed04 SHA512 ead47a9f194846d704e229d62163233a7b063dab504e665d620f59be5c9abe2b31facf14cad612b102d4bf64d60d9f6f53c0b4bca0ba78d1e62cbd9bda77e0b1
diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml
new file mode 100644
index 000000000..8ae183900
--- /dev/null
+++ b/sci-libs/vegas/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ The vegas package is for evaluating multidimensional integrals using an improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J. Comput. Phys. 27(1978) 192).
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">vegas</remote-id>
+ <remote-id type="github">gplepage/vegas</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild b/sci-libs/vegas/vegas-6.0.1.ebuild
new file mode 100644
index 000000000..7654563e4
--- /dev/null
+++ b/sci-libs/vegas/vegas-6.0.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Adaptive multidimensional Monte Carlo integration."
+HOMEPAGE="https://github.com/gplepage/vegas"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ >=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch
deleted file mode 100644
index e68c5f4fe..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90
---- wannier90-1.1.old/src/wannier_lib.F90 2007-12-20 10:58:37.000000000 +0100
-+++ wannier90-1.1.new/src/wannier_lib.F90 2008-04-28 17:27:19.000000000 +0200
-@@ -166,6 +166,12 @@
- exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands)
- end if
-
-+ if (postproc_setup) then
-+ call kmesh_write()
-+ write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh ',io_time(),' (sec)'
-+ write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.'
-+ endif
-+
-
- call kmesh_dealloc()
- call param_dealloc()
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch
deleted file mode 100644
index 391a34ca2..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90
---- wannier90-1.1.old/src/disentangle.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/disentangle.F90 2009-03-07 15:48:05.000000000 +0100
-@@ -1784,9 +1784,9 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
-+ write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
- if (icompflag.eq.1) then
-@@ -2551,8 +2551,8 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
-diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90
---- wannier90-1.1.old/src/overlap.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/overlap.F90 2009-03-07 15:48:36.000000000 +0100
-@@ -141,8 +141,8 @@
- nn_found=.true.
- nn=inn
- else
-- call io_error('Error reading '//trim(seedname)//'.mmn.&
-- & More than one matching nearest neighbour found')
-+ call io_error('Error reading '//trim(seedname)// &
-+ '.mmn. More than one matching nearest neighbour found')
- endif
- endif
- end do
-diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90
---- wannier90-1.1.old/src/parameters.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/parameters.F90 2009-03-07 15:50:46.000000000 +0100
-@@ -1054,8 +1054,9 @@
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_species
- do nat=1,atoms_species_num(nsp)
-- write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-- '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
-+ write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') &
-+& '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-+& '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
- end do
- end do
- write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*'
-@@ -1073,8 +1074,8 @@
- write(stdout,'(1x,a)') '| Frac. Coord. l mr r z-axis x-axis Z/a |'
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_proj
-- write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),&
-- & 2x,f4.1,1x,a1)') '|',proj_site(1,nsp),proj_site(2,nsp),&
-+ write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')&
-+& '|',proj_site(1,nsp),proj_site(2,nsp),&
- proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),&
- proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),&
- proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|'
-@@ -2738,8 +2739,8 @@
- dummy=utility_strip(in_data(line))
- dummy=adjustl(dummy)
- pos1=index(dummy,':')
-- if(pos1==0) call io_error('param_read_projection: malformed projection &
-- &definition: '//trim(dummy))
-+ if(pos1==0) &
-+ call io_error('param_read_projection: malformed projection definition: '//trim(dummy))
- sites=0
- ctemp=dummy(:pos1-1)
- ! Read the atomic site
-@@ -2980,11 +2981,11 @@
- endif
- end if
- if(sites==-1) then
-- if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: &
-- &too many projections defined')
-+ if(counter+sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- else
-- if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:&
-- & too many projections defined')
-+ if(counter+sites*sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- end if
- !
- if(sites==-1) then
-@@ -3025,8 +3026,8 @@
-
- ! check there are enough projections and add random projections if required
- if (.not. lpartrandom) then
-- if (counter.ne.num_proj) call io_error('param_get_projections:&
-- & Fewer projections defined than the number of Wannier functions requested')
-+ if (counter.ne.num_proj) call io_error(&
-+ 'param_get_projections: Fewer projections defined than the number of Wannier functions requested')
- else
- call random_seed()
- do loop=counter+1,num_proj
diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
deleted file mode 100644
index c9656ac31..000000000
--- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl
---- wannier90-2.0.1.1.orig/tests/run_test.pl 2016-02-08 11:51:52.000000000 +0000
-+++ wannier90-2.0.1.1/tests/run_test.pl 2017-01-05 12:10:29.584850729 +0000
-@@ -2,7 +2,7 @@
- #
- use Cwd;
- my $cwd = cwd();
--$wanex="../wannier90.x" ;
-+$wanex="../src/wannier90.x" ;
- $wanex=$cwd."/".$wanex ;
- print " Running test set of inputs\n";
- @tests_found = <./test*>;
diff --git a/sci-mathematics/cipi/cipi-1.0-r1.ebuild b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
new file mode 100644
index 000000000..6cd189e33
--- /dev/null
+++ b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake flag-o-matic
+
+DESCRIPTION="Computing information projections iteratively"
+HOMEPAGE="https://github.com/tom111/cipi"
+SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="doc"
+
+DEPEND="
+ dev-libs/boost:=
+ doc? ( virtual/latex-base )"
+RDEPEND="${DEPEND}"
+
+DOCS="AUTHORS README"
+
+CMAKE_IN_SOURCE_BUILD="yes"
+
+PATCHES=(
+ "${FILESDIR}/${P}-boost.patch"
+)
+
+src_prepare() {
+ cmake_src_prepare
+ append-ldflags -Wl,--copy-dt-needed-entries
+}
+
+src_configure() {
+ mycmakeargs=(
+ -DENABLE_DOC=$(usex doc ON OFF)
+ )
+
+ cmake_src_configure
+}
+
+pkg_postinst() {
+ elog
+ elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}"
+ elog
+ if use doc; then
+ elog "A pdf manual has been installed to /usr/share/${PN}-${PV}"
+ fi
+}
diff --git a/sci-mathematics/cipi/files/cipi-1.0-boost.patch b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
new file mode 100644
index 000000000..66aa9fd3f
--- /dev/null
+++ b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
@@ -0,0 +1,11 @@
+--- a/src/CMakeLists.txt 2024-02-16 21:36:58.808186061 +0100
++++ b/src/CMakeLists.txt 2024-02-16 21:36:55.288131610 +0100
+@@ -8,7 +8,7 @@
+ Message("Boost found" ${Boost_LIBRARY_DIR})
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR})
+ #MESSAGE("Boost was found" ${Boost_INCLUDE_DIR})
+- TARGET_LINK_LIBRARIES (cipi boost_thread-mt)
++ TARGET_LINK_LIBRARIES (cipi boost_thread)
+ ENDIF (Boost_FOUND)
+
+ INSTALL(PROGRAMS cipi DESTINATION bin)
diff --git a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch b/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
deleted file mode 100644
index 798d17fd3..000000000
--- a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
+++ /dev/null
@@ -1,254 +0,0 @@
-From: Mehdi Dogguy <mehdi@debian.org>
-Date: Sun, 27 Apr 2014 13:46:16 +0200
-Subject: Port to OCamlgraph 1.8.5
-
----
- src/impact/reason_graph.ml | 2 +-
- src/kernel/stmts_graph.ml | 10 +++++-----
- src/logic/property_status.ml | 8 ++++----
- src/misc/service_graph.ml | 4 ++--
- src/pdg_types/pdgTypes.ml | 6 +++---
- src/postdominators/print.ml | 2 +-
- src/semantic_callgraph/register.ml | 4 ++--
- src/slicing/printSlice.ml | 10 +++++-----
- src/syntactic_callgraph/register.ml | 4 ++--
- src/wp/cil2cfg.ml | 12 ++++++------
- 10 files changed, 31 insertions(+), 31 deletions(-)
-
-diff --git a/src/impact/reason_graph.ml b/src/impact/reason_graph.ml
-index eabacb0..ce19b4a 100644
---- a/src/impact/reason_graph.ml
-+++ b/src/impact/reason_graph.ml
-@@ -139,7 +139,7 @@ module Printer (X: AdditionalInfo) = struct
-
- let graph_attributes _ = [`Label "Impact graph"]
-
-- let default_vertex_attributes _g = [`Style [`Filled]; `Shape `Box]
-+ let default_vertex_attributes _g = [`Style `Filled; `Shape `Box]
- let default_edge_attributes _g = []
-
- let vertex_attributes v =
-diff --git a/src/kernel/stmts_graph.ml b/src/kernel/stmts_graph.ml
-index a8fe121..16059c3 100644
---- a/src/kernel/stmts_graph.ml
-+++ b/src/kernel/stmts_graph.ml
-@@ -157,12 +157,12 @@ module TP = struct
-
- let vertex_attributes s =
- match s.skind with
-- | Loop _ -> [`Color 0xFF0000; `Style [`Filled]]
-- | If _ -> [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
-- | Return _ -> [`Color 0x0000FF; `Style [`Filled]]
-+ | Loop _ -> [`Color 0xFF0000; `Style `Filled]
-+ | If _ -> [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
-+ | Return _ -> [`Color 0x0000FF; `Style `Filled]
- | Block _ -> [`Shape `Box; `Fontsize 8]
-- | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style [`Filled]]
-- | Instr (Skip _) -> [`Color 0x00FFFF ; `Style [`Filled]]
-+ | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style `Filled]
-+ | Instr (Skip _) -> [`Color 0x00FFFF ; `Style `Filled]
- | _ -> []
- let default_vertex_attributes _ = []
-
-diff --git a/src/logic/property_status.ml b/src/logic/property_status.ml
-index f7c278d..47485f6 100644
---- a/src/logic/property_status.ml
-+++ b/src/logic/property_status.ml
-@@ -1481,12 +1481,12 @@ module Consolidation_graph = struct
- let s = get_status p in
- let color = status_color p s in
- let style = match s with
-- | Never_tried -> [`Style [`Bold]; `Width 0.8 ]
-- | _ -> [`Style [`Filled]]
-+ | Never_tried -> [`Style `Bold; `Width 0.8 ]
-+ | _ -> [`Style `Filled]
- in
- style @ [ label v; `Color color; `Shape `Box ]
- | Emitter _ as v ->
-- [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style [`Filled] ]
-+ [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style `Filled ]
- | Tuning_parameter _ as v ->
- [ label v; (*`Style `Dotted;*) `Color 0xb0c4de; ]
- (*| Correctness_parameter _ (*as v*) -> assert false (*[ label v; `Color 0xb0c4de ]*)*)
-@@ -1495,7 +1495,7 @@ module Consolidation_graph = struct
- | None -> []
- | Some s ->
- let c = emitted_status_color s in
-- [ `Color c; `Fontcolor c; `Style [`Bold] ]
-+ [ `Color c; `Fontcolor c; `Style `Bold ]
-
- let default_vertex_attributes _ = []
- let default_edge_attributes _ = []
-diff --git a/src/misc/service_graph.ml b/src/misc/service_graph.ml
-index 4f866c5..d158028 100644
---- a/src/misc/service_graph.ml
-+++ b/src/misc/service_graph.ml
-@@ -289,7 +289,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
- color e
- else
- match CallG.E.label e with
-- | Inter_services -> [ `Style [`Invis] ]
-+ | Inter_services -> [ `Style `Invis ]
- | Inter_functions | Both -> color e
-
- let default_edge_attributes _ = []
-@@ -303,7 +303,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
- sg_attributes =
- [ `Label ("S " ^ cs);
- `Color (Extlib.number_to_color id);
-- `Style [`Bold] ] }
-+ `Style `Bold ] }
-
- end
-
-diff --git a/src/pdg_types/pdgTypes.ml b/src/pdg_types/pdgTypes.ml
-index 05754e4..74cdebf 100644
---- a/src/pdg_types/pdgTypes.ml
-+++ b/src/pdg_types/pdgTypes.ml
-@@ -626,7 +626,7 @@ module Pdg = struct
-
- let graph_attributes _ = [`Rankdir `TopToBottom ]
-
-- let default_vertex_attributes _ = [`Style [`Filled]]
-+ let default_vertex_attributes _ = [`Style `Filled]
- let vertex_name v = string_of_int (Node.id v)
-
- let vertex_attributes v =
-@@ -711,13 +711,13 @@ module Pdg = struct
- if Dpd.is_ctrl d then (`Arrowtail `Odot)::attrib else attrib
- in
- let attrib =
-- if Dpd.is_addr d then (`Style [`Dotted])::attrib else attrib
-+ if Dpd.is_addr d then (`Style `Dotted)::attrib else attrib
- in
- attrib
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (`Style [`Filled]) :: attrib in
-+ let attrib = (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
-diff --git a/src/postdominators/print.ml b/src/postdominators/print.ml
-index f2e3a25..15f4ff2 100644
---- a/src/postdominators/print.ml
-+++ b/src/postdominators/print.ml
-@@ -63,7 +63,7 @@ module Printer = struct
-
- let graph_attributes (title, _) = [`Label title]
-
-- let default_vertex_attributes _g = [`Style [`Filled]]
-+ let default_vertex_attributes _g = [`Style `Filled]
- let default_edge_attributes _g = []
-
- let vertex_attributes (s, has_postdom) =
-diff --git a/src/semantic_callgraph/register.ml b/src/semantic_callgraph/register.ml
-index 1c79dcc..071f061 100644
---- a/src/semantic_callgraph/register.ml
-+++ b/src/semantic_callgraph/register.ml
-@@ -102,8 +102,8 @@ module Service =
- let name = Kernel_function.get_name
- let attributes v =
- [ `Style
-- [if Kernel_function.is_definition v then `Bold
-- else `Dotted] ]
-+ (if Kernel_function.is_definition v then `Bold
-+ else `Dotted) ]
- let entry_point () =
- try Some (fst (Globals.entry_point ()))
- with Globals.No_such_entry_point _ -> None
-diff --git a/src/slicing/printSlice.ml b/src/slicing/printSlice.ml
-index c5363f9..211e0bb 100644
---- a/src/slicing/printSlice.ml
-+++ b/src/slicing/printSlice.ml
-@@ -227,7 +227,7 @@ module PrintProject = struct
-
- let graph_attributes (name, _) = [`Label name]
-
-- let default_vertex_attributes _ = [`Style [`Filled]]
-+ let default_vertex_attributes _ = [`Style `Filled]
-
- let vertex_name v = match v with
- | Src fi -> SlicingMacros.fi_name fi
-@@ -280,16 +280,16 @@ module PrintProject = struct
-
- let edge_attributes (e, call) =
- let attrib = match e with
-- | (Src _, Src _) -> [`Style [`Invis]]
-- | (OptSliceCallers _, _) -> [`Style [`Invis]]
-- | (_, OptSliceCallers _) -> [`Style [`Invis]]
-+ | (Src _, Src _) -> [`Style `Invis]
-+ | (OptSliceCallers _, _) -> [`Style `Invis]
-+ | (_, OptSliceCallers _) -> [`Style `Invis]
- | _ -> []
- in match call with None -> attrib
- | Some call -> (`Label (string_of_int call.sid)):: attrib
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (*(`Label name) ::*) (`Style [`Filled]) :: attrib in
-+ let attrib = (*(`Label name) ::*) (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
-diff --git a/src/syntactic_callgraph/register.ml b/src/syntactic_callgraph/register.ml
-index d4669c4..d41980e 100644
---- a/src/syntactic_callgraph/register.ml
-+++ b/src/syntactic_callgraph/register.ml
-@@ -37,8 +37,8 @@ module Service =
- let name v = nodeName v.cnInfo
- let attributes v =
- [ match v.cnInfo with
-- | NIVar (_,b) when not !b -> `Style [`Dotted]
-- | _ -> `Style [`Bold] ]
-+ | NIVar (_,b) when not !b -> `Style `Dotted
-+ | _ -> `Style `Bold ]
- let equal v1 v2 = id v1 = id v2
- let compare v1 v2 =
- let i1 = id v1 in
-diff --git a/src/wp/cil2cfg.ml b/src/wp/cil2cfg.ml
-index 6d8cf09..ba5f410 100644
---- a/src/wp/cil2cfg.ml
-+++ b/src/wp/cil2cfg.ml
-@@ -1278,9 +1278,9 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
- | Vstart | Vend | Vexit -> [`Color 0x0000FF; `Shape `Doublecircle]
- | VfctIn | VfctOut -> [`Color 0x0000FF; `Shape `Box]
- | VblkIn _ | VblkOut _ -> [`Shape `Box]
-- | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style [`Filled]]
-+ | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style `Filled]
- | Vtest _ | Vswitch _ ->
-- [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
-+ [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
- | Vcall _ | Vstmt _ -> []
- in (`Label (String.escaped label))::attr
-
-@@ -1290,15 +1290,15 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
- let attr = [] in
- let attr = (`Label (String.escaped (PE.edge_txt e)))::attr in
- let attr =
-- if is_back_edge e then (`Constraint false)::(`Style [`Bold])::attr
-+ if is_back_edge e then (`Constraint false)::(`Style `Bold)::attr
- else attr
- in
- let attr = match (edge_type e) with
- | Ethen | EbackThen -> (`Color 0x00FF00)::attr
- | Eelse | EbackElse -> (`Color 0xFF0000)::attr
-- | Ecase [] -> (`Color 0x0000FF)::(`Style [`Dashed])::attr
-+ | Ecase [] -> (`Color 0x0000FF)::(`Style `Dashed)::attr
- | Ecase _ -> (`Color 0x0000FF)::attr
-- | Enext -> (`Style [`Dotted])::attr
-+ | Enext -> (`Style `Dotted)::attr
- | Eback -> attr (* see is_back_edge above *)
- | Enone -> attr
- in
-@@ -1308,7 +1308,7 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (`Style [`Filled]) :: attrib in
-+ let attrib = (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
---
diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild
index 9577bf240..173e0715e 100644
--- a/sci-mathematics/lie/lie-2.2.2.ebuild
+++ b/sci-mathematics/lie/lie-2.2.2.ebuild
@@ -21,7 +21,7 @@ RDEPEND="
sys-libs/ncurses:=
"
DEPEND="${RDEPEND}"
-BDEPEND="${RDEPEND}
+BDEPEND="
sys-devel/bison
"
diff --git a/sci-mathematics/ltl2ba/Manifest b/sci-mathematics/ltl2ba/Manifest
index 4d6528d6b..659c1c6e6 100644
--- a/sci-mathematics/ltl2ba/Manifest
+++ b/sci-mathematics/ltl2ba/Manifest
@@ -1 +1,3 @@
DIST ltl2ba-1.1.tar.gz 29629 BLAKE2B 06ba7f7b5e3c6b72d2f0ea3b991346c803669e24d66dc38e311109ee08ed6dcc72bfd9f2ebe0f8864b0f80f010a4438029f4f5dbbf0087469ca2d07cdfce6b3f SHA512 8d010e2bb59fa5d682a56a50133865da938fd3bfcde6386184880eec6989bc1b694d6af9146b4b708cefdcdbcf98248f87074b8c973ea8cab65d658b394ccf69
+DIST ltl2ba-1.2.tar.gz 33026 BLAKE2B f19359e33d4eeb4dde75425ed03d940c08f46dd265b1b9c6773807e7dca67fd44f694f685d4153ca786118e336fab736104a865c5d0e9883390fca694f72b492 SHA512 148ffb1b4dbe134b69c6e946a4a9f1a95a809bf36ef3533117eedeceb721dd4c8a3238bbda2de5782a79b7aee70e33adf6ff193917441092a1ccb4e56a53a655
+DIST ltl2ba-1.3.tar.gz 38265 BLAKE2B bd74d9b9e22589ac00fbaa15f745dd6371894f68b50f85507694648274d9391ad3a90cdf1ee6c342abbceb04d0e2eb5d71473d43969b469a933517cfcd1e16c1 SHA512 1bcef13d98879c083dc907939c652e694802ed91c33a5d90bbeb6fc22d6265a0b153932c5fb3f8557aad30582322c16d0be822bf4208f40faf9384b367a84aa6
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+ default
+ sed -i Makefile \
+ -e "s/CC=gcc/#CC=gcc/g" \
+ -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+ append-cflags -fcommon
+ default
+}
+
+src_install() {
+ dobin ltl2ba
+ dodoc README
+}
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+ default
+ sed -i Makefile \
+ -e "s/CC=gcc/#CC=gcc/g" \
+ -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+ append-cflags -fcommon
+ default
+}
+
+src_install() {
+ dobin ltl2ba
+ dodoc README
+}
diff --git a/sci-physics/apfelxx/Manifest b/sci-physics/apfelxx/Manifest
new file mode 100644
index 000000000..b461f2a76
--- /dev/null
+++ b/sci-physics/apfelxx/Manifest
@@ -0,0 +1 @@
+DIST apfelxx-4.8.0.tar.gz 21695802 BLAKE2B f28d28bafed79ec679fd44bbd3cba668b108668dceaffbc80091a022d1884121a9d2fb08e89ae439663765877aadb7c214b6196d2ea35ad8c25ba545ec3492ee SHA512 23fcde7262637cbe0ff0173a530d0e2d3f39a9daa8b8757e4769c41c4af72569b0e0b8ab59ad5a8dc08ec7718d40bd34abed66671d2116f4242d06b6c2e7c1cc
diff --git a/sci-physics/apfelxx/apfelxx-4.8.0.ebuild b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
new file mode 100644
index 000000000..d31224fa3
--- /dev/null
+++ b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Object oriented rewriting of the APFEL evolution code"
+HOMEPAGE="https://github.com/vbertone/apfelxx"
+SRC_URI="https://github.com/vbertone/apfelxx/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+RDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+ default
+ cmake_src_prepare
+ sed -i "/prefix./s/\/lib/\/$(get_libdir)/g" CMakeLists.txt || die
+ sed -i "s#DESTINATION lib#DESTINATION $(get_libdir)#g" CMakeLists.txt || die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ python_optimize
+}
diff --git a/sci-physics/apfelxx/metadata.xml b/sci-physics/apfelxx/metadata.xml
new file mode 100644
index 000000000..27c6de8e1
--- /dev/null
+++ b/sci-physics/apfelxx/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">
+ APFEL++ is a C++ rewriting of the Fortran 77 evolution code APFEL. However, APFEL++ is based on a completely new code design and guarantees a better performance along with a more optimal memory management. The new modular structure allows for better maintainability and easier extensibility. This makes APFEL++ suitable for a wide range of tasks: from the solution of the DGLAP evolution equations to the computation of deep-inelastic-scattering (DIS) and single-inclusive-annihilation cross sections. Also more complex computations, such as differential semi-inclusive DIS and Drell-Yan cross sections, are easily implementable in APFEL++.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">vbertone/apfelxx</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/cernlib/Manifest b/sci-physics/cernlib/Manifest
new file mode 100644
index 000000000..d8be46729
--- /dev/null
+++ b/sci-physics/cernlib/Manifest
@@ -0,0 +1,2 @@
+DIST cernlib-2023.10.31.0-free.tar.gz 39191038 BLAKE2B 941592a65f0c8d7d0c6c3907c96d8209568579dac455ed28657a5635677d73e6580f48667a641a6ca9dd296bf82a40f6a75c5fc801fcefb7f8e9101b4dcd3202 SHA512 d015f89942bab695444d37847a8138c3a8736ceeb6f4826c659553bf1ae5eab2a77b2871645a125ea189e62520856955070fbb3ed2d208d35f82ee8b8559d089
+DIST cernlib-2023.10.31.0.tar.gz 39547453 BLAKE2B f37686e4a43b969a8cb604874b6181adf8529b9fc383ccd2e42fc369f92d4693ca8db682bc58638cb58e9941cf22551cfec26b33075e15fc6a0b3fab3dcf7d82 SHA512 9bc866d08e3bce2f571f9f4e21e34ca6c99467088d4dce4cbc9b6c62d8ee2b9018668fd66795996a5f6abb1082ac9559cf08bc7f5201421dbffcdd0db9459008
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
new file mode 100644
index 000000000..c5c919678
--- /dev/null
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
@@ -0,0 +1,72 @@
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
+
+DESCRIPTION="CERN program library for High Energy Physics"
+HOMEPAGE="https://cernlib.web.cern.ch/cernlib/"
+SRC_URI="
+ free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz )
+ !free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}.tar.gz )
+"
+
+LICENSE="
+ free? ( BSD LGPL-2+ GPL-1+ )
+ !free? ( all-rights-reserved )
+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+free"
+RESTRICT="mirror"
+
+RDEPEND="
+ x11-libs/motif:0
+ x11-libs/libXaw
+ x11-libs/libXau
+ virtual/lapack
+ dev-lang/cfortran
+ x11-libs/xbae
+ net-libs/libnsl
+ virtual/libcrypt:=
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/pkgconfig
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-cfortran.patch
+ "${FILESDIR}"/${P}-ctest.patch
+ "${FILESDIR}"/${P}-man.patch
+)
+
+src_unpack() {
+ default
+ if use free; then
+ mv ${P}-free ${P} || die
+ fi
+}
+
+src_prepare() {
+ cmake_src_prepare
+ # cfortran.patch
+ # Remove cfortran.h since it is already installed from dev-lang/cfortran
+ # thereby we avoid collisions if e.g. sci-physics/root[fortran] is installed.
+ rm cfortran/cfortran.h || die
+}
+
+src_configure() {
+ # docs follow rpm like spliting into packages cernlib, cernlib-devel, etc.
+ # we move them into a folder that agrees with gentoo doc structure.
+ sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ # man.patch
+ # The CMakeLists.txt already compresses the manual before install
+ # therefore we install it manually and avoid QA problems.
+ doman contrib/man/man1/*.1
+ doman contrib/man/man8/*.8
+}
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
new file mode 100644
index 000000000..b4426b3eb
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..ead47c54 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -735,7 +735,6 @@ add_subdirectory(code_motif)
+ ########################################################################
+ set(CERNLIB_MMAP 1)
+ install(FILES
+-${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cfortran.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/comis.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cspack.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/geant315.h
+@@ -757,7 +756,7 @@ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/paw.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/zebra.h
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/ COMPONENT libs )
+
+-set(head cfortran.h comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h )
++set(head comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h )
+
+ install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_INSTALL_INCLUDEDIR}/cfortran/)")
+ foreach ( m ${head} )
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
new file mode 100644
index 000000000..b329bb900
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
@@ -0,0 +1,31 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..78a28e11 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -162,9 +162,10 @@ macro(CLATestTarget ast)
+ list(FIND a "<" NEEDSHELL)
+ list(JOIN a " " MYCMD)
+ if (NEEDSHELL STREQUAL "-1")
+- add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
++ add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+ if (CERNLIB_ENABLE_MEMORYTEST)
+- add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
++ add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS}
++ ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+ endif()
+ else()
+ add_test(NAME test${exec} COMMAND sh -c "${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD}" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+@@ -182,9 +183,11 @@ macro(CLBTestTarget ast)
+ list(JOIN a " " MYCMD)
+ if (NEEDSHELL STREQUAL "-1")
+ if (CERNLIB_ENABLE_MEMORYTEST)
+- add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
++ add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS}
++ ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
+ endif()
+- add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
++ add_test(NAME test${exec} COMMAND
++ ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
+ else()
+ if (CERNLIB_ENABLE_MEMORYTEST)
+ add_test(NAME memory_test${exec} COMMAND sh -c "${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD}" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch
new file mode 100644
index 000000000..636943899
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch
@@ -0,0 +1,22 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..0db67942 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -410,7 +413,7 @@ else()
+ COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz."
+ )
+ endif()
+- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
++#install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
+ endforeach ( m ${man1} )
+
+ foreach ( m ${man8} )
+@@ -425,7 +428,7 @@ else()
+ COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz."
+ )
+ endif()
+- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8)
++#install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8)
+ endforeach ( m ${man8} )
+
+ #install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/patchy5/yexpand.script DESTINATION ${CMAKE_INSTALL_BINDIR}/ RENAME yexpand.script${COMPSUFFIXBIN} )
diff --git a/sci-physics/cernlib/metadata.xml b/sci-physics/cernlib/metadata.xml
new file mode 100644
index 000000000..dcbfb9b47
--- /dev/null
+++ b/sci-physics/cernlib/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>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">
+ The CERN Program Library is a large collection of general purpose
+ libraries and modules maintained and offered in both source and
+ object code form on the CERN central computers. Most of these
+ programs were developed at CERN and are therefore oriented towards
+ the needs of a physics research laboratory that is general
+ mathematics, data analysis, detectors simulation, data-handling
+ etc... applicable to a wide range of problems.
+ </longdescription>
+ <use>
+ <flag name="free"> Use free sources </flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/collier/Manifest b/sci-physics/collier/Manifest
new file mode 100644
index 000000000..709444249
--- /dev/null
+++ b/sci-physics/collier/Manifest
@@ -0,0 +1 @@
+DIST collier-1.2.8.tar.gz 933258 BLAKE2B 9849ae140ed055a24010f020920f377a78665cb6f2c16ba060082c3573594a2f5772779b4a5596d306220b49ec2ffb7249705c0f05ea4eb22784518acb1038a0 SHA512 119b597da04dcd529efc35b5f96d2b2ad1f2f4403c3d0521a24b49fba973c5557378b68994ea6d30ca92057d32a30a6de299b2c707d56c231d197f33632297d9
diff --git a/sci-physics/collier/collier-1.2.8.ebuild b/sci-physics/collier/collier-1.2.8.ebuild
new file mode 100644
index 000000000..c9410cf34
--- /dev/null
+++ b/sci-physics/collier/collier-1.2.8.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit fortran-2 cmake
+
+MY_P=COLLIER-${PV}
+
+DESCRIPTION="A Complex One-Loop LIbrary with Extended Regularizations"
+HOMEPAGE="https://collier.hepforge.org/index.html"
+SRC_URI="https://collier.hepforge.org/downloads/?f=${P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="static-libs"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-1.2.7-mod.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -Dstatic=$(usex static-libs ON OFF)
+ -DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)
+ -DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake/collier
+ )
+ cmake_src_configure
+}
diff --git a/sci-physics/collier/files/collier-1.2.7-mod.patch b/sci-physics/collier/files/collier-1.2.7-mod.patch
new file mode 100644
index 000000000..030900b5c
--- /dev/null
+++ b/sci-physics/collier/files/collier-1.2.7-mod.patch
@@ -0,0 +1,40 @@
+--- a/CMakeLists.txt 2023-05-08 17:21:39.559979698 +0200
++++ b/CMakeLists.txt 2023-05-08 17:43:20.599147534 +0200
+@@ -282,7 +282,36 @@
+ message("Collier install include prefix: ${INCLUDE_INSTALL_DIR}")
+ message("Collier install library prefix: ${LIB_INSTALL_DIR}")
+
+-set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod")
++set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/cache.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/buildtensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_aux2.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_stat.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_aux.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_coefs.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_global.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_init.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_tensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/combinatorics.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_2pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_3pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_4pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_5pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_6pt.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_global.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_statistics.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globalc.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globald.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/inittensors.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/master.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionab.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionc.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiond.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionefg.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiontn.mod"
++ "${CMAKE_Fortran_MODULE_DIRECTORY}/tensorreduction.mod"
++)
+ set_target_properties(collier PROPERTIES PUBLIC_HEADER "${COLLIER_HEADERS}")
+
+ include(PackageConfigInstall)
diff --git a/sci-physics/collier/metadata.xml b/sci-physics/collier/metadata.xml
new file mode 100644
index 000000000..72f8361a4
--- /dev/null
+++ b/sci-physics/collier/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://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>
+ A package for evaluation of scalar and tensor one-loop integrals
+ based on the FF package by G.J. van Oldenborgh.
+ It features an easy Fortran, C++, and Mathematica interface
+ to the scalar one-loop functions of FF and in addition provides
+ the 2-, 3-, and 4-point tensor coefficient functions.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
index 6cee48279..fb57ea648 100644
--- a/sci-physics/formcalc/formcalc-9.10-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -3,6 +3,8 @@
EAPI=8
+inherit fortran-2
+
MY_PN=FormCalc
MY_P=${MY_PN}-${PV}
@@ -36,14 +38,9 @@ src_compile() {
src_install() {
MMADIR=/usr/share/Mathematica/Applications
+ # unversioned directory
dosym ${MY_P} ${MMADIR}/${MY_PN}
- dodir ${MMADIR}/${MY_P}
- insinto ${MMADIR}
- doins -r "${S}"
- # Copy executable, etc. permissions
- for f in $(find * ! -type l); do
- fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
- done
+ mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
index a5cd57431..91d88dd99 100644
--- a/sci-physics/formcalc/formcalc-9.9-r1.ebuild
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -3,6 +3,8 @@
EAPI=8
+inherit fortran-2
+
MY_PN=FormCalc
MY_P=${MY_PN}-${PV}
@@ -38,14 +40,9 @@ src_compile() {
src_install() {
MMADIR=/usr/share/Mathematica/Applications
+ # unversioned directory
dosym ${MY_P} ${MMADIR}/${MY_PN}
- dodir ${MMADIR}/${MY_P}
- insinto ${MMADIR}
- doins -r "${S}"
- # Copy executable, etc. permissions
- for f in $(find * ! -type l); do
- fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
- done
+ mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
# switch to system form
dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
diff --git a/sci-physics/hepunits/Manifest b/sci-physics/hepunits/Manifest
index f831328d4..9b6a3c900 100644
--- a/sci-physics/hepunits/Manifest
+++ b/sci-physics/hepunits/Manifest
@@ -1 +1,2 @@
DIST hepunits-2.3.2.tar.gz 13327 BLAKE2B 16986f4cf96eb927e5ae7268dc2975957846678bff0569fc5d5b9d36bb5dae251905283a07e5fcdd895b20982e1e2d32bce5048752d654ca085286e89b65837f SHA512 48d0a4939e19fc6f26b3bb5f8515d8e0d9d4cbed172c14ae30609c2039bdb77625dad8e1e628178481ee0f203d7d36cd2e0d3306f3b344fe14cd68827c4d9477
+DIST hepunits-2.3.3.tar.gz 13491 BLAKE2B ec212be4e53e7ea5aa195852ea6ad4f3aac8e3eb49676e6bef76d525be861ecd4480821b248d746950b45affccd31bf23d5232aee13058bb48ec8d76c4f70a14 SHA512 7a29dd6220c1fbe610f15ef66f02e499d7e2ade8c39827e3229ae74035d127ca7805b9e32c3859c5af4b001725d21514fd81f0408d7f0dc76e9ee34aa66191e8
diff --git a/sci-physics/hepunits/hepunits-2.3.2.ebuild b/sci-physics/hepunits/hepunits-2.3.2.ebuild
index 9816df84b..34b3977a8 100644
--- a/sci-physics/hepunits/hepunits-2.3.2.ebuild
+++ b/sci-physics/hepunits/hepunits-2.3.2.ebuild
@@ -20,4 +20,4 @@ fi
RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
diff --git a/sci-physics/hepunits/hepunits-2.3.3.ebuild b/sci-physics/hepunits/hepunits-2.3.3.ebuild
new file mode 100644
index 000000000..2fb8bb148
--- /dev/null
+++ b/sci-physics/hepunits/hepunits-2.3.3.ebuild
@@ -0,0 +1,25 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="units and constants in the HEP system of units"
+HOMEPAGE="https://github.com/scikit-hep/hepunits"
+
+LICENSE="BSD"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scikit-hep/hepunits"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/hepunits/hepunits-9999.ebuild b/sci-physics/hepunits/hepunits-9999.ebuild
index 9816df84b..2fb8bb148 100644
--- a/sci-physics/hepunits/hepunits-9999.ebuild
+++ b/sci-physics/hepunits/hepunits-9999.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -20,4 +20,6 @@ fi
RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/hoppet/Manifest b/sci-physics/hoppet/Manifest
new file mode 100644
index 000000000..cc73bfc3b
--- /dev/null
+++ b/sci-physics/hoppet/Manifest
@@ -0,0 +1 @@
+DIST hoppet-1.2.0.tgz 575911 BLAKE2B 4d4dc1874b45b7237384ad3955808b5f4995c86b4d44165ef0c4d8b1da21880cdd1a3f1f1537f02ad7928baef5207e950be411465989ab876bcb806f355725cf SHA512 65ceb170cd417f229f8a974aa995138b8ee7ea5ef04538a5382b353181951e9d4489045234cd45c1ea8f88a5faf4755e3a0e246065711f137676bbf726a29f1f
diff --git a/sci-physics/hoppet/hoppet-1.2.0.ebuild b/sci-physics/hoppet/hoppet-1.2.0.ebuild
new file mode 100644
index 000000000..337881026
--- /dev/null
+++ b/sci-physics/hoppet/hoppet-1.2.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2022-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+DESCRIPTION="Higher Order Perturbative Parton Evolution Toolkit"
+HOMEPAGE="
+ https://hoppet.hepforge.org/
+ https://github.com/gavinsalam/hoppet
+"
+SRC_URI="https://hoppet.hepforge.org/downloads/${P}.tgz"
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64"
+
+
+src_configure() {
+ default
+ # own custom configure
+ ./configure --prefix="${EPREFIX}"/usr FFLAGS="${FFLAGS} -fPIC" || die
+}
+
+src_install() {
+ # Fix install to ED
+ sed -i "s#scripts/install-sh hoppet-config#\##g" Makefile || die
+ sed -i "s#/usr/lib/libhoppet#${ED}/usr/$(get_libdir)/libhoppet#g" src/Makefile || die
+ sed -i "s#/usr/include/hoppet#${ED}/usr/include/hoppet#g" src/Makefile || die
+ emake install
+ emake install-mod
+ dobin hoppet-config
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/hoppet/metadata.xml b/sci-physics/hoppet/metadata.xml
new file mode 100644
index 000000000..37900a238
--- /dev/null
+++ b/sci-physics/hoppet/metadata.xml
@@ -0,0 +1,19 @@
+<?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">
+ HOPPET is a Fortran 95 package for carrying out DGLAP evolution and other common manipulations of parton distribution functions (PDFs).
+ </longdescription>
+ <upstream>
+ <remote-id type="github">gavinsalam/hoppet</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/lhapdf-sets/Manifest b/sci-physics/lhapdf-sets/Manifest
index 6b51079a6..6e1d34375 100644
--- a/sci-physics/lhapdf-sets/Manifest
+++ b/sci-physics/lhapdf-sets/Manifest
@@ -4,8 +4,10 @@ DIST CT14nlo.tar.gz 27067462 BLAKE2B b8d46593a62e80c320c76fb89f646ba0f31ab988110
DIST CT14qed_proton.tar.gz 11064380 BLAKE2B b0b5834473a90d2adfedfa4dd467847349fc1b60907d387d1007387dcf557fac37871ea7430161edc0ecf6f8e8839077283dc8fcad610f03dd192efd70890c3f SHA512 a41f6f82e5505f66014e5523210c272254fb8018bbfac542eb1941e60c1c897ee687bfef1afbd981132cb772240fdd4d19b5dcd2b36b01f8e34ea959d9acd4f7
DIST MRST2004qed.tar.gz 185079 BLAKE2B 62e0371de965698100755b14b0c282095b84b40800a58cd6776c458b03982f032f3b2464eb76174084dd22de9fd962e202a4896327b0a00579c3a632dac24ccc SHA512 404aacf0e241f572cc42ad4cf963deef1acd3d365fa68cfa3518878f921858046377ea39caf663fdced2cdde07af2f6ce695737f7fea229489df3d3f38283c95
DIST MRST2007lomod.tar.gz 56685 BLAKE2B 8515b6f77302621f4b37f550840f07f0351e7ea98de16a37ceb4cb0f2ea64aa4b027462ffc442f34d1f4c349d67fac7b35353606d8920f17621c7187e508c689 SHA512 8e55627a01c85d90a62e4fb11b115c2faac2220479b6d558d3d6f1b801fc5c3e88abc377cd5437ccaeedd34b2ca42d6e833014566b796e5e1eebcf4d620e5dc0
+DIST NNPDF23_nlo_as_0118.tar.gz 21655966 BLAKE2B f92d0b90f27d1a096f327e5aa45cc4d36ad3789db6fcc477b21d6170495c8508edcc86000baf20e50366895a8a1fd1b7d30c136b77ea35c466b65016b66c3829 SHA512 5570273743d4efb9676e3b5f461d8944b841cbcb3f80949f63520f05c184bd551a2a3be3961d20d5de80e7e35e88f26e5eb5c20903d20ed44e2f33038d6c66af
DIST NNPDF23_nlo_as_0119_qed_mc.tar.gz 25223180 BLAKE2B 05dd8772d559e8f08e28dc16da6b256d875563b140e1954cedac9b5f541e9cd325c4dfd5adbb13af434e036cbafa9bfe19325f69ae00ed599cfac6791629d989 SHA512 fc6998d50a61bbe65eef827021c0f453164795c079daef6a4932f825f8db4ae318bbf0e8781b61f1d3ffa9a495b5c4813af3aa31c77694657a44356d93fa970f
DIST NNPDF23_nnlo_as_0119_qed_mc.tar.gz 28940412 BLAKE2B 57c7c98bb863258f87e236fea2d0233ac61350012aec6ba5cced75de0b4b945a5633d7fd487b0913b822df1c3ef804de2aacf34b1319d6973d959dc02ebbc9b2 SHA512 5088c30acbd1da4e412ba9f6a997ceaa34f426f41c7ebacaf4d2e8aa49b8b45052913e8d873b293d9f140c01e82c05735b66dd527a9aa124b86f73bf5e4d8c53
+DIST NNPDF31_nnlo_as_0118.tar.gz 43193739 BLAKE2B b826eaebb6483b844bc18cfca36be8ead1dc409641e445f8d31db58f31bde623b7e7753a94c0e2ee0dfe24b28909b9d06b17641a783c223d8ab7ce8e55902a5c SHA512 a62330979f4001933b52e2b1bd3142b4dacd27aeed1e49969108a842e00e7db59a7fe8d80b755c283f3bc706b36e3ec4597e124d95ad3a7f334fb956bebe7ae0
DIST NNPDF31_nnlo_as_0118_luxqed.tar.gz 47462442 BLAKE2B 2b473d943ec49e28de63d002e4eadfd3002c63aa6ef9b4e792adf7acf8bb3a771f91298ac6575034407653d15aa4191da6090aaaa34d8a8091cb1a5d4562479a SHA512 5faafc9a2b23dc0a82c7f3ca26a6691cfa476f83741beab2b41a77e63fa5f10428bf43579670636689c0080421f4b08ec058aa63c047f04f6d892b1b848fd702
DIST PDF4LHC15_nlo_asvar.tar.gz 578871 BLAKE2B a42a24d4af82f892e0dccfeeacedfcbb074be1ddc9649d55ff6c15e3923901173337ba4197248410d2a40e72ab627af9a0cea09e5ee98c37130aceb34402d9d4 SHA512 ef96970050b78f5a5bc54b43ee2d7ed0eb76796ea23ce864f1c8ff6de2d68f99023d5c4530f4e73197948c39886fcb832ed26dfa126ca0396e4fd08e353df8a0
DIST cteq66.tar.gz 8647237 BLAKE2B 3ac47b6eee434f89ff329cfcb8268782af4ffa552ca4b412a59254e9b10410518f9fe9543b47f193d9cd31b06fc1101556df2be01c25ca17febcb9fb1855e5ca SHA512 25d0fa01dcdb59d71c7092367af8258471a2bc6dfd146766cc79f90ffb0feafa0f2011d0a37a7d75315c10ba7c7a6e3fa583d9c0a28119b072228ac800294e48
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
index edd3639d2..784d94f97 100644
--- a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -17,6 +17,8 @@ IUSE_LHAPDF_SETS="
lhapdf_sets_cteq66
lhapdf_sets_cteq6l1
lhapdf_sets_mrst2004qed
+ lhapdf_sets_nnpdf23_nlo_as_0118
+ lhapdf_sets_nnpdf31_nnlo_as_0118
"
COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current"
@@ -36,7 +38,9 @@ SRC_URI="
lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz )
lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz )
- lhapdf_sets_mrst2004qed? ( ${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_mrst2004qed? ( ${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_nnpdf23_nlo_as_0118? ( ${COMMON_URI}/NNPDF23_nlo_as_0118.tar.gz )
+ lhapdf_sets_nnpdf31_nnlo_as_0118? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118.tar.gz )
"
MY_PV=$(ver_cut 1-3)
diff --git a/sci-physics/mcfm/mcfm-10.2.1.ebuild b/sci-physics/mcfm/mcfm-10.2.1.ebuild
index 9a928e4c9..bfc795247 100644
--- a/sci-physics/mcfm/mcfm-10.2.1.ebuild
+++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
MY_PN=MCFM
MY_P=${MY_PN}-${PV}
@@ -29,9 +29,6 @@ DEPEND="
>=sci-libs/handyg-0.1.5
"
RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
PATCHES=(
"${FILESDIR}"/${P}-rest.patch
diff --git a/sci-physics/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml
index bdee6992b..35b6c2bd9 100644
--- a/sci-physics/oneloop/metadata.xml
+++ b/sci-physics/oneloop/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-physics@gentoo.org</email>
<name>Gentoo Physics Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="bitbucket">hameren/oneloop</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
index 8b98d1e1d..9344d1513 100644
--- a/sci-physics/oneloop/oneloop-2020.07.31.ebuild
+++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
@@ -5,7 +5,7 @@ EAPI=8
# python only needed for create.py to get binaries
PYTHON_COMPAT=( python3_{10..11} )
-inherit toolchain-funcs python-any-r1
+inherit toolchain-funcs python-any-r1 fortran-2
DESCRIPTION="Library of one-loop scalar functions"
HOMEPAGE="https://bitbucket.org/hameren/oneloop"
@@ -16,12 +16,9 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
BDEPEND="
${PYTHON_DEPS}
app-arch/unzip
- virtual/fortran
"
PATCHES=(
diff --git a/sci-physics/particle/Manifest b/sci-physics/particle/Manifest
index fbbcdada4..2f92c548b 100644
--- a/sci-physics/particle/Manifest
+++ b/sci-physics/particle/Manifest
@@ -1 +1,3 @@
DIST particle-0.23.0.tar.gz 313512 BLAKE2B 33a0dc1cf612af8242b5080d0862f3b1e587254b46fa90f235cd6edba3919594c5077733600dfe88ad0959be889271c301324789abf0511a7fbe588942086877 SHA512 582c42beade0b28f28f3ee9f83f6d8cc75558f8a9aa5fbe3679c7aa68af40bd04f374741211d6f214bb828c24a017a89b541f780739a36d61d85a2fd5e00b530
+DIST particle-0.23.1.tar.gz 313729 BLAKE2B fc35163955e065b350dfa0825612a64214baeb1f5be41404af259136e6689e23419891513c059ccdfbe2cbf5891596fccd0b0b7f283031bb3352600b5be43441 SHA512 1b4f4516357fd9725d9d5b0a481467896e93e23a8956b2ce321b9cac1d200a8ee8dd9cc1b22d940b4708f29abe3417988677ac685b78287abe10afafa79fb381
+DIST particle-0.24.0.tar.gz 314302 BLAKE2B bbb2d52a80b4d9aafaf86a3cc1b28106253bf0edfe5a6127c03242a32973feaefeb32562063e5ff0438f5df946a905d03baa36c445093ce185d3be71c10e5135 SHA512 5a73079d9120ab509162189ba5992c615fc00e00d37a6556338130739bbf53fd5db01e973cb1b509ef7ce569021c0462ac77e5fcafe40df31e5cef0a89923a2a
diff --git a/sci-physics/particle/particle-0.23.0.ebuild b/sci-physics/particle/particle-0.23.0.ebuild
index c1f823d9d..88da33c3e 100644
--- a/sci-physics/particle/particle-0.23.0.ebuild
+++ b/sci-physics/particle/particle-0.23.0.ebuild
@@ -22,13 +22,15 @@ RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
test? (
>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/tabulate[${PYTHON_USEDEP}]
)
"
-BDEPEND="${RDEPEND}"
distutils_enable_tests pytest
src_prepare() {
diff --git a/sci-physics/particle/particle-0.23.1.ebuild b/sci-physics/particle/particle-0.23.1.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.23.1.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+ >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+ dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+ default
+
+ sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+ epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/particle/particle-0.24.0.ebuild b/sci-physics/particle/particle-0.24.0.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.24.0.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+ >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+ dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+ default
+
+ sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+ epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/particle/particle-9999.ebuild b/sci-physics/particle/particle-9999.ebuild
index c1f823d9d..43f1e67ca 100644
--- a/sci-physics/particle/particle-9999.ebuild
+++ b/sci-physics/particle/particle-9999.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_11 )
+PYTHON_COMPAT=( python3_{11..12} )
DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -22,13 +22,15 @@ RDEPEND="
>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
test? (
>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/tabulate[${PYTHON_USEDEP}]
)
"
-BDEPEND="${RDEPEND}"
distutils_enable_tests pytest
src_prepare() {
diff --git a/sci-physics/pyhepmc/Manifest b/sci-physics/pyhepmc/Manifest
new file mode 100644
index 000000000..1351fa866
--- /dev/null
+++ b/sci-physics/pyhepmc/Manifest
@@ -0,0 +1 @@
+DIST pyhepmc-2.11.0.tar.gz 361596 BLAKE2B 18264f61bdef3c27f8aa4d48d25257c03f98cc89745533641119cf7ba6d5fe36c084d25ccaeed6769dc9226fd5f2c27060006030447a8ac8409ff6d752437d2c SHA512 31975d0bee5037c1cc36753ce6324342ed6a48b2d3f91f53d61f445f38f0fa3ecbeb0e29fcbc7f6778bafcc23c1f6a689b9516eae8da4cc620cd7c72b89e0b00
diff --git a/sci-physics/pyhepmc/metadata.xml b/sci-physics/pyhepmc/metadata.xml
new file mode 100644
index 000000000..6f6a9a0bb
--- /dev/null
+++ b/sci-physics/pyhepmc/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ pyhepmc largely mirrors the C++ interface of the HepMC3 library, which is documented here. Parts of the documentation have been copied from HepMC3. Documentation is available as Python docstrings, so you can use Python's help() browser to learn about the API. Alternatively, you can consult the online reference generated from these docstrings which includes some examples.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">pyhepmc</remote-id>
+ <remote-id type="github">scikit-hep/pyhepmc</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
new file mode 100644
index 000000000..c28b094bb
--- /dev/null
+++ b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Pythonic wrapper for the HepMC3 C++ library."
+HOMEPAGE="https://github.com/scikit-hep/pyhepmc"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.0[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ ${RDEPEND}
+ dev-build/cmake
+"
diff --git a/sci-physics/pyhf/pyhf-0.7.3.ebuild b/sci-physics/pyhf/pyhf-0.7.3.ebuild
index 8b2d02304..d97cd71f9 100644
--- a/sci-physics/pyhf/pyhf-0.7.3.ebuild
+++ b/sci-physics/pyhf/pyhf-0.7.3.ebuild
@@ -32,4 +32,4 @@ RDEPEND="
>=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}]
>=dev-python/click-8.0.0[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
diff --git a/sci-physics/pylhe/Manifest b/sci-physics/pylhe/Manifest
new file mode 100644
index 000000000..11dbc6d26
--- /dev/null
+++ b/sci-physics/pylhe/Manifest
@@ -0,0 +1,2 @@
+DIST pylhe-0.7.0.gh.tar.gz 140203 BLAKE2B 6c167b37bb6c978752de79586e4f655169b5134c6cd7637807e649323ebaca50d8a360b1ca32eeff2cc162efe5e13d7de92f72d5a9263a7b2c48a5b87b7b919c SHA512 1a338ab4e1c5dd1d8d80e4a03ad84eb59f19ebb151a4b1393b68ee6ecade920c88db6cb940d56bd1f238e833f59b266507ab678124ea49b4086fe05b7f9baa88
+DIST pylhe-0.8.0.gh.tar.gz 144541 BLAKE2B 5c6a6511acd1adefad6bf3769fdb5ac2a528a8cc939bb1209d7fd4dc31eef9060d129c330b34e3cfc7b640c9b82f68f043e4604f3a535865240ceda0a33dd691 SHA512 6fc3c525cbb5f2ebe8678d1e03940fde8bdc837f1da6a667c70069584de476ea73c72e817cc84637e018ca7cf21e8bb0f7b2721fe54ef78a9b0eee7900ec400e
diff --git a/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
new file mode 100644
index 000000000..ea678ce8c
--- /dev/null
+++ b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
@@ -0,0 +1,8 @@
+--- a/pytest.ini 2024-03-20 07:36:32.600030197 +0100
++++ b/pytest.ini 2024-03-20 07:36:45.896874886 +0100
+@@ -1,4 +1,4 @@
+ [pytest]
+ docstyle_convention = numpy
+ junit_family = xunit2
+-addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --cov=pylhe --cov-report=term-missing --cov-config=.coveragerc --cov-report xml --doctest-modules --doctest-glob='*.rst'
++addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --doctest-modules --doctest-glob='*.rst'
diff --git a/sci-physics/pylhe/metadata.xml b/sci-physics/pylhe/metadata.xml
new file mode 100644
index 000000000..86ede8deb
--- /dev/null
+++ b/sci-physics/pylhe/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Small and thin Python interface to read Les Houches Event (LHE) files.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">pylhe</remote-id>
+ <remote-id type="github">scikit-hep/pylhe</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/pylhe/pylhe-0.7.0.ebuild b/sci-physics/pylhe/pylhe-0.7.0.ebuild
new file mode 100644
index 000000000..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.7.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe"
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+ >=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+ >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+ >=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+ test? (
+ >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+ )
+"
+PATCHES=(
+ "${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
diff --git a/sci-physics/pylhe/pylhe-0.8.0.ebuild b/sci-physics/pylhe/pylhe-0.8.0.ebuild
new file mode 100644
index 000000000..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.8.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe"
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+ >=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+ >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+ >=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+ test? (
+ >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+ )
+"
+PATCHES=(
+ "${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
index 19a247ba2..672957c56 100644
--- a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
+++ b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
@@ -15,12 +15,6 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
-
PATCHES=(
"${FILESDIR}"/${P}-cxx.patch
)
diff --git a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
index ccea20aa5..6486e70b9 100644
--- a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
+++ b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake
+inherit cmake fortran-2
DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
@@ -15,12 +15,6 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND="
- virtual/fortran
-"
-
PATCHES=(
"${FILESDIR}"/${P}-cxx.patch
)
diff --git a/sci-physics/qgraf/Manifest b/sci-physics/qgraf/Manifest
index ebe52e211..32519be3c 100644
--- a/sci-physics/qgraf/Manifest
+++ b/sci-physics/qgraf/Manifest
@@ -1 +1,3 @@
-DIST qgraf-3.6.5.tgz 449818 BLAKE2B 630cbd798423f17a1a20ab80f65c88e755347c9583a70cf43e3914186bc7c71bb8b854227197b9705c2d6538627fe56bf3fe497b3823a7130ff660192d2270c8 SHA512 b98fbc8c2fa64b5f3596b4a8b68bfab75a0bebf74615fc680d5b4487ec3c8de40ed4a7b310f2036c25f3fd91a76cb57db7c647b38e8580eed2b9d8bd0c50bcc7
+DIST qgraf-3.4.2.tgz 358979 BLAKE2B 06c5cf82faab531d6d17387d62e80b2e395ad0ffd80a69dc49608588f4acdf23d226877db047d3906963b5f64d85329665fed0e10359ddbb649122fb328b78f8 SHA512 e86f94480eaf7cd0b4d79b60ec1420c21f0285133f2184d1c0a1d05ec0d9abc3e483d100d43c38fafc06bf8cecea413c0304adcb64d900522e877b1a24e7b61b
+DIST qgraf-3.5.2.tgz 426930 BLAKE2B 0bd50cbefee9a91cdfe9a15a53fb018c1b15088b211a03dde63f08410bbac4acd7586ef4cece17debd5197d3d5b7a8c889aeec27d7f3f137df7ef95f1687a709 SHA512 1e1fbafc80c60a663537a5ca555f405ec1517beccf09e2f68fcd9c84963b4b20d3a66e77980c4c4ff68f82950dc41f4492dc0272fdf5e3c105861fcf4c0e8c80
+DIST qgraf-3.6.7.tgz 460592 BLAKE2B d4275d7e5b9138eab3a2848b1e75883a4d52b61bdddd2ecbefe674559a56d9315bb03bd86c5a607f01d708c634f35b180f4cfde99242e65a40bf3f81ce6fa9e3 SHA512 c721eb82975a6077da77a82f7875d0e0346e21932d0312109d1bab68391a0210fc3f7ff79327d515668dedee0c5fce4e01d7433177232c43a4e39d8204f01405
diff --git a/sci-physics/qgraf/qgraf-3.6.5.ebuild b/sci-physics/qgraf/qgraf-3.4.2.ebuild
index 68e0ebf97..cdab94002 100644
--- a/sci-physics/qgraf/qgraf-3.6.5.ebuild
+++ b/sci-physics/qgraf/qgraf-3.4.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit toolchain-funcs
+inherit toolchain-funcs fortran-2
DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
@@ -16,12 +16,8 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE="doc examples"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
src_compile() {
- $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS}
+ $(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
}
src_install() {
diff --git a/sci-physics/qgraf/qgraf-3.5.2.ebuild b/sci-physics/qgraf/qgraf-3.5.2.ebuild
new file mode 100644
index 000000000..4194295a4
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.5.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
+SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+ $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
+}
+
+src_install() {
+ dobin ${PN}
+
+ use doc && dodoc *.pdf
+ if use examples; then
+ docinto examples
+ dodoc phi3 qed qcd *.sty *.dat
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
diff --git a/sci-physics/qgraf/qgraf-3.6.7.ebuild b/sci-physics/qgraf/qgraf-3.6.7.ebuild
new file mode 100644
index 000000000..4194295a4
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.6.7.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
+SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+ $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
+}
+
+src_install() {
+ dobin ${PN}
+
+ use doc && dodoc *.pdf
+ if use examples; then
+ docinto examples
+ dodoc phi3 qed qcd *.sty *.dat
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
diff --git a/sci-physics/rivet/Manifest b/sci-physics/rivet/Manifest
deleted file mode 100644
index f5c46bd86..000000000
--- a/sci-physics/rivet/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST Rivet-3.1.5.tar.gz 30576082 BLAKE2B 2fcf0f03219832d48546235f25d844837c37aa20e3972c35184741d1e14d70224bd7db597cd01e946dde4768b941ce9cf1dee3b3c385cb8a81e7b291c7edb1d3 SHA512 8dea32ef1ec7596904f1209a89343ed767e57b67e5fb85a230fd52a05231c901ea9f4663e6cea145e72d5d1beaf94dd642afaa1d5814843672b33073bb359c3f
-DIST Rivet-3.1.6.tar.gz 28804847 BLAKE2B b4e5a35285a4abdedaefbeaa06e5a703e5bf3b1ef4721db3d664dac5197b63845d228ab0dc0370b7b5095dccc3c9b5f3456ef59aabdcfb6c2f65cfbccd322635 SHA512 dd57d40db15fd55bae06a0faffbea80a15558763caf1f6f1defdde69d3abda709bdf806a1d9703f5e5796743af0482643c577332f69892de858aa5802e26279e
-DIST Rivet-3.1.7.tar.gz 30411263 BLAKE2B 7275c0e83ec834d5d6c0fe04c3c026a0440f8cfc6769937dcd0d023580c63407526c413f3ec64461767ceb302e0a53e98225e109f613b791e9a7544fbd4fdb2b SHA512 c7190a6d611419ad47cb0985e343a942155eca779379b3e7ca37732f98a3beb5badcd45f9325b6c877832477824f88daa6ae4cde2effd27e7bcc09e544de4c41
diff --git a/sci-physics/rivet/files/rivet-3.1.5-doc.patch b/sci-physics/rivet/files/rivet-3.1.5-doc.patch
deleted file mode 100644
index ae01b1812..000000000
--- a/sci-physics/rivet/files/rivet-3.1.5-doc.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- 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:: \
- $(abs_srcdir)/coverage/mk-coverage-htmls || true
-
diff --git a/sci-physics/rivet/files/rivet-3.1.5-test.patch b/sci-physics/rivet/files/rivet-3.1.5-test.patch
deleted file mode 100644
index 915473eb1..000000000
--- a/sci-physics/rivet/files/rivet-3.1.5-test.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/test/Makefile.am
-+++ b/test/Makefile.am
-@@ -26,7 +26,7 @@
- LIBLOCATION=$(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
deleted file mode 100644
index 68fd4436c..000000000
--- a/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-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
deleted file mode 100644
index 7f9434874..000000000
--- a/sci-physics/rivet/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?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
deleted file mode 100644
index b5156ce06..000000000
--- a/sci-physics/rivet/rivet-3.1.5.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_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 "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-physics/rivet/rivet-3.1.6.ebuild b/sci-physics/rivet/rivet-3.1.6.ebuild
deleted file mode 100644
index bbdf10c78..000000000
--- a/sci-physics/rivet/rivet-3.1.6.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit python-single-r1 flag-o-matic autotools
-
-MY_PN="Rivet"
-MY_PF=${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 "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-physics/rivet/rivet-3.1.7.ebuild b/sci-physics/rivet/rivet-3.1.7.ebuild
deleted file mode 100644
index b0234d1e0..000000000
--- a/sci-physics/rivet/rivet-3.1.7.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit python-single-r1 flag-o-matic autotools optfeature
-
-MY_PN="Rivet"
-MY_PF=${MY_PN}-${PV}
-
-DESCRIPTION="Rivet toolkit (Robust Independent Validation of Experiment and Theory)"
-HOMEPAGE="
- https://rivet.hepforge.org/
- https://gitlab.com/hepcedar/rivet
-"
-SRC_URI="https://www.hepforge.org/archive/rivet/${MY_PF}.tar.gz"
-S=${WORKDIR}/${MY_PF}
-
-LICENSE="GPL-3+"
-SLOT="3"
-KEYWORDS="~amd64"
-IUSE="+hepmc3 hepmc2 +zlib"
-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
- zlib? ( sys-libs/zlib )
-
- ${PYTHON_DEPS}
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- virtual/fortran
- >=dev-python/cython-0.29.24
-"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-3.1.6-binreloc.patch
- "${FILESDIR}"/${P}-ldflags.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
- econf \
- $(use_with zlib zlib "${ESYSROOT}/usr") \
- $(usex hepmc2 "--with-hepmc=${ESYSROOT}/usr" "") \
- $(usex hepmc3 "--with-hepmc3=${ESYSROOT}/usr" "") \
- --with-yoda="${ESYSROOT}/usr" \
- --with-fastjet="${ESYSROOT}/usr"
-}
-
-src_install() {
- default
- python_optimize
- find "${ED}" -name '*.la' -delete || die
-}
-
-pkg_postinstall() {
- optfeature "plotting support" virtual/latex-base media-gfx/imagemagick app-text/ghostscript-gpl
-}
diff --git a/sci-physics/scikit-hep-testdata/Manifest b/sci-physics/scikit-hep-testdata/Manifest
new file mode 100644
index 000000000..1051bc85d
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/Manifest
@@ -0,0 +1 @@
+DIST scikit-hep-testdata-0.4.39.gh.tar.gz 340561478 BLAKE2B 9d0fc60c8bd9c11b5cd786389489b095a5498c7e08c744106d3bacd3f203f4b186f50a5e1ef6cbdcb23fc5d975807277cc25397ea8049e2acccbbc06c53f65d2 SHA512 fe31302178b8148b0486fe314a9d40c7a4318e53113878769484cc79dd55e5adb977357a175ffad887a205e1ea3e99a4f5be192581cca61554ba2187daad3bd2
diff --git a/sci-physics/scikit-hep-testdata/metadata.xml b/sci-physics/scikit-hep-testdata/metadata.xml
new file mode 100644
index 000000000..ea2e37599
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/metadata.xml
@@ -0,0 +1,19 @@
+<?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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ A common package to provide example files (e.g. ROOT) for testing and developing packages against. The sample of files is representative of typical files found "in the wild".
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">scikit-hep-testdata</remote-id>
+ <remote-id type="github">scikit-hep/scikit-hep-testdata</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
new file mode 100644
index 000000000..47d0f0bbd
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
@@ -0,0 +1,30 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A package to provide example files for testing and developing packages against."
+HOMEPAGE="https://github.com/scikit-hep/scikit-hep-testdata"
+# pypi does not include the data nor tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${P}"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+# otherwise we don't install the data
+export SKHEP_DATA=1
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/setuptools-scm[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/spheno/Manifest b/sci-physics/spheno/Manifest
index afe87bb28..5db72217b 100644
--- a/sci-physics/spheno/Manifest
+++ b/sci-physics/spheno/Manifest
@@ -1 +1,2 @@
-DIST ?f=SPheno-3.3.8.tar.gz 1415645 BLAKE2B 830cdbcd8f213f0de0cd0b72455d5919e390069f097bca5a0cabdbfb77ec21549c9455139ff960a0cdbd425368805c1f2d11384c240a8e82f66e33864f4fce7b SHA512 e6c923586eae198f62121e0410f9f1f87e7badfd58d90e3b5f600e8364ea054dfb8b58c1c39d74ec6067112fa6cad727797230bce6cfc6040e2bf4c6d01b0eae
+DIST spheno-3.3.8.tar.gz 1415645 BLAKE2B 830cdbcd8f213f0de0cd0b72455d5919e390069f097bca5a0cabdbfb77ec21549c9455139ff960a0cdbd425368805c1f2d11384c240a8e82f66e33864f4fce7b SHA512 e6c923586eae198f62121e0410f9f1f87e7badfd58d90e3b5f600e8364ea054dfb8b58c1c39d74ec6067112fa6cad727797230bce6cfc6040e2bf4c6d01b0eae
+DIST spheno-4.0.5.tar.gz 1587855 BLAKE2B d3cb92740be416934a928147d980e180be623dbbfeac7a1b0b16e7e4a36d2b3088e455b5348f6e65cfa2ac8d90286c0b65a81498527419ed4eaa42622651408b SHA512 387099c3d9c9c7baf4a5da6d46b819d53dc703f72cc3a73fac7c2e63b66623e328294ac131e128253002ab03a81e96c686702ac90a58479ae573f228d3a51379
diff --git a/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
new file mode 100644
index 000000000..1abf36367
--- /dev/null
+++ b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
@@ -0,0 +1,29 @@
+--- a/src/Makefile 2023-05-04 12:33:44.804394098 +0200
++++ b/src/Makefile 2023-05-04 12:34:37.023776033 +0200
+@@ -21,9 +21,9 @@
+ #
+
+ # Intels ifort, default in optimized mode
+-F90 = ifort
+-comp = -c -O -module ${Mdir} -I${InDir}
+-LFlagsB = -O
++F90 = ${F90}
++comp = -c -O -J${Mdir} -I${InDir} ${FFLAGS} ${FCFLAGS} ${CFLAGS}
++LFlagsB = -O ${LDFLAGS}
+
+ # Intels ifort, debug modus
+ ifeq (${F90},ifortg)
+@@ -81,11 +81,11 @@
+ #
+ .f90.a:
+ ${F90} ${comp} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .F90.a:
+ ${F90} ${comp} ${PreDef} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .f90.o:
+ ${F90} ${comp} $<
diff --git a/sci-physics/spheno/spheno-3.3.8.ebuild b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
index 9a740b89e..7ed53c4c7 100644
--- a/sci-physics/spheno/spheno-3.3.8.ebuild
+++ b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
@@ -3,14 +3,14 @@
EAPI=8
-inherit toolchain-funcs
+inherit fortran-2
MY_PN=SPheno
MY_P=${MY_PN}-${PV}
DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
HOMEPAGE="https://spheno.hepforge.org/"
-SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz"
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${MY_P}"
LICENSE="all-rights-reserved"
@@ -18,16 +18,11 @@ RESTRICT="bindist mirror"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
src_compile() {
# single thread force needed since fortan mods depend on each other
- export MAKEOPTS=-j1
- tc-export FC AR
- emake AR="${AR}" F90="${FC}"
+ emake -j1 F90="${FC}"
}
src_install() {
@@ -35,7 +30,8 @@ src_install() {
# convenience symlink since the package is lowercase but the default produced binary is uppercase
dosym ${MY_PN} /usr/bin/${PN}
dolib.a lib/lib${MY_PN}.a
- doheader include/*
+ mv include ${PN}
+ doheader -r ${PN}
dodoc doc/*
docinto examples
dodoc input/*
diff --git a/sci-physics/spheno/spheno-4.0.5.ebuild b/sci-physics/spheno/spheno-4.0.5.ebuild
new file mode 100644
index 000000000..7ed53c4c7
--- /dev/null
+++ b/sci-physics/spheno/spheno-4.0.5.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN=SPheno
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
+HOMEPAGE="https://spheno.hepforge.org/"
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+
+PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
+
+src_compile() {
+ # single thread force needed since fortan mods depend on each other
+ emake -j1 F90="${FC}"
+}
+
+src_install() {
+ dobin bin/${MY_PN}
+ # convenience symlink since the package is lowercase but the default produced binary is uppercase
+ dosym ${MY_PN} /usr/bin/${PN}
+ dolib.a lib/lib${MY_PN}.a
+ mv include ${PN}
+ doheader -r ${PN}
+ dodoc doc/*
+ docinto examples
+ dodoc input/*
+ docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-physics/tauola/tauola-1.1.8.ebuild b/sci-physics/tauola/tauola-1.1.8.ebuild
index 61ec51d9f..4d4742dd1 100644
--- a/sci-physics/tauola/tauola-1.1.8.ebuild
+++ b/sci-physics/tauola/tauola-1.1.8.ebuild
@@ -21,7 +21,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}
doc? (
- app-doc/doxygen[dot]
+ app-text/doxygen[dot]
app-text/ghostscript-gpl
app-text/texlive
)
diff --git a/sci-physics/uproot/Manifest b/sci-physics/uproot/Manifest
new file mode 100644
index 000000000..bb52077be
--- /dev/null
+++ b/sci-physics/uproot/Manifest
@@ -0,0 +1 @@
+DIST uproot-5.3.1.tar.gz 919910 BLAKE2B 6c138a56ecabb08905e1edde8c776c3dfae6cca3213bbc3546e7241979052178e1c9718c1fcf298573669bcc4c004806cd54ab16050405038f76f3ef356fb184 SHA512 2525f372caa3b25e3a11b170ce981ce253a7b9ca1fdb2c04b6bb1093b166d206a28e9bc22ffa19dead76870f521cee44a812cbf41a087b34fb9a3bc52c210733
diff --git a/sci-physics/uproot/metadata.xml b/sci-physics/uproot/metadata.xml
new file mode 100644
index 000000000..1b293facb
--- /dev/null
+++ b/sci-physics/uproot/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Uproot is a library for reading and writing ROOT files in pure Python and NumPy.
+
+ Unlike the standard C++ ROOT implementation, Uproot is only an I/O library, primarily intended to stream data into machine learning libraries in Python. Unlike PyROOT and root_numpy, Uproot does not depend on C++ ROOT. Instead, it uses Numpy to cast blocks of data from the ROOT file as Numpy arrays.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">uproot</remote-id>
+ <remote-id type="github">scikit-hep/uproot5</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/uproot/uproot-5.3.1.ebuild b/sci-physics/uproot/uproot-5.3.1.ebuild
new file mode 100644
index 000000000..cfc3880e9
--- /dev/null
+++ b/sci-physics/uproot/uproot-5.3.1.ebuild
@@ -0,0 +1,28 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="ROOT I/O in pure Python and Numpy."
+HOMEPAGE="https://github.com/scikit-hep/uproot"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/awkward-2.4.6[${PYTHON_USEDEP}]
+ >=dev-python/cramjam-2.5.0[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+# way too many missing packages, isal, deflate, xxhash, http servers etc
+# distutils_enable_tests pytest
diff --git a/sci-visualization/forge/forge-1.0.5.ebuild b/sci-visualization/forge/forge-1.0.5.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-1.0.5.ebuild
+++ b/sci-visualization/forge/forge-1.0.5.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sci-visualization/forge/forge-1.0.7.ebuild b/sci-visualization/forge/forge-1.0.7.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-1.0.7.ebuild
+++ b/sci-visualization/forge/forge-1.0.7.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sci-visualization/forge/forge-9999.ebuild b/sci-visualization/forge/forge-9999.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-9999.ebuild
+++ b/sci-visualization/forge/forge-9999.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sys-cluster/easybuild-easyblocks/Manifest b/sys-cluster/easybuild-easyblocks/Manifest
index 2a6fcf00a..955f41791 100644
--- a/sys-cluster/easybuild-easyblocks/Manifest
+++ b/sys-cluster/easybuild-easyblocks/Manifest
@@ -1 +1,2 @@
DIST easybuild-easyblocks-4.6.2.tar.gz 539757 BLAKE2B e33db4b390cdbe11237c5f5750426f15d264cf081e2846c7b9de9254f7a0fbdc1459795920fcc131ceb5681f0acc905a74f96cd841b73b523e030246b78393e8 SHA512 72cb4c057efdfeb4c45fbf1e036a6f231e7f01ad6e593d1c2352b27f002ed4f45cd625c4125b90b708b15f226fb9519a345217f7882c2155b399894986a4505c
+DIST easybuild-easyblocks-4.9.0.tar.gz 574066 BLAKE2B 404ea11287d03edf497c85e9d58eba05d3257aed609eb3f65e3d1543e08e0be27a64fd7459ba30578a3bd2be2051020f711f6598af082d2cdec3fad65116a0ed SHA512 c75695c66f4683128be268471e996abde83fc9cc5f937699b81da5ea94bf02df84bc6b0a88c657a904730afbc4048e3a44cfbc5288a546c1962a51960393d5c7
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild
index 8f194c8ed..6c5f7a6e6 100644
--- a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild
@@ -20,7 +20,7 @@ KEYWORDS="~amd64"
RDEPEND="
>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
src_prepare() {
# already there from easybuild_framework
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
new file mode 100644
index 000000000..d4cc85067
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
@@ -0,0 +1,36 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ # already there from easybuild_framework
+ rm easybuild/__init__.py || die
+ default
+}
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
new file mode 100644
index 000000000..b32a81c59
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
@@ -0,0 +1,37 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+ SUB_P=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ # already there from easybuild_framework
+ rm easybuild/__init__.py || die
+ default
+}
diff --git a/sys-cluster/easybuild-easyconfigs/Manifest b/sys-cluster/easybuild-easyconfigs/Manifest
index c9dfce712..b8328d6aa 100644
--- a/sys-cluster/easybuild-easyconfigs/Manifest
+++ b/sys-cluster/easybuild-easyconfigs/Manifest
@@ -1 +1,2 @@
DIST easybuild-easyconfigs-4.6.2.tar.gz 7991765 BLAKE2B 02e7b629858177db19b7a63fcacd4898805ccfabd7bac343e05015d545d057bb04416b0b89245d3e3c206bc0f129920dda7d7ae1e421e9f7ce690ee6d01acd90 SHA512 4632dc0714b3e070b58a8192cb8054f0e21357701f59df054593ea754f5598c8e6446acd77c0e41f2fb920d31297ea5a5164fd81b26b926835868f24623cdce8
+DIST easybuild-easyconfigs-4.9.0.tar.gz 9636057 BLAKE2B 5b7710c99eb0d728d4df6582db40b7dc72d86cfca32548c79344a2b918e53e56360c97225ab2cf577bf2ba170bf67de211758afb83e696ec157165316b01cf02 SHA512 a39dc1eddc569163b21abdca9633a4c35519f609a03012ef7ec3f58c40a58961450b626c3701c325a2e485e5a00d161d737239c19ea657546b52b2c16de307f5
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild
index 65ebf61c0..08434dc1c 100644
--- a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild
@@ -22,4 +22,4 @@ RDEPEND="
>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
>=sys-cluster/easybuild-easyblocks-${SUB_P}.${SUB_PP}[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
new file mode 100644
index 000000000..5d5750a61
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+ SUB_P=9999
+ SUB_PP=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+ >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
new file mode 100644
index 000000000..5d5750a61
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+ SUB_P=9999
+ SUB_PP=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+ >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-framework/Manifest b/sys-cluster/easybuild-framework/Manifest
index 633cd3bdc..6845b4e9c 100644
--- a/sys-cluster/easybuild-framework/Manifest
+++ b/sys-cluster/easybuild-framework/Manifest
@@ -1 +1,2 @@
DIST easybuild-framework-4.6.2.tar.gz 2019284 BLAKE2B a32ae1fc43d490b32fc6c44790493204de935d16257846ec46830fc4d18a7343b860317c0ba33a16d89f12f657c33f7bb7359a70bf26a17c4e0dd16b8c78e2cd SHA512 ac8a06301c6c95edded262cb55b02ea8ada9ea14dfb7b7354a3bb29fcd9ad9a8d0011edbf2175085b8cec721f08a2b5f5e74aaa191d381a787eb5438c6c7f8cc
+DIST easybuild-framework-4.9.0.tar.gz 2064113 BLAKE2B 637498e7d52f0e9a6e9bd25c843052d9fc3c730f93b40c37381263b8861b0dd1b8ebf1d13af514d841d43284eb81b7555fcdaacbc1ac2c1bd655748c01540677 SHA512 b7b52d8987f13d9f859df0874adb7b855f8b4961215d9e9cb4a63a15911affe1591d718076277419be0c31e76845cf5cbe4fe553676ac71b8ff33a82d3c17a0e
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild
index a7e11912c..0f7421835 100644
--- a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild
+++ b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild
@@ -26,7 +26,7 @@ dev-python/cryptography[${PYTHON_USEDEP}]
dev-python/rich[${PYTHON_USEDEP}]
dev-python/archspec[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-test.patch
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
new file mode 100644
index 000000000..c88f89f6f
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-python/flake8[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/autopep8[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/archspec[${PYTHON_USEDEP}]
+ dev-python/cryptography[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
new file mode 100644
index 000000000..c88f89f6f
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-python/flake8[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/autopep8[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/archspec[${PYTHON_USEDEP}]
+ dev-python/cryptography[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild/Manifest b/sys-cluster/easybuild/Manifest
index 6ae785a0e..b17222baf 100644
--- a/sys-cluster/easybuild/Manifest
+++ b/sys-cluster/easybuild/Manifest
@@ -1 +1,2 @@
DIST easybuild-4.6.2.tar.gz 10680 BLAKE2B ed9dcaf1e138dd0d56fbff51151b5e0a6c0842495a950fe6a37a16435ab679bd0f60d34a703f6791b1486001fa3508e23d8a82ae6cc39f90137f03b5a93f5a0e SHA512 34097122968d31cf7fa8503f1566ff43c4fd34849c02050eb2f7304028479afd224128a0b83c195150b9ff6680b903a6b20fee715c9511bde292e2c4ac88397b
+DIST easybuild-4.9.0.tar.gz 10622 BLAKE2B bf7c69db95d49e2d992541baa145346e173fc35eab6002afd59a62d7c2007fea41672d81a3f1cf0e170f630dcf4bbea957b254fbffd5237738180d2df0976964 SHA512 3a1a4433e58d90f90dd8ba2700f7dcc07a07333d7f103ea23f82145af76a41af436d9e606fbe95fc5cfcf4be07399a3b3d5cc10c57c0bd77ea8018ba4e852c8d
diff --git a/sys-cluster/easybuild/easybuild-4.6.2.ebuild b/sys-cluster/easybuild/easybuild-4.6.2.ebuild
index 7259225ef..fe08d45ad 100644
--- a/sys-cluster/easybuild/easybuild-4.6.2.ebuild
+++ b/sys-cluster/easybuild/easybuild-4.6.2.ebuild
@@ -22,7 +22,7 @@ RDEPEND="
~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
pkg_postinst() {
elog "Remember to set the module install path"
diff --git a/sys-cluster/easybuild/easybuild-4.9.0.ebuild b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
new file mode 100644
index 000000000..9a38672aa
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-libs/openssl
+ dev-tcltk/tclx
+ || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+ ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+pkg_postinst() {
+ elog "Remember to set the module install path"
+ elog "ml use \$installpath/modules/all"
+ elog "where --installpath is passed to eb"
+
+ optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-cluster/easybuild/easybuild-9999.ebuild b/sys-cluster/easybuild/easybuild-9999.ebuild
new file mode 100644
index 000000000..9a38672aa
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-libs/openssl
+ dev-tcltk/tclx
+ || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+ ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+pkg_postinst() {
+ elog "Remember to set the module install path"
+ elog "ml use \$installpath/modules/all"
+ elog "where --installpath is passed to eb"
+
+ optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-devel/DPC++/DPC++-2021.12.ebuild b/sys-devel/DPC++/DPC++-2021.12.ebuild
index 48e7b5d44..348b6f8d6 100644
--- a/sys-devel/DPC++/DPC++-2021.12.ebuild
+++ b/sys-devel/DPC++/DPC++-2021.12.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -62,7 +62,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )
diff --git a/sys-devel/DPC++/DPC++-2022.09.ebuild b/sys-devel/DPC++/DPC++-2022.09.ebuild
index 7532e3c1b..ee2077566 100644
--- a/sys-devel/DPC++/DPC++-2022.09.ebuild
+++ b/sys-devel/DPC++/DPC++-2022.09.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -62,7 +62,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )
diff --git a/sys-devel/DPC++/DPC++-2022.12.ebuild b/sys-devel/DPC++/DPC++-2022.12.ebuild
index 25ac88770..be9a59fec 100644
--- a/sys-devel/DPC++/DPC++-2022.12.ebuild
+++ b/sys-devel/DPC++/DPC++-2022.12.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -64,7 +64,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )