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-rw-r--r--app-office/visidata/Manifest5
-rw-r--r--app-office/visidata/visidata-2.11-r1.ebuild90
-rw-r--r--app-office/visidata/visidata-2.11.1.ebuild88
-rw-r--r--app-office/visidata/visidata-2.11_p20230217-r1.ebuild90
-rw-r--r--app-office/visidata/visidata-2.8.ebuild11
-rw-r--r--dev-java/jama/Manifest1
-rw-r--r--dev-java/jama/jama-1.0.3.ebuild32
-rw-r--r--dev-java/jama/metadata.xml11
-rw-r--r--dev-java/parsington/Manifest1
-rw-r--r--dev-java/parsington/metadata.xml14
-rw-r--r--dev-java/parsington/parsington-3.1.0.ebuild48
-rw-r--r--dev-java/parsington/parsington-9999.ebuild48
-rw-r--r--dev-java/scijava-common/Manifest1
-rw-r--r--dev-java/scijava-common/metadata.xml14
-rw-r--r--dev-java/scijava-common/scijava-common-2.94.2.ebuild68
-rw-r--r--dev-java/scijava-common/scijava-common-9999.ebuild68
-rw-r--r--dev-java/scijava-optional/Manifest1
-rw-r--r--dev-java/scijava-optional/metadata.xml11
-rw-r--r--dev-java/scijava-optional/scijava-optional-1.0.1.ebuild44
-rw-r--r--dev-java/scijava-optional/scijava-optional-9999.ebuild44
-rw-r--r--dev-java/scijava-table/Manifest1
-rw-r--r--dev-java/scijava-table/metadata.xml11
-rw-r--r--dev-java/scijava-table/scijava-table-1.0.2.ebuild54
-rw-r--r--dev-java/scijava-table/scijava-table-9999.ebuild54
-rw-r--r--dev-lang/conceptual/Manifest1
-rw-r--r--dev-lang/conceptual/conceptual-1.5.1b.ebuild43
-rw-r--r--dev-lang/conceptual/metadata.xml14
-rw-r--r--dev-lang/pgi/Manifest1
-rw-r--r--dev-lang/pgi/files/pgi-13.5-glibc.patch31
-rw-r--r--dev-lang/pgi/files/pgi-13.5-terminal.patch39
-rw-r--r--dev-lang/pgi/metadata.xml15
-rw-r--r--dev-lang/pgi/pgi-13.5.ebuild105
-rw-r--r--dev-libs/oneCCL/Manifest1
-rw-r--r--dev-libs/oneCCL/oneCCL-2021.10.ebuild62
-rw-r--r--dev-libs/oneDNN/Manifest1
-rw-r--r--dev-libs/oneDNN/oneDNN-3.2.1.ebuild60
-rw-r--r--dev-libs/tut/Manifest1
-rw-r--r--dev-libs/tut/metadata.xml11
-rw-r--r--dev-libs/tut/tut-0_p20200320.ebuild48
-rw-r--r--dev-python/Forthon/Forthon-0.8.49.ebuild23
-rw-r--r--dev-python/Forthon/Forthon-0.9.4.ebuild17
-rw-r--r--dev-python/Forthon/Manifest2
-rw-r--r--dev-python/Forthon/metadata.xml23
-rw-r--r--dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild4
-rw-r--r--dev-python/POT/Manifest1
-rw-r--r--dev-python/POT/POT-0.7.0.ebuild29
-rw-r--r--dev-python/POT/metadata.xml12
-rw-r--r--dev-python/PeakUtils/Manifest1
-rw-r--r--dev-python/PeakUtils/PeakUtils-1.3.3.ebuild28
-rw-r--r--dev-python/PeakUtils/metadata.xml19
-rw-r--r--dev-python/amply/Manifest1
-rw-r--r--dev-python/amply/amply-0.1.4.ebuild25
-rw-r--r--dev-python/amply/metadata.xml11
-rw-r--r--dev-python/annexremote/annexremote-1.5.0.ebuild18
-rw-r--r--dev-python/annexremote/annexremote-1.6.0.ebuild18
-rw-r--r--dev-python/anys/Manifest1
-rw-r--r--dev-python/anys/anys-0.2.0.ebuild28
-rw-r--r--dev-python/anys/anys-0.2.1.ebuild4
-rw-r--r--dev-python/archspec/archspec-0.1.4.ebuild3
-rw-r--r--dev-python/arrayfire-python/Manifest2
-rw-r--r--dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild35
-rw-r--r--dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild39
-rw-r--r--dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch20
-rw-r--r--dev-python/arrayfire-python/metadata.xml21
-rw-r--r--dev-python/asciitree/asciitree-0.3.3.ebuild4
-rw-r--r--dev-python/asdf/Manifest1
-rw-r--r--dev-python/asdf/asdf-2.14.3.ebuild2
-rw-r--r--dev-python/asdf/asdf-2.8.3.ebuild47
-rw-r--r--dev-python/astropy-healpix/astropy-healpix-0.7.ebuild4
-rw-r--r--dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild5
-rw-r--r--dev-python/astropy/Manifest1
-rw-r--r--dev-python/astropy/astropy-5.0.ebuild59
-rw-r--r--dev-python/av/av-8.0.3.ebuild6
-rw-r--r--dev-python/av/metadata.xml4
-rw-r--r--dev-python/bcbio-gff/Manifest1
-rw-r--r--dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild18
-rw-r--r--dev-python/bcbio-gff/metadata.xml12
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild4
-rw-r--r--dev-python/bz2file/Manifest1
-rw-r--r--dev-python/bz2file/bz2file-0.98.ebuild23
-rw-r--r--dev-python/bz2file/files/bz2file-0.98-always-threading.patch22
-rw-r--r--dev-python/bz2file/metadata.xml11
-rw-r--r--dev-python/ccdproc/ccdproc-2.3.0.ebuild4
-rw-r--r--dev-python/ccdproc/metadata.xml1
-rw-r--r--dev-python/colorcet/Manifest1
-rw-r--r--dev-python/colorcet/colorcet-2.0.6.ebuild31
-rw-r--r--dev-python/colorcet/colorcet-3.0.1.ebuild3
-rw-r--r--dev-python/colorlover/Manifest1
-rw-r--r--dev-python/colorlover/colorlover-0.3.0.ebuild18
-rw-r--r--dev-python/colorlover/metadata.xml12
-rw-r--r--dev-python/cymbal/cymbal-1.0.0.ebuild6
-rw-r--r--dev-python/dandi-schema/Manifest3
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.5.1.ebuild42
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.7.1.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.2.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.3.ebuild (renamed from dev-python/dandi-schema/dandi-schema-0.6.0.ebuild)2
-rw-r--r--dev-python/datrie/datrie-0.8.2-r1.ebuild2
-rw-r--r--dev-python/delegator/delegator-0.1.1.ebuild6
-rw-r--r--dev-python/delegator/metadata.xml2
-rw-r--r--dev-python/dijitso/Manifest1
-rw-r--r--dev-python/dijitso/dijitso-2017.1.0.ebuild26
-rw-r--r--dev-python/dijitso/metadata.xml17
-rw-r--r--dev-python/dnaio/Manifest4
-rw-r--r--dev-python/dnaio/dnaio-0.4.2.ebuild22
-rw-r--r--dev-python/dnaio/dnaio-0.4.3.ebuild22
-rw-r--r--dev-python/dnaio/dnaio-0.5.0.ebuild22
-rw-r--r--dev-python/dnaio/dnaio-0.5.1.ebuild22
-rw-r--r--dev-python/dpath/Manifest1
-rw-r--r--dev-python/dpath/dpath-2.1.6.ebuild18
-rw-r--r--dev-python/dpath/metadata.xml16
-rw-r--r--dev-python/dpctl/Manifest1
-rw-r--r--dev-python/dpctl/dpctl-0.14.5.ebuild69
-rw-r--r--dev-python/extension-helpers/Manifest1
-rw-r--r--dev-python/extension-helpers/extension-helpers-0.1.ebuild28
-rw-r--r--dev-python/ezdxf/ezdxf-0.16.5.ebuild7
-rw-r--r--dev-python/ffc/Manifest1
-rw-r--r--dev-python/ffc/ffc-2019.1.0.ebuild23
-rw-r--r--dev-python/ffc/metadata.xml19
-rw-r--r--dev-python/fiat/Manifest1
-rw-r--r--dev-python/fiat/fiat-2019.1.0.ebuild19
-rw-r--r--dev-python/fiat/metadata.xml22
-rw-r--r--dev-python/fscacher/Manifest4
-rw-r--r--dev-python/fscacher/fscacher-0.1.4.ebuild6
-rw-r--r--dev-python/fscacher/fscacher-0.2.0.ebuild6
-rw-r--r--dev-python/fslpy/fslpy-3.10.0.ebuild6
-rw-r--r--dev-python/geopandas/Manifest2
-rw-r--r--dev-python/geopandas/geopandas-0.13.2.ebuild (renamed from dev-python/geopandas/geopandas-0.12.2.ebuild)8
-rw-r--r--dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild4
-rw-r--r--dev-python/gmsh_interop/metadata.xml4
-rw-r--r--dev-python/grabbit/grabbit-0.2.6.ebuild4
-rw-r--r--dev-python/gwcs/Manifest1
-rw-r--r--dev-python/gwcs/gwcs-0.16.1.ebuild42
-rw-r--r--dev-python/hdbscan/Manifest1
-rw-r--r--dev-python/hdbscan/hdbscan-0.8.26.ebuild33
-rw-r--r--dev-python/hdbscan/hdbscan-0.8.29.ebuild3
-rw-r--r--dev-python/heudiconv/Manifest1
-rw-r--r--dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild12
-rw-r--r--dev-python/heudiconv/heudiconv-0.13.0.ebuild42
-rw-r--r--dev-python/holoviews/Manifest1
-rw-r--r--dev-python/holoviews/holoviews-1.14.2.ebuild31
-rw-r--r--dev-python/holoviews/holoviews-1.15.3.ebuild3
-rw-r--r--dev-python/imageutils/Manifest1
-rw-r--r--dev-python/imageutils/imageutils-0.3.8.ebuild16
-rw-r--r--dev-python/imageutils/metadata.xml16
-rw-r--r--dev-python/interleave/interleave-0.2.0.ebuild7
-rw-r--r--dev-python/json_tricks/Manifest1
-rw-r--r--dev-python/json_tricks/json_tricks-3.15.5.ebuild21
-rw-r--r--dev-python/json_tricks/metadata.xml26
-rw-r--r--dev-python/jupyterlab_launcher/Manifest1
-rw-r--r--dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild26
-rw-r--r--dev-python/jupyterlab_launcher/metadata.xml8
-rw-r--r--dev-python/lazy_ops/lazy_ops-0.2.0.ebuild2
-rw-r--r--dev-python/llvmlite/Manifest1
-rw-r--r--dev-python/llvmlite/llvmlite-0.40.1.ebuild63
-rw-r--r--dev-python/logzero/logzero-1.7.0.ebuild4
-rw-r--r--dev-python/looseversion/Manifest2
-rw-r--r--dev-python/looseversion/looseversion-1.0.2.ebuild26
-rw-r--r--dev-python/looseversion/looseversion-1.0.3.ebuild26
-rw-r--r--dev-python/looseversion/metadata.xml25
-rw-r--r--dev-python/matrix2latex/Manifest1
-rw-r--r--dev-python/matrix2latex/matrix2latex-1.10.ebuild28
-rw-r--r--dev-python/neo/neo-0.11.0.ebuild5
-rw-r--r--dev-python/neo/neo-0.11.1.ebuild6
-rw-r--r--dev-python/num2words/num2words-0.5.10.ebuild4
-rw-r--r--dev-python/numba/Manifest2
-rw-r--r--dev-python/numba/numba-0.57.1.ebuild (renamed from dev-python/numba/numba-0.56.3.ebuild)12
-rw-r--r--dev-python/numcodecs/Manifest4
-rw-r--r--dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch11
-rw-r--r--dev-python/numcodecs/numcodecs-0.10.0.ebuild35
-rw-r--r--dev-python/numcodecs/numcodecs-0.11.0.ebuild49
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.0.ebuild35
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.1.ebuild35
-rw-r--r--dev-python/numpy/numpy-1.23.5.ebuild11
-rw-r--r--dev-python/nwbinspector/Manifest1
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.14.ebuild39
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.19.ebuild2
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild2
-rw-r--r--dev-python/palettable/Manifest1
-rw-r--r--dev-python/palettable/palettable-3.3.0.ebuild34
-rw-r--r--dev-python/palettable/palettable-9999.ebuild34
-rw-r--r--dev-python/panel/Manifest2
-rw-r--r--dev-python/panel/panel-0.11.0.ebuild61
-rw-r--r--dev-python/panel/panel-0.14.1.ebuild55
-rw-r--r--dev-python/panel/panel-0.14.2.ebuild5
-rw-r--r--dev-python/persim/Manifest3
-rw-r--r--dev-python/persim/persim-0.1.3.ebuild37
-rw-r--r--dev-python/persim/persim-0.2.0.ebuild44
-rw-r--r--dev-python/persim/persim-0.3.0.ebuild47
-rw-r--r--dev-python/plac/Manifest1
-rw-r--r--dev-python/plac/metadata.xml (renamed from dev-python/dnaio/metadata.xml)10
-rw-r--r--dev-python/plac/plac-1.3.5.ebuild18
-rw-r--r--dev-python/probeinterface/Manifest1
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.11.ebuild35
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.14.ebuild4
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.16.ebuild4
-rw-r--r--dev-python/pybind11-stubgen/Manifest2
-rw-r--r--dev-python/pybind11-stubgen/metadata.xml4
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild6
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild24
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild24
-rw-r--r--dev-python/pyct/pyct-0.4.8.ebuild5
-rw-r--r--dev-python/pynndescent/metadata.xml4
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.6.ebuild3
-rw-r--r--dev-python/pynrrd/Manifest1
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.2.ebuild5
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.3.ebuild5
-rw-r--r--dev-python/pynrrd/pynrrd-1.0.0.ebuild30
-rw-r--r--dev-python/pynwb/Manifest2
-rw-r--r--dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch54
-rw-r--r--dev-python/pynwb/pynwb-2.1.0-r2.ebuild43
-rw-r--r--dev-python/pynwb/pynwb-2.2.0-r1.ebuild3
-rw-r--r--dev-python/pynwb/pynwb-2.3.1-r1.ebuild1
-rw-r--r--dev-python/pynwb/pynwb-2.3.2.ebuild (renamed from dev-python/pynwb/pynwb-2.3.1.ebuild)6
-rw-r--r--dev-python/pytest-doctestplus/Manifest1
-rw-r--r--dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild24
-rw-r--r--dev-python/python-igraph/Manifest2
-rw-r--r--dev-python/python-igraph/python-igraph-0.10.4.ebuild5
-rw-r--r--dev-python/python-vxi11/Manifest1
-rw-r--r--dev-python/python-vxi11/metadata.xml20
-rw-r--r--dev-python/python-vxi11/python-vxi11-0.9.ebuild21
-rw-r--r--dev-python/python-vxi11/python-vxi11-9999.ebuild21
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild4
-rw-r--r--dev-python/pyvista/pyvista-0.33.2.ebuild4
-rw-r--r--dev-python/pyviz_comms/Manifest1
-rw-r--r--dev-python/pyviz_comms/metadata.xml2
-rw-r--r--dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild22
-rw-r--r--dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild4
-rw-r--r--dev-python/reproject/metadata.xml3
-rw-r--r--dev-python/reproject/reproject-0.8.ebuild4
-rw-r--r--dev-python/repsep_utils/Manifest2
-rw-r--r--dev-python/repsep_utils/repsep_utils-0.3.1.ebuild22
-rw-r--r--dev-python/repsep_utils/repsep_utils-0.3.ebuild22
-rw-r--r--dev-python/schema/schema-0.7.4.ebuild6
-rw-r--r--dev-python/scooby/scooby-0.5.7.ebuild6
-rw-r--r--dev-python/snakemake/Manifest2
-rw-r--r--dev-python/snakemake/metadata.xml5
-rw-r--r--dev-python/snakemake/snakemake-7.32.3.ebuild (renamed from dev-python/snakemake/snakemake-7.24.2.ebuild)1
-rw-r--r--dev-python/sphinx-argparse/Manifest1
-rw-r--r--dev-python/sphinx-argparse/metadata.xml11
-rw-r--r--dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild26
-rw-r--r--dev-python/sphinx-astropy/Manifest1
-rw-r--r--dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild31
-rw-r--r--dev-python/spikeinterface/spikeinterface-0.96.1.ebuild2
-rw-r--r--dev-python/spikeinterface/spikeinterface-0.97.0.ebuild2
-rw-r--r--dev-python/traits/Manifest1
-rw-r--r--dev-python/traits/metadata.xml1
-rw-r--r--dev-python/traits/traits-6.1.1.ebuild37
-rw-r--r--dev-python/traits/traits-6.3.2.ebuild3
-rw-r--r--dev-python/traits/traits-6.4.1.ebuild10
-rw-r--r--dev-python/tridesclous/tridesclous-1.6.4.ebuild5
-rw-r--r--dev-python/tridesclous/tridesclous-1.6.6.ebuild2
-rw-r--r--dev-python/ufl/Manifest1
-rw-r--r--dev-python/ufl/metadata.xml19
-rw-r--r--dev-python/ufl/ufl-2019.1.0.ebuild29
-rw-r--r--dev-python/umap-learn/metadata.xml3
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.2.ebuild5
-rw-r--r--dev-python/unyt/Manifest3
-rw-r--r--dev-python/unyt/metadata.xml12
-rw-r--r--dev-python/unyt/unyt-2.7.2.ebuild32
-rw-r--r--dev-python/unyt/unyt-2.8.0.ebuild32
-rw-r--r--dev-python/visvis/Manifest1
-rw-r--r--dev-python/visvis/visvis-1.13.0.ebuild25
-rw-r--r--dev-python/wraps/Manifest1
-rw-r--r--dev-python/wraps/metadata.xml1
-rw-r--r--dev-python/wraps/wraps-0.1.0-r1.ebuild30
-rw-r--r--dev-python/wraps/wraps-0.2.0.ebuild4
-rw-r--r--dev-python/xgboost/metadata.xml3
-rw-r--r--dev-python/xgboost/xgboost-1.6.2.ebuild3
-rw-r--r--dev-python/xopen/Manifest4
-rw-r--r--dev-python/xopen/metadata.xml16
-rw-r--r--dev-python/xopen/xopen-0.9.0.ebuild21
-rw-r--r--dev-python/xopen/xopen-1.0.0.ebuild21
-rw-r--r--dev-python/xopen/xopen-1.0.1.ebuild21
-rw-r--r--dev-python/xopen/xopen-1.1.0.ebuild21
-rw-r--r--dev-python/yte/Manifest1
-rw-r--r--dev-python/yte/metadata.xml (renamed from dev-util/waf/metadata.xml)8
-rw-r--r--dev-python/yte/yte-1.5.1.ebuild24
-rw-r--r--dev-python/zarr/Manifest1
-rw-r--r--dev-python/zarr/zarr-2.11.1.ebuild61
-rw-r--r--dev-python/zarr/zarr-2.11.3.ebuild5
-rw-r--r--dev-python/zarr/zarr-2.12.0.ebuild5
-rw-r--r--dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild2
-rw-r--r--dev-util/waf/Manifest1
-rw-r--r--dev-util/waf/waf-2.0.21.ebuild65
-rw-r--r--dev-vcs/dandi-cli/Manifest6
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild79
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild79
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.51.0.ebuild)5
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.50.0.ebuild)15
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.49.0.ebuild)15
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch29
-rw-r--r--dev-vcs/datalad/Manifest1
-rw-r--r--dev-vcs/datalad/datalad-0.18.0.ebuild4
-rw-r--r--dev-vcs/datalad/datalad-0.18.1.ebuild4
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-rw-r--r--sci-libs/itk/files/itk-5.3.0-uint8.patch10
-rw-r--r--sci-libs/itk/itk-5.2.1-r2.ebuild2
-rw-r--r--sci-libs/itk/itk-5.3.0-r1.ebuild (renamed from sci-libs/itk/itk-5.3.0.ebuild)50
-rw-r--r--sci-libs/itk/metadata.xml1
-rw-r--r--sci-libs/labbookdb/labbookdb-0.1.ebuild4
-rw-r--r--sci-libs/nibabel/Manifest3
-rw-r--r--sci-libs/nibabel/nibabel-3.2.1.ebuild41
-rw-r--r--sci-libs/nibabel/nibabel-4.0.0.ebuild4
-rw-r--r--sci-libs/nibabel/nibabel-5.0.0.ebuild4
-rw-r--r--sci-libs/nipy/Manifest2
-rw-r--r--sci-libs/nipy/nipy-0.4.2.ebuild55
-rw-r--r--sci-libs/nipy/nipy-0.5.0-r1.ebuild49
-rw-r--r--sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild2
-rw-r--r--sci-libs/nipype/nipype-1.5.0.ebuild4
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r1.ebuild (renamed from sci-libs/nipype/nipype-1.8.4.ebuild)9
-rw-r--r--sci-libs/oneDAL/Manifest1
-rw-r--r--sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch162
-rw-r--r--sci-libs/oneDAL/oneDAL-2023.2.1.ebuild85
-rw-r--r--sci-libs/pybids/pybids-0.10.2.ebuild4
-rw-r--r--sci-libs/pybids/pybids-0.12.4.ebuild4
-rw-r--r--sci-libs/pybids/pybids-0.6.5.ebuild4
-rw-r--r--sci-libs/pydicom/Manifest3
-rw-r--r--sci-libs/pydicom/pydicom-1.1.0.ebuild27
-rw-r--r--sci-libs/pydicom/pydicom-2.2.2.ebuild15
-rw-r--r--sci-libs/pydicom/pydicom-2.3.1.ebuild (renamed from sci-libs/pydicom/pydicom-1.4.2.ebuild)16
-rw-r--r--sci-libs/scikits_video/Manifest1
-rw-r--r--sci-libs/scikits_video/metadata.xml19
-rw-r--r--sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild32
-rw-r--r--sci-libs/spams-python/Manifest1
-rw-r--r--sci-libs/spams-python/metadata.xml24
-rw-r--r--sci-libs/spams-python/spams-python-2.6.2.ebuild60
-rw-r--r--sci-libs/xblas/Manifest1
-rw-r--r--sci-libs/xblas/metadata.xml17
-rw-r--r--sci-libs/xblas/xblas-1.0.248-r1.ebuild110
-rw-r--r--sci-libs/xraylib/Manifest1
-rw-r--r--sci-libs/xraylib/metadata.xml42
-rw-r--r--sci-libs/xraylib/xraylib-4.0.0.ebuild96
-rw-r--r--sci-mathematics/frama-c/frama-c-22.0.ebuild2
-rw-r--r--sci-mathematics/gap/Manifest2
-rw-r--r--sci-mathematics/gap/files/gap-4.11.0-autoconf.patch86
-rw-r--r--sci-mathematics/gap/gap-4.11.0.ebuild140
-rw-r--r--sci-mathematics/gap/metadata.xml30
-rw-r--r--sci-mathematics/pulp/pulp-2.7.0.ebuild2
-rw-r--r--sci-mathematics/scilab-bin/Manifest1
-rw-r--r--sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild78
-rw-r--r--sci-misc/openfst/Manifest2
-rw-r--r--sci-misc/openfst/files/kaldi-openfst-1.4.1.patch269
-rw-r--r--sci-misc/openfst/files/kaldi.patch599
-rw-r--r--sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch83
-rw-r--r--sci-misc/openfst/metadata.xml4
-rw-r--r--sci-misc/openfst/openfst-1.8.2.ebuild (renamed from sci-misc/openfst/openfst-1.8.1.ebuild)4
-rw-r--r--sci-misc/pqdump/Manifest119
-rw-r--r--sci-misc/pqdump/pqdump-0.1.0.ebuild146
-rw-r--r--sci-physics/feynarts/feynarts-3.11.ebuild4
-rw-r--r--sci-physics/formcalc/formcalc-9.10-r1.ebuild4
-rw-r--r--sci-physics/formcalc/formcalc-9.9-r1.ebuild4
-rw-r--r--sci-physics/hepunits/Manifest1
-rw-r--r--sci-physics/hepunits/hepunits-2.3.2.ebuild23
-rw-r--r--sci-physics/hepunits/hepunits-9999.ebuild23
-rw-r--r--sci-physics/hepunits/metadata.xml19
-rw-r--r--sci-physics/particle/Manifest1
-rw-r--r--sci-physics/particle/metadata.xml19
-rw-r--r--sci-physics/particle/particle-0.23.0.ebuild42
-rw-r--r--sci-physics/particle/particle-9999.ebuild42
-rw-r--r--sci-physics/rivet/Manifest1
-rw-r--r--sci-physics/rivet/rivet-3.1.7.ebuild78
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild4
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild5
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild5
-rw-r--r--sys-cluster/easybuild/easybuild-4.6.2.ebuild3
-rw-r--r--sys-cluster/modules/modules-4.6.0.ebuild78
-rw-r--r--sys-devel/DPC++/DPC++-2022.12.ebuild1
-rw-r--r--sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch12
-rw-r--r--sys-devel/oneDPL/Manifest1
-rw-r--r--sys-devel/oneDPL/oneDPL-2022.2.0.ebuild66
-rw-r--r--x11-misc/xdg-java/Manifest1
-rw-r--r--x11-misc/xdg-java/metadata.xml14
-rw-r--r--x11-misc/xdg-java/xdg-java-0.1.1.ebuild45
-rw-r--r--x11-misc/xdg-java/xdg-java-9999.ebuild45
660 files changed, 3984 insertions, 16853 deletions
diff --git a/app-office/visidata/Manifest b/app-office/visidata/Manifest
index 125ed2aa0..841bc773a 100644
--- a/app-office/visidata/Manifest
+++ b/app-office/visidata/Manifest
@@ -1 +1,4 @@
-DIST visidata-2.8.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3
+DIST visidata-2.11.1.gh.tar.gz 1928973 BLAKE2B bb9c40121175db262d4e0256b4e5b71313228590b9517e42589158d1a6279add0c1eacf1fe0ae5d38bd013b53c3ccad92ba0c4e39d40e27605c1502c84c40a5d SHA512 01905795ae6216e3cf662b43732394c68b43ffc8a4dc40da8552ebefaba4535fa3937aec1825cb108267dd83ab1b6a1072d1e698d416eae883dba915ca40b332
+DIST visidata-2.11.gh.tar.gz 1927455 BLAKE2B 95f868028fabb488f550b2ba15b60104a2d54dff972946ac38996d2906464e306e396adbf8dee32107aaf19a48d0e5d087aeeec82909e1d09b1d84b1e61138b7 SHA512 01512d47da329ba95aa7ceb5678a652fba5e06f6ff7ef0216b6271bf5b63a10712d425a2a1668ef6399b74f9fa9cb8d2d0f7bfa9316488ef5d64285ddcdde31a
+DIST visidata-2.11_p20230217.gh.tar.gz 2062327 BLAKE2B c7cd07ac816a31c2294d431c6426fc44f8a2cf015e7994d8b918c9e60cce2e7700ac77919c5a9e5c3ad5ccf41cb5b04e34fc84016a0c6faa8bd4e8e470275d0a SHA512 eaf2060c6fe6d1fed713cb0318d12233f279151a1a97b11ae3a7ccf07a065d716cf81872b76aa71a15dda3bfd85c09e7e03f9be2fae857f8edbded86e06b597f
+DIST visidata-2.8.gh.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3
diff --git a/app-office/visidata/visidata-2.11-r1.ebuild b/app-office/visidata/visidata-2.11-r1.ebuild
new file mode 100644
index 000000000..208587336
--- /dev/null
+++ b/app-office/visidata/visidata-2.11-r1.ebuild
@@ -0,0 +1,90 @@
+# 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 optfeature
+
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="http://visidata.org"
+SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests fail on recent Python:
+# https://github.com/saulpw/visidata/issues/1905
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/odfpy[${PYTHON_USEDEP}]
+ dev-python/openpyxl[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-vcs/git
+ $(python_gen_impl_dep sqlite)
+ )
+"
+
+#distutils_enable_sphinx docs \
+# dev-python/recommonmark \
+# dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ rm tests/load-http.vd || die "Could not remove network-dependent test."
+ rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+ rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+ rm tests/describe-error.vd || die "Could not remove network-dependent test"
+ rm tests/describe.vd || die "Could not remove network-dependent test"
+ rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+ distutils-r1_python_prepare_all
+}
+
+python_test() {
+ git init || die "Git init failed."
+ git add tests/golden/ || die "Git add failed."
+ # this test script eventually calls pytest under the hood
+ dev/test.sh || die "Tests failed."
+ rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+ optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+ optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+ optfeature "integration with png" dev-python/pypng
+ optfeature "integration with http" dev-python/requests
+ optfeature "integration with postgres" dev-python/psycopg-binary
+ optfeature "integration with xlsx" dev-python/openpyxl
+ optfeature "integration with xls" dev-python/xlrd
+ optfeature "integration with hdf5" dev-python/h5py
+ optfeature "integration with ttf/otf" dev-python/fonttools
+ optfeature "integration with xml/htm/html" dev-python/lxml
+ optfeature "integration with dta (Stata)" dev-python/pandas
+ optfeature "integration with shapefiles" sci-libs/pyshp
+ optfeature "integration with namestand" dev-python/graphviz
+ optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+ optfeature "integration with vobject" dev-python/vobject
+ optfeature "integration with tabulate" dev-python/tabulate
+ optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+ # optfeature "pdf tables" tabula # no package presently
+ #optfeature "integration with mbtiles" mapbox-vector-tile
+ #optfeature "integration with xpt (SAS)" xport
+ #optfeature "integration with sas7bdat (SAS)" sas7bdat
+ #optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.11.1.ebuild b/app-office/visidata/visidata-2.11.1.ebuild
new file mode 100644
index 000000000..3a5c510b4
--- /dev/null
+++ b/app-office/visidata/visidata-2.11.1.ebuild
@@ -0,0 +1,88 @@
+# 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_11 )
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="https://www.visidata.org/"
+SRC_URI="https://github.com/saulpw/visidata/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/odfpy[${PYTHON_USEDEP}]
+ dev-python/openpyxl[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-vcs/git
+ $(python_gen_impl_dep sqlite)
+ )
+"
+
+#distutils_enable_sphinx docs \
+# dev-python/recommonmark \
+# dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ rm tests/load-http.vd || die "Could not remove network-dependent test."
+ rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+ rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+ rm tests/describe-error.vd || die "Could not remove network-dependent test"
+ rm tests/describe.vd || die "Could not remove network-dependent test"
+ rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+ distutils-r1_python_prepare_all
+}
+
+python_test() {
+ git init || die "Git init failed."
+ git add tests/golden/ || die "Git add failed."
+ # this test script eventually calls pytest under the hood
+ dev/test.sh || die "Tests failed."
+ rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+ optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+ optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+ optfeature "integration with png" dev-python/pypng
+ optfeature "integration with http" dev-python/requests
+ optfeature "integration with postgres" dev-python/psycopg-binary
+ optfeature "integration with xlsx" dev-python/openpyxl
+ optfeature "integration with xls" dev-python/xlrd
+ optfeature "integration with hdf5" dev-python/h5py
+ optfeature "integration with ttf/otf" dev-python/fonttools
+ optfeature "integration with xml/htm/html" dev-python/lxml
+ optfeature "integration with dta (Stata)" dev-python/pandas
+ optfeature "integration with shapefiles" sci-libs/pyshp
+ optfeature "integration with namestand" dev-python/graphviz
+ optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+ optfeature "integration with vobject" dev-python/vobject
+ optfeature "integration with tabulate" dev-python/tabulate
+ optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+ # optfeature "pdf tables" tabula # no package presently
+ #optfeature "integration with mbtiles" mapbox-vector-tile
+ #optfeature "integration with xpt (SAS)" xport
+ #optfeature "integration with sas7bdat (SAS)" sas7bdat
+ #optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.11_p20230217-r1.ebuild b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild
new file mode 100644
index 000000000..5edfdcb23
--- /dev/null
+++ b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild
@@ -0,0 +1,90 @@
+# 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_{11..11} )
+
+inherit distutils-r1 optfeature
+
+MY_HASH="5ff7883563eeac32fe192c5b2d4290a4e1e91cc2"
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="http://visidata.org"
+SRC_URI="https://github.com/saulpw/visidata/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/odfpy[${PYTHON_USEDEP}]
+ dev-python/openpyxl[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-vcs/git
+ $(python_gen_impl_dep sqlite)
+ )
+"
+
+S="${WORKDIR}/${PN}-${MY_HASH}"
+
+#distutils_enable_sphinx docs \
+# dev-python/recommonmark \
+# dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ rm tests/load-http.vd || die "Could not remove network-dependent test."
+ rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+ rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+ rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+ rm tests/describe-error.vd || die "Could not remove network-dependent test"
+ rm tests/describe.vd || die "Could not remove network-dependent test"
+ rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+ distutils-r1_python_prepare_all
+}
+
+python_test() {
+ git init || die "Git init failed."
+ git add tests/golden/ || die "Git add failed."
+ # this test script eventually calls pytest under the hood
+ dev/test.sh || die "Tests failed."
+ rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+ optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+ optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+ optfeature "integration with png" dev-python/pypng
+ optfeature "integration with http" dev-python/requests
+ optfeature "integration with postgres" dev-python/psycopg-binary
+ optfeature "integration with xlsx" dev-python/openpyxl
+ optfeature "integration with xls" dev-python/xlrd
+ optfeature "integration with hdf5" dev-python/h5py
+ optfeature "integration with ttf/otf" dev-python/fonttools
+ optfeature "integration with xml/htm/html" dev-python/lxml
+ optfeature "integration with dta (Stata)" dev-python/pandas
+ optfeature "integration with shapefiles" sci-libs/pyshp
+ optfeature "integration with namestand" dev-python/graphviz
+ optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+ optfeature "integration with vobject" dev-python/vobject
+ optfeature "integration with tabulate" dev-python/tabulate
+ optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+ # optfeature "pdf tables" tabula # no package presently
+ #optfeature "integration with mbtiles" mapbox-vector-tile
+ #optfeature "integration with xpt (SAS)" xport
+ #optfeature "integration with sas7bdat (SAS)" sas7bdat
+ #optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild
index f3cf9e123..11c164d7e 100644
--- a/app-office/visidata/visidata-2.8.ebuild
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -1,20 +1,23 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1 optfeature
DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
HOMEPAGE="http://visidata.org"
-SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+# Tests fail on recent Python:
+# https://github.com/saulpw/visidata/issues/1905
+RESTRICT="test"
RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]"
BDEPEND="
diff --git a/dev-java/jama/Manifest b/dev-java/jama/Manifest
new file mode 100644
index 000000000..47e1c0f12
--- /dev/null
+++ b/dev-java/jama/Manifest
@@ -0,0 +1 @@
+DIST jama-1.0.3-sources.tar.gz 82188 BLAKE2B 35de815f770b192cd1b86a56ddf1919e12675d898ec4473489d3ce2c3899185f9d96eda39b6f7520fc67edfd17fe58b585f788f6a6967220150fc9a334b219ea SHA512 9bedf8f35ea1d400194b5a3b49914ebd04b5a31247959886f1967d062ceffae30993d34cd2f15d3942285a45c6930e2d4518f4ed0cc013ce853cc26aca021b0d
diff --git a/dev-java/jama/jama-1.0.3.ebuild b/dev-java/jama/jama-1.0.3.ebuild
new file mode 100644
index 000000000..9a88f35c4
--- /dev/null
+++ b/dev-java/jama/jama-1.0.3.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN="Jama"
+
+JAVA_PKG_IUSE="doc source test"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="JAMA is a basic linear algebra package for Java. "
+HOMEPAGE="https://math.nist.gov/javanumerics/jama/"
+
+SRC_URI="https://math.nist.gov/javanumerics/jama/${MY_PN}-${PV}.tar.gz -> ${P}-sources.tar.gz"
+S="${WORKDIR}/${MY_PN}"
+KEYWORDS="~amd64"
+
+LICENSE="public-domain"
+SLOT="0"
+
+BDEPEND=">=virtual/jdk-1.8:*"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR=(
+ "./"
+ "util"
+)
+JAVA_MAIN_CLASS="gov.math.nist.Main"
+
+JAVA_TEST_SRC_DIR="test"
diff --git a/dev-java/jama/metadata.xml b/dev-java/jama/metadata.xml
new file mode 100644
index 000000000..f3dd4314e
--- /dev/null
+++ b/dev-java/jama/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+ JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts.
+ </longdescription>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-java/parsington/Manifest b/dev-java/parsington/Manifest
new file mode 100644
index 000000000..970430d78
--- /dev/null
+++ b/dev-java/parsington/Manifest
@@ -0,0 +1 @@
+DIST parsington-3.1.0-sources.tar.gz 45883 BLAKE2B 39d37c772ba12f845fc6a53762e474f534dbb4920bc7178e885d560550a60c4e3949406d94a604b2b8740b9d337a504783111ccf28d480da10454db55abe853c SHA512 d1596e67b691148838116a02a88b2c520f0887952d254939cec0c77f225601be5f7d19f44c6b310126c7d210c726ec3399d77f8d91d590c377a2cd22814a68a7
diff --git a/dev-java/parsington/metadata.xml b/dev-java/parsington/metadata.xml
new file mode 100644
index 000000000..3c4854834
--- /dev/null
+++ b/dev-java/parsington/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+ Parsington is an infix-to-postfix and infix-to-syntax-tree expression parser for mathematical expressions written in Java. It is simple yet fancy, handling (customizable) operators, functions, variables and constants in a similar way to what the Java language itself supports.
+ </longdescription>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">scijava/parsington</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-java/parsington/parsington-3.1.0.ebuild b/dev-java/parsington/parsington-3.1.0.ebuild
new file mode 100644
index 000000000..c583c89e9
--- /dev/null
+++ b/dev-java/parsington/parsington-3.1.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-jupiter"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A mathematical expression parser for infix expression strings"
+HOMEPAGE="https://github.com/scijava/parsington"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/parsington.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:parsington:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:parsington:3.1.0"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND=">=dev-java/junit-5.9.1:5"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ "${CDEPEND}"
+ )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS="org.scijava.parsington.Main"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-5"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/parsington/parsington-9999.ebuild b/dev-java/parsington/parsington-9999.ebuild
new file mode 100644
index 000000000..c583c89e9
--- /dev/null
+++ b/dev-java/parsington/parsington-9999.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-jupiter"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A mathematical expression parser for infix expression strings"
+HOMEPAGE="https://github.com/scijava/parsington"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/parsington.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:parsington:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:parsington:3.1.0"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND=">=dev-java/junit-5.9.1:5"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ "${CDEPEND}"
+ )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS="org.scijava.parsington.Main"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-5"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-common/Manifest b/dev-java/scijava-common/Manifest
new file mode 100644
index 000000000..093710215
--- /dev/null
+++ b/dev-java/scijava-common/Manifest
@@ -0,0 +1 @@
+DIST scijava-common-2.94.2-sources.tar.gz 558014 BLAKE2B eb045006f96ee9eddd6413049162c8f99d90cf8c44b0c2bce916423eba6234241b6e8324b8ffc4300e228eb7e337d9b89e8f570bc744078c8e7859c0965dd46a SHA512 a56c0d957307ecd610b3b72dd98481118ca7a380f44662a6d1bae93d5dcd5d1bb55a630d9724403e6d16430d84a7e5452962d9dca06ddd97c30a4414672b2a86
diff --git a/dev-java/scijava-common/metadata.xml b/dev-java/scijava-common/metadata.xml
new file mode 100644
index 000000000..374f9940a
--- /dev/null
+++ b/dev-java/scijava-common/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+ SciJava Common is a common library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ2 and SCIFIO.
+ </longdescription>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">scijava/scijava-common</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-common/scijava-common-2.94.2.ebuild b/dev-java/scijava-common/scijava-common-2.94.2.ebuild
new file mode 100644
index 000000000..f384bf8bd
--- /dev/null
+++ b/dev-java/scijava-common/scijava-common-2.94.2.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SciJava Common is a shared library for SciJava software."
+HOMEPAGE="
+ https://imagej.net/libs/scijava#scijava-common
+ https://github.com/scijava/scijava-common
+ "
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-common.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-common:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+ dev-java/parsington:0
+ dev-java/jaxws-api:0
+ dev-java/jaxb-api:2
+"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ ${CDEPEND}
+ test? (
+ >=dev-java/junit-4.13.2
+ >=dev-java/mockito-2.19.0:2
+ )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+ ${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+ "src/main/resources"
+)
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+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
new file mode 100644
index 000000000..f384bf8bd
--- /dev/null
+++ b/dev-java/scijava-common/scijava-common-9999.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SciJava Common is a shared library for SciJava software."
+HOMEPAGE="
+ https://imagej.net/libs/scijava#scijava-common
+ https://github.com/scijava/scijava-common
+ "
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-common.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-common:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+ dev-java/parsington:0
+ dev-java/jaxws-api:0
+ dev-java/jaxb-api:2
+"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ ${CDEPEND}
+ test? (
+ >=dev-java/junit-4.13.2
+ >=dev-java/mockito-2.19.0:2
+ )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+ ${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+ "src/main/resources"
+)
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+JAVA_TEST_SRC_DIR="src/test/java"
+JAVA_TEST_RESOURCE_DIRS=(
+ "src/test/resources"
+)
diff --git a/dev-java/scijava-optional/Manifest b/dev-java/scijava-optional/Manifest
new file mode 100644
index 000000000..eb3283b48
--- /dev/null
+++ b/dev-java/scijava-optional/Manifest
@@ -0,0 +1 @@
+DIST scijava-optional-1.0.1-sources.tar.gz 7659 BLAKE2B c5a99b5ffcd5c8a09cc40d360d31796002993352b581509bbb78d4464f0119313b743bdf94b22532bd5bcc3a8baf614273378031154588245805cc6bccf39de5 SHA512 e083586fb6015354bc7520bed04d4c7c745445e01ffb6ba86bb91505f65ba06dfb50cbcecf3971fcb9161c16a2e112af31e247edffae973bf310e13bded99e89
diff --git a/dev-java/scijava-optional/metadata.xml b/dev-java/scijava-optional/metadata.xml
new file mode 100644
index 000000000..e7e56ccca
--- /dev/null
+++ b/dev-java/scijava-optional/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">scijava/scijava-optional</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild
new file mode 100644
index 000000000..54010f802
--- /dev/null
+++ b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Helpers for emulating named and default arguments"
+HOMEPAGE="https://github.com/scijava/scijava-optional"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-optional:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-optional:1.0.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ >=dev-java/junit-4.13.2:4
+ )
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-optional/scijava-optional-9999.ebuild b/dev-java/scijava-optional/scijava-optional-9999.ebuild
new file mode 100644
index 000000000..54010f802
--- /dev/null
+++ b/dev-java/scijava-optional/scijava-optional-9999.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Helpers for emulating named and default arguments"
+HOMEPAGE="https://github.com/scijava/scijava-optional"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-optional:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-optional:1.0.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ >=dev-java/junit-4.13.2:4
+ )
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-table/Manifest b/dev-java/scijava-table/Manifest
new file mode 100644
index 000000000..ba3cb11b6
--- /dev/null
+++ b/dev-java/scijava-table/Manifest
@@ -0,0 +1 @@
+DIST scijava-table-1.0.2-sources.tar.gz 37037 BLAKE2B 61a6b2da5cb355e00feb49895ae1a9a978ba50ee75e60c4f74d1490d1c167ca3a19452621ba25afccc975f4fbf3636ae09c0d25019e04980c4247fc18d859951 SHA512 17bbb1f798f7ee718fd2fbd9f9c81419cb5054b40d82cac9fa3b9f882e9ba46b410979038d8031d6f6dea53902f0865e68d59e55e1b02ab717da40aed5726b70
diff --git a/dev-java/scijava-table/metadata.xml b/dev-java/scijava-table/metadata.xml
new file mode 100644
index 000000000..d86e34de2
--- /dev/null
+++ b/dev-java/scijava-table/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">scijava/scijava-table</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-table/scijava-table-1.0.2.ebuild b/dev-java/scijava-table/scijava-table-1.0.2.ebuild
new file mode 100644
index 000000000..c2e06ac37
--- /dev/null
+++ b/dev-java/scijava-table/scijava-table-1.0.2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Table structures for SciJava."
+HOMEPAGE="https://github.com/scijava/scijava-table"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-table.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-table:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-table:1.0.3"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+ >=dev-java/scijava-common-2.89.0:0
+ >=dev-java/scijava-optional-1.0.1:0
+"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ ${CDEPEND}
+ test? ( >=dev-java/junit-4.13.2:4 )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+ ${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-table/scijava-table-9999.ebuild b/dev-java/scijava-table/scijava-table-9999.ebuild
new file mode 100644
index 000000000..c2e06ac37
--- /dev/null
+++ b/dev-java/scijava-table/scijava-table-9999.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Table structures for SciJava."
+HOMEPAGE="https://github.com/scijava/scijava-table"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scijava/scijava-table.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="org.scijava:scijava-table:9999"
+else
+ SRC_URI="
+ https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="org.scijava:scijava-table:1.0.3"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+ >=dev-java/scijava-common-2.89.0:0
+ >=dev-java/scijava-optional-1.0.1:0
+"
+
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ ${CDEPEND}
+ test? ( >=dev-java/junit-4.13.2:4 )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+ ${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-lang/conceptual/Manifest b/dev-lang/conceptual/Manifest
deleted file mode 100644
index e981b3cd2..000000000
--- a/dev-lang/conceptual/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conceptual-1.5.1b.tar.gz 5416709 BLAKE2B 9ac64c9e509613b3dcafa80a05d295845644b58b09797a4c9ee046b26969b7222648c93d9950e906e586195f2b5eecc7392be7b69ffd3e28d624c79ca0f2099e SHA512 08aab08cbbc56be54ef0ffbaf6acbe5013c312e62451e97faf3278f1a63a015a9b5f20d21899c9d125522331731e60fb17208c446640cc5d2bae622ea714d82d
diff --git a/dev-lang/conceptual/conceptual-1.5.1b.ebuild b/dev-lang/conceptual/conceptual-1.5.1b.ebuild
deleted file mode 100644
index 53cfee813..000000000
--- a/dev-lang/conceptual/conceptual-1.5.1b.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-JAVA_PKG_OPT_USE="gui"
-
-inherit java-pkg-opt-2 python-single-r1
-
-DESCRIPTION="A Network Correctness and Performance Testing Language"
-HOMEPAGE="http://conceptual.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE="gui"
-KEYWORDS="~amd64"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- virtual/mpi
- ${PYTHON_DEPS}
- gui? (
- virtual/jdk:*
- dev-java/jython
- )"
-DEPEND="${RDEPEND}"
-
-src_compile() {
- default
- use gui && emake gui
-}
-
-src_install () {
- default
- if use gui; then
- java-pkg_newjar gui/ncptlGUI-1.5.1b.jar ${PN}.jar
- java-pkg_dolauncher
- fi
- python_optimize
-}
diff --git a/dev-lang/conceptual/metadata.xml b/dev-lang/conceptual/metadata.xml
deleted file mode 100644
index c73b3a9fa..000000000
--- a/dev-lang/conceptual/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>ottxor@gentoo.org</email>
- <name>Christoph Junghans</name>
- </maintainer>
- <use>
- <flag name="gui">Build the Java base graphical interface</flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">conceptual</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-lang/pgi/Manifest b/dev-lang/pgi/Manifest
deleted file mode 100644
index 27c00897e..000000000
--- a/dev-lang/pgi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pgilinux-2013-135.tar.gz 949594228 SHA256 94dc015b5758486905643a729f7ece5c68038667385cbd08406b8799fcf9a22c SHA512 1bbd26f14c6757677c30fc2f4598f2b26072d34f0fe90a8914b55b0e52472adc1d342398372581ee9eef43480b5207d7998322f9621d0993f0a82d9055b7a5c6 WHIRLPOOL ad299eb206748f921ab826093a2a728ea100b0b51f2eca30562a956ed5885791c1b6465d3877586e626bb3ba6d397e6cd0d13e8bc736f2ccbf64e2e5601e7d8f
diff --git a/dev-lang/pgi/files/pgi-13.5-glibc.patch b/dev-lang/pgi/files/pgi-13.5-glibc.patch
deleted file mode 100644
index 434f12cb5..000000000
--- a/dev-lang/pgi/files/pgi-13.5-glibc.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff -ru opt/pgi/linux86/13.5/include/bits/types.h opt/pgi-b/linux86/13.5/include/bits/types.h
---- opt/pgi/linux86/13.5/include/bits/types.h 2013-05-07 21:45:39.000000000 +0200
-+++ opt/pgi-b/linux86/13.5/include/bits/types.h 2013-06-02 01:24:19.000000000 +0200
-@@ -136,6 +136,7 @@
- #include <bits/typesizes.h> /* Defines __*_T_TYPE macros. */
-
-
-+__STD_TYPE __SQUAD_TYPE __syscall_slong_t;
- __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */
- __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */
- __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */
-diff -ru opt/pgi/linux86-64/13.5/include/bits/types.h opt/pgi-b/linux86-64/13.5/include/bits/types.h
---- opt/pgi/linux86-64/13.5/include/bits/types.h 2013-05-07 21:45:39.000000000 +0200
-+++ opt/pgi-b/linux86-64/13.5/include/bits/types.h 2013-06-02 01:23:51.000000000 +0200
-@@ -135,7 +135,7 @@
- #endif
- #include <bits/typesizes.h> /* Defines __*_T_TYPE macros. */
-
--
-+__STD_TYPE __SQUAD_TYPE __syscall_slong_t;
- __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */
- __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */
- __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */
-@@ -156,7 +156,6 @@
- __STD_TYPE __SUSECONDS_T_TYPE __suseconds_t; /* Signed count of microseconds. */
-
- __STD_TYPE __DADDR_T_TYPE __daddr_t; /* The type of a disk address. */
--__STD_TYPE __SWBLK_T_TYPE __swblk_t; /* Type of a swap block maybe? */
- __STD_TYPE __KEY_T_TYPE __key_t; /* Type of an IPC key. */
-
- /* Clock ID used in clock and timer functions. */
diff --git a/dev-lang/pgi/files/pgi-13.5-terminal.patch b/dev-lang/pgi/files/pgi-13.5-terminal.patch
deleted file mode 100644
index 9b5b67474..000000000
--- a/dev-lang/pgi/files/pgi-13.5-terminal.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-diff -ru pgi-a/install pgi/install
---- pgi-a/install 2013-06-01 01:24:11.522714654 +0200
-+++ pgi/install 2013-06-01 01:27:36.372713265 +0200
-@@ -83,7 +83,7 @@
- else
- licensefile=$SRC/common/BETA_LICENSE
- fi
--more $licensefile
-+#more $licensefile
- echo
- echo -n 'Do you accept these terms? (accept,decline) '
- read x
-@@ -296,7 +296,7 @@
- echo
- echo 'In order to install the ACML software, please read and accept the'
- echo 'following license.'
-- more $SRC/common/LICENSE_ACML.txt
-+ #more $SRC/common/LICENSE_ACML.txt
- echo
- echo -n 'Do you accept these terms? (accept,decline) '
- read x
-@@ -342,7 +342,7 @@
- echo
- echo 'In order to install the CUDA software, please read and accept the'
- echo 'following license.'
-- more $SRC/common/LICENSE_NVIDIA_CUDA.txt
-+ #more $SRC/common/LICENSE_NVIDIA_CUDA.txt
- echo
- echo -n 'Do you accept these terms? (accept,decline) '
- read x
-@@ -398,7 +398,7 @@
- echo
- echo 'In order to install the JAVA software, please read and accept the'
- echo 'following license.'
-- more $SRC/common/LICENSE_JRE_6U21.txt
-+ #more $SRC/common/LICENSE_JRE_6U21.txt
- echo
- echo -n 'Do you accept these terms? (accept,decline) '
- read x
diff --git a/dev-lang/pgi/metadata.xml b/dev-lang/pgi/metadata.xml
deleted file mode 100644
index b9e493f21..000000000
--- a/dev-lang/pgi/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>gentryx@gmx.de</email>
- </maintainer>
- <maintainer type="project">
- <email>cluster@gentoo.org</email>
- <name>Gentoo Cluster Project</name>
- </maintainer>
- <use>
- <flag name="java">Install a PGI-tuned JRE.</flag>
- <flag name="cuda">Install PGI's CUDA components (e.g. for OpenACC)</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-lang/pgi/pgi-13.5.ebuild b/dev-lang/pgi/pgi-13.5.ebuild
deleted file mode 100644
index 19ec7445b..000000000
--- a/dev-lang/pgi/pgi-13.5.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="PGI compiler suite"
-HOMEPAGE="https://www.pgroup.com"
-SRC_URI="pgilinux-2013-135.tar.gz"
-
-LICENSE="PGI"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda java"
-
-RDEPEND="net-misc/curl"
-
-RESTRICT="mirror strip fetch"
-
-QA_PREBUILT="
- opt/pgi/linux86/2013/cuda/4.2/lib/lib*.so.*
- opt/pgi/linux86-64/13.5/bin/*
- opt/pgi/linux86-64/13.5/lib/lib*
- opt/pgi/linux86-64/13.5/lib/*.o
- opt/pgi/linux86-64/13.5/libso/lib*
- opt/pgi/linux86-64/13.5/libso/*.o
- opt/pgi/linux86-64/13.5/cray/lib*
- opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl
- opt/pgi/linux86-64/13.5/REDIST/lib*.so
- opt/pgi/linux86-64/2013/cuda/5.0/nvvm/cicc
- opt/pgi/linux86-64/2013/cuda/4.2/nvvm/cicc
- opt/pgi/linux86-64/2013/acml/5.3.0/lib/lib*
- opt/pgi/linux86-64/2013/acml/5.3.0/libso/lib*.so
- opt/pgi/linux86/13.5/etc/pgi_license_tool/curl
- opt/pgi/linux86/13.5/bin/*
- opt/pgi/linux86/13.5/lib/lib*
- opt/pgi/linux86/13.5/lib/*.o
- opt/pgi/linux86/13.5/libso/lib*
- opt/pgi/linux86/13.5/cray/lib*
- opt/pgi/linux86/2013/cuda/5.0/nvvm/cicc
- opt/pgi/linux86/2013/cuda/4.2/nvvm/cicc
- opt/pgi/linux86/2013/acml/4.4.0/lib/lib*
- opt/pgi/linux86/2013/acml/4.4.0/libso/lib*.so
-"
-
-S="${WORKDIR}"
-
-PATCHES=( "${FILESDIR}"/${P}-terminal.patch )
-
-pkg_nofetch() {
- einfo "PGI doesn't provide direct download links. Please download"
- einfo "${ARCHIVE} from ${HOMEPAGE}"
-}
-
-src_install() {
- dodir /opt/pgi
-
- command="accept
-1
-${ED}/opt/pgi"
-
- command="${command}
-n"
-
- if use cuda; then
- command="${command}
-y
-accept"
- else
- command="${command}
-n"
- fi
-
- if use java; then
- command="${command}
-
-accept"
- else
- command="${command}
-no"
- fi
-
- command="${command}
-y
-n
-n
-y
-"
- ./install <<EOF
-${command}
-EOF
- # fix problems with PGI's C++ compiler and current glibc:
- cd "${ED}"
- epatch "${FILESDIR}/${P}-glibc.patch"
-
- # java symlink might be broken if useflag is disabled:
- if ! use java; then
- rm opt/pgi/linux86-64/13.5/jre || die
- fi
-
- # replace PGI's curl with the stock version:
- dodir /opt/pgi/linux86-64/13.5/etc/pgi_license_tool
- dosym ../../../../../../usr/bin/curl /opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl
- dodir /opt/pgi/linux86/13.5/etc/pgi_license_tool
- dosym ../../../../../../usr/bin/curl /opt/pgi/linux86/13.5/etc/pgi_license_tool/curl
-}
diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest
index 95c5b9e72..2eb21d0f6 100644
--- a/dev-libs/oneCCL/Manifest
+++ b/dev-libs/oneCCL/Manifest
@@ -1,2 +1,3 @@
+DIST oneCCL-2021.10.tar.gz 37777252 BLAKE2B fb8d4429cbd7366efdd6e392d8132631c4dbc770962781a49b5b2df6e0c0a9b9b6c97043997066879b22ea85bf76e507bdcc27a78e40beffa7520d2a420b35ef SHA512 3ff845bf28e18c195411f5ed4542f172648feeb385fc456b6222d527018f48625c9be7e96a0f9b973f8af7ad1cc122a83ac8e169eeb59d5a35ed901910fdbace
DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790
DIST oneCCL-2021.8.tar.gz 36868388 BLAKE2B b27f04efaddf2c31befd70388f0aa84b9cb5266b5d4e4a300064e0dc98e4d7eee3590288dc0b8cc1640fe0a9b928a0dfdf16a2ea45db9bd1517a8ca2dd00bdfe SHA512 879d1b73e594d5ff2c5a5aee08dfb4aded11c4974a9efcc199e7c2ee87b00c2441edb1dcb073bb4ed2587d752efcafe338072959b7b0f89fc1692dc377f748c2
diff --git a/dev-libs/oneCCL/oneCCL-2021.10.ebuild b/dev-libs/oneCCL/oneCCL-2021.10.ebuild
new file mode 100644
index 000000000..a67659f4a
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.10.ebuild
@@ -0,0 +1,62 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+ dev-libs/level-zero:=
+ sys-apps/hwloc:=
+ sys-block/libfabric:=
+ sys-devel/ittapi
+ sys-cluster/pmix
+ mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2021.8-use-system-libs.patch"
+)
+
+src_prepare() {
+ # No -Werror
+ find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+ # Use system libs instead
+ rm -r deps/* || die
+
+ # 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=(
+ -DBUILD_EXAMPLES=OFF
+ # BUILD_CONFIG causes sandbox violation
+ -DBUILD_CONFIG=OFF
+ -DCCL_ENABLE_ZE=ON
+ # TODO: Find out how to execute the tests
+ -DBUILD_FT=OFF
+ -DENABLE_MPI_TESTS=OFF
+ -DENABLE_MPI="$(usex mpi)"
+ # Use system fabric
+ -DLIBFABRIC_DIR="${ESYSROOT}/usr"
+ )
+ cmake_src_configure
+}
diff --git a/dev-libs/oneDNN/Manifest b/dev-libs/oneDNN/Manifest
index b66805cea..80f52571c 100644
--- a/dev-libs/oneDNN/Manifest
+++ b/dev-libs/oneDNN/Manifest
@@ -1,2 +1,3 @@
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/oneDNN-3.2.1.ebuild b/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
new file mode 100644
index 000000000..1c66ec72c
--- /dev/null
+++ b/dev-libs/oneDNN/oneDNN-3.2.1.ebuild
@@ -0,0 +1,60 @@
+# 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 "${ED}/usr/share/doc/dnnl" || die
+}
diff --git a/dev-libs/tut/Manifest b/dev-libs/tut/Manifest
deleted file mode 100644
index 30c2a9334..000000000
--- a/dev-libs/tut/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tut-0_p20200320.tar.gz 262793 BLAKE2B fb8d16a7ca099dda88d300fb2521affb59fc7c84d52ba3a278cbd573621f1b922a3330097bd756844841582d6d0b5d76d8c90529e6f18a3020cd4ae0655e4591 SHA512 54b34519c90d8ab5e8264572c43245122d8c0f9d41a8acf86ad29f2cd4f35bf481b00f3aaedd922febd79b6da148fd90bb9d1521a148e7a7d6d01204805df1fb
diff --git a/dev-libs/tut/metadata.xml b/dev-libs/tut/metadata.xml
deleted file mode 100644
index 7a070008d..000000000
--- a/dev-libs/tut/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">mrzechonek/tut-framework</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-libs/tut/tut-0_p20200320.ebuild b/dev-libs/tut/tut-0_p20200320.ebuild
deleted file mode 100644
index f4f13064e..000000000
--- a/dev-libs/tut/tut-0_p20200320.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="doc/webgen"
-DOCS_DEPEND="media-gfx/graphviz"
-
-inherit docs
-
-COMMIT="a8e49ef56dc8be5256b5305ec6702d50c5b36c09"
-
-DESCRIPTION="C++ Template Unit Test Framework"
-HOMEPAGE="https://mrzechonek.github.io/tut-framework/"
-SRC_URI="https://github.com/mrzechonek/tut-framework/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples"
-
-S="${WORKDIR}/${PN}-framework-${COMMIT}"
-
-BDEPEND="dev-util/waf"
-
-src_configure() {
- waf configure || die "waf configure failed"
-}
-
-src_compile() {
- waf build || die "waf compile failed"
- docs_compile
-}
-
-src_install() {
- default
- # install function does not work for some reason
- #waf install || die "waf install failed"
- cp -r build/* . || die
-
- doheader -r include/*
-
- if use examples ; then
- dodoc -r example
- fi
-}
diff --git a/dev-python/Forthon/Forthon-0.8.49.ebuild b/dev-python/Forthon/Forthon-0.8.49.ebuild
deleted file mode 100644
index f24277001..000000000
--- a/dev-python/Forthon/Forthon-0.8.49.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface generator for Fortran based codes"
-HOMEPAGE="https://github.com/dpgrote/Forthon"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# no tests in package
-
-python_install_all() {
- dodoc -r example simpleexample docs
-
- distutils-r1_python_install_all
-}
diff --git a/dev-python/Forthon/Forthon-0.9.4.ebuild b/dev-python/Forthon/Forthon-0.9.4.ebuild
deleted file mode 100644
index fa6e3fde3..000000000
--- a/dev-python/Forthon/Forthon-0.9.4.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface generator for Fortran based codes"
-HOMEPAGE="https://github.com/dpgrote/Forthon"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# no tests in package
diff --git a/dev-python/Forthon/Manifest b/dev-python/Forthon/Manifest
deleted file mode 100644
index fc38dbbbb..000000000
--- a/dev-python/Forthon/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Forthon-0.8.49.tar.gz 83622 BLAKE2B 0c9d6af9a68cb05bf75fc638f3bb080aab25a5f575d2fb92c97ff3d1ae7f6925680d15fad8ae8e67c23b12c2b230ddd5bf0ef8e5900f5f379e4a3b843a449888 SHA512 50b8f2af32af061e0349a97076c50c54b22581c2b2c857a5529eca7714f2ad22ace25d792072397ba64b267ec9a24b1a670f454667ee9e3aae97331311870035
-DIST Forthon-0.9.4.tar.gz 86694 BLAKE2B 962e732543a0d5197a26b0d2036952fc056f0d23f771fd286fae874b33386422d2bf15ba51b31d596348c2291ef6490830d80d709e0cbe420179603956ce6567 SHA512 1e48bcd5610e1431474d9f9721ea375650a36ddffb796fd3ff8b710c53fe6814d7ae6b12d054451ac2c44febff126500c1ea6e66acdeda65c3a1818295dbbf50
diff --git a/dev-python/Forthon/metadata.xml b/dev-python/Forthon/metadata.xml
deleted file mode 100644
index 8ddc1aa0d..000000000
--- a/dev-python/Forthon/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
- Forthon generates links between Fortran95 and Python. Python is a high
- level, object oriented, interactive and scripting language that allows
- a flexible and versatile interface to computational tools. The Forthon
- package generates the necessary wrapping code which allows access to
- the Fortran database and to the Fortran subroutines and
- functions. This provides a development package where the
- computationally intensive parts of a code can be written in efficient
- Fortran, and the high level controlling code can be written in the
- much more versatile Python language.
- </longdescription>
-</pkgmetadata>
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 6f675dc80..cb24f5d19 100644
--- a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
+++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
@@ -5,11 +5,11 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
DESCRIPTION="Create calibration matrix to correct for magneto-resistance in resistive sensors"
HOMEPAGE="https://gitlab.science.ru.nl/hfml/MRcalib"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
diff --git a/dev-python/POT/Manifest b/dev-python/POT/Manifest
deleted file mode 100644
index 9db8bb97b..000000000
--- a/dev-python/POT/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST POT-0.7.0.tar.gz 189869 BLAKE2B 40f651d70e3177cc1d778b635e8609057cebe1685c36ed65d1d5ec26ae3c5665fb872b7efcd98d90012ed3e2a0251ddd8fafcae551254ee68697788cfd9e984e SHA512 a52f748ebee128732cd17281aace1f95bf638cbc8e1610774aef947b27b5172bcbf434c9e6a36ef4d2920940331d6ced1ff5315ca1b7705fda14489c34e5b6ff
diff --git a/dev-python/POT/POT-0.7.0.ebuild b/dev-python/POT/POT-0.7.0.ebuild
deleted file mode 100644
index e25d01017..000000000
--- a/dev-python/POT/POT-0.7.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python Optimal Transport Library"
-HOMEPAGE="https://github.com/PythonOT/POT"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_test() {
- pytest -c /dev/null -vv || die "tests failed for ${EPYTHON}"
-}
diff --git a/dev-python/POT/metadata.xml b/dev-python/POT/metadata.xml
deleted file mode 100644
index 2f2c0b51c..000000000
--- a/dev-python/POT/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/PeakUtils/Manifest b/dev-python/PeakUtils/Manifest
deleted file mode 100644
index 8b9972e10..000000000
--- a/dev-python/PeakUtils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PeakUtils-1.3.3.tar.gz 118684 BLAKE2B 978128ca36150487b54d491845b2eb4d28718760a43e5e71eb8a11142dd6dca3ffbb60e7a9c2e604c4b9868180f5fbe1a13c89a8390ecac34dce50f5e1b83548 SHA512 c6bc49907221b11ca4af204f55b24e8ca2b8267e989d9971523d33077519027ffc140883c8dca5988f04a4adf2e02d5c15b595d5474b2be410cc8ca87840cf4a
diff --git a/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild b/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild
deleted file mode 100644
index 983d2c645..000000000
--- a/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Peak detection utilities for 1D data"
-HOMEPAGE="https://bitbucket.org/lucashnegri/peakutils"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- >=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-DEPEND="${RDEPEND}"
-BDEPEND="
- test? (
- dev-python/pandas
- )
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/PeakUtils/metadata.xml b/dev-python/PeakUtils/metadata.xml
deleted file mode 100644
index ba9535089..000000000
--- a/dev-python/PeakUtils/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
-As the name implies, this package provides utilities related to the
-detection of peaks on 1D data. Includes functions to perform
-baseline estimation, to find the indexes of the peaks in the data
-and performing Gaussian fitting or centroid computation to further
-increase the resolution of the peak detection.
-</longdescription>
- <upstream>
- <remote-id type="bitbucket">lucashnegri/peakutils</remote-id>
- <remote-id type="pypi">PeakUtils</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/amply/Manifest b/dev-python/amply/Manifest
deleted file mode 100644
index 09b9588e7..000000000
--- a/dev-python/amply/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST amply-0.1.4.tar.gz 28182 BLAKE2B 78ae51f18355968c7713351267fe8a60adc797c9e0e37092f538935026898b51413f346a0faecc748a290f3fd3e4c313cfab6d0ddacfe34f76ecdb4ecd562ffb SHA512 cb9140a157059edd69f634499946b1e006993037eed44c6eb844e211454d975455e00cc5da8771a09b4345d77c30515b7c106420b15dae8ca54ac599399fb3ed
diff --git a/dev-python/amply/amply-0.1.4.ebuild b/dev-python/amply/amply-0.1.4.ebuild
deleted file mode 100644
index ae3e3b63d..000000000
--- a/dev-python/amply/amply-0.1.4.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Allows you to load and manipulate AMPL/GLPK data as Python data structures"
-HOMEPAGE="https://github.com/willu47/amply/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="EPL-1.0"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]"
-
-RDEPEND="
- dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/amply/metadata.xml b/dev-python/amply/metadata.xml
deleted file mode 100644
index 3d5e87252..000000000
--- a/dev-python/amply/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="pypi">amply</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild
index 90511a157..a6dacd5c9 100644
--- a/dev-python/annexremote/annexremote-1.5.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.5.0.ebuild
@@ -3,31 +3,21 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-# Reported upstream:
+# Tests require nose, reported upstream:
# https://github.com/Lykos153/AnnexRemote/issues/61
RESTRICT="test"
-COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
-RDEPEND="
- ${COMMON_DEPEND}
-"
-DEPEND="
- ${COMMON_DEPEND}
-"
-
-distutils_enable_tests nose
-
python_install_all() {
distutils-r1_python_install_all
dodoc README.md
diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild
index 90511a157..a6dacd5c9 100644
--- a/dev-python/annexremote/annexremote-1.6.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.6.0.ebuild
@@ -3,31 +3,21 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-# Reported upstream:
+# Tests require nose, reported upstream:
# https://github.com/Lykos153/AnnexRemote/issues/61
RESTRICT="test"
-COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
-RDEPEND="
- ${COMMON_DEPEND}
-"
-DEPEND="
- ${COMMON_DEPEND}
-"
-
-distutils_enable_tests nose
-
python_install_all() {
distutils-r1_python_install_all
dodoc README.md
diff --git a/dev-python/anys/Manifest b/dev-python/anys/Manifest
index d5c7418ba..bb3dbee15 100644
--- a/dev-python/anys/Manifest
+++ b/dev-python/anys/Manifest
@@ -1,2 +1 @@
-DIST anys-0.2.0.tar.gz 17799 BLAKE2B d481c43df1a3161f75a32b6fc7a38d3e18dc996f05dd08abb3891ca9570a2a841b159547f1c6889b73d2476a141404baba4ad3e10c318bc2e230c9d136b02ff6 SHA512 72bdc9df4cd805604f5497418a90738fccbc0ffd2dddf81324fe50d0d8ab13e036ff829e284dea8473427af396f02ceb01a191ad7d6946427478a12c04ca2ffd
DIST anys-0.2.1.tar.gz 17850 BLAKE2B c7eda2e245108f9a0a0263af45589d7b0df78767517e9b56768626e43badc5100f01a844d17b10e34a19c0a0fbfa951ba97a374cb8951e7a5560e11867b12d78 SHA512 5a46d9e8aa97401f11dcc7a26a3d8dc759c59b5485222cb6ba1df3d4b2d8d67455102943f044850d289cd3e32bcaf6413ed4a4dfbee26c049a6ef32dfa5cd87e
diff --git a/dev-python/anys/anys-0.2.0.ebuild b/dev-python/anys/anys-0.2.0.ebuild
deleted file mode 100644
index 0f1bb884f..000000000
--- a/dev-python/anys/anys-0.2.0.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="Matchers for pytest"
-HOMEPAGE="https://github.com/jwodder/anys"
-SRC_URI="https://github.com/jwodder/anys/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-python/wheel[${PYTHON_USEDEP}]
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.2.0-coverage.patch"
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
index 659e797cf..88e61a12e 100644
--- a/dev-python/anys/anys-0.2.1.ebuild
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild
index 5e8eee157..f1b1cb0f1 100644
--- a/dev-python/archspec/archspec-0.1.4.ebuild
+++ b/dev-python/archspec/archspec-0.1.4.ebuild
@@ -2,11 +2,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=poetry
-inherit distutils-r1
+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"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/arrayfire-python/Manifest b/dev-python/arrayfire-python/Manifest
deleted file mode 100644
index 6d077c449..000000000
--- a/dev-python/arrayfire-python/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST arrayfire-python-3.6.20181017.tar.gz 115659 BLAKE2B a58f8a3e929b9b04a7ce4339624833a9bcf513c790e6bf66edabaaeb01b590d651d6a89584ccf04387e9844dc506b1d21ea3392a2b6361802404820c1ff9d91a SHA512 8ae9d0c3e4b27ff237c47a55358ab6421eef4a3d251583e8d64b48ff40a8b9e6773e6fc27473c228141a5c9be86ba096bacd8ee1716d2f82f5dd97440b87bec4
-DIST arrayfire-python-3.6.20181017_p1.tar.gz 126376 BLAKE2B 33699c33a12a9231baac11a462502dbda2eb0e743256b7d4bff0b9b0925652efa9504ed5dc123b86493b7751bed85cd4050807297da087fe765dbc44ba985520 SHA512 2977365f7817528cf0c73fe0c21704efba9c5b30b902a5b3449ed6b4487492ed1baa2a60c03b42087232d8a119f5a0b0af9aa16cf8d83a05092c0eb78fa8e147
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild
deleted file mode 100644
index 443642962..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/arrayfire/arrayfire-python"
-else
- SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- sci-libs/arrayfire
-"
-DEPEND="${RDEPEND}"
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-python_test() {
- ${EPYTHON} -m arrayfire.tests || \
- die "tests failed with ${EPYTHON}"
-}
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild
deleted file mode 100644
index 7907a4e33..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/arrayfire/arrayfire-python"
-else
- COMMIT=534b8c2ab4db5b08347f4d3d2f86a58ba8fcfdb6
- SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- sci-libs/arrayfire
-"
-DEPEND="${RDEPEND}"
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-PATCHES=( "${FILESDIR}"/${P}-skip_tests.patch )
-
-python_test() {
- ${EPYTHON} -m tests || \
- die "tests failed with ${EPYTHON}"
-}
diff --git a/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch b/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch
deleted file mode 100644
index eb4eb54cf..000000000
--- a/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff --git a/tests/simple/__init__.py b/tests/simple/__init__.py
-index 4950136..41c9cf2 100644
---- a/tests/simple/__init__.py
-+++ b/tests/simple/__init__.py
-@@ -11,7 +11,6 @@
-
- from ._util import tests
- from .algorithm import simple_algorithm
--from .arith import simple_arith
- from .array_test import simple_array
- from .blas import simple_blas
- from .data import simple_data
-@@ -28,7 +27,6 @@ from .statistics import simple_statistics
- __all__ = [
- "tests",
- "simple_algorithm",
-- "simple_arith",
- "simple_array",
- "simple_blas",
- "simple_data",
diff --git a/dev-python/arrayfire-python/metadata.xml b/dev-python/arrayfire-python/metadata.xml
deleted file mode 100644
index 8cbbb986a..000000000
--- a/dev-python/arrayfire-python/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
- ArrayFire is a high performance library for parallel computing
- wih an easy-to-use API. This package project Python bindings
- for the ArrayFire library.
- </longdescription>
- <upstream>
- <remote-id type="github">arrayfire/arrayfire-python</remote-id>
- <remote-id type="pypi">arrayfire</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild
index 3f8f82f8b..29d5ecf87 100644
--- a/dev-python/asciitree/asciitree-0.3.3.ebuild
+++ b/dev-python/asciitree/asciitree-0.3.3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="ASCII trees in python"
diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest
index fc182f25b..ac7f18004 100644
--- a/dev-python/asdf/Manifest
+++ b/dev-python/asdf/Manifest
@@ -1,2 +1 @@
DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655
-DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df
diff --git a/dev-python/asdf/asdf-2.14.3.ebuild b/dev-python/asdf/asdf-2.14.3.ebuild
index d5e292123..2c935c1fb 100644
--- a/dev-python/asdf/asdf-2.14.3.ebuild
+++ b/dev-python/asdf/asdf-2.14.3.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
>=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}]
>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
- >=dev-python/semantic_version-2.8[${PYTHON_USEDEP}]
+ >=dev-python/semantic-version-2.8[${PYTHON_USEDEP}]
"
distutils_enable_tests pytest
diff --git a/dev-python/asdf/asdf-2.8.3.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild
deleted file mode 100644
index 09aab4068..000000000
--- a/dev-python/asdf/asdf-2.8.3.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for the Advanced Scientific Data Format"
-HOMEPAGE="https://asdf.readthedocs.io/en/latest/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Reported upstream:
-# https://github.com/asdf-format/asdf/issues/1319
-RESTRICT="test"
-
-BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]
- test? (
- dev-python/astropy[${PYTHON_USEDEP}]
- dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
- dev-python/psutil[${PYTHON_USEDEP}]
- dev-python/gwcs[${PYTHON_USEDEP}]
- )
- doc? ( media-gfx/graphviz )
-"
-
-RDEPEND="
- >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}]
- >=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.10[${PYTHON_USEDEP}]
- >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
- >=dev-python/semantic_version-2.8[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-python/matplotlib dev-python/docutils
-
-python_test() {
- # discovers things in docs dir if we do not
- # explicitly set it to run on the tests dir
- epytest asdf/tests
-}
diff --git a/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild
index 36f38c205..9bf99f7e2 100644
--- a/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild
+++ b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild
@@ -5,12 +5,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="HEALPix for Astropy"
HOMEPAGE="https://github.com/astropy/astropy-healpix"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P/-/_}.tar.gz"
S="${WORKDIR}/${P/-/_}"
LICENSE="BSD"
diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild
index 34b71dbda..be72affc7 100644
--- a/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild
+++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild
@@ -5,15 +5,14 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1 xdg-utils
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi xdg-utils
MYPV=${PV/_/}
S=${WORKDIR}/${PN}-${MYPV}
DESCRIPTION="Helpers for Astropy and Affiliated packages"
HOMEPAGE="https://github.com/astropy/astropy-helpers"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${PN}-${MYPV}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest
index da0e68d73..3d86b9bab 100644
--- a/dev-python/astropy/Manifest
+++ b/dev-python/astropy/Manifest
@@ -1,2 +1 @@
-DIST astropy-5.0.tar.gz 7823746 BLAKE2B e769f9ea26e156a2342dc75b307c16c2c38108adf0dfd931812b2eb3234941055c013378a492306f2247c16b4804fe569ba1cbfd8427df1aac2b808976082cf9 SHA512 3c0b0cdef434f27ee399fbfc3d55b95ce8395624caf8e73a205dba7742c39d8a2bcea9bf61c2c20235da7388d40c657c5474bfc7e3dc3c9e5911e39bab47cdb9
DIST astropy-5.2.1.tar.gz 8284422 BLAKE2B ded3556d6b16fe7abbbd019c23c0297f4690b13f054a1b98ab6aaeb20b92debefbc6e7c6c5eff8c65dfaa271826885027d6ba4a92f94218632162501a30b025b SHA512 46da7b065e119fa36233ced928abab31d6022fd116d2ed6825cb88b456ab57130772eea1de8cff7b5b7f30aadf46b933ad56a47cf6d2d68c0fa7593f322a6ea0
diff --git a/dev-python/astropy/astropy-5.0.ebuild b/dev-python/astropy/astropy-5.0.ebuild
deleted file mode 100644
index 6f32f60ed..000000000
--- a/dev-python/astropy/astropy-5.0.ebuild
+++ /dev/null
@@ -1,59 +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="Core functionality for performing astrophysics with Python"
-HOMEPAGE="https://astropy.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-#TODO: Package all these pytest deps:
-# pytest-remotedata>=0.3.1
-# pytest-openfiles>=0.3.1
-# pytest-astropy-header>=0.1.2
-# pytest-arraydiff>=0.1
-# pytest-filter-subpackage>=0.1
-RESTRICT="test"
-
-RDEPEND="
- dev-libs/expat:0=
- >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
- >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}]
- >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}]
- >=dev-python/packaging-19.0[${PYTHON_USEDEP}]
- sci-astronomy/wcslib:0=
- >=sci-libs/cfitsio-3.350:0=
- sys-libs/zlib:0=
-"
-BDEPEND="${RDEPEND}
- dev-python/astropy-helpers[${PYTHON_USEDEP}]
- dev-python/extension-helpers[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/setuptools-scm[${PYTHON_USEDEP}]
- test? (
- dev-libs/libxml2
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/ipython[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/objgraph[${PYTHON_USEDEP}]
- dev-python/pytest-xdist[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- )"
-
-distutils_enable_tests pytest
-# TODO: Fix this
-# NameError: name 'disabled_intersphinx_mapping' is not defined
-#distutils_enable_sphinx docs \
-# dev-python/matplotlib \
-# dev-python/graphviz \
-# dev-python/sphinx-astropy \
-# dev-python/pyyaml \
-# dev-python/scipy
diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild
index 91c9535df..75236266d 100644
--- a/dev-python/av/av-8.0.3.ebuild
+++ b/dev-python/av/av-8.0.3.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Pythonic bindings for FFmpeg's libraries."
-HOMEPAGE="https://github.com/mikeboers/PyAV https://pypi.org/project/av/"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
+HOMEPAGE="https://github.com/PyAV-Org/PyAV https://pypi.org/project/av/"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/av/metadata.xml b/dev-python/av/metadata.xml
index 325d9cc57..2231a73ae 100644
--- a/dev-python/av/metadata.xml
+++ b/dev-python/av/metadata.xml
@@ -5,4 +5,8 @@
<email>jpizarrocallejas@gmail.com</email>
<name>Jorge Pizarro Callejas</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mikeboers/PyAV</remote-id>
+ <remote-id type="pypi">av</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/bcbio-gff/Manifest b/dev-python/bcbio-gff/Manifest
deleted file mode 100644
index a4a0d0677..000000000
--- a/dev-python/bcbio-gff/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bcbio-gff-0.6.6.tar.gz 19099 BLAKE2B d86840ecb3b3073ddb4810fad976fa306e9b7cd13bb3779f4b0832deef01388ed39a529fde75b2dbae1078132889007bf4cef728c0fb41ddc7f363209382914a SHA512 b8880181b8308cd729936cda9102c0ea4793aeb551d75d639fe23712245fd0c4c1a72de7d96e0739d92260503c2b45d22bf73ddfe6f260629b29409097050da5
diff --git a/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild b/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild
deleted file mode 100644
index 73f412971..000000000
--- a/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Read and write Generic Feature Format (GFF) with Biopython"
-HOMEPAGE="https://pypi.python.org/pypi/bcbio-gff"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="HPND" # same as biopython
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/six[${PYTHON_USEDEP}]"
diff --git a/dev-python/bcbio-gff/metadata.xml b/dev-python/bcbio-gff/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/bcbio-gff/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
index 02581b74c..0a0c64b4b 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -6,11 +6,11 @@ EAPI=8
PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=rdepend
DISTUTILS_IN_SOURCE_BUILD=1
-inherit distutils-r1 optfeature
+inherit distutils-r1 optfeature pypi
DESCRIPTION="Statistical and interactive HTML plots for Python"
HOMEPAGE="https://bokeh.org/"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz
+SRC_URI+="
https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py
"
diff --git a/dev-python/bz2file/Manifest b/dev-python/bz2file/Manifest
deleted file mode 100644
index f8c6f14de..000000000
--- a/dev-python/bz2file/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bz2file-0.98.tar.gz 11333 BLAKE2B 4ec4687f609521a637c20a512b544cd99d7c334f7cffaeff71d2a893eefe131a10bd548b9f1e829c899cdcf181f5e877e092cf08d709bb3f1ba9901d3386b3e6 SHA512 2d28e71fe71b5fea4008d65a1fa91d5c6fafcacc09f891c5deaaa985661576bd97f2e33fe9f8c5943841f09c153f2079a2511329c066e57c775fb0b089b30b20
diff --git a/dev-python/bz2file/bz2file-0.98.ebuild b/dev-python/bz2file/bz2file-0.98.ebuild
deleted file mode 100644
index 0324854a1..000000000
--- a/dev-python/bz2file/bz2file-0.98.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Read and write bzip2-compressed files"
-HOMEPAGE="https://github.com/nvawda/bz2file"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${P}-always-threading.patch )
-
-python_test() {
- distutils_install_for_testing
- ${EPYTHON} test_bz2file.py || die "tests failed for ${EPYTHON}"
-}
diff --git a/dev-python/bz2file/files/bz2file-0.98-always-threading.patch b/dev-python/bz2file/files/bz2file-0.98-always-threading.patch
deleted file mode 100644
index ec11bce25..000000000
--- a/dev-python/bz2file/files/bz2file-0.98-always-threading.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-threading is always available in newer pythons
-
-https://github.com/nvawda/bz2file/issues/7
-
---- a/test_bz2file.py
-+++ b/test_bz2file.py
-@@ -496,15 +496,6 @@ class BZ2FileTest(BaseTest):
- for t in threads:
- t.join()
-
-- def testWithoutThreading(self):
-- if not hasattr(support, "import_fresh_module"):
-- return
-- module = support.import_fresh_module("bz2file", blocked=("threading",))
-- with module.BZ2File(self.filename, "wb") as f:
-- f.write(b"abc")
-- with module.BZ2File(self.filename, "rb") as f:
-- self.assertEqual(f.read(), b"abc")
--
- def testMixedIterationAndReads(self):
- self.createTempFile()
- linelen = len(self.TEXT_LINES[0])
diff --git a/dev-python/bz2file/metadata.xml b/dev-python/bz2file/metadata.xml
deleted file mode 100644
index bb126c586..000000000
--- a/dev-python/bz2file/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="pypi">bz2file</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
index 03fd9123d..481ce2e7b 100644
--- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild
+++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data"
HOMEPAGE="https://github.com/astropy/ccdproc"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/ccdproc/metadata.xml b/dev-python/ccdproc/metadata.xml
index 387ed8dcd..72370beb3 100644
--- a/dev-python/ccdproc/metadata.xml
+++ b/dev-python/ccdproc/metadata.xml
@@ -12,5 +12,6 @@ and bad pixel tracking through the reduction steps.
</longdescription>
<upstream>
<remote-id type="github">astropy/ccdproc</remote-id>
+ <remote-id type="pypi">ccdproc</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/colorcet/Manifest b/dev-python/colorcet/Manifest
index 9692f6be6..a743f1d71 100644
--- a/dev-python/colorcet/Manifest
+++ b/dev-python/colorcet/Manifest
@@ -1,2 +1 @@
-DIST colorcet-2.0.6.tar.gz 2924576 BLAKE2B 7354047b9cad133d7376d9ad19a6c09f6aa0c70e5cf0b5df6405064fdea2013df97e3beda7bba2d2483134ce3c3d63287dd911d2c2c9ed52b932eb0069dfb3a0 SHA512 b447e21a8922f0df94fd73791b8794467cc1a6a576367f073693450121fe936837da558e9ce79b930db64bcbc910f0528d84dd90eaf8ffe68b5546ac81a37813
DIST colorcet-3.0.1.tar.gz 3036207 BLAKE2B fabdd32dafc1828d50236ec93aa78e46aa125fe3564e732c2ece203cb71578d2d23303ccb2d069c938f513bd7df6a35f692b74b0c692546544f9e04fc28e9cae SHA512 92ede4947ef3af8b8cc3a4822c0e738cc8f0730fafb9f58a4a2c9bd3cda9c1e6ed254b9eec92f0306de95643eccd644b8ad955bc079ad20c00ee62e5f611431e
diff --git a/dev-python/colorcet/colorcet-2.0.6.ebuild b/dev-python/colorcet/colorcet-2.0.6.ebuild
deleted file mode 100644
index ba5c3db0a..000000000
--- a/dev-python/colorcet/colorcet-2.0.6.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
-
-# Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably
-# incorrect" for this package. It isn't. This package imports from neither
-# "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime.
-PYTHON_COMPAT=( python3_{10..11} pypy3 )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Collection of perceptually uniform colormaps"
-HOMEPAGE="https://holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Reported upstream:
-# https://github.com/holoviz/colorcet/issues/103
-RESTRICT="test"
-
-DEPEND="
- >=dev-python/param-1.7.0[${PYTHON_USEDEP}]
- >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}"
-
-distutils_enable_tests pytest
diff --git a/dev-python/colorcet/colorcet-3.0.1.ebuild b/dev-python/colorcet/colorcet-3.0.1.ebuild
index 25182e5d2..08ea7d55a 100644
--- a/dev-python/colorcet/colorcet-3.0.1.ebuild
+++ b/dev-python/colorcet/colorcet-3.0.1.ebuild
@@ -9,11 +9,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} pypy3 )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Collection of perceptually uniform colormaps"
HOMEPAGE="https://holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/colorlover/Manifest b/dev-python/colorlover/Manifest
deleted file mode 100644
index 0df2f3e30..000000000
--- a/dev-python/colorlover/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST colorlover-0.3.0.tar.gz 9060 BLAKE2B 33d060d7b324f47b785964e53473b4c2e70a130cfa9cf933222fe65dc6cbe93e7dd7054f6a38ab9ca79ac82e119e8b973266a06f4892bbb3b954cfcea4cb45b0 SHA512 4c39176c3375894202ecee86f3b4c45cd814720b4ce990e4d0605530a4fe2d71e28caa01aba143a86fc824c266cdf6f350cf84de6e1b01bfa2bdfae92a48bb2b
diff --git a/dev-python/colorlover/colorlover-0.3.0.ebuild b/dev-python/colorlover/colorlover-0.3.0.ebuild
deleted file mode 100644
index abf84b9b9..000000000
--- a/dev-python/colorlover/colorlover-0.3.0.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="color scales in python for humans"
-HOMEPAGE="https://github.com/plotly/colorlover"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# no tests in package
diff --git a/dev-python/colorlover/metadata.xml b/dev-python/colorlover/metadata.xml
deleted file mode 100644
index 2f2c0b51c..000000000
--- a/dev-python/colorlover/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild
index bada7bbe6..c5d9eec8e 100644
--- a/dev-python/cymbal/cymbal-1.0.0.ebuild
+++ b/dev-python/cymbal/cymbal-1.0.0.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Add functionality missing from the python libclang bindings"
-HOMEPAGE="https://pypi.org/project/cymbal"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+HOMEPAGE="https://pypi.org/project/cymbal/"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
index 58b4b1500..c33eb24f9 100644
--- a/dev-python/dandi-schema/Manifest
+++ b/dev-python/dandi-schema/Manifest
@@ -1,4 +1,3 @@
-DIST dandi-schema-0.5.1.gh.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804
-DIST dandi-schema-0.6.0.gh.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd
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
diff --git a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
deleted file mode 100644
index c0ac63b6b..000000000
--- a/dev-python/dandi-schema/dandi-schema-0.5.1.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/python-email-validator[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.3.4-coverage.patch"
-)
-
-src_configure() {
- echo "__version__ = '${PV}'" >> dandischema/_version.py
-}
-
-distutils_enable_tests pytest
-
-python_test() {
- export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
-}
diff --git a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
index c0ac63b6b..6f026c947 100644
--- a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
@@ -20,7 +20,7 @@ RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/pydantic[${PYTHON_USEDEP}]
- dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
index c0ac63b6b..6f026c947 100644
--- a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
@@ -20,7 +20,7 @@ RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/pydantic[${PYTHON_USEDEP}]
- dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
diff --git a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild
index c0ac63b6b..6f026c947 100644
--- a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild
@@ -20,7 +20,7 @@ RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/pydantic[${PYTHON_USEDEP}]
- dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
diff --git a/dev-python/datrie/datrie-0.8.2-r1.ebuild b/dev-python/datrie/datrie-0.8.2-r1.ebuild
index 6c05c8216..e8f9f9336 100644
--- a/dev-python/datrie/datrie-0.8.2-r1.ebuild
+++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
# Fails to compile with pep517
#DISTUTILS_USE_PEP517=setuptools
diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild
index d417f89d8..0a22057ef 100644
--- a/dev-python/delegator/delegator-0.1.1.ebuild
+++ b/dev-python/delegator/delegator-0.1.1.ebuild
@@ -4,12 +4,12 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
+PYPI_NO_NORMALIZE=1
+PYPI_PN=delegator.py
+inherit distutils-r1 pypi
DESCRIPTION="Subprocesses for Humans 2.0."
HOMEPAGE="https://github.com/amitt001/delegator.py"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}.py/${PN}.py-${PV}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/delegator/metadata.xml b/dev-python/delegator/metadata.xml
index 33a95485e..57368da50 100644
--- a/dev-python/delegator/metadata.xml
+++ b/dev-python/delegator/metadata.xml
@@ -10,7 +10,7 @@
<name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="github">amitt001/delegator</remote-id>
+ <remote-id type="github">amitt001/delegator.py</remote-id>
<remote-id type="pypi">delegator.py</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/dijitso/Manifest b/dev-python/dijitso/Manifest
deleted file mode 100644
index d822cce7e..000000000
--- a/dev-python/dijitso/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dijitso-2017.1.0.tar.gz 51223 BLAKE2B dd36d97ae3051779a4a21f277fddd02460f3572029b70a1fa5a799a54749cbd807bf9e12a41f2138cc917dfa3ea43368a96bb079dc2e99b6be6900f735e425ce SHA512 994c3d88ca207b3d3065f9376546580492a06eda51a340fc16bbd768248dc26a2984af064e9d970657509b003e403db329aea9ca9cca2f428764b7ec0a367040
diff --git a/dev-python/dijitso/dijitso-2017.1.0.ebuild b/dev-python/dijitso/dijitso-2017.1.0.ebuild
deleted file mode 100644
index cef1e1eb7..000000000
--- a/dev-python/dijitso/dijitso-2017.1.0.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Python module for distributed just-in-time shared library building"
-HOMEPAGE="https://bitbucket.org/fenics-project/dijitso/"
-SRC_URI="https://bitbucket.org/fenics-project/dijitso/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/mpi4py[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
-"
-# TODO: fix this, seems to require self
-#distutils_enable_sphinx doc/sphinx/source
-distutils_enable_tests --install pytest
diff --git a/dev-python/dijitso/metadata.xml b/dev-python/dijitso/metadata.xml
deleted file mode 100644
index 483c5a2ef..000000000
--- a/dev-python/dijitso/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-This module was written to improve a core component of the FEniCS
-framework, namely the just in time compilation of C++ code that is
-generated from Python modules, but is only called from within a C++
-library, and thus do not need wrapping in a nice Python interface.
-</longdescription>
- <upstream>
- <remote-id type="bitbucket">fenics-project/dijitso</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/dnaio/Manifest b/dev-python/dnaio/Manifest
deleted file mode 100644
index d56f36ebe..000000000
--- a/dev-python/dnaio/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST dnaio-0.4.2.tar.gz 125495 BLAKE2B 8034cbf2951345d7be0c0041d6ea24fc16d8e11669e04659216cd9551bc3da00b33a1c89e3b5453884e808c217b7d0ec232617da524037d834081ae3ae37f4e2 SHA512 9cd5d150fe49f6887bc3ac92975f2ec7d8f07370cfc8d8f8d556ad7b2143340c65bde87c80e02396358ea644a891dab39384641a143879e31328bfffff4c21b6
-DIST dnaio-0.4.3.tar.gz 126329 BLAKE2B 03c1f0d77d1c9452ec16e2fcf50312b24ac932fbe120462d2ac8cea26a0d0ed0f6b2f65c0a1570ba116e81fd59d57469e44b9a17112a03f704d6a906802528be SHA512 79a015c3ab61b9608cace1e435ca0d749ab67bf8b6acffb1b8cafcf2614061b46254c63583e44d7995ba4548bcd19e476297a66a20aa530eb98b6cda09690e64
-DIST dnaio-0.5.0.tar.gz 126321 BLAKE2B b26dc2e8f65efcc4aebe42f3ef252cc54a2c91beed65d060b51fbf4a6f3364325f884cf5d2e8269e1424d575200e4e716bc0a111c150ee403ead4cc176ed9ea6 SHA512 2e6a0dd04558b70ee08a81fd1d118525734df52701735cc27bab4c423c2030ec2fb6e83ddf02c491e1eb250c471d230b8fa72993c3a20ae844716c9542059c67
-DIST dnaio-0.5.1.tar.gz 126820 BLAKE2B d6e89ddceeb14ed50022f14e16c071e15af9bf832478dddfb4b6c086579822ea8b682f8e2c868a9f26a87637aae6959d822a8d9788ba980073740fe2e89c69fc SHA512 127e3dcc8291c21e8adce71211692e9c2284d49df336bb923c53fc5fea7dcb9d9b9f047f95642f3300240dac3d43cf6e987b3148b4ffa239d70f3b6c7ef043a5
diff --git a/dev-python/dnaio/dnaio-0.4.2.ebuild b/dev-python/dnaio/dnaio-0.4.2.ebuild
deleted file mode 100644
index d5c738db4..000000000
--- a/dev-python/dnaio/dnaio-0.4.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="efficient reader for FASTA and FASTQ files"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/xopen
-"
-
-# no tests in package
diff --git a/dev-python/dnaio/dnaio-0.4.3.ebuild b/dev-python/dnaio/dnaio-0.4.3.ebuild
deleted file mode 100644
index d5c738db4..000000000
--- a/dev-python/dnaio/dnaio-0.4.3.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="efficient reader for FASTA and FASTQ files"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/xopen
-"
-
-# no tests in package
diff --git a/dev-python/dnaio/dnaio-0.5.0.ebuild b/dev-python/dnaio/dnaio-0.5.0.ebuild
deleted file mode 100644
index d5c738db4..000000000
--- a/dev-python/dnaio/dnaio-0.5.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="efficient reader for FASTA and FASTQ files"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/xopen
-"
-
-# no tests in package
diff --git a/dev-python/dnaio/dnaio-0.5.1.ebuild b/dev-python/dnaio/dnaio-0.5.1.ebuild
deleted file mode 100644
index 2a7885b90..000000000
--- a/dev-python/dnaio/dnaio-0.5.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="efficient reader for FASTA and FASTQ files"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/xopen
-"
-
-# no tests in package
diff --git a/dev-python/dpath/Manifest b/dev-python/dpath/Manifest
new file mode 100644
index 000000000..81aa6ca1c
--- /dev/null
+++ b/dev-python/dpath/Manifest
@@ -0,0 +1 @@
+DIST dpath-2.1.6.tar.gz 28142 BLAKE2B 78cb4a8eb7278cd0c1818ffba9d77a917d89f3454a047a82d9031028b34ea2969fe98ed7086d26f6697a166b81cd50439b7b3bd545ab7e6cadcd0606c24be61e SHA512 2f2dac39b6e1ad2effd8d61ac4acf6619205423389ecebc54061aa10ec11ce3236ea666b632a7dca349e9b7a6579815c97e01c930eaa1a99d965e37b9825b82c
diff --git a/dev-python/dpath/dpath-2.1.6.ebuild b/dev-python/dpath/dpath-2.1.6.ebuild
new file mode 100644
index 000000000..55da56b96
--- /dev/null
+++ b/dev-python/dpath/dpath-2.1.6.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# 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="Accessing and searching dictionaries via /slashed/paths"
+HOMEPAGE="https://pypi.org/project/dpath/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+distutils_enable_tests pytest
diff --git a/dev-python/dpath/metadata.xml b/dev-python/dpath/metadata.xml
new file mode 100644
index 000000000..347155fb7
--- /dev/null
+++ b/dev-python/dpath/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">dpath-maintainers/dpath-python</remote-id>
+ <remote-id type="pypi">dpath</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dpctl/Manifest b/dev-python/dpctl/Manifest
index 20d7c42f5..d402c3e9e 100644
--- a/dev-python/dpctl/Manifest
+++ b/dev-python/dpctl/Manifest
@@ -1 +1,2 @@
DIST dpctl-0.14.1_rc2.gh.tar.gz 409028 BLAKE2B 481be08bb6a7b1a439580d600b0e14036f10793e568314f9373ffa46daad7d3e43d33fc66c3c48ec7e3de71e9d0a7256cdfdd984c38fa7f1694dcc0227dae93f SHA512 91ab20a51893e3afc9e140ab9dfd1aa19b24e58227a001faefb9ceba6ffc4aa235214663c7456e977acf556796be097eabacc9b01b94eb42e8c70677a2f2dd9d
+DIST dpctl-0.14.5.gh.tar.gz 552066 BLAKE2B f668ceea99125dad1e0a6989db5bd59df087840d09b1a1538c38cddd0f482f4fc4053ef400e86ddedee4b1906575a441fb97d2caaf3c3718d8aac503d942c0b5 SHA512 6df39eec93da38b86df4cdfdf90350ff11f95d4884bb762289af9b0a6e240d45ed7cc7243677ca7403b042f8938f8acfa42a974d6cff673cd846c0b0f22d0803
diff --git a/dev-python/dpctl/dpctl-0.14.5.ebuild b/dev-python/dpctl/dpctl-0.14.5.ebuild
new file mode 100644
index 000000000..65526b110
--- /dev/null
+++ b/dev-python/dpctl/dpctl-0.14.5.ebuild
@@ -0,0 +1,69 @@
+# Copyright 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
+
+DESCRIPTION="Data Parallel Control "
+HOMEPAGE="https://github.com/IntelPython/dpctl"
+SRC_URI="https://github.com/IntelPython/dpctl/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[${PYTHON_USEDEP}]
+ dev-python/scikit-build[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+ dev-util/cmake
+ dev-vcs/git
+ sys-devel/DPC++
+"
+
+DEPEND="
+ dev-libs/level-zero
+ dev-libs/opencl-icd-loader
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ sci-libs/oneDAL
+ sys-devel/DPC++:0/6
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.14.0-find-opencl.patch"
+ "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch"
+ "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch"
+ #"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch"
+)
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+
+ # Build system reads version from git tag
+ git init -q || die
+ git config --global user.email "larry@gentoo.org" || die
+ git config --global user.name "Larry the Cow" || die
+ git add . || die
+ git commit -qm "init" || die
+ git tag -a "${PV}" -m "${PN} version ${PV}" || die
+
+ distutils-r1_python_prepare_all
+}
+
+python_test() {
+ export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages"
+ # We don't use epytest because it overwrites our PYTHONPATH
+ pytest -vv || die
+}
diff --git a/dev-python/extension-helpers/Manifest b/dev-python/extension-helpers/Manifest
index 1e59aebf1..33d56a849 100644
--- a/dev-python/extension-helpers/Manifest
+++ b/dev-python/extension-helpers/Manifest
@@ -1,2 +1 @@
-DIST extension-helpers-0.1.tar.gz 24306 BLAKE2B 8fa5134bd26f4c5b9a66694d1c057c969607bfe9a05d5c470cdccda87bbff329174916bccc390ff80fdce72af5b764d0b3a7c34b632c01e33e3c84f913c6527b SHA512 d8394f5f0de28dfa2c204b918a39b5f3b990057bfdb7a21907b0b9ae3bacd5b95c5f25b32a08a50606fbae35b93629dcfe1fee512c6aa4f4e7c08c22bcfd3fbb
DIST extension-helpers-1.0.0.tar.gz 23463 BLAKE2B 0b1edffabc112120ac85c6445255986145143da9552221390a0827516a20e2877cad47e5968f6c7d293550db566574f86c877758d6233e51ca0762c3ff2e9327 SHA512 30234591100e5e8b7bda4392d72421911773a3aabb40c003367e8b335edcea3285f79fd962edd3d09b96ed7b4b936a97086376dfff50b18df85b55c612d61f8d
diff --git a/dev-python/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
deleted file mode 100644
index 976e33986..000000000
--- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Utilities for building and installing packages in the Astropy ecosystem"
-HOMEPAGE="https://github.com/astropy/astropy-helpers"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-#TODO: Package all these pytest deps:
-# pytest-doctestplus>=0.2.0
-# pytest-remotedata>=0.3.1
-# pytest-openfiles>=0.3.1
-# pytest-astropy-header>=0.1.2
-# pytest-arraydiff>=0.1
-# pytest-filter-subpackage>=0.1
-RESTRICT="test"
-
-distutils_enable_tests pytest
-distutils_enable_sphinx docs dev-python/sphinx-astropy
diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
index 27c8ff04b..b3a0148f7 100644
--- a/dev-python/ezdxf/ezdxf-0.16.5.ebuild
+++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
@@ -5,12 +5,11 @@ EAPI=8
#FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not.
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Python interface to DXF"
-HOMEPAGE="https://pypi.org/project/ezdxf"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
+HOMEPAGE="https://pypi.org/project/ezdxf/"
+SRC_URI="$(pypi_sdist_url ${PN} ${PV} .zip)"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/ffc/Manifest b/dev-python/ffc/Manifest
deleted file mode 100644
index 266151bd7..000000000
--- a/dev-python/ffc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ffc-2019.1.0.tar.gz 1365806 BLAKE2B a9c2e03f3cc178d279fea89eb95090a8417351ccde61f1a357e14610d952dd20870617bf32daf1bf79d2535997d4ce7e1a8971d9b03a0ee2636d4e18d208bd17 SHA512 c7deaeb5a0deadd998ba7809b7725e2d28a84bf82706427b5273310292d50380d132088ca04bc9a3945b543709226b7c2c2cbb28dde63fc06033f9d1f123433e
diff --git a/dev-python/ffc/ffc-2019.1.0.ebuild b/dev-python/ffc/ffc-2019.1.0.ebuild
deleted file mode 100644
index a164e1356..000000000
--- a/dev-python/ffc/ffc-2019.1.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Compiler for multilinear forms by generating C or C++ code"
-HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
-SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- ~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
- ~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- "
diff --git a/dev-python/ffc/metadata.xml b/dev-python/ffc/metadata.xml
deleted file mode 100644
index 744ca900c..000000000
--- a/dev-python/ffc/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-FFC works as a compiler for multilinear forms by generating code (C or
-C++) for the evaluation of a multilinear form given in mathematical
-notation. This new approach to form evaluation makes it possible to
-combine generality with efficiency; the form can be given in
-mathematical notation and the generated code is as efficient as
-hand-optimized code.
-</longdescription>
- <upstream>
- <remote-id type="bitbucket">fenics-project/ffc</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/fiat/Manifest b/dev-python/fiat/Manifest
deleted file mode 100644
index 17a7b25c7..000000000
--- a/dev-python/fiat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST fiat-2019.1.0.tar.gz 108440 BLAKE2B ebf4f9e342e063be3be51daf28d433274a3238f6dda7515e350d374427157490d86dfbfd4faba13fef1def58623ff38ed3df445815b5cbe2e1f6afd4b0dfa374 SHA512 15de17b2a28ba5071c0dd9ecc05ec36eeae76de3aa9f068577d43b7526778116e2ded412fa8c26189e7c505881dd2b68b2c45704c8446d9ef9d9d3797c3592e6
diff --git a/dev-python/fiat/fiat-2019.1.0.ebuild b/dev-python/fiat/fiat-2019.1.0.ebuild
deleted file mode 100644
index b50646eb3..000000000
--- a/dev-python/fiat/fiat-2019.1.0.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="FInite element Automatic Tabulator"
-HOMEPAGE="https://github.com/FEniCS/fiat"
-SRC_URI="https://github.com/FEniCS/fiat/archive/2019.1.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml
deleted file mode 100644
index 23d9fd64c..000000000
--- a/dev-python/fiat/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The FInite element Automatic Tabulator FIAT supports generation of
-arbitrary order instances of the Lagrange elements on lines, triangles,
-and tetrahedra. It is also capable of generating arbitrary order
-instances of Jacobi-type quadrature rules on the same element shapes.
-Further, H(div) and H(curl) conforming finite element spaces such as the
-families of Raviart-Thomas, Brezzi-Douglas-Marini and Nedelec are
-supported on triangles and tetrahedra. Upcoming versions will also
-support Hermite and nonconforming elements.
-</longdescription>
- <upstream>
- <remote-id type="bitbucket">fenics-project/fiat</remote-id>
- <remote-id type="github">FEniCS/fiat</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/fscacher/Manifest b/dev-python/fscacher/Manifest
index 67c5c736e..779c470e4 100644
--- a/dev-python/fscacher/Manifest
+++ b/dev-python/fscacher/Manifest
@@ -1,2 +1,2 @@
-DIST fscacher-0.1.4.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c
-DIST fscacher-0.2.0.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e
+DIST fscacher-0.1.4.gh.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c
+DIST fscacher-0.2.0.gh.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e
diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild
index b15c37615..50dcd6914 100644
--- a/dev-python/fscacher/fscacher-0.1.4.ebuild
+++ b/dev-python/fscacher/fscacher-0.1.4.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Cache results of operations on heavy file trees"
HOMEPAGE="https://github.com/con/fscacher"
-SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
SLOT="0"
LICENSE="MIT"
diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild
index 8bb00f6f4..f466d0675 100644
--- a/dev-python/fscacher/fscacher-0.2.0.ebuild
+++ b/dev-python/fscacher/fscacher-0.2.0.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Cache results of operations on heavy file trees"
HOMEPAGE="https://github.com/con/fscacher"
-SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
SLOT="0"
LICENSE="MIT"
diff --git a/dev-python/fslpy/fslpy-3.10.0.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild
index d25cfb22f..3f6262707 100644
--- a/dev-python/fslpy/fslpy-3.10.0.ebuild
+++ b/dev-python/fslpy/fslpy-3.10.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx
@@ -18,7 +18,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/dill[${PYTHON_USEDEP}]
>=dev-python/h5py-2.9[${PYTHON_USEDEP}]
- >=dev-python/indexed_gzip-0.7.0[${PYTHON_USEDEP}]
+ >=dev-python/indexed-gzip-0.7.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1[${PYTHON_USEDEP}]
>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
>=dev-python/trimesh-2.37.29[${PYTHON_USEDEP}]
diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest
index 23cd9b3d5..037a125d3 100644
--- a/dev-python/geopandas/Manifest
+++ b/dev-python/geopandas/Manifest
@@ -1 +1 @@
-DIST geopandas-0.12.2.gh.tar.gz 6360014 BLAKE2B ded0b7fdff88f91ad02f690013b92b4fd7378742fbe01473a0351164df526fe4ca7cbfb1097b79311d2f6c3fa4301199cf7862befe970e4b6fa6a0d8c1317c38 SHA512 6470bf45360bb6486607870ee643f295a8823ce3109b777ec9d1eb576bc11c717d3dc40777481748ffe8d17a6d9869245efff5298bea274ec108ca9d0b1502ba
+DIST geopandas-0.13.2.gh.tar.gz 6388249 BLAKE2B 910f32ea7d798bbdeee77be190c57daf7bdc719901a2183b5328ec13619ff9b4145d1717afed8fc71da154d84f388ce2bc30c541478f95ed121c7d8681c691ae SHA512 4dff4bfeca2490081c02c41edf92037fa8a8f4b030b6f6a0cdc231b3119f829604af39277125db9535c66aac0698d2d4dcfac2bb58b92d31bea83f0ee296e21a
diff --git a/dev-python/geopandas/geopandas-0.12.2.ebuild b/dev-python/geopandas/geopandas-0.13.2.ebuild
index 10edebed5..921c13417 100644
--- a/dev-python/geopandas/geopandas-0.12.2.ebuild
+++ b/dev-python/geopandas/geopandas-0.13.2.ebuild
@@ -25,9 +25,10 @@ distutils_enable_tests pytest
python_test() {
local deselect=(
- # disable tests due to networking being blocked
- geopandas/io/tests/test_file.py::test_read_file_remote_zipfile_url
- geopandas/io/tests/test_file.py::test_read_file_remote_geojson_url
+ # needs network access
+ geopandas/io/tests/test_file.py::test_read_file_url
+ # fails with RuntimeError thrown by matplotlib
+ geopandas/tests/test_plotting.py::TestGeoplotAccessor::test_pandas_kind
)
epytest ${deselect[@]/#/--deselect }
@@ -37,4 +38,5 @@ pkg_postinst() {
optfeature "plotting" dev-python/matplotlib
optfeature "spatial indexes and spatial joins" sci-libs/rtree
optfeature "geocoding" sci-geosciences/geopy
+ optfeature "geodatabase access" dev-python/psycopg dev-python/sqlalchemy
}
diff --git a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
index 88e1a333a..3185102ba 100644
--- a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
+++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Interoperability with Gmsh for Python"
HOMEPAGE="https://github.com/inducer/gmsh_interop/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/gmsh_interop/metadata.xml b/dev-python/gmsh_interop/metadata.xml
index 2f2c0b51c..ed015f298 100644
--- a/dev-python/gmsh_interop/metadata.xml
+++ b/dev-python/gmsh_interop/metadata.xml
@@ -9,4 +9,8 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">gmsh_interop</remote-id>
+ <remote-id type="github">inducer/gmsh_interop</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild
index c7e710a70..722048089 100644
--- a/dev-python/grabbit/grabbit-0.2.6.ebuild
+++ b/dev-python/grabbit/grabbit-0.2.6.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
diff --git a/dev-python/gwcs/Manifest b/dev-python/gwcs/Manifest
index 91b72eae3..4e040149b 100644
--- a/dev-python/gwcs/Manifest
+++ b/dev-python/gwcs/Manifest
@@ -1,2 +1 @@
-DIST gwcs-0.16.1.tar.gz 171068 BLAKE2B 0406a7b8545b56d7811b8326c148f0d413dd6ae38f90c9e50d984fd9a35d2f130d61821a237acc2bec2746e012d199f4ed08231299520de46ffa1554fe4d860b SHA512 2414f1c40be632e7b7cdb6657f54869a2aa8aefce6074ff0e6c5c277fd6c125d72c42b76e9344f100367f810bfcd5dc49b4e6ec6318b08a975799a918debb9cc
DIST gwcs-0.18.3.tar.gz 184361 BLAKE2B a4afcf3d6281f65f1ff6733bb83f82ba089fc56d2a21c2d6f5fd8370ef518b97376ebe718a9e4f9fa34ae80fc66baecf9e32835bb18f1737bf3f47e972e31118 SHA512 51aac4dd1f3b835b274f265cf26d4f9cf757435bb8355d43a31b7eba665991c233b46f9e0a87d22985c04fdabc0455958b99f37aeb55a04a9c0b4901d5069891
diff --git a/dev-python/gwcs/gwcs-0.16.1.ebuild b/dev-python/gwcs/gwcs-0.16.1.ebuild
deleted file mode 100644
index cef67f6ea..000000000
--- a/dev-python/gwcs/gwcs-0.16.1.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
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-inherit distutils-r1
-
-DESCRIPTION="Generalized World Coordinate System"
-HOMEPAGE="https://gwcs.readthedocs.io/en/latest/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Tests do not pass, reported upstream:
-# https://github.com/spacetelescope/gwcs/issues/437
-RESTRICT=test
-
-BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]
- test? (
- dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
- )
-"
-
-RDEPEND="
- dev-python/asdf[${PYTHON_USEDEP}]
- >=dev-python/astropy-4.1[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-
-# TODO: package stsci-rtd-theme
-#distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/sphinx-automodapi dev-python/sphinx_rtd_theme
-distutils_enable_tests pytest
-
-python_test() {
- # discovers things in docs dir if we do not
- # explicitly set it to run on the tests dir
- pytest -vv gwcs/tests || die " Tests failed with ${EPYTHON}"
-}
diff --git a/dev-python/hdbscan/Manifest b/dev-python/hdbscan/Manifest
index b162353da..7ffc42c8b 100644
--- a/dev-python/hdbscan/Manifest
+++ b/dev-python/hdbscan/Manifest
@@ -1,2 +1 @@
-DIST hdbscan-0.8.26.tar.gz 10776639 BLAKE2B 7f1cb7b479746e3ff262cce90d48cca42dccabc131a60300ae5448455260eb27387ab2eeeee19257930ee646d06df80fa2997cf1819da18178c5522a8a27a30c SHA512 7337f4246511d22e8e11308e7776aad6929f26674daecc1e174b01673782837815a40820a6565406315b1ae14ed059c4945810ac997abfde9e24abda352de622
DIST hdbscan-0.8.29.tar.gz 11666106 BLAKE2B de324386d7d2178f74ea958fa75e5eccb9dcdeba3d85cecce1150930e2d687caecbc79469de6ad62806c5bd860962bba57f27323c69f3abc6b0d4694a553656d SHA512 fd349c1c6c09f0288a9a2501eb7794fb03139c11261a835d90f1c9cd80955a4d8d075ff3864ddb9cfcbc204a3d0662011074bdb29b66b72d5469f76bc4f7ecca
diff --git a/dev-python/hdbscan/hdbscan-0.8.26.ebuild b/dev-python/hdbscan/hdbscan-0.8.26.ebuild
deleted file mode 100644
index 91e83eb87..000000000
--- a/dev-python/hdbscan/hdbscan-0.8.26.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="A high performance implementation of HDBSCAN clustering."
-HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="test"
-# Tests fail, reported to upstream
-# https://github.com/scikit-learn-contrib/hdbscan/issues/501
-
-DEPEND=""
-RDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdbscan/hdbscan-0.8.29.ebuild b/dev-python/hdbscan/hdbscan-0.8.29.ebuild
index e13b6da0e..33947fd22 100644
--- a/dev-python/hdbscan/hdbscan-0.8.29.ebuild
+++ b/dev-python/hdbscan/hdbscan-0.8.29.ebuild
@@ -5,11 +5,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A high performance implementation of HDBSCAN clustering."
HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest
index 55669a6ad..e3afb5ed5 100644
--- a/dev-python/heudiconv/Manifest
+++ b/dev-python/heudiconv/Manifest
@@ -1 +1,2 @@
DIST heudiconv-0.11.6.tar.gz 9070519 BLAKE2B df6c66080bbaa89f74490f136674eabd64e9b2844ae7daef82ef4b4ef8c42ed16d3ae3b790534cc13ec121e63de8486838eb7e7becbcdbffff2df6e8bd2bd54c SHA512 c4d1f0caaed9713360ad2614bc276f2cc0e356c54b1b37c8912d762db429313c75d0f081886cb6ea0b8fd171bc5fc5a338fd3b670a8b10a3fbed0c6f9dfb7477
+DIST heudiconv-0.13.0.tar.gz 9158053 BLAKE2B 9f87fbcd5ea8ccca39cc029f1bdd84906412a22e5d18e2afe280d19737f0dda4c03248ba93f58c06aae4b15366477e8a5d1c41d09d1b1d3a10ff673aaa050e26 SHA512 b867ee0a60ad98099a3802e290ebb24b858befbd45e93772fafe437a87ea867c5076680ea3ed7856272397267c740ef2eade9f64ffc0d4216d4a37be39add158
diff --git a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild b/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild
index 847424235..8dbfcfa0f 100644
--- a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild
+++ b/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild
@@ -4,15 +4,14 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
DESCRIPTION="Flexible DICOM conversion to structured directory layouts"
HOMEPAGE="
https://github.com/nipy/heudiconv
https://heudiconv.readthedocs.io/en/latest/
"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="Apache-2.0"
@@ -29,6 +28,7 @@ RDEPEND="
"
BDEPEND="
test? (
+ dev-python/mock[${PYTHON_USEDEP}]
dev-python/six[${PYTHON_USEDEP}]
)
"
@@ -39,4 +39,10 @@ PATCHES=(
"${FILESDIR}/${P}-gitenv.patch"
)
+# Reported upstream:
+# https://github.com/nipy/heudiconv/issues/679
+EPYTEST_DESELECT=(
+ heudiconv/tests/test_main.py::test_prepare_for_datalad
+)
+
distutils_enable_tests pytest
diff --git a/dev-python/heudiconv/heudiconv-0.13.0.ebuild b/dev-python/heudiconv/heudiconv-0.13.0.ebuild
new file mode 100644
index 000000000..7f7db0b0e
--- /dev/null
+++ b/dev-python/heudiconv/heudiconv-0.13.0.ebuild
@@ -0,0 +1,42 @@
+# 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="Flexible DICOM conversion to structured directory layouts"
+HOMEPAGE="
+ https://github.com/nipy/heudiconv
+ https://heudiconv.readthedocs.io/en/latest/
+"
+
+SLOT="0"
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/versioningit[${PYTHON_USEDEP}]
+ sci-biology/dcm2niix
+ sci-biology/dcmstack[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ sci-libs/nipype[${PYTHON_USEDEP}]
+ sci-libs/pydicom[${PYTHON_USEDEP}]
+ "
+BDEPEND="
+ test? (
+ dev-python/mock[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upstream:
+# https://github.com/nipy/heudiconv/issues/679
+EPYTEST_DESELECT=(
+ heudiconv/tests/test_main.py::test_prepare_for_datalad
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/holoviews/Manifest b/dev-python/holoviews/Manifest
index 806b0513d..ec3bb1815 100644
--- a/dev-python/holoviews/Manifest
+++ b/dev-python/holoviews/Manifest
@@ -1,2 +1 @@
-DIST holoviews-1.14.2.tar.gz 6929549 BLAKE2B 72746a846ea7628b45e61b892ea940df4b2d7886efda054eedb859caac5dc3b66ed1c0aa9a4df8766905e35a973f6ee9226558cf6fb68394d17fe7c2f77982b2 SHA512 473a344f36c6ab1abc0847df46f4dc015fe225b9285a86152a78e13402770d5e7fdbd51aef21ff5cc53fbab89898237a260bea86dadef91ccb30bbce9344daf0
DIST holoviews-1.15.3.tar.gz 6905214 BLAKE2B 60bb7008dd5af474295245eb0dbce240cfb4dcaf4122bc6073561e829c506b670201ac7d2b7ae1eea640929eb0993148c22c1a3e8d8ccb8e00582a2fbd3e696b SHA512 b1d4b64503511c61ede67d6d45472acde1afb854e19f7a30acb35d7fab2400ffe1e43db7b6e85eefe542b8353982af9cb41d505412bb0674cb20926c24f76494
diff --git a/dev-python/holoviews/holoviews-1.14.2.ebuild b/dev-python/holoviews/holoviews-1.14.2.ebuild
deleted file mode 100644
index 4c8af05d9..000000000
--- a/dev-python/holoviews/holoviews-1.14.2.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..10} )
-
-# HoloViews imports from "distutils" at runtime.
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Make data analysis and visualization seamless and simple"
-HOMEPAGE="https://holoviews.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=dev-python/param-1.9.3[${PYTHON_USEDEP}]
- >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}
- dev-python/colorcet[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.0.0[${PYTHON_USEDEP}]
- >=dev-python/panel-0.8.0[${PYTHON_USEDEP}]
- >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}]
-"
diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild
index 425290441..783d9b1cb 100644
--- a/dev-python/holoviews/holoviews-1.15.3.ebuild
+++ b/dev-python/holoviews/holoviews-1.15.3.ebuild
@@ -8,11 +8,10 @@ PYTHON_COMPAT=( python3_{10..10} )
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Make data analysis and visualization seamless and simple"
HOMEPAGE="https://holoviews.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/imageutils/Manifest b/dev-python/imageutils/Manifest
deleted file mode 100644
index ccb3920ff..000000000
--- a/dev-python/imageutils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST imageutils-0.3.8.tar.gz 3531 BLAKE2B 58b8248faa79f36cb24451c5d174fba421cc4c8664d9093047dfd4460f0c80941912859fe6507d2f2a0814f00d6a64631617ad6731e1dddb7525e6ed087ad825 SHA512 5399fe0586929b5fa4e3d70177179f3c050527115f32ac84d16c0ace1d650c789555329cc86a533fa38778cce5bcb0b6c12886195876e7103535b74b508998f6
diff --git a/dev-python/imageutils/imageutils-0.3.8.ebuild b/dev-python/imageutils/imageutils-0.3.8.ebuild
deleted file mode 100644
index 09db367f1..000000000
--- a/dev-python/imageutils/imageutils-0.3.8.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Various utilities for working with images"
-HOMEPAGE="https://pypi.org/project/imageutils/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
diff --git a/dev-python/imageutils/metadata.xml b/dev-python/imageutils/metadata.xml
deleted file mode 100644
index b75b1ab3a..000000000
--- a/dev-python/imageutils/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-astronomy@gentoo.org</email>
- <name>Gentoo Astronomy Project</name>
- </maintainer>
- <longdescription lang="en">
-imageutils is a collection of image processing utilities that are generally
-useful to astronomers. These will likely become part of the core AstroPy
-package before the 1.0 release.
-</longdescription>
- <upstream>
- <remote-id type="github">astropy/imageutils</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild
index 7dbb9d5c9..4434b8fdd 100644
--- a/dev-python/interleave/interleave-0.2.0.ebuild
+++ b/dev-python/interleave/interleave-0.2.0.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10)
+PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Yield from multiple iterators as values become available"
HOMEPAGE="https://github.com/jwodder/interleave"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/json_tricks/Manifest b/dev-python/json_tricks/Manifest
deleted file mode 100644
index 24618b3f4..000000000
--- a/dev-python/json_tricks/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST json_tricks-3.15.5.tar.gz 41517 BLAKE2B beca160278281161ad480848da7971b4bcd0c3624ada8e1092edaf5c56abedf3fb4f5bc96c4efbd714cbdc07c3ba5d63fa4e97efcd040f1f6bc5406d6a841580 SHA512 e43ead9ffd3966f5c548f70bacd58baa275d63e3a55fbd49d84d477fc0bea30cbeaeac46c308b6251bc141efb949c2e73444432c14608d9a8fc5dfc6c7c246d6
diff --git a/dev-python/json_tricks/json_tricks-3.15.5.ebuild b/dev-python/json_tricks/json_tricks-3.15.5.ebuild
deleted file mode 100644
index f659a2a18..000000000
--- a/dev-python/json_tricks/json_tricks-3.15.5.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Extra features for Python's JSON"
-HOMEPAGE="https://github.com/mverleg/pyjson_tricks"
-SRC_URI="https://github.com/mverleg/pyjson_tricks/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/py${PN}-${PV}"
-
-distutils_enable_tests pytest
-distutils_enable_sphinx docs
diff --git a/dev-python/json_tricks/metadata.xml b/dev-python/json_tricks/metadata.xml
deleted file mode 100644
index 2967a86bd..000000000
--- a/dev-python/json_tricks/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">
- The json-tricks package brings several pieces of functionality to
- Python handling of json files: (1) Store and load numpy arrays in
- human-readable format; (2) Store and load class instances both
- generic and customized; (3) Store and load date/times as a
- dictionary (including timezone); (4) Preserve map order {} using
- OrderedDict; (5) Allow for comments in json files by starting lines
- with #; (6) Sets, complex numbers, Decimal, Fraction, enums,
- compression, duplicate keys, pathlib Paths ...
- </longdescription>
- <upstream>
- <remote-id type="pypi">json-tricks</remote-id>
- <remote-id type="github">mverleg/pyjson_tricks</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/jupyterlab_launcher/Manifest b/dev-python/jupyterlab_launcher/Manifest
deleted file mode 100644
index c1d49b101..000000000
--- a/dev-python/jupyterlab_launcher/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jupyterlab_launcher-0.13.1.tar.gz 20418 BLAKE2B 1cfe0e357da0926468a7dfb8b6b2d6eb870593b6bb9ac5c798a90f876c76b82c07cca7948bbdfdc0f4e49cefb67c0ba56edc0d7334e969a76cec2407353afd63 SHA512 f7b4267379fd21e80688e565f788277b92aad748971c077e694246ae01c7f56b5a6a50d4fa9d3bfecc561b723d6bcbbb988f019268d2752076ec6293f9960406
diff --git a/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild b/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild
deleted file mode 100644
index 80abd3be5..000000000
--- a/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.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_{8..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Jupyter Launcher"
-HOMEPAGE="https://jupyter.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-# TODO: fix this
-RESTRICT="test"
-
-RDEPEND="
- >=dev-python/jsonschema-2.6.0[${PYTHON_USEDEP}]
- >=dev-python/notebook-4.2.0[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/jupyterlab_launcher/metadata.xml b/dev-python/jupyterlab_launcher/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-python/jupyterlab_launcher/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild
index a873e6b85..d624fb2aa 100644
--- a/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild
+++ b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 pypi
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
index 86f967801..ccc9695f0 100644
--- a/dev-python/llvmlite/Manifest
+++ b/dev-python/llvmlite/Manifest
@@ -1 +1,2 @@
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
diff --git a/dev-python/llvmlite/llvmlite-0.40.1.ebuild b/dev-python/llvmlite/llvmlite-0.40.1.ebuild
new file mode 100644
index 000000000..bacb0358b
--- /dev/null
+++ b/dev-python/llvmlite/llvmlite-0.40.1.ebuild
@@ -0,0 +1,63 @@
+# 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/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild
index 59f029e95..2c3f44eb1 100644
--- a/dev-python/logzero/logzero-1.7.0.ebuild
+++ b/dev-python/logzero/logzero-1.7.0.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 pypy3 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Robust and effective logging for Python 2 and 3"
HOMEPAGE="https://pypi.org/project/logzero"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/looseversion/Manifest b/dev-python/looseversion/Manifest
deleted file mode 100644
index 1fe929b12..000000000
--- a/dev-python/looseversion/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST looseversion-1.0.2.gh.tar.gz 8144 BLAKE2B 1c3b76c6f77499ac39863897771bbc2246e5d1ad47e3ae4f0c21d4bb6a717270ebe6550ea53b188740ed74bf5a7fef31d743486f0ee54ddb9758d2806374dbdf SHA512 d166c49a1788fe6453d4187af62a860f9c66ce7b71ec924ad3a6d19101d9619394bb81e17e52054b5a8e693051ca40c4269e415f4af513d35212eab678837569
-DIST looseversion-1.0.3.tar.gz 6874 BLAKE2B ce0cc5af699c7db85f180ba0e4b465411d15a1bd4f669fc34ede985f0ceca63a01d9ab7755b722018770633342bfe6eeeb59b98026616641aca1a522acd47f7b SHA512 262f6b33516020bf38878cdf0dfcd3e51507d20f40a348a8fcd8ba66c2eaef564738c275297c3efe8daf9ff5efc5b7dffa8d76f77626c3eefdac7b097db27f78
diff --git a/dev-python/looseversion/looseversion-1.0.2.ebuild b/dev-python/looseversion/looseversion-1.0.2.ebuild
deleted file mode 100644
index 0150e69f5..000000000
--- a/dev-python/looseversion/looseversion-1.0.2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="A backwards/forwards-compatible fork of distutils' LooseVersion"
-HOMEPAGE="https://github.com/effigies/looseversion"
-SRC_URI="https://github.com/effigies/looseversion/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="PSF-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND=""
-BEPEND=""
-
-distutils_enable_tests pytest
-
-python_test() {
- epytest tests.py
-}
diff --git a/dev-python/looseversion/looseversion-1.0.3.ebuild b/dev-python/looseversion/looseversion-1.0.3.ebuild
deleted file mode 100644
index aa8ebcc32..000000000
--- a/dev-python/looseversion/looseversion-1.0.3.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=flit
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="A backwards/forwards-compatible fork of distutils' LooseVersion"
-HOMEPAGE="https://github.com/effigies/looseversion"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="PSF-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND=""
-BEPEND=""
-
-distutils_enable_tests pytest
-
-python_test() {
- epytest tests.py
-}
diff --git a/dev-python/looseversion/metadata.xml b/dev-python/looseversion/metadata.xml
deleted file mode 100644
index 20b71d2b7..000000000
--- a/dev-python/looseversion/metadata.xml
+++ /dev/null
@@ -1,25 +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">
- A backwards/forwards-compatible fork of distutils.version.LooseVersion, for times
- when PEP-440 isn't what you need. The goal of this package is to be a drop-in
- replacement for the original LooseVersion. It implements an identical interface
- and comparison logic to LooseVersion. The only major change is that a
- looseversion.LooseVersion is comparable to a distutils.version.LooseVersion,
- which means tools should not need to worry whether all dependencies that use
- LooseVersion have migrated.
- </longdescription>
- <upstream>
- <remote-id type="github">effigies/looseversion</remote-id>
- <remote-id type="pypi">looseversion</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/matrix2latex/Manifest b/dev-python/matrix2latex/Manifest
deleted file mode 100644
index 996d52a66..000000000
--- a/dev-python/matrix2latex/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST matrix2latex-1.10.tar.gz 594004 BLAKE2B 0950af176071470781f45a37955ce4222299c0cae276ea7b0b767d372b3c5fc1eff4f67c26d3702dd0bc2a06c8eca5569e8fbb67b247c0bba698df2bdf8a762a SHA512 61570aa8dbb396b1c33fd327acae67b1c5b7c1655a60ad73da0ed01627c569f88f318aec92cbef1df25fc2da6e68ecf38fb1a94d26777bd50caffa694f587efe
diff --git a/dev-python/matrix2latex/matrix2latex-1.10.ebuild b/dev-python/matrix2latex/matrix2latex-1.10.ebuild
deleted file mode 100644
index 0d84ff9e9..000000000
--- a/dev-python/matrix2latex/matrix2latex-1.10.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="A tool to create LaTeX tables from python lists and arrays"
-HOMEPAGE="https://github.com/TheChymera/matrix2latex"
-SRC_URI="https://github.com/TheChymera/matrix2latex/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}-${COMMIT}"
-
-distutils_enable_sphinx doc_sphinx
-distutils_enable_tests pytest
-
-python_prepare_all() {
- # this has been renamed in newer versions of sphinx
- sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' doc_sphinx/conf.py
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/neo/neo-0.11.0.ebuild b/dev-python/neo/neo-0.11.0.ebuild
index c66b2b951..dedbcea6e 100644
--- a/dev-python/neo/neo-0.11.0.ebuild
+++ b/dev-python/neo/neo-0.11.0.ebuild
@@ -3,15 +3,14 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
MY_PN="python-neo"
DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
-SRC_URI="https://github.com/NeuralEnsemble/python-neo/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/neo/neo-0.11.1.ebuild b/dev-python/neo/neo-0.11.1.ebuild
index c7a36d0e3..6f43494f8 100644
--- a/dev-python/neo/neo-0.11.1.ebuild
+++ b/dev-python/neo/neo-0.11.1.ebuild
@@ -3,14 +3,12 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-#SRC_URI="https://github.com/NeuralEnsemble/python-neo/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild
index 78a73cb5e..f57281b6e 100644
--- a/dev-python/num2words/num2words-0.5.10.ebuild
+++ b/dev-python/num2words/num2words-0.5.10.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Modules to convert numbers to words."
HOMEPAGE="https://github.com/savoirfairelinux/num2words"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index 7f3f072b4..d77998df2 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1,2 +1,2 @@
-DIST numba-0.56.3.tar.gz 2492552 BLAKE2B a8a3070ef6ca709594f308c751700a8c2cae1077c15b12291632a2022ca47460af245f02253555f4dfd4a93ef179c262baa36127b135158e48d60783f2ee0bb4 SHA512 42a1d9007ff89a58a79a80743e883e013a7a53b5035e1754b4c9f1ec715834a036eee32bff42ab0aa89132a7b6cb15decd9e918a9e49c42ce5a024e10ece3169
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/numba-0.56.3.ebuild b/dev-python/numba/numba-0.57.1.ebuild
index 85fb09a85..814dc36f9 100644
--- a/dev-python/numba/numba-0.56.3.ebuild
+++ b/dev-python/numba/numba-0.57.1.ebuild
@@ -4,14 +4,14 @@
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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -19,11 +19,11 @@ KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="openmp threads"
RDEPEND="
- >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.40.0
+ >=dev-python/llvmlite-0.40.0[${PYTHON_USEDEP}]
+ <=dev-python/llvmlite-0.41.0
>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.24[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 )
+ <dev-python/numpy-1.25[${PYTHON_USEDEP}]
+ threads? ( >=dev-cpp/tbb-2021.6 )
"
BDEPEND="
dev-python/pip[${PYTHON_USEDEP}]
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
index 8527c31e4..d256ba401 100644
--- a/dev-python/numcodecs/Manifest
+++ b/dev-python/numcodecs/Manifest
@@ -1,3 +1 @@
-DIST numcodecs-0.10.0.tar.gz 4519035 BLAKE2B c94edb258d23b815048c758fb1f36f6291e6b0f5b8ae9f72ea9d7a6bfd5a35891882380f309f1c26ca47b62d1825a11b1bbff289d2970d739ccfad7a5f4d610d SHA512 098602d79ac4d7cbb6c261f513b0ab6206c4b74f5f5cbb6e500434bcdeb6b2c023b0afa272c2a300081abf8bd0ec363ca0985e954b284e96fb70e95c369abf77
-DIST numcodecs-0.9.0.tar.gz 4514267 BLAKE2B d7042ff0296a8246f063f55f31d790fcfbd59de07c08ff0d57e1bd4c7094c6f375ef55714866061f449dcca87d39abd36c56218d23aca0fd6bcfae491fb10097 SHA512 1525e5a7f7a7427752d3ccfbbb82b7afbfc90fcbc2c9e886e31d286c64478d85747de7e6bf16a8e980af96cf952d1202a15affa02cf6a22b4aac3725a0c8a65f
-DIST numcodecs-0.9.1.tar.gz 4514374 BLAKE2B b418ee0fd27cb5f7bf8def3b124f31af7c0e2e2610dca55351c105933f7471e2465f24fa24e53ee607abcf26d690ba2b368e77618c703a4dbc8a926be48c9c1d SHA512 639cc5a5656e026f85e893009831f98420e3818f73bab95f0afd0a5bd64c901082826921e40c1b6e1f75cad82b3be2cf36787fa74ba7f0fd011dac070b24e0f8
+DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2
diff --git a/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch
new file mode 100644
index 000000000..2d5e7f86e
--- /dev/null
+++ b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch
@@ -0,0 +1,11 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -87,7 +87,7 @@ exclude_lines = [
+ ]
+
+ [tool.pytest.ini_options]
+-addopts = "--cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx"
++addopts = "--pyargs numcodecs --doctest-modules --doctest-glob=*.pyx"
+ doctest_optionflags = [
+ "NORMALIZE_WHITESPACE",
+ "ELLIPSIS",
diff --git a/dev-python/numcodecs/numcodecs-0.10.0.ebuild b/dev-python/numcodecs/numcodecs-0.10.0.ebuild
deleted file mode 100644
index b2030d332..000000000
--- a/dev-python/numcodecs/numcodecs-0.10.0.ebuild
+++ /dev/null
@@ -1,35 +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="Data storage buffer compression and transformation codecs"
-HOMEPAGE="https://github.com/zarr-developers/numcodecs"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Fails to collect tests for yet unknown reasons:
-# https://github.com/zarr-developers/numcodecs/issues/304
-RESTRICT="test"
-
-RDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-DEPEND="
- test? (
- ${RDEPEND}
- dev-python/entrypoints[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/numcodecs/numcodecs-0.11.0.ebuild b/dev-python/numcodecs/numcodecs-0.11.0.ebuild
new file mode 100644
index 000000000..500a52b89
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.11.0.ebuild
@@ -0,0 +1,49 @@
+# 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}]
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-nocov.patch"
+)
+
+# Reported upstream:
+# https://github.com/zarr-developers/numcodecs/issues/436
+EPYTEST_DESELECT=(
+ tests/test_json.py::test_non_numpy_inputs
+ tests/test_msgpacks.py::test_non_numpy_inputs
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+ cd "${T}" || die
+ epytest --pyargs numcodecs
+}
diff --git a/dev-python/numcodecs/numcodecs-0.9.0.ebuild b/dev-python/numcodecs/numcodecs-0.9.0.ebuild
deleted file mode 100644
index b2030d332..000000000
--- a/dev-python/numcodecs/numcodecs-0.9.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
-
-DESCRIPTION="Data storage buffer compression and transformation codecs"
-HOMEPAGE="https://github.com/zarr-developers/numcodecs"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Fails to collect tests for yet unknown reasons:
-# https://github.com/zarr-developers/numcodecs/issues/304
-RESTRICT="test"
-
-RDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-DEPEND="
- test? (
- ${RDEPEND}
- dev-python/entrypoints[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/numcodecs/numcodecs-0.9.1.ebuild b/dev-python/numcodecs/numcodecs-0.9.1.ebuild
deleted file mode 100644
index b2030d332..000000000
--- a/dev-python/numcodecs/numcodecs-0.9.1.ebuild
+++ /dev/null
@@ -1,35 +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="Data storage buffer compression and transformation codecs"
-HOMEPAGE="https://github.com/zarr-developers/numcodecs"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Fails to collect tests for yet unknown reasons:
-# https://github.com/zarr-developers/numcodecs/issues/304
-RESTRICT="test"
-
-RDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-DEPEND="
- test? (
- ${RDEPEND}
- dev-python/entrypoints[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/numpy/numpy-1.23.5.ebuild b/dev-python/numpy/numpy-1.23.5.ebuild
index 51be775b9..5a9224e54 100644
--- a/dev-python/numpy/numpy-1.23.5.ebuild
+++ b/dev-python/numpy/numpy-1.23.5.ebuild
@@ -3,12 +3,10 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+)"
-
FORTRAN_NEEDED=lapack
-
-inherit distutils-r1 flag-o-matic fortran-2 toolchain-funcs
+inherit distutils-r1 flag-o-matic fortran-2 pypi toolchain-funcs
DOC_PV=${PV}
# For when docs aren't ready yet, set to last version
@@ -19,8 +17,7 @@ HOMEPAGE="
https://github.com/numpy/numpy/
https://pypi.org/project/numpy/
"
-SRC_URI="
- mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz
+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
@@ -29,7 +26,7 @@ SRC_URI="
"
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"
+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="
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
index 78267d7a8..d4db5e2f3 100644
--- a/dev-python/nwbinspector/Manifest
+++ b/dev-python/nwbinspector/Manifest
@@ -1,3 +1,2 @@
-DIST nwbinspector-0.4.14.gh.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa
DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c
DIST nwbinspector-0.4.26.gh.tar.gz 575576 BLAKE2B 5ec888fc578dd0225b346426b93193f1a08cf92fa9c11e7653773c6bd74603c9e3456514209b3e2a12cf9d868f6004b64700c98212f3837b4b77096dff23ea72 SHA512 901df8422aa3b8666f01e9a6389c22f7caca30007494cb8680ee228bb58a9192f4f35a2426f38f068df5e938fe192db6db4d5626d00ca96e766114dd301efce3
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
deleted file mode 100644
index 5f5bc2045..000000000
--- a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# 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_10 )
-inherit distutils-r1
-
-DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
-SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND=""
-RDEPEND="
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/natsort[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
-"
-BDEPEND=""
-
-distutils_enable_tests pytest
-
-python_test() {
- local EPYTEST_IGNORE=(
- tests/test_inspector.py
- tests/unit_tests/test_time_series.py
- )
- epytest
-}
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
index a80527994..b4b5f7448 100644
--- a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild
index 46f158e0e..271dbfb1d 100644
--- a/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
diff --git a/dev-python/palettable/Manifest b/dev-python/palettable/Manifest
deleted file mode 100644
index 2fd3a2291..000000000
--- a/dev-python/palettable/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST palettable-3.3.0.tar.gz 105475 BLAKE2B bd3745e428b8273c1ce8ebca89cb99ba988fbf6bcfc11a387a946938dd8e573a8b9aadf3288b3a4c9a794add1c3b64f77519188a7025a1cb85de129e476429a4 SHA512 6689b009d3a7face36c0d3eaf2bee6a5e8f364f25f30e06924ec61d730c95921ef37cfc857a93b07a772a7b347e805ae8139f056478378a6c8669f853d5df810
diff --git a/dev-python/palettable/palettable-3.3.0.ebuild b/dev-python/palettable/palettable-3.3.0.ebuild
deleted file mode 100644
index 1288d9233..000000000
--- a/dev-python/palettable/palettable-3.3.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="library of color palettes for python"
-HOMEPAGE="https://github.com/jiffyclub/palettable"
-
-if [ ${PV} == "9999" ] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/jiffyclub/palettable.git"
-else
- SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/matplotlib[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_test() {
- distutils_install_for_testing
- pytest -vv || die "tests failed for ${EPYTHON}"
-}
diff --git a/dev-python/palettable/palettable-9999.ebuild b/dev-python/palettable/palettable-9999.ebuild
deleted file mode 100644
index 1288d9233..000000000
--- a/dev-python/palettable/palettable-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="library of color palettes for python"
-HOMEPAGE="https://github.com/jiffyclub/palettable"
-
-if [ ${PV} == "9999" ] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/jiffyclub/palettable.git"
-else
- SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-python/matplotlib[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_test() {
- distutils_install_for_testing
- pytest -vv || die "tests failed for ${EPYTHON}"
-}
diff --git a/dev-python/panel/Manifest b/dev-python/panel/Manifest
index 5bd9272be..459ed3f61 100644
--- a/dev-python/panel/Manifest
+++ b/dev-python/panel/Manifest
@@ -1,3 +1 @@
-DIST panel-0.11.0.tar.gz 9682808 BLAKE2B 2f953aaa9e791433d254219ad3cf9efdd486164e713f41a3539628a6c87f5b7b800ebd166537d021799ce74dddd3bc259343e6ec4161d0d87393864502215a00 SHA512 6fa2e04dd758583db851fa7d36592b7fb10ad2838b1f51fb53cb9ead4b5504a975ca040525f3f210ff0a67e8ce579195d980570b2d7616308cc126c61a9e9f59
-DIST panel-0.14.1.tar.gz 20052944 BLAKE2B 225c42562f7b5922380eca6f58da38ef228dbcb46ada930f7e0423fe2ce0d81d23d026b3f375a5bd46b521f6e49293f861cf92bc4d5044414818e0e1f787b0de SHA512 4d730a4555fffcb543b22900a17ad377eadb36a890ecc6cf873726da12c067d1cfeaf9626a0e4559b5c08e5646abb5c5cc0f28201341d9989f2c8fb345f8ecbd
DIST panel-0.14.2.tar.gz 20352366 BLAKE2B 429a2da7e92cc1b0f3a42fc120eddc4a8a54e3805c1ca249aad7c243cef0092959e62a13b0f9c64c4765a6d2533b6519a90640e85d4d512a257df40fff1a4522 SHA512 c611e4bc592edeca5920441102cf7baea336016b9f90778c05fc61c57a4b8b48c80e16c182daa1763440be10c6a0ffabb80699bf6aaa96e03566b4ac55b56f4b
diff --git a/dev-python/panel/panel-0.11.0.ebuild b/dev-python/panel/panel-0.11.0.ebuild
deleted file mode 100644
index 072c763ad..000000000
--- a/dev-python/panel/panel-0.11.0.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-# Panel imports from "distutils" at runtime.
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="High-level app and dashboarding solution for Python"
-HOMEPAGE="https://panel.holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that
-# away below. Our patched Panel thus requires Bokeh only at runtime.
-DEPEND="
- >=dev-python/param-1.10.0[${PYTHON_USEDEP}]
- >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}
- dev-python/markdown[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}]
- >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}]
- >=net-libs/nodejs-15.11.0
-"
-
-src_prepare() {
- # Install Jupyter configuration files to "/etc" rather than "/usr/etc".
- sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die
-
- # Prevent Panel from violating network sandboxing. By default, "setup.py"
- # invokes "npm" to rebuild Node.js packages bundled with Panel when these
- # packages were built by Panel developers with a different version of Bokeh
- # than that installed on the local system. Since disabling this
- # functionality invites backend and frontend complications, we encourage
- # server administrators to manually perform this functionality below.
- sed -i -e '/^\s*_build_paneljs()$/d' setup.py || die
-
- default_src_prepare
-}
-
-pkg_postinst() {
- panel_pkg_postinst() {
- PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')"
- elog "Node.js packages bundled with Panel under ${EPYTHON} may be"
- elog "desynchronized from Bokeh and require manual rebuilding with:"
- elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\""
- elog
- }
-
- python_foreach_impl panel_pkg_postinst
-}
diff --git a/dev-python/panel/panel-0.14.1.ebuild b/dev-python/panel/panel-0.14.1.ebuild
deleted file mode 100644
index aa535f46f..000000000
--- a/dev-python/panel/panel-0.14.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-# Panel imports from "distutils" at runtime.
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="High-level app and dashboarding solution for Python"
-HOMEPAGE="https://panel.holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that
-# away below. Our patched Panel thus requires Bokeh only at runtime.
-DEPEND="
- >=dev-python/param-1.10.0[${PYTHON_USEDEP}]
- >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}
- dev-python/markdown[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}]
- >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}]
- >=net-libs/nodejs-15.11.0
-"
-
-PATCHES=( "${FILESDIR}/${P}-disable_lite_build.patch" )
-
-src_prepare() {
- # Install Jupyter configuration files to "/etc" rather than "/usr/etc".
- sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die
-
- default_src_prepare
-}
-
-pkg_postinst() {
- panel_pkg_postinst() {
- PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')"
- elog "Node.js packages bundled with Panel under ${EPYTHON} may be"
- elog "desynchronized from Bokeh and require manual rebuilding with:"
- elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\""
- elog
- }
-
- python_foreach_impl panel_pkg_postinst
-}
diff --git a/dev-python/panel/panel-0.14.2.ebuild b/dev-python/panel/panel-0.14.2.ebuild
index 866110947..bf4df1861 100644
--- a/dev-python/panel/panel-0.14.2.ebuild
+++ b/dev-python/panel/panel-0.14.2.ebuild
@@ -4,15 +4,12 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..10} )
-
# Panel imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="High-level app and dashboarding solution for Python"
HOMEPAGE="https://panel.holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/persim/Manifest b/dev-python/persim/Manifest
index 44487ab15..b45fc4da3 100644
--- a/dev-python/persim/Manifest
+++ b/dev-python/persim/Manifest
@@ -1,4 +1 @@
-DIST persim-0.1.3.tar.gz 24345 BLAKE2B df407f22226797274e64766fac98733a7c006b7577bd21432bd109f17674192b1e520744e897b5baa207aef2f9bedaa6beab6412d550090c21072860c9a9f2d1 SHA512 4d177367213353eac3bd57b1450bace3ded25480b256f700d1d5daf7f8fc63204af3bdff45f71c85d8ac4a2d3f923fac00a568d43753b321c25ab98e77010349
-DIST persim-0.2.0.tar.gz 35005 BLAKE2B c3399ec13274e7fd105dccf5abdf85b973ec387196fd8659636173fa4e19bb6d8b9d8dba10d1382239d32d938a6f472b9201c7a54df7924802af3adc40d8aa8a SHA512 0bcfcc2fbf8d0449d680a8805281d01481513c060fa9ecc5f3d44ed70cda791d625bfe77fee954a186f77032f6447907f987c679a2c3bd7adc17a46eb753d083
-DIST persim-0.3.0.tar.gz 49716 BLAKE2B 8cea73e9486ecebfc5f73975341e6094d1c374d3c13b3b849988357ebec7d77ce4f59512388e7748b83c67fe32d3481dc1c9d7a74984d5faa7f8928bfcd282dd SHA512 575f21e8ae2cac7a609d8eb3691f1e7550139be2c0cbb63ff3dceefd923e42888b1ca40eef39c631e1351cdbe3c1c5a4371f4a61f0075588b13ced98ae2663a2
DIST persim-0.3.1.tar.gz 50438 BLAKE2B 774f0adc67ec6af7e297e73a75a3c4eb6004b0ec43d685eca29e20b0b6ef214fafed638e4c1c6eb10b5dad0b836883f3396c6ed323d4530d832c2e655f5353c2 SHA512 b35884d202a98449b719527987fdf07b88b42252d403f7f0b18a2507f63db496d49e389eca5019c540ebcdc99b63b07df73f43bc7780488a6e7e6958e0017b70
diff --git a/dev-python/persim/persim-0.1.3.ebuild b/dev-python/persim/persim-0.1.3.ebuild
deleted file mode 100644
index e8aad47df..000000000
--- a/dev-python/persim/persim-0.1.3.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
-
-PYTHON_COMPAT=( python3_{10..10} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Distances and representations of persistence diagrams"
-HOMEPAGE="https://persim.scikit-tda.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/hopcroftkarp[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/plotly[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/scikit-tda/persim/issues/64
- test/test_persim.py::test_integer_diagrams
- test/test_persim.py::TestEmpty::test_empyt_diagram_list
- test/test_persim.py::TestTransforms::test_lists_of_lists
- test/test_persim.py::TestTransforms::test_n_pixels
- test/test_persim.py::TestTransforms::test_multiple_diagrams
-)
diff --git a/dev-python/persim/persim-0.2.0.ebuild b/dev-python/persim/persim-0.2.0.ebuild
deleted file mode 100644
index 792839a0b..000000000
--- a/dev-python/persim/persim-0.2.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Distances and representations of persistence diagrams"
-HOMEPAGE="https://persim.scikit-tda.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/hopcroftkarp[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/plotly[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/scikit-tda/persim/issues/65
- test/test_persim.py::test_integer_diagrams
- test/test_persim.py::TestEmpty::test_empyt_diagram_list
- test/test_persim.py::TestTransforms::test_lists_of_lists
- test/test_persim.py::TestTransforms::test_n_pixels
- test/test_persim.py::TestTransforms::test_multiple_diagrams
- test/test_persistence_imager.py::test_empty_diagram_list
- test/test_persistence_imager.py::test_fit_diagram
- test/test_persistence_imager.py::test_fit_diagram_list
- test/test_persistence_imager.py::test_mixed_pairs
- test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists
- test/test_persistence_imager.py::TestTransformOutput::test_n_pixels
- test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams
-)
diff --git a/dev-python/persim/persim-0.3.0.ebuild b/dev-python/persim/persim-0.3.0.ebuild
deleted file mode 100644
index 91b9514ad..000000000
--- a/dev-python/persim/persim-0.3.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Distances and representations of persistence diagrams"
-HOMEPAGE="https://persim.scikit-tda.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/hopcroftkarp[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/plotly[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
-"
-BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/scikit-tda/persim/issues/66
- test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs
- test/test_persim.py::test_integer_diagrams
- test/test_persim.py::TestEmpty::test_empyt_diagram_list
- test/test_persim.py::TestTransforms::test_lists_of_lists
- test/test_persim.py::TestTransforms::test_n_pixels
- test/test_persim.py::TestTransforms::test_multiple_diagrams
- test/test_persistence_imager.py::test_empty_diagram_list
- test/test_persistence_imager.py::test_fit_diagram
- test/test_persistence_imager.py::test_fit_diagram_list
- test/test_persistence_imager.py::test_mixed_pairs
- test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists
- test/test_persistence_imager.py::TestTransformOutput::test_n_pixels
- test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams
-)
diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest
new file mode 100644
index 000000000..e50aa7618
--- /dev/null
+++ b/dev-python/plac/Manifest
@@ -0,0 +1 @@
+DIST plac-1.3.5.tar.gz 38074 BLAKE2B 8c770ea43d94a5fa80fa22f0e1fb6433e7901769315e0ecd9d6889d773e454b428265c3cd43792867dd56757cc6e31dcbda76052b46266878f07e493cf899c14 SHA512 9de705fbcc7585f9be8bb648ca3136cf0f031702e3def3ae069be6cff0e71969fe193e1420bd4018392f4a323cfe9131f86a10a2a2ecd0001fd1e82ad63a0d4a
diff --git a/dev-python/dnaio/metadata.xml b/dev-python/plac/metadata.xml
index e97c4322a..98f0f918b 100644
--- a/dev-python/dnaio/metadata.xml
+++ b/dev-python/plac/metadata.xml
@@ -1,12 +1,16 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
</maintainer>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ialbert/plac</remote-id>
+ <remote-id type="pypi">plac</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/plac/plac-1.3.5.ebuild b/dev-python/plac/plac-1.3.5.ebuild
new file mode 100644
index 000000000..dcc47aa3d
--- /dev/null
+++ b/dev-python/plac/plac-1.3.5.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# 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="Parsing the Command Line the Easy Way"
+HOMEPAGE="https://pypi.org/project/plac/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest
index 7d88bcad7..53fb37ba4 100644
--- a/dev-python/probeinterface/Manifest
+++ b/dev-python/probeinterface/Manifest
@@ -1,3 +1,2 @@
-DIST probeinterface-0.2.11.gh.tar.gz 194474 BLAKE2B 806d1d83a47fdd3a3196386d08ac5cee7f8561547be819fe814f67265e5b1e31e35107a047ed5c5ae533123b318ab6dca4b37ec8ddb6d30431644402b499b5d2 SHA512 a7e12fba55b952dea3b062dde37178b02259424ec82f788bb210a94cf7fb48d325045f2451c3e764b68563948fe81b60d1d378827a15ae5470931b120b2bc10d
DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84
diff --git a/dev-python/probeinterface/probeinterface-0.2.11.ebuild b/dev-python/probeinterface/probeinterface-0.2.11.ebuild
deleted file mode 100644
index 15579b701..000000000
--- a/dev-python/probeinterface/probeinterface-0.2.11.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 2021-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
-
-DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
-HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
-SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-BDEPEND="
- test? (
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- )
-"
-
-EPYTEST_DESELECT=(
- # Requires network access:
- # https://github.com/SpikeInterface/probeinterface/issues/70
- tests/test_library.py::test_download_probeinterface_file
- tests/test_library.py::test_get_from_cache
- tests/test_library.py::test_get_probe
- tests/test_wiring.py::test_wire_probe
-)
-distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
index d3827a5e9..75dd43bd4 100644
--- a/dev-python/probeinterface/probeinterface-0.2.14.ebuild
+++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
@@ -1,10 +1,10 @@
-# Copyright 2021-2022 Gentoo Authors
+# 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 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
diff --git a/dev-python/probeinterface/probeinterface-0.2.16.ebuild b/dev-python/probeinterface/probeinterface-0.2.16.ebuild
index d3827a5e9..75dd43bd4 100644
--- a/dev-python/probeinterface/probeinterface-0.2.16.ebuild
+++ b/dev-python/probeinterface/probeinterface-0.2.16.ebuild
@@ -1,10 +1,10 @@
-# Copyright 2021-2022 Gentoo Authors
+# 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 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
diff --git a/dev-python/pybind11-stubgen/Manifest b/dev-python/pybind11-stubgen/Manifest
index 783143fe7..7b5f755b5 100644
--- a/dev-python/pybind11-stubgen/Manifest
+++ b/dev-python/pybind11-stubgen/Manifest
@@ -1,3 +1 @@
DIST pybind11-stubgen-0.10.4.tar.gz 12605 BLAKE2B 5cb3e4301a896066ac26a7e6b9af83c77fb16fd5a3e48713a597e981a68e41cd90ddf0e351c177b7385966e8720100ef03b0524dfd381f17c87a2016a6eba808 SHA512 b43795c5fef6eee5198ec7590338f8a2dabbc4a2530de49f50a3b1a410da60188da86f7148a74ff014068c8d9ce5b058695902e236407ab221d640ac9b15903d
-DIST pybind11-stubgen-0.8.6.tar.gz 10993 BLAKE2B f3073dac1bff941cbf2470d50d11a090a99ff335a08cca3efc217d06c3a0cab266cf9769a1a7bdc5349da7cc3120e8a6b54f60df775ee27fcfbf0b5003867726 SHA512 6a8338f78d636b865bb76a3e769997f1c781acb57a0bb4f68f59ae2d6f3c60efe2b2ec7a9034f4e172b3d4bc4c74c990a4a24c6b2df242573fa7f03b97a84851
-DIST pybind11-stubgen-0.8.7.tar.gz 10993 BLAKE2B e672e955535bb7d797a3ee692f3fb13658d589bedc60c207dc094efff2e6281aec81636b0719a61567be46eb2fb27b7235e38cc06c436dea2689ae32b4b53b18 SHA512 56f3d84027d7cb06cce608ac7403a3fea902277d6e44fa3e284227656bca036ba956ef6b51a4f963a0b19e8fe30c0ddfac6670ea338905bf3ac39668748da668
diff --git a/dev-python/pybind11-stubgen/metadata.xml b/dev-python/pybind11-stubgen/metadata.xml
index 2f2c0b51c..ad7b36abc 100644
--- a/dev-python/pybind11-stubgen/metadata.xml
+++ b/dev-python/pybind11-stubgen/metadata.xml
@@ -9,4 +9,8 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">sizmailov/pybind11-stubgen</remote-id>
+ <remote-id type="pypi">pybind11-stubgen</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
index f983beb99..e1aaab3b6 100644
--- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
+++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
@@ -3,12 +3,12 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
+PYTHON_COMPAT=( python3_{10..11} )
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild
deleted file mode 100644
index 9451a6082..000000000
--- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
-
-DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
-HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- ${PYTHON_DEPS}
- dev-python/pybind11[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}"
-
-# no tests in package
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild
deleted file mode 100644
index 3f2b0f779..000000000
--- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
-
-DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
-HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- ${PYTHON_DEPS}
- dev-python/pybind11[${PYTHON_USEDEP}]
-"
-RDEPEND="${DEPEND}"
-
-# no tests in package
diff --git a/dev-python/pyct/pyct-0.4.8.ebuild b/dev-python/pyct/pyct-0.4.8.ebuild
index 6201e2cf2..d8ef9bfa2 100644
--- a/dev-python/pyct/pyct-0.4.8.ebuild
+++ b/dev-python/pyct/pyct-0.4.8.ebuild
@@ -4,15 +4,12 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} pypy3 )
-
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Python packaging Common Tasks"
HOMEPAGE="https://holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/pynndescent/metadata.xml b/dev-python/pynndescent/metadata.xml
index 2f2c0b51c..7930c1730 100644
--- a/dev-python/pynndescent/metadata.xml
+++ b/dev-python/pynndescent/metadata.xml
@@ -9,4 +9,8 @@
<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
index 241b0b746..770630cac 100644
--- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild
+++ b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
@@ -5,11 +5,10 @@ EAPI=8
PYTHON_COMPAT=( python3_10 )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/pynrrd/Manifest b/dev-python/pynrrd/Manifest
index 72f9e8c2a..e174359e3 100644
--- a/dev-python/pynrrd/Manifest
+++ b/dev-python/pynrrd/Manifest
@@ -1,2 +1,3 @@
DIST pynrrd-0.4.2.tar.gz 43129 BLAKE2B 2001d151e38bbd02a648759475af13dd1be4bb7c12b7f8a3c7294e7fe1c281aeb9b35e39cce8254088b1c2f766aabe7343be0da4d48208375bb21be6dce9ba61 SHA512 8c5e4c1cb89dc84be3cf06e40d3f5bd45ea355c4e103027a62b088c4a73b03d1032cea1de0b153ef13fefd9b06d5a9b1954456a4542ae27cb74a278835b759ca
DIST pynrrd-0.4.3.tar.gz 43162 BLAKE2B 266c57029e48e923dd5371184f59471e069890668ac15a75cfafc178cfe1a718f33bc6bcc704172e0fca0bdc9c52091da79e404b6bfb85838eef0c3e0807409c SHA512 d6264fce3b270e5ae9d889e7d58a18ae7bf3fecf5a1fe168dc584dece2052efd32170b21a02fa630c35e0e45e7109c745069710169ec38819639a4585344e0f6
+DIST pynrrd-1.0.0.tar.gz 45061 BLAKE2B c08bcd70c3565cd690b228793651e57e08d2095a72b7f7102e6274f1518873acb1ee5645302fbb68b7cf1afafe3c5c734a33e561eea1caaacb5434c049dcc325 SHA512 c622812a4e000e6a4b5d82db2eac02822968c38bb9b8ab5d35cfa498a636bf221078d8722f8ac2cdd91b0430f0b5b6768fb33a63112c3045038f6d44d121e7b5
diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
index f25908cb3..2993f8f3a 100644
--- a/dev-python/pynrrd/pynrrd-0.4.2.ebuild
+++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# 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
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
index f25908cb3..2993f8f3a 100644
--- a/dev-python/pynrrd/pynrrd-0.4.3.ebuild
+++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# 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
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
diff --git a/dev-python/pynrrd/pynrrd-1.0.0.ebuild b/dev-python/pynrrd/pynrrd-1.0.0.ebuild
new file mode 100644
index 000000000..d46aba486
--- /dev/null
+++ b/dev-python/pynrrd/pynrrd-1.0.0.ebuild
@@ -0,0 +1,30 @@
+# 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="Simple pure-python module for reading and writing nrrd files"
+HOMEPAGE="https://github.com/mhe/pynrrd"
+SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/nptyping[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="test? ( ${RDEPEND} )"
+
+distutils_enable_tests unittest
+
+python_test() {
+ ${EPYTHON} -m unittest discover -v nrrd/tests || \
+ die "unittests failed for ${EPYTHON}"
+}
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index 808263ac7..d80f44e8e 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,3 +1,3 @@
-DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025
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
diff --git a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
deleted file mode 100644
index bf496b900..000000000
--- a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.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/pynwb-2.1.0-r2.ebuild b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
deleted file mode 100644
index e95649217..000000000
--- a/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
+++ /dev/null
@@ -1,43 +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="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=sci-libs/hdf5-1.12.2
- >=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}/${P}-versions.patch"
- )
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
index 52fab7a63..5a286c3b6 100644
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
@@ -5,11 +5,10 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
index 585dcc37d..382bfdb60 100644
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
@@ -9,7 +9,6 @@ inherit distutils-r1 pypi
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="$(pypi_sdist_url pynwb)"
SLOT="0"
LICENSE="BSD"
diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild b/dev-python/pynwb/pynwb-2.3.2.ebuild
index cce90c5d1..6599fbf8f 100644
--- a/dev-python/pynwb/pynwb-2.3.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.3.2.ebuild
@@ -9,7 +9,6 @@ inherit distutils-r1 pypi
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="$(pypi_sdist_url pynwb)"
SLOT="0"
LICENSE="BSD"
@@ -25,11 +24,6 @@ RDEPEND="
"
BDEPEND=""
-# Remove in next release
-PATCHES=(
- "${FILESDIR}/${P}-typing.patch"
- )
-
EPYTEST_DESELECT=(
# Reported upsream:
# https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest
index 47318a5ee..fa08cd21b 100644
--- a/dev-python/pytest-doctestplus/Manifest
+++ b/dev-python/pytest-doctestplus/Manifest
@@ -1,2 +1 @@
-DIST pytest-doctestplus-0.11.2.tar.gz 34943 BLAKE2B a45779ff3d65e1b920282f400d67b618f620a9a905da69edff96db799f30e1b93562e69bd567a49629194b962a080b1f675619b0c6995227a1391c3d0e74be20 SHA512 fed49a551be78f51db60161ccfa592e461719cca76e2a48e3267e8a22dbec60d02d8fbb757a88cb5cf4dc22143e27d3d20f25b51855be835254c72fd8260abbd
DIST pytest-doctestplus-0.12.1.tar.gz 36434 BLAKE2B 95baa9f6185423fdd3e61ec0c269de54a4cf3298f2db90087b1413608663e4200e48158240cf565c8cc267244fbf8d60a0a5241b3b8f1fa8c1187e34824b17ae SHA512 46b999abd5632fa5c5743900b8b78ee7b6be742959daeb85296ebdf820d7533cff0a78d1c8aed7f5d5a15436998b2f7fe3e571133be14fce056276900493fef9
diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
deleted file mode 100644
index c9149842e..000000000
--- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Pytest plugin with advanced doctest features"
-HOMEPAGE="https://astropy.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# TODO: fix this
-# AttributeError: type object 'reprec' has no attribute 'assertoutcome'
-RESTRICT="test"
-
-RDEPEND="dev-python/pytest[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest
index a0620dd02..335664088 100644
--- a/dev-python/python-igraph/Manifest
+++ b/dev-python/python-igraph/Manifest
@@ -1 +1 @@
-DIST python-igraph-0.10.4.tar.gz 4209850 BLAKE2B 2f3b75569ea93d08b50c4af7331a1e072d1ded66a6437d52ca054ee2603f60cbbec9371107d8c6eeda5a8215b0fa5ee6eac420dbda9247ab2246d70b01d25aa5 SHA512 675388c3a9a346534c66ec96f4a427b34e88e15a1d401af4f283ee7f1f17fad85bd1636a85af58b6d1969238b40e0314d7b6db4b84723e0eb1f3afbc660f0300
+DIST igraph-0.10.4.tar.gz 4209850 BLAKE2B 2f3b75569ea93d08b50c4af7331a1e072d1ded66a6437d52ca054ee2603f60cbbec9371107d8c6eeda5a8215b0fa5ee6eac420dbda9247ab2246d70b01d25aa5 SHA512 675388c3a9a346534c66ec96f4a427b34e88e15a1d401af4f283ee7f1f17fad85bd1636a85af58b6d1969238b40e0314d7b6db4b84723e0eb1f3afbc660f0300
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 f0096ae23..5ef24cedf 100644
--- a/dev-python/python-igraph/python-igraph-0.10.4.ebuild
+++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
@@ -5,12 +5,11 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Python interface for igraph"
HOMEPAGE="https://igraph.org"
-SRC_URI="mirror://pypi/i/igraph/igraph-${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="$(pypi_sdist_url igraph)"
S="${WORKDIR}/igraph-${PV}"
LICENSE="MIT"
diff --git a/dev-python/python-vxi11/Manifest b/dev-python/python-vxi11/Manifest
deleted file mode 100644
index 1f4c7aece..000000000
--- a/dev-python/python-vxi11/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST python-vxi11-0.9.tar.gz 21446 BLAKE2B 33d5af56aabf6583f630f4b8d7e31fc8fb962ef8c6952cf1894a69a304cd2f2f0c3d1bc2c17000a5b029c977c8a7c782657c9d9fab7ced484e41514ab77432f5 SHA512 d3136ca8d6cdd7bc695d52ab2adbad956936de6ab99b4be58f3b11111b1f0afc8720239ef6754da79f1c719bbd2ccec1c8a58249a4408b8536b7fd387c0164d0
diff --git a/dev-python/python-vxi11/metadata.xml b/dev-python/python-vxi11/metadata.xml
deleted file mode 100644
index 80031f312..000000000
--- a/dev-python/python-vxi11/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>marbre@linux.sungazer.de</email>
- <name>Marius Brehler</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
-Python VXI-11 is a Python implementation of the VXI-11 Ethernet
-instrument control protocol. It is compatible with VXI-11,
-LXI instruments and VXI-11 to GPIB bridges (HP E2050A, etc.).
-</longdescription>
- <upstream>
- <remote-id type="github">python-ivi/python-vxi11</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/python-vxi11/python-vxi11-0.9.ebuild b/dev-python/python-vxi11/python-vxi11-0.9.ebuild
deleted file mode 100644
index fe2292148..000000000
--- a/dev-python/python-vxi11/python-vxi11-0.9.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
-
-DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet"
-HOMEPAGE="https://github.com/python-ivi/python-vxi11"
-
-if [[ ${PV} == 9999 ]] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/python-ivi/python-vxi11"
-else
- SRC_URI="https://github.com/python-ivi/python-vxi11/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
diff --git a/dev-python/python-vxi11/python-vxi11-9999.ebuild b/dev-python/python-vxi11/python-vxi11-9999.ebuild
deleted file mode 100644
index fe2292148..000000000
--- a/dev-python/python-vxi11/python-vxi11-9999.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
-
-DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet"
-HOMEPAGE="https://github.com/python-ivi/python-vxi11"
-
-if [[ ${PV} == 9999 ]] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/python-ivi/python-vxi11"
-else
- SRC_URI="https://github.com/python-ivi/python-vxi11/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
index c50848555..a775be3bf 100644
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
+++ b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
@@ -6,11 +6,11 @@ EAPI=8
PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517=setuptools
DISTUTILS_SINGLE_IMPL=1
-inherit distutils-r1
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
HOMEPAGE="https://github.com/Lightning-AI/lightning"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
diff --git a/dev-python/pyvista/pyvista-0.33.2.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild
index ed4a21a4e..d59653fae 100644
--- a/dev-python/pyvista/pyvista-0.33.2.ebuild
+++ b/dev-python/pyvista/pyvista-0.33.2.ebuild
@@ -5,12 +5,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..10} )
DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1"
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Easier Pythonic interface to VTK"
HOMEPAGE="https://docs.pyvista.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
KEYWORDS="~amd64 ~x86"
diff --git a/dev-python/pyviz_comms/Manifest b/dev-python/pyviz_comms/Manifest
index 9f4d81ce1..0d6a5ac51 100644
--- a/dev-python/pyviz_comms/Manifest
+++ b/dev-python/pyviz_comms/Manifest
@@ -1,2 +1 @@
-DIST pyviz_comms-2.0.1.tar.gz 125046 BLAKE2B d0913fb873396ddb11db2781cb65cd4b2a9dd22ce496af58a656a2c17c4d0ca1af1351a618b293c5eca964dc7f32840c577a831139a0e5e9cd7667886c97aa2c SHA512 da913ee537588cd7e643c034f14b141e28699ddddb1dcd89053b3b9482bc330582f381e4257cd07546049da67f20b1f25cf9ffb4d11c9ef457bd4915781a751c
DIST pyviz_comms-2.2.0.tar.gz 31910 BLAKE2B 42175d8750e9cb8dea4888970028898a9ee1e34b2ca5c895d2a1db40d9eec2f7eb86aec41090431b723ffcfdd0411016c04015e286d467a4c9d89eb710e7e08c SHA512 de6dba5b5d93a9a496b6895f4bf884dd80afd4124e1519bbd243b7672827f04f51d353f3941678be3780a250640e03b0c4ea0a3f87b8b9892980845bdca07439
diff --git a/dev-python/pyviz_comms/metadata.xml b/dev-python/pyviz_comms/metadata.xml
index 8127bb8b0..3a0ec5dc8 100644
--- a/dev-python/pyviz_comms/metadata.xml
+++ b/dev-python/pyviz_comms/metadata.xml
@@ -7,7 +7,7 @@
</maintainer>
<stabilize-allarches/>
<upstream>
- <remote-id type="pypi">pyviz_comms</remote-id>
+ <remote-id type="pypi">pyviz-comms</remote-id>
<remote-id type="github">holoviz/pyviz_comms</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild
deleted file mode 100644
index 8526bd511..000000000
--- a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="Bidirectional communication for the HoloViz ecosystem"
-HOMEPAGE="https://holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/param[${PYTHON_USEDEP}]"
-
-# Tarballs do not include tests, reported upstream:
-# https://github.com/holoviz/pyviz_comms/issues/104
-#distutils_enable_tests pytest
diff --git a/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
index 8526bd511..7f50fc279 100644
--- a/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
+++ b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Bidirectional communication for the HoloViz ecosystem"
HOMEPAGE="https://holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/reproject/metadata.xml b/dev-python/reproject/metadata.xml
index 4f4367037..56a54a20b 100644
--- a/dev-python/reproject/metadata.xml
+++ b/dev-python/reproject/metadata.xml
@@ -5,4 +5,7 @@
<email>sci-astronomy@gentoo.org</email>
<name>Gentoo Astronomy Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">reproject</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild
index 62ad23af9..cf57e7d73 100644
--- a/dev-python/reproject/reproject-0.8.ebuild
+++ b/dev-python/reproject/reproject-0.8.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Reproject astronomical images"
HOMEPAGE="https://reproject.readthedocs.io/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/repsep_utils/Manifest b/dev-python/repsep_utils/Manifest
index 489a3a719..1c65b16d9 100644
--- a/dev-python/repsep_utils/Manifest
+++ b/dev-python/repsep_utils/Manifest
@@ -1 +1,3 @@
DIST repsep_utils-0.2.tar.gz 11147 BLAKE2B 89726b7e163c954ae9826a32c6997f4c678e6586240db52b37355ca59c16743b8c19e89d12d175cb55435aced5498a22e9e825d0c2d95f9046a52ac6daadefb3 SHA512 ba499cecb3dac38c1ca8e91eee3e1f9edafbc906e8acc046cd1eaead8253a9ac61f489ffca23cdb4ac6a595ecef40cc6a3374b3618c8162a4f38f499c1a4cc4e
+DIST repsep_utils-0.3.1.tar.gz 12021 BLAKE2B cfe6e0dbeaddf751a1f222a19e7c430b4c3acd4ea28061164ecc213cadccb7bcb42e9b1fe16bf73f93d735edba3887553ac49b04f763ec888177ab653d05b07b SHA512 a5897a6b2a778d8079f9d5947b22def7c42922d0c607e711f2c2957b569991098f1ed3ce53ff2f74183cb4466b87f87596aafec9f2e4c1efb38c317ef29df8da
+DIST repsep_utils-0.3.tar.gz 11893 BLAKE2B b02ec74d55bbfbe15052573049660a39c87681862ff3d38a7560666191b9b2cec6ea230898349c8feef4d5654e1524b16fa90c13b1238ea1d5d51ae6eaffa283 SHA512 9df1fb77d09d18387625e7cceed9aa31faf35fd72d076425cbabc30c7020e6f8257161628940f131f6209ac2aab6336c07ffb3aa333c2ec48e2a3c47708cc2b4
diff --git a/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild
new file mode 100644
index 000000000..975d97f9d
--- /dev/null
+++ b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Utilities Supporting RepSeP-style documents"
+HOMEPAGE="https://github.com/TheChymera/repsep_utils"
+SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-tex/pythontex"
+
+src_install() {
+ dobin "bin/repsep"
+
+ insinto "/usr/share/repsep"
+ doins repsep/*
+}
diff --git a/dev-python/repsep_utils/repsep_utils-0.3.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.ebuild
new file mode 100644
index 000000000..975d97f9d
--- /dev/null
+++ b/dev-python/repsep_utils/repsep_utils-0.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Utilities Supporting RepSeP-style documents"
+HOMEPAGE="https://github.com/TheChymera/repsep_utils"
+SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-tex/pythontex"
+
+src_install() {
+ dobin "bin/repsep"
+
+ insinto "/usr/share/repsep"
+ doins repsep/*
+}
diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild
index d8c8b0c2a..faa082e58 100644
--- a/dev-python/schema/schema-0.7.4.ebuild
+++ b/dev-python/schema/schema-0.7.4.ebuild
@@ -4,12 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_10 pypy3 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Schema validation just got Pythonic"
-HOMEPAGE="https://pypi.org/project/schema"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+HOMEPAGE="https://pypi.org/project/schema/"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild
index b876c3425..4cd053b50 100644
--- a/dev-python/scooby/scooby-0.5.7.ebuild
+++ b/dev-python/scooby/scooby-0.5.7.ebuild
@@ -4,12 +4,10 @@
EAPI=7
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Easily report Python package versions and hardware resources"
-HOMEPAGE="https://pypi.org/project/scooby"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+HOMEPAGE="https://pypi.org/project/scooby/"
LICENSE="MIT"
KEYWORDS="~amd64 ~x86"
diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest
index fbef82cf7..9beeb00c6 100644
--- a/dev-python/snakemake/Manifest
+++ b/dev-python/snakemake/Manifest
@@ -1 +1 @@
-DIST snakemake-7.24.2.gh.tar.gz 8849295 BLAKE2B 3ea9149ef8dbba080063cd2038ec75c42332ec3024f4ddeca0e3b2feb73d536f96484622fd9f45c51682c329cf575f3745048529e62b56f14afbea9e97b80ebe SHA512 f12e8c864a55940adbba04f3f88522e1a46739d73e77baf9b9b462cd1256336733d0591b8bc7d331231d30852ea29f2ac305745774cee78c1b6e46c4699b08a8
+DIST snakemake-7.32.3.gh.tar.gz 8886818 BLAKE2B d407e8bf65bacb5a1d3decaa54caee602f6588239c6c42062897bfaee3a13d6afd6d4afcab85a3b1de0994e2d46fcd4851e9dfd500b164a5c05a73aeba38f92a SHA512 675d1206bda44309f38b4cde441584f4c6243c1c63fb3ab07a781e3538c604e66ef013f75a27dd3b11f620611cf583e4e2fca5531a5492cef5cbd85f44f0b77e
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index d9550c50f..74c76cce1 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/metadata.xml
@@ -5,8 +5,11 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
<upstream>
- <remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
<remote-id type="pypi">snakemake</remote-id>
<remote-id type="github">snakemake/snakemake</remote-id>
</upstream>
diff --git a/dev-python/snakemake/snakemake-7.24.2.ebuild b/dev-python/snakemake/snakemake-7.32.3.ebuild
index fb9895514..94dd9e925 100644
--- a/dev-python/snakemake/snakemake-7.24.2.ebuild
+++ b/dev-python/snakemake/snakemake-7.32.3.ebuild
@@ -52,6 +52,7 @@ RDEPEND="
dev-python/throttler[${PYTHON_USEDEP}]
dev-python/toposort[${PYTHON_USEDEP}]
dev-python/wrapt[${PYTHON_USEDEP}]
+ dev-python/yte[${PYTHON_USEDEP}]
sci-mathematics/pulp[${PYTHON_USEDEP}]
"
diff --git a/dev-python/sphinx-argparse/Manifest b/dev-python/sphinx-argparse/Manifest
deleted file mode 100644
index db92db585..000000000
--- a/dev-python/sphinx-argparse/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sphinx-argparse-0.3.2.tar.gz 45841 BLAKE2B 7f8a7159974bca803705736c848973d605594732983462d7636d82125e195d8ab87b76c247c9081e626cfe17d0f8d12a66d79076c643b0fe780c4f3eb5bbdc23 SHA512 fcc179d85ac9d30e327f75b02086c8f831856b099d9a26bc10adc4f20b57781a117a5dac2d6882e1f7c07604157dda2c2344c29ae3c475022ce252cde96646bb
diff --git a/dev-python/sphinx-argparse/metadata.xml b/dev-python/sphinx-argparse/metadata.xml
deleted file mode 100644
index 3b119bca0..000000000
--- a/dev-python/sphinx-argparse/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">ashb/sphinx-argparse</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
deleted file mode 100644
index 2660d4912..000000000
--- a/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 2020-2022 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
-
-DESCRIPTION="Sphinx extension that automatically documents argparse commands and options"
-HOMEPAGE="
- https://pypi.org/project/sphinx-argparse/
- https://github.com/ashb/sphinx-argparse
-"
-SRC_URI="https://github.com/ashb/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/sphinx[${PYTHON_USEDEP}]
- dev-python/commonmark[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest
index 1084d6cfa..7cbf6d7c8 100644
--- a/dev-python/sphinx-astropy/Manifest
+++ b/dev-python/sphinx-astropy/Manifest
@@ -1,2 +1 @@
-DIST sphinx-astropy-1.7.0.tar.gz 18266 BLAKE2B 363733c5a3e5974cdf0f62f879babc9a28617ff61d15292649acd189798e24611c2d84e69af5dc05b89241f395cc997233f966bdf8e8a84ccfe235f873d533c2 SHA512 4b9af1528805c5017695be6ad9d0b789437da4ea01080190d5c0e44a76d927098864002cfd2a59529924a8d2844e26d2e7635fb3f0417ed90502e7e47d0239d3
DIST sphinx-astropy-1.8.0.tar.gz 18310 BLAKE2B 0d13ba59b2ffcb792e66e58d2a87057b79da811d38e6fd101b074b0edbf5ad6d76e79300f5863521b0bbb1b40921ba6773f8d37c32d68dd36078cb2d0497e2ff SHA512 f02fe8d3ed58ffeff190492c07e2df91a2bd5bcc8e82c6685002e543585a5fc1294ebd46821b7dc0a364540f3a45adacf1b90261b7da95657bc99dcd6130f4d5
diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
deleted file mode 100644
index cf6e3a5c5..000000000
--- a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Sphinx extensions and configuration specific to the Astropy project"
-HOMEPAGE="https://astropy.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# Requires access to the internet
-RESTRICT="test"
-
-RDEPEND="
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}]
- dev-python/numpydoc[${PYTHON_USEDEP}]
- >=dev-python/sphinx-1.7[${PYTHON_USEDEP}]
- dev-python/sphinx-automodapi[${PYTHON_USEDEP}]
- dev-python/sphinx-gallery[${PYTHON_USEDEP}]
- dev-python/pillow[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
index 6dae8d191..ef6a472f4 100644
--- a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
+++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
index 5c4e65481..2a25d4eee 100644
--- a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
+++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/traits/Manifest b/dev-python/traits/Manifest
index 8e8de91b3..c33b93d1f 100644
--- a/dev-python/traits/Manifest
+++ b/dev-python/traits/Manifest
@@ -1,3 +1,2 @@
-DIST traits-6.1.1.tar.gz 567019 BLAKE2B 4b6ed46c87b1fda2a2001299106b5aacafbe8b148ba0564c4f39b67a8de76f6713366c8b00841db254a26c87a7b2b73b6935ecade770d92ad972aa8a0425cecf SHA512 7f7e9f11d4861c02164ae1ce595888859c8ce23213290cfc3ac11df100d33beeeea4c7def6799b70ef2d090b3f7bd98407f3605affff0867914d0fe0164dd50f
DIST traits-6.3.2.tar.gz 9517139 BLAKE2B 9c6209a24fd07def86699174a66e2e0b3332670d974a75ead9486187c37e1c2c25b2a0c47e5444a03577931411ce6938b3b9ba195261a46c86d660c5abe9b502 SHA512 792004d88d2a00a1e9ba03974d58ec692b620f3c45aaf3bd82f93396818df8663a86903d43806c877230a66c5c8fee4d68268ed9355c166af00b5d060ba14c7d
DIST traits-6.4.1.tar.gz 9527016 BLAKE2B 12036eeb845cc3014b0cba9984e1c1686a6720630678d440a2059c47916c08284b1f823ca566dcb6c1c86594ebec5400bb2a8c44d43d765a25d00e157fbbda74 SHA512 04b936195d57320c02fee9f0d5e7dbcfee28add422c151bd4aaa6d1c58c59f8de7fe54b4df039bb2023ffc9dae9570bba52210cd015ce462e0f736e9439327e5
diff --git a/dev-python/traits/metadata.xml b/dev-python/traits/metadata.xml
index ec9460dd1..2e84467ab 100644
--- a/dev-python/traits/metadata.xml
+++ b/dev-python/traits/metadata.xml
@@ -21,6 +21,7 @@
* Visualization: With the TraitsUI package, GUIs can be generated automatically from traited objects.
</longdescription>
<upstream>
+ <remote-id type="github">enthought/traits</remote-id>
<remote-id type="pypi">traits</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild
deleted file mode 100644
index 7282ebfa8..000000000
--- a/dev-python/traits/traits-6.1.1.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
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
-HOMEPAGE="https://docs.enthought.com/traits/
- https://github.com/enthought/traits
- https://pypi.org/project/traits/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-# Reported upstream: https://github.com/enthought/traits/issues/1731
-RESTRICT="test"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-distutils_enable_tests unittest
-# ToDo: Fix doc building:
-# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
-#distutils_enable_sphinx docs/source --no-autodoc
-
-python_prepare_all() {
- sed -i -e "s/'-O3'//g" setup.py || die
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- cd "${BUILD_DIR}"/lib || die
- ${EPYTHON} -m unittest discover || die
-}
diff --git a/dev-python/traits/traits-6.3.2.ebuild b/dev-python/traits/traits-6.3.2.ebuild
index 3d81493f5..4d3c699a5 100644
--- a/dev-python/traits/traits-6.3.2.ebuild
+++ b/dev-python/traits/traits-6.3.2.ebuild
@@ -5,14 +5,13 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
HOMEPAGE="
https://docs.enthought.com/traits/
https://github.com/enthought/traits
"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/traits/traits-6.4.1.ebuild b/dev-python/traits/traits-6.4.1.ebuild
index 3d81493f5..ebd3fb97a 100644
--- a/dev-python/traits/traits-6.4.1.ebuild
+++ b/dev-python/traits/traits-6.4.1.ebuild
@@ -3,16 +3,16 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
HOMEPAGE="
https://docs.enthought.com/traits/
https://github.com/enthought/traits
"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-distutils_enable_tests unittest
+distutils_enable_tests pytest
# ToDo: Fix doc building:
# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
#distutils_enable_sphinx docs/source --no-autodoc
@@ -31,6 +31,6 @@ python_prepare_all() {
}
python_test() {
- cd "${BUILD_DIR}"/lib || die
- ${EPYTHON} -m unittest discover || die
+ cd "${T}" || die
+ epytest --pyargs traits
}
diff --git a/dev-python/tridesclous/tridesclous-1.6.4.ebuild b/dev-python/tridesclous/tridesclous-1.6.4.ebuild
index a65c30298..131156160 100644
--- a/dev-python/tridesclous/tridesclous-1.6.4.ebuild
+++ b/dev-python/tridesclous/tridesclous-1.6.4.ebuild
@@ -3,13 +3,12 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="offline/online spike sorting"
HOMEPAGE="https://github.com/tridesclous/tridesclous"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/tridesclous/tridesclous-1.6.6.ebuild b/dev-python/tridesclous/tridesclous-1.6.6.ebuild
index 13697e657..fb401397f 100644
--- a/dev-python/tridesclous/tridesclous-1.6.6.ebuild
+++ b/dev-python/tridesclous/tridesclous-1.6.6.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/ufl/Manifest b/dev-python/ufl/Manifest
deleted file mode 100644
index 636d9ef3e..000000000
--- a/dev-python/ufl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ufl-2019.1.0.tar.gz 308107 BLAKE2B b89ac7bc5614d5fc61f3d5a91bdd64c8ef0b8589500e2ca4c0cc33a3488f17630ce006a9908ac53606cfa5867781943a247791ae043c8e15c040de1eabd20199 SHA512 2e79c5c05ddea1edc2aca55eafb5fcb246f24a31d9f7312dca19cfa284f7c039b1cb3d5450bbd628eed29b0881f3f3abdc9be106fd33f86a73720eaba5bea3d5
diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml
deleted file mode 100644
index 3dff10f36..000000000
--- a/dev-python/ufl/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The Unified Form Language (UFL) is a domain specific language for
-declaration of finite element discretizations of variational forms. More
-precisely, it defines a flexible interface for choosing finite element
-spaces and defining expressions for weak forms in a notation close to
-mathematical notation.
-</longdescription>
- <upstream>
- <remote-id type="bitbucket">fenics-project/ufl</remote-id>
- <remote-id type="github">FEniCS/ufl</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/ufl/ufl-2019.1.0.ebuild b/dev-python/ufl/ufl-2019.1.0.ebuild
deleted file mode 100644
index ef75774a2..000000000
--- a/dev-python/ufl/ufl-2019.1.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Unified Form Language for declaration of for FE discretizations"
-HOMEPAGE="https://github.com/FEniCS/ufl"
-SRC_URI="https://github.com/FEniCS/ufl/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
-
-python_test() {
- distutils_install_for_testing
- pytest -vv || die "pytest failed for ${EPYTHON}"
-}
-
-pkg_postinst() {
- optfeature "Support for evaluating Bessel functions" dev-python/scipy
-}
diff --git a/dev-python/umap-learn/metadata.xml b/dev-python/umap-learn/metadata.xml
index 2f2c0b51c..36f603448 100644
--- a/dev-python/umap-learn/metadata.xml
+++ b/dev-python/umap-learn/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">umap-learn</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
index 45b45b7f1..ea2769294 100644
--- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild
+++ b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
@@ -4,12 +4,11 @@
EAPI=8
PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
DESCRIPTION="Uniform Manifold Approximation and Projection"
HOMEPAGE="https://umap-learn.readthedocs.io/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/unyt/Manifest b/dev-python/unyt/Manifest
deleted file mode 100644
index 8120c74f7..000000000
--- a/dev-python/unyt/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST old_json_registry.txt 12950 BLAKE2B 54197911cbb4c3167ffe88673db87cc7dec96a55dd762162293eb0616996ec1324d91e6b4bbba4f77be227e63bf52013bcab155ca49a75e14844ae52d82337b7 SHA512 9fe6d46e24257542646e40e7364b93d52f21b6a449532cfaf4a7e913d47b76ac6c5b0579db4bc9449de816e127db90b6d330cb7620376846236829c4bc2f2346
-DIST unyt-2.7.2.tar.gz 584585 BLAKE2B 1ff1083709195510d915979c07e1aa0e0605897d41d8b3eb9497dfa21e86ba6cebc623d6cb42dba85580a416f0ad1c4c4a2be20fd492fc421e19a42c61f8c66a SHA512 73c8585b847baba927357e093336936c2505da28665dc06b79d29eb667604ef195d2c9a68aa851c0231a08f440dc7a711c4ea19ea334675dd78c11e7441aff72
-DIST unyt-2.8.0.tar.gz 324621 BLAKE2B b950ac0ca37795212edcf0a93a418c3287d5019fd9a6509bde50a62795433bcb828595508ffdc0f615b6e1e2426e7cfebf8cd3c65068e9754f79d58783ae7e7e SHA512 b3279023044d54b83833e2503876da67c6a8ce25fe1d3359e045cb9f5f8e5389bb3e1f5e1564479ebef3191c451614c3bd28b9f79ade89d3f9c00dceb04b021c
diff --git a/dev-python/unyt/metadata.xml b/dev-python/unyt/metadata.xml
deleted file mode 100644
index 2f2c0b51c..000000000
--- a/dev-python/unyt/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/unyt/unyt-2.7.2.ebuild b/dev-python/unyt/unyt-2.7.2.ebuild
deleted file mode 100644
index 893f0c03f..000000000
--- a/dev-python/unyt/unyt-2.7.2.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="package for handling numpy arrays with units"
-HOMEPAGE="https://github.com/yt-project/unyt"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz
- https://raw.githubusercontent.com/yt-project/unyt/v${PV}/unyt/tests/data/old_json_registry.txt
-"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
- mkdir -p "${S}"/unyt/tests/data || die
- mv "${DISTDIR}"/old_json_registry.txt "${S}"/unyt/tests/data/
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/unyt/unyt-2.8.0.ebuild b/dev-python/unyt/unyt-2.8.0.ebuild
deleted file mode 100644
index 893f0c03f..000000000
--- a/dev-python/unyt/unyt-2.8.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="package for handling numpy arrays with units"
-HOMEPAGE="https://github.com/yt-project/unyt"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz
- https://raw.githubusercontent.com/yt-project/unyt/v${PV}/unyt/tests/data/old_json_registry.txt
-"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
- mkdir -p "${S}"/unyt/tests/data || die
- mv "${DISTDIR}"/old_json_registry.txt "${S}"/unyt/tests/data/
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/visvis/Manifest b/dev-python/visvis/Manifest
index 5b433e036..2caf8e4e4 100644
--- a/dev-python/visvis/Manifest
+++ b/dev-python/visvis/Manifest
@@ -1,2 +1 @@
-DIST visvis-1.13.0.tar.gz 5095145 BLAKE2B 4c47002902d7ee15f4ccc684b53daec09657422d9e53438a0e91d11ea17b76fd8e413b6caab8fee63752116247b526454bc7830751db1d3bb6d12adab914cc1a SHA512 a2272250060e418c7b78acb51599bf5d440d6d20ffe41d5fbfb3b68f6486b6d9312300dfa94697ff23bdadb2e79a871dc75bf0ba53be3267107d392236693d6a
DIST visvis-1.14.0.tar.gz 4892032 BLAKE2B 564e328d4265676bec35798149ff1283b7289fe04e946ca78b6068ae6f70d1dff809a4ec19b94b1d49a9c3ac7f0b186996070736d3eb4ba4897feac7d03edb6a SHA512 d056ec8a83ac9cee4cbb05806145287fa9dab8064fbc910463255d4510f082ca29f393c309c7b649c6d625f1c368bf5ef28f44de1ebb30ccd1d5650fadb76a81
diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild
deleted file mode 100644
index 68d53d30e..000000000
--- a/dev-python/visvis/visvis-1.13.0.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_SETUPTOOLS=no
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="An object oriented approach to visualization of 1D to 4D data"
-HOMEPAGE="https://github.com/almarklein/visvis"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pyopengl[${PYTHON_USEDEP}]
- dev-python/imageio[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest
index 94118dae2..44510a1dd 100644
--- a/dev-python/wraps/Manifest
+++ b/dev-python/wraps/Manifest
@@ -1,2 +1 @@
-DIST wraps-0.1.0.tar.gz 25356 BLAKE2B 844293a5f7dfd84aa17f636d4863182118d40aa6ae53e044e77b77207be5b744cc78ef5235b889a963332fedb6922ce8ad829075099d9428be335366fe22cc56 SHA512 0e34d811869be2b22ec61638acb21342693e0fa44cf3d152dde179903c26771a9e26c673d2f37107122ba4bc92fe944b18ed16ebece7df0c07178845fc72bebb
DIST wraps-0.2.0.tar.gz 25308 BLAKE2B b68359d34995f7bc39535e97458807a5d55e3547124ccb8b34f9cd34fe1d3b38921a3a0c16df031410022f74d414aba97af9e9f60a20fb635428030bc400b130 SHA512 daf72785c3215db06f4bf06704f02c7ecfd1ef5c58dbf5c50b2dee14755d73b519f8a13be9658bf825c296689d9b3effd08aec4254779812583c1024522751f0
diff --git a/dev-python/wraps/metadata.xml b/dev-python/wraps/metadata.xml
index dd3bf5227..d94ee3bee 100644
--- a/dev-python/wraps/metadata.xml
+++ b/dev-python/wraps/metadata.xml
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="github">nekitdev/wraps</remote-id>
+ <remote-id type="pypi">wraps</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/wraps/wraps-0.1.0-r1.ebuild b/dev-python/wraps/wraps-0.1.0-r1.ebuild
deleted file mode 100644
index 4f51a06f2..000000000
--- a/dev-python/wraps/wraps-0.1.0-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=poetry
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION=" Meaningful and safe wrapping types. "
-HOMEPAGE="https://github.com/nekitdev/wraps"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="test"
-# package does not have test suite (yet)
-
-RDEPEND="
- >=dev-python/attrs-21.4.0[${PYTHON_USEDEP}]
- >=dev-python/typing-extensions-4.2.0[${PYTHON_USEDEP}]
- "
-
-PATCHES=(
- "${FILESDIR}/${P}-poetry_groups.patch"
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild
index 0e4ec817c..b06b511cd 100644
--- a/dev-python/wraps/wraps-0.2.0.ebuild
+++ b/dev-python/wraps/wraps-0.2.0.ebuild
@@ -5,12 +5,10 @@ EAPI=8
DISTUTILS_USE_PEP517=poetry
PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION=" Meaningful and safe wrapping types. "
HOMEPAGE="https://github.com/nekitdev/wraps"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/xgboost/metadata.xml b/dev-python/xgboost/metadata.xml
index a83159655..f862a0379 100644
--- a/dev-python/xgboost/metadata.xml
+++ b/dev-python/xgboost/metadata.xml
@@ -5,4 +5,7 @@ SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
<maintainer type="person">
<email>heroxbd@gentoo.org</email>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">xgboost</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/xgboost/xgboost-1.6.2.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild
index 645522c9c..780adec11 100644
--- a/dev-python/xgboost/xgboost-1.6.2.ebuild
+++ b/dev-python/xgboost/xgboost-1.6.2.ebuild
@@ -5,11 +5,10 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="XGBoost Python Package"
HOMEPAGE="https://xgboost.readthedocs.io"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
diff --git a/dev-python/xopen/Manifest b/dev-python/xopen/Manifest
deleted file mode 100644
index 7c783a2c0..000000000
--- a/dev-python/xopen/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST xopen-0.9.0.tar.gz 13334 BLAKE2B e3131bccf25b486eb9e23abcde03b09287edbff7fe78f558d158700e21219a330f3bf50390de4bd9f0598f1079261ff42b5d3bfd58a5b81e44b0051f592b2d7f SHA512 1cc8f32aaa9e626855e038ce3422d485a73c3d7d3af6e0957b8d735bc2c673f1780896686e9541a25fb25a57d7fe37d63099b23cada112ee2be382ccc0b52def
-DIST xopen-1.0.0.tar.gz 17487 BLAKE2B b805c8bc9bbfd57027a83e6d12d5bfdcb53cd9a4d3d938e9c97160e05e0684ee061121b800bcfdbfa3eb84bd10205c1a29a9c787563377a015a962132ee3c4d5 SHA512 d0ca9118d7ff871ee71605e3bbdf8271aca1179d8fbc4ec4e4ce86c0d822dcd74bb4c7927a8aa5796f01cb5cd14ef88414d9dc1f26e734b0037e81a180fbff09
-DIST xopen-1.0.1.tar.gz 18237 BLAKE2B 4019176c80d135551de09a057fe24c1ae96ccff3a2dc59129dbc6262e13b95993618701deae7795df49bfc9cfeb6503c2c9de4d25f1d7499a6ccce91878e49fd SHA512 045fd685b1a9f2dcd91e4ec28b5d3e1dba5ff71bee22165b0b6f1ca4d0fec91fd9551118e1f096d94d543e67512f7bc0c5bf58954115908b03544cf7afcef7b7
-DIST xopen-1.1.0.tar.gz 17836 BLAKE2B bdc70e4b9f08bbacadc8ca7bfb543a554104d41d092c771524277d83e616d29d2425724c35f82b2480e42ee60b9671d18742537c157acfea857669007ba63979 SHA512 74e366febede75afd09760a0f04fe13738bc432fe6801507435efb8020d4431aa37aab9500e55d78de5030474f473b379aff7764205e07647454d12118a26997
diff --git a/dev-python/xopen/metadata.xml b/dev-python/xopen/metadata.xml
deleted file mode 100644
index 822323020..000000000
--- a/dev-python/xopen/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>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>
-</pkgmetadata>
diff --git a/dev-python/xopen/xopen-0.9.0.ebuild b/dev-python/xopen/xopen-0.9.0.ebuild
deleted file mode 100644
index 7c32e8298..000000000
--- a/dev-python/xopen/xopen-0.9.0.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="Open compressed files transparently"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- app-arch/pigz
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/xopen/xopen-1.0.0.ebuild b/dev-python/xopen/xopen-1.0.0.ebuild
deleted file mode 100644
index 7c32e8298..000000000
--- a/dev-python/xopen/xopen-1.0.0.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="Open compressed files transparently"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- app-arch/pigz
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/xopen/xopen-1.0.1.ebuild b/dev-python/xopen/xopen-1.0.1.ebuild
deleted file mode 100644
index 7c32e8298..000000000
--- a/dev-python/xopen/xopen-1.0.1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="Open compressed files transparently"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- app-arch/pigz
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/xopen/xopen-1.1.0.ebuild b/dev-python/xopen/xopen-1.1.0.ebuild
deleted file mode 100644
index 3c721232d..000000000
--- a/dev-python/xopen/xopen-1.1.0.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-inherit distutils-r1
-
-DESCRIPTION="Open compressed files transparently"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- app-arch/pigz
-"
-
-distutils_enable_tests pytest
diff --git a/dev-python/yte/Manifest b/dev-python/yte/Manifest
new file mode 100644
index 000000000..e0bd09674
--- /dev/null
+++ b/dev-python/yte/Manifest
@@ -0,0 +1 @@
+DIST yte-1.5.1.tar.gz 6764 BLAKE2B ebe65bf961e028cb87ec0c7f8e552bcd5890329c0e66b9227becc21480a3b3ce5734090acc3fe32d44efcf2ecc7a2456f7056e75eccf7def75781910bef7dbc5 SHA512 5012e47d1ad8c20cb755b9c605d866d56850f0d16381f74c8d405232de95f43a6ea9ab65eb07cf23a14eeaa18e9105e0f0642a54f2847584bfffe432ce909267
diff --git a/dev-util/waf/metadata.xml b/dev-python/yte/metadata.xml
index 026cdb22b..ea4e4616a 100644
--- a/dev-util/waf/metadata.xml
+++ b/dev-python/yte/metadata.xml
@@ -1,8 +1,16 @@
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">yte-template-engine/yte</remote-id>
+ <remote-id type="pypi">yte</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/yte/yte-1.5.1.ebuild b/dev-python/yte/yte-1.5.1.ebuild
new file mode 100644
index 000000000..bb3b6354a
--- /dev/null
+++ b/dev-python/yte/yte-1.5.1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="A YAML template engine with Python expressions"
+HOMEPAGE="https://pypi.org/project/yte/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+ dev-python/dpath[${PYTHON_USEDEP}]
+ 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 08592fdcc..87617bcb1 100644
--- a/dev-python/zarr/Manifest
+++ b/dev-python/zarr/Manifest
@@ -1,3 +1,2 @@
-DIST zarr-2.11.1.tar.gz 3492813 BLAKE2B ff31cc2d11f5f863770f91136694108ab76525c644dd57861a4a57ca03dae0bb8cde5c20a2654f3566ffb69900d581e7592f576b9c0d2746e4fb95ed6991c740 SHA512 e0079a69f65a1bc230049469f50bf52af036d85d84f7c163ecdc2a4a8d7b75b07b59c1fcdecd83f578682914a6463641e9341d2c18f939c57f1e78f298f6b7ea
DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65
DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild
deleted file mode 100644
index fb138aad0..000000000
--- a/dev-python/zarr/zarr-2.11.1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1
-
-DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
-HOMEPAGE="https://github.com/zarr-developers/zarr-python"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-python/asciitree[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/numcodecs[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
-"
-
-DEPEND="
- test? (
- dev-python/msgpack[${PYTHON_USEDEP}]
- )
-"
-
-# Reported upsream
-# https://github.com/zarr-developers/zarr-python/issues/961
-EPYTEST_DESELECT=(
- zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
- zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
- zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
- zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
- zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild
index aecd66ba9..f18e92d44 100644
--- a/dev-python/zarr/zarr-2.11.3.ebuild
+++ b/dev-python/zarr/zarr-2.11.3.ebuild
@@ -4,13 +4,12 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
HOMEPAGE="https://github.com/zarr-developers/zarr-python"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild
index aecd66ba9..f18e92d44 100644
--- a/dev-python/zarr/zarr-2.12.0.ebuild
+++ b/dev-python/zarr/zarr-2.12.0.ebuild
@@ -4,13 +4,12 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
HOMEPAGE="https://github.com/zarr-developers/zarr-python"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild
index 47c21433e..58cb87329 100644
--- a/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild
+++ b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=poetry
inherit distutils-r1 pypi
diff --git a/dev-util/waf/Manifest b/dev-util/waf/Manifest
deleted file mode 100644
index f3196a0cf..000000000
--- a/dev-util/waf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST waf-2.0.21.tar.bz2 684459 BLAKE2B ba7d85c50d4ba1ad566620f7da2779ac1a4e0a5fcc5bcc639c64a59750bf9df40318070f771098d21335cc8d494b4043ecbdae1baa67c4bce3ce791ce2e538d5 SHA512 b76c32d5992757af1f483dc59dc439e414d06d0325eaf1c8ac20bc20ee62bee25d8a97099d80e6d8e3a2ca9c9aeadf0543c2ba5005479e9617c1fbcfd60ba6b8
diff --git a/dev-util/waf/waf-2.0.21.ebuild b/dev-util/waf/waf-2.0.21.ebuild
deleted file mode 100644
index e7d0a83bc..000000000
--- a/dev-util/waf/waf-2.0.21.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit python-single-r1
-
-DESCRIPTION="Piece of software used to help building software projects"
-HOMEPAGE="https://waf.io/"
-SRC_URI="https://waf.io/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="doc examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-BDEPEND="doc? ( $(python_gen_cond_dep \
- 'dev-python/sphinx[${PYTHON_USEDEP}]' )
-)"
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
- rm waf || die
-
- default
-}
-
-src_configure() {
- ${EPYTHON} ./waf-light configure || die "waf configure failed"
-}
-
-src_compile() {
- ${EPYTHON} ./waf-light build || die "waf build failed"
- use doc && build_sphinx docs/sphinx
-}
-
-src_install() {
- default
-
- # Set INSTALL to EPREFIX
- # Set REVISION to PR
- # set dirname to empty because python_get_sitedir
- # installs directly to a dir with the correct name
- # Set location of waflib to location of Gentoo
- # Python sitedir
- sed -e "/INSTALL=/s:=.*:='${EPREFIX}':" \
- -e "/REVISION=/s:=.*:='${PR}':" \
- -e "/dirname =/s:=.*:= '':" \
- -e "s:/lib/:$(python_get_sitedir)/:" \
- -e "/^#\(==>\|BZ\|<==\)/d" \
- -i waf || die
- python_doscript waf
-
- python_domodule waflib
-
- if use examples ; then
- dodoc -r demos
- fi
-}
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index a9f6d958f..d249e7c33 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,5 +1,3 @@
-DIST dandi-0.46.6.tar.gz 218868 BLAKE2B 7900c153172aa9669d0eae6bc2293ef51d1640b2fdd4e40eb887b1aba555d61617f95fb76601f1e81aeb9e0a54901c711bfb3c95eb478853490b29a0c1ee20e7 SHA512 db04e261205be716d6a098fbb63760411d3869c692df78954b50b649228747e0c18a9a32d3a9b0a5f21f55432e6a6cadad2142ee99168d02f02cfe51bf7eef93
-DIST dandi-0.48.0.tar.gz 228206 BLAKE2B 5cef713220839751b873170223bead06effddedf4b0d98d7de134fb87d64a4cc49521dd26d6a90777d331e77649c271466af9e30fd2511d72a3e505b5a904fbe SHA512 2e6686169105299f39f66d32542ce0e2d9d9fd9035f306c537771218ef8ced9832e6ea7911259623112604d83675aa52322410078eb7d00b6f83ec77a2cbc2c6
-DIST dandi-0.49.0.tar.gz 227445 BLAKE2B d698327fa12fa4dc1d3b1816181c8eb99eed1ac57a8ea9d5fddf96b9b8267313993053f39deeddfc3f4f3123a609d82b79dba69bb4decf30a2cd9903daa1effd SHA512 f3174a16fe1ddea894fad3ed8fdafca3b7664bdb110b5a8e3e3305f08705afa1ef985729aafea95ffdd59b1073fa9bb284ae00856291f4bd80bc9afd8e7f1bc8
-DIST dandi-0.50.0.tar.gz 236960 BLAKE2B b36f890e7d7de77ed2202d54516c897fb293ca5b360849199a0cd5fbe61ff07056b328eb3454f72b974a53ddef24ede5180c7f32b32b663c4bbe77f513301fa3 SHA512 91beb1b2330ab425a7cb4f744e2f11c3e5ab5f631903b05b676be898dba4ca16c42c2f9abb21b45858b50bb00c181fab341303846c9ccf416ddcd88c19136ffa
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
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
deleted file mode 100644
index 963aacdd4..000000000
--- a/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
+++ /dev/null
@@ -1,79 +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..10} )
-
-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="$(pypi_sdist_url dandi)"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test etelemetry"
-
-RDEPEND="
- dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/click-didyoumean[${PYTHON_USEDEP}]
- =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/fscacher[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/interleave[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/nwbinspector[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pycryptodome[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyout[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/semantic_version[${PYTHON_USEDEP}]
- dev-python/tenacity[${PYTHON_USEDEP}]
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/zarr[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
- test? (
- dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
- dev-python/pyfakefs[${PYTHON_USEDEP}]
- dev-python/pytest-mock[${PYTHON_USEDEP}]
- media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
- )
-"
-# Upstream might be amenable to dropping opencv:
-# https://github.com/dandi/dandi-cli/issues/944
-
-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-0.48.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild
deleted file mode 100644
index 963aacdd4..000000000
--- a/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild
+++ /dev/null
@@ -1,79 +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..10} )
-
-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="$(pypi_sdist_url dandi)"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test etelemetry"
-
-RDEPEND="
- dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/click-didyoumean[${PYTHON_USEDEP}]
- =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/fscacher[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/interleave[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/nwbinspector[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pycryptodome[${PYTHON_USEDEP}]
- >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/pynwb[${PYTHON_USEDEP}]
- dev-python/pyout[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/semantic_version[${PYTHON_USEDEP}]
- dev-python/tenacity[${PYTHON_USEDEP}]
- dev-python/wheel[${PYTHON_USEDEP}]
- dev-python/zarr[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
- test? (
- dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
- dev-python/pyfakefs[${PYTHON_USEDEP}]
- dev-python/pytest-mock[${PYTHON_USEDEP}]
- media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
- )
-"
-# Upstream might be amenable to dropping opencv:
-# https://github.com/dandi/dandi-cli/issues/944
-
-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-0.51.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild
index e4da9cb75..c626dbe8b 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.51.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1 pypi
@@ -21,6 +21,7 @@ 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}]
@@ -41,7 +42,7 @@ RDEPEND="
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/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.50.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild
index 8bbba64e8..060424cdb 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.50.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1 pypi
@@ -21,7 +21,8 @@ KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
+ <sci-biology/bidsschematools-0.7.0[${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}]
@@ -41,7 +42,7 @@ RDEPEND="
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/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
@@ -51,9 +52,11 @@ RDEPEND="
BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
dev-python/pyfakefs[${PYTHON_USEDEP}]
dev-python/pytest-mock[${PYTHON_USEDEP}]
+ dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
)
"
@@ -62,6 +65,10 @@ BDEPEND="
S="${WORKDIR}/${MY_P}"
+PATCHES=(
+ "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
+)
+
distutils_enable_tests pytest
src_prepare() {
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.49.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
index 8bbba64e8..beb2ffcc7 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.49.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.55.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1 pypi
@@ -21,8 +21,9 @@ KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
+ =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
dev-python/appdirs[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
@@ -41,7 +42,7 @@ RDEPEND="
dev-python/python-dateutil[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/semantic_version[${PYTHON_USEDEP}]
+ dev-python/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
@@ -51,9 +52,11 @@ RDEPEND="
BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
dev-python/pyfakefs[${PYTHON_USEDEP}]
dev-python/pytest-mock[${PYTHON_USEDEP}]
+ dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
)
"
@@ -62,6 +65,10 @@ BDEPEND="
S="${WORKDIR}/${MY_P}"
+PATCHES=(
+ "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
+)
+
distutils_enable_tests pytest
src_prepare() {
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch
new file mode 100644
index 000000000..4cd55ca7e
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch
@@ -0,0 +1,29 @@
+From d16bf0855e9ef7c029e8aca969ddfa04c1d7fdfd Mon Sep 17 00:00:00 2001
+From: "John T. Wodder II" <git@varonathe.org>
+Date: Thu, 25 May 2023 14:17:36 -0400
+Subject: [PATCH] Fix test for newer hdf5
+
+---
+ dandi/tests/test_files.py | 9 ++++++++-
+ 1 file changed, 8 insertions(+), 1 deletion(-)
+
+diff --git a/dandi/tests/test_files.py b/dandi/tests/test_files.py
+index 4dbf0f223..3e44cf6b1 100644
+--- a/dandi/tests/test_files.py
++++ b/dandi/tests/test_files.py
+@@ -374,7 +374,14 @@ def test_validate_bogus(tmp_path):
+ errors = dandi_file(path).get_validation_errors()
+ # ATM we would get 2 errors -- since could not be open in two places,
+ # but that would be too rigid to test. Let's just see that we have expected errors
+- assert any(e.message.startswith("Unable to open file") for e in errors)
++ assert any(
++ e.message.startswith(
++ ("Unable to open file", "Unable to synchronously open file")
++ )
++ for e in errors
++ )
++ # Recent versions of hdf5 changed the error message, hence the need to
++ # check for two different patterns.
+
+
+ def test_upload_zarr(new_dandiset, tmp_path):
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
index 92f325b66..78bcf187d 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,2 +1,3 @@
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
diff --git a/dev-vcs/datalad/datalad-0.18.0.ebuild b/dev-vcs/datalad/datalad-0.18.0.ebuild
index 69b1a5cb5..cd90c1db2 100644
--- a/dev-vcs/datalad/datalad-0.18.0.ebuild
+++ b/dev-vcs/datalad/datalad-0.18.0.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# 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 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
diff --git a/dev-vcs/datalad/datalad-0.18.1.ebuild b/dev-vcs/datalad/datalad-0.18.1.ebuild
index 69b1a5cb5..cd90c1db2 100644
--- a/dev-vcs/datalad/datalad-0.18.1.ebuild
+++ b/dev-vcs/datalad/datalad-0.18.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# 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 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
diff --git a/dev-vcs/datalad/datalad-0.18.3.ebuild b/dev-vcs/datalad/datalad-0.18.3.ebuild
new file mode 100644
index 000000000..cd90c1db2
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.18.3.ebuild
@@ -0,0 +1,74 @@
+# 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/docs/meetings/logs/20130130.log b/docs/meetings/logs/20130130.log
deleted file mode 100644
index cde74b5cc..000000000
--- a/docs/meetings/logs/20130130.log
+++ /dev/null
@@ -1,262 +0,0 @@
-[22:01:44] *** Joins: jlec (~jlec@gentoo/developer/jlec)
-[22:01:53] <tomka> here
-[22:01:53] <willikins> tomka, you have notes! [17:16] <darkside_> thats a fun OSX error o_0 [18:46] <hwoarang> how about moving the tatt source code to the arch-tools repository please?!
-[22:02:13] <jlec> hi
-[22:02:59] <bicatali> let's wait another minute or so, although not sure we'll be so many of us
-[22:03:53] <jlec> Actually the science channel looks quite full
-[22:04:32] <bicatali> may be we should switch the meeting there then
-[22:04:53] <bicatali> ok, let's start
-[22:05:06] <jlec> I am supressing the join/part messages so I don't know when they all joined
-[22:05:06] <bicatali> 1. alternatives
-[22:05:26] <jlec> Who is willing to work on that?
-[22:06:03] <bicatali> i'm working on an eselect fork, some fixes are already on github.com/gentoo-science/eselect.git
-[22:06:31] <tomka> I'm mostly in maintenance mode, not going to take over new projects, sorry.
-[22:06:33] <jlec> How much work do you think needs to be done until we can start merging it into the main eselect?
-[22:06:45] <bicatali> more fixes will follow this week end to do the alternatives_for into the eselect
-[22:07:04] <jlec> is ulm following the changes?
-[22:07:15] <bicatali> these last fixes should be enough for ulm to review and pull
-[22:07:24] <jlec> perfect.
-[22:07:41] <jlec> That you are taking care of eselect.
-[22:07:45] <bicatali> then there is the ldscript issue, which i have not started
-[22:07:46] <bicatali> yep
-[22:08:12] <jlec> yeah about the ldscript thing.
-[22:08:12] *** Joins: heroxbd (~user@gentoo/developer/heroxbd)
-[22:08:17] <bicatali> after those fixes the eclass will need to be rewritten, but it should be much more simple
-[22:08:31] <heroxbd> sorry I'm late, it's 5am here.
-[22:08:44] <jlec> no problem
-[22:08:48] <jlec> we just started
-[22:08:55] <heroxbd> ;)
-[22:09:07] <jlec> bicatali: so we are waiting for you to fix eselect
-[22:09:21] <bicatali> so has anyone tried the eselect-9999 from the science overlay?
-[22:09:39] <jlec> not yet, but I will switch to tomorrow
-[22:10:11] * heroxbd is wondering if it is about blas/atlas/gotoblas selection
-[22:10:19] <bicatali> i would like a tester for the current eclass/eselect with multiple blas
-[22:10:25] <jlec> heroxbd: alternatives framework
-[22:10:32] <heroxbd> I see
-[22:10:53] <bicatali> heroxbd: you need to unmask eselect-9999::science
-[22:11:13] <heroxbd> bicatali: I'd like to be a tester, too.
-[22:11:19] <bicatali> the other issue is what we do with library sonames
-[22:11:31] <jlec> right
-[22:11:43] <jlec> But I still disagree with equalizing them
-[22:12:02] <jlec> You are right we reduce the rebuilding when one implementation is drop
-[22:12:04] <jlec> ped
-[22:12:07] <bicatali> so debian changes soname for atlas and openblas to blas
-[22:12:28] <jlec> But we loose the ability to use different blas implementations for different programms
-[22:13:31] <jlec> What do we gain in addition to the rebuilds to set all sonames to blas?
-[22:13:33] <bicatali> i don't think we want users to compile R against openblas-threaded and octave against atlas
-[22:13:49] <jlec> Why not?
-[22:14:37] <bicatali> it's calling for bugs while rebuilding, and what do we do if the user removes one provider?
-[22:15:00] <jlec> portage should catch that and preserve libs.
-[22:15:03] <bicatali> and truely, once you choose one, you don't move
-[22:15:25] <jlec> Not that I would recommend using different blas for different apps
-[22:15:31] <jlec> But it's about choice
-[22:15:35] <bicatali> we could do more eselect modules: blas-threads, blas-serial, blas-int64
-[22:16:21] <heroxbd> just to confirm, they cannot be made ABI at all. So we are exclued with this probability, is that true?
-[22:16:27] <jlec> so instead of splitting into different providers, splitting into different types of implementation.
-[22:16:30] <heroxbd> ABI-compatible I mean
-[22:16:59] <jlec> bicatali: that sounds like a good idea
-[22:17:29] <bicatali> yes, so we would use the mutlibuild eclass for each, then add some use flags threads, int64, etc... for the dependent packages
-[22:18:02] <jlec> bicatali: but what about the libs which are splitted in to different so files? How do you handle sonames there?
-[22:18:15] <bicatali> this makes sense: sometimes a threaded program does want a serial blas to avoid oversuscribing
-[22:18:38] <bicatali> same soname for a given eselect module?
-[22:19:20] <bicatali> right now i would suggest lets split, then later on let's worry about soname/ldscript
-[22:19:49] <jlec> split what?
-[22:20:22] <bicatali> let's make several blas eselect modules: blas-serial, blas-threads, ...
-[22:20:59] <bicatali> and add use flags to virtual/blas
-[22:22:15] <jlec> And would that look for different providers for e.g. blas-serial?
-[22:22:30] <jlec> so atlas and reference are installed and provide serial
-[22:22:40] <jlec> How can the user choose?
-[22:22:51] <bicatali> use flag?
-[22:23:19] <bicatali> threads? ( virtual/blas[threads] )
-[22:23:56] <jlec> so we have can do eselect blas-thread set atlas ?
-[22:23:59] <bicatali> the worry about this is: much work to change ebuilds
-[22:24:34] <bicatali> eselect blas-threads to select atlas-threads
-[22:24:47] <bicatali> eselect blas-serial to select atlas...
-[22:25:14] <jlec> and what if want now reference ?
-[22:25:44] <bicatali> only on eselect blas-serial and virtual/blas with -threads
-[22:26:25] <jlec> So you want to control everything over virtual/blas?
-[22:26:57] <bicatali> on the package level yes, or do several virtual/blas-*
-[22:27:30] <bicatali> it seems it needs more thinking, so let's set this for another time
-[22:27:56] <jlec> yes fine. Perhaps you could write up a draft of your ideas
-[22:28:34] * heroxbd considers a written guideline for us and the users necessary
-[22:28:41] <bicatali> so actions: i'll finish the eselect, heroxbd will test the current builds with it
-[22:28:55] <jlec> I will also test
-[22:29:13] <jlec> sounds good
-[22:29:14] <bicatali> anyone wants to investigate multibuilds?
-[22:29:16] <heroxbd> no problem
-[22:29:29] <heroxbd> I've been googling for it
-[22:29:34] <jlec> bicatali: I can take a look
-[22:29:49] <jlec> but we need to have a chat about your exact ideas
-[22:30:08] <bicatali> yes. and let's start an alternatives wiki page
-[22:30:37] <bicatali> btw anyone with another word than 'alternatives' is welcome
-[22:31:05] * jlec slowly gets bicatali plan
-[22:31:39] <bicatali> time to switch to the 2. documentation
-[22:31:52] <jlec> WE need more.
-[22:32:04] <heroxbd> exactly
-[22:32:23] <jlec> I am trying to work on the whole contribution/community part
-[22:32:43] <jlec> And I am currently in progress to move the mpi.eclass/empi thing to the tree.
-[22:33:08] <jlec> This also need more documentation, which is probably more a business of the clusterteam
-[22:33:31] <jlec> Which other documentations are top priority?
-[22:33:33] <bicatali> regarding https://wiki.gentoo.org/wiki/Project:Science: it would be nice if everyone reads all the pages/subpages and resources
-[22:34:36] <bicatali> like the Gentoo Electronics project and herd are empty
-[22:34:49] <bicatali> but is it?
-[22:34:56] <bicatali> the mail alias is not
-[22:35:26] <jlec> bicatali: I will go through it and send mails to the aliases.
-[22:35:57] <jlec> !herd sci-electronics
-[22:36:00] <willikins> jlec: (sci-electronics) calchan, rafaelmartins, tomjbe, xmw
-[22:37:38] <jlec> And wee need to increase the staffing needs
-[22:37:45] <jlec> As we really need staff
-[22:37:58] <jlec> BTW please try to recruit
-[22:38:19] <bicatali> so let's push some jobs in the next gmn
-[22:38:19] <jlec> we are super fast in recruiting currently so the process is really fast
-[22:38:28] <jlec> good idea
-[22:39:10] <bicatali> who would like to review all the wiki pages to make them consistent?
-[22:39:30] <heroxbd> I can, haven't read it carefully yet
-[22:39:32] <bicatali> i've tried quite a bit already, but it needs more reviewing
-[22:39:46] <tomka> What's inconsistent?
-[22:39:57] <bicatali> jlec: want to ping the herds to include themselves in the wiki?
-[22:40:06] <jlec> It seems to be quite consistent
-[22:40:12] <bicatali> herds, members and mail aliases
-[22:40:18] <jlec> bicatali: ask for input on their pages
-[22:40:29] <jlec> I will also go through it
-[22:41:04] <tomka> Recruitment looks pretty much boilerplate.
-[22:41:09] <tomka> It's the same on every sub-page.
-[22:41:23] <tomka> But missing on sci-biology
-[22:41:27] <bicatali> just want to make sure we can get rid of http://www.gentoo.org/proj/en/science/index.xml
-[22:41:28] <tomka> are they fully staffed?
-[22:41:42] <bicatali> which is still the first google result for gentoo science
-[22:43:08] <jlec> I will first take a look that everything from the old xml site is covered by the wiki and then clean/improve the wiki pages.
-[22:43:12] <heroxbd> so the task is to review the wiki to make sure it has the full coverage of proj/science/xml and then redirect it.
-[22:43:48] <bicatali> yes, the blas-lapack page i will start the rewrite with the alternatives
-[22:43:48] <heroxbd> !herd sci-biology
-[22:43:49] <willikins> heroxbd: (sci-biology) je_fro, jlec, weaver
-[22:44:05] <bicatali> !herd sci-geosciences
-[22:44:06] <willikins> bicatali: (sci-geosciences) fordfrog
-[22:44:06] <jlec> heroxbd: it's just me
-[22:44:20] <heroxbd> ;)
-[22:44:32] <bicatali> so these sub-projects make sense?
-[22:44:59] <jlec> you mean the packages in the wiki or the herd subdivision?
-[22:45:05] <heroxbd> I think so, there would be more stuff.
-[22:45:36] <bicatali> we have both sub-herds and sub-projects
-[22:46:00] <bicatali> ok, let's keep it that way and get more people i guess
-[22:46:28] <jlec> sub-projects don't make really sense.
-[22:46:33] <jlec> sub-herds do
-[22:47:17] <jlec> I think the sub-projects should be things like the alternative framework rather then different science fields
-[22:47:29] <bicatali> well we had this: http://www.gentoo.org/proj/en/science/electronics/
-[22:48:09] <jlec> so we can add the electronics test bench sub project
-[22:48:36] <bicatali> first make sure that electronics is active...
-[22:49:02] <jlec> So I will ask the current sub-projects if they are willing to merge into the parent
-[22:49:14] <jlec> or otherwise maintain their subpage
-[22:49:24] <bicatali> yes, and then re-organize the wiki
-[22:49:26] <jlec> rafaelmartins: what about sci-electronics?
-[22:49:34] <jlec> !seen rafaelmartins
-[22:49:37] <willikins> jlec: rafaelmartins was last seen 4 hours, 44 minutes and 31 seconds ago, joining #gentoo-prefix
-[22:50:35] <heroxbd> we can make alternative framework itself a subproject in parallel to the fields.
-[22:51:22] <bicatali> i'd rather see the alternatives part of the eselect, i'll talk to ulm
-[22:51:32] <jlec> kk
-[22:52:00] <rafaelmartins> jlec: hello
-[22:52:05] <jlec> hi
-[22:52:08] * rafaelmartins jumps in the meeting
-[22:52:18] <heroxbd> hi
-[22:52:21] <jlec> I will send around mails
-[22:52:26] <jlec> that's better
-[22:52:30] <rafaelmartins> so, we are having low activity lately
-[22:52:31] <bicatali> actions: wiki review herobxd, jlec. wiki reorg: jlec?. alternatives write-up start: bicatali
-[22:52:37] <bicatali> rafaelmartins: oi
-[22:52:45] <rafaelmartins> bicatali: oi :)
-[22:53:01] <jlec> bicatali: I will take care of the wiki
-[22:54:14] <bicatali> finally: 3. new leader
-[22:54:21] <bicatali> i nominate jlec
-[22:54:46] * heroxbd nods
-[22:54:46] <jlec> Thanks. I accept the nomination.
-[22:54:53] <tomka> I second that.
-[22:54:59] <rafaelmartins> about electronics, quickly:
-[22:55:33] <rafaelmartins> I'am not doing a lot of work on this. mainly maintaining just the stuff I use to play for fun, not working with any eng-related stuff at this point
-[22:56:12] <rafaelmartins> I assumed as lead mainly because calchan wasn't able to do it at that time, my plan is to schedule a subproject lead election soon
-[22:56:37] <bicatali> rafaelmartins: pushing for new recruits and updating the wiki should be enough for electronics to survive
-[22:56:42] <jlec> rafaelmartins: I will take care of the wiki and do the rest by mail to the alias
-[22:56:50] <rafaelmartins> so, the subproject still exists, but with quite low activity at this point
-[22:56:59] <heroxbd> rafaelmartins: or would like to merge the sub project into science?
-[22:57:10] <rafaelmartins> bicatali: yeah, we got some people interested, but they disappear :(
-[22:57:34] <rafaelmartins> heroxbd: I'd like to hear calchan's opinion on this
-[22:57:52] <heroxbd> rafaelmartins: ok
-[22:57:59] <rafaelmartins> we can keep everything as is now, just migrating the project page to the wiki and decide on it later
-[22:58:05] <bicatali> rafaelmartins: could you help jlec merging the old page into https://wiki.gentoo.org/wiki/Project:Electronics
-[22:58:16] <rafaelmartins> bicatali: of course
-[22:58:49] *** Joins: fbissey (~fbissey@132.181.64.206)
-[22:58:53] <bicatali> ok voting: i vote for jlec as new leader
-[22:59:08] <rafaelmartins> +1 for jlec
-[22:59:10] <fbissey> Just in time for the vote
-[22:59:17] <bicatali> hey fbissey
-[22:59:23] <heroxbd> I vote for jlec, too
-[22:59:27] <heroxbd> fbissey: hi
-[22:59:39] <fbissey> no surprise that jlec is put in the driving seat
-[22:59:52] <tomka> +1 for jlec
-[23:00:49] <bicatali> jlec: clearly you are our new leader, please someone kicks me out from this channel!
-[23:01:08] <jlec> THank you everbody
-[23:01:12] <heroxbd> bicatali: ;)
-[23:01:15] <fbissey> congrats!
-[23:01:50] <jlec> ANd thank you bicatali doing the work the last years
-[23:01:55] <heroxbd> jlec: hey you haven't voted yet
-[23:01:59] <tomka> yeah thanks bicatali
-[23:02:24] <fbissey> thanks for putting up with us bicatali
-[23:02:50] <heroxbd> bicatali: yeah, thanks. And may I ask why you stepped down and what's your plan with science herd next?
-[23:03:02] <bicatali> i'll try to clean up my leadership with a bug free alternatives
-[23:03:36] <fbissey> I remember jlec and I came to gentoo at the same time and he is lead and I haven't made it to developer yet
-[23:03:52] <bicatali> heroxbd: jlec is more involved than me. i'm going to work on an automated gentoo
-[23:04:07] <heroxbd> fbissey: wow
-[23:04:38] <jlec> I think we set some nice clean up for the next months.
-[23:04:39] <heroxbd> bicatali: that's cluster deployment?
-[23:04:58] <jlec> Getting the alternatives into the tree should be top priority.
-[23:05:11] <heroxbd> jlec: agreed.
-[23:05:43] <heroxbd> jlec: and as the wiki reorg/review overlaps, you can assign me some jobs in detail.
-[23:05:59] <bicatali> heroxbd: no, some minimal gentoo core + cvmfs ala coreos to automate stabilizing
-[23:06:20] <bicatali> anyone keeping logs?
-[23:06:31] <jlec> I am logging
-[23:06:54] <heroxbd> ain't there a 4. open floor?
-[23:07:15] <heroxbd> just some FYI: first some news from roverlay.
-[23:07:18] <bicatali> heroxbd: yes you are right
-[23:08:27] <heroxbd> I started co-maintaining the roverlay with calchan, it is automated generatedfrom cran. once it's mature, I'll write up some doc
-[23:08:49] <bicatali> that is good news
-[23:09:13] <heroxbd> sorry, creepy internet connection
-[23:09:32] <bicatali> jlec: want to post meeting log on the wiki then?
-[23:09:48] <jlec> bicatali: I will
-[23:09:56] <fbissey> heroxbd: can it take other R repo like bioconductor?
-[23:11:04] <heroxbd> fbissey, I think it high possible, as the overlay generation tools are actively developed by another student.
-[23:11:13] <heroxbd> *highly
-[23:11:32] <heroxbd> it has been a google summer of code project
-[23:12:57] <heroxbd> FYI2, among the Prefix users, many are from academic field. They submit bugs, and are good candidatesfor recruitment.
-[23:14:38] <jlec> heroxbd: sounds great.
-[23:14:45] <bicatali> ok folks, thanks, i'm off the meeting
-[23:14:53] <jlec> make them fix the quizzes and get them a bug
-[23:14:57] <fbissey> bye bicatali
-[23:15:05] <jlec> bicatali thanks for all
-[23:15:07] <jlec> bye
-[23:15:28] <heroxbd> bicatali: see you
-[23:17:30] <jlec> Okay guys, anymore more openfloor topics?
-[23:17:34] <heroxbd> are we waiting for closing the meeting?
-[23:18:08] <fbissey> I have some stuff but I will probably post on list for discusion
-[23:18:19] <jlec> If there is nothing else, I would close it
-[23:18:47] <jlec> We can schedule the next meeting sooner, in 1-2 months or so
-[23:19:12] <jlec> fbissey: Or do you want to discuss now. It is up to you.
-[23:19:31] <fbissey> I can introduce it.
-[23:19:58] <fbissey> blas/lapack setup in python package is horrible
-[23:20:26] <fbissey> motivated by work I am doing with people in sage I trying to get stuff to simplify that
-[23:20:27] <jlec> We should wait for this a little
-[23:20:39] <heroxbd> fbissey: python build system tries to do all the smart but wrong guessing
-[23:21:00] <jlec> After bicatali fixed eselect and we decided about the soname thing, we shoudl have an ldscript
-[23:21:10] <jlec> then it will become easier
-[23:21:13] <fbissey> there is a python module to interface with pkg-config that makes some things easier
-[23:21:22] <heroxbd> good idea
-[23:21:42] <jlec> fbissey: best would be to simply have libblas.so as ldscript
-[23:21:57] <jlec> but that should be implemented after we fixed the rest
-[23:21:59] <fbissey> that make things easy agreed.
-[23:23:57] <fbissey> nothing more from me
-[23:24:05] <jlec> fine
-[23:24:18] <jlec> So I will close the meeting here. Thanks for attending.
-[23:24:29] <jlec> I will post the meeting log on the wiki
-[23:24:36] <heroxbd> Thanks all
-[23:24:47] <tomka> thanks
-[23:25:30] *** Parts: fbissey (~fbissey@132.181.64.206) ("Konversation terminated!")
-[23:33:09] *** Quits: tomka (~tomka@gentoo/developer/tomka) (Quit: tomka)
-[23:44:50] *** Joins: Calchan (~calchan@gentoo/developer/calchan)
diff --git a/docs/meetings/sci-electronics-201010-agenda b/docs/meetings/sci-electronics-201010-agenda
deleted file mode 100644
index 2e3c18a3c..000000000
--- a/docs/meetings/sci-electronics-201010-agenda
+++ /dev/null
@@ -1,14 +0,0 @@
-Topics
-------
-
-- Open bugs (http://xrl.us/bh4cdg).
-- Packages lacking in the main tree:
- - Add your package here...
-- Creation of the sci-electronics subproject.
-
-
-Schedule
---------
-
-- When: 2010-10-17 2000 UTC (rafaelmartins, dilfridge)
-- Where: #gentoo-meetings @ Freenode
diff --git a/docs/proj/contrib.xml b/docs/proj/contrib.xml
deleted file mode 100644
index fd474808b..000000000
--- a/docs/proj/contrib.xml
+++ /dev/null
@@ -1,182 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
-<guide link="/doc/en/" lang="en">
-
- <title>Contributing to the Scientific Project</title>
-
- <author title="Author">
- <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
- <!-- others add your name here -->
- </author>
-
- <abstract>
- This document provides information on how one can get involved and
- help out with the Gentoo Scientific Project
- </abstract>
-
- <!-- The content of this document is licensed under the CC-BY-SA license -->
- <!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
- <license/>
-
- <version>0.1</version>
- <date>2009-01-21</date>
-
- <chapter>
- <title>Overview</title>
- <section>
- <body>
- <p>
- This document aims to provide information on how one can get
- involved and help out with the Gentoo Scientific Project.
- Scientific packages are very diverse and many of us want our
- pet application in the main tree for easy installation. Due to
- the small size of our team, we can not implement all of
- them, so we really appreciate any contribution.
- </p>
- <p>
- There are few obvious areas where one can help as we
- describe below. The Scientific Project tends to set strong
- requirements on testing, especially on core packages.
- Comments, thoughts, and feedback is greatly welcomed!
- </p>
- </body>
- </section>
- </chapter>
-
- <chapter>
- <title>Bugs</title>
- <section>
- <title>Reporting</title>
- <body>
- <p>
- All good software has bugs. They are too many combinations of
- compilers, USE flags and versions to test them all. So if
- you find the time to report them, we would love to hear
- about it. We have the standard bugzilla system for
- this. Don't be afraid of all these fields to fill in, it's
- not that bad!
- </p>
- </body>
- </section>
- <section>
- <title>Resolving</title>
- <body>
- <p>
- The Scientific Team in Gentoo has always had a high number of
- bugs. Fortunately, many of them are new packages. Any help in resolving
- issues, improving submitted ebuilds is greatly appreciated.
- </p>
- <p>
- <uri link="http://tinyurl.com/2qxmvu">Bugs for the Scientific Team.</uri>
- <uri link="http://tinyurl.com/2nm6ag">Bugs for the Biology Team.</uri>
- <uri link="http://tinyurl.com/368f2d">Bugs for the Chemistry Team.</uri>
- <uri link="http://tinyurl.com/2lknlo">Bugs for the Electronics Team.</uri>
- <uri link="http://tinyurl.com/2pcntk">Bugs for the Mathematics Team.</uri>
- <uri link="http://tinyurl.com/3789aa">Bugs for the Physics Team.</uri>
- </p>
- </body>
- </section>
- </chapter>
-
- <chapter>
- <title>Writing ebuilds</title>
- <section>
- <body>
- <p>
- You don't see your application in the main tree or in the
- overlays and you don't want to wait for someone else to
- create the ebuilds? The most obvious solution is to develop
- your own ebuilds. If you do so, it's always nice to share
- them. You can post them to our bugzilla system and then one
- of our devs will comment out. The <uri link="http://overlays.gentoo.org/proj/sunrise">sunrise
- overlay</uri> allows you more directly to commit your
- ebuilds if you don't want to wait for science access.
- </p>
- </body>
- </section>
- </chapter>
-
- <chapter>
- <title>Communication</title>
- <section>
- <title>Mailing List</title>
- <body>
- <p>
- Join our
- <uri link="http://www.gentoo.org/main/en/lists.xml"> gentoo-science mailing list
- </uri> and asking/answering questions.
- </p>
- </body>
- </section>
- <section>
- <title>IRC</title>
- <body>
- <p>
- Meet some of us in #gentoo-science. It is a fairly quiet
- channel, but slowly growing and we are responsive. We can
- answer your questions, help you developing your ebuilds,
- share ideas, etc...
- </p>
- </body>
- </section>
- <title>Direct emails</title>
- <body>
- <p>
- If you feel your questions are more private and don't need
- to be known from the rest of the world, you can always
- directly send an email to our developers
- listed <uri link="http://www.gentoo.org/main/en/proj/science/index.xml">here</uri>
- and the listed sub-projects. If you want to mail all of us, send a mail to the herd.
- </p>
- </body>
- </chapter>
-
- <chapter>
- <title>Writing Documentation</title>
- <body>
- <section>
- <p>
- You may not be interested in fixing ebuilds and testing
- packages, but want to share your knowledge about some
- software, configuration or tips and tricks. The best way to
- do this is to write some documentation. You can even write
- official Gentoo documentation such as our
- <uri link="http://www.gentoo.org/main/en/proj/science/blas-lapack.xml">blas/lapack
- guide</uri>.
- </p>
- </section>
- </body>
- </chapter>
-
- <chapter>
- <title>Seriously getting involved</title>
- <section>
- <body>
- <p>
- If you would like to join our team of volunteers and become
- an official Gentoo Developer, show activity in anywhere you
- can: bugzilla, overlays, mailing lists, irc, forums,...
- Please refer to
- <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=1&amp;chap=2">
- Becoming a Developer</uri> in the
- <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml">
- Gentoo Developer Handbook</uri>.
- </p>
- <p>
- Benefits are huge :-) :
- <dl>
- <dd>
- <ul>
- <li>Receive a warm welcome from us</li>
- <li>Impress your geek friends</li>
- <!--<li>Loose your social life, but</li>-->
- <li>Get a free beer first time we meet in person!</li>
- </ul>
- </dd>
- </dl>
- </p>
-
- </body>
- </section>
- </chapter>
-</guide>
diff --git a/docs/proj/index.xml b/docs/proj/index.xml
deleted file mode 100644
index b672ed36e..000000000
--- a/docs/proj/index.xml
+++ /dev/null
@@ -1,106 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet href="/xsl/project.xsl" type="text/xsl"?>
-<?xml-stylesheet href="/xsl/guide.xsl" type="text/xsl"?>
-<!DOCTYPE project SYSTEM "/dtd/project.dtd">
-
-<project>
- <name>Science</name>
- <longname>The Gentoo Scientific Project</longname>
- <date>2009-01-21</date>
- <author title="author">
- <mail link="sci@gentoo.org">Science Team</mail>
- </author>
-
- <description>
- The Gentoo Scientific Project handles all Gentoo related Math and Science items.
- </description>
-
- <longdescription>
- <p>
- The Gentoo Scientific Project handles math and science related activities in Gentoo.
- This includes maintaining packages that belong to various math
- and science related herds, fortran compilers, documentations and communications.
- </p>
- </longdescription>
-
- <goals>
- <p>
- The goals of Scientific Gentoo are to provide a simple but optimal
- installation and configuration of a wide variety of math and
- science applications. Scientific computing is an area where custom optimization
- provides great benefit. We also provide tools to easily switch configurations, and relevant
- documentations. We give special attention to ways to test the
- packages, through regression suites, and benchmarks.
- </p>
- </goals>
-
-
- <!-- Staff -->
- <dev role="member" description="General package maintainer">bicatali</dev>
- <dev role="contributor" description="Ebuild development, general bug fixing, electronics and physics">dilfridge</dev>
- <dev role="member" description="General package maintainer">je_fro</dev>
- <dev role="contributor" description="Ebuild development (sage), general bug fixing and keep opendx running">kiwifb</dev>
- <dev role="member" description="General package maintainer, g-octave developer">rafaelmartins</dev>
- <dev role="member" description="General package maintainer">xarthisius</dev>
- <dev role="member" description="g-cran developer">tulcod</dev>
- <dev role="member" description="General package maintainer, sci-electronics">tomjbe</dev>
- <dev role="my role in the science project" description="what i do mainly">dev-username</dev>
-
- <!-- Subprojects
- <subproject ref="/proj/en/science/astronomy/index.xml" />
- <subproject ref="/proj/en/science/biology/index.xml" />
- <subproject ref="/proj/en/science/chemistry/index.xml" />
- <subproject ref="/proj/en/science/electronics/index.xml" />
- <subproject ref="/proj/en/science/math/index.xml" />
- <subproject ref="/proj/en/science/physics/index.xml" />
- -->
-
- <resource link="contrib.xml">Guide on contributing to the science project</resource>
- <resource link="http://overlays.gentoo.org/proj/science">Official overlay</resource>
- <resource link="http://news.gmane.org/gmane.linux.gentoo.science/">Mailing list archives</resource>
- <resource link="irc://irc.freenode.net/gentoo-science">#gentoo-science IRC Channel</resource>
-
-<extrachapter position="bottom">
-<title>The Science Overlay</title>
-<section>
-<body>
-<p>
- New packages and more complex version bumps are held in
- an <uri link="http://overlays.gentoo.org/proj/science/">Overlay</uri>. They
- help both the science and hp-cluster team and the wiki contains some
- temporary information.
-</p>
-</body>
-</section>
-</extrachapter>
-
-<recruitment>
- <job>
- <summary>Scientific package maintainer</summary>
- <details>
- The sci team and its various subprojects are always looking for a
- general package maintainer to help our understaffed
- team. Tasks are troubleshooting, version bumping and
- stabilizing, new ebuilds and eclassed introduction.
- </details>
- <requirements>
- Experience with Linux, various package build systems (autotools, cmake)
- and makefiles, and bash.
- </requirements>
- <contact>sci</contact>
- </job>
- <job>
- <summary>CAD Programs</summary>
- <details>
- Computer Aided Design open source programs are getting more popular
- and yet to have decent support in Gentoo. We need to put an end
- on this.
- </details>
- <requirements>
- Knowledge of a few CAD programs and good ebuild skills.
- </requirements>
- <contact>sci</contact>
- </job>
-</recruitment>
-
-</project>
diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass
deleted file mode 100644
index 7237f0db3..000000000
--- a/eclass/alternatives-2.eclass
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 2010-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Based in part upon 'alternatives.exlib' from Exherbo, which is:
-# Copyright 2008, 2009 Bo Ørsted Andresen
-# Copyright 2008, 2009 Mike Kelly
-# Copyright 2009 David Leverton
-
-# @ECLASS: alternatives-2.eclass
-# @MAINTAINER:
-# Gentoo Science Project <sci@gentoo.org>
-# @BLURB: Manage alternative implementations.
-# @DESCRIPTION:
-# Autogenerate eselect modules for alternatives and ensure that valid provider
-# is set.
-#
-# Remove eselect modules when last provider is unmerged.
-#
-# If your package provides pkg_postinst or pkg_prerm phases, you need to be
-# sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate.
-
-case "${EAPI:-0}" in
- 0|1|2|3|4)
- die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}"
- ;;
- 5|6|7)
- ;;
- *)
- die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}"
- ;;
-esac
-
-DEPEND=">=app-admin/eselect-1.4.13-r101"
-RDEPEND="${DEPEND}
- !app-eselect/eselect-blas
- !app-eselect/eselect-cblas
- !app-eselect/eselect-lapack"
-
-# @ECLASS-VARIABLE: ALTERNATIVES_DIR
-# @INTERNAL
-# @DESCRIPTION:
-# Alternatives directory with symlinks managed by eselect.
-ALTERNATIVES_DIR="/etc/env.d/alternatives"
-
-# @FUNCTION: alternatives_for
-# @USAGE: <alternative> <provider> <importance> <source> <target> [<source> <target> [...]]
-# @DESCRIPTION:
-# Set up alternative provider.
-#
-# EXAMPLE:
-# @CODE
-# alternatives_for sh bash 0 \
-# /usr/bin/sh bash
-# @CODE
-alternatives_for() {
- debug-print-function ${FUNCNAME} "${@}"
-
- dodir /etc/env.d/alternatives
-
- ALTERNATIVESDIR_ROOT="${D%/}" \
- eselect alternatives add ${@} || die
-
- ALTERNATIVES_CREATED+=( ${1} )
-}
-
-# @FUNCTION: cleanup_old_alternatives_module
-# @USAGE: <alternative>
-# @DESCRIPTION:
-# Remove old alternatives module.
-cleanup_old_alternatives_module() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local alt=${1} old_module="${EROOT%/}/usr/share/eselect/modules/${alt}.eselect"
-
- if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then
- local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')"
- if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then
- einfo "rm ${old_module}"
- rm "${old_module}" || eerror "rm ${old_module} failed"
- fi
- fi
-}
-
-# @FUNCTION: alternatives-2_pkg_postinst
-# @DESCRIPTION:
-# Create eselect modules for all provided alternatives if necessary and ensure
-# that valid provider is set.
-#
-# Also remove old eselect modules for provided alternatives.
-#
-# Provided alternatives are set up using alternatives_for().
-alternatives-2_pkg_postinst() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local alt
-
- for alt in ${ALTERNATIVES_CREATED[@]}; do
- if ! eselect ${alt} show > /dev/null; then
- einfo "Creating Alternative for ${alt}"
- eselect alternatives create ${alt}
- fi
-
- # Set alternative provider if there is no valid provider selected
- eselect alternatives update "${alt}"
-
- cleanup_old_alternatives_module ${alt}
- done
-}
-
-# @FUNCTION: alternatives-2_pkg_prerm
-# @DESCRIPTION:
-# Ensure a valid provider is set in case the package is unmerged and
-# remove autogenerated eselect modules for alternative when last
-# provider is unmerged.
-#
-# Provided alternatives are set up using alternatives_for().
-alternatives-2_pkg_prerm() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local alt ret
-
- # If we are uninstalling, update alternatives to valid provider
- [[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore"
- for alt in ${ALTERNATIVES_CREATED[@]}; do
- eselect alternatives update "${alt}"
- ret=$?
-
- case ${ret} in
- 0) : ;;
- 2)
- # This was last provider for the alternative, remove eselect module
- einfo "Cleaning up unused alternatives module for ${alt}"
- eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}"
- ;;
- *)
- eerror "eselect alternatives update returned \"${ret}\""
- ;;
- esac
- done
-}
-
-EXPORT_FUNCTIONS pkg_postinst pkg_prerm
diff --git a/eclass/numeric-int64-multibuild.eclass b/eclass/numeric-int64-multibuild.eclass
deleted file mode 100644
index 9dd23cebf..000000000
--- a/eclass/numeric-int64-multibuild.eclass
+++ /dev/null
@@ -1,414 +0,0 @@
-# Copyright 1999-2021 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: numeric-int64-multibuild.eclass
-# @MAINTAINER:
-# sci team <sci@gentoo.org>
-# @AUTHOR:
-# Author: Mark Wright <gienah@gentoo.org>
-# Author: Justin Lecher <jlec@gentoo.org>
-# @BLURB: Build functions for Fortran multilib int64 multibuild packages
-# @DESCRIPTION:
-# The numeric-int64-multibuild.eclass exports USE flags and utility functions
-# necessary to build packages for multilib int64 multibuild in a clean
-# and uniform manner.
-
-if [[ ! ${_NUMERIC_INT64_MULTILIB_ECLASS} ]]; then
-
-# EAPI=5 is required for meaningful MULTILIB_USEDEP.
-case ${EAPI:-0} in
- 5)
- inherit multilib ;;
- 6|7) ;;
- *) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-inherit alternatives-2 eutils fortran-2 multilib-build numeric toolchain-funcs
-
-IUSE="int64"
-
-# @ECLASS-VARIABLE: NUMERIC_INT32_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for int32 build
-NUMERIC_INT32_SUFFIX="int32"
-
-# @ECLASS-VARIABLE: NUMERIC_INT64_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for int64 build
-NUMERIC_INT64_SUFFIX="int64"
-
-# @ECLASS-VARIABLE: NUMERIC_STATIC_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for static build
-NUMERIC_STATIC_SUFFIX="static"
-
-# @FUNCTION: numeric-int64_is_int64_build
-# @DESCRIPTION:
-# Returns shell true if the current multibuild is a int64 build,
-# else returns shell false.
-#
-# Example:
-#
-# @CODE
-# $(numeric-int64_is_int64_build) && \
-# openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT"
-# @CODE
-numeric-int64_is_int64_build() {
- debug-print-function ${FUNCNAME} "${@}"
- if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_INT64_SUFFIX}" ]]; then
- return 0
- else
- return 1
- fi
-}
-
-# @FUNCTION: numeric-int64_is_static_build
-# @DESCRIPTION:
-# Returns shell true if current multibuild is a static build,
-# else returns shell false.
-#
-# Example:
-#
-# @CODE
-# if $(numeric-int64_is_static_build); then
-# dolib.a lib*a
-# fi
-# @CODE
-numeric-int64_is_static_build() {
- debug-print-function ${FUNCNAME} "${@}"
- if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_STATIC_SUFFIX}" ]]; then
- return 0
- else
- return 1
- fi
-}
-
-# @FUNCTION: numeric-int64_get_module_name
-# @USAGE: [<module_name>]
-# @DESCRIPTION:
-# Return the numeric module name, without the .pc extension,
-# for the current fortran int64 build. If the current build is not an int64
-# build, and the ebuild does not have dynamic, threads or openmp USE flags or
-# they are disabled, then the module_name is ${NUMERIC_MODULE_NAME} or
-# <module_name> if <module_name> is specified.
-#
-# Takes an optional <module_name> parameter. If no <module_name> is specified,
-# uses ${NUMERIC_MODULE_NAME} as the base to calculate the module_name for the
-# current build.
-#
-# Example:
-#
-# @CODE
-# NUMERIC_MODULE_NAME=blas
-# profname=$(numeric-int64_get_module_name)
-#
-# int32 build:
-# -> profname == blas
-#
-# int64 build:
-# -> profname == blas-int64
-# @CODE
-numeric-int64_get_module_name() {
- debug-print-function ${FUNCNAME} "${@}"
- local module_name="${1:-${NUMERIC_MODULE_NAME}}"
- if has dynamic ${IUSE} && use dynamic; then
- module_name+="-dynamic"
- fi
- if $(numeric-int64_is_int64_build); then
- module_name+="-${NUMERIC_INT64_SUFFIX}"
- fi
- # choose posix threads over openmp when the two are set
- # yet to see the need of having the two profiles simultaneously
- if in_iuse threads && use threads; then
- module_name+="-threads"
- elif in_iuse openmp && use openmp; then
- module_name+="-openmp"
- fi
- echo "${module_name}"
-}
-
-# @FUNCTION: _numeric-int64_get_numeric_alternative
-# @INTERNAL
-_numeric-int64_get_numeric_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- local alternative_name="${1}"
- if $(numeric-int64_is_int64_build); then
- alternative_name+="-${NUMERIC_INT64_SUFFIX}"
- fi
- echo "${alternative_name}"
-}
-
-# @FUNCTION: numeric-int64_get_blas_alternative
-# @DESCRIPTION:
-# Returns the eselect blas alternative for the current
-# int build type. Which is blas-int64 if called from an int64 build,
-# or blas otherwise.
-numeric-int64_get_blas_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- _numeric-int64_get_numeric_alternative blas
-}
-
-# @FUNCTION: numeric-int64_get_cblas_alternative
-# @DESCRIPTION:
-# Returns the eselect cblas alternative for the current
-# int build type. Which is cblas-int64 if called from an int64 build,
-# or cblas otherwise.
-numeric-int64_get_cblas_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- _numeric-int64_get_numeric_alternative cblas
-}
-
-# @FUNCTION: numeric-int64_get_xblas_alternative
-# @DESCRIPTION:
-# Returns the eselect xblas alternative for the current
-# int build type. Which is xblas-int64 if called from an int64 build,
-# or xblas otherwise.
-numeric-int64_get_xblas_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- _numeric-int64_get_numeric_alternative xblas
-}
-
-# @FUNCTION: numeric-int64_get_lapack_alternative
-# @DESCRIPTION:
-# Returns the eselect lapack alternative for the current
-# int build type. Which is lapack-int64 if called from an int64 build,
-# or lapack otherwise.
-numeric-int64_get_lapack_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- _numeric-int64_get_numeric_alternative lapack
-}
-
-# @FUNCTION: numeric-int64_get_blas_module_name
-# @DESCRIPTION:
-# Returns the pkg-config file name, without the .pc extension,
-# for the currently selected blas-int64 module if we are performing an int64
-# build, or the currently selected blas module otherwise.
-numeric-int64_get_blas_module_name() {
- debug-print-function ${FUNCNAME} "${@}"
- local blas_alternative=$(numeric-int64_get_blas_alternative)
- local blas_symlinks=( $(eselect "${blas_alternative}" files) )
- local blas_prof_symlink="$(readlink -f ${blas_symlinks[0]})"
- local blas_prof_file="${blas_prof_symlink##*/}"
- echo "${blas_prof_file%.pc}"
-}
-
-# @FUNCTION: numeric-int64_get_xblas_module_name
-# @DESCRIPTION:
-# Returns the xblas pkg-config file name,
-# without the .pc extension, for the current build. Which is xblas-int64 if
-# we are performing an int64 build, or xblas otherwise.
-numeric-int64_get_xblas_module_name() {
- debug-print-function ${FUNCNAME} "${@}"
- local xblas_provider="xblas"
- if $(numeric-int64_is_int64_build); then
- xblas_provider+="-${INT64_SUFFIX}"
- fi
- echo "${xblas_provider}"
-}
-
-# @FUNCTION: numeric-int64_get_fortran_int64_abi_fflags
-# @DESCRIPTION:
-# Return the Fortran compiler flag to enable 64 bit integers for
-# array indices if we are performing an int64 build, or the empty string
-# otherwise.
-#
-# Example:
-#
-# @CODE
-# src_configure() {
-# my_configure() {
-# export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)"
-# econf $(use_enable fortran)
-# }
-# numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_configure
-# }
-# @CODE
-numeric-int64_get_fortran_int64_abi_fflags() {
- debug-print-function ${FUNCNAME} "${@}"
- $(numeric-int64_is_int64_build) && echo "$(fortran_int64_abi_fflags)"
-}
-
-# @FUNCTION: numeric-int64_get_multibuild_int_variants
-# @DESCRIPTION:
-# Returns the array of int64 and int32
-# multibuild combinations.
-numeric-int64_get_multibuild_int_variants() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=( int32 ) variant
-
- in_iuse int64 && use int64 && MULTIBUILD_VARIANTS+=( int64 )
-
- echo "${MULTIBUILD_VARIANTS[@]}"
-}
-
-# @FUNCTION: numeric-int64_get_multibuild_variants
-# @DESCRIPTION:
-# Returns the array of int64, int32 and static
-# multibuild combinations.
-numeric-int64_get_multibuild_variants() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=$(numeric-int64_get_multibuild_int_variants)
- if in_iuse static-libs && use static-libs; then
- for variant in ${MULTIBUILD_VARIANTS[@]}; do
- MULTIBUILD_VARIANTS+=( static_${variant} )
- done
- fi
- echo "${MULTIBUILD_VARIANTS[@]}"
-}
-
-# @FUNCTION: numeric-int64_get_all_abi_variants
-# @DESCRIPTION:
-# Returns the array of int64, int32 and static build combinations
-# combined with all multilib ABI variants.
-numeric-int64_get_all_abi_variants() {
- debug-print-function ${FUNCNAME} "${@}"
- local abi ret=() variant
-
- for abi in $(multilib_get_enabled_abi_pairs); do
- for variant in $(numeric-int64_get_multibuild_variants); do
- if [[ ${variant} =~ int64 ]]; then
- [[ ${abi} =~ amd64 ]] && ret+=( ${abi}_${variant} )
- else
- ret+=( ${abi}_${variant} )
- fi
- done
- done
- echo "${ret[@]}"
-}
-
-# @FUNCTION: numeric-int64_ensure_blas_int_support
-# @DESCRIPTION:
-# Check the blas supports the necessary int types in the currently
-# selected blas module.
-#
-# Example:
-#
-# @CODE
-# src_prepare() {
-# numeric-int64_ensure_blas_int_support
-# ...
-# @CODE
-numeric-int64_ensure_blas_int_support() {
- local MULTILIB_INT64_VARIANTS=( $(numeric-int64_get_multibuild_variants) )
- local MULTIBUILD_ID
- for MULTIBUILD_ID in "${MULTILIB_INT64_VARIANTS[@]}"; do
- local blas_module_name=$(numeric-int64_get_blas_module_name)
- $(tc-getPKG_CONFIG) --exists "${blas_module_name}" \
- || die "${PN} requires the pkgbuild module ${blas_module_name}"
- done
-}
-
-# @FUNCTION: numeric-int64-multibuild_install_alternative
-# @USAGE: <alternative name> <provider name> [extra files sources] [extra files dest]
-# @DESCRIPTION:
-# Install alternatives pc file and extra files for all providers for all multilib ABIs.
-numeric-int64-multibuild_install_alternative() {
- debug-print-function ${FUNCNAME} "${@}"
- [[ $# -lt 2 ]] && die "${FUNCNAME} needs at least two arguments"
- pc_file() {
- debug-print-function ${FUNCNAME} "${@}"
- numeric-int64_is_static_build && return
- local alternative=$(_numeric-int64_get_numeric_alternative "$1")
- local module_name=$(numeric-int64_get_module_name)
- printf \
- "/usr/$(get_libdir)/pkgconfig/${alternative}.pc ${module_name}.pc " \
- >> "${T}"/alternative-${alternative}.sh || die
- }
- pc_install() {
- debug-print-function ${FUNCNAME} "${@}"
- numeric-int64_is_static_build && return
- local alternative=$(_numeric-int64_get_numeric_alternative "$1")
- local module_name=$(numeric-int64_get_module_name $2)
- shift 2
- alternatives_for \
- ${alternative} ${module_name} 0 \
- $(cat "${T}"/alternative-${alternative}.sh) ${@}
- rm "${T}"/alternative-${alternative}.sh || die
- }
- numeric-int64-multibuild_foreach_all_abi_variants pc_file ${@}
- numeric-int64-multibuild_foreach_int_abi pc_install ${@}
-}
-
-# @FUNCTION: numeric-int64-multibuild_multilib_wrapper
-# @USAGE: <argv>...
-# @DESCRIPTION:
-# Initialize the environment for ABI selected for multibuild.
-#
-# Example:
-#
-# @CODE
-# multibuild_foreach_variant run_in_build_dir \
-# numeric-int64-multibuild_multilib_wrapper my_src_install
-# @CODE
-numeric-int64-multibuild_multilib_wrapper() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local v="${MULTIBUILD_VARIANT%_*}"
- # MULTIBUILD_VARIANT could be abi_x86_64.amd64_static_int32
- v=${v%_${NUMERIC_STATIC_SUFFIX}}
- local ABI="${v#*.}"
- # hack: our int64 and int32 ABIs can correspond to the same ABI
- # in multilib, resulting in multiple sed replacements of headers
- # and thus error like "Flag not listed in wrapper template."
- # Using MULTILIB_ABI_FLAG="${ABI}", the corresponding header
- # is ignored.
- local MULTILIB_ABI_FLAG
- case ${MULTIBUILD_VARIANT} in
- *_${NUMERIC_STATIC_SUFFIX}*|*_${NUMERIC_INT64_SUFFIX})
- MULTILIB_ABI_FLAG="${ABI}"
- ;;
- *_${NUMERIC_INT32_SUFFIX})
- MULTILIB_ABI_FLAG="${v%.*}"
- ;;
- esac
-
- multilib_toolchain_setup "${ABI}"
- readonly ABI
- "${@}" || die
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_int_abi
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric variant (e.g. int32, int64)
-numeric-int64-multibuild_foreach_int_abi() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_int_variants) )
- multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_variant
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric abi and static-libs (e.g. int32, int64, static)
-numeric-int64-multibuild_foreach_variant() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_variants) )
- multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_all_abi_variants
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric variant (e.g. int32, int64, static) _AND_
-# enabled multilib ABI
-numeric-int64-multibuild_foreach_all_abi_variants() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) )
- multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_copy_sources
-# @DESCRIPTION:
-# Thin wrapper around multibuild_copy_sources()
-numeric-int64-multibuild_copy_sources() {
- debug-print-function ${FUNCNAME} "${@}"
- local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) )
- multibuild_copy_sources
-}
-
-_NUMERIC_INT64_MULTILIB_ECLASS=1
-fi
diff --git a/eclass/numeric.eclass b/eclass/numeric.eclass
deleted file mode 100644
index 431b7afec..000000000
--- a/eclass/numeric.eclass
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: numeric.eclass
-# @MAINTAINER:
-# jlec@gentoo.org
-# @BLURB: Maintance bits needed for *lapack* and *blas* packages
-# @DESCRIPTION:
-# Various functions which make the maintenance numerical algebra packages
-# easier.
-
-if [[ ! ${_NUMERIC_ECLASS} ]]; then
-
-case ${EAPI:-0} in
- 0|1|2|3|4|5)
- inherit multilib ;;
- 6|7) ;;
- *) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-# @VARIABLE: NUMERIC_MODULE_NAME
-# @DESCRIPTION:
-# The base pkg-config module name of the package being built.
-# NUMERIC_MODULE_NAME is used by the numeric-int64_get_module_name to
-# determine the pkg-config module name based on whether the package
-# has dynamic, threads or openmp USE flags and if so, if the user has
-# turned them or, and if the current multibuild is a int64 build or not.
-#
-# @CODE
-# NUMERIC_MODULE_NAME="openblas"
-# inherit ... numeric-int64-multibuild
-# @CODE
-: ${NUMERIC_MODULE_NAME:=blas}
-
-# @FUNCTION: create_pkgconfig
-# @USAGE: [ additional arguments ]
-# @DESCRIPTION:
-# Creates and installs pkg-config file. The function should only be executed in
-# src_install(). For further information about optional arguments please consult
-# http://people.freedesktop.org/~dbn/pkg-config-guide.html
-#
-# @CODE
-# Optional arguments are:
-#
-# -p | --prefix Offset for current package (${EPREFIX}/usr)
-# -e | --exec-prefix Offset for current package (${prefix})
-# -L | --libdir Libdir to use (${prefix}/$(get_libdir))
-# -I | --includedir Includedir to use (${prefix}/include)
-# -n | --name A human-readable name (PN}
-# -d | --description A brief description (DESCRIPTION)
-# -V | --version Version of the package (PV)
-# -u | --url Web presents (HOMEPAGE)
-# -r | --requires Packages required by this package (unset)
-# -l | --libs Link flags specific to this package (unset)
-# -c | --cflags Compiler flags specific to this package (unset)
-# --requires-private Like --requires, but not exposed (unset)
-# --conflicts Packages that this one conflicts with (unset)
-# --libs-private Like --libs, but not exposed (unset)
-# @CODE
-create_pkgconfig() {
- debug-print-function ${FUNCNAME} "${@}"
- local pcfilename pcrequires pcrequirespriv pcconflicts pclibs pclibspriv pccflags
- local pcprefix="${EPREFIX}/usr"
- local pcexecprefix="${pcprefix}"
- local pclibdir="${EPREFIX}/usr/$(get_libdir)"
- local pcincldir="${pcprefix}/include"
- local pcname=${PN}
- local pcdescription="${DESCRIPTION}"
- local pcurl=${HOMEPAGE}
- local pcversion=${PV}
-
- [[ "${EBUILD_PHASE}" != "install" ]] && \
- die "create_pkgconfig should only be used in src_install()"
-
- while (($#)); do
- case ${1} in
- -p | --prefix )
- shift; pcprefix=${1} ;;
- -e | --exec-prefix )
- shift; pcexecprefix=${1} ;;
- -L | --libdir )
- shift; pclibdir=${1} ;;
- -I | --includedir )
- shift; pcincldir=${1} ;;
- -n | --name )
- shift; pcname=${1} ;;
- -d | --description )
- shift; pcdescription=${1} ;;
- -V | --version )
- shift; pcversion=${1} ;;
- -u | --url )
- shift; pcurl=${1} ;;
- -r | --requires )
- shift; pcrequires=${1} ;;
- --requires-private )
- shift; pcrequirespriv=${1} ;;
- --conflicts )
- shift; pcconflicts=${1};;
- -l | --libs )
- shift; pclibs=${1} ;;
- --libs-private )
- shift; pclibspriv=${1} ;;
- -c | --cflags )
- shift; pccflags=${1} ;;
- -* )
- ewarn "Unknown option ${1}" ;;
- * )
- pcfilename=${1} ;;
- esac
- shift
- done
-
- [[ -z ${pcfilename} ]] && die "Missing name for pkg-config file"
-
- cat > "${T}"/${pcfilename}.pc <<- EOF
- prefix="${pcprefix}"
- exec_prefix="${pcexecprefix}"
- libdir="${pclibdir}"
- includedir="${pcincldir}"
-
- Name: ${pcname}
- Description: ${pcdescription}
- Version: ${pcversion}
- URL: ${pcurl}
- Requires: ${pcrequires}
- Requires.private: ${pcrequirespriv}
- Conflicts: ${pcconflicts}
- Libs: -L\${libdir} ${pclibs}
- Libs.private: ${pclibspriv}
- Cflags: -I\${includedir} ${pccflags}
- EOF
-
- insinto /usr/$(get_libdir)/pkgconfig
- doins "${T}"/${pcfilename}.pc
-}
-
-_NUMERIC_ECLASS=1
-fi
diff --git a/licenses/CeCILL-1.1 b/licenses/CeCILL-1.1
deleted file mode 100644
index b4efe1181..000000000
--- a/licenses/CeCILL-1.1
+++ /dev/null
@@ -1,513 +0,0 @@
- FREE SOFTWARE LICENSING AGREEMENT CeCILL
- ========================================
-
-
-Notice
-------
-
-
-This Agreement is a free software license that is the result of discussions
-between its authors in order to ensure compliance with the two main
-principles guiding its drafting:
- - firstly, its conformity with French law, both as regards the law of
- torts and intellectual property law, and the protection that it offers
- to authors and the holders of economic rights over software.
- - secondly, compliance with the principles for the distribution of free
- software: access to source codes, extended user-rights.
-
-The following bodies are the authors of this license CeCILL (Ce : CEA, C :
-CNRS, I : INRIA, LL : Logiciel Libre):
-
-Commissariat l'Energie Atomique - CEA, a public scientific, technical and
-industrial establishment, having its principal place of business at 31-33
-rue de la Fdration, 75752 PARIS cedex 15, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business at
-3 rue Michel-Ange 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique - INRIA, a
-public scientific and technological establishment, having its principal
-place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le
-Chesnay cedex.
-
-
-PREAMBLE
---------
-
-
-The purpose of this Free Software Licensing Agreement is to grant users the
-right to modify and redistribute the software governed by this license
-within the framework of an "open source" distribution model.
-
-The exercising of these rights is conditional upon certain obligations for
-users so as to ensure that this status is retained for subsequent
-redistribution operations.
-
-As a counterpart to the access to the source code and rights to copy, modify
-and redistribute granted by the license, users are provided only with a
-limited warranty and the software's author, the holder of the economic
-rights, and the successive licensors only have limited liability.
-
-In this respect, it is brought to the user's attention that the risks
-associated with loading, using, modifying and/or developing or reproducing
-the software by the user given its nature of Free Software, that may
-mean that it is complicated to manipulate, and that also therefore means
-that it is reserved for developers and experienced professionals having
-in-depth computer knowledge. Users are therefore encouraged to load and test
-the Software's suitability as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and, more
-generally, to use and operate it in the same conditions of security.
-This Agreement may be freely reproduced and published, provided it is
-not altered, and that no Articles are either added or removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of the
-economic rights decides to submit the operation thereof to its provisions.
-
-
-Article 1 - DEFINITIONS
-------------------------
-
-
-For the purposes of this Agreement, when the following expressions commence
-with a capital letter, they shall have the following meaning:
-
-Agreement: means this Licensing Agreement, and any or all of its subsequent
-versions.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" at the time when the
-Licensee accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and/or Object Code
-form and, where applicable, its documentation, "as is" at the time when it
-is distributed for the first time under the terms and conditions of the
-Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of the
-Source Code.
-
-Holder: means the holder of the economic rights over the Initial
-Software.
-
-Licensee(s): mean(s) the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any or all other individual or legal entity,
-that distributes the Software under the Agreement.
-
-Contributions: mean any or all modifications, corrections, translations,
-adaptations and/or new functionalities integrated into the Software by any
-or all Contributor, and the Static Modules.
-
-Module: means a set of sources files including their documentation that,
-once compiled in executable form, enables supplementary functionalities or
-services to be developed in addition to those offered by the Software.
-
-Dynamic Module: means any or all module, created by the Contributor, that
-is independent of the Software, so that this module and the Software are in
-two different executable forms that are run in separate address spaces,
-with one calling the other when they are run.
-
-Static Module: means any or all module, created by the Contributor and
-connected to the Software by a static link that makes their object codes
-interdependent. This module and the Software to which it is connected, are
-combined in a single executable.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
-Article 2 - PURPOSE
--------------------
-
-
-The purpose of the Agreement is to enable the Licensor to grant the
-Licensee a free, non-exclusive, transferable and worldwide License for the
-Software as set forth in Article 5 hereinafter for the whole term of
-protection of the rights over said Software.
-
-
-Article 3 - ACCEPTANCE
-----------------------
-
-
-3.1. The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement by the occurrence of the first of the
-following events:
-- (i) loading the Software by any or all means, notably, by downloading
- from a remote server, or by loading from a physical medium;
-- (ii) the first time the Licensee exercises any of the rights granted
- hereunder.
-
-3.2. One copy of the Agreement, containing a notice relating to the
-specific nature of the Software, to the limited warranty, and to the
-limitation to use by experienced users has been provided to the Licensee
-prior to its acceptance as set forth in Article 3.1 hereinabove, and the
-Licensee hereby acknowledges that it is aware thereof.
-
-
-Article 4 - EFFECTIVE DATE AND TERM
------------------------------------
-
-
-4.1. EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by the
-Licensee as set forth in Article 3.1.
-
-4.2. TERM
-
-The Agreement shall remain in force during the whole legal term of
-protection of the economic rights over the Software.
-
-
-Article 5 - SCOPE OF THE RIGHTS GRANTED
----------------------------------------
-
-
-The Licensor hereby grants to the Licensee, that accepts such, the
-following rights as regards the Software for any or all use, and for the
-term of the Agreement, on the basis of the terms and conditions set forth
-hereinafter.
-
-Otherwise, the Licensor grants to the Licensee free of charge exploitation
-rights on the patents he holds on whole or part of the inventions
-implemented in the Software.
-
-5.1. RIGHTS OF USE
-
-The Licensee is authorized to use the Software, unrestrictedly, as regards
-the fields of application, with it being hereinafter specified that this
-relates to:
-- permanent or temporary reproduction of all or part of the Software by
- any or all means and in any or all form.
-- loading, displaying, running, or storing the Software on any or all
- medium.
-- entitlement to observe, study or test the operation thereof so as to
- establish the ideas and principles that form the basis for any or all
- constituent elements of said Software. This shall apply when the
- Licensee carries out any or all loading, displaying, running,
- transmission or storage operation as regards the Software, that it is
- entitled to carry out hereunder.
-
-5.2. entitlement to make CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modification to the Software, and the right to
-reproduce the resulting Software.
-
-The Licensee is authorized to make any or all Contribution to the Software
-provided that it explicitly mentions its name as the author of said
-Contribution and the date of the development thereof.
-
-5.3. DISTRIBUTION AND PUBLICATION RIGHTS
-
-In particular, the right of distribution and publication includes the right
-to transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, a copy or copies of the Software
-by means of any or all process.
-The Licensee is further authorized to redistribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-5.3.1. REDISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to redistribute true copies of the Software in
-Source Code or Object Code form, provided that said redistribution complies
-with all the provisions of the Agreement and is accompanied by:
-- a copy of the Agreement,
-- a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-and that, in the event that only the Software's Object Code is
-redistributed, the Licensee allows future Licensees unhindered access to
-the Software's full Source Code by providing them with the terms and
-conditions for access thereto, it being understood that the additional cost
-of acquiring the Source Code shall not exceed the cost of transferring the
-data.
-
-5.3.2. REDISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
-conditions for the redistribution of the Modified Software shall then be
-subject to all the provisions hereof.
-
-The Licensee is authorized to redistribute the Modified Software, in Source
-Code or Object Code form, provided that said redistribution complies with
-all the provisions of the Agreement and is accompanied by:
-- a copy of the Agreement,
-- a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-and that, in the event that only the Modified Software's Object Code is
-redistributed, the Licensee allows future Licensees unhindered access to
-the Modified Software's full Source Code by providing them with the terms
-and conditions for access thereto, it being understood that the additional
-cost of acquiring the Source Code shall not exceed the cost of transferring
-the data.
-
-
-5.3.3. redistribution OF DYNAMIC MODULES
-
-When the Licensee has developed a Dynamic Module, the terms and conditions
-hereof do not apply to said Dynamic Module, that may be distributed under
-a separate Licensing Agreement.
-
-5.3.4. COMPATIBILITY WITH THE GPL LICENSE
-
-In the event that the Modified or unmodified Software is included in a code
-that is subject to the provisions of the GPL License, the Licensee is
-authorized to redistribute the whole under the GPL License.
-
-In the event that the Modified Software includes a code that is subject to
-the provisions of the GPL License, the Licensee is authorized to
-redistribute the Modified Software under the GPL License.
-
-
-Article 6 - INTELLECTUAL PROPERTY
-----------------------------------
-
-
-6.1. OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or all
-use of the Initial Software is subject to compliance with the terms and
-conditions under which the Holder has elected to distribute its work and no
-one shall be entitled to and it shall have sole entitlement to modify the
-terms and conditions for the distribution of said Initial Software.
-
-The Holder undertakes to maintain the distribution of the Initial Software
-under the conditions of the Agreement, for the duration set forth in
-article 4.2..
-
-6.2. OVER THE CONTRIBUTIONS
-
-The intellectual property rights over the Contributions belong to the
-holder of the economic rights as designated by effective legislation.
-
-6.3. OVER THE DYNAMIC MODULES
-
-The Licensee having developed a Dynamic Module is the holder of the
-intellectual property rights over said Dynamic Module and is free to choose
-the agreement that shall govern its distribution.
-
-6.4. JOINT PROVISIONS
-
-6.4.1. The Licensee expressly undertakes:
-- not to remove, or modify, in any or all manner, the intellectual
- property notices affixed to the Software;
-- to reproduce said notices, in an identical manner, in the copies of
- the Software.
-
-6.4.2. The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights of the Holder and/or Contributors and to take,
-where applicable, vis--vis its staff, any or all measures required to
-ensure respect for said intellectual property rights of the Holder and/or
-Contributors.
-
-
-Article 7 - RELATED SERVICES
------------------------------
-
-
-7.1. Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of service. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall then be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2. Similarly, any or all Licensor shall be entitled to offer to its
-Licensees, under its own responsibility, a warranty, that shall only be
-binding upon itself, for the redistribution of the Software and/or the
-Modified Software, under terms and conditions that it shall decide upon
-itself. Said warranty, and the financial terms and conditions of its
-application, shall be subject to a separate instrument executed between the
-Licensor and the Licensee.
-
-
-Article 8 - LIABILITY
-----------------------
-
-
-8.1. Subject to the provisions of Article 8.2, should the Licensor fail to
-fulfill all or part of its obligations hereunder, the Licensee shall be
-entitled to claim compensation for the direct loss suffered as a result of
-a fault on the part of the Licensor, subject to providing evidence of it.
-
-8.2. The Licensor's liability is limited to the commitments made under this
-Licensing Agreement and shall not be incurred as a result , in particular:
-(i) of loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss due to the Software's use or
-performance that is suffered by the Licensee, when the latter is a
-professional using said Software for professional purposes and (iii)
-consequential loss due to the Software's use or performance. The Parties
-expressly agree that any or all pecuniary or business loss (i.e. loss of
-data, loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party, shall
-constitute consequential loss and shall not provide entitlement to any or
-all compensation from the Licensor.
-
-
-Article 9 - WARRANTY
----------------------
-
-
-9.1. The Licensee acknowledges that the current situation as regards
-scientific and technical know-how at the time when the Software was
-distributed did not enable all possible uses to be tested and verified, nor
-for the presence of any or all faults to be detected. In this respect, the
-Licensee's attention has been drawn to the risks associated with loading,
-using, modifying and/or developing and reproducing the Software that are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means, the
-product's suitability for its requirements, its due and proper functioning,
-and for ensuring that it shall not cause damage to either persons or
-property.
-
-9.2. The Licensor hereby represents, in good faith, that it is entitled to
-grant all the rights on the Software (including in particular the rights
-set forth in Article 5 hereof over the Software).
-
-9.3. The Licensee acknowledges that the Software is supplied "as is" by the
-Licensor without any or all other express or tacit warranty, other than
-that provided for in Article 9.2 and, in particular, without any or all
-warranty as to its market value, its secured, innovative or relevant
-nature.
-
-Specifically, the Licensor does not warrant that the Software is free from
-any or all error, that it shall operate continuously, that it shall be
-compatible with the Licensee's own equipment and its software
-configuration, nor that it shall meet the Licensee's requirements.
-
-9.4. The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any or all third party intellectual right
-relating to a patent, software or to any or all other property right.
-Moreover, the Licensor shall not hold the Licensee harmless against any or
-all proceedings for infringement that may be instituted in respect of the
-use, modification and redistribution of the Software. Nevertheless, should
-such proceedings be instituted against the Licensee, the Licensor shall
-provide it with technical and legal assistance for its defense. Such
-technical and legal assistance shall be decided upon on a case-by-case
-basis between the relevant Licensor and the Licensee pursuant to a
-memorandum of understanding. The Licensor disclaims any or all liability as
-regards the Licensee's use of the Software's name. No warranty shall be
-provided as regards the existence of prior rights over the name of the
-Software and as regards the existence of a trademark.
-
-
-Article 10 - TERMINATION
--------------------------
-
-
-10.1. In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement thirty
-(30) days after notice has been sent to the Licensee and has remained
-ineffective.
-
-10.2. The Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any or all
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance with
-the terms and conditions hereof.
-
-
-Article 11 - MISCELLANEOUS PROVISIONS
---------------------------------------
-
-
-11.1. EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to perform
-the Agreement, that may be attributable to an event of force majeure, an
-act of God or an outside cause, such as, notably, defective functioning, or
-interruptions affecting the electricity or telecommunications networks,
-blocking of the network following a virus attack, the intervention of the
-government authorities, natural disasters, water damage, earthquakes, fire,
-explosions, strikes and labor unrest, war, etc.
-
-11.2. The fact that either Party may fail, on one or several occasions, to
-invoke one or several of the provisions hereof, shall under no
-circumstances be interpreted as being a waiver by the interested Party of
-its entitlement to invoke said provision(s) subsequently.
-
-11.3. The Agreement cancels and replaces any or all previous agreement,
-whether written or oral, between the Parties and having the same purpose,
-and constitutes the entirety of the agreement between said Parties
-concerning said purpose. No supplement or modification to the terms and
-conditions hereof shall be effective as regards the Parties unless it is
-made in writing and signed by their duly authorized representatives.
-
-11.4. In the event that one or several of the provisions hereof were to
-conflict with a current or future applicable act or legislative text, said
-act or legislative text shall take precedence, and the Parties shall make
-the necessary amendments so as to be in compliance with said act or
-legislative text. All the other provisions shall remain effective.
-Similarly, the fact that a provision of the Agreement may be null and
-void, for any reason whatsoever, shall not cause the Agreement as a whole
-to be null and void.
-
-11.5. LANGUAGE
-
-The Agreement is drafted in both French and English. In the event of a
-conflict as regards construction, the French version shall be deemed
-authentic.
-
-
-Article 12 - NEW VERSIONS OF THE AGREEMENT
--------------------------------------------
-
-
-12.1. Any or all person is authorized to duplicate and distribute copies of
-this Agreement.
-
-12.2. So as to ensure coherence, the wording of this Agreement is protected
-and may only be modified by the authors of the License, that reserve the
-right to periodically publish updates or new versions of the Agreement,
-each with a separate number. These subsequent versions may address new issues
-encountered by Free Software.
-
-12.3. Any or all Software distributed under a given version of the
-Agreement may only be subsequently distributed under the same version of
-the Agreement, or a subsequent version, subject to the provisions of
-article 5.3.4.
-
-
-Article 13 - GOVERNING LAW AND JURISDICTION
--------------------------------------------
-
-
-13.1. The Agreement is governed by French law. The Parties agree to
-endeavor to settle the disagreements or disputes that may arise during the
-performance of the Agreement out-of-court.
-
-13.2. In the absence of an out-of-court settlement within two (2) months as
-from their occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the first Party to take action.
-
-
- Version 1.1 of 10/26/2004
-
-
-
-
-
-
-
-
-
-
-
diff --git a/licenses/PGI b/licenses/PGI
deleted file mode 100644
index a54f86c9b..000000000
--- a/licenses/PGI
+++ /dev/null
@@ -1,262 +0,0 @@
-PGI End-User License Agreement
-
-NOTICE: PLEASE READ THIS DOCUMENT CAREFULLY BEFORE DOWNLOADING, COPYING OR
-USING THE LICENSED SOFTWARE. THIS END-USER LICENSE AGREEMENT ("ELA") IS A
-LEGAL AGREEMENT BETWEEN YOU, THE LICENSEE (A SINGLE PERSON, INSTITUTION, OR
-LEGAL ENTITY) ("YOU"), AND STMICROELECTRONICS, N.V., A DUTCH CORPORATION,
-HAVING ITS PRINCIPAL PLACE OF BUSINESS AT STRAWINSKYLAAN 1725, TOWER B 17TH
-FLOOR, 1077 XX AMSTERDAM, THE NETHERLANDS, ACTING FOR THE PURPOSE OF THIS
-ELA THROUGH ITS SWISS BRANCH, 39, CHEMIN DU CHAMP DES FILLES, C. P. 21, CH
-1228 PLAN-LES-OUATES, GENEVA, SWITZERLAND ("ST") FOR THE LICENSED SOFTWARE,
-ASSOCIATED MEDIA, PRINTED MATERIAL, ELECTRONIC DOCUMENTATION OR ANY PORTION
-THEREOF ("SOFTWARE"). ST IS WILLING TO LICENSE THE SOFTWARE TO YOU ONLY
-UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS ELA.
-PLEASE READ THE ELA CAREFULLY. BY DOWNLOADING OR INSTALLING THIS SOFTWARE,
-YOU ACCEPT ALL OF THE TERMS OF THE ELA. PLEASE INDICATE YOUR ACCEPTANCE OF
-ALL OF THE THESE TERMS BY SELECTING THE "ACCEPT" BUTTON AT THE BOTTOM OF
-THE ELA. IF YOU ARE UNWILLING TO BE BOUND BY ALL OF THE TERMS, PLEASE
-SELECT THE "DECLINE" BUTTON AT THE BOTTOM OF THE ELA AND THE DOWNLOAD OR
-INSTALL PROCESS WILL STOP.
-
-
-1) Ownership
-
- The Software distributed and licensed to You hereunder, including, if
- and when provided, any updates furnished to You for free or for
- additional fees, is proprietary to ST or its licensors (ST and
- licensors hereafter referred to as "Licensor"). The Licensors retain
- title to and ownership of the Software, including the copy provided
- herein, and reserve all rights not expressly granted in this ELA.
-
-2) Granting of License
-
-2A) Except as set forth in Sections 3 and 4 below, under the terms and
- conditions of this ELA, You are hereby granted a limited, revocable,
- nontransferable, and nonexclusive license to use the Software subject
- to the restrictions and other terms within. That use must be
- (i) only by You,
- (ii) only on a computer system running a specific operating system
- on which the Software is designed to run and for which portions
- of the Software and subsequent components in the compilation
- process are intended to produce an executable image ("Target
- Systems") for which the corresponding fee has been paid,
- (iii) only on the network(s) and only by the number of users for
- which the corresponding fee has been paid, and
- (iv) only to target no more than the maximum number of CPUs, or
- the maximum number of processes, for which the corresponding
- fee has been paid.
- Except as set forth in Section 2B below, any other use of the
- Software is strictly prohibited.
-
-2B) You may distribute an end-user application that You build with the
- Software that provides significant functionality distinct from that
- included with the Software ("End-User Application") to users within
- Your organization as well as third party users outside Your
- organization ("Sublicensees") for only such uses and/or Target
- Systems for which the Software was designed and intended. You agree
- that any sublicense shall not relieve You from Your obligations under
- this ELA. The Software includes the run-time files, libraries and
- executables ("Run-Time Files") that are bound into Your application
- by the linker or otherwise required by Your application. You may
- also distribute separate dynamically-linked or executable Run-Time
- Files required during the execution of Your End-User Application.
- Whenever an End-User Application is used internally within Your
- organization or by outside third parties, You shall contractually
- require that all Sublicensees abide by the following restrictions:
- (i) they shall not use the "PGI", "The Portland Group", "ST", or
- "STMicroelectronics" name, logo, or trademarks in marketing the
- End-User Application without prior written permission from ST,
- (ii) they will maintain a valid copyright on the End-User
- Application,
- (iii) they will, without limitation, indemnify, hold harmless, and
- defend ST and other applicable Licensors and their respective
- affiliates and suppliers from and against any and all claims,
- lawsuits, costs, and expenses, including attorney's fees, that
- arise or result from their use or distribution of the End-User
- Application, and
- (iv) they shall strictly prohibit the further distribution of the
- Run-Time Files by the user of the End-User Application.
- Notwithstanding the above, the only Run-Time Files that may be
- distributed as noted in this Section 2B are in the folders or
- directories whose names begin with "REDIST".
-
-3) Software from Microsoft
-
- You acknowledge that as part of the Software You may receive Run-Time
- Files in the form of Microsoft Foundation Classes ("MFCs"), Active
- Template Libraries ("ATLs"), and/or "C" Runtime files ("CRTs") in
- binary form only ("Microsoft Distributable Code"). Notwithstanding
- any other provision of this ELA, You acknowledge and agree
- (A) that You have a limited right to use the Microsoft
- Distributable Code to design, develop, or test for use with the
- Software only,
- (B) that You or Your end-users of the Microsoft Distributable Code
- may only use it to create programs that run natively on
- Microsoft platforms, and
- (C) to the following restrictions: You and Your end-users:
- (i) will not alter any copyright, trademark, patent, or other
- legal notice or disclaimer in the Microsoft Distributable
- Code,
- (ii) will not run the Microsoft Distributable Code on a
- platform other than a Microsoft platform, and
- (iii) will not include Microsoft Distributable Code in
- malicious, deceptive, or unlawful programs.
- Further, You will require end users of the Microsoft Distributable
- Code to agree to terms at least as protective as this ELA.
-
-4) Software from Sun Microsystems and/or Oracle America, Inc.
-
- You acknowledge that as part of the Software you are receiving access
- to Java(tm) 2 Runtime Environment (J2RE), version 1.4.2 or subsequent
- versions ("Java Code"). Notwithstanding any other provision of this
- ELA, You are hereby granted a limited, revocable, nontransferable,
- and nonexclusive license, without the right to sublicense, to use the
- Java Code complete and unmodified for the sole purpose of running
- Java applets and applications intended to run on the JavaTM 2
- Platform Standard Edition 5.0 (J2SE 5.0) or subsequent versions on
- Java-enabled general purpose desktop computers and servers.
-
-5) Restrictions
-
-5A) You may make one (1) copy of the Software in machine-readable form,
- solely for archival or backup purposes, provided the copyright notice
- and other proprietary legends on the Software are included on any
- archival/backup copies. You may not modify, adapt, translate,
- reverse engineer, de-compile, disassemble, or create derivative
- works, in whole or in part, based on the Software. You may not rent,
- lease, loan, share, or electronically transfer the Software to
- others.
-
-5B) The term "proprietary" as used in this ELA or in the Software does
- not establish a confidential relationship between the Licensor and
- You and does not in itself provide You any rights to the Software.
- You acknowledge that the Licensors have valuable intellectual
- property rights in the Software and agree to respect and protect such
- intellectual property rights. No right, title, or interest in or to
- any trademark, service mark, logo or trade name of the Licensors is
- granted under this ELA.
-
-5C) You acknowledge and agree that the Software is not designed or
- intended for use in nuclear activities or life support systems. The
- Licensors disclaim any express or implied warranty of fitness for
- such uses.
-
-5D) You will not modify or distribute any of the Software so that any
- part of it becomes subject to an Excluded License. As used in this
- ELA, an "Excluded License" is one that requires, as a condition of
- use, modification, or distribution, that
- (i) the Software be disclosed or distributed in source code form; or
- (ii) others have a right to modify it, or
- (iii) the Software loses its proprietary nature.
- Therefore, without the prior written permission of the applicable
- Licensors, You may not modify the Software directly in any way. In
- particular, You may not introduce or commingle with the Software any
- source or object code that is governed by an open source or public
- license of any kind.
-
-6) Limited Warranty
-
- THE SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. TO
- THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE LICENSORS FURTHER
- DISCLAIM ALL WARRANTIES, INCLUDING WITHOUT LIMITATION ANY IMPLIED
- WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND
- NONINFRINGEMENT. THE ENTIRE RISK ARISING OUT OF THE USE OR
- PERFORMANCE OF THE SOFTWARE AND DOCUMENTATION REMAINS WITH YOU. TO
- THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL
- THE LICENSORS BE LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, INDIRECT,
- SPECIAL, PUNITIVE, OR OTHER DAMAGES WHATSOEVER (INCLUDING, WITHOUT
- LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS
- INTERRUPTION, LOSS OF BUSINESS INFORMATION, LOSS OF DATA OR OTHER
- PECUNIARY LOSS) ARISING OUT OF THIS ELA OR THE USE OF OR INABILITY TO
- USE THE SOFTWARE, EVEN IF THE LICENSORS HAVE BEEN ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGES. NOTWITHSTANDING THE FOREGOING, TO THE
- EXTENT THAT ST MAY BE HELD LEGALLY LIABLE TO YOU BY A COURT OF
- COMPETENT JURISDICTION UNDER CONTRACT, TORT, OR ANY OTHER LEGAL
- THEORY, THE MAXIMUM LIABILITY OF THE LICENSORS SHALL NOT EXCEED THE
- APPLICABLE PURCHASE PRICE OF THE SOFTWARE OR ONE THOUSAND DOLLARS
- ($1,000), WHICHEVER IS GREATER.
-
-7) Indemnity and Audit
-
-7A) You agree to indemnify, defend, and hold the Licensors harmless from
- and against any and all claims, liabilities, damages, penalties,
- settlements, and costs and expenses (including, without limitation,
- reasonable attorneys' fees and court or arbitration costs), asserted
- by any and all third parties (collectively "Claims") against the
- Licensors, and their respective employees, directors, officers, and
- agents alleging or resulting from:
- (i) Your breach of any term or condition of this ELA;
- (ii) alleged or actual infringement of the intellectual property or
- other proprietary rights of a third party by You or Your
- sublicensees; unauthorized alteration of the Software or
- derivative products by You or Your sublicensees;
- (iii) combination of the Software or derivative products with other
- software, products or materials not in accordance with the
- terms of this ELA; or
- (iv) any acts or omissions by You, Your employees, directors,
- officers, and agents or sublicensees either under this ELA or
- outside its scope, including personal injury, death, or
- property damage to anyone or anything.
-
-7B) ST reserves the right, upon reasonable prior written notice to You
- and during Your normal business hours, to audit Your use of the
- Software and any derivative products made therefrom to confirm Your
- compliance with the terms of this ELA.
-
-8) Software Export
-
- All Software and technical data delivered under this ELA are subject
- to US export control laws and may be subject to export or import
- regulations in other countries. You agree to comply strictly with
- all such laws and regulations and acknowledge that You have the
- responsibility to obtain such licenses to export, re-export, or
- import as may be required after delivery to You.
-
-9) Software Manuals
-
- All proprietary documentation provided with the Software is copyrighted
- and may not be copied, photographed, reproduced, translated or reduced
- to any electronic medium or machine-readable form in whole or in part
- without the express, written, prior approval of ST.
-
-10) Government Use
-
- The Software is a "commercial item," as that term is defined at 48
- C.F.R. 2.101 (OCT 1995), consisting of "commercial computer software"
- and "commercial computer software documentation," as such terms are
- used in 48 C.F.R. 12.212 (SEPT 1995) and is provided to the U.S.
- Government only as a commercial end item. Consistent with 48 C.F.R.
- 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (JUNE 1995), all
- U.S. Government licensees and end users acquire the Software with
- only those rights set forth herein.
-
-11) Termination
-
- The license granted to You in this ELA is effective until terminated.
- The license may be terminated by ST at any time without prior notice.
- You may terminate the license at any time by returning and/or
- destroying the Software together with all copies. Upon termination
- of the license for any reason, you agree to destroy all copies of the
- Software.
-
-12) Surviving Terms
-
- In the event this ELA is terminated for any reason, the following
- provisions shall survive termination and shall remain in full force
- and effect: 1, 5, 6, 7, 8, 9, 10, 12, and 13.
-
-13) Controlling Law and Complete Agreement
-
- This Agreement shall be construed and interpreted under the laws of
- the state of New York, not including its conflict of laws principles.
- If any provision of this ELA, or portion thereof, is found to be
- unenforceable, that provision shall be enforced to the maximum extent
- possible and the remainder of this ELA shall continue in full force
- and effect.
-
-YOU ACKNOWLEDGE THAT YOU HAVE READ THIS ELA AND AGREE TO BE BOUND BY ITS
-TERMS. YOU FURTHER AGREE THAT IT IS THE COMPLETE AND EXCLUSIVE STATEMENT
-OF AGREEMENT BETWEEN YOU AND ST AND THAT IT SUPERSEDES ANY PRIOR AGREEMENT,
-ORAL OR WRITTEN, ANY PROPOSAL, AND ANY OTHER COMMUNICATIONS BETWEEN YOU AND
-ST RELATING TO THE SUBJECT MATTER OF THIS ELA.
-
diff --git a/licenses/ligplot+ b/licenses/ligplot+
deleted file mode 100644
index 7457f6622..000000000
--- a/licenses/ligplot+
+++ /dev/null
@@ -1,138 +0,0 @@
-LIGPLOT - Automated representation of protein-ligand interactions
- ----------------------------------------------------------------
-
- CONFIDENTIALITY AGREEMENT
- -------------------------
-
-
-
-In regard to the LIGPLOT , specified in the Appendix herewith
-(the Software) supplied to us, the copyright and other
-intellectual property rights to which belong to the authors, we
-
-
- __________________________________________________________________
-
-undertake to the authors that we shall be bound by the following terms
-and conditions:-
-
-1. We will receive the Software and any related documentation in
-confidence and will not use the same except for the purpose of the
-department's own research. The Software will be used only by such of
-our officers or employees to whom it must reasonably be communicated
-to enable us to undertake our research and who agree to be bound by
-the same confidence. The department shall procure and enforce such
-agreement from its staff for the benefit of the authors.
-
-2. The publication of research using the Software must reference
-"Wallace A C, Laskowski R A, Thornton J M (1995). LIGPLOT: A program
-to generate schematic diagrams of protein-ligand interactions. Protein
-Engineering, 8, 127-134."
-
-3. Research shall take place solely at the department's premises at
-
-
- __________________________________________________________________
-
-4. All forms of the Software will be kept in a reasonably secure place
- to prevent unauthorised access.
-
-5. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking
-maintained) with the following copyright notice: " Copyright 1994
-A C Wallace, R A Laskowski, & J M Thornton All Rights Reserved".
-
-6. The Software may be modified but any changes made shall be made
-available to the authors.
-
-7. The Software shall be used exclusively for academic teaching and
-research. The Software will not be used for any commercial research or
-research associated with an industrial company.
-
-8. The confidentiality obligation in paragraph one shall not apply:
-
- (i) to information and data known to the department at the time of
- receipt hereunder (as evidenced by its written records);
-
- (ii) to information and data which was at the time of receipt in the
- public domain or thereafter becomes so through no wrongful act of
- the department;
-
- (iii) to information and data which the department receives from a third
- party not in breach of any obligation of confidentiality owed to
- the authors.
-
-Please sign this Undertaking and return a copy of it to indicate that you
-have read, understood and accepted the above terms.
-
-
-
- For and on behalf of _____________________________
-
- _________________________________________________
-
- ..................................................
-
- Dated ............................................
-
-
-
-e-mail address ___________________________
-
-
-
-Please complete the above form, sign it, and then send it, or fax it, to:-
-
-
-Roman Laskowski
-European Bioinformatics Institute,
-Wellcome Trust Genome Campus,
-Hinxton,
-Cambridge, CB10 1SD,
-United Kingdom
-
-Fax:- +44 (0)1223 494 468
-
-roman@ebi.ac.uk
-
-
-If you have any problems either installing the software or running it,
-please e-mail your problems to:-
-
- roman@ebi.ac.uk
-
-
-APPENDIX - Files supplied as part of the LIGPLOT program
---------------------------------------------------------
-
-Source program files:-
-1. ligplot.c
-2. ligplot.h
-3. hbadd.c
-4. hbadd.h
-5. dimer.c
-6. dimer.h
-
-Script files:-
-1. ligplot.scr
-2. ligonly.scr
-3. dimplot.scr
-4. dimonly.scr
-
-Parameter file:-
-1. ligplot.prm
-
-Installation instructions:-
-1. install.doc
-
-Documentation:-
-1. manual.tar.Z
-2. README
-
-Confidentiality Agreement:-
-1. confid.txt
-
-
-
- v.4.4.2 - 7 Mar 2003
-
diff --git a/licenses/polyphen b/licenses/polyphen
deleted file mode 100644
index 250b86ed7..000000000
--- a/licenses/polyphen
+++ /dev/null
@@ -1,7 +0,0 @@
-The software provided herein is free for academic instruction and research
-use only. Commercial licenses are available to legal entities, including
-companies and organizations (both for-profit and non-profit), requiring the
-software for general commercial use. To obtain a commercial license please,
-contact us via e-mail.
-
-e-mail: iadzhubey@rics.bwh.harvard.edu \ No newline at end of file
diff --git a/licenses/signalp b/licenses/signalp
deleted file mode 100644
index 7e5b15f19..000000000
--- a/licenses/signalp
+++ /dev/null
@@ -1,218 +0,0 @@
- ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
- ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF SignalP 3.0
-
- By downloading the Software you are consenting to be bound by and become
- a party to this agreement as the "Licensee". If you do not agree to all
- of the terms of this agreement, you must not click the Acceptance
- button, not install the product nor use the product, and you do not
- become a LICENSEE under this agreement.
-
- If you are not a member of a publicly funded Academic and/or Education
- and/or Research Institution you must obtain a commercial license, please
- send mail to (software@cbs.dtu.dk). This software license agreement is
- entered into by and between Center for Biological Sequence Analysis,
- Technical University of Denmark (hereinafter "CBS") and the "LICENSEE".
-
- WHEREAS CBS has the right to license all copyrights and other property
- rights in the Licensed Software identified as SignalP 3.0 and developed
- by CBS and CBS desires to license the Software so that it becomes
- available for public use and benefit.
-
- WHEREAS LICENSEE is a public funded Academic and/or Education and/or
- Research Institution.
-
- WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
- the Software for internal research purposes only.
-
- NOW, THEREFORE, in consideration of the mutual promises and covenants
- contained herein, the parties agree as follows:
-
- 1. Definitions
-
- "Licensed Software" means the specific version SignalP 3.0 pursuant
- to this Agreement. Any opinion, findings, conclusions or recommendations
- expressed in the Licensed Software are those of the authors and do not
- necessarily reflect the views of CBS.
-
- 2. License
-
- Subject to the terms and conditions of this Agreement a non-exclusive,
- non-transferable License to use and copy the Licensed Software is made
- available free of charge for the LICENSEE which is a non-profit
- educational, academic and/or research institution. The License is only
- granted for personal and internal use in research only at one Site,
- where a Site is defined as a set of contiguous buildings in one
- location. The software will be used at only one location of LICENSEE.
-
- This license does not entitle Licensee to receive from CBS copies of the
- Licensed software on disks, tapes or CD's, hard-copy documentation,
- technical support, telephone assistance, or enhancements or updates to
- the Licensed Software.
-
- The user and any research assistants, co-workers or other workers who
- may use the Software agree to not give the program to third parties or
- grant licenses on software, which include the Software, alone or
- integrated into other software, to third parties. Modification of the
- source code is prohibited without the prior written consent of CBS.
-
- 3. Ownership
-
- Except as expressly licensed in this Agreement, CBS shall retain title
- to the Licensed Software, and any upgrades and modifications created by
- CBS.
-
- 4. Consideration
-
- In consideration for the license rights granted by CBS, LICENSEE will
- obtain this academic license free of charge.
-
- 5. Copies
-
- LICENSEE shall have the right to make copies of the Licensed Software
- for internal use at the Site and for back-up purposes under this
- Agreement, but agrees that all such copies shall contain the copyright
- notices and all other reasonable and appropriate proprietary markings or
- confidential legends that appear on the Licensed Software provided
- hereunder.
-
- 6. Support
-
- CBS shall have no obligation to offer support services to LICENSEE, and
- nothing contained herein shall be interpreted as to require CBS to
- provide maintenance, installation services, version updates, debugging,
- consultation or end-user support of any kind.
-
- 7. Software Protection
-
- LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
- The software code shall be treated as trade secrets and confidential
- information of CBS, and LICENSEE agrees to use best efforts to hold the
- same in confidence. LICENSEE's obligation for confidentiality shall not
- extend to any information which is or becomes generally available to the
- public, is already known to or subsequently disclosed by third parties
- to LICENSEE and at its free disposal, or is independently developed by
- LICENSEE or its affiliates without the use of the confidential
- information disclosed by CBS, or is required by law or legal process.
-
- Except as other wise expressly permitted in this Agreement, Licensee my
- not (i) modify or create any derivative works of the Licensed Software
- or documentation, including customization, translation or localization;
- (ii) decompile, disassemble, reverse engineer, or otherwise attempt to
- derive the source code for the Product; (iii) redistribute, encumber,
- sell, rent, lease, sublicense, or otherwise transfer rights to the
- Licensed Software; (iv) remove or alter any trademark, logo, copyright
- or other proprietary notices, legends, symbols or labels in the Product;
- or (v) publish any results of benchmark tests run on the Product to a
- third party without CBS's prior written consent.
-
- 8. Representations of CBS to LICENSEE
-
- CBS represents to LICENSEE that (i) CBS has the right to grant the
- License and to enter into this agreement, (ii) that, to the best of
- CBS's knowledge, the Licensed software does not infringe any patent,
- copyright or trade secrets of any third party, provided however that
- such representation and warranty shall not apply to any addition to, or
- modifications or adaptation of, the Licensed Software made by LICENSEE
- and (iii) CBS undertakes to use best efforts to cooperate with and
- assist LICENSEE, at LICENSEE's expense, in defending itself against any
- action based on the alleged infringement of any third party patent,
- copyright or trade secret rights resulting from or relating to the use
- or licensing of the Licensed Software by LICENSEE.
-
- 9. Indemnity and Disclaimer of Warranties
-
- Except as expressly set forth in this agreement, CBS makes no
- representations or warranties, express or implied.
-
- The product is provided free of charge, and, therefore, on an "as is"
- basis, without warranty of any kind, express or implied, including
- without limitation the warranties that it is free of defects, virus
- free, able to operate on an uninterrupted basis, merchantable, fit for a
- particular purpose or non-interfering. The entire risk as to the quality
- and performance of the Licensed Software is borne by LICENSEE.
-
- By way of example, but not limitation, CBS makes no representations or
- warranties of merchantability or fitness for any particular application
- or, except as set forth in paragraph 8, that the use of the Software
- will not infringe any patents, copyrights or trademarks or other rights
- of third parties. The entire risk as to the quality and performance of
- the product is borne by LICENSEE. CBS shall not be liable for any
- liability or damages with respect to any claim by LICENSEE or any third
- party on account of, or arising from the license or use of the Software.
-
- Should the Licensed Software prove defective in any respect, LICENSEE
- and not LICENSOR or it's affiliates should assume the entire cost of any
- service and repair. This disclaimer of warranty constitutes an essential
- part of this agreement. No use of the licensed product is authorized
- hereunder except under this disclaimer.
-
- In no event will LICENSOR or its affiliates be liable for any indirect,
- special, incidental or consequential damages arising out of the use of
- or inability to use the product, including, without limitation, damages
- for lost profits, loss of goodwill, work stoppage, computer failure or
- malfunction, or any and all other commercial damages or losses, even if
- advised of the possibility thereof, and regardless of the legal or
- equitable theory (contract, tort or otherwise) upon which the claim is
- based.
-
- 10. Promotional Advertising & References
-
- LICENSEE may not use the name of the Licensed Software in its
- promotional advertising, product literature, and other similar
- promotional materials to be disseminated to the public or any portion
- thereof. LICENSEE agrees not to identify CBS in any promotional
- advertising or other promotional materials to be disseminated to the
- public, or any portion thereof without CBS's prior written consent.
- LICENSEE agrees that any reference to the software for crystallographic
- computations will cite one or more publications as set forth in the
- manual and in agreement with common scientific practice. CBS shall not
- use LICENSEE's name in publicity or advertising involving this Agreement
- or otherwise without LICENSEE's prior written consent which may be
- withheld at LICENSEE's sole discretion.
-
- 11. Term
-
- This Agreement and the license rights granted herein shall become
- effective as of the date this Agreement is executed by both parties and
- shall be perpetual unless terminated in accordance with this Section.
-
- CBS may terminate this Agreement at any time.
-
- Either party may terminate this Agreement at any time effective upon the
- other party's breach of any agreement, covenant, or representation made
- in this Agreement, such breach remaining uncorrected sixty (60) days
- after written notice thereof.
-
- LICENSEE shall have the right, at any time, to terminate this Agreement
- without cause by written notice to CBS specifying the date of
- termination.
-
- Upon termination, LICENSEE shall destroy all full and partial copies of
- the Licensed Software.
-
- 12. Governing Law
-
- This Agreement shall be construed in accordance with the laws of
- Denmark.
-
- 13. General
-
- The parties agree that this Agreement is the complete and exclusive
- agreement among the parties and supersedes all proposals and prior
- agreements whether written or oral, and all other communications among
- the parties relating to the subject matter of this Agreement. This
- Agreement cannot be modified except in writing and signed by both
- parties. Failure by either party at any time to enforce any of the
- provisions of this Agreement shall not constitute a waiver by such party
- of such provision nor in any way affect the validity of this Agreement.
-
- The invalidity of singular provisions does not affect the validity of
- the entire understanding. The parties are obligated, however, to replace
- the invalid provisions by a regulation which comes closest to the
- economic intent of the invalid provision. The same shall apply mutatis
- mutandis in case of a gap.
-
- IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
- duly executed on the date of the download of the software and by
- accepting the license conditions by pressing the Acceptance button.
-
diff --git a/licenses/tmhmm b/licenses/tmhmm
deleted file mode 100644
index 529d135d5..000000000
--- a/licenses/tmhmm
+++ /dev/null
@@ -1,217 +0,0 @@
- ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
- ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF TMHMM 2.0c
-
- By downloading the Software you are consenting to be bound by and become
- a party to this agreement as the "Licensee". If you do not agree to all
- of the terms of this agreement, you must not click the Acceptance
- button, not install the product nor use the product, and you do not
- become a LICENSEE under this agreement.
-
- If you are not a member of a publicly funded Academic and/or Education
- and/or Research Institution you must obtain a commercial license, please
- send mail to (software@cbs.dtu.dk). This software license agreement is
- entered into by and between Center for Biological Sequence Analysis,
- Technical University of Denmark (hereinafter "CBS") and the "LICENSEE".
-
- WHEREAS CBS has the right to license all copyrights and other property
- rights in the Licensed Software identified as TMHMM 2.0c and developed
- by CBS and CBS desires to license the Software so that it becomes
- available for public use and benefit.
-
- WHEREAS LICENSEE is a public funded Academic and/or Education and/or
- Research Institution.
-
- WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
- the Software for internal research purposes only.
-
- NOW, THEREFORE, in consideration of the mutual promises and covenants
- contained herein, the parties agree as follows:
-
- 1. Definitions
-
- "Licensed Software" means the specific version TMHMM 2.0c pursuant
- to this Agreement. Any opinion, findings, conclusions or recommendations
- expressed in the Licensed Software are those of the authors and do not
- necessarily reflect the views of CBS.
-
- 2. License
-
- Subject to the terms and conditions of this Agreement a non-exclusive,
- non-transferable License to use and copy the Licensed Software is made
- available free of charge for the LICENSEE which is a non-profit
- educational, academic and/or research institution. The License is only
- granted for personal and internal use in research only at one Site,
- where a Site is defined as a set of contiguous buildings in one
- location. The software will be used at only one location of LICENSEE.
-
- This license does not entitle Licensee to receive from CBS copies of the
- Licensed software on disks, tapes or CD's, hard-copy documentation,
- technical support, telephone assistance, or enhancements or updates to
- the Licensed Software.
-
- The user and any research assistants, co-workers or other workers who
- may use the Software agree to not give the program to third parties or
- grant licenses on software, which include the Software, alone or
- integrated into other software, to third parties. Modification of the
- source code is prohibited without the prior written consent of CBS.
-
- 3. Ownership
-
- Except as expressly licensed in this Agreement, CBS shall retain title
- to the Licensed Software, and any upgrades and modifications created by
- CBS.
-
- 4. Consideration
-
- In consideration for the license rights granted by CBS, LICENSEE will
- obtain this academic license free of charge.
-
- 5. Copies
-
- LICENSEE shall have the right to make copies of the Licensed Software
- for internal use at the Site and for back-up purposes under this
- Agreement, but agrees that all such copies shall contain the copyright
- notices and all other reasonable and appropriate proprietary markings or
- confidential legends that appear on the Licensed Software provided
- hereunder.
-
- 6. Support
-
- CBS shall have no obligation to offer support services to LICENSEE, and
- nothing contained herein shall be interpreted as to require CBS to
- provide maintenance, installation services, version updates, debugging,
- consultation or end-user support of any kind.
-
- 7. Software Protection
-
- LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
- The software code shall be treated as trade secrets and confidential
- information of CBS, and LICENSEE agrees to use best efforts to hold the
- same in confidence. LICENSEE's obligation for confidentiality shall not
- extend to any information which is or becomes generally available to the
- public, is already known to or subsequently disclosed by third parties
- to LICENSEE and at its free disposal, or is independently developed by
- LICENSEE or its affiliates without the use of the confidential
- information disclosed by CBS, or is required by law or legal process.
-
- Except as other wise expressly permitted in this Agreement, Licensee my
- not (i) modify or create any derivative works of the Licensed Software
- or documentation, including customization, translation or localization;
- (ii) decompile, disassemble, reverse engineer, or otherwise attempt to
- derive the source code for the Product; (iii) redistribute, encumber,
- sell, rent, lease, sublicense, or otherwise transfer rights to the
- Licensed Software; (iv) remove or alter any trademark, logo, copyright
- or other proprietary notices, legends, symbols or labels in the Product;
- or (v) publish any results of benchmark tests run on the Product to a
- third party without CBS's prior written consent.
-
- 8. Representations of CBS to LICENSEE
-
- CBS represents to LICENSEE that (i) CBS has the right to grant the
- License and to enter into this agreement, (ii) that, to the best of
- CBS's knowledge, the Licensed software does not infringe any patent,
- copyright or trade secrets of any third party, provided however that
- such representation and warranty shall not apply to any addition to, or
- modifications or adaptation of, the Licensed Software made by LICENSEE
- and (iii) CBS undertakes to use best efforts to cooperate with and
- assist LICENSEE, at LICENSEE's expense, in defending itself against any
- action based on the alleged infringement of any third party patent,
- copyright or trade secret rights resulting from or relating to the use
- or licensing of the Licensed Software by LICENSEE.
-
- 9. Indemnity and Disclaimer of Warranties
-
- Except as expressly set forth in this agreement, CBS makes no
- representations or warranties, express or implied.
-
- The product is provided free of charge, and, therefore, on an "as is"
- basis, without warranty of any kind, express or implied, including
- without limitation the warranties that it is free of defects, virus
- free, able to operate on an uninterrupted basis, merchantable, fit for a
- particular purpose or non-interfering. The entire risk as to the quality
- and performance of the Licensed Software is borne by LICENSEE.
-
- By way of example, but not limitation, CBS makes no representations or
- warranties of merchantability or fitness for any particular application
- or, except as set forth in paragraph 8, that the use of the Software
- will not infringe any patents, copyrights or trademarks or other rights
- of third parties. The entire risk as to the quality and performance of
- the product is borne by LICENSEE. CBS shall not be liable for any
- liability or damages with respect to any claim by LICENSEE or any third
- party on account of, or arising from the license or use of the Software.
-
- Should the Licensed Software prove defective in any respect, LICENSEE
- and not LICENSOR or it's affiliates should assume the entire cost of any
- service and repair. This disclaimer of warranty constitutes an essential
- part of this agreement. No use of the licensed product is authorized
- hereunder except under this disclaimer.
-
- In no event will LICENSOR or its affiliates be liable for any indirect,
- special, incidental or consequential damages arising out of the use of
- or inability to use the product, including, without limitation, damages
- for lost profits, loss of goodwill, work stoppage, computer failure or
- malfunction, or any and all other commercial damages or losses, even if
- advised of the possibility thereof, and regardless of the legal or
- equitable theory (contract, tort or otherwise) upon which the claim is
- based.
-
- 10. Promotional Advertising & References
-
- LICENSEE may not use the name of the Licensed Software in its
- promotional advertising, product literature, and other similar
- promotional materials to be disseminated to the public or any portion
- thereof. LICENSEE agrees not to identify CBS in any promotional
- advertising or other promotional materials to be disseminated to the
- public, or any portion thereof without CBS's prior written consent.
- LICENSEE agrees that any reference to the software for crystallographic
- computations will cite one or more publications as set forth in the
- manual and in agreement with common scientific practice. CBS shall not
- use LICENSEE's name in publicity or advertising involving this Agreement
- or otherwise without LICENSEE's prior written consent which may be
- withheld at LICENSEE's sole discretion.
-
- 11. Term
-
- This Agreement and the license rights granted herein shall become
- effective as of the date this Agreement is executed by both parties and
- shall be perpetual unless terminated in accordance with this Section.
-
- CBS may terminate this Agreement at any time.
-
- Either party may terminate this Agreement at any time effective upon the
- other party's breach of any agreement, covenant, or representation made
- in this Agreement, such breach remaining uncorrected sixty (60) days
- after written notice thereof.
-
- LICENSEE shall have the right, at any time, to terminate this Agreement
- without cause by written notice to CBS specifying the date of
- termination.
-
- Upon termination, LICENSEE shall destroy all full and partial copies of
- the Licensed Software.
-
- 12. Governing Law
-
- This Agreement shall be construed in accordance with the laws of
- Denmark.
-
- 13. General
-
- The parties agree that this Agreement is the complete and exclusive
- agreement among the parties and supersedes all proposals and prior
- agreements whether written or oral, and all other communications among
- the parties relating to the subject matter of this Agreement. This
- Agreement cannot be modified except in writing and signed by both
- parties. Failure by either party at any time to enforce any of the
- provisions of this Agreement shall not constitute a waiver by such party
- of such provision nor in any way affect the validity of this Agreement.
-
- The invalidity of singular provisions does not affect the validity of
- the entire understanding. The parties are obligated, however, to replace
- the invalid provisions by a regulation which comes closest to the
- economic intent of the invalid provision. The same shall apply mutatis
- mutandis in case of a gap.
-
- IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
- duly executed on the date of the download of the software and by
- accepting the license conditions by pressing the Acceptance button.
diff --git a/media-libs/imglib2/Manifest b/media-libs/imglib2/Manifest
new file mode 100644
index 000000000..3ce824e00
--- /dev/null
+++ b/media-libs/imglib2/Manifest
@@ -0,0 +1 @@
+DIST imglib2-6.2.0-sources.tar.gz 1088844 BLAKE2B 919b4261199415e0e575bba297900e5dc177785b70511d797a7f962675adaa61f19467d37d664c12a4dc91df3f1f6cd575309c7f508c4792706942670c6946c0 SHA512 e3381979884dac13d051f1754be0837049e430b71c382666d036fa1d3403bc233a7b39c3b0c587852b08d7d12851043111a1ab206e4049d117dedf847da687e9
diff --git a/media-libs/imglib2/imglib2-6.2.0.ebuild b/media-libs/imglib2/imglib2-6.2.0.ebuild
new file mode 100644
index 000000000..d024676c7
--- /dev/null
+++ b/media-libs/imglib2/imglib2-6.2.0.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A multidimensional, type-agnostic image processing library."
+HOMEPAGE="
+ http://imglib2.net/
+ https://github.com/imglib/imglib2
+"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/imglib/imglib2.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="net.imglib2:imglib2:9999"
+else
+ SRC_URI="
+ https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+# jmh-core: According to the pom version 1.36 is required,
+# however, jmh-core-1.35 is latest available in Gentoo
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ >=dev-java/jama-1.0.3
+ >=dev-java/junit-4.13.2
+ >=dev-java/jmh-core-1.35
+ )
+"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/media-libs/imglib2/imglib2-9999.ebuild b/media-libs/imglib2/imglib2-9999.ebuild
new file mode 100644
index 000000000..d024676c7
--- /dev/null
+++ b/media-libs/imglib2/imglib2-9999.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A multidimensional, type-agnostic image processing library."
+HOMEPAGE="
+ http://imglib2.net/
+ https://github.com/imglib/imglib2
+"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/imglib/imglib2.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="net.imglib2:imglib2:9999"
+else
+ SRC_URI="
+ https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+# jmh-core: According to the pom version 1.36 is required,
+# however, jmh-core-1.35 is latest available in Gentoo
+BDEPEND="
+ >=virtual/jdk-1.8:*
+ test? (
+ >=dev-java/jama-1.0.3
+ >=dev-java/junit-4.13.2
+ >=dev-java/jmh-core-1.35
+ )
+"
+
+RDEPEND="
+ >=virtual/jre-1.8:*
+"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/media-libs/imglib2/metadata.xml b/media-libs/imglib2/metadata.xml
new file mode 100644
index 000000000..b5cf3918a
--- /dev/null
+++ b/media-libs/imglib2/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+ ImgLib2 is a general-purpose, multidimensional image processing library.
+
+ It provides an interface-driven design that supports numeric and non-numeric data types (8-bit unsigned integer, 32-bit floating point, etc.) in an extensible way. It implements several data sources and sample organizations, including one single primitive array, one array per plane, N-dimensional array “cells” cached to and from disk on demand, and planes read on demand from disk.
+ </longdescription>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">imglib/imglib2</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/media-libs/scifio-jai-imageio/Manifest b/media-libs/scifio-jai-imageio/Manifest
new file mode 100644
index 000000000..3d8ce4b51
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/Manifest
@@ -0,0 +1 @@
+DIST scifio-jai-imageio-1.1.1-sources.tar.gz 826853 BLAKE2B 5bd31431f2b3b1286005ac740d0847281d46f2a4784d823f2a668544a0a69fd006b8b449919008bb51a15a07031a2c8f8c41046ed2f240632c4e7a47616b66da SHA512 041c743c3d5d64110d0f20396bf8d40e06b7806addc40165d6cde1e00edd37ffa22fc1b9887a00c14c701f59c549b3aebf9a7238a71efdac91d018627764e73a
diff --git a/media-libs/scifio-jai-imageio/metadata.xml b/media-libs/scifio-jai-imageio/metadata.xml
new file mode 100644
index 000000000..ff4226a63
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+ SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core. Java API to handle JPEG and JPEG2000 files. Used by Bio-Formats to read images compressed with JPEG2000 and lossless JPEG.
+ </longdescription>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">scifio/scifio-jai-imageio</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild
new file mode 100644
index 000000000..bdc989735
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core."
+HOMEPAGE="http://jai-imageio.dev.java.net/"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="io.scif:scifio-jai-imageio:9999"
+else
+ SRC_URI="
+ https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+ "src/main/resources"
+)
diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild
new file mode 100644
index 000000000..bdc989735
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core."
+HOMEPAGE="http://jai-imageio.dev.java.net/"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git"
+ S="${WORKDIR}/${P}"
+ MAVEN_ID="io.scif:scifio-jai-imageio:9999"
+else
+ SRC_URI="
+ https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+ "
+ S="${WORKDIR}/${PN}-${P}"
+ MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+ "src/main/resources"
+)
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index d117605d1..5916259b7 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,5 +1,4 @@
-DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
-DIST cernbox-client-2.9.2-6339.src.rpm 6243132 BLAKE2B c73c3c338f9d3fb7fa7b22efe9b6ff1380d80f3804e2e732873f5804ed31d98fb04f9dbcdc0f614136c08081bea825d70948f94a6c0c9dddfe20eca66e41c4c1 SHA512 ec0edff177a5b77144eef173e4e3f5d549762faa6682618124f5c64e37f657c3aa00f639723cf2c48b6c4d1049373cd24b41d347cd9bf3c7bb291ab3340d6b2a
-DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
-DIST ownCloud-2.11.1.8438.tar.xz 5655380 BLAKE2B da34adafabfc8c2b0bbfdff99a81b56f2d2639b5168b2165a847a6d5a4efe4e86578984c0f0c20564d0978aab18bb1a62330539bdd137f608a5cfc3ff8d84cf0 SHA512 fe38471f62e7233a7ba04f7fd2c7c7231957e6927c39d0bcf3f6f77fd6cbb1223618bbf6a8cc5fa15de10a35c7f07f2f5df0e49acbc2af5fe9333cda2eb41c92
-DIST ownCloud-2.11.1.8946.tar.xz 5654496 BLAKE2B 6b5b82730460071ae590b35d653824f4e56d506d87929c5d4ebb31eef921d0cb0141a44d7f0c996b8d1afffa5874d3e4dda75feaba740e652df2939633475fcd SHA512 b44f72e22c539a731901d9c146f00edbf0a4dabb992d6cde06be1b50506d5bc4a8aa861c6ea0207eed72aaea8c8af8651ce07f9e9154e6e44ccdecdd27e35b75
+DIST cernbox-client-4.1.0-11373.src.rpm 4621882 BLAKE2B db5106e4e214cee38f729543017adc45a7f4a00e95e57953c6d18b5272e6db88a7d5d820e68272e17d80c3ce962ad3ce689f053a2cff5fe0b7ec2788885cc0d8 SHA512 2deb9c19cbfffd7c37ac06c244c94e996a369ac511d4d71634b7f86f16093cfe7e6d44a97446bcf919924ded392669903344ea38da8bb70cc47317729d355cee
+DIST libregraphapi-1.0.1.tar.gz 105266 BLAKE2B b5122ca5bb757c58bba0f29eaf119685c0ed119a9a72951f4098d8180e5bf05332b36fa6c884ca29b0414051c9c6d6ca081e3c7eeb7b9810202f11c1a70c5190 SHA512 aaa710642c36b4038dc61e7df4fc904a82a2ab6c34da03c3f5328075e41ab319f6616866b7f9ae472ff256b421751f8f5ce7ce0a6d3451bda75cfa3b307df082
+DIST ownCloud-4.1.0.11250.tar.xz 4122856 BLAKE2B 63bdd6047a75e07f6097fec37fb8092675ede50aada272bb8817e0d6ac1aa690cb7257a3d984bac58ed6320543f038cd2c89c49d9161d70ec8a3268997c42af3 SHA512 5f8f43cc8e3ceb2beeebe11fd93937df54e66ce9020a628da232523176815968364667a093cdea6bdf44dca9e1b67878ef76f38c48287327efc0fc3f85f22fb5
+DIST ownCloud-4.2.0.11670.tar.xz 4126004 BLAKE2B 60a5855239b32bfb6769d38de3eced3dcb6c642d702fa33439dfebdc97947dfaed1f0081d2ec8913edc7ab8688872115abd739e21eae7d06e96cbcd92abb5565 SHA512 277d18581155f663c0c18b44a6c0fb9b31c84695e0980da486028b91c1d1c9f5a7ba956afbc11fb2e7fc4679e46a30c2d737667208f5c0599a39bf91a109ce99
diff --git a/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
deleted file mode 100644
index c4eeaa7be..000000000
--- a/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake rpm xdg
-
-DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
-
-# Origin is classic owncloud-client, branded for CERN during compilation.
-ORIGIN_PN="ownCloud"
-BRANDED_P="cernbox"
-BRANDED_PV="2.7.1"
-BRANDED_REL="2596"
-HOMEPAGE="https://cernbox.cern.ch/"
-SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
- https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
- https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
-
-LICENSE="CC-BY-3.0 GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="dolphin gnome-keyring nautilus test"
-
-COMMON_DEPEND=">=dev-db/sqlite-3.4:3
- dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
- dev-qt/qtconcurrent:5
- dev-qt/qtcore:5
- dev-qt/qtdbus:5
- dev-qt/qtgui:5
- dev-qt/qtnetwork:5[ssl]
- dev-qt/qtsql:5
- dev-qt/qtwidgets:5
- dev-qt/qtxml:5
- sys-fs/inotify-tools
- dolphin? (
- kde-frameworks/kcoreaddons:5
- kde-frameworks/kio:5
- )
- nautilus? ( dev-python/nautilus-python )"
-
-RDEPEND="${COMMON_DEPEND}"
-DEPEND="${COMMON_DEPEND}
- dev-qt/linguist-tools:5
- kde-frameworks/extra-cmake-modules
- test? (
- dev-util/cmocka
- dev-qt/qttest:5
- )"
-
-RESTRICT="!test? ( test )"
-
-S=${WORKDIR}/${ORIGIN_PN}-${PV}
-
-PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch )
-
-src_unpack() {
- rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
- mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
-}
-
-src_prepare() {
- # Keep tests in ${T}
- sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
-
- if ! use nautilus; then
- pushd shell_integration > /dev/null || die
- cmake_comment_add_subdirectory nautilus
- popd > /dev/null || die
- fi
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
- -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
- -DBUILD_TESTING=$(usex test)
- )
-
- cmake_src_configure
-}
diff --git a/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild
index c698f7562..741aa66f1 100644
--- a/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -10,21 +10,24 @@ DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
# Origin is classic owncloud-client, branded for CERN during compilation.
ORIGIN_PN="ownCloud"
BRANDED_P="cernbox"
-BRANDED_PV="2.9.2"
-BRANDED_REL="6339"
+BRANDED_PV="4.1.0"
+BRANDED_REL="11373"
+REGRAPHAPI_PV="1.0.1"
HOMEPAGE="https://cernbox.cern.ch/"
SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
- https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
- https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
+ https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz
+ -> libregraphapi-${REGRAPHAPI_PV}.tar.gz"
LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="dolphin gnome-keyring nautilus test"
+IUSE="dolphin keyring nautilus test"
RESTRICT="!test? ( test )"
RDEPEND=">=dev-db/sqlite-3.4:3
- dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
+ dev-libs/qtkeychain[keyring?,qt5(+)]
dev-qt/qtconcurrent:5
dev-qt/qtcore:5
dev-qt/qtdbus:5
@@ -57,7 +60,16 @@ src_unpack() {
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
}
+PATCHES=(
+ "${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
+ "${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch
+ "${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch
+)
+
src_prepare() {
+ mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \
+ src/libsync/libregraphapisrc-src || die
+
# Keep tests in ${T}
sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
diff --git a/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild
index c698f7562..741aa66f1 100644
--- a/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -10,21 +10,24 @@ DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
# Origin is classic owncloud-client, branded for CERN during compilation.
ORIGIN_PN="ownCloud"
BRANDED_P="cernbox"
-BRANDED_PV="2.9.2"
-BRANDED_REL="6339"
+BRANDED_PV="4.1.0"
+BRANDED_REL="11373"
+REGRAPHAPI_PV="1.0.1"
HOMEPAGE="https://cernbox.cern.ch/"
SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
- https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
- https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
+ https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz
+ -> libregraphapi-${REGRAPHAPI_PV}.tar.gz"
LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="dolphin gnome-keyring nautilus test"
+IUSE="dolphin keyring nautilus test"
RESTRICT="!test? ( test )"
RDEPEND=">=dev-db/sqlite-3.4:3
- dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
+ dev-libs/qtkeychain[keyring?,qt5(+)]
dev-qt/qtconcurrent:5
dev-qt/qtcore:5
dev-qt/qtdbus:5
@@ -57,7 +60,16 @@ src_unpack() {
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
}
+PATCHES=(
+ "${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
+ "${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch
+ "${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch
+)
+
src_prepare() {
+ mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \
+ src/libsync/libregraphapisrc-src || die
+
# Keep tests in ${T}
sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
diff --git a/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch b/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch
deleted file mode 100644
index c2ccbcc5e..000000000
--- a/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/branding/cernbox-theme.h 2021-10-21 13:10:22.832842670 +0200
-+++ b/branding/cernbox-theme.h 2021-10-21 13:14:57.394479817 +0200
-@@ -62,7 +62,7 @@
-
-
- QString about() const {
-- QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" MIRALL_STRINGIFY(APPLICATION_DOMAIN))), Utility::escape(QStringLiteral(MIRALL_STRINGIFY(APPLICATION_DOMAIN))));
-+ QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" APPLICATION_DOMAIN)), Utility::escape(QStringLiteral(APPLICATION_DOMAIN)));
-
-
- return devString;
diff --git a/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
new file mode 100644
index 000000000..d9762292e
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
@@ -0,0 +1,17 @@
+Index: ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt
+--- ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt.orig
++++ ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt
+@@ -3,12 +3,7 @@ set(LibreGraphAPIVersion v0.13.2)
+ find_package(LibreGraphAPI QUIET)
+ if (NOT TARGET OpenAPI::LibreGraphAPI)
+ message(WARNING "Failed to find system OpenAPI::LibreGraphAPI: fetching ${LibreGraphAPIVersion}")
+- include(FetchContent)
+- FetchContent_Populate(LibreGraphAPISrc
+- QUIET
+- GIT_REPOSITORY https://github.com/owncloud/libre-graph-api-cpp-qt-client.git
+- GIT_TAG ${LibreGraphAPIVersion})
+- add_subdirectory(${libregraphapisrc_SOURCE_DIR}/client ${libregraphapisrc_BINARY_DIR}/client EXCLUDE_FROM_ALL)
++ add_subdirectory(libregraphapisrc-src/client libregraphapisrc-src/client EXCLUDE_FROM_ALL)
+ endif()
+
+ set(libsync_SRCS
diff --git a/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch
new file mode 100644
index 000000000..266596b7b
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch
@@ -0,0 +1,16 @@
+diff -Naur ownCloud-3.2.0.10193.orig/src/CMakeLists.txt ownCloud-3.2.0.10193/src/CMakeLists.txt
+--- ownCloud-3.2.0.10193.orig/src/CMakeLists.txt 2023-02-15 18:27:55.000000000 +0100
++++ ownCloud-3.2.0.10193/src/CMakeLists.txt 2023-02-22 22:55:29.352847663 +0100
+@@ -16,12 +16,6 @@
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fstack-protector-strong")
+ endif()
+ endif()
+-
+- string(TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER)
+- if(CMAKE_BUILD_TYPE_LOWER MATCHES "(release|relwithdebinfo|minsizerel)")
+- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_FORTIFY_SOURCE=2")
+- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FORTIFY_SOURCE=2")
+- endif()
+ endif()
+
+ if(WIN32)
diff --git a/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch
new file mode 100644
index 000000000..5e00e23aa
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch
@@ -0,0 +1,73 @@
+From: Fabian Müller <fmueller@owncloud.com>
+Bug: https://github.com/owncloud/client/pull/10969
+
+Fix installation of branded client in parallel to unbranded client.
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 4d73f2cc3..49228dbb6 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -54,10 +54,12 @@ endif(NOT BUILD_LIBRARIES_ONLY)
+
+ add_subdirectory(plugins)
+
+-install(EXPORT ownCloudConfig DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud" NAMESPACE ownCloud::)
++install(EXPORT ${APPLICATION_SHORTNAME}Config DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}" NAMESPACE ownCloud::)
+
+-ecm_setup_version(PROJECT VARIABLE_PREFIX ownCloud
+- PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake"
+- SOVERSION ${MIRALL_SOVERSION})
++ecm_setup_version(PROJECT
++ VARIABLE_PREFIX ${APPLICATION_SHORTNAME}
++ PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake"
++ SOVERSION ${MIRALL_SOVERSION}
++)
+
+-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud")
++install(FILES "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}")
+diff --git a/src/csync/CMakeLists.txt b/src/csync/CMakeLists.txt
+index fcf665e44..15c0a8130 100644
+--- a/src/csync/CMakeLists.txt
++++ b/src/csync/CMakeLists.txt
+@@ -98,10 +98,10 @@ INSTALL(
+ ../common/filesystembase.h
+ ../common/utility.h
+ DESTINATION
+- ${INCLUDE_INSTALL_DIR}/ownCloud/common
++ ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/common
+ )
+
+-INSTALL(TARGETS csync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++INSTALL(TARGETS csync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
+
+ configure_file(config_csync.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config_csync.h)
+
+diff --git a/src/libsync/CMakeLists.txt b/src/libsync/CMakeLists.txt
+index 3995bcfe9..eeaef8450 100644
+--- a/src/libsync/CMakeLists.txt
++++ b/src/libsync/CMakeLists.txt
+@@ -85,7 +85,7 @@ INSTALL(
+ ${CMAKE_CURRENT_BINARY_DIR}/owncloudlib.h
+ logger.h
+ accessmanager.h
+- DESTINATION ${INCLUDE_INSTALL_DIR}/ownCloud/libsync
++ DESTINATION ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/libsync
+ )
+
+ add_library(libsync SHARED ${libsync_SRCS})
+@@ -138,4 +138,4 @@ set_target_properties(libsync PROPERTIES
+ VERSION ${MIRALL_VERSION}
+ SOVERSION ${MIRALL_SOVERSION}
+ )
+-install(TARGETS libsync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++install(TARGETS libsync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
+diff --git a/src/resources/CMakeLists.txt b/src/resources/CMakeLists.txt
+index 6f50bf3be..7e0ff05b7 100644
+--- a/src/resources/CMakeLists.txt
++++ b/src/resources/CMakeLists.txt
+@@ -42,4 +42,4 @@ if(Qt5LinguistTools_FOUND)
+ )
+ endif()
+
+-install(TARGETS owncloudResources EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++install(TARGETS owncloudResources EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
diff --git a/net-misc/cernbox-client/metadata.xml b/net-misc/cernbox-client/metadata.xml
index c67ea7b66..e8384eb02 100644
--- a/net-misc/cernbox-client/metadata.xml
+++ b/net-misc/cernbox-client/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>o.freyermuth@googlemail.com</email>
@@ -26,5 +26,7 @@
</use>
<upstream>
<doc>https://cernbox.web.cern.ch/cernbox/</doc>
+ <remote-id type="github">owncloud/client</remote-id>
+ <remote-id type="github">owncloud/libre-graph-api-cpp-qt-client</remote-id>
</upstream>
</pkgmetadata>
diff --git a/profiles/package.mask b/profiles/package.mask
index 147869ad2..9f3b8e7f5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,28 +30,9 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (17 Mar 2023)
-# Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely
-# requires bumping the version which would also require bumping
-# sci-libs/itk
-sci-biology/ants
-# revdep of above
-sci-biology/samri
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
-# Needs bump of PYTHON_COMPAT to at least python3_10
-sci-biology/chiron
-sci-biology/trans-abyss
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
-# Depends on dev-python/nose, needs porting to pytest
-sci-biology/RSeQC
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (10 Feb 2023)
-# Fetch restricted ebuilds without proper manifest entry
-dev-lang/pgi
-sci-biology/signalp
-sci-biology/tmhmm
-sci-chemistry/ligplot+
-sci-chemistry/nmrview
-sci-chemistry/rosetta-tools
+# 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/profiles/package.use.mask b/profiles/package.use.mask
index 79c0fcb5c..39a6df0b7 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -18,7 +18,3 @@
# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
# vtk<9 no longer available in ::gentoo
sci-libs/gdcm python
-
-# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
-# gui sandbox error
-dev-lang/conceptual gui
diff --git a/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild
new file mode 100644
index 000000000..ec394603d
--- /dev/null
+++ b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild
@@ -0,0 +1,44 @@
+# 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_HASH="a7059ef691e74aeb018edaf37df49c99f6efed60"
+
+DESCRIPTION="Conversion and validation tools for BEP 032"
+HOMEPAGE="https://github.com/INT-NIT/BEP032tools"
+SRC_URI="https://github.com/INT-NIT/BEP032tools/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/neo[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ dev-python/parameterized[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/${PN}-${MY_HASH}"
+
+# Require nixio
+EPYTEST_DESELECT=(
+ "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_0_nix"
+ "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_multi_split"
+ "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ice::test_data_file_conversion_0_nix"
+)
+# Require dynamically fetched data
+EPYTEST_DESELECT+=(
+ "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_nwb_to_bids"
+ "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_validation"
+)
+
+distutils_enable_tests pytest
diff --git a/sci-biology/BEP032tools/Manifest b/sci-biology/BEP032tools/Manifest
new file mode 100644
index 000000000..1e97ed9b1
--- /dev/null
+++ b/sci-biology/BEP032tools/Manifest
@@ -0,0 +1 @@
+DIST BEP032tools-0.0.1_alpha.gh.tar.gz 79175 BLAKE2B dc3d999401d2d4361bfc66b72a39fa02bd6148a377bf63b5bdcc788f4018e486e89743b35ad8f61e232b22f79fed6199dad462aaab60e3bbd1425de117b9c576 SHA512 bf929e5f00cfdd47bbdb9f2240bab97468da5bcb72857e8272eb25857ce7d525b6a97cbc459ace8629d67eb9238b8ddd537e2b6269b73d0173a945b39d5eb59e
diff --git a/dev-python/palettable/metadata.xml b/sci-biology/BEP032tools/metadata.xml
index a5b9b813a..8d24d17e7 100644
--- a/dev-python/palettable/metadata.xml
+++ b/sci-biology/BEP032tools/metadata.xml
@@ -2,15 +2,15 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>marbre@linux.sungazer.de</email>
- <name>Marius Brehler</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">jiffyclub/palettable</remote-id>
- <remote-id type="pypi">palettable</remote-id>
+ <remote-id type="github">INT-NIT/BEP032tools</remote-id>
+ <remote-id type="pypi">BEP032tools</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild b/sci-biology/BlastToSam/BlastToSam-1.1.ebuild
deleted file mode 100644
index 775889330..000000000
--- a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 java-pkg-2 java-ant-2
-
-DESCRIPTION="Convert NCBI BLAST+ Pairwise/XML (-outfmt 0 or 5) output to SAM v1.4"
-HOMEPAGE="https://github.com/AstrorEnales/BlastToSam"
-EGIT_REPO_URI="https://github.com/AstrorEnales/BlastToSam.git"
-EGIT_COMMIT="8f543ff1640b64e44701cb534e2959ff46469b2e"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=">=virtual/jre-1.5:*"
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.5:*
- dev-java/ant-core
- dev-java/jython
-"
-
-src_compile() {
- ant compile || die
-}
-
-src_install() {
- java-pkg_dojar build/jar/BlastToSam.jar
- java-pkg_dolauncher
- dodoc README.md
-}
diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml
deleted file mode 100644
index 5a3c7d51d..000000000
--- a/sci-biology/BlastToSam/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">AstrorEnales/BlastToSam</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
index 8e6d2925e..7b070e595 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
@@ -1,17 +1,19 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
HOMEPAGE="http://www.genome.umd.edu/masurca.html
http://bioinformatics.oxfordjournals.org/content/29/21/2669
- https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
+ https://github.com/alekseyzimin/masurca"
SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
LICENSE="BSD GPL-2 GPL-3"
SLOT="0"
-KEYWORDS="~amd64"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
DEPEND="
>=dev-lang/perl-5.8
diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
new file mode 100644
index 000000000..7b070e595
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html
+ http://bioinformatics.oxfordjournals.org/content/29/21/2669
+ https://github.com/alekseyzimin/masurca"
+SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="BSD GPL-2 GPL-3"
+SLOT="0"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
+
+DEPEND="
+ >=dev-lang/perl-5.8
+ app-arch/bzip2
+"
+RDEPEND="${DEPEND}"
+
+src_compile(){
+ ./install.sh || die
+}
+src_install(){
+ dobin masurca
+}
diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest
index 330ac8de3..fd6029f04 100644
--- a/sci-biology/MaSuRCA/Manifest
+++ b/sci-biology/MaSuRCA/Manifest
@@ -1 +1,2 @@
DIST MaSuRCA-4.0.1.tar.gz 26502309 BLAKE2B 658c3a85d3d16bc966f50def9b0f98503f25f89893a18f6b7c361592dc2b20875f4c2b78e55e7279e47d0d381e9f973185da7cf7a1529c617c82b0789dea4183 SHA512 5a52dc6667b501ef5ee33f8c30a516a466b39b061ae3bee93f3e6a9cc9dd21503365671d93858165290b3200c859772324fdb12f8bdab235b3ff08c158c4dd66
+DIST MaSuRCA-4.1.0.tar.gz 26532049 BLAKE2B 93cf8cc2bcb4d2c56961f66c0e045ad7776011b4a5f78e5944c5e9b74004c553fc38e542a163aa2efca0aff0e2726fc38eea1aba8f2da287c5154c9eae4e9bcf SHA512 6de57abff87de2fd8c30bcc7efbd6c37358d37eab518d36ccbe48f036af6e1bc22a655abb59f32df613d99c84a5deca272c8c894395f255bcbceb4da5368e64a
diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml
index 138cb7705..8a631d677 100644
--- a/sci-biology/MaSuRCA/metadata.xml
+++ b/sci-biology/MaSuRCA/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">alekseyzimin/masurca</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/MeV/metadata.xml b/sci-biology/MeV/metadata.xml
index bd7adb92f..334d55097 100644
--- a/sci-biology/MeV/metadata.xml
+++ b/sci-biology/MeV/metadata.xml
@@ -9,6 +9,6 @@
<name>Gentoo Biology Project</name>
</maintainer>
<upstream>
- <remote-id type="sourceforge">downloads</remote-id>
+ <remote-id type="sourceforge">mev-tm4</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/RSeQC/Manifest b/sci-biology/RSeQC/Manifest
deleted file mode 100644
index 5319e5fa5..000000000
--- a/sci-biology/RSeQC/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST RSeQC-4.0.0.tar.gz 101873 BLAKE2B 0a63ef39d3aa27e8ad419ad4d4e335563d870600d03e131fd02e4d4fd8fb403007f8b3a7ec0d57e8731ac616c6a4e07f3d6664668ea0e79aef911c1e54088afb SHA512 77ec4ad2c0f460b8bafe00dcfac6b1d9ddf65f933a55892c376eb7009f5820531dd167acc675b07186e81daa2a904914643dfcb7c220ef7b290d0c8ad3833c42
-DIST fetchChromSizes 2695 BLAKE2B a41f8e0085121f097c0fe93922b221b276f00a5d6af1da76f347ca121882e5d899d482900f51a0da4bff22b0b3158f0e274a67c60d7b7499c1bc3ead96beccd6 SHA512 23405beabb4f42b5cc5b569d9948d070e354ef2be10030b51ba3510865ab4e25bee8aab7283d9b6cbd7df454159a6f89e58ad8f5ee6a541046ad5a72f65019e8
diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
deleted file mode 100644
index 9df8930e5..000000000
--- a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Utilities for RNA-seq data quality control"
-HOMEPAGE="https://sourceforge.net/projects/rseqc/"
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
- https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/nose[${PYTHON_USEDEP}]
-"
-RDEPEND="
- >=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]
- sci-biology/bx-python[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pyBigWig[${PYTHON_USEDEP}]
-"
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # avoid file collision with bx-python
- rm lib/psyco_full.py || die
-}
diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml
deleted file mode 100644
index 5c8442330..000000000
--- a/sci-biology/RSeQC/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">rseqc</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest
deleted file mode 100644
index cb1b89168..000000000
--- a/sci-biology/Trinotate/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Trinotate-3.2.2.tar.gz 12902856 BLAKE2B 741b5b7386c5de646a4a1f3aa4ffc7ed9c4891e64a977efc5cd482eb0cd9315fbddc1db35f20f6fbbf136e28942542f72d33c078524971968a932f5af5d6551b SHA512 9e302eee948974c647fdcc6a352b17d55f3bd1331f6d3ddc49e0fc35f5603dcc370e9c6020e7b33dcd57324a954eab2ed3e81f2e34ef83af2fd97c793f1dfc48
diff --git a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
deleted file mode 100644
index 794de03ae..000000000
--- a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit perl-module
-
-DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
-HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
-SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-${PN}-v${PV}"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/ncbi-tools++
- sci-biology/trinityrnaseq
- sci-biology/TransDecoder
-"
-
-# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
-# >=sci-biology/rnammer-2.3.2
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
-# >=sci-biology/signalp-4
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
-
-# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'.
-# In the 'rnammer' software configuration, edit the rnammer script to point
-# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-
-src_install(){
- perl_set_version
- dobin Trinotate
- insinto /usr/share/"${PN}"
- doins -r admin sample_data util TrinotateWeb
- perl_domodule -r PerlLib/*
- dodoc notes README.md README.txt Changelog.txt
-}
diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml
deleted file mode 100644
index eaf731f09..000000000
--- a/sci-biology/Trinotate/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">Trinotate/Trinotate</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest
index c00c77f25..ef2d97caf 100644
--- a/sci-biology/ants/Manifest
+++ b/sci-biology/ants/Manifest
@@ -1 +1,2 @@
-DIST ants-2.4.1.tar.gz 2473738 BLAKE2B 9abe2ade15bd8348452a23e15d8c862771ca2c8f971c44f185febfb1ee725b1ceb7e89359c8dfee31bd9c4087f10104831fe56bd1528ea7f5a81d52c1a4a4709 SHA512 533ca8adb934e8fe4e24425b3f8a9a8f0b67999d9593f8c8842e0298087d5bc58f65d1fcbfe78ac7dc17d0e786badc4a65bbde80d82d21c277ee6c1b3af7eae4
+DIST ants-2.4.3.tar.gz 2474986 BLAKE2B 56a057673ff65e7ed3037ee34cea481e960122f32d2fd04b347644126793a2ba0a9249823b45e360abf2019136659b3ba4a24e49677458d69cc0b614266faca1 SHA512 50b42e30bec9077a00450253a39a8296ca841a3b3511f623a759071e6fbda9b6ab480b4f26566c621dc85107913f2782f2a1c4ecdeaa8361dc132209a432c544
+DIST ants_testdata-2.4.3.tar.xz 25058064 BLAKE2B ca3bb9998d7ded8fc9821a341a3a5b847a40fe93cccbc61458b5a6f9bab102a14fa297aad2425a5602b70c51e756edab2609213b01e06f7dc63eca2e67846351 SHA512 2689bdf1cb6bc4e608511efab574c8a0a5de839a376e9af91e277bae352744fa58463258ea604ea73041b7b596a3ab3a36e0f5a28c098ee5e7a1a9f8b8873779
diff --git a/sci-biology/ants/ants-2.4.1-r1.ebuild b/sci-biology/ants/ants-2.4.3.ebuild
index 70d5d8873..2dfa2a56d 100644
--- a/sci-biology/ants/ants-2.4.1-r1.ebuild
+++ b/sci-biology/ants/ants-2.4.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -10,40 +10,49 @@ MY_PN="ANTs"
DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
HOMEPAGE="https://stnava.github.io/ANTs/"
-SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="
+ https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ test? (
+ https://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
+ )
+"
S="${WORKDIR}/${MY_PN}-${PV}"
SLOT="0"
LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
IUSE="test vtk"
-RESTRICT="test"
+RESTRICT="!test? ( test )"
DEPEND="
- !vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] )
+ !vtk? ( =sci-libs/itk-5.3*[fftw,-vtkglue] )
vtk? (
- =sci-libs/itk-5.2*[fftw,vtkglue]
- =sci-libs/vtk-9.1*
+ =sci-libs/itk-5.3*[fftw,vtkglue]
+ =sci-libs/vtk-9.2*
)
"
RDEPEND="${DEPEND}"
-PATCHES=(
- "${FILESDIR}/${P}-fix-compile.patch"
-)
+src_unpack() {
+ default
+ if use test; then
+ mkdir -p "${S}/.ExternalData/SHA512" || die "Could not create test data directory."
+ tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/SHA512/" > /dev/null || die "Could not unpack test data."
+ fi
+}
src_configure() {
local mycmakeargs=(
-DBUILD_EXAMPLES=OFF
-DUSE_SYSTEM_ITK=ON
-DITK_USE_SYSTEM_FFTW=ON
- -DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/"
+ -DITK_DIR="${EPREFIX}/usr/include/ITK-5.3/"
-DBUILD_TESTING="$(usex test ON OFF)"
-DUSE_VTK=$(usex vtk ON OFF)
-DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
)
use vtk && mycmakeargs+=(
- -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/"
+ -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.2/"
)
cmake_src_configure
}
diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest
index ab53258d3..283f2cedf 100644
--- a/sci-biology/bidsschematools/Manifest
+++ b/sci-biology/bidsschematools/Manifest
@@ -1,3 +1,3 @@
-DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd
-DIST bidsschematools-0.5.1.tar.gz 1159308 BLAKE2B a53355b24e87ea7008fa64ca4f7e71c7bf29effc52f4aa3f855af633ce83817d5551eead4224d39f8cd46693dc48a7d9325a7ad8698e159b468e902982c5a940 SHA512 f1d9ab6b37c8fd4fd6a6aa821ef718c1af7f3d453d44c2c76c104f5601d40e5a328b0332255a591d8431e8c0ca3406dccd852c6c1fc8d832657b27a6b0076adc
DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1
+DIST bidsschematools-0.7.0.tar.gz 1227313 BLAKE2B 350621d8052ca8ee45be970c4f8973c34d5c7dfd9da0777758009d8f725691efaa665926d9f97723e2331f5511aedf3601fd1df520746b6ec4aebd6ef27a2cf6 SHA512 391e3ed1a96202bada1486de377ea4d96e8622cced132cbb014a697578dbd1c5fdfa3eb2ce6f44b5031136c987e2298a5bc702c1c5751e35479512cfe57a383b
+DIST bidsschematools-0.7.1.tar.gz 1226794 BLAKE2B 6bbc672ac047bd1475b5b79f5cb74b61f190207531be810018768a6cf62e2cae36ccef4893bee041a53ed546f8ae6f104bb64d2f0b89550c80c911d6a48fcee5 SHA512 8cf9e94496108c15360bcc25a1c8e5900350e1fb3da9886c2d089481ae69c94a634ea0cf67e2a1120a93c2982c07061cda8d0d8ecba9715f848c01388108517e
diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
index 13aabaa37..96b6cd57f 100644
--- a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
+++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 2022-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,11 +6,10 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A Python library for working with the BIDS schema"
HOMEPAGE="https://github.com/bids-standard/bids-specification"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild
index 0e62efa42..98b773243 100644
--- a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
+++ b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,20 +6,23 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A Python library for working with the BIDS schema"
HOMEPAGE="https://github.com/bids-standard/bids-specification"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="render"
+# Documented upstream:
+# https://github.com/conda-forge/bidsschematools-feedstock/pull/2
+#RESTRICT="test"
RDEPEND="
dev-python/pyyaml[${PYTHON_USEDEP}]
render? (
+ dev-python/markdown-it-py[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/tabulate[${PYTHON_USEDEP}]
)
@@ -28,6 +31,12 @@ DEPEND=""
distutils_enable_tests pytest
+# Reported upstream:
+# https://github.com/bids-standard/bids-specification/issues/1500
+EPYTEST_DESELECT=(
+ "bidsschematools/tests/test_validator.py::test_bids_datasets[ds000248]"
+)
+
src_prepare() {
if ! use render; then
rm "${S}/bidsschematools/render.py"
diff --git a/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild
index 13aabaa37..b5b12165d 100644
--- a/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild
+++ b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,11 +6,10 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A Python library for working with the BIDS schema"
HOMEPAGE="https://github.com/bids-standard/bids-specification"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
index a94c2be48..dc0c49e6f 100644
--- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
+++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_SETUPTOOLS="rdepend"
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
diff --git a/sci-biology/canu/Manifest b/sci-biology/canu/Manifest
deleted file mode 100644
index f7859b395..000000000
--- a/sci-biology/canu/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST canu-2.1.1.tar.xz 2281796 BLAKE2B ada9326054e0455fac824545baa0ed86d5e53325256a388b9a1bdfa393a2b9ad8926f64b5c871bc10acc9b2d8bac96bcb80682e6ed7c19d01d6ed3b7764111af SHA512 9be64df3c46c6eb98dde915959df346292ac033e650b428b16187e700637b91a87e67ccdf23a241dfbcef7bdb3df289e412d38a2233831eba855fd84dc6ea7c0
diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
deleted file mode 100644
index 987fb99f2..000000000
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit java-pkg-2 perl-module python-r1
-
-DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
-HOMEPAGE="https://canu.readthedocs.io/en/latest"
-SRC_URI="https://github.com/marbl/canu/releases/download/v${PV}/${P}.tar.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- dev-lang/perl
- virtual/perl-File-Path
- sci-visualization/gnuplot
- sci-biology/minimap2
-"
-# =sci-biology/mhap-2.1.3 if we unbundle it
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.8:*
- dev-java/ant-core
-"
-
-# Detected file collision(s):
-# * sci-biology/wgs-assembler-8.3_rc2:0::science
-# * /usr/bin/bogart
-# * /usr/bin/bogus
-# * /usr/bin/fastqAnalyze
-# * /usr/bin/fastqSample
-# * /usr/bin/fastqSimulate
-# * /usr/bin/fastqSimulate-sort
-# * /usr/bin/meryl
-# * /usr/bin/overlapInCore
-# * /usr/bin/utgcns
-
-# Perl 5.12.0, or File::Path 2.08
-# Java SE 8
-# https://github.com/marbl/MHAP uses Apache maven
-
-# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
-
-src_compile(){
- cd src || die
- emake
-}
-
-src_install(){
- # installs
- # /usr/bin
- # /usr/lib/libcanu.a
- # /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu
- # /usr/share/java/classes/mhap-2.1.3.jar
- rm -rf Linux-amd64/obj
- insinto /usr
- doins -r Linux-amd64/{bin,share}
- insinto /usr/$(get_libdir)
- dolib.a Linux-amd64/lib/libcanu.a
- rm Linux-amd64/lib/libcanu.a || die
- perl_set_version
- perl_domodule -r Linux-amd64/lib
-}
diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/canu/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/chiron/Manifest b/sci-biology/chiron/Manifest
deleted file mode 100644
index 2cde5a081..000000000
--- a/sci-biology/chiron/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST chiron-0.6.1.1.tar.gz 53281188 BLAKE2B 56c623ec0d2f8970cd03d892d321362145b44890a0384d5209a2bd8c19b22509ec0557e539f021240a447e836ca6cd3531f3c9ac827b6ece715b086fca73d9f3 SHA512 b74e7f3cea9d206bc0c456189ec643de684a866bdb2dd6fd9d05ac11efd2b980d1aa09f7fc2a2aa3d5df56ca60e7a57c23d63e20df3df10f3ab82c5289d8a52f
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild
deleted file mode 100644
index 162a03129..000000000
--- a/sci-biology/chiron/chiron-0.6.1.1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="A deep neural network basecaller for nanopore sequencing"
-HOMEPAGE="https://github.com/haotianteng/chiron
- https://www.biorxiv.org/content/early/2017/09/12/179531"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MPL-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- sci-biology/mappy[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-biology/biopython[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- sci-libs/tensorflow[${PYTHON_USEDEP}]
-"
diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/chiron/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest
deleted file mode 100644
index 30063661a..000000000
--- a/sci-biology/cutadapt/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST cutadapt-2.10.tar.gz 282198 BLAKE2B 87784fd092d3417775f3a627d68bea1d3421f6392ae90f65e9b5f231f10a4da8cfacecc8c6fc3cd8420d0255ffc44ec72188bc901d1768f18f3b78077a165314 SHA512 afefb101a25daa071e5945e442de46cd594a6f4ba5915e9d11943280039223ff5d686b358de44f11b6367f203767d97b76fc529eae70b072139e55831189e594
-DIST cutadapt-3.3.tar.gz 294579 BLAKE2B 1cf833d65a9611e50d747b6ce544dbf639ccc8eab8c5e83425d47bfe5526a0a25faab10cec7b41fad5b012ccf0552948a778b81dac3d5768674326d210dd4540 SHA512 d8895453455aff31c613a4e031559c08646ce2bf072d85ed7b195e5863700a02a1ed44bfb409b63849aadf1db7cf40dea33d0ead4f056307365dc91aa6c93234
diff --git a/sci-biology/cutadapt/cutadapt-2.10.ebuild b/sci-biology/cutadapt/cutadapt-2.10.ebuild
deleted file mode 100644
index c0c263469..000000000
--- a/sci-biology/cutadapt/cutadapt-2.10.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://github.com/marcelm/cutadapt"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND