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-rw-r--r--app-arch/libdeflate/Manifest1
-rw-r--r--app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch54
-rw-r--r--app-arch/libdeflate/libdeflate-1.2.ebuild27
-rw-r--r--app-arch/libdeflate/metadata.xml5
-rw-r--r--app-office/visidata/visidata-2.8.ebuild2
-rw-r--r--dev-cpp/Fastor/metadata.xml3
-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild2
-rw-r--r--dev-cpp/highwayhash/metadata.xml3
-rw-r--r--dev-cpp/xor_singleheader/metadata.xml3
-rw-r--r--dev-lang/icc/Manifest3
-rw-r--r--dev-lang/icc/icc-18.0.2.199-r1.ebuild41
-rw-r--r--dev-lang/icc/icc-19.0.4.243.ebuild40
-rw-r--r--dev-lang/icc/icc-19.1.1.217.ebuild41
-rw-r--r--dev-lang/icc/metadata.xml16
-rw-r--r--dev-lang/ifc/Manifest3
-rw-r--r--dev-lang/ifc/ifc-18.0.2.199-r1.ebuild40
-rw-r--r--dev-lang/ifc/ifc-19.0.4.243.ebuild39
-rw-r--r--dev-lang/ifc/ifc-19.1.1.217.ebuild43
-rw-r--r--dev-lang/ifc/metadata.xml17
-rw-r--r--dev-lang/vtune/Manifest3
-rw-r--r--dev-lang/vtune/metadata.xml15
-rw-r--r--dev-lang/vtune/vtune-18.0.2.0.551022.ebuild49
-rw-r--r--dev-lang/vtune/vtune-19.0.4.0.597835.ebuild48
-rw-r--r--dev-lang/vtune/vtune-2020.1.0.607630.ebuild52
-rw-r--r--dev-lang/yaggo/metadata.xml3
-rw-r--r--dev-libs/intel-common/Manifest4
-rw-r--r--dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild95
-rw-r--r--dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild101
-rw-r--r--dev-libs/intel-common/intel-common-19.0.4.243.ebuild101
-rw-r--r--dev-libs/intel-common/intel-common-19.1.1.217.ebuild102
-rw-r--r--dev-libs/intel-common/metadata.xml15
-rw-r--r--dev-libs/lief/lief-0.11.5.ebuild2
-rw-r--r--dev-libs/oneCCL/Manifest1
-rw-r--r--dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch104
-rw-r--r--dev-libs/oneCCL/metadata.xml (renamed from sci-libs/ipp/metadata.xml)8
-rw-r--r--dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild61
-rw-r--r--dev-libs/oneDNN/Manifest1
-rw-r--r--dev-libs/oneDNN/metadata.xml11
-rw-r--r--dev-libs/oneDNN/oneDNN-2.7.2.ebuild60
-rw-r--r--dev-libs/simclist/metadata.xml3
-rw-r--r--dev-libs/tut/metadata.xml5
-rw-r--r--dev-ml/lacaml/metadata.xml1
-rw-r--r--dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild22
-rw-r--r--dev-python/MagnetoResistance-tool/Manifest1
-rw-r--r--dev-python/MagnetoResistance-tool/metadata.xml11
-rw-r--r--dev-python/affine/affine-2.3.0.ebuild2
-rw-r--r--dev-python/annexremote/annexremote-1.5.0.ebuild5
-rw-r--r--dev-python/annexremote/annexremote-1.6.0.ebuild5
-rw-r--r--dev-python/anys/anys-0.2.1.ebuild2
-rw-r--r--dev-python/archspec/Manifest1
-rw-r--r--dev-python/archspec/archspec-0.1.4.ebuild20
-rw-r--r--dev-python/archspec/metadata.xml20
-rw-r--r--dev-python/asciitree/asciitree-0.3.3.ebuild4
-rw-r--r--dev-python/asciitree/metadata.xml5
-rw-r--r--dev-python/asdf/Manifest1
-rw-r--r--dev-python/asdf/asdf-2.14.3.ebuild47
-rw-r--r--dev-python/asdf/asdf-2.8.3.ebuild7
-rw-r--r--dev-python/astropy-healpix/astropy-healpix-0.6.ebuild2
-rw-r--r--dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild2
-rw-r--r--dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild2
-rw-r--r--dev-python/astropy/astropy-5.0.ebuild2
-rw-r--r--dev-python/astroscrappy/astroscrappy-1.1.0.ebuild2
-rw-r--r--dev-python/av/av-8.0.3.ebuild2
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild4
-rw-r--r--dev-python/cadquery-ocp/Manifest1
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild195
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild2
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild70
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild4
-rw-r--r--dev-python/cadquery/Manifest1
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20210804.ebuild56
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild4
-rw-r--r--dev-python/ccdproc/ccdproc-2.3.0.ebuild4
-rw-r--r--dev-python/click-didyoumean/Manifest2
-rw-r--r--dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild24
-rw-r--r--dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild22
-rw-r--r--dev-python/cligj/cligj-0.7.2.ebuild2
-rw-r--r--dev-python/colorcet/Manifest1
-rw-r--r--dev-python/colorcet/colorcet-2.0.6.ebuild10
-rw-r--r--dev-python/colorcet/colorcet-3.0.1.ebuild28
-rw-r--r--dev-python/cymbal/cymbal-1.0.0.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.4.3.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.5.1.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.5.3.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.6.0.ebuild2
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.7.1.ebuild2
-rw-r--r--dev-python/delegator/delegator-0.1.1.ebuild2
-rw-r--r--dev-python/dpctl/Manifest2
-rw-r--r--dev-python/dpctl/dpctl-0.13.0.ebuild62
-rw-r--r--dev-python/dpctl/dpctl-0.14.0.ebuild62
-rw-r--r--dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch82
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch13
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch47
-rw-r--r--dev-python/dpctl/metadata.xml12
-rw-r--r--dev-python/dpnp/Manifest2
-rw-r--r--dev-python/dpnp/dpnp-0.10.0.ebuild57
-rw-r--r--dev-python/dpnp/dpnp-0.11.0.ebuild57
-rw-r--r--dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch97
-rw-r--r--dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch80
-rw-r--r--dev-python/dpnp/metadata.xml12
-rw-r--r--dev-python/extension-helpers/extension-helpers-0.1.ebuild2
-rw-r--r--dev-python/ezdxf/ezdxf-0.16.5.ebuild2
-rw-r--r--dev-python/fiat/metadata.xml1
-rw-r--r--dev-python/fiona/fiona-1.8.21.ebuild4
-rw-r--r--dev-python/fscacher/fscacher-0.1.4.ebuild2
-rw-r--r--dev-python/fscacher/fscacher-0.2.0.ebuild2
-rw-r--r--dev-python/fslpy/Manifest2
-rw-r--r--dev-python/fslpy/fslpy-3.10.0.ebuild (renamed from dev-python/fslpy/fslpy-3.8.1.ebuild)18
-rw-r--r--dev-python/geopandas/Manifest2
-rw-r--r--dev-python/geopandas/geopandas-0.12.1.ebuild (renamed from dev-python/geopandas/geopandas-0.10.2.ebuild)14
-rw-r--r--dev-python/geopandas/metadata.xml30
-rw-r--r--dev-python/gffpandas/gffpandas-1.2.0.ebuild2
-rw-r--r--dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild2
-rw-r--r--dev-python/grabbit/grabbit-0.2.6.ebuild2
-rw-r--r--dev-python/gwcs/Manifest1
-rw-r--r--dev-python/gwcs/gwcs-0.16.1.ebuild9
-rw-r--r--dev-python/gwcs/gwcs-0.18.3.ebuild42
-rw-r--r--dev-python/hdf5storage/hdf5storage-0.1.17.ebuild2
-rw-r--r--dev-python/hdf5storage/hdf5storage-0.1.18.ebuild2
-rw-r--r--dev-python/hdf5storage/hdf5storage-9999.ebuild2
-rw-r--r--dev-python/hdmf/hdmf-3.1.1-r1.ebuild2
-rw-r--r--dev-python/hdmf/hdmf-3.3.2-r1.ebuild2
-rw-r--r--dev-python/holoviews/Manifest1
-rw-r--r--dev-python/holoviews/holoviews-1.14.2.ebuild6
-rw-r--r--dev-python/holoviews/holoviews-1.15.3.ebuild46
-rw-r--r--dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild8
-rw-r--r--dev-python/hopcroftkarp/metadata.xml19
-rw-r--r--dev-python/interleave/interleave-0.2.0.ebuild2
-rw-r--r--dev-python/json_tricks/metadata.xml2
-rw-r--r--dev-python/kmapper/metadata.xml3
-rw-r--r--dev-python/latexify_py/Manifest1
-rw-r--r--dev-python/latexify_py/latexify_py-0.2.0.ebuild34
-rw-r--r--dev-python/latexify_py/metadata.xml8
-rw-r--r--dev-python/llvmlite/Manifest2
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch13
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch (renamed from dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch)0
-rw-r--r--dev-python/llvmlite/llvmlite-0.39.1.ebuild (renamed from dev-python/llvmlite/llvmlite-0.39.0.ebuild)8
-rw-r--r--dev-python/logzero/logzero-1.7.0.ebuild2
-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/meshpy/meshpy-2020.1.ebuild2
-rw-r--r--dev-python/meshpy/metadata.xml1
-rw-r--r--dev-python/mkl-service/Manifest1
-rw-r--r--dev-python/mkl-service/metadata.xml12
-rw-r--r--dev-python/mkl-service/mkl-service-2.4.0.ebuild38
-rw-r--r--dev-python/mkl_fft/Manifest1
-rw-r--r--dev-python/mkl_fft/metadata.xml12
-rw-r--r--dev-python/mkl_fft/mkl_fft-1.3.1.ebuild39
-rw-r--r--dev-python/mkl_random/Manifest1
-rw-r--r--dev-python/mkl_random/metadata.xml12
-rw-r--r--dev-python/mkl_random/mkl_random-1.2.2.ebuild41
-rw-r--r--dev-python/mkl_umath/Manifest1
-rw-r--r--dev-python/mkl_umath/metadata.xml12
-rw-r--r--dev-python/mkl_umath/mkl_umath-0.1.1.ebuild37
-rw-r--r--dev-python/multimethod/multimethod-1.8.ebuild2
-rw-r--r--dev-python/num2words/num2words-0.5.10.ebuild2
-rw-r--r--dev-python/numba-dpex/Manifest1
-rw-r--r--dev-python/numba-dpex/metadata.xml12
-rw-r--r--dev-python/numba-dpex/numba-dpex-0.19.0.ebuild40
-rw-r--r--dev-python/numba/Manifest3
-rw-r--r--dev-python/numba/files/numba-0.51.2-skip_tests.patch46
-rw-r--r--dev-python/numba/files/numba-0.56.4-allow-py3.11.patch13
-rw-r--r--dev-python/numba/metadata.xml4
-rw-r--r--dev-python/numba/numba-0.56.3.ebuild (renamed from dev-python/numba/numba-0.56.0.ebuild)10
-rw-r--r--dev-python/numba/numba-0.56.4.ebuild85
-rw-r--r--dev-python/numcodecs/numcodecs-0.10.0.ebuild2
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.0.ebuild2
-rw-r--r--dev-python/numcodecs/numcodecs-0.9.1.ebuild2
-rw-r--r--dev-python/numpy/Manifest4
-rw-r--r--dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch50
-rw-r--r--dev-python/numpy/metadata.xml24
-rw-r--r--dev-python/numpy/numpy-1.23.5.ebuild187
-rw-r--r--dev-python/nwbinspector/Manifest6
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.12.ebuild7
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.14.ebuild6
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.19.ebuild (renamed from dev-python/nwbinspector/nwbinspector-0.3.9.ebuild)8
-rw-r--r--dev-python/panel/Manifest2
-rw-r--r--dev-python/panel/files/panel-0.14.1-disable_lite_build.patch47
-rw-r--r--dev-python/panel/panel-0.11.0.ebuild6
-rw-r--r--dev-python/panel/panel-0.14.1.ebuild55
-rw-r--r--dev-python/panel/panel-0.14.2.ebuild64
-rw-r--r--dev-python/param/Manifest3
-rw-r--r--dev-python/param/param-1.10.1.ebuild14
-rw-r--r--dev-python/param/param-1.12.3.ebuild22
-rw-r--r--dev-python/persim/persim-0.1.3.ebuild17
-rw-r--r--dev-python/persim/persim-0.2.0.ebuild24
-rw-r--r--dev-python/persim/persim-0.3.0.ebuild25
-rw-r--r--dev-python/persim/persim-0.3.1.ebuild25
-rw-r--r--dev-python/probeinterface/Manifest3
-rw-r--r--dev-python/probeinterface/metadata.xml (renamed from dev-python/click-didyoumean/metadata.xml)3
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.11.ebuild35
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.14.ebuild37
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.5.ebuild35
-rw-r--r--dev-python/py2bit/Manifest1
-rw-r--r--dev-python/py2bit/py2bit-0.3.0.ebuild13
-rw-r--r--dev-python/py2bit/py2bit-0.3.1.ebuild32
-rw-r--r--dev-python/py2bit/py2bit-9999.ebuild13
-rw-r--r--dev-python/pyBigWig/Manifest1
-rw-r--r--dev-python/pyBigWig/pyBigWig-0.3.17.ebuild7
-rw-r--r--dev-python/pyBigWig/pyBigWig-0.3.18.ebuild25
-rw-r--r--dev-python/pyBigWig/pyBigWig-9999.ebuild7
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild2
-rw-r--r--dev-python/pyct/pyct-0.4.8.ebuild6
-rw-r--r--dev-python/pyerfa/pyerfa-2.0.0.1.ebuild2
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.6.ebuild2
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.2.ebuild2
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.3.ebuild2
-rw-r--r--dev-python/pynwb/Manifest2
-rw-r--r--dev-python/pynwb/files/pynwb-2.2.0-versions.patch21
-rw-r--r--dev-python/pynwb/pynwb-2.0.0.ebuild46
-rw-r--r--dev-python/pynwb/pynwb-2.0.1-r1.ebuild (renamed from dev-python/pynwb/pynwb-2.0.1.ebuild)6
-rw-r--r--dev-python/pynwb/pynwb-2.1.0-r2.ebuild (renamed from dev-python/pynwb/pynwb-2.1.0-r1.ebuild)6
-rw-r--r--dev-python/pynwb/pynwb-2.2.0-r1.ebuild57
-rw-r--r--dev-python/pyout/files/pyout-0.7.2-blessed.patch140
-rw-r--r--dev-python/pyout/pyout-0.7.1-r1.ebuild (renamed from dev-python/pyout/pyout-0.7.2.ebuild)9
-rw-r--r--dev-python/pyout/pyout-0.7.2-r1.ebuild (renamed from dev-python/pyout/pyout-0.7.1.ebuild)6
-rw-r--r--dev-python/pyparsing/Manifest1
-rw-r--r--dev-python/pyparsing/metadata.xml21
-rw-r--r--dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild29
-rw-r--r--dev-python/pysolar/pysolar-0.8.ebuild2
-rw-r--r--dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild2
-rw-r--r--dev-python/python-gantt/metadata.xml5
-rw-r--r--dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild2
-rw-r--r--dev-python/python-igraph/python-igraph-0.9.11.ebuild2
-rw-r--r--dev-python/pytorch-lightning/Manifest2
-rw-r--r--dev-python/pytorch-lightning/metadata.xml2
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild29
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild31
-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/pyviz_comms-2.0.1.ebuild10
-rw-r--r--dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild22
-rw-r--r--dev-python/pyvote/metadata.xml5
-rw-r--r--dev-python/pyvote/pyvote-0.1.ebuild2
-rw-r--r--dev-python/pyzo/metadata.xml3
-rw-r--r--dev-python/rasterio/rasterio-1.2.10-r1.ebuild2
-rw-r--r--dev-python/rasterstats/rasterstats-0.16.0.ebuild2
-rw-r--r--dev-python/reproject/reproject-0.8.ebuild2
-rw-r--r--dev-python/repsep_utils/metadata.xml13
-rw-r--r--dev-python/schema/schema-0.7.4.ebuild2
-rw-r--r--dev-python/scooby/scooby-0.5.7.ebuild2
-rw-r--r--dev-python/snakemake/metadata.xml1
-rw-r--r--dev-python/snuggs/snuggs-1.4.7.ebuild2
-rw-r--r--dev-python/sphinx-argparse/Manifest2
-rw-r--r--dev-python/sphinx-argparse/metadata.xml3
-rw-r--r--dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild (renamed from dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild)15
-rw-r--r--dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild2
-rw-r--r--dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild2
-rw-r--r--dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild2
-rw-r--r--dev-python/texext/Manifest2
-rw-r--r--dev-python/texext/texext-0.6.7.ebuild (renamed from dev-python/texext/texext-0.6.6.ebuild)8
-rw-r--r--dev-python/traits/Manifest3
-rw-r--r--dev-python/traits/traits-6.1.1.ebuild8
-rw-r--r--dev-python/traits/traits-6.3.2.ebuild (renamed from dev-python/traits/traits-6.0.0.ebuild)26
-rw-r--r--dev-python/traits/traits-6.4.1.ebuild36
-rw-r--r--dev-python/transforms3d/transforms3d-0.3.1.ebuild2
-rw-r--r--dev-python/typish/typish-1.9.3.ebuild2
-rw-r--r--dev-python/ufl/metadata.xml1
-rw-r--r--dev-python/umap-learn/umap-learn-0.5.2.ebuild2
-rw-r--r--dev-python/visvis/visvis-1.13.0.ebuild2
-rw-r--r--dev-python/wraps/Manifest3
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch16
-rw-r--r--dev-python/wraps/wraps-0.1.0-r1.ebuild (renamed from dev-python/wraps/wraps-0.1.0.ebuild)5
-rw-r--r--dev-python/wraps/wraps-0.2.0.ebuild30
-rw-r--r--dev-python/xgboost/Manifest2
-rw-r--r--dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch31
-rw-r--r--dev-python/xgboost/xgboost-1.6.2.ebuild (renamed from dev-python/xgboost/xgboost-1.3.1.ebuild)10
-rw-r--r--dev-python/zarr/zarr-2.11.1.ebuild2
-rw-r--r--dev-python/zarr/zarr-2.11.3.ebuild2
-rw-r--r--dev-python/zarr/zarr-2.12.0.ebuild2
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547 files changed, 6724 insertions, 5362 deletions
diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
index f26d506d5..b320be20c 100644
--- a/app-arch/libdeflate/Manifest
+++ b/app-arch/libdeflate/Manifest
@@ -1,5 +1,4 @@
DIST libdeflate-1.11.tar.gz 162862 BLAKE2B 70ee15bdbe697083f84eef4bfce069b3bff8499a8daf53037a52fd247a47cd04867c1d93265e1b88232da52919ad15333e90d787dff05f7d8e5abe7a9613a07a SHA512 71badc0d934dde5fa79c0d8661b3a38a45d7189fba6f1c77986b2fb6baa03233b8474f0a83f004242410421c2063d2f98f02ca4f8a7a7a14cc7bcd3a9be4fbbc
-DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb
DIST libdeflate-1.6.tar.gz 139031 BLAKE2B c9390408322dc71f27d86fb69e0dd47996a725a3f4ddbe1d395e07dcd1b1f2b6fde1a9decfa8d7a0bd841defff67a659b1f2efd2609db7d79626e038cb44e020 SHA512 b7225c7defb3e9b1177c434aa0de80e525de06160894282e9d3e736d6c17d2ee107e321042104a67dfa3649d982a022ee30fe30380259b8aa65ac75d1d02e334
DIST libdeflate-1.7.tar.gz 144143 BLAKE2B 6aa947a4e2489f5a3e5681d56c2272b0a694981ed2607fa4112d90a8b4565ba1066364ffcac2fe8836bacbbad0346bce5efea54b4abae55022a33ee7d983e570 SHA512 82b297af2d3128a244e561893cce1d3664de410469ba6745c3f68fc3a1962c62467c427f3857bb679578e0f704cd0eba1a64b13c30505addd310ff9af1883068
DIST libdeflate-1.8.tar.gz 145823 BLAKE2B 3597e41cbcae17b5b6b5bbb196af6ea52ac55b279f42e1ca3b12ba45638602e8a3f7520d84d7be637675c04fd82e096cb03d15f5fd742a31db5ba22cbd6e71f4 SHA512 b40caecdf783487488a5bd8213304175348b9db9bc1efdf6d5222fb912f61698b5e196522195a3640d7ff61ba953a93c0c8f75e07f548ac8b9d9c5dd5a787544
diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
deleted file mode 100644
index 790aa6de9..000000000
--- a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- libdeflate-1.2/Makefile 2019-01-15 06:37:48.000000000 +0100
-+++ libdeflate-1.2/Makefile 2019-01-22 14:06:13.427054892 +0100
-@@ -21,7 +21,7 @@
- 1>&2 2>/dev/null; then echo $(1); fi)
-
- override CFLAGS := \
-- $(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon \
-+ $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon \
- -Wall -Wundef \
- $(call cc-option,-Wpedantic) \
- $(call cc-option,-Wdeclaration-after-statement) \
-@@ -34,6 +34,9 @@
- ##############################################################################
-
- PREFIX ?= /usr
-+BINDIR ?= $(PREFIX)/bin
-+INCDIR ?= $(PREFIX)/include
-+LIBDIR ?= $(PREFIX)/lib
-
- SOVERSION := 0
- STATIC_LIB_SUFFIX := .a
-@@ -240,20 +243,20 @@
- all:$(DEFAULT_TARGETS)
-
- install:all
-- install -Dm644 -t $(DESTDIR)$(PREFIX)/lib $(STATIC_LIB)
-- install -Dm755 -t $(DESTDIR)$(PREFIX)/lib $(SHARED_LIB)
-- ln -sf $(SHARED_LIB) $(DESTDIR)$(PREFIX)/lib/libdeflate.so
-- install -Dm644 -t $(DESTDIR)$(PREFIX)/include libdeflate.h
-- install -Dm755 gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip
-- ln -f $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+ install -Dm644 -t $(DESTDIR)$(LIBDIR) $(STATIC_LIB)
-+ install -Dm755 -t $(DESTDIR)$(LIBDIR) $(SHARED_LIB)
-+ ln -sf $(SHARED_LIB) $(DESTDIR)$(LIBDIR)/libdeflate.so
-+ install -Dm644 -t $(DESTDIR)$(INCDIR) libdeflate.h
-+ install -Dm755 gzip $(DESTDIR)$(BINDIR)/libdeflate-gzip
-+ ln -f $(DESTDIR)$(BINDIR)/libdeflate-gzip $(DESTDIR)$(BINDIR)/libdeflate-gunzip
-
- uninstall:
-- rm -f $(DESTDIR)$(PREFIX)/lib/$(STATIC_LIB) \
-- $(DESTDIR)$(PREFIX)/lib/$(SHARED_LIB) \
-- $(DESTDIR)$(PREFIX)/lib/libdeflate.so \
-- $(DESTDIR)$(PREFIX)/include/libdeflate.h \
-- $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip \
-- $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+ rm -f $(DESTDIR)$(LIBDIR)/$(STATIC_LIB) \
-+ $(DESTDIR)$(LIBDIR)/$(SHARED_LIB) \
-+ $(DESTDIR)$(LIBDIR)/libdeflate.so \
-+ $(DESTDIR)$(INCDIR)/libdeflate.h \
-+ $(DESTDIR)$(BINDIR)/libdeflate-gzip \
-+ $(DESTDIR)$(BINDIR)/libdeflate-gunzip
-
- test_programs:$(TEST_PROGRAMS)
-
diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild b/app-arch/libdeflate/libdeflate-1.2.ebuild
deleted file mode 100644
index c5924c064..000000000
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate"
-SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-PATCHES=( "${FILESDIR}"/libdeflate-1.2-respect_EPREFIX.patch )
-
-src_install() {
- if ! use static-libs; then
- find "${ED}" -name '*.a' -delete || die
- fi
- emake install DESTDIR="${ED}" LIBDIR=/usr/"$(get_libdir)"
- dodoc NEWS README.md
-}
diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml
index 6e347494a..fe240766f 100644
--- a/app-arch/libdeflate/metadata.xml
+++ b/app-arch/libdeflate/metadata.xml
@@ -8,9 +8,12 @@
<maintainer type="person">
<email>gentoo@aisha.cc</email>
<name>Aisha Tammy</name>
- </maintainer>
+ </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ebiggers/libdeflate</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild
index ab4d506ab..f3cf9e123 100644
--- a/app-office/visidata/visidata-2.8.ebuild
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 optfeature
diff --git a/dev-cpp/Fastor/metadata.xml b/dev-cpp/Fastor/metadata.xml
index e97c4322a..9937ac435 100644
--- a/dev-cpp/Fastor/metadata.xml
+++ b/dev-cpp/Fastor/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">romeric/Fastor</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 432004f11..38e0dfbd0 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..11} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit cmake python-any-r1
COMMIT="39f885951a9b8b11f931f917935a16066a945056"
diff --git a/dev-cpp/highwayhash/metadata.xml b/dev-cpp/highwayhash/metadata.xml
index ef6b5dcd5..ce99f4b00 100644
--- a/dev-cpp/highwayhash/metadata.xml
+++ b/dev-cpp/highwayhash/metadata.xml
@@ -5,4 +5,7 @@
<email>junghans@gentoo.org</email>
<name>Christoph Junghans</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">google/highwayhash</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-cpp/xor_singleheader/metadata.xml b/dev-cpp/xor_singleheader/metadata.xml
index e97c4322a..cebb00f2c 100644
--- a/dev-cpp/xor_singleheader/metadata.xml
+++ b/dev-cpp/xor_singleheader/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">FastFilter/xor_singleheader</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/icc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild
deleted file mode 100644
index 84641de62..000000000
--- a/dev-lang/icc/icc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# avoid file collision with ifc #476330
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "icc-common-ps-18.0.2-199-18.0.2-199.noarch.rpm"
- "icc-common-ps-ss-bec-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "icc-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "icc-doc-18.0-18.0.2-199.noarch.rpm"
- "icc-doc-ps-18.0-18.0.2-199.noarch.rpm")
- fi
-}
diff --git a/dev-lang/icc/icc-19.0.4.243.ebuild b/dev-lang/icc/icc-19.0.4.243.ebuild
deleted file mode 100644
index 9a166f221..000000000
--- a/dev-lang/icc/icc-19.0.4.243.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# avoid file collision with ifc #476330
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-19.0.4-243-19.0.4-243.noarch.rpm"
- "icc-common-ps-19.0.4-243-19.0.4-243.noarch.rpm"
- "icc-common-ps-ss-bec-19.0.4-243-19.0.4-243.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-ss-bec-19.0.4-243-19.0.4-243.x86_64.rpm")
-
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-19.0.4-243-19.0.4-243.x86_64.rpm"
- "icc-ps-ss-bec-32bit-19.0.4-243-19.0.4-243.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=(
- "icc-doc-19.0-19.0.4-243.noarch.rpm"
- "icc-doc-ps-19.0-19.0.4-243.noarch.rpm")
- fi
-}
diff --git a/dev-lang/icc/icc-19.1.1.217.ebuild b/dev-lang/icc/icc-19.1.1.217.ebuild
deleted file mode 100644
index 226b9c784..000000000
--- a/dev-lang/icc/icc-19.1.1.217.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-INTEL_DIST_DAT_RPMS=(
- "icc-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "icc-common-ps-${MY_PV}-${MY_PV}.noarch.rpm"
- "idesupport-icc-common-ps-19.1-${MY_PV}.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "icc-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-INTEL_DIST_X86_RPMS=(
- "icc-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "icc-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "icc-doc-19.1-${MY_PV}.noarch.rpm" )
- fi
-}
diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml
deleted file mode 100644
index 7c4d1a96d..000000000
--- a/dev-lang/icc/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The Intel® C++ Compiler is a full featured C/C++ compiler for Intel
-based architectures. The compiler supports multi-threading, automatic
-processor dispatch, vectorization, auto-parallelization, OpenMP, data
-prefetching, loop unrolling. The package comes with extensive
-documentation. The product can be installed as a non-commercial as
-well. License, terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/ifc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild b/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
deleted file mode 100644
index f37dd5491..000000000
--- a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-18.0.2-199-18.0.2-199.noarch.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-18.0-18.0.2-199.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/ifc-19.0.4.243.ebuild b/dev-lang/ifc/ifc-19.0.4.243.ebuild
deleted file mode 100644
index a45765a2f..000000000
--- a/dev-lang/ifc/ifc-19.0.4.243.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-19.0.4-243-19.0.4-243.noarch.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-19.0.4-243-19.0.4-243.x86_64.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.0-19.0.4-243.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/ifc-19.1.1.217.ebuild b/dev-lang/ifc/ifc-19.1.1.217.ebuild
deleted file mode 100644
index 4157a3eec..000000000
--- a/dev-lang/ifc/ifc-19.1.1.217.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-${MY_PV}-${MY_PV}.noarch.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-${MY_PV}-${MY_PV}.x86_64.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.1-${MY_PV}.noarch.rpm" )
- fi
-}
-
-src_install() {
- # already provided in dev-libs/intel-common
- rm \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/omp_lib.f90 \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib.mod \
- "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib_kinds.mod \
- || die "rm failed"
-
- intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml
deleted file mode 100644
index 0cc12d890..000000000
--- a/dev-lang/ifc/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The Intel® Fortran Compiler is a full featured FORTRAN 77/95 and
-substantial FORTRAN 2003 compiler for Intel based architectures. The
-compiler supports multi-threading with automatic processor dispatch,
-vectorization, auto-parallelization, OpenMP, data prefetching, loop
-unrolling. The package comes with extensive documentation.
-The product can be installed as a non-commercial as well. License,
-terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest
deleted file mode 100644
index 0007a0681..000000000
--- a/dev-lang/vtune/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml
deleted file mode 100644
index 718cc299c..000000000
--- a/dev-lang/vtune/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-The Intel® VTune™ Profiler collects key profiling data and presents
-it with a powerful interface that simplifies its analysis and
-interpretation. The package comes with extensive documentation. The
-product can be installed as a non-commercial as well. License, terms
-of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild b/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
deleted file mode 100644
index 9ec0beef6..000000000
--- a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-INTEL_SUBDIR=vtune_amplifier
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-18.0.2.199[compiler]"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-amplifier-2018-cli-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-common-pset-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-gui-common-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-sep-2018.2-551022.noarch.rpm"
- "vtune-amplifier-2018-target-2018.2-551022.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-amplifier-2018-cli-2018.2-551022.x86_64.rpm"
- "vtune-amplifier-2018-collector-64linux-2018.2-551022.x86_64.rpm"
- "vtune-amplifier-2018-gui-2018.2-551022.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-amplifier-2018-cli-32bit-2018.2-551022.i486.rpm"
- "vtune-amplifier-2018-collector-32linux-2018.2-551022.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2018-doc-2018.2-551022.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild b/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild
deleted file mode 100644
index e090c10b7..000000000
--- a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-INTEL_SUBDIR=vtune_amplifier
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-19.0.4.243[compiler]"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-amplifier-2019-cli-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-common-pset-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-gui-common-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-sep-2019.4-597835.noarch.rpm"
- "vtune-amplifier-2019-target-2019.4-597835.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-amplifier-2019-cli-2019.4-597835.x86_64.rpm"
- "vtune-amplifier-2019-collector-64linux-2019.4-597835.x86_64.rpm"
- "vtune-amplifier-2019-gui-2019.4-597835.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-amplifier-2019-cli-32bit-2019.4-597835.i486.rpm"
- "vtune-amplifier-2019-collector-32linux-2019.4-597835.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2019-doc-2019.4-597835.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild b/dev-lang/vtune/vtune-2020.1.0.607630.ebuild
deleted file mode 100644
index e1ec58882..000000000
--- a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-INTEL_SUBDIR=vtune_profiler
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Profiler"
-HOMEPAGE="https://software.intel.com/en-us/vtune"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]"
-
-MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630
-
-QA_PREBUILT="*"
-
-INTEL_DIST_DAT_RPMS=(
- "vtune-profiler-2020-cli-common-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-common-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-common-pset-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-sep-${MY_PV}.noarch.rpm"
- "vtune-profiler-2020-target-${MY_PV}.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "vtune-profiler-2020-cli-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-collector-64linux-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-gui-${MY_PV}.x86_64.rpm"
- "vtune-profiler-2020-vpp-server-${MY_PV}.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
- "vtune-profiler-2020-cli-32bit-${MY_PV}.i486.rpm"
- "vtune-profiler-2020-collector-32linux-${MY_PV}.i486.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "vtune-profiler-2020-doc-${MY_PV}.noarch.rpm" )
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
-
- local path="PATH="
- use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
- use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
- echo "${path}" > "${T}"/35vtune || die
- doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/yaggo/metadata.xml b/dev-lang/yaggo/metadata.xml
index 138cb7705..61d3a34e2 100644
--- a/dev-lang/yaggo/metadata.xml
+++ b/dev-lang/yaggo/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">gmarcais/yaggo</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest
deleted file mode 100644
index 21dea448d..000000000
--- a/dev-libs/intel-common/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
-DIST parallel_studio_xe_2019_update3_professional_edition.tgz 4777019188 BLAKE2B 1ebbc23d1370bb396b452dc73d4a79b4ea7be0e304e3d38b3cba77372df6af097ea1109535d166b56a6c50e28e3330a1ed49c6a9270411b14ccf48f32a9eaedd SHA512 622b1a8877f06247a0a93cb98d2cc6d5b359aa2c9cf7ff6f45a8e1dca34fecea10d603d632a7b3454d809d6e38cb860b40ae3f782e250279768937af6ceb015d
-DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d
-DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404
diff --git a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild b/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
deleted file mode 100644
index 5397d76b6..000000000
--- a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-l-all-common-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-l-all-vars-18.0.2-199-18.0.2-199.noarch.rpm"
- "comp-nomcu-vars-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
- "comp-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-18.0-18.0.2-199.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-2018.2-199-2018.2-199.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-2018-2018.2-199.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-18.0.2-199-18.0.2-199.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-18.0.2-199-18.0.2-199.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-18.0.2-199-18.0.2-199.noarch.rpm"
- "openmp-common-ifort-18.0.2-199-18.0.2-199.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-18.0.2-199-18.0.2-199.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild b/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild
deleted file mode 100644
index dc06e4551..000000000
--- a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update3_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV=$(ver_rs 3 '-') # 19.0.3-199
-MY_PV2=$(ver_cut 1-2) # 19.0
-MY_PV3='20'$(ver_cut 1) # 2019
-MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild b/dev-libs/intel-common/intel-common-19.0.4.243.ebuild
deleted file mode 100644
index df8f5574c..000000000
--- a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2019_update4_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV=$(ver_rs 3 '-') # 19.0.3-199
-MY_PV2=$(ver_cut 1-2) # 19.0
-MY_PV3='20'$(ver_cut 1) # 2019
-MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild b/dev-libs/intel-common/intel-common-19.1.1.217.ebuild
deleted file mode 100644
index 4ba98edad..000000000
--- a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-INTEL_DIST_PV=2020_update1_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-SLOT="0"
-
-MY_PV="$(ver_rs 3 '-')" # 19.1.1-217
-MY_PV2="$(ver_cut 1-2)" # 19.1
-MY_PV3="2019" # 2019
-MY_PV4="${MY_PV3}.7-$(ver_cut 4)" # 2019.7-217 sic!
-
-CHECKREQS_DISK_BUILD=750M
-
-QA_PREBUILT="*"
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
- "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm"
- "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
- "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
- "comp-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm"
- "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm")
-
-pkg_setup() {
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" )
- fi
-
- if use mpi; then
- INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" )
-
- if use doc; then
- INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" )
- fi
- fi
-
- if use openmp; then
- INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" )
- INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" )
- INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" )
-
- if use compiler; then
- INTEL_DIST_DAT_RPMS+=(
- "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm"
- "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm")
- INTEL_DIST_AMD64_RPMS+=(
- "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm")
- INTEL_DIST_X86_RPMS+=(
- "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm")
- fi
- fi
-}
-
-src_install() {
- intel-sdp-r1_src_install
- local path rootpath ldpath arch fenv=35intelsdp
- cat > ${fenv} <<-EOF
- NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
- INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
- EOF
- for arch in $(isdp_get-sdp-installed-arches); do
- path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
- done
- if use mpi && use amd64; then
- path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
- ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
- fi
- cat >> ${fenv} <<-EOF
- PATH=${path#:}
- ROOTPATH=${rootpath#:}
- LDPATH=${ldpath#:}
- EOF
-
- doenvd ${fenv}
-
- cat >> "${T}"/40-${PN} <<- EOF
- SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
- EOF
- insinto /etc/revdep-rebuild/
- doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/metadata.xml b/dev-libs/intel-common/metadata.xml
deleted file mode 100644
index 026b5a33d..000000000
--- a/dev-libs/intel-common/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-This package contains the core files to be installed for the Intel
-compilers and libraries. Probably useless if installed standalone.
-</longdescription>
- <use>
- <flag name="compiler">Install the libraries needed for the icc and ifort compilers</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-libs/lief/lief-0.11.5.ebuild b/dev-libs/lief/lief-0.11.5.ebuild
index 519729525..c2c38e5ba 100644
--- a/dev-libs/lief/lief-0.11.5.ebuild
+++ b/dev-libs/lief/lief-0.11.5.ebuild
@@ -4,7 +4,7 @@
EAPI=7
CMAKE_ECLASS=cmake
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
+PYTHON_COMPAT=( python3_10 pypy3 )
# Upstream has two alternate approaches to building its Python API:
# 1. A working "CMakeList.txt" only supporting a single Python target.
diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest
new file mode 100644
index 000000000..825fc0a11
--- /dev/null
+++ b/dev-libs/oneCCL/Manifest
@@ -0,0 +1 @@
+DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790
diff --git a/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
new file mode 100644
index 000000000..e92608f4a
--- /dev/null
+++ b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
@@ -0,0 +1,104 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 74c4fc0..92c4d16 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -87,15 +87,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE
+ SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support")
+
+ set(CCL_COMMON_INSTALL_PREFIX "intel64")
+-set(CMAKE_INSTALL_LIBDIR "lib")
+ set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+ set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+ set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}")
+ set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}")
+-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env")
+-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc")
+-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing")
+-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles")
++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env")
++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}")
++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles")
+ set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples")
+ set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests")
+ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+@@ -103,23 +101,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+ # setup dependency directories
+ set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps")
+
+-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/")
+-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/")
++set(MPI_INCLUDE_DIR "/usr/include/")
++set(MPI_LIB_DIR "/usr/lib64/")
+ message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}")
+ message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}")
+
+ if ("${LIBFABRIC_DIR}" STREQUAL "")
+- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include")
+- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/")
++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/")
++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/")
+ else()
+ set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/")
+- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib")
++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/")
+ endif()
+ message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}")
+ message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}")
+
+-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/")
+-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/")
++set(HWLOC_INCLUDE_DIR "/usr/include/")
++set(HWLOC_LIB_DIR "/usr/lib64/")
+ message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}")
+ message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}")
+
+@@ -128,7 +126,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64")
+ message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}")
+ message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}")
+
+-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/")
++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero")
+ message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}")
+
+ set(CMAKE_SKIP_INSTALL_RPATH TRUE)
+@@ -241,8 +239,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party-
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE})
+-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE})
+-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE})
+
+ # copy kernels
+ if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 7b4cff9..e8296a0 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -263,8 +263,8 @@ list(APPEND SRC_LINK_LIBS
+ pthread
+ ${EXTERNAL_LIBS}
+ fabric
+- ${HWLOC_LIB_DIR}/libhwloc.a
+- ${ITT_LIB_DIR}/libittnotify.a)
++ libhwloc.so
++ libittnotify.so)
+
+ if (ENABLE_MPI)
+ set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI")
+@@ -335,16 +335,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "")
+ install(DIRECTORY ${DEPS_DIR}/ofi/lib/
+ DESTINATION ${CCL_INSTALL_LIB})
+ endif()
+-
+-if (ENABLE_MPI)
+- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*")
+- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN})
+- install(DIRECTORY ${DEPS_DIR}/mpi/include/
+- DESTINATION ${CCL_INSTALL_INCLUDE})
+- install(DIRECTORY ${DEPS_DIR}/mpi/lib/
+- DESTINATION ${CCL_INSTALL_LIB})
+- install(DIRECTORY ${DEPS_DIR}/mpi/etc/
+- DESTINATION ${CCL_INSTALL_ETC})
+- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/
+- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/)
+-endif()
diff --git a/sci-libs/ipp/metadata.xml b/dev-libs/oneCCL/metadata.xml
index 7bd17909e..cbb320b12 100644
--- a/sci-libs/ipp/metadata.xml
+++ b/dev-libs/oneCCL/metadata.xml
@@ -5,9 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
- <longdescription lang="en">
-Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a
-library of multi-core-ready, optimized software functions for
-multimedia data processing, and communications applications.
-</longdescription>
+ <upstream>
+ <remote-id type="github">oneapi-src/oneCCL</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild
new file mode 100644
index 000000000..76ab29af2
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+ dev-libs/level-zero:=
+ sys-apps/hwloc:=
+ sys-block/libfabric:=
+ sys-devel/ittapi
+ mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2021.7.1-use-system-libs.patch"
+)
+
+src_prepare() {
+ # No -Werror
+ find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+ # Use system libs instead
+ rm -r deps/* || 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
new file mode 100644
index 000000000..3f702434b
--- /dev/null
+++ b/dev-libs/oneDNN/Manifest
@@ -0,0 +1 @@
+DIST oneDNN-2.7.2.tar.gz 6409290 BLAKE2B 8e6fb262a77469cfaddd633bf11334d04ffb641fa798f0de23e458086c66c9b7e932d45d52baf8a93453495df9280f6a97dc3f220d7674850d1ca6c525ce2a7f SHA512 faf8ea953f552afaafcc597f647a98187c8c6dabd8a532fc1b8037626fa77a8a6543dce3247d953a470391d39189ba421ab7de589a8bb7c4c38e22327ab1c401
diff --git a/dev-libs/oneDNN/metadata.xml b/dev-libs/oneDNN/metadata.xml
new file mode 100644
index 000000000..0d6dc84a7
--- /dev/null
+++ b/dev-libs/oneDNN/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">oneapi-src/oneDNN</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild b/dev-libs/oneDNN/oneDNN-2.7.2.ebuild
new file mode 100644
index 000000000..1c66ec72c
--- /dev/null
+++ b/dev-libs/oneDNN/oneDNN-2.7.2.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/simclist/metadata.xml b/dev-libs/simclist/metadata.xml
index 8426fdb21..62c13e1e4 100644
--- a/dev-libs/simclist/metadata.xml
+++ b/dev-libs/simclist/metadata.xml
@@ -15,4 +15,7 @@
<flag name="dump">Disable building of dump and restore functionalities</flag>
<flag name="hash">Allow list_hash() to work exclusively on memory locations</flag>
</use>
+ <upstream>
+ <remote-id type="github">mij/simclist</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-libs/tut/metadata.xml b/dev-libs/tut/metadata.xml
index 026cdb22b..7a070008d 100644
--- a/dev-libs/tut/metadata.xml
+++ b/dev-libs/tut/metadata.xml
@@ -1,8 +1,11 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mrzechonek/tut-framework</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml
index 1094bf3da..24157e1f0 100644
--- a/dev-ml/lacaml/metadata.xml
+++ b/dev-ml/lacaml/metadata.xml
@@ -15,5 +15,6 @@
</longdescription>
<upstream>
<remote-id type="bitbucket">mmottl/lacaml</remote-id>
+ <remote-id type="github">mmottl/lacaml</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
new file mode 100644
index 000000000..6f675dc80
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
@@ -0,0 +1,22 @@
+# 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
+
+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"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/MagnetoResistance-tool/Manifest b/dev-python/MagnetoResistance-tool/Manifest
new file mode 100644
index 000000000..b8d0afd21
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/Manifest
@@ -0,0 +1 @@
+DIST MagnetoResistance-tool-0.0.2.tar.gz 21657 BLAKE2B 5d1a2f497f742df04aac5db6afe83373e6e3e3cea3891585c22d1585186665f0d597b3dccd5f2adfef4e58bc41f680b974974cb12c56e3ef29f69122407cfff5 SHA512 4866197feb96912edc19691ba7ea54303ed168d8ab72c534ad910a3a77ce6e8ccf0f19744eca5044936c29bde131d4c352abbd57547f1c30b3ae59d4aac36986
diff --git a/dev-python/MagnetoResistance-tool/metadata.xml b/dev-python/MagnetoResistance-tool/metadata.xml
new file mode 100644
index 000000000..aed122741
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/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="person">
+ <email>andrewammerlaan@gentoo.org</email>
+ <name>Andrew Ammerlaan</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">MagnetoResistance-tool</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/affine/affine-2.3.0.ebuild b/dev-python/affine/affine-2.3.0.ebuild
index a298cec26..7cc363d92 100644
--- a/dev-python/affine/affine-2.3.0.ebuild
+++ b/dev-python/affine/affine-2.3.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild
index b35e3c274..90511a157 100644
--- a/dev-python/annexremote/annexremote-1.5.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.5.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Helper module to easily develop git-annex remotes"
@@ -14,6 +14,9 @@ LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
+# Reported upstream:
+# https://github.com/Lykos153/AnnexRemote/issues/61
+RESTRICT="test"
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild
index b35e3c274..90511a157 100644
--- a/dev-python/annexremote/annexremote-1.6.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.6.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Helper module to easily develop git-annex remotes"
@@ -14,6 +14,9 @@ LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
+# Reported upstream:
+# https://github.com/Lykos153/AnnexRemote/issues/61
+RESTRICT="test"
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
index d74bb76f9..659e797cf 100644
--- a/dev-python/anys/anys-0.2.1.ebuild
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest
new file mode 100644
index 000000000..5351b4321
--- /dev/null
+++ b/dev-python/archspec/Manifest
@@ -0,0 +1 @@
+DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild
new file mode 100644
index 000000000..5e8eee157
--- /dev/null
+++ b/dev-python/archspec/archspec-0.1.4.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=poetry
+inherit distutils-r1
+
+DESCRIPTION="labels for various aspects of a system architecture like CPU, etc."
+HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/six-1.16.0[${PYTHON_USEDEP}]
+ <=dev-python/six-2.0.0[${PYTHON_USEDEP}]
+ >=dev-python/click-7.1.2[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
diff --git a/dev-python/archspec/metadata.xml b/dev-python/archspec/metadata.xml
new file mode 100644
index 000000000..3688592b1
--- /dev/null
+++ b/dev-python/archspec/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">archspec</remote-id>
+ <remote-id type="github">archspec/archspec</remote-id>
+ <bugs-to>https://github.com/archspec/archspec/issues</bugs-to>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild
index 0ced423c8..3f8f82f8b 100644
--- a/dev-python/asciitree/asciitree-0.3.3.ebuild
+++ b/dev-python/asciitree/asciitree-0.3.3.ebuild
@@ -3,12 +3,12 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="ASCII trees in python"
HOMEPAGE="https://github.com/mbr/asciitree"
-SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/0.3.3.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-python/asciitree/metadata.xml b/dev-python/asciitree/metadata.xml
index f6f63a810..8b000b491 100644
--- a/dev-python/asciitree/metadata.xml
+++ b/dev-python/asciitree/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mbr/asciitree</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest
index 3b2cf6ef8..fc182f25b 100644
--- a/dev-python/asdf/Manifest
+++ b/dev-python/asdf/Manifest
@@ -1 +1,2 @@
+DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655
DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df
diff --git a/dev-python/asdf/asdf-2.14.3.ebuild b/dev-python/asdf/asdf-2.14.3.ebuild
new file mode 100644
index 000000000..2463f0a6c
--- /dev/null
+++ b/dev-python/asdf/asdf-2.14.3.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Python library for the Advanced Scientific Data Format"
+HOMEPAGE="https://asdf.readthedocs.io/en/latest/"
+SRC_URI="mirror://pypi/${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/asdf/asdf-2.8.3.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild
index 96663e49a..edce106b0 100644
--- a/dev-python/asdf/asdf-2.8.3.ebuild
+++ b/dev-python/asdf/asdf-2.8.3.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_{8..9} )
+PYTHON_COMPAT=( python3_{10..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -15,6 +15,9 @@ 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? (
diff --git a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
index ce6ec0cd3..1169e9965 100644
--- a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
+++ b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
index 393066583..81cd07a63 100644
--- a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
+++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1 xdg-utils
diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
index 844b614bd..02f378b8a 100644
--- a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
+++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/dev-python/astropy/astropy-5.0.ebuild b/dev-python/astropy/astropy-5.0.ebuild
index c650533d6..43e7ac903 100644
--- a/dev-python/astropy/astropy-5.0.ebuild
+++ b/dev-python/astropy/astropy-5.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
index f4ef741da..79054f7ab 100644
--- a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
+++ b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild
index 57a8bbdfb..91c9535df 100644
--- a/dev-python/av/av-8.0.3.ebuild
+++ b/dev-python/av/av-8.0.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
index d6dfa1901..02581b74c 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=rdepend
DISTUTILS_IN_SOURCE_BUILD=1
inherit distutils-r1 optfeature
@@ -25,7 +25,7 @@ RDEPEND="
>=dev-python/pillow-7.1.0[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
>=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}]
- >=www-servers/tornado-5.1[${PYTHON_USEDEP}]
+ >=dev-python/tornado-5.1[${PYTHON_USEDEP}]
"
BDEPEND="
test? (
diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest
index 4818fac84..9b34bca41 100644
--- a/dev-python/cadquery-ocp/Manifest
+++ b/dev-python/cadquery-ocp/Manifest
@@ -1,2 +1 @@
-DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8
DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
deleted file mode 100644
index ec0b8526d..000000000
--- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
+++ /dev/null
@@ -1,195 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
-inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
-
-MY_PN=OCP
-MY_PV="${PV//_/-}"
-MY_P="${MY_PN}-${MY_PV}"
-OCCT_PV=$(ver_cut 1-3)
-
-DESCRIPTION="Python wrapper for OCCT generated using pywrap"
-HOMEPAGE="https://github.com/CadQuery/OCP"
-SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file
-# generated by the src_prepare() phase. OCP currently requires opencascade
-# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also:
-# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994
-BDEPEND="
- >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}]
- >=dev-util/cmake-3.16
-"
-RDEPEND="
- ${PYTHON_DEPS}
- sci-libs/opencascade:0/7.5[json,tbb,vtk]
- >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
-"
-DEPEND="${RDEPEND}
- $(python_gen_cond_dep '
- >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]')
-"
-
-S="${WORKDIR}/${MY_P}"
-
-# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare().
-CMAKE_IN_SOURCE_BUILD=True
-
-# Ensure the path returned by get_llvm_prefix() contains clang.
-llvm_check_deps() {
- has_version -r "sys-devel/clang:${LLVM_SLOT}"
-}
-
-cadquery-ocp_check_reqs() {
- CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE}
-}
-
-pkg_pretend() {
- cadquery-ocp_check_reqs
-}
-
-pkg_setup() {
- cadquery-ocp_check_reqs
- llvm_pkg_setup
- python-single-r1_pkg_setup
-}
-
-# OCP currently requires manual configuration, compilation, and installation
-# loosely inspired by the conda-specific "build-bindings-job.yml" file.
-#
-# Note that the cmake_src_prepare() function called below handles user patches.
-src_prepare() {
- # Most recently installed version of Clang.
- local _CLANG_VERSION="$(CPP=clang clang-fullversion)"
-
- # Most recently installed version (excluding trailing patch) of VTK.
- local _VTK_VERSION="$(best_version -r sci-libs/vtk)"
- _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")"
-
- # Absolute dirname of the most recently installed Clang include directory,
- # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also:
- # https://bugs.gentoo.org/619490
- local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include"
-
- # Absolute filename of the most recently installed Clang shared library.
- local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so"
-
- # Absolute dirname of OCCT's include and shared library directories.
- local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade-${OCCT_PV}"
- local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade-${OCCT_PV}"
-
- # Absolute dirname of a temporary directory to store symbol tables for this
- # OCCT version dumped below by the "dump_symbols.py" script.
- local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols"
- local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux"
-
- # Absolute dirname of VTK's include directory,
- local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}"
-
- # Ensure the above paths exist as a crude sanity test.
- test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found."
- test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found."
- test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found."
- test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found."
- test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found."
-
- # "dev-python/clang-python" atom targeting this Clang version.
- local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}"
-
- # Ensure "dev-python/clang-python" targets this Clang version.
- has_version -r "=${_CLANG_PYTHON_ATOM}" ||
- die "${_CLANG_PYTHON_ATOM} not installed."
-
- # Remove all vendored paths.
- rm -r conda opencascade pywrap *.dat || die
-
- # Inject a symlink to OCCT's include directory.
- ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die
-
- # Inject a symlink from OCCT's shared library directory into this temporary
- # directory as required by the "dump_symbols.py" script.
- mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die
- ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die
-
- # Update all hardcoded OCCT shared library versions in "dump_symbols.py".
- sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \
- dump_symbols.py || die
-
- # Dump (i.e., generate) symbol tables for this OCCT version.
- einfo 'Dumping OCCT symbol tables...'
- ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die
-
- # Generate OCCT bindings in the "OCP/" subdirectory.
- einfo 'Building OCP CMake binary tree...'
- ${EPYTHON} -m bindgen \
- --verbose \
- --njobs $(makeopts_jobs) \
- --libclang "${_CLANG_LIB_FILE}" \
- --include "${_CLANG_INCLUDE_DIR}" \
- --include "${_VTK_INCLUDE_DIR}" \
- all ocp.toml || die
-
- # Remove the source "FindOpenCascade.cmake" after generating bindings,
- # which copied that file to the target "OCP/FindOpenCascade.cmake".
- rm FindOpenCascade.cmake || die
-
- #FIXME: Submit an issue recommending upstream replace their
- #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level
- #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl
- # find_package(vtk 9 CONFIG REQUIRED)
- # if(TARGET VTK::VTK)
- # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES)
- # endif()
-
- # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with
- # standard OCCT paths derived above. That file is both fundamentally
- # broken and useless, as the ${CASROOT} environment variable and
- # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file
- # already reliably identify all requisite OpenCASCADE paths. Failure to
- # patch this file results in src_configure() failures resembling:
- # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES)
- sed -i \
- -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \
- -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \
- -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \
- OCP/FindOpenCascade.cmake || die
-
- # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed
- # as an absolute path both here and below to minimize eclass issues.
- CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -B "${S}/OCP.build"
- -DPYTHON_EXECUTABLE="${PYTHON}"
- -Wno-dev
- )
-
- CMAKE_USE_DIR="${S}/OCP" cmake_src_configure
-}
-
-src_compile() {
- CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile
-}
-
-# OCP currently ships no test suite, so we synthesize a crude import unit test.
-src_test() {
- PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \
- 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ'
-}
-
-src_install() {
- python_moduleinto .
- python_domodule "${S}/OCP.build/"OCP*.so
-}
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
index 064952018..e165d6578 100644
--- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
+++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
index e5aef7ccf..4bccc9e86 100644
--- a/dev-python/cadquery-pywrap/Manifest
+++ b/dev-python/cadquery-pywrap/Manifest
@@ -1,2 +1 @@
-DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872
DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
deleted file mode 100644
index 19494930c..000000000
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit llvm distutils-r1
-
-DESCRIPTION="C++ binding generator based on libclang and pybind11"
-HOMEPAGE="https://github.com/CadQuery/pywrap"
-
-#FIXME: Uncomment on bumping to the next stable release.
-# MY_PN=occt
-# MY_PV=$(ver_cut 1-2)
-# MY_P="${MY_PN}${MY_PV}"
-# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz"
-
-# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.2 has yet to be
-# officially released. We instead package a commit known to work as expected.
-MY_COMMIT="f8869e5a47fd3e3e1d31e7ab89b46c158f7487bf"
-SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-# Dependencies are intentionally listed in "setup.py" order.
-RDEPEND="
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
- dev-python/clang-python[${PYTHON_USEDEP}]
- dev-python/cymbal[${PYTHON_USEDEP}]
- dev-python/toml[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/toposort[${PYTHON_USEDEP}]
- dev-python/pyparsing[${PYTHON_USEDEP}]
- dev-python/pybind11[${PYTHON_USEDEP}]
- dev-python/schema[${PYTHON_USEDEP}]
- sci-libs/vtk
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/pywrap-${MY_COMMIT}"
-
-src_prepare() {
- # Relax Jinja version requirements. See also upstream pull request:
- # https://github.com/CadQuery/pywrap/pull/34
- sed -i -e "s~'jinja2==\\(.*\\)',~'jinja2>=\\1,<4',~" setup.py || die
- sed -i \
- -e 's~^\({%- macro super(cls,classes,typedefs\)\() -%}\)$~\1=[]\2~' \
- bindgen/macros.j2 || die
-
- #FIXME: Submit an upstream issue. This violates PEP 440 standards.
- # Sanitize the "bindgen" version to avoid Gentoo QA notices.
- sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die
-
- # Replace conda- with Gentoo-specific prefix dirnames.
- sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py ||
- die
-
- # Reduce all hardcoded header includes to noops.
- sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die
-
- distutils-r1_src_prepare
-}
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
index b2213cef7..7a3b772f3 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit llvm distutils-r1
@@ -29,7 +29,7 @@ SLOT="0"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
dev-python/clang-python[${PYTHON_USEDEP}]
dev-python/cymbal[${PYTHON_USEDEP}]
dev-python/toml[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest
index 380c3e6ae..2b4ddbec1 100644
--- a/dev-python/cadquery/Manifest
+++ b/dev-python/cadquery/Manifest
@@ -1,2 +1 @@
-DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3
DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17
diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
deleted file mode 100644
index 3eafde559..000000000
--- a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_SINGLE_IMPL=1
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python parametric CAD scripting framework based on OCCT"
-HOMEPAGE="https://cadquery.readthedocs.io"
-
-# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but
-# CadQuery 2.2 has yet to be officially released. We instead package a commit
-# known to work as expected with OCCT 7.5.2.
-MY_COMMIT="9b657093c30147293034068dd9d58ec2b728e61a"
-
-#FIXME: Uncomment on bumping to the next stable release.
-# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz"
-SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its
-# Anaconda focus, "setup.py" currently fails to list dependencies.
-BDEPEND="
- test? (
- $(python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
- ')
- )
-"
-RDEPEND="
- >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
- >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}]
- dev-python/ezdxf[${PYTHON_USEDEP}]
- dev-python/ipython[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/nptyping[${PYTHON_USEDEP}]
- sci-libs/nlopt[python,${PYTHON_USEDEP}]
- ')
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-${MY_COMMIT}"
-
-distutils_enable_tests pytest
-
-#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints".
-# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
index 26aa07b6d..543bf100b 100644
--- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
+++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
@@ -5,7 +5,7 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
DISTUTILS_SINGLE_IMPL=1
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
@@ -31,7 +31,7 @@ BDEPEND="
test? (
$(python_gen_cond_dep '
dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
')
)
"
diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
index 015dd2910..7789636c3 100644
--- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild
+++ b/dev-python/ccdproc/ccdproc-2.3.0.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_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/click-didyoumean/Manifest b/dev-python/click-didyoumean/Manifest
deleted file mode 100644
index 5c8198fe3..000000000
--- a/dev-python/click-didyoumean/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST click-didyoumean-0.2.0.tar.gz 309305 BLAKE2B 498571996758c57e015dd2f5de8966ace78defb2b1f9faa5a99c6020fb143bafa03e240f183f46a962dc9a3d39e1e9a7a49855f6f6e2dfd5452c546f015b17ce SHA512 690438809d103d2f2b54fc1dabb912b359f5355ba242bb37ef420cd8fcc3ed226911d7216acdcb3574bb0e93231c3a3ca7b00e9e99365955387cfeddeed449ae
-DIST click-didyoumean-0.3.0.tar.gz 309301 BLAKE2B 2b667b5e94dd690e5b7a2e96b83197f52e201b002a32fff4a8dbb4bd5497d5b816b40d9da98729821e1d17a795a3776c1553a746aa4c4144cf7fe6540768e1ca SHA512 4927ee392f27950c3f7ef5e0f1d5a5e2421172f3e9d34ec76986c9c7ea698cfa1981678a06fb8682577d6ed04c242c42bdd1d796d7623a1c99dfdbdb61c80fca
diff --git a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
deleted file mode 100644
index b9a65c5d8..000000000
--- a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( pypy3 python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="Enable git-like did-you-mean feature in click"
-HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
-SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="test"
-# Tests actually pass, but not included in archive:
-# https://github.com/click-contrib/click-didyoumean/issues/11
-DEPEND="
- dev-python/click
-"
-RDEPEND="${DEPEND}"
-
-distutils_enable_tests pytest
diff --git a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild
deleted file mode 100644
index 9fe4373c8..000000000
--- a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
-PYTHON_COMPAT=( pypy3 python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="Enable git-like did-you-mean feature in click"
-HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
-SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-DEPEND="
- dev-python/click
-"
-RDEPEND="${DEPEND}"
-
-distutils_enable_tests pytest
diff --git a/dev-python/cligj/cligj-0.7.2.ebuild b/dev-python/cligj/cligj-0.7.2.ebuild
index c90584b75..b5d65668f 100644
--- a/dev-python/cligj/cligj-0.7.2.ebuild
+++ b/dev-python/cligj/cligj-0.7.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/colorcet/Manifest b/dev-python/colorcet/Manifest
index 0bb308038..9692f6be6 100644
--- a/dev-python/colorcet/Manifest
+++ b/dev-python/colorcet/Manifest
@@ -1 +1,2 @@
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
index c8024aa51..ba5c3db0a 100644
--- a/dev-python/colorcet/colorcet-2.0.6.ebuild
+++ b/dev-python/colorcet/colorcet-2.0.6.ebuild
@@ -1,12 +1,13 @@
-# 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
# 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_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -17,6 +18,9 @@ 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}]
diff --git a/dev-python/colorcet/colorcet-3.0.1.ebuild b/dev-python/colorcet/colorcet-3.0.1.ebuild
new file mode 100644
index 000000000..25182e5d2
--- /dev/null
+++ b/dev-python/colorcet/colorcet-3.0.1.ebuild
@@ -0,0 +1,28 @@
+# 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}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ >=dev-python/param-1.7.0[${PYTHON_USEDEP}]
+ >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild
index a16fcd44c..bada7bbe6 100644
--- a/dev-python/cymbal/cymbal-1.0.0.ebuild
+++ b/dev-python/cymbal/cymbal-1.0.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild
index cf3c8a34f..f1733c147 100644
--- a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Schemata for DANDI archive project"
diff --git a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
index 19a906634..71a3ff4a4 100644
--- a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild
index 19a906634..71a3ff4a4 100644
--- a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
index 19a906634..71a3ff4a4 100644
--- a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
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 19a906634..71a3ff4a4 100644
--- a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild
index 1ae0a527a..c9d19ba4c 100644
--- a/dev-python/delegator/delegator-0.1.1.ebuild
+++ b/dev-python/delegator/delegator-0.1.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/dpctl/Manifest b/dev-python/dpctl/Manifest
new file mode 100644
index 000000000..aab57723a
--- /dev/null
+++ b/dev-python/dpctl/Manifest
@@ -0,0 +1,2 @@
+DIST dpctl-0.13.0.gh.tar.gz 363708 BLAKE2B 82eaf296cb0aaaad1a9c23334b027d4b38ef8d580c43a6ea1fb7542b20f5511c09edf7fdd3bd98a5b48cdf55176fcaeea787c6d93ef65fc6c94004cbb0c61255 SHA512 5ddefe9671ef77e0ff507e3c92c80b147a4f19f50ee9b64dd940960e181edea16b5dbbdb990aa3dc37da80e6015979f702fba60210b8677a83780224cdd30e76
+DIST dpctl-0.14.0.gh.tar.gz 399378 BLAKE2B 3a9cbea965941c8c0a85938f0736705fd0bbdc611e02a44363a670119555ff95fbae130526caa25f42ee499d5b36c83b8c574db1b2368a1cbe7855b84fabe9f1 SHA512 37d76653112556ebeadec846cc6b156cb84e7b82bc6a9477072a3721b3a830c5fcb7d6e92e76aa7c7449547e925b07d5dda42d2777813e7d1db1d97ea852e22a
diff --git a/dev-python/dpctl/dpctl-0.13.0.ebuild b/dev-python/dpctl/dpctl-0.13.0.ebuild
new file mode 100644
index 000000000..4c240bfb1
--- /dev/null
+++ b/dev-python/dpctl/dpctl-0.13.0.ebuild
@@ -0,0 +1,62 @@
+# 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}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${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[${PYTHON_USEDEP}]
+ sci-libs/oneDAL
+ sys-devel/DPC++:0/5
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.14.0-dont-fetch-level-zero.patch"
+ "${FILESDIR}/${PN}-0.13.0-dont-fetch-pybind.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="${ESYSROOT}/usr/lib/llvm/intel"
+
+ # For some reason this is required to build successfully
+ mkdir -p _skbuild/linux-x86_64-3.8/setuptools/lib.linux-x86_64-cpython-38/dpctl || die
+ cp dpctl/_version.py _skbuild/linux-x86_64-3.8/setuptools/lib.linux-x86_64-cpython-38/dpctl || die
+ mkdir -p _skbuild/linux-x86_64-3.9/setuptools/lib.linux-x86_64-cpython-39/dpctl || die
+ cp dpctl/_version.py _skbuild/linux-x86_64-3.9/setuptools/lib.linux-x86_64-cpython-39/dpctl || die
+ mkdir -p _skbuild/linux-x86_64-3.10/setuptools/lib.linux-x86_64-cpython-310/dpctl || die
+ cp dpctl/_version.py _skbuild/linux-x86_64-3.10/setuptools/lib.linux-x86_64-cpython-310/dpctl || die
+ mkdir -p _skbuild/linux-x86_64-3.11/setuptools/lib.linux-x86_64-cpython-311/dpctl || die
+ cp dpctl/_version.py _skbuild/linux-x86_64-3.11/setuptools/lib.linux-x86_64-cpython-311/dpctl || die
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/dpctl/dpctl-0.14.0.ebuild b/dev-python/dpctl/dpctl-0.14.0.ebuild
new file mode 100644
index 000000000..0bab26875
--- /dev/null
+++ b/dev-python/dpctl/dpctl-0.14.0.ebuild
@@ -0,0 +1,62 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Control "
+HOMEPAGE="https://github.com/IntelPython/dpctl"
+SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${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=(
+ "${FILESDIR}/${P}-find-opencl.patch"
+ "${FILESDIR}/${P}-dont-fetch-level-zero.patch"
+ "${FILESDIR}/${P}-dont-fetch-pybind.patch"
+ "${FILESDIR}/${P}-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
+}
diff --git a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
new file mode 100644
index 000000000..b7dab5c75
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 23ae1dd..e144e90 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -26,15 +26,7 @@ install(FILES ${_dpctl_capi_headers}
+ # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
+ include(GNUInstallDirs)
+
+-# Fetch pybind11
+-include(FetchContent)
+-
+-FetchContent_Declare(
+- pybind11
+- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.9.2.tar.gz
+- URL_HASH SHA256=6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1
+-)
+-FetchContent_MakeAvailable(pybind11)
++include(/usr/share/cmake/pybind11/pybind11Config.cmake)
+
+ add_subdirectory(dpctl)
+
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
new file mode 100644
index 000000000..ac0301886
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
@@ -0,0 +1,82 @@
+diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
+index 2929c33..731f054 100644
+--- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
++++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
+@@ -26,76 +26,10 @@
+
+ function(get_level_zero_headers)
+
+- if(EXISTS level-zero)
+- # Update the checkout
+- execute_process(
+- COMMAND ${GIT_EXECUTABLE} fetch
+- RESULT_VARIABLE result
+- ERROR_VARIABLE error
+- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- ERROR_STRIP_TRAILING_WHITESPACE
+- )
+-
+- if(NOT result EQUAL 0)
+- message(FATAL_ERROR
+- "Could not update Level Zero sources."
+- )
+- endif()
+- else()
+- # Clone the Level Zero git repo
+- execute_process(
+- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git
+- RESULT_VARIABLE result
+- ERROR_VARIABLE error
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- ERROR_STRIP_TRAILING_WHITESPACE
+- )
+-
+- if(NOT result EQUAL 0)
+- message(FATAL_ERROR
+- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero."
+- )
+- endif()
+- endif()
+-
+- # Use git describe to get latest tag name
+- execute_process(
+- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0
+- RESULT_VARIABLE result
+- OUTPUT_VARIABLE latest_tag
+- ERROR_VARIABLE error
+- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- ERROR_STRIP_TRAILING_WHITESPACE
+- )
+-
+- if(NOT result EQUAL 0)
+- message(FATAL_ERROR
+- "Could not get the name for the latest release."
+- )
+- endif()
+-
+- # Use git describe to get latest tag name
+- execute_process(
+- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag}
+- RESULT_VARIABLE result
+- ERROR_VARIABLE error
+- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- ERROR_STRIP_TRAILING_WHITESPACE
+- )
+-
+- if(NOT result EQUAL 0)
+- message(FATAL_ERROR
+- "Could not checkout the latest release."
+- )
+- endif()
+-
+ # Populate the path to the headers
+ find_path(LEVEL_ZERO_INCLUDE_DIR
+ NAMES zet_api.h
+- PATHS ${CMAKE_BINARY_DIR}/level-zero/include
++ PATHS /usr/include/level_zero
+ NO_DEFAULT_PATH
+ NO_CMAKE_ENVIRONMENT_PATH
+ NO_CMAKE_PATH
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
new file mode 100644
index 000000000..b2b8c5d81
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index da138c1..ecab139 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -28,15 +28,7 @@ install(FILES ${_dpctl_capi_headers}
+ # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
+ include(GNUInstallDirs)
+
+-# Fetch pybind11
+-include(FetchContent)
+-
+-FetchContent_Declare(
+- pybind11
+- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.1.tar.gz
+- URL_HASH SHA256=111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad
+-)
+-FetchContent_MakeAvailable(pybind11)
++include(/usr/share/cmake/pybind11/pybind11Config.cmake)
+
+ add_subdirectory(dpctl)
+
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch
new file mode 100644
index 000000000..3841816ee
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch
@@ -0,0 +1,13 @@
+diff --git a/libsyclinterface/cmake/modules/FindIntelSycl.cmake b/libsyclinterface/cmake/modules/FindIntelSycl.cmake
+index 84e8946..ccc2591 100644
+--- a/libsyclinterface/cmake/modules/FindIntelSycl.cmake
++++ b/libsyclinterface/cmake/modules/FindIntelSycl.cmake
+@@ -134,7 +134,7 @@ if(${clangxx_result} MATCHES "0")
+ find_file(
+ IntelSycl_OPENCL_LIBRARY
+ NAMES "libOpenCL.so"
+- PATHS ${IntelSycl_LIBRARY_DIR}
++ PATHS /usr/lib64
+ )
+ endif()
+
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
new file mode 100644
index 000000000..44b950cb6
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
@@ -0,0 +1,47 @@
+From d0d3e6f1a9ffbac91f24cc06abce6dcad6509a6b Mon Sep 17 00:00:00 2001
+From: Julien Jerphanion <git@jjerphan.xyz>
+Date: Tue, 6 Dec 2022 10:24:26 +0100
+Subject: [PATCH 1/2] MAINT Include tuple in 'utils/strided_iters.hpp'
+
+This include directive seems to have been forgotten and it is impossible
+for me to compile dpctl without it.
+---
+ dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
+index c24ed54941..595ad3f4a7 100644
+--- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
++++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
+@@ -30,6 +30,7 @@
+ #include <array>
+ #include <numeric> // std::iota
+ #include <vector>
++#include <tuple>
+
+ /* An N-dimensional array can be stored in a single
+ * contiguous chunk of memory by contiguously laying
+
+From f75ccd8c8aeaae92f0cb03874f93be5e7a63a6a7 Mon Sep 17 00:00:00 2001
+From: Julien Jerphanion <git@jjerphan.xyz>
+Date: Tue, 6 Dec 2022 14:45:40 +0100
+Subject: [PATCH 2/2] Make clang-format happy
+
+---
+ dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
+index 595ad3f4a7..0abd7f4f2a 100644
+--- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
++++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
+@@ -29,8 +29,8 @@
+ #include <algorithm> // sort
+ #include <array>
+ #include <numeric> // std::iota
+-#include <vector>
+ #include <tuple>
++#include <vector>
+
+ /* An N-dimensional array can be stored in a single
+ * contiguous chunk of memory by contiguously laying
diff --git a/dev-python/dpctl/metadata.xml b/dev-python/dpctl/metadata.xml
new file mode 100644
index 000000000..06d339ee1
--- /dev/null
+++ b/dev-python/dpctl/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/dpctl</remote-id>
+ <remote-id type="pypi">dpctl</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dpnp/Manifest b/dev-python/dpnp/Manifest
new file mode 100644
index 000000000..a2dfe5862
--- /dev/null
+++ b/dev-python/dpnp/Manifest
@@ -0,0 +1,2 @@
+DIST dpnp-0.10.0.gh.tar.gz 443009 BLAKE2B c15cce02d1cdd99217f4ee6dca853138d16318695075509e4042bd21cb098c13abf3b8351cc537ca1d1f2d875bfa51675431183665f87c8bd381c347766bc29c SHA512 3ecff347a371ff2173ce4573444afe1201fe2b1a9a75a8a68879fe1930b15b979875391b29d0c57e4e97d860e94f2af2b75bbb6dbf2232011bed92812c8ba01b
+DIST dpnp-0.11.0.gh.tar.gz 477797 BLAKE2B e33d63c9334e56e69efe73ab37d14fa133869eae518b484f1627587ea8cb869c7f3039d8d7ecc7656fec4e70d8ddc182d3e757f20cc497c6f497d29c851daafb SHA512 ca4697773bc92260a763861581009c60489694e31effb452d7ce3bf7961345b4cbdfdb5797f8d345caa838032b7d8e74eac935116c99d3b2fe019bbb6da1d92a
diff --git a/dev-python/dpnp/dpnp-0.10.0.ebuild b/dev-python/dpnp/dpnp-0.10.0.ebuild
new file mode 100644
index 000000000..51e17faa0
--- /dev/null
+++ b/dev-python/dpnp/dpnp-0.10.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+# Breaks the installation of the backend library
+#DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Extension for NumPy"
+HOMEPAGE="https://github.com/IntelPython/dpnp"
+SRC_URI="https://github.com/IntelPython/dpnp/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-util/cmake
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-cpp/tbb
+ dev-python/dpctl[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/mkl
+ sys-devel/DPC++:=
+"
+DEPEND="${RDEPEND}
+ sys-devel/oneDPL
+"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${P}-fix-compile.patch"
+)
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export DPL_ROOT="${ESYSROOT}/usr/include/include/oneapi/dpl"
+ # Parallel build broken
+ export MAKEOPTS="-j1"
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ export BUILD_DIR_LIBS="${BUILD_DIR}/lib/dpnp"
+ distutils-r1_python_compile
+}
diff --git a/dev-python/dpnp/dpnp-0.11.0.ebuild b/dev-python/dpnp/dpnp-0.11.0.ebuild
new file mode 100644
index 000000000..51e17faa0
--- /dev/null
+++ b/dev-python/dpnp/dpnp-0.11.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+# Breaks the installation of the backend library
+#DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Extension for NumPy"
+HOMEPAGE="https://github.com/IntelPython/dpnp"
+SRC_URI="https://github.com/IntelPython/dpnp/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-util/cmake
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-cpp/tbb
+ dev-python/dpctl[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/mkl
+ sys-devel/DPC++:=
+"
+DEPEND="${RDEPEND}
+ sys-devel/oneDPL
+"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${P}-fix-compile.patch"
+)
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export DPL_ROOT="${ESYSROOT}/usr/include/include/oneapi/dpl"
+ # Parallel build broken
+ export MAKEOPTS="-j1"
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ export BUILD_DIR_LIBS="${BUILD_DIR}/lib/dpnp"
+ distutils-r1_python_compile
+}
diff --git a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
new file mode 100644
index 000000000..deaa95d0b
--- /dev/null
+++ b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
@@ -0,0 +1,97 @@
+diff --git a/0.build.sh b/0.build.sh
+index c089b1d..3bb0739 100755
+--- a/0.build.sh
++++ b/0.build.sh
+@@ -10,14 +10,14 @@ python setup.py clean
+ DPLROOT=/opt/intel/oneapi/dpl/latest python setup.py build_clib
+
+ # inplace build
+-CC=dpcpp python setup.py build_ext --inplace
++CC=${CC} python setup.py build_ext --inplace
+
+ # development build. Root privileges needed
+ # python setup.py develop
+
+ echo
+ echo =========example3==============
+-dpcpp -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
++${CXX} -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
+ # LD_DEBUG=libs,bindings,symbols ./example3
+ ./example3
+
+diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
+index 81f073c..bcc4ecc 100644
+--- a/dpnp/backend/CMakeLists.txt
++++ b/dpnp/backend/CMakeLists.txt
+@@ -88,24 +88,6 @@ if (CMAKE_VERSION VERSION_EQUAL 3.19.1)
+ )
+ endif()
+
+-if(UNIX)
+- set(CMAKE_CXX_COMPILER "dpcpp")
+- # add_compile_options(-fPIC)
+-elseif(WIN32)
+- set(CMAKE_CXX_COMPILER "dpcpp")
+- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
+- # set(CMAKE_LINKER "lld-link")
+- # include (Platform/Windows-Clang)
+- # set(CMAKE_LINKER "dpcpp")
+- # set(CMAKE_AR "llvm-ar")
+- # set(CMAKE_RANLIB "llvm-ranlib")
+- # set(CMAKE_CXX_FLAGS "/EHsc")
+-
+- add_compile_options(/EHsc) # /Ox /W3 /GL /DNDEBUG /MD /EHsc
+-else()
+- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
+-endif()
+-
+ # set language version
+ set(CMAKE_CXX_STANDARD 17)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+@@ -280,6 +262,7 @@ endif()
+ # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
+
+ install(TARGETS dpnp_backend_c
++ DESTINATION ${DPNP_INSTALL_PREFIX}
+ PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+ )
+
+diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
+index dc9f322..35432fa 100644
+--- a/utils/command_build_clib.py
++++ b/utils/command_build_clib.py
+@@ -60,8 +60,8 @@ else:
+ Set compiler for the project
+ """
+ # default variables (for Linux)
+-_project_compiler = "dpcpp"
+-_project_linker = "dpcpp"
++_project_compiler = os.environ.get("CXX")
++_project_linker = os.environ.get("CXX")
+ _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel"]
+ _project_cmplr_flag_sycl = ["-fsycl"]
+ _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
+@@ -113,8 +113,8 @@ except ImportError:
+
+ # other OS specific
+ if IS_WIN:
+- _project_compiler = "dpcpp"
+- _project_linker = "lld-link"
++ _project_compiler = os.environ.get("CXX")
++ _project_linker = os.environ.get("CXX")
+ _project_cmplr_flag_sycl = []
+ _project_cmplr_flag_stdcpp_static = []
+ _project_cmplr_flag_compatibility = []
+diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
+index 0ef0e24..84f2469 100644
+--- a/utils/command_build_cmake_clib.py
++++ b/utils/command_build_cmake_clib.py
+@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
+ "-S" + backend_directory,
+ "-B" + abs_build_temp_path,
+ "-DCMAKE_BUILD_TYPE=" + config,
+- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
+ "-DDPNP_INSTALL_STRUCTURED=OFF",
+ # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
+ "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
new file mode 100644
index 000000000..2ccc0a6b8
--- /dev/null
+++ b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
@@ -0,0 +1,80 @@
+diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
+index 409a29f..11d21f1 100644
+--- a/dpnp/backend/CMakeLists.txt
++++ b/dpnp/backend/CMakeLists.txt
+@@ -98,30 +98,7 @@ string(CONCAT COMMON_LINK_FLAGS
+ "-fsycl "
+ "-fsycl-device-code-split=per_kernel "
+ )
+-if(UNIX)
+- set(CMAKE_CXX_COMPILER "dpcpp")
+- # add_compile_options(-fPIC)
+-elseif(WIN32)
+- set(CMAKE_CXX_COMPILER "dpcpp")
+- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
+- # set(CMAKE_LINKER "lld-link")
+- # include (Platform/Windows-Clang)
+- # set(CMAKE_LINKER "dpcpp")
+- # set(CMAKE_AR "llvm-ar")
+- # set(CMAKE_RANLIB "llvm-ranlib")
+- # set(CMAKE_CXX_FLAGS "/EHsc")
+
+- string(APPEND COMMON_COMPILER_FLAGS
+- "/EHsc "
+-# "/Ox "
+-# "/W3 "
+-# "/GL "
+-# "/DNDEBUG "
+-# "/MD "
+- )
+-else()
+- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
+-endif()
+
+ # set language version
+ set(CMAKE_CXX_STANDARD 17)
+@@ -327,6 +304,7 @@ endif()
+ # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
+
+ install(TARGETS dpnp_backend_c
++ DESTINATION ${DPNP_INSTALL_PREFIX}
+ PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+ )
+
+diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
+index 3d1177b..d8fbdac 100644
+--- a/utils/command_build_clib.py
++++ b/utils/command_build_clib.py
+@@ -61,8 +61,8 @@ else:
+ Set compiler for the project
+ """
+ # default variables (for Linux)
+-_project_compiler = "dpcpp"
+-_project_linker = "dpcpp"
++_project_compiler = os.environ.get("CXX")
++_project_linker = os.environ.get("CXX")
+ _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func"]
+ _project_cmplr_flag_sycl = ["-fsycl"]
+ _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
+@@ -114,7 +114,7 @@ except ImportError:
+
+ # other OS specific
+ if IS_WIN:
+- _project_compiler = "dpcpp"
++ _project_compiler = os.environ.get("CXX")
+ _project_linker = "lld-link"
+ _project_cmplr_flag_sycl = []
+ _project_cmplr_flag_stdcpp_static = []
+diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
+index 0ef0e24..84f2469 100644
+--- a/utils/command_build_cmake_clib.py
++++ b/utils/command_build_cmake_clib.py
+@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
+ "-S" + backend_directory,
+ "-B" + abs_build_temp_path,
+ "-DCMAKE_BUILD_TYPE=" + config,
+- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
+ "-DDPNP_INSTALL_STRUCTURED=OFF",
+ # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
+ "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/dpnp/metadata.xml b/dev-python/dpnp/metadata.xml
new file mode 100644
index 000000000..868959c89
--- /dev/null
+++ b/dev-python/dpnp/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/dpnp</remote-id>
+ <remote-id type="pypi">dpnp</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
index 8119b0206..976e33986 100644
--- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild
+++ b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
index 43bf7c371..27c8ff04b 100644
--- a/dev-python/ezdxf/ezdxf-0.16.5.ebuild
+++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
@@ -4,7 +4,7 @@
EAPI=8
#FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not.
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml
index d08e0d509..23d9fd64c 100644
--- a/dev-python/fiat/metadata.xml
+++ b/dev-python/fiat/metadata.xml
@@ -17,5 +17,6 @@ support Hermite and nonconforming elements.
</longdescription>
<upstream>
<remote-id type="bitbucket">fenics-project/fiat</remote-id>
+ <remote-id type="github">FEniCS/fiat</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/fiona/fiona-1.8.21.ebuild b/dev-python/fiona/fiona-1.8.21.ebuild
index 51ded0d37..231038559 100644
--- a/dev-python/fiona/fiona-1.8.21.ebuild
+++ b/dev-python/fiona/fiona-1.8.21.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_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild
index 3f55c8604..b15c37615 100644
--- a/dev-python/fscacher/fscacher-0.1.4.ebuild
+++ b/dev-python/fscacher/fscacher-0.1.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Cache results of operations on heavy file trees"
diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild
index bb632800e..8bb00f6f4 100644
--- a/dev-python/fscacher/fscacher-0.2.0.ebuild
+++ b/dev-python/fscacher/fscacher-0.2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Cache results of operations on heavy file trees"
diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest
index 196e885ac..f2c52a88e 100644
--- a/dev-python/fslpy/Manifest
+++ b/dev-python/fslpy/Manifest
@@ -1 +1 @@
-DIST fslpy-3.8.1.tar.gz 4698603 BLAKE2B 33740081a065b6684b864eaf50910a38e26ce7aa10d18bf8faaeaf34ee87dfa22e8f2ee3cebc5681f2356cfb519a59ba07232a3cfb81526258ef92f3ced893ea SHA512 1b5d945f6aae6557e892e5700f228170bab8a235c77d06b162fc2afc16663f3bdbe18e54e4e20dad46ac873ccbf0cdc2649e5ac1c53e17b0d78c45e91e8a1896
+DIST fslpy-3.10.0.tar.gz 4695461 BLAKE2B 9ce74ed6175fb84fe0f123375273a9450c03b659c977b48e3fb874509d5b3f728c75aff850931e1af4fd398fb5eda80a6eef90b2a582e8db3f2135704b4124ed SHA512 b9b12350308d2aee5d10c16582abd96f17b56893287fc32ab3942e8edce8add1f96e1f5c83cca761707be9b2442262e28d961879d5d02e1001006805a74e1cda
diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild
index f28e7283e..ce3b7008f 100644
--- a/dev-python/fslpy/fslpy-3.8.1.ebuild
+++ b/dev-python/fslpy/fslpy-3.10.0.ebuild
@@ -3,8 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
-
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx
DESCRIPTION="The FSL Python Library"
@@ -16,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
+ dev-python/dill[${PYTHON_USEDEP}]
>=dev-python/h5py-2.9[${PYTHON_USEDEP}]
>=dev-python/indexed_gzip-0.7.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1[${PYTHON_USEDEP}]
@@ -27,17 +28,20 @@ RDEPEND="
>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
"
-PATCHES=(
- "${FILESDIR}/fslpy-2.7.0-coverage.patch"
-)
-
distutils_enable_tests pytest
distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+python_prepare_all() {
+ # Do not depend on coverage
+ sed -i -e 's/--cov=fsl//g' setup.cfg || die
+
+ distutils-r1_python_prepare_all
+}
+
src_test() {
virtx distutils-r1_src_test
}
python_test() {
- epytest --niters=50 -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
+ epytest -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
}
diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest
index c541ed559..2abc44bd1 100644
--- a/dev-python/geopandas/Manifest
+++ b/dev-python/geopandas/Manifest
@@ -1 +1 @@
-DIST geopandas-0.10.2.tar.gz 6317604 BLAKE2B 5eb0d84c11eda99b43bc15b179a971c5e56fb36d40c771b523161dd6ddac4faee4bac483ccd1bdb9f10f73dfd2adf6d72703cc180359cd68383bfba9410f4f5b SHA512 339660c423955b9f110eb390c3d1dc88eeb1ed74fa300870ae277d312e9b2e6733463bc45b445c73a9f8b6dee82d82f203c7b75c0a4aad7e36e43e5c7ec78f42
+DIST geopandas-0.12.1.gh.tar.gz 6358329 BLAKE2B a1d16656e19284b855338379e4329e964772db32ed833cce65118c9f03519a69b3be090af66829b39c2afdf520a8e98773de3ceebc0aef818c586cba913b81ea SHA512 42f70d7d919e819e0ab5872d7389ede769868599221c1717ea18c0f4fe24ec3cc736ef7c7b26766c43abaa456e46a4f9283ab9f4364d13ae171aaf705ff3d168
diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.12.1.ebuild
index e63aaa1bc..1fd17dda0 100644
--- a/dev-python/geopandas/geopandas-0.10.2.ebuild
+++ b/dev-python/geopandas/geopandas-0.12.1.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
-inherit distutils-r1
+inherit distutils-r1 optfeature
DESCRIPTION="Python tools for geographic data"
HOMEPAGE="https://github.com/geopandas/geopandas"
-SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -32,3 +32,9 @@ python_test() {
epytest ${deselect[@]/#/--deselect }
}
+
+pkg_postinst() {
+ optfeature "plotting" dev-python/matplotlib
+ optfeature "spatial indexes and spatial joins" sci-libs/rtree
+ optfeature "geocoding" sci-geosciences/geopy
+}
diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml
index a9b62a0d8..a102c7148 100644
--- a/dev-python/geopandas/metadata.xml
+++ b/dev-python/geopandas/metadata.xml
@@ -1,19 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- GeoPandas is a project to add support for geographic data to pandas
- objects. It currently implements GeoSeries and GeoDataFrame types
- which are subclasses of pandas.Series and pandas.DataFrame
- respectively. GeoPandas objects can act on shapely geometry objects
- and perform geometric operations.
-</longdescription>
- <upstream>
- <remote-id type="github">geopandas/geopandas</remote-id>
- <remote-id type="pypi">geopandas</remote-id>
- </upstream>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ GeoPandas is a project to add support for geographic data to pandas
+ objects. It currently implements GeoSeries and GeoDataFrame types
+ which are subclasses of pandas.Series and pandas.DataFrame
+ respectively. GeoPandas objects can act on shapely geometry objects
+ and perform geometric operations.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">geopandas/geopandas</remote-id>
+ <remote-id type="pypi">geopandas</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
index 12ec9927c..96ed950c1 100644
--- a/dev-python/gffpandas/gffpandas-1.2.0.ebuild
+++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
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 785646336..88e1a333a 100644
--- a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
+++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild
index 93e08ccf4..c7e710a70 100644
--- a/dev-python/grabbit/grabbit-0.2.6.ebuild
+++ b/dev-python/grabbit/grabbit-0.2.6.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/gwcs/Manifest b/dev-python/gwcs/Manifest
index 4c4dc60c1..91b72eae3 100644
--- a/dev-python/gwcs/Manifest
+++ b/dev-python/gwcs/Manifest
@@ -1 +1,2 @@
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
index 373410501..c75d7b534 100644
--- a/dev-python/gwcs/gwcs-0.16.1.ebuild
+++ b/dev-python/gwcs/gwcs-0.16.1.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
@@ -14,6 +14,9 @@ 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[${PYTHON_USEDEP}]
test? (
diff --git a/dev-python/gwcs/gwcs-0.18.3.ebuild b/dev-python/gwcs/gwcs-0.18.3.ebuild
new file mode 100644
index 000000000..c75d7b534
--- /dev/null
+++ b/dev-python/gwcs/gwcs-0.18.3.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Generalized World Coordinate System"
+HOMEPAGE="https://gwcs.readthedocs.io/en/latest/"
+SRC_URI="mirror://pypi/${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/hdf5storage/hdf5storage-0.1.17.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild
index 22f9151e0..edafef12b 100644
--- a/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild
index 22f9151e0..edafef12b 100644
--- a/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/hdf5storage/hdf5storage-9999.ebuild b/dev-python/hdf5storage/hdf5storage-9999.ebuild
index 3a6391eb0..f88ed9f94 100644
--- a/dev-python/hdf5storage/hdf5storage-9999.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-9999.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index 866b5e553..b3f479f18 100644
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
index 1bec3913c..c63395b7d 100644
--- a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="The Hierarchical Data Modeling Framework"
diff --git a/dev-python/holoviews/Manifest b/dev-python/holoviews/Manifest
index 94e17efc1..806b0513d 100644
--- a/dev-python/holoviews/Manifest
+++ b/dev-python/holoviews/Manifest
@@ -1 +1,2 @@
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
index 505133d78..4c8af05d9 100644
--- a/dev-python/holoviews/holoviews-1.14.2.ebuild
+++ b/dev-python/holoviews/holoviews-1.14.2.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild
new file mode 100644
index 000000000..425290441
--- /dev/null
+++ b/dev-python/holoviews/holoviews-1.15.3.ebuild
@@ -0,0 +1,46 @@
+# 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"
+# Reported upstream:
+# https://github.com/holoviz/holoviews/issues/5592
+RESTRICT="test"
+
+DEPEND="
+ >=dev-python/param-1.9.3[${PYTHON_USEDEP}]
+ >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/bokeh[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/nbconvert[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ sci-visualization/dash[${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}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild
index 5dfb4bc6b..341aa57f2 100644
--- a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild
+++ b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
DESCRIPTION="python frontend for the fast ripser tda tool"
-HOMEPAGE="https://ripser.scikit-tda.org/"
+HOMEPAGE="https://ripser.scikit-tda.org/ https://github.com/sofiatolaosebikan/hopcroftkarp"
COMMIT="2846e1dd3265d95d2bddb0cf4190b830cbb4efe6"
SRC_URI="https://github.com/sofiatolaosebikan/hopcroftkarp/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}"/${PN}-${COMMIT}
diff --git a/dev-python/hopcroftkarp/metadata.xml b/dev-python/hopcroftkarp/metadata.xml
index 2f2c0b51c..6959005e7 100644
--- a/dev-python/hopcroftkarp/metadata.xml
+++ b/dev-python/hopcroftkarp/metadata.xml
@@ -1,12 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
+ <maintainer type="person">
+ <email>gentoo@aisha.cc</email>
+ <name>Aisha Tammy</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">sofiatolaosebikan/hopcroftkarp</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild
index c8a9c9ca1..7dbb9d5c9 100644
--- a/dev-python/interleave/interleave-0.2.0.ebuild
+++ b/dev-python/interleave/interleave-0.2.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10})
+PYTHON_COMPAT=( python3_10)
inherit distutils-r1
diff --git a/dev-python/json_tricks/metadata.xml b/dev-python/json_tricks/metadata.xml
index f5804b4b0..2967a86bd 100644
--- a/dev-python/json_tricks/metadata.xml
+++ b/dev-python/json_tricks/metadata.xml
@@ -21,6 +21,6 @@
</longdescription>
<upstream>
<remote-id type="pypi">json-tricks</remote-id>
+ <remote-id type="github">mverleg/pyjson_tricks</remote-id>
</upstream>
</pkgmetadata>
-
diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml
index e97c4322a..006b418f5 100644
--- a/dev-python/kmapper/metadata.xml
+++ b/dev-python/kmapper/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">scikit-tda/kepler-mapper</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/latexify_py/Manifest b/dev-python/latexify_py/Manifest
new file mode 100644
index 000000000..7a500fe7d
--- /dev/null
+++ b/dev-python/latexify_py/Manifest
@@ -0,0 +1 @@
+DIST latexify_py-0.2.0.tar.gz 30995 BLAKE2B 2b55c83ea073b221096b4e44fad362d421f5d526bdff79a825b67a5fb419ff6185cd9f18a49727b988409f257318845a90f78223cf6eb9dd264ce6d1c0b71b82 SHA512 17250784d7a009705854d3f6118b3c854c4e86e007a45740c2b6d314ff25503b3561327b610b17e49652fa59ff6612bae8e74ea4caedeaa4f6a0b1e446fe086c
diff --git a/dev-python/latexify_py/latexify_py-0.2.0.ebuild b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
new file mode 100644
index 000000000..bd42c3cf3
--- /dev/null
+++ b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1
+
+DESCRIPTION="Generate LaTeX expression from Python code"
+HOMEPAGE="https://github.com/google/latexify_py"
+SRC_URI="https://github.com/google/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/dill[${PYTHON_USEDEP}]
+"
+
+BDEPEND="test? (
+ dev-python/notebook[${PYTHON_USEDEP}]
+ dev-python/twine[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_tests pytest
+
+DOCS=( README.md docs )
+
+python_test() {
+ PYTHONPATH="${S}/src" epytest
+}
diff --git a/dev-python/latexify_py/metadata.xml b/dev-python/latexify_py/metadata.xml
new file mode 100644
index 000000000..ae9640ffb
--- /dev/null
+++ b/dev-python/latexify_py/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
index 1749985b0..86f967801 100644
--- a/dev-python/llvmlite/Manifest
+++ b/dev-python/llvmlite/Manifest
@@ -1 +1 @@
-DIST llvmlite-0.39.0.gh.tar.gz 237009 BLAKE2B 41e485c636d285d039cd559c6386f79d05d51c266b31e24c68a30a921e9131d422e5782befdbdac7407b61fd44cab4b14863fdefa1c76ced235dd89eb0328110 SHA512 3493afc14c08b06bfb26230409d678b9a72d3957e412a4a6a6367aea0bc743fc46191ba050aa70e403424567038ab9fc2721c839df8035e4511dbf9ee4caddfa
+DIST llvmlite-0.39.1.gh.tar.gz 237119 BLAKE2B c2538994a6b9116d9a124ad8b8fff9c06d654bcdd345fb25251505b7577c6dffdfa56c9226250dbc2de6253cf6154523ec0d3cd849697a66cabf5b522c5e76ca SHA512 16b341300e4034aff4ce9553fec6b5923b9f4cb261c1ec0ee2cef6d87addcbebe8f4805dbc2fb30f357800fa029c3b6fc8ed62a5fdaad7c262e723c3b9c4ad32
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
new file mode 100644
index 000000000..d35979ebc
--- /dev/null
+++ b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 02b1604..a45c9b8 100644
+--- a/setup.py
++++ b/setup.py
+@@ -33,7 +33,7 @@ except ImportError:
+
+
+ min_python_version = "3.7"
+-max_python_version = "3.11" # exclusive
++max_python_version = "3.12" # exclusive
+
+
+ def _guard_py_ver():
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
index 17eb80e87..17eb80e87 100644
--- a/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch
+++ b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
diff --git a/dev-python/llvmlite/llvmlite-0.39.0.ebuild b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
index a2c3a6750..c95aa079d 100644
--- a/dev-python/llvmlite/llvmlite-0.39.0.ebuild
+++ b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 llvm
DESCRIPTION="Python wrapper around the llvm C++ library"
@@ -24,7 +25,10 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
-PATCHES=( "${FILESDIR}/${P}-llvm12.patch" )
+PATCHES=(
+ "${FILESDIR}/${P}-llvm12.patch"
+ "${FILESDIR}/${P}-allow-py3.11.patch"
+)
src_prepare() {
sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild
index 717426899..59f029e95 100644
--- a/dev-python/logzero/logzero-1.7.0.ebuild
+++ b/dev-python/logzero/logzero-1.7.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
+PYTHON_COMPAT=( python3_10 pypy3 )
inherit distutils-r1
diff --git a/dev-python/looseversion/Manifest b/dev-python/looseversion/Manifest
new file mode 100644
index 000000000..1fe929b12
--- /dev/null
+++ b/dev-python/looseversion/Manifest
@@ -0,0 +1,2 @@
+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
new file mode 100644
index 000000000..0150e69f5
--- /dev/null
+++ b/dev-python/looseversion/looseversion-1.0.2.ebuild
@@ -0,0 +1,26 @@
+# 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 -> ${P}.gh.tar.gz"
+
+LICENSE="PSF-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RDEPEND=""
+BEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ epytest tests.py
+}
diff --git a/dev-python/looseversion/looseversion-1.0.3.ebuild b/dev-python/looseversion/looseversion-1.0.3.ebuild
new file mode 100644
index 000000000..aa8ebcc32
--- /dev/null
+++ b/dev-python/looseversion/looseversion-1.0.3.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=flit
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="A backwards/forwards-compatible fork of distutils' LooseVersion"
+HOMEPAGE="https://github.com/effigies/looseversion"
+SRC_URI="mirror://pypi/${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
new file mode 100644
index 000000000..20b71d2b7
--- /dev/null
+++ b/dev-python/looseversion/metadata.xml
@@ -0,0 +1,25 @@
+<?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/meshpy/meshpy-2020.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild
index 191589690..78ee45fbc 100644
--- a/dev-python/meshpy/meshpy-2020.1.ebuild
+++ b/dev-python/meshpy/meshpy-2020.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml
index fff86775c..77991f7a8 100644
--- a/dev-python/meshpy/metadata.xml
+++ b/dev-python/meshpy/metadata.xml
@@ -15,5 +15,6 @@ Hang Si. Both are included in the package in slightly modified versions.
</longdescription>
<upstream>
<remote-id type="pypi">MeshPy</remote-id>
+ <remote-id type="github">inducer/meshpy</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/mkl-service/Manifest b/dev-python/mkl-service/Manifest
new file mode 100644
index 000000000..f0b775c11
--- /dev/null
+++ b/dev-python/mkl-service/Manifest
@@ -0,0 +1 @@
+DIST mkl-service-2.4.0.gh.tar.gz 18705 BLAKE2B 12896adba1c001a581ff10a18cf11b3b87344687807307ae7ee002583281ac8072730b9496ce94c48d8d9ded5ae815c432e1944715091043c222bd93e2728ed8 SHA512 fc33b0a3670fcac5564c020ee870a800b113b93f344eddf63874303347c7151b7f00052adf5a9544ff7557892aefb6088ee9c53cce043536f4456bd9903dc232
diff --git a/dev-python/mkl-service/metadata.xml b/dev-python/mkl-service/metadata.xml
new file mode 100644
index 000000000..813808eb0
--- /dev/null
+++ b/dev-python/mkl-service/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/mkl-service</remote-id>
+ <remote-id type="pypi">mkl-service</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl-service/mkl-service-2.4.0.ebuild b/dev-python/mkl-service/mkl-service-2.4.0.ebuild
new file mode 100644
index 000000000..decfc57bb
--- /dev/null
+++ b/dev-python/mkl-service/mkl-service-2.4.0.ebuild
@@ -0,0 +1,38 @@
+# 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="Python hooks for Intel Math Kernel Library runtime control settings"
+HOMEPAGE="https://github.com/IntelPython/mkl-service"
+SRC_URI="https://github.com/IntelPython/mkl-service/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_fft/Manifest b/dev-python/mkl_fft/Manifest
new file mode 100644
index 000000000..24960cd58
--- /dev/null
+++ b/dev-python/mkl_fft/Manifest
@@ -0,0 +1 @@
+DIST mkl_fft-1.3.1.gh.tar.gz 41796 BLAKE2B 880c5fef47e8f489c51c7ae69516ca073fe49583a1a11c16289d5313161190d0f4fe2be43defe51b26c6d1f5a4df8c40da8fe65c10911f40483e0400d177f859 SHA512 5d9bb76a5d5dfcf93a05fe6e1ebc267ba7011370ef40e84d6e017e90db301cedb1fb202b1f0851133537fa8bf09260bc9b3f5eb497efc049d6153a4de088854f
diff --git a/dev-python/mkl_fft/metadata.xml b/dev-python/mkl_fft/metadata.xml
new file mode 100644
index 000000000..95348817f
--- /dev/null
+++ b/dev-python/mkl_fft/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/mkl_fft</remote-id>
+ <remote-id type="pypi">mkl-fft</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild
new file mode 100644
index 000000000..9b9c72d41
--- /dev/null
+++ b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="NumPy-based Python interface to Intel MKL FFT functionality"
+HOMEPAGE="https://github.com/IntelPython/mkl_fft"
+SRC_URI="https://github.com/IntelPython/mkl_fft/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_random/Manifest b/dev-python/mkl_random/Manifest
new file mode 100644
index 000000000..a826880d4
--- /dev/null
+++ b/dev-python/mkl_random/Manifest
@@ -0,0 +1 @@
+DIST mkl_random-1.2.2.gh.tar.gz 80274 BLAKE2B f59091c2bdb4b0136e218e3a1341d1852aa9fcec097dc435330f9b175a71aefc1d7fe7fb56411f562f4f56bbff52fa46dec3506a36f73fecd91646b7b1ac56d4 SHA512 dd691fb9873cf54e4f488a20de9c85993536bbeaedb7fbd731e9c021e3b40992f45a01268f3166ce08e766b9374745ac2ee81e99eb013c7406d40d365241cb31
diff --git a/dev-python/mkl_random/metadata.xml b/dev-python/mkl_random/metadata.xml
new file mode 100644
index 000000000..394347ca5
--- /dev/null
+++ b/dev-python/mkl_random/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/mkl_random</remote-id>
+ <remote-id type="pypi">mkl-random</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_random/mkl_random-1.2.2.ebuild b/dev-python/mkl_random/mkl_random-1.2.2.ebuild
new file mode 100644
index 000000000..7bd845de9
--- /dev/null
+++ b/dev-python/mkl_random/mkl_random-1.2.2.ebuild
@@ -0,0 +1,41 @@
+# 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="Python interface to Intel Math Kernel Library's random number generation"
+HOMEPAGE="https://github.com/IntelPython/mkl_random"
+SRC_URI="https://github.com/IntelPython/mkl_random/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+ export C_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/"
+ export CPLUS_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_umath/Manifest b/dev-python/mkl_umath/Manifest
new file mode 100644
index 000000000..6e1df7796
--- /dev/null
+++ b/dev-python/mkl_umath/Manifest
@@ -0,0 +1 @@
+DIST mkl_umath-0.1.1.gh.tar.gz 47263 BLAKE2B cb336ad38853298152ebef56e20dac5c6154352a1e443097db27c21ef3099b1ce93ba14a8a9d93ec163aecd0bef2ad8bbff436ae3f4f35ff1029ac6c34a808f5 SHA512 7e545c294d879ca602d2527945b9bb6782cf4e01c44cbde617c3ffcf8d639e428fecc3c9427b4089d70dbc8ae723630a8148917df18109b9c1727a25ad651775
diff --git a/dev-python/mkl_umath/metadata.xml b/dev-python/mkl_umath/metadata.xml
new file mode 100644
index 000000000..f23ce9644
--- /dev/null
+++ b/dev-python/mkl_umath/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/mkl_umath</remote-id>
+ <remote-id type="pypi">mkl-umath</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild
new file mode 100644
index 000000000..1210fdfd8
--- /dev/null
+++ b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild
@@ -0,0 +1,37 @@
+# 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="Package implementing NumPy's UFuncs based on SVML and MKL VML"
+HOMEPAGE="https://github.com/IntelPython/mkl_umath"
+SRC_URI="https://github.com/IntelPython/mkl_umath/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+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="${ESYSROOT}/usr/lib/llvm/intel"
+ export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild
index 4d3c7837c..595a728a4 100644
--- a/dev-python/multimethod/multimethod-1.8.ebuild
+++ b/dev-python/multimethod/multimethod-1.8.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild
index e846480bd..858258d04 100644
--- a/dev-python/num2words/num2words-0.5.10.ebuild
+++ b/dev-python/num2words/num2words-0.5.10.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/numba-dpex/Manifest b/dev-python/numba-dpex/Manifest
new file mode 100644
index 000000000..9cbab6ce8
--- /dev/null
+++ b/dev-python/numba-dpex/Manifest
@@ -0,0 +1 @@
+DIST numba-dpex-0.19.0.gh.tar.gz 207313 BLAKE2B 10cb770f13eb298f3808a326521066ea5c850a1712ece52d6cccb239c598220224afeb2c3d167d915082f3d9c020c22c0819da7d6ec1b5a3a19a1fad8cce0824 SHA512 328897a553e465563f835f86e443dc2695d66bcf23b40eb578886254a8476aa3d6321fdd3a657d0a7952df886f54b59609cf6ce0ccd44c94820d72675dc3fbc8
diff --git a/dev-python/numba-dpex/metadata.xml b/dev-python/numba-dpex/metadata.xml
new file mode 100644
index 000000000..c98aa52a0
--- /dev/null
+++ b/dev-python/numba-dpex/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">IntelPython/numba-dpex</remote-id>
+ <remote-id type="pypi">numba-dpex</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/numba-dpex/numba-dpex-0.19.0.ebuild b/dev-python/numba-dpex/numba-dpex-0.19.0.ebuild
new file mode 100644
index 000000000..8a8a343b6
--- /dev/null
+++ b/dev-python/numba-dpex/numba-dpex-0.19.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Extension for Numba"
+HOMEPAGE="https://github.com/IntelPython/numba-dpex"
+SRC_URI="https://github.com/IntelPython/numba-dpex/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ sys-devel/DPC++
+"
+
+RDEPEND="
+ dev-python/dpctl[${PYTHON_USEDEP}]
+ dev-python/dpnp[${PYTHON_USEDEP}]
+ dev-python/numba[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index 6282580a9..7f3f072b4 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1 +1,2 @@
-DIST numba-0.56.0.tar.gz 2488023 BLAKE2B ebfc00e2f131de54cf97db0f7bb6034a650c76db1b001fc68adec7800f4890b598d83cbcf8e5beb7f8023b770b310a2d837bfc0a43d5b901f2e09a40908ec307 SHA512 cedeb683120505a02ce2911efc46c0137cc03a25b1a6864b1ff68fe69655abfbe1d9880785ea718cd14577c985e1baa8b2cb3ecaf5c591c843b9021fa182c284
+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
diff --git a/dev-python/numba/files/numba-0.51.2-skip_tests.patch b/dev-python/numba/files/numba-0.51.2-skip_tests.patch
deleted file mode 100644
index 327271a04..000000000
--- a/dev-python/numba/files/numba-0.51.2-skip_tests.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-diff --git a/numba/tests/test_jitclasses.py b/numba/tests/test_jitclasses.py
-index 87f1165..c1c5f35 100644
---- a/numba/tests/test_jitclasses.py
-+++ b/numba/tests/test_jitclasses.py
-@@ -909,6 +909,7 @@ class TestJitClass(TestCase, MemoryLeakMixin):
- self.assertEqual(t[2:2:1], 2)
- self.assertEqual(t[6:6:1], 3)
-
-+ @unittest.skip("Gentoo has not reverted the LLVM 'truncate longlabel' patch")
- def test_jitclass_longlabel_not_truncated(self):
- # See issue #3872, llvm 7 introduced a max label length of 1024 chars
- # Numba ships patched llvm 7.1 (ppc64le) and patched llvm 8 to undo this
-diff --git a/numba/tests/test_np_functions.py b/numba/tests/test_np_functions.py
-index 01c15fd..3d9e228 100644
---- a/numba/tests/test_np_functions.py
-+++ b/numba/tests/test_np_functions.py
-@@ -2028,6 +2028,7 @@ class TestNPFunctions(MemoryLeakMixin, TestCase):
- params = {'ary': ary, 'to_begin': a, 'to_end': b}
- _check(params)
-
-+ @unittest.skip("unhandled type error")
- def test_ediff1d_edge_cases(self):
- # NOTE: NumPy 1.16 has a variety of behaviours for type conversion, see
- # https://github.com/numpy/numpy/issues/13103, as this is not resolved
-diff --git a/numba/tests/test_record_dtype.py b/numba/tests/test_record_dtype.py
-index 6d479c4..2357206 100644
---- a/numba/tests/test_record_dtype.py
-+++ b/numba/tests/test_record_dtype.py
-@@ -796,7 +796,7 @@ class TestRecordDtype(unittest.TestCase):
- # len(transformed) is generally 10, but could be longer if a large
- # number of typecodes are in use. Checking <20 should provide enough
- # tolerance.
-- self.assertLess(len(transformed), 20)
-+ self.assertLessEqual(len(transformed), 20)
-
- struct_arr = types.Array(rec, 1, 'C')
- transformed = mangle_type(struct_arr)
-@@ -804,7 +804,7 @@ class TestRecordDtype(unittest.TestCase):
- self.assertNotIn('first', transformed)
- self.assertNotIn('second', transformed)
- # Length is usually 50 - 5 chars tolerance as above.
-- self.assertLess(len(transformed), 50)
-+ self.assertLessEqual(len(transformed), 50)
-
- def test_record_two_arrays(self):
- """
diff --git a/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
new file mode 100644
index 000000000..07c1b5d88
--- /dev/null
+++ b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 68feca4..1d254ec 100644
+--- a/setup.py
++++ b/setup.py
+@@ -20,7 +20,7 @@ except ImportError:
+
+
+ min_python_version = "3.7"
+-max_python_version = "3.11" # exclusive
++max_python_version = "3.12" # exclusive
+ min_numpy_build_version = "1.11"
+ min_numpy_run_version = "1.18"
+ max_numpy_run_version = "1.24"
diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml
index e97c4322a..63bc398e0 100644
--- a/dev-python/numba/metadata.xml
+++ b/dev-python/numba/metadata.xml
@@ -9,4 +9,8 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">numba/numba</remote-id>
+ <remote-id type="pypi">numba</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/numba/numba-0.56.0.ebuild b/dev-python/numba/numba-0.56.3.ebuild
index 15eae53a7..f8cd62036 100644
--- a/dev-python/numba/numba-0.56.0.ebuild
+++ b/dev-python/numba/numba-0.56.3.ebuild
@@ -3,9 +3,9 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=setuptools
inherit optfeature multiprocessing distutils-r1
DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
@@ -22,15 +22,14 @@ RDEPEND="
>=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
<=dev-python/llvmlite-0.40.0
>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.23[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.1 )
+ <dev-python/numpy-1.24[${PYTHON_USEDEP}]
+ threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 )
"
BDEPEND="
dev-python/pip[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
"
-DISTUTILS_IN_SOURCE_BUILD=1
distutils_enable_tests unittest
distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
@@ -73,7 +72,6 @@ python_compile() {
# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
python_test() {
- distutils_install_for_testing
${EPYTHON} setup.py build_ext --inplace || die \
"${EPYTHON} failed to build_ext"
${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
diff --git a/dev-python/numba/numba-0.56.4.ebuild b/dev-python/numba/numba-0.56.4.ebuild
new file mode 100644
index 000000000..63ecebdf4
--- /dev/null
+++ b/dev-python/numba/numba-0.56.4.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# py3.11 fails to compile:
+# error: ‘CFrame’ does not name a type; did you mean ‘_frame’?
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit optfeature multiprocessing distutils-r1
+
+DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
+HOMEPAGE="https://numba.pydata.org/
+ https://github.com/numba"
+SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="openmp threads"
+
+RDEPEND="
+ >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
+ <=dev-python/llvmlite-0.40.0
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+ <dev-python/numpy-1.24[${PYTHON_USEDEP}]
+ threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 )
+"
+BDEPEND="
+ dev-python/pip[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests unittest
+distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
+ "${FILESDIR}/${PN}-0.56.4-allow-py3.11.patch"
+)
+
+pkg_setup() {
+ if ! use openmp; then
+ export NUMBA_DISABLE_OPENMP=1 || die
+ else
+ unset NUMBA_DISABLE_OPENMP || die
+ fi
+ if ! use threads; then
+ export NUMBA_DISABLE_TBB=1 || die
+ else
+ unset NUMBA_DISABLE_TBB || die
+ export TBBROOT="${EPREFIX}/usr" || die
+ fi
+}
+
+python_prepare_all() {
+ # This conf.py only works in a git repo
+ if use doc; then
+ git init -q || die
+ git config user.email "larry@gentoo.org" || die
+ git config user.name "Larry the Cow" || die
+ git add . || die
+ git commit -m "init" || die
+ fi
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ # FIXME: parallel python building fails. See Portage bug #614464 and
+ # gentoo/sci issue #1080.
+ export MAKEOPTS=-j1 || die
+ distutils-r1_python_compile
+}
+
+# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
+python_test() {
+ ${EPYTHON} setup.py build_ext --inplace || die \
+ "${EPYTHON} failed to build_ext"
+ ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
+ "${EPYTHON} failed unittests"
+}
+
+pkg_postinst() {
+ optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
+}
diff --git a/dev-python/numcodecs/numcodecs-0.10.0.ebuild b/dev-python/numcodecs/numcodecs-0.10.0.ebuild
index 7219b5b7b..b2030d332 100644
--- a/dev-python/numcodecs/numcodecs-0.10.0.ebuild
+++ b/dev-python/numcodecs/numcodecs-0.10.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Data storage buffer compression and transformation codecs"
diff --git a/dev-python/numcodecs/numcodecs-0.9.0.ebuild b/dev-python/numcodecs/numcodecs-0.9.0.ebuild
index 7219b5b7b..b2030d332 100644
--- a/dev-python/numcodecs/numcodecs-0.9.0.ebuild
+++ b/dev-python/numcodecs/numcodecs-0.9.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Data storage buffer compression and transformation codecs"
diff --git a/dev-python/numcodecs/numcodecs-0.9.1.ebuild b/dev-python/numcodecs/numcodecs-0.9.1.ebuild
index 7219b5b7b..b2030d332 100644
--- a/dev-python/numcodecs/numcodecs-0.9.1.ebuild
+++ b/dev-python/numcodecs/numcodecs-0.9.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Data storage buffer compression and transformation codecs"
diff --git a/dev-python/numpy/Manifest b/dev-python/numpy/Manifest
new file mode 100644
index 000000000..fdd711d83
--- /dev/null
+++ b/dev-python/numpy/Manifest
@@ -0,0 +1,4 @@
+DIST numpy-1.23.5.tar.gz 10731755 BLAKE2B d2ed6d359a51343a1618f64604e4d5c030115caa63f2aadf2fc150775630e40fbebaad28f5657faae1365264fd45bc9efb00854bf9cd393b7628c96d6fc87db9 SHA512 8f3ece76dbe79bc887275332d25f851ade2087de3026de5fb7ed793590b3e7d274f590357296e152373b4e9a245d4d563393ba7198bca6d44631b941acb89c2c
+DIST numpy-html-1.23.5.zip 27964271 BLAKE2B 0aa26d7c39f2d6b119e404dfb9642967770881ee0d640157a9ed11d16f21cd43109bed3c08f89fda457ec470292d945e2bf8b2dab56e4b36192d5e8eb3757b44 SHA512 218a2e893816af767c7cedd1f2256e05f68e59491c29277c95de653a206aaff35c5fe3bc6afd6d6d5ea7957748ec565593eb30d004e36e94c894ea4a6884902a
+DIST numpy-ref-1.23.5.pdf 7715485 BLAKE2B 7fbb0ce29e86fc7cd4932a6a9f0221b579b6cae695231edfebf863e5b4c2920796d802ccf9ae3e05b331964ac7c4f51099578d91b6b7fb357c6de2110a5f7cba SHA512 6036c6a36f332b83f371c7530a6ba6f354b1334d667d2a52993a1e52aa9d94d524e216f768928a006c717ed4b4131879f6e491a294ecfd3a0d1b0f9f937a887a
+DIST numpy-user-1.23.5.pdf 4123384 BLAKE2B d4587c9f979e1ef4734768598d6e106f2b4b0c8222f901a6c4caf0920e41622201252c5bd172b16346e0357138b5ff27c59e56c851be5ae3b7712624bd9cc5b4 SHA512 58e1ab96d2cfbd96df205c86f0a1a09e204349f70d21df7f8481c21ded8b46f4b9ede3216d5cce6c2b9bfc0aacbecdfa198bdb2d4c258a0dd4acb6e3ba421f9c
diff --git a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
new file mode 100644
index 000000000..d87a16a4b
--- /dev/null
+++ b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch
@@ -0,0 +1,50 @@
+Originally added in: https://gitweb.gentoo.org/repo/gentoo.git/commit/dev-python/numpy/files?id=e5ce90a04e79f6413604e96e4803cb95ada7c859
+https://bugs.gentoo.org/567938
+--- a/numpy/distutils/system_info.py
++++ b/numpy/distutils/system_info.py
+@@ -505,33 +505,7 @@ def get_info(name, notfound_action=0):
+ 'blas_armpl': blas_armpl_info,
+ 'lapack_armpl': lapack_armpl_info,
+ 'fftw3_armpl': fftw3_armpl_info,
+- 'atlas': atlas_info, # use lapack_opt or blas_opt instead
+- 'atlas_threads': atlas_threads_info, # ditto
+- 'atlas_blas': atlas_blas_info,
+- 'atlas_blas_threads': atlas_blas_threads_info,
+- 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead
+- 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto
+- 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead
+- 'atlas_3_10_threads': atlas_3_10_threads_info, # ditto
+- 'atlas_3_10_blas': atlas_3_10_blas_info,
+- 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info,
+- 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt instead
+- 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, # ditto
+- 'flame': flame_info, # use lapack_opt instead
+- 'mkl': mkl_info,
+- # openblas which may or may not have embedded lapack
+- 'openblas': openblas_info, # use blas_opt instead
+- # openblas with embedded lapack
+- 'openblas_lapack': openblas_lapack_info, # use blas_opt instead
+- 'openblas_clapack': openblas_clapack_info, # use blas_opt instead
+- 'blis': blis_info, # use blas_opt instead
+- 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead
+- 'blas_mkl': blas_mkl_info, # use blas_opt instead
+ 'accelerate': accelerate_info, # use blas_opt instead
+- 'openblas64_': openblas64__info,
+- 'openblas64__lapack': openblas64__lapack_info,
+- 'openblas_ilp64': openblas_ilp64_info,
+- 'openblas_ilp64_lapack': openblas_ilp64_lapack_info,
+ 'x11': x11_info,
+ 'fft_opt': fft_opt_info,
+ 'fftw': fftw_info,
+@@ -951,10 +925,7 @@ class system_info:
+ return [b for b in [a.strip() for a in libs.split(',')] if b]
+
+ def get_libraries(self, key='libraries'):
+- if hasattr(self, '_lib_names'):
+- return self.get_libs(key, default=self._lib_names)
+- else:
+- return self.get_libs(key, '')
++ return self.get_libs(key, '')
+
+ def library_extensions(self):
+ c = customized_ccompiler()
diff --git a/dev-python/numpy/metadata.xml b/dev-python/numpy/metadata.xml
new file mode 100644
index 000000000..26b229a9c
--- /dev/null
+++ b/dev-python/numpy/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>python@gentoo.org</email>
+ <name>Python</name>
+ </maintainer>
+ <longdescription lang="en">
+ NumPy is a general-purpose array-processing Python package designed to
+ efficiently manipulate large multi-dimensional arrays of arbitrary
+ records without sacrificing too much speed for small multi-dimensional
+ arrays. There are also basic facilities for discrete fourier transform,
+ basic linear algebra and random number generation.
+ It is the successor of Numeric and numarray.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">numpy/numpy</remote-id>
+ <remote-id type="pypi">numpy</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/numpy/numpy-1.23.5.ebuild b/dev-python/numpy/numpy-1.23.5.ebuild
new file mode 100644
index 000000000..51be775b9
--- /dev/null
+++ b/dev-python/numpy/numpy-1.23.5.ebuild
@@ -0,0 +1,187 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_REQ_USE="threads(+)"
+
+FORTRAN_NEEDED=lapack
+
+inherit distutils-r1 flag-o-matic fortran-2 toolchain-funcs
+
+DOC_PV=${PV}
+# For when docs aren't ready yet, set to last version
+#DOC_PV=1.23.0
+DESCRIPTION="Fast array and numerical python library"
+HOMEPAGE="
+ https://numpy.org/
+ https://github.com/numpy/numpy/
+ https://pypi.org/project/numpy/
+"
+SRC_URI="
+ mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz
+ doc? (
+ https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-html.zip -> numpy-html-${DOC_PV}.zip
+ https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-ref.pdf -> numpy-ref-${DOC_PV}.pdf
+ https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-user.pdf -> numpy-user-${DOC_PV}.pdf
+ )
+"
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~alpha amd64 arm arm64 hppa ~ia64 ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~x64-solaris ~x86-solaris"
+IUSE="doc lapack"
+
+RDEPEND="
+ lapack? (
+ >=virtual/cblas-3.8
+ >=virtual/lapack-3.8
+ )
+"
+BDEPEND="
+ ${RDEPEND}
+ >=dev-python/cython-0.29.30[${PYTHON_USEDEP}]
+ lapack? (
+ virtual/pkgconfig
+ )
+ doc? (
+ app-arch/unzip
+ )
+ test? (
+ >=dev-python/hypothesis-5.8.0[${PYTHON_USEDEP}]
+ >=dev-python/pytz-2019.3[${PYTHON_USEDEP}]
+ >=dev-python/cffi-1.14.0[${PYTHON_USEDEP}]
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}"/numpy-1.22.0-no-hardcode-blasv2.patch
+)
+
+distutils_enable_tests pytest
+
+src_unpack() {
+ default
+ if use doc; then
+ unzip -qo "${DISTDIR}"/numpy-html-${DOC_PV}.zip -d html || die
+ fi
+}
+
+python_prepare_all() {
+ # Allow use with setuptools 60.x
+ # See numpy-1.22.1-revert-setuptools-upper-bound.patch for details
+ export SETUPTOOLS_USE_DISTUTILS=stdlib
+
+ if use lapack; then
+ local incdir="${EPREFIX}"/usr/include
+ local libdir="${EPREFIX}"/usr/$(get_libdir)
+ cat >> site.cfg <<-EOF || die
+ [blas]
+ include_dirs = ${incdir}
+ library_dirs = ${libdir}
+ blas_libs = cblas,blas
+ [lapack]
+ library_dirs = ${libdir}
+ lapack_libs = lapack
+ EOF
+ else
+ export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None
+ fi
+
+ export CC="$(tc-getCC) ${CFLAGS}"
+
+ append-flags -fno-strict-aliasing
+
+ # See progress in http://projects.scipy.org/scipy/numpy/ticket/573
+ # with the subtle difference that we don't want to break Darwin where
+ # -shared is not a valid linker argument
+ if [[ ${CHOST} != *-darwin* ]]; then
+ append-ldflags -shared
+ fi
+
+ # only one fortran to link with:
+ # linking with cblas and lapack library will force
+ # autodetecting and linking to all available fortran compilers
+ append-fflags -fPIC
+ if use lapack; then
+ NUMPY_FCONFIG="config_fc --noopt --noarch"
+ # workaround bug 335908
+ [[ $(tc-getFC) == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95"
+ fi
+
+ # don't version f2py, we will handle it.
+ sed -i -e '/f2py_exe/s: + os\.path.*$::' numpy/f2py/setup.py || die
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ export MAKEOPTS=-j1 #660754
+
+ distutils-r1_python_compile ${NUMPY_FCONFIG}
+}
+
+python_test() {
+ local EPYTEST_DESELECT=(
+ # very disk- and memory-hungry
+ numpy/lib/tests/test_io.py::test_large_zip
+
+ # precision problems
+ numpy/core/tests/test_umath_accuracy.py::TestAccuracy::test_validate_transcendentals
+
+ # runs the whole test suite recursively, that's just crazy
+ numpy/core/tests/test_mem_policy.py::test_new_policy
+
+ # very slow, unlikely to be practically useful
+ numpy/typing/tests/test_typing.py
+ )
+
+ if use arm && [[ $(uname -m || echo "unknown") == "armv8l" ]] ; then
+ # Degenerate case. arm32 chroot on arm64.
+ # bug #774108
+ EPYTEST_DESELECT+=(
+ numpy/core/tests/test_cpu_features.py::Test_ARM_Features::test_features
+ )
+ fi
+
+ if use x86 ; then
+ EPYTEST_DESELECT+=(
+ # https://github.com/numpy/numpy/issues/18388
+ numpy/core/tests/test_umath.py::TestRemainder::test_float_remainder_overflow
+ # https://github.com/numpy/numpy/issues/18387
+ numpy/random/tests/test_generator_mt19937.py::TestRandomDist::test_pareto
+ # more precision problems
+ numpy/core/tests/test_einsum.py::TestEinsum::test_einsum_sums_int16
+ )
+ fi
+ if use arm || use x86 ; then
+ EPYTEST_DESELECT+=(
+ # too large for 32-bit platforms
+ numpy/core/tests/test_ufunc.py::TestUfunc::test_identityless_reduction_huge_array
+ )
+ fi
+
+ distutils_install_for_testing --single-version-externally-managed \
+ --record "${TMPDIR}/record.txt" ${NUMPY_FCONFIG}
+
+ cd "${TEST_DIR}/lib" || die
+ epytest -k "not _fuzz"
+}
+
+python_install() {
+ # https://github.com/numpy/numpy/issues/16005
+ local mydistutilsargs=( build_src )
+ distutils-r1_python_install ${NUMPY_FCONFIG}
+ python_optimize
+}
+
+python_install_all() {
+ local DOCS=( LICENSE.txt README.md THANKS.txt )
+
+ if use doc; then
+ local HTML_DOCS=( "${WORKDIR}"/html/. )
+ DOCS+=( "${DISTDIR}"/${PN}-{user,ref}-${DOC_PV}.pdf )
+ fi
+
+ distutils-r1_python_install_all
+}
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
index ba201f8da..1db41ecc8 100644
--- a/dev-python/nwbinspector/Manifest
+++ b/dev-python/nwbinspector/Manifest
@@ -1,3 +1,3 @@
-DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e
-DIST nwbinspector-0.4.12.tar.gz 455926 BLAKE2B 4bb8b493367593fdd575535e574b8494980a60a6ed1983a08f895c106e03e25ad6cd76b6c72cfcc42a34778d5059c90940bc9907dc9d87569df79aeae1698135 SHA512 60bb799beaff61612e7993069a34f62e0b6053dc3e820474f33c020c02f8c7b11bed0bca7e2bb335edfd60b06159be90b1a50dfcd497f6a3fb0916dc49cf17b7
-DIST nwbinspector-0.4.14.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa
+DIST nwbinspector-0.4.12.gh.tar.gz 455926 BLAKE2B 4bb8b493367593fdd575535e574b8494980a60a6ed1983a08f895c106e03e25ad6cd76b6c72cfcc42a34778d5059c90940bc9907dc9d87569df79aeae1698135 SHA512 60bb799beaff61612e7993069a34f62e0b6053dc3e820474f33c020c02f8c7b11bed0bca7e2bb335edfd60b06159be90b1a50dfcd497f6a3fb0916dc49cf17b7
+DIST nwbinspector-0.4.14.gh.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa
+DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
index bea484ec2..5f5bc2045 100644
--- a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
@@ -1,15 +1,15 @@
-# Copyright 2022 Gentoo Authors
+# 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_{8..10} )
+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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -19,6 +19,7 @@ RESTRICT="!test? ( test )"
DEPEND=""
RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/natsort[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
index a2b20f5af..5f5bc2045 100644
--- a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
@@ -1,15 +1,15 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 2022-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
-SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
index e248266d4..a80527994 100644
--- a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
@@ -1,15 +1,15 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 2022-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
-SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
@@ -19,10 +19,12 @@ RESTRICT="!test? ( test )"
DEPEND=""
RDEPEND="
+ dev-python/click[${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=""
diff --git a/dev-python/panel/Manifest b/dev-python/panel/Manifest
index dacf388f1..5bd9272be 100644
--- a/dev-python/panel/Manifest
+++ b/dev-python/panel/Manifest
@@ -1 +1,3 @@
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/files/panel-0.14.1-disable_lite_build.patch b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch
new file mode 100644
index 000000000..387cfb61b
--- /dev/null
+++ b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch
@@ -0,0 +1,47 @@
+Subject: Prevent Panel from violating network sandboxing.
+
+ * By default, "setup.py" invokes "npm" to rebuild Node.js packages bundled with Panel.
+ * Without this patch we get `error: HTTPSConnectionPool`
+ * A `sed` fix of the `_build_paneljs()` line will break the syntax.
+ * Using the `PANEL_LITE_BUILD` variable might do the trick instead of a patch, but thus far it didn't
+Author: Horea Christian <gentoo@chymera.eu>
+diff --git a/setup.py b/setup.py
+index d2541dfb..8cfbf933 100644
+--- a/setup.py
++++ b/setup.py
+@@ -54,8 +54,6 @@ class CustomDevelopCommand(develop):
+ """Custom installation for development mode."""
+
+ def run(self):
+- if not PANEL_LITE_BUILD:
+- _build_paneljs()
+ develop.run(self)
+
+
+@@ -63,8 +61,6 @@ class CustomInstallCommand(install):
+ """Custom installation for install mode."""
+
+ def run(self):
+- if not PANEL_LITE_BUILD:
+- _build_paneljs()
+ install.run(self)
+
+
+@@ -72,8 +68,6 @@ class CustomSdistCommand(sdist):
+ """Custom installation for sdist mode."""
+
+ def run(self):
+- if not PANEL_LITE_BUILD:
+- _build_paneljs()
+ sdist.run(self)
+
+
+@@ -92,8 +86,6 @@ try:
+
+ def run(self):
+ """Do nothing so the command intentionally fails."""
+- if not PANEL_LITE_BUILD:
+- _build_paneljs()
+ bdist_wheel.run(self)
+
+ _COMMANDS['bdist_wheel'] = CustomBdistWheelCommand
diff --git a/dev-python/panel/panel-0.11.0.ebuild b/dev-python/panel/panel-0.11.0.ebuild
index 594377dcd..072c763ad 100644
--- a/dev-python/panel/panel-0.11.0.ebuild
+++ b/dev-python/panel/panel-0.11.0.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
# Panel imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
diff --git a/dev-python/panel/panel-0.14.1.ebuild b/dev-python/panel/panel-0.14.1.ebuild
new file mode 100644
index 000000000..aa535f46f
--- /dev/null
+++ b/dev-python/panel/panel-0.14.1.ebuild
@@ -0,0 +1,55 @@
+# 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
new file mode 100644
index 000000000..866110947
--- /dev/null
+++ b/dev-python/panel/panel-0.14.2.ebuild
@@ -0,0 +1,64 @@
+# 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}/${PN}-0.14.1-disable_lite_build.patch" )
+
+# This does not work, need to patch..
+#export PANEL_LITE_BUILD=1
+
+src_prepare() {
+ # Install Jupyter configuration files to "/etc" rather than "/usr/etc".
+ sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die
+
+ default_src_prepare
+}
+
+# This also does not work, still need patch :(
+#src_compile() {
+# export PANEL_LITE_BUILD=1
+# distutils-r1_src_compile
+#}
+
+pkg_postinst() {
+ panel_pkg_postinst() {
+ PANEL_DIR="$(${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/param/Manifest b/dev-python/param/Manifest
index bec3c8061..d26e110b2 100644
--- a/dev-python/param/Manifest
+++ b/dev-python/param/Manifest
@@ -1 +1,2 @@
-DIST param-1.10.1.tar.gz 74216 BLAKE2B 98486a386b31f400647fa3da3d280867935a0e5c493de4b31dccfa7c5650a3b55e2590e09cbf15097d700e54dbdd33fda12ead4489ed745977ec0065b27735da SHA512 8f4693651b1abd12126248e1508b0bed7796a1a4d33cd0ed05cc1e176d1216f9bc504f8637220a92585e7682f2d0ad2600a5b24427702536d4ef679971e9c4a7
+DIST param-1.10.1.gh.tar.gz 132562 BLAKE2B ec4f8f6fada02aa91049cc665efddc75ab289a4f86cbd8951d9720c8174b5236415df884e630ede57b76d01da62b477a5db50b97cb46d04d46e37503ec0410a0 SHA512 ca035325829bbb9fdcfadc8fabac8d5a690e38b0942d30d8963f14259f0dc8ebeeba84723904aae8804898f6ea6d5cfa97d2a1103db29f0d6d3355577abe8d14
+DIST param-1.12.3.gh.tar.gz 460593 BLAKE2B 45e004f4df4d70ceb3d5ff654e260d2fdb28cd47c904408ccda86233502464907bc2e709840b060189a81242f348d3cd6e3f021a157be67962365f93a0b08327 SHA512 c7181dfb7ccffaab7521744566d601470678dc35a2ecd9b55fc5adda73a7cd4998f583f4a7b5930a5c811913cd5a9f2152fbc270a541b749c32b0901985cead2
diff --git a/dev-python/param/param-1.10.1.ebuild b/dev-python/param/param-1.10.1.ebuild
index 3be942fe3..8e8ec8053 100644
--- a/dev-python/param/param-1.10.1.ebuild
+++ b/dev-python/param/param-1.10.1.ebuild
@@ -1,16 +1,22 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters"
HOMEPAGE="https://param.holoviz.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+# Pypi sources do not include tests
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
SLOT="0"
+
+# Some tests require nose:
+#distutils_enable_tests unittest
diff --git a/dev-python/param/param-1.12.3.ebuild b/dev-python/param/param-1.12.3.ebuild
new file mode 100644
index 000000000..9ce9e3762
--- /dev/null
+++ b/dev-python/param/param-1.12.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters"
+HOMEPAGE="https://param.holoviz.org"
+# Pypi sources do not include tests, reported upstream:
+# https://github.com/holoviz/param/issues/678
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests pytest
diff --git a/dev-python/persim/persim-0.1.3.ebuild b/dev-python/persim/persim-0.1.3.ebuild
index 722ae4d39..e8aad47df 100644
--- a/dev-python/persim/persim-0.1.3.ebuild
+++ b/dev-python/persim/persim-0.1.3.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -24,3 +25,13 @@ RDEPEND="${PYTHON_DEPS}
"
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
index 8ca453bf9..792839a0b 100644
--- a/dev-python/persim/persim-0.2.0.ebuild
+++ b/dev-python/persim/persim-0.2.0.ebuild
@@ -1,9 +1,10 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -24,3 +25,20 @@ RDEPEND="${PYTHON_DEPS}
"
distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/scikit-tda/persim/issues/65
+ test/test_persim.py::test_integer_diagrams
+ test/test_persim.py::TestEmpty::test_empyt_diagram_list
+ test/test_persim.py::TestTransforms::test_lists_of_lists
+ test/test_persim.py::TestTransforms::test_n_pixels
+ test/test_persim.py::TestTransforms::test_multiple_diagrams
+ test/test_persistence_imager.py::test_empty_diagram_list
+ test/test_persistence_imager.py::test_fit_diagram
+ test/test_persistence_imager.py::test_fit_diagram_list
+ test/test_persistence_imager.py::test_mixed_pairs
+ test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists
+ test/test_persistence_imager.py::TestTransformOutput::test_n_pixels
+ test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams
+)
diff --git a/dev-python/persim/persim-0.3.0.ebuild b/dev-python/persim/persim-0.3.0.ebuild
index 6e1d989aa..91b9514ad 100644
--- a/dev-python/persim/persim-0.3.0.ebuild
+++ b/dev-python/persim/persim-0.3.0.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -26,3 +27,21 @@ RDEPEND="${PYTHON_DEPS}
BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )"
distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/scikit-tda/persim/issues/66
+ test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs
+ test/test_persim.py::test_integer_diagrams
+ test/test_persim.py::TestEmpty::test_empyt_diagram_list
+ test/test_persim.py::TestTransforms::test_lists_of_lists
+ test/test_persim.py::TestTransforms::test_n_pixels
+ test/test_persim.py::TestTransforms::test_multiple_diagrams
+ test/test_persistence_imager.py::test_empty_diagram_list
+ test/test_persistence_imager.py::test_fit_diagram
+ test/test_persistence_imager.py::test_fit_diagram_list
+ test/test_persistence_imager.py::test_mixed_pairs
+ test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists
+ test/test_persistence_imager.py::TestTransformOutput::test_n_pixels
+ test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams
+)
diff --git a/dev-python/persim/persim-0.3.1.ebuild b/dev-python/persim/persim-0.3.1.ebuild
index 6e1d989aa..91b9514ad 100644
--- a/dev-python/persim/persim-0.3.1.ebuild
+++ b/dev-python/persim/persim-0.3.1.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -26,3 +27,21 @@ RDEPEND="${PYTHON_DEPS}
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/probeinterface/Manifest b/dev-python/probeinterface/Manifest
new file mode 100644
index 000000000..b2c8e3956
--- /dev/null
+++ b/dev-python/probeinterface/Manifest
@@ -0,0 +1,3 @@
+DIST probeinterface-0.2.11.gh.tar.gz 194474 BLAKE2B 806d1d83a47fdd3a3196386d08ac5cee7f8561547be819fe814f67265e5b1e31e35107a047ed5c5ae533123b318ab6dca4b37ec8ddb6d30431644402b499b5d2 SHA512 a7e12fba55b952dea3b062dde37178b02259424ec82f788bb210a94cf7fb48d325045f2451c3e764b68563948fe81b60d1d378827a15ae5470931b120b2bc10d
+DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
+DIST probeinterface-0.2.5.gh.tar.gz 154572 BLAKE2B fdd339fdeec0c71f404fb96665b7d92db29d15f84163924d4508cbe17bf88b4a95e0296c48cf8f878034ed0ce3b249e750363ad32385b2e9d3e83900a760bebe SHA512 fdf170e1e4057445b0c8701105c7e6283258b460b1250e992f9896d6d3a0feacf3eb7dc6f8b35b77f591e1654930bd20d548758ea01b5d4cdb15a57dac24c4f9
diff --git a/dev-python/click-didyoumean/metadata.xml b/dev-python/probeinterface/metadata.xml
index d206a1b1c..58f800ce0 100644
--- a/dev-python/click-didyoumean/metadata.xml
+++ b/dev-python/probeinterface/metadata.xml
@@ -10,7 +10,6 @@
<name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="github">click-contrib/click-didyoumean</remote-id>
- <remote-id type="pypi">click-didyoumean</remote-id>
+ <remote-id type="github">SpikeInterface/probeinterface</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/probeinterface/probeinterface-0.2.11.ebuild b/dev-python/probeinterface/probeinterface-0.2.11.ebuild
new file mode 100644
index 000000000..15579b701
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.11.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
new file mode 100644
index 000000000..d3827a5e9
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.5.ebuild b/dev-python/probeinterface/probeinterface-0.2.5.ebuild
new file mode 100644
index 000000000..15579b701
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.5.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_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[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/py2bit/Manifest b/dev-python/py2bit/Manifest
index 4b58d5605..afd79913c 100644
--- a/dev-python/py2bit/Manifest
+++ b/dev-python/py2bit/Manifest
@@ -1 +1,2 @@
DIST py2bit-0.3.0.tar.gz 16059 BLAKE2B b66621b91db8c0370933d1531c25e3e9d2cf34cc453e085f5acf92175f16bc4a87368d5b97f4ad1f6b0aeb715ac91e02f752f27d660e733cbcf9788f7fb9ff0b SHA512 914ee4490605a005c5c83e914e5d469dcb860a76cf52dd2337086954d9a37f21addca7a581eb8ff612b77f7969334057de4ab5d5ce2c6e15fb88e56abd36e193
+DIST py2bit-0.3.1.tar.gz 16771 BLAKE2B 044f6c638bc001694a5ee1c0924bebfeccd26616dbeb7f7a692df71dde6937851227d8a4263c9f0c4e44a34d53900340bdf95818aa2c9c699d26b36a75e64158 SHA512 e9cb16e6f617f5f9c4a324abc949562da8aa0b4792e7011148103462ec49f3f38ab29a2c1821a374ec99726c292de2888de506966510a10211ee24295e9f775c
diff --git a/dev-python/py2bit/py2bit-0.3.0.ebuild b/dev-python/py2bit/py2bit-0.3.0.ebuild
index 7c6c27ef2..4b1c29658 100644
--- a/dev-python/py2bit/py2bit-0.3.0.ebuild
+++ b/dev-python/py2bit/py2bit-0.3.0.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -23,3 +24,9 @@ SLOT="0"
DEPEND="sci-libs/lib2bit"
RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/py2bit/py2bit-0.3.1.ebuild b/dev-python/py2bit/py2bit-0.3.1.ebuild
new file mode 100644
index 000000000..4b1c29658
--- /dev/null
+++ b/dev-python/py2bit/py2bit-0.3.1.ebuild
@@ -0,0 +1,32 @@
+# 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
+
+DESCRIPTION="Python library for accessing 2bit files"
+HOMEPAGE="https://github.com/dpryan79/py2bit"
+
+if [[ ${PV} == 9999 ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/dpryan79/py2bit"
+else
+ SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-libs/lib2bit"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/py2bit/py2bit-9999.ebuild b/dev-python/py2bit/py2bit-9999.ebuild
index 7c6c27ef2..4b1c29658 100644
--- a/dev-python/py2bit/py2bit-9999.ebuild
+++ b/dev-python/py2bit/py2bit-9999.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -23,3 +24,9 @@ SLOT="0"
DEPEND="sci-libs/lib2bit"
RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest
index 96d66a343..b27a43a9b 100644
--- a/dev-python/pyBigWig/Manifest
+++ b/dev-python/pyBigWig/Manifest
@@ -1 +1,2 @@
DIST pyBigWig-0.3.17.tar.gz 65490 BLAKE2B 5ae3ad5792357ae36082022aa34548fb7ad105909eccc27305064f8f948714f462e1d239c3af7f9b75b84f5658bcb03231d7d1d3b0ebc8025c96d2e7835f1bfb SHA512 b52fec3a85984708660dd454f5569900a5cce7804d02e719bddbdc7ed2f9f4ab1131e55b0a01ae977b18bb0bbd079e13ec887d5df108d8abfebdd04ad56e503f
+DIST pyBigWig-0.3.18.tar.gz 66478 BLAKE2B 0d2e20bed5f59fb8c79026f453c4d5c3e4f9b663e96614b3ef8cbb939357c8895edfa92184da018efdd40e14bbf357f13cc32f898d9cf89419382e7be89b01c8 SHA512 e782f059a8c47043498b2c4b1c0b63f3a1863d03f641c469995536bded220714c61fe0a2f1dbe5841152fe54d0d43b544e14ec4999447d4d808e01b452fa5e88
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild
index eaa5d5375..acaca2306 100644
--- a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild
+++ b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="quick access to and creation of bigWig files"
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild
new file mode 100644
index 000000000..acaca2306
--- /dev/null
+++ b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild
@@ -0,0 +1,25 @@
+# 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
+
+DESCRIPTION="quick access to and creation of bigWig files"
+HOMEPAGE="https://github.com/dpryan79/pyBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig"
+else
+ SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-biology/libBigWig"
+RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild
index eaa5d5375..acaca2306 100644
--- a/dev-python/pyBigWig/pyBigWig-9999.ebuild
+++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="quick access to and creation of bigWig files"
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 f73f2dd4b..f983beb99 100644
--- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
+++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
diff --git a/dev-python/pyct/pyct-0.4.8.ebuild b/dev-python/pyct/pyct-0.4.8.ebuild
index f40dc6d49..6201e2cf2 100644
--- a/dev-python/pyct/pyct-0.4.8.ebuild
+++ b/dev-python/pyct/pyct-0.4.8.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
# HoloViews imports from "distutils" at runtime.
DISTUTILS_USE_SETUPTOOLS=rdepend
diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
index 2e5bdf3e0..70b444b30 100644
--- a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pynndescent/pynndescent-0.5.6.ebuild b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
index 1e9eb00e4..241b0b746 100644
--- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild
+++ b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
index aa922e6ed..f25908cb3 100644
--- a/dev-python/pynrrd/pynrrd-0.4.2.ebuild
+++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
index aa922e6ed..f25908cb3 100644
--- a/dev-python/pynrrd/pynrrd-0.4.3.ebuild
+++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index ddb67415a..3a1d1f7a9 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,3 +1,3 @@
-DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a
DIST pynwb-2.0.1.tar.gz 452718 BLAKE2B d29347d748bd37bdf9326e0f9cc88b84742714ba78e6b0c56a923a4dd723c94e69ab3f325b5a5c66aef3ef819228abd64704268240fbdd369dac41b25e226b43 SHA512 897fa3bce93e733222a94bf9f043ed39c606c29f392f932a21c1004eebc1866d4caf50905a8e59baca87744af04d93e9957a7efb7e775422af5022787c4d086e
DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025
+DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57
diff --git a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
new file mode 100644
index 000000000..6141f629a
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
@@ -0,0 +1,21 @@
+diff --git a/setup.py b/tmp/setup.py
+index 39e75824..f7948f64 100755
+--- a/setup.py
++++ b/setup.py
+@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
+ schema_dir = 'nwb-schema/core'
+
+ reqs = [
+- 'h5py>=2.10,<4',
+- 'hdmf>=3.4.2,<4',
+- 'numpy>=1.16,<1.24',
+- 'pandas>=1.1.5,<2',
+- 'python-dateutil>=2.7.3,<3',
++ 'h5py',
++ 'hdmf',
++ 'numpy',
++ 'pandas',
++ 'python-dateutil',
+ 'setuptools'
+ ]
+
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild
deleted file mode 100644
index e133d027b..000000000
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- sci-libs/hdf5[ros3(-)]
- <dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${P}-versions.patch"
- )
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
- tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
- # Reported upstream and fixed in newer version:
- # https://github.com/NeurodataWithoutBorders/pynwb/issues/1412#issuecomment-934153799
- tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_dandi_read
- tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_read
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild b/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
index 3fe21370f..3d3e0cbb9 100644
--- a/dev-python/pynwb/pynwb-2.0.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
@@ -16,7 +16,7 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/hdf5[ros3(-)]
+ >=sci-libs/hdf5-1.12.2
<dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
index c24dae23a..14eed0e2f 100644
--- a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.1.0-r2.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_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
@@ -16,7 +16,7 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/hdf5[ros3(-)]
+ >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
new file mode 100644
index 000000000..041418fbb
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="mirror://pypi/${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/1580
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_non_external_format
+ tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_nonmatch_starting_frame
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data_construct_mode
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format_construct_mode
+ tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_starting_frame
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
+ tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pyout/files/pyout-0.7.2-blessed.patch b/dev-python/pyout/files/pyout-0.7.2-blessed.patch
new file mode 100644
index 000000000..89e189916
--- /dev/null
+++ b/dev-python/pyout/files/pyout-0.7.2-blessed.patch
@@ -0,0 +1,140 @@
+From 0f7c6d6f2abb304c9c473afb504cb03d17fef036 Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Sat, 7 Jan 2023 21:49:32 -0500
+Subject: [PATCH 1/2] Accepting either bless* library
+
+---
+ pyout/field.py | 7 ++++++-
+ pyout/tabular.py | 9 +++++++--
+ pyout/tests/terminal.py | 9 +++++++--
+ pyout/tests/test_interface.py | 7 ++++++-
+ pyout/tests/test_tabular.py | 7 ++++++-
+ 5 files changed, 32 insertions(+), 7 deletions(-)
+
+diff --git a/pyout/field.py b/pyout/field.py
+index 5105081..99c310f 100644
+--- a/pyout/field.py
++++ b/pyout/field.py
+@@ -495,7 +495,12 @@ class TermProcessors(StyleProcessors):
+
+ Parameters
+ ----------
+- term : blessings.Terminal
++ term : blessed.Terminal or blessings.Terminal
++
++ Notes
++ -----
++ * Eventually we may want to retire blessings:
++ https://github.com/pyout/pyout/issues/136
+ """
+
+ def __init__(self, term):
+diff --git a/pyout/tabular.py b/pyout/tabular.py
+index 2a776a1..0d4797a 100644
+--- a/pyout/tabular.py
++++ b/pyout/tabular.py
+@@ -7,7 +7,12 @@
+ from logging import getLogger
+ import os
+
+-from blessings import Terminal
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++ from blessed import Terminal
++except ImportError:
++ from blessings import Terminal
+
+ from pyout import interface
+ from pyout.field import TermProcessors
+@@ -16,7 +21,7 @@
+
+
+ class TerminalStream(interface.Stream):
+- """Stream interface implementation using blessings.Terminal.
++ """Stream interface implementation using blessed/blessings.Terminal.
+ """
+
+ def __init__(self, stream=None, interactive=None):
+diff --git a/pyout/tests/terminal.py b/pyout/tests/terminal.py
+index 53aabd7..2d8857c 100644
+--- a/pyout/tests/terminal.py
++++ b/pyout/tests/terminal.py
+@@ -6,12 +6,17 @@
+ from functools import partial
+ import re
+
+-import blessings
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++ import blessed as bls
++except ImportError:
++ import blessings as bls
+
+ from pyout.tests.utils import assert_contains
+
+
+-class Terminal(blessings.Terminal):
++class Terminal(bls.Terminal):
+
+ def __init__(self, *args, **kwargs):
+ super(Terminal, self).__init__(
+diff --git a/pyout/tests/test_interface.py b/pyout/tests/test_interface.py
+index 5205ef3..8348323 100644
+--- a/pyout/tests/test_interface.py
++++ b/pyout/tests/test_interface.py
+@@ -1,6 +1,11 @@
+ import pytest
+
+-pytest.importorskip("blessings")
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++ pytest.importorskip("blessed")
++except pytest.skip.Exception:
++ pytest.importorskip("blessings")
+
+ import inspect
+
+diff --git a/pyout/tests/test_tabular.py b/pyout/tests/test_tabular.py
+index 2044e92..a1d35e5 100644
+--- a/pyout/tests/test_tabular.py
++++ b/pyout/tests/test_tabular.py
+@@ -1,7 +1,12 @@
+ # -*- coding: utf-8 -*-
+ import pytest
+
+-pytest.importorskip("blessings")
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++ pytest.importorskip("blessed")
++except pytest.skip.Exception:
++ pytest.importorskip("blessings")
+
+ from collections import Counter
+ from collections import OrderedDict
+
+From 5f6691c114578217a124d2ac1b24468993178e27 Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Sat, 7 Jan 2023 23:48:37 -0500
+Subject: [PATCH 2/2] Preferring blessings
+
+---
+ setup.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index b376c2e..43005e7 100644
+--- a/setup.py
++++ b/setup.py
+@@ -2,7 +2,7 @@
+
+ requires = {
+ "core": [
+- "blessings; sys_platform != 'win32'",
++ "blessed; sys_platform != 'win32'",
+ "jsonschema>=3.0.0",
+ ],
+ "tests": ["pytest", "pytest-timeout"],
diff --git a/dev-python/pyout/pyout-0.7.2.ebuild b/dev-python/pyout/pyout-0.7.1-r1.ebuild
index 6cf80ec85..9cd796883 100644
--- a/dev-python/pyout/pyout-0.7.2.ebuild
+++ b/dev-python/pyout/pyout-0.7.1-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Terminal styling for structured data"
@@ -13,10 +13,11 @@ SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.
SLOT="0"
LICENSE="MIT"
KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
RDEPEND="
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/blessings[${PYTHON_USEDEP}]
+ dev-python/blessed[${PYTHON_USEDEP}]
"
DEPEND="
test? (
@@ -26,6 +27,10 @@ DEPEND="
distutils_enable_tests pytest
+
+PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" )
+
+
python_prepare_all() {
sed -i -e '/pytest-runner/d' setup.py || die
distutils-r1_python_prepare_all
diff --git a/dev-python/pyout/pyout-0.7.1.ebuild b/dev-python/pyout/pyout-0.7.2-r1.ebuild
index 6cf80ec85..7e262b158 100644
--- a/dev-python/pyout/pyout-0.7.1.ebuild
+++ b/dev-python/pyout/pyout-0.7.2-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Terminal styling for structured data"
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/blessings[${PYTHON_USEDEP}]
+ dev-python/blessed[${PYTHON_USEDEP}]
"
DEPEND="
test? (
@@ -26,6 +26,8 @@ DEPEND="
distutils_enable_tests pytest
+PATCHES=( "${FILESDIR}/${P}-blessed.patch" )
+
python_prepare_all() {
sed -i -e '/pytest-runner/d' setup.py || die
distutils-r1_python_prepare_all
diff --git a/dev-python/pyparsing/Manifest b/dev-python/pyparsing/Manifest
deleted file mode 100644
index 736d09882..000000000
--- a/dev-python/pyparsing/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyparsing_2.4.7.tar.gz 648158 BLAKE2B 24525b4ee7876e245b9eb270f0e3e22fe2d8b398f9777ad3b3657b8a1227dcbd25983aa64a3f3018debdbffc1a042c732e6b3a09800e081c7acac7b97da15317 SHA512 c7a546729f86a2b5176e2482b566b9fd715b03e495aaef4d720b21307bb03f385dbc849247f8d266cb3d92be0a83c34ce4995b655ce85318355d5a0d42d6991e
diff --git a/dev-python/pyparsing/metadata.xml b/dev-python/pyparsing/metadata.xml
deleted file mode 100644
index 2692e21d7..000000000
--- a/dev-python/pyparsing/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Science Project</name>
- </maintainer>
- <longdescription lang="en">
- The pyparsing module is an alternative approach to creating and
- executing simple grammars, vs. the traditional lex/yacc approach, or the
- use of regular expressions. The pyparsing module provides a library of
- classes that client code uses to construct the grammar directly in
- Python code.
- </longdescription>
- <stabilize-allarches/>
- <upstream>
- <remote-id type="sourceforge">pyparsing</remote-id>
- <remote-id type="pypi">pyparsing</remote-id>
- <remote-id type="github">pyparsing/pyparsing</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild b/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild
deleted file mode 100644
index 55da214a2..000000000
--- a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2004-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# please keep this ebuild at EAPI 7 -- sys-apps/portage dep
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..10} pypy3 )
-inherit distutils-r1
-
-MY_P=${P/-/_}
-DESCRIPTION="Easy-to-use Python module for text parsing"
-HOMEPAGE="https://github.com/pyparsing/pyparsing https://pypi.org/project/pyparsing/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz"
-S=${WORKDIR}/${PN}-${MY_P}
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~x64-cygwin ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
-IUSE="examples"
-
-distutils_enable_tests setup.py
-
-python_install_all() {
- if use examples; then
- docompress -x /usr/share/doc/${PF}/examples
- dodoc -r examples
- fi
- distutils-r1_python_install_all
-}
diff --git a/dev-python/pysolar/pysolar-0.8.ebuild b/dev-python/pysolar/pysolar-0.8.ebuild
index 65027edb9..6865958e5 100644
--- a/dev-python/pysolar/pysolar-0.8.ebuild
+++ b/dev-python/pysolar/pysolar-0.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
AUTHOR=pingswept
diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
index 17b19cbb0..c9149842e 100644
--- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
+++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/python-gantt/metadata.xml b/dev-python/python-gantt/metadata.xml
index 3febd988f..18071f943 100644
--- a/dev-python/python-gantt/metadata.xml
+++ b/dev-python/python-gantt/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -13,4 +13,7 @@
Python-Gantt makes it possible to easily draw gantt charts from Python
and export outputs as scalable vector graphics (SVG).
</longdescription>
+ <upstream>
+ <remote-id type="github">stefanSchinkel/gantt</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
index f2d829835..b5fdf845b 100644
--- a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
+++ b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/python-igraph/python-igraph-0.9.11.ebuild b/dev-python/python-igraph/python-igraph-0.9.11.ebuild
index 4d2a6ee5f..0cf01c443 100644
--- a/dev-python/python-igraph/python-igraph-0.9.11.ebuild
+++ b/dev-python/python-igraph/python-igraph-0.9.11.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pytorch-lightning/Manifest b/dev-python/pytorch-lightning/Manifest
index f9f1f6b1d..2876dd7d6 100644
--- a/dev-python/pytorch-lightning/Manifest
+++ b/dev-python/pytorch-lightning/Manifest
@@ -1 +1 @@
-DIST pytorch-lightning-1.5.8.tar.gz 444592 BLAKE2B 7fa8e230811381a0aea43f4d098f9d833350183cfe10ea2f51aa6c4a8c9835ed979d103572b352c2831361d5802caf66a674da0fccf948ba9b14cdb7d77d325e SHA512 e9c08b5614f8041e2511977b0e42be5d209efbf20a80ae8067bf7ac4dedd5d30908a33542fb3f1601814dba769ffeb545ba8a66ff368ff038e8fdc5f630dc808
+DIST pytorch-lightning-1.8.6.tar.gz 576205 BLAKE2B a8a2d0a14d331303f45319f3aa840f4bc0a21e6c6ac3bac8e7d72f92947126f64e06da36a62eed6ff0c33caae935905348ccb1379b53ee73cd35e569973d6551 SHA512 85e6474637f5d237c22cf0775ee8d6f56c000c3c0376af2087b68d0c4311608d35d02e856ef1dddca1c481e531ee0fb246357b91f5c185637a740c80a0152510
diff --git a/dev-python/pytorch-lightning/metadata.xml b/dev-python/pytorch-lightning/metadata.xml
index 2e30eb3db..df24db4ac 100644
--- a/dev-python/pytorch-lightning/metadata.xml
+++ b/dev-python/pytorch-lightning/metadata.xml
@@ -6,7 +6,7 @@
<name>Science Project</name>
</maintainer>
<upstream>
- <remote-id type="github">PyTorchLightning/pytorch-lightning</remote-id>
+ <remote-id type="github">Lightning-AI/lightning</remote-id>
<remote-id type="pypi">pytorch-lightning</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
deleted file mode 100644
index cf51f4e9b..000000000
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.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} )
-
-inherit distutils-r1
-
-DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
-HOMEPAGE="https://github.com/PyTorchLightning/pytorch-lightning"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- sci-libs/pytorch[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/future[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/fsspec[${PYTHON_USEDEP}]
- sci-visualization/tensorboard[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/ratelimit[${PYTHON_USEDEP}]
-"
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
new file mode 100644
index 000000000..c50848555
--- /dev/null
+++ b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_SINGLE_IMPL=1
+inherit distutils-r1
+
+DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
+HOMEPAGE="https://github.com/Lightning-AI/lightning"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ sci-visualization/tensorboard[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/ratelimit[${PYTHON_USEDEP}]
+ ')
+"
diff --git a/dev-python/pyvista/pyvista-0.33.2.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild
index c8b5a59dc..ed4a21a4e 100644
--- a/dev-python/pyvista/pyvista-0.33.2.ebuild
+++ b/dev-python/pyvista/pyvista-0.33.2.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_{8..9} )
+PYTHON_COMPAT=( python3_{10..10} )
DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1"
inherit distutils-r1
diff --git a/dev-python/pyviz_comms/Manifest b/dev-python/pyviz_comms/Manifest
index 315e51357..9f4d81ce1 100644
--- a/dev-python/pyviz_comms/Manifest
+++ b/dev-python/pyviz_comms/Manifest
@@ -1 +1,2 @@
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/pyviz_comms-2.0.1.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild
index df1d2bfe2..8526bd511 100644
--- a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild
+++ b/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -16,3 +16,7 @@ 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
new file mode 100644
index 000000000..8526bd511
--- /dev/null
+++ b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
@@ -0,0 +1,22 @@
+# 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/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml
index d208f0f55..5fbf687f3 100644
--- a/dev-python/pyvote/metadata.xml
+++ b/dev-python/pyvote/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -16,4 +16,7 @@
(or normal) probability density function for outcomes, or a fixed
outcome probability.
</longdescription>
+ <upstream>
+ <remote-id type="github">TheChymera/pyvote</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild
index b7ef458e2..95d95cb1b 100644
--- a/dev-python/pyvote/pyvote-0.1.ebuild
+++ b/dev-python/pyvote/pyvote-0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml
index ae9640ffb..8019eb9d1 100644
--- a/dev-python/pyzo/metadata.xml
+++ b/dev-python/pyzo/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">pyzo/pyzo</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
index 7ae9776c7..c2aa347f1 100644
--- a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
+++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
index 3567cdb42..5074a1566 100644
--- a/dev-python/rasterstats/rasterstats-0.16.0.ebuild
+++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild
index 2daccec83..91e7586c0 100644
--- a/dev-python/reproject/reproject-0.8.ebuild
+++ b/dev-python/reproject/reproject-0.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml
index aa31ba351..9656580bb 100644
--- a/dev-python/repsep_utils/metadata.xml
+++ b/dev-python/repsep_utils/metadata.xml
@@ -1,15 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>chr@chymera.eu</email>
- <name>Horea Christian</name>
- </maintainer>
- <longdescription lang="en">
+ <maintainer type="person">
+ <email>chr@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <longdescription lang="en">
Utilities for compiling and developing RepSeP-style articles, such as the
reference implementation. The package contains generic boilerplate code for
PythonTeX-interaction, as used by all RepSeP-style articles, as well as an
executable file allowing single-script execution for development and
debugging purposes.
</longdescription>
+ <upstream>
+ <remote-id type="github">TheChymera/repsep_utils</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild
index 05e8712bb..d8c8b0c2a 100644
--- a/dev-python/schema/schema-0.7.4.ebuild
+++ b/dev-python/schema/schema-0.7.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
+PYTHON_COMPAT=( python3_10 pypy3 )
inherit distutils-r1
diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild
index 19d343eca..b876c3425 100644
--- a/dev-python/scooby/scooby-0.5.7.ebuild
+++ b/dev-python/scooby/scooby-0.5.7.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index 440b5758f..d9550c50f 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/metadata.xml
@@ -8,5 +8,6 @@
<upstream>
<remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
<remote-id type="pypi">snakemake</remote-id>
+ <remote-id type="github">snakemake/snakemake</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/snuggs/snuggs-1.4.7.ebuild b/dev-python/snuggs/snuggs-1.4.7.ebuild
index ebae883ff..be3395de7 100644
--- a/dev-python/snuggs/snuggs-1.4.7.ebuild
+++ b/dev-python/snuggs/snuggs-1.4.7.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_PEP517="setuptools"
inherit distutils-r1
diff --git a/dev-python/sphinx-argparse/Manifest b/dev-python/sphinx-argparse/Manifest
index cc6a6ba19..db92db585 100644
--- a/dev-python/sphinx-argparse/Manifest
+++ b/dev-python/sphinx-argparse/Manifest
@@ -1 +1 @@
-DIST sphinx-argparse-0.3.1.tar.gz 42953 BLAKE2B 76c74a270a638b1b894548bc898918fbfa5fde6bcf1ccbf5e69a3daaada829bc1ae27ad8befd18e834646dc2fc3b025f36807c2be894911cc0c6d65294174898 SHA512 3d289c90165eb6a3d7a94dff8e6a429a49eb404ce373e80e007a0cd9abaae1e1236f5393df2fbf11701c349dade9d199640dc398064da4fd50a58a90eb3f8f12
+DIST sphinx-argparse-0.3.2.tar.gz 45841 BLAKE2B 7f8a7159974bca803705736c848973d605594732983462d7636d82125e195d8ab87b76c247c9081e626cfe17d0f8d12a66d79076c643b0fe780c4f3eb5bbdc23 SHA512 fcc179d85ac9d30e327f75b02086c8f831856b099d9a26bc10adc4f20b57781a117a5dac2d6882e1f7c07604157dda2c2344c29ae3c475022ce252cde96646bb
diff --git a/dev-python/sphinx-argparse/metadata.xml b/dev-python/sphinx-argparse/metadata.xml
index ae9640ffb..3b119bca0 100644
--- a/dev-python/sphinx-argparse/metadata.xml
+++ b/dev-python/sphinx-argparse/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ashb/sphinx-argparse</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
index 5b380202e..2660d4912 100644
--- a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild
+++ b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild
@@ -3,25 +3,24 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+PYTHON_COMPAT=( python3_{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"
+HOMEPAGE="
+ https://pypi.org/project/sphinx-argparse/
+ https://github.com/ashb/sphinx-argparse
+"
SRC_URI="https://github.com/ashb/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-DEPEND=""
-RDEPEND="${DEPEND}
+RDEPEND="
dev-python/sphinx[${PYTHON_USEDEP}]
dev-python/commonmark[${PYTHON_USEDEP}]
"
distutils_enable_tests pytest
-# requires self to build own documentation
-distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse
diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
index be4395414..cf6e3a5c5 100644
--- a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
+++ b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
index f98b972ae..afac4215c 100644
--- a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
+++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
index 7680d8206..8279d642c 100644
--- a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
+++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/texext/Manifest b/dev-python/texext/Manifest
index acfea3010..3300b31c6 100644
--- a/dev-python/texext/Manifest
+++ b/dev-python/texext/Manifest
@@ -1 +1 @@
-DIST texext-0.6.6.tar.gz 38121 BLAKE2B 655ac678ecf1de5f7fa34148bff93c4ba8a28253117afccc197da3e44592024a6ec523452c2e02697275f4061ae2452beae74e9d3fa305eb1faddffb33c992ac SHA512 117a74c85fc36af8921a145e387b560e3c6c115090f777539178021cafac0075077fc81c62d18fa2bbee0b0f59e256274a9526f2a688d00a99ecbda2ac944ccd
+DIST texext-0.6.7.gh.tar.gz 42823 BLAKE2B 224cb700f5ee74de75c41d8248a1cbb494f773f8124638974fbabdbffcd2bf72237c55b15e12ea8e5a5086dab02fde798efe5f3519befddb1a4535ed233414a3 SHA512 abdc57f9fd38b3d6e261347a3ba2d7d7400d8b7bd79c2763a40cc34aa72a079fe55dae1fc0117f2da604331a449b2d9168f320a6ecc2f13c62a6615c000523f8
diff --git a/dev-python/texext/texext-0.6.6.ebuild b/dev-python/texext/texext-0.6.7.ebuild
index 15d6a83d1..fdeb2350a 100644
--- a/dev-python/texext/texext-0.6.6.ebuild
+++ b/dev-python/texext/texext-0.6.7.ebuild
@@ -1,15 +1,15 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
+EAPI=8
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Sphinx extensions for working with LaTeX math"
HOMEPAGE="https://github.com/matthew-brett/texext"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/matthew-brett/texext/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/traits/Manifest b/dev-python/traits/Manifest
index 4c0fe0428..8e8de91b3 100644
--- a/dev-python/traits/Manifest
+++ b/dev-python/traits/Manifest
@@ -1,2 +1,3 @@
-DIST traits-6.0.0.tar.gz 441607 BLAKE2B d8f28e8ccdca8d65a4abb71210f6fe36d6fd2eb07ce5e8f1d374a64cf44e9ce95a318274c68b6791c91f2e105c4f9385e4a743d33434b608ce1d939693958e33 SHA512 b89f844b18c97e2fd2239fc74253e83f255aa231a3d02207a5acf27da7686c32c57cb7c36ffb92a59f7bfa4d98a5e1a95ae2b70e34aa4577a7ae82c8c6756e1e
DIST traits-6.1.1.tar.gz 567019 BLAKE2B 4b6ed46c87b1fda2a2001299106b5aacafbe8b148ba0564c4f39b67a8de76f6713366c8b00841db254a26c87a7b2b73b6935ecade770d92ad972aa8a0425cecf SHA512 7f7e9f11d4861c02164ae1ce595888859c8ce23213290cfc3ac11df100d33beeeea4c7def6799b70ef2d090b3f7bd98407f3605affff0867914d0fe0164dd50f
+DIST traits-6.3.2.tar.gz 9517139 BLAKE2B 9c6209a24fd07def86699174a66e2e0b3332670d974a75ead9486187c37e1c2c25b2a0c47e5444a03577931411ce6938b3b9ba195261a46c86d660c5abe9b502 SHA512 792004d88d2a00a1e9ba03974d58ec692b620f3c45aaf3bd82f93396818df8663a86903d43806c877230a66c5c8fee4d68268ed9355c166af00b5d060ba14c7d
+DIST traits-6.4.1.tar.gz 9527016 BLAKE2B 12036eeb845cc3014b0cba9984e1c1686a6720630678d440a2059c47916c08284b1f823ca566dcb6c1c86594ebec5400bb2a8c44d43d765a25d00e157fbbda74 SHA512 04b936195d57320c02fee9f0d5e7dbcfee28add422c151bd4aaa6d1c58c59f8de7fe54b4df039bb2023ffc9dae9570bba52210cd015ce462e0f736e9439327e5
diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild
index 677be0b9e..7282ebfa8 100644
--- a/dev-python/traits/traits-6.1.1.ebuild
+++ b/dev-python/traits/traits-6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -16,10 +16,12 @@ SRC_URI="mirror://pypi/${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[${PYTHON_USEDEP}]"
-distutils_enable_tests nose
+distutils_enable_tests unittest
# ToDo: Fix doc building:
# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
#distutils_enable_sphinx docs/source --no-autodoc
diff --git a/dev-python/traits/traits-6.0.0.ebuild b/dev-python/traits/traits-6.3.2.ebuild
index 0d6ffae85..3d81493f5 100644
--- a/dev-python/traits/traits-6.0.0.ebuild
+++ b/dev-python/traits/traits-6.3.2.ebuild
@@ -1,43 +1,35 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
-HOMEPAGE="https://docs.enthought.com/traits/
+HOMEPAGE="
+ https://docs.enthought.com/traits/
https://github.com/enthought/traits
- https://pypi.org/project/traits/"
+"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- dev-python/nose[${PYTHON_USEDEP}]
- ${RDEPEND}
- )"
+distutils_enable_tests unittest
+# ToDo: Fix doc building:
+# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
+#distutils_enable_sphinx docs/source --no-autodoc
python_prepare_all() {
sed -i -e "s/'-O3'//g" setup.py || die
distutils-r1_python_prepare_all
}
-python_compile() {
- python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
- distutils-r1_python_compile
-}
-
python_test() {
cd "${BUILD_DIR}"/lib || die
${EPYTHON} -m unittest discover || die
diff --git a/dev-python/traits/traits-6.4.1.ebuild b/dev-python/traits/traits-6.4.1.ebuild
new file mode 100644
index 000000000..3d81493f5
--- /dev/null
+++ b/dev-python/traits/traits-6.4.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
+HOMEPAGE="
+ https://docs.enthought.com/traits/
+ https://github.com/enthought/traits
+"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+
+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/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
index ed719c6a5..fe3dedf84 100644
--- a/dev-python/transforms3d/transforms3d-0.3.1.ebuild
+++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_USE_SETUPTOOLS=no
inherit distutils-r1
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
index 3c32b1184..f597d0175 100644
--- a/dev-python/typish/typish-1.9.3.ebuild
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Functionality for types"
diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml
index 142da2a70..3dff10f36 100644
--- a/dev-python/ufl/metadata.xml
+++ b/dev-python/ufl/metadata.xml
@@ -14,5 +14,6 @@ mathematical notation.
</longdescription>
<upstream>
<remote-id type="bitbucket">fenics-project/ufl</remote-id>
+ <remote-id type="github">FEniCS/ufl</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
index f0dc3dab5..45b45b7f1 100644
--- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild
+++ b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild
index 05eb0e162..68d53d30e 100644
--- a/dev-python/visvis/visvis-1.13.0.ebuild
+++ b/dev-python/visvis/visvis-1.13.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_SETUPTOOLS=no
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest
index 84f3a1b37..94118dae2 100644
--- a/dev-python/wraps/Manifest
+++ b/dev-python/wraps/Manifest
@@ -1 +1,2 @@
-DIST wraps-0.1.0.tar.gz 11126 BLAKE2B 6db25f60750fedcc44896e7d30f90400994a5c8c8fbb8bcad33696dfa4b3eb53f41c6a4e29a69c11610c6d32084019e9dbbdcdc6d7e462a0fda7f3cc3459c0fc SHA512 597afa975c0cc434ab861699d9de59c3815d240c59364c064346ab267f1f3c1177163db7c3fff20c6e2e68bed9eb9eff7eb068488d1bf427eca84925ba8e2e9f
+DIST wraps-0.1.0.tar.gz 25356 BLAKE2B 844293a5f7dfd84aa17f636d4863182118d40aa6ae53e044e77b77207be5b744cc78ef5235b889a963332fedb6922ce8ad829075099d9428be335366fe22cc56 SHA512 0e34d811869be2b22ec61638acb21342693e0fa44cf3d152dde179903c26771a9e26c673d2f37107122ba4bc92fe944b18ed16ebece7df0c07178845fc72bebb
+DIST wraps-0.2.0.tar.gz 25308 BLAKE2B b68359d34995f7bc39535e97458807a5d55e3547124ccb8b34f9cd34fe1d3b38921a3a0c16df031410022f74d414aba97af9e9f60a20fb635428030bc400b130 SHA512 daf72785c3215db06f4bf06704f02c7ecfd1ef5c58dbf5c50b2dee14755d73b519f8a13be9658bf825c296689d9b3effd08aec4254779812583c1024522751f0
diff --git a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
index 8a6de2917..c1b2ccd3e 100644
--- a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
+++ b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
@@ -1,14 +1,14 @@
--- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
+++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
-@@ -37,29 +37,6 @@
+@@ -36,31 +36,6 @@
- typing-extensions = ">= 4.2.0"
+ typing-extensions = ">= 4.3.0"
-[tool.poetry.group.format]
-optional = true
-
-[tool.poetry.group.format.dependencies]
--black = "22.6.0"
+-black = "22.8.0"
-
-[tool.poetry.group.format.dependencies.isort]
-version = "5.10.1"
@@ -18,17 +18,19 @@
-optional = true
-
-[tool.poetry.group.check.dependencies]
--mypy = "0.961"
+-mypy = "0.971"
-
-[tool.poetry.group.test]
-optional = true
-
-[tool.poetry.group.test.dependencies]
--pytest = "7.1.2"
+-pytest = "7.1.3"
-pytest-cov = "3.0.0"
+-anyio = "3.6.1"
+-trio = "0.21.0"
-
- [tool.black]
- line_length = 100
+ [tool.poetry.group.docs]
+ optional = true
@@ -67,29 +44,6 @@
line_length = 100
diff --git a/dev-python/wraps/wraps-0.1.0.ebuild b/dev-python/wraps/wraps-0.1.0-r1.ebuild
index 79df009b5..4f51a06f2 100644
--- a/dev-python/wraps/wraps-0.1.0.ebuild
+++ b/dev-python/wraps/wraps-0.1.0-r1.ebuild
@@ -4,13 +4,13 @@
EAPI=8
DISTUTILS_USE_PEP517=poetry
-PYTHON_COMPAT=( python3_{8..11} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION=" Meaningful and safe wrapping types. "
HOMEPAGE="https://github.com/nekitdev/wraps"
-SRC_URI="https://github.com/nekitdev/wraps/releases/download/v${PV}/${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
@@ -24,7 +24,6 @@ RDEPEND="
"
PATCHES=(
- "${FILESDIR}/${P}-includes.patch"
"${FILESDIR}/${P}-poetry_groups.patch"
)
diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild
new file mode 100644
index 000000000..0e4ec817c
--- /dev/null
+++ b/dev-python/wraps/wraps-0.2.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{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}/${PN}-0.1.0-poetry_groups.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest
index 1bcc6ae18..7c74e59be 100644
--- a/dev-python/xgboost/Manifest
+++ b/dev-python/xgboost/Manifest
@@ -1 +1 @@
-DIST xgboost-1.3.1.tar.gz 764139 BLAKE2B cde5e36b07fd4e2dba4961921bc169b730c775a12d8ec98a80d3f442a894f4bcc946094122df8d9fc5e76c8f505d4c57416e2deb13fe88751a9f51d8e4e09cad SHA512 ffe5851bd600d3a2f9b92850df6a028ec2c7d5f40ce4bad8e21b24e128a251e577e4344d8ce5cc50d6c17accf23bf283ff605d93fe6e12b9bfea6b544c57f428
+DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b
diff --git a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch b/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch
deleted file mode 100644
index 8c2d3d180..000000000
--- a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-The BUILD_TEMP_DIR variable is set in the build phase but is no
-longer available in the install phase. We write the variable to
-a tmp file and read it later in the install phase as a workaround
-diff --git a/setup.py b/setup.py
-index 6244066..934e7cf 100644
---- a/setup.py
-+++ b/setup.py
-@@ -137,6 +137,11 @@ class BuildExt(build_ext.build_ext): # pylint: disable=too-many-ancestors
- build_dir = self.build_temp
- global BUILD_TEMP_DIR # pylint: disable=global-statement
- BUILD_TEMP_DIR = build_dir
-+ tmp_workdir = os.environ["WORKDIR"]
-+ py_vers = os.environ["EPYTHON"]
-+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "w")
-+ f.write(BUILD_TEMP_DIR)
-+ f.close()
- libxgboost = os.path.abspath(
- os.path.join(CURRENT_DIR, os.path.pardir, 'lib', lib_name()))
-
-@@ -229,6 +234,11 @@ class InstallLib(install_lib.install_lib):
- dst = os.path.join(self.install_dir, 'xgboost', 'lib', lib_name())
-
- global BUILD_TEMP_DIR # pylint: disable=global-statement
-+ tmp_workdir = os.environ["WORKDIR"]
-+ py_vers = os.environ["EPYTHON"]
-+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "r")
-+ BUILD_TEMP_DIR = f.read()
-+ f.close()
- libxgboost_path = lib_name()
-
- dft_lib_dir = os.path.join(CURRENT_DIR, os.path.pardir, 'lib')
diff --git a/dev-python/xgboost/xgboost-1.3.1.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild
index 25145f93d..645522c9c 100644
--- a/dev-python/xgboost/xgboost-1.3.1.ebuild
+++ b/dev-python/xgboost/xgboost-1.6.2.ebuild
@@ -1,10 +1,10 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="XGBoost Python Package"
@@ -15,11 +15,7 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-PATCHES=( "${FILESDIR}/${P}-fix-install.patch" )
-
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
-
-PATCHES=( "${FILESDIR}/${P}-fix-install.patch" )
diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild
index 8cb175408..fb138aad0 100644
--- a/dev-python/zarr/zarr-2.11.1.ebuild
+++ b/dev-python/zarr/zarr-2.11.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild
index 1fa4e9af9..d0781c09f 100644
--- a/dev-python/zarr/zarr-2.11.3.ebuild
+++ b/dev-python/zarr/zarr-2.11.3.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild
index 1fa4e9af9..d0781c09f 100644
--- a/dev-python/zarr/zarr-2.12.0.ebuild
+++ b/dev-python/zarr/zarr-2.12.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/dev-util/makefile2graph/metadata.xml b/dev-util/makefile2graph/metadata.xml
index 138cb7705..41bb35aa0 100644
--- a/dev-util/makefile2graph/metadata.xml
+++ b/dev-util/makefile2graph/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">lindenb/makefile2graph</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-util/plog/metadata.xml b/dev-util/plog/metadata.xml
index 7203fb853..40a8e36c6 100644
--- a/dev-util/plog/metadata.xml
+++ b/dev-util/plog/metadata.xml
@@ -4,4 +4,7 @@
<maintainer type="person">
<email>heroxbd@gentoo.org</email>
</maintainer>
+ <upstream>
+ <remote-id type="github">SergiusTheBest/plog</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index 2a70c8348..ac01f9406 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,3 +1,4 @@
DIST dandi-0.45.1.tar.gz 321362 BLAKE2B d07296be6bd4237fea4aa83c0b087de45234157aa6aa457f8d44f56b514a4deca11226831182b84c19a72b398183b3b181beb3946c7f8cce2d842ac80f0b57e2 SHA512 07d97420651bbd82d8d4146322ff80873489bd49869834ace9986f1ddc1880be5ff6bd1d625d8b4607a90de8007aeba152e8161af05c25a804cb18c7a0c78e29
-DIST dandi-cli-0.38.0.gh.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054
+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-cli-0.39.4.gh.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
index a12843df7..e3f36d1de 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.39.4.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_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
@@ -14,7 +14,7 @@ SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
index 1dbc002dd..52d57dfd5 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
@@ -18,7 +18,7 @@ SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
index b5f95e030..f5e9d67cf 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild
@@ -1,27 +1,30 @@
-# 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_{8..10} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
dev-python/appdirs[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
- ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}]
+ =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
dev-python/fscacher[${PYTHON_USEDEP}]
dev-python/humanize[${PYTHON_USEDEP}]
@@ -29,6 +32,7 @@ RDEPEND="
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[${PYTHON_USEDEP}]
@@ -43,7 +47,7 @@ RDEPEND="
dev-python/zarr[${PYTHON_USEDEP}]
"
-DEPEND="
+BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
dev-python/responses[${PYTHON_USEDEP}]
@@ -55,22 +59,10 @@ DEPEND="
# Upstream might be amenable to dropping opencv:
# https://github.com/dandi/dandi-cli/issues/944
-# Some tests require deep copy with git history
-# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299
-EPYTEST_DESELECT=(
- "dandi/tests/test_utils.py::test_get_instance_dandi_with_api"
- "dandi/tests/test_utils.py::test_get_instance_url"
- "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old"
- "dandi/tests/test_utils.py::test_get_instance_bad_cli_version"
-)
+S="${WORKDIR}/${MY_P}"
distutils_enable_tests pytest
-PATCHES=(
- "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch"
- "${FILESDIR}/${PN}-0.37.0-pep517.patch"
-)
-
src_prepare() {
if use etelemetry; then
default
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild
new file mode 100644
index 000000000..f5e9d67cf
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild
@@ -0,0 +1,79 @@
+# 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
+
+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="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test etelemetry"
+
+RDEPEND="
+ dev-python/appdirs[${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/datalad/Manifest b/dev-vcs/datalad/Manifest
index 5ad5852a2..92f325b66 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,5 +1,2 @@
-DIST datalad-0.15.1.tar.gz 1357778 BLAKE2B 7c12c3ff1bd8d260e8e7cfd9e477a1f0798f6fc0fbdbc335229bcf88362ebc7280eeb92bb59c45e0f66677297680e4d8d7bc8f56c7ac171f921bc389c1ceef7c SHA512 d5ae7859486748cbf40bd27f3351fa5620b8342c6a4347b8e3e0cb331de5fa33b9384071adbb899fd7878641a210a11b360a9ea68d0c7437eae709244fa08fd1
-DIST datalad-0.15.2.tar.gz 1361038 BLAKE2B c515b374f0781693ed0f1d0d2c260a0bdb1c9e998b782a2232c501b4ab7c022adc38f00a79d0aed04ffde4ade5c696705d53bf16dbaec2378c74ef4ab35a7a15 SHA512 f0206855439c2d376172218ec6bf1ffa3277508256a5a49a2ec65a57bb5720e039481329c16459ed62eb1c9ed0126dc178ca34fa2c3b8dfdf8b8a0706a2b8658
-DIST datalad-0.16.1.tar.gz 1472447 BLAKE2B b62f2fb37d0bc5cdaa8fd36f1bdea1beab4b4c071ba32c45b1ba5f2036788e4dc4767b406b20c0e0ccf3a5e02fbcb77b73ac9d8f254d02d6004ce909a94bffb5 SHA512 7236e635f8c9b9fbc9f82776d325dce1585d9a99d767b66f2877fb935d788c36335562ae8679821dea1b433f5d122f687e0c6b2098d8e388b8f8f6134751cc5b
-DIST datalad-0.17.0.tar.gz 1510529 BLAKE2B 797a4d15139a88d20f03d1b81cf8b19088cf91925852a0a0d2079b3a64debfaa4945c31f21cc701ac507b00c1eabe10eb57653d8cbef1914d2c7babc48324458 SHA512 fea35a574f13b4957149f87553c80eceaebde064921e5fa28960b088e6d8f38a2eb2cbf797c9e031bd696bdca1400c2baa4c3e94c2b78bf8c1349a752928b09c
-DIST datalad-0.17.2.tar.gz 1512123 BLAKE2B 83f1d437f6a2d300c169710fd12c8e126e5ab89aee9f0ccda48325c13c26a7e895fc11d33e61a266d7e4f5ac976244950851080055639b679819f659286c3c57 SHA512 7eceaea6bd0f0e251f194d8c1846e5abfff46174c536a42c1c0f891ca06f9688f8d291dec706f4ca51128d6588ceaf28039d80e63ebc5a15417bca3c74f0d866
+DIST datalad-0.18.0.tar.gz 1425155 BLAKE2B 8d7cbf7f56b1de82c74fa823b2d4512112f1b4c4be106cac433c8db696b2e7f77da758c0bb62b7cb9fe0fbb08d49431dda2818d08d5c60b5052154895c335b33 SHA512 0df8276edc3872c73fee7286ea4e578648a6fb2a630fa49a4f8945e0d6ff88353d9b11d29d942c0ce22ed17a8223e71f99d8b519a6a8afbc2ac9e6da89d95ee5
+DIST datalad-0.18.1.tar.gz 1425820 BLAKE2B 574e864feb500062f829dfea3f9c8c51f9ad2e0e68e70966c2a5ea315fafffb259de9a0f57427c0aae1ee93c24ec9a3a91ef42637d109d912cf5b6c41ac07b11 SHA512 19f011428fe66d9f21410ae33276133f26cf2b1a367c23a83c56ab48a0e038837ba18163e12ab2d74eba7d0ec9ce2e660a21494ddba0da3a2df6da2c043c4aad
diff --git a/dev-vcs/datalad/datalad-0.15.1.ebuild b/dev-vcs/datalad/datalad-0.15.1.ebuild
deleted file mode 100644
index f7d178584..000000000
--- a/dev-vcs/datalad/datalad-0.15.1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-arch/p7zip
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wrapt[${PYTHON_USEDEP}]
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/whoosh[${PYTHON_USEDEP}]
- )
- misc? (
- dev-python/argcomplete[${PYTHON_USEDEP}]
- dev-python/pyperclip[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- )
- publish? (
- dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- dev-python/PyGithub[${PYTHON_USEDEP}]
- )
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests nose
-
-python_test() {
- export DATALAD_TESTS_NONETWORK=1
- ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
-}
diff --git a/dev-vcs/datalad/datalad-0.15.2.ebuild b/dev-vcs/datalad/datalad-0.15.2.ebuild
deleted file mode 100644
index f7d178584..000000000
--- a/dev-vcs/datalad/datalad-0.15.2.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-arch/p7zip
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wrapt[${PYTHON_USEDEP}]
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/whoosh[${PYTHON_USEDEP}]
- )
- misc? (
- dev-python/argcomplete[${PYTHON_USEDEP}]
- dev-python/pyperclip[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- )
- publish? (
- dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- dev-python/PyGithub[${PYTHON_USEDEP}]
- )
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests nose
-
-python_test() {
- export DATALAD_TESTS_NONETWORK=1
- ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
-}
diff --git a/dev-vcs/datalad/datalad-0.16.1.ebuild b/dev-vcs/datalad/datalad-0.16.1.ebuild
deleted file mode 100644
index 52b13b5ea..000000000
--- a/dev-vcs/datalad/datalad-0.16.1.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
-
-DESCRIPTION="Keep code, data, containers under control with git and git-annex"
-HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test +downloaders +metadata +publish misc"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-arch/p7zip
- dev-python/annexremote[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
- dev-python/distro[${PYTHON_USEDEP}]
- dev-python/iso8601[${PYTHON_USEDEP}]
- dev-python/humanize[${PYTHON_USEDEP}]
- dev-python/fasteners[${PYTHON_USEDEP}]
- app-arch/patool[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/wrapt[${PYTHON_USEDEP}]
- downloaders? (
- dev-python/boto[${PYTHON_USEDEP}]
- dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings-alt[${PYTHON_USEDEP}]
- dev-python/msgpack[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- )
- metadata? (
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/whoosh[${PYTHON_USEDEP}]
- )
- misc? (
- dev-python/argcomplete[${PYTHON_USEDEP}]
- dev-python/pyperclip[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- )
- publish? (
- dev-vcs/python-gitlab[${PYTHON_USEDEP}]
- dev-python/PyGithub[${PYTHON_USEDEP}]
- )
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- dev-python/beautifulsoup4[${PYTHON_USEDEP}]
- dev-python/httpretty[${PYTHON_USEDEP}]
- dev-python/vcrpy[${PYTHON_USEDEP}]
- )
-"
-
-# Noticed by upstream:
-# https://github.com/datalad/datalad/issues/6623
-PATCHES=( "${FILESDIR}/${P}-input.patch" )
-
-distutils_enable_tests nose
-
-python_test() {
- export DATALAD_TESTS_NONETWORK=1
- ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
-}
diff --git a/dev-vcs/datalad/datalad-0.17.2.ebuild b/dev-vcs/datalad/datalad-0.18.0.ebuild
index 86d141996..69b1a5cb5 100644
--- a/dev-vcs/datalad/datalad-0.17.2.ebuild
+++ b/dev-vcs/datalad/datalad-0.18.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
@@ -18,17 +18,19 @@ IUSE="test +downloaders +metadata +publish misc"
RESTRICT="!test? ( test )"
RDEPEND="
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
app-arch/p7zip
app-arch/patool[${PYTHON_USEDEP}]
dev-python/annexremote[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${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[${PYTHON_USEDEP}]
@@ -49,20 +51,19 @@ RDEPEND="
dev-vcs/python-gitlab[${PYTHON_USEDEP}]
)
"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
+ ${RDEPEND}
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/mypy[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
)
"
-
-EPYTEST_DESELECT=(
- # Reported upstream: https://github.com/datalad/datalad/issues/6870
- datalad/distributed/tests/test_ria_basics.py::test_version_check
- datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper
-)
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
distutils_enable_tests pytest
diff --git a/dev-vcs/datalad/datalad-0.17.0.ebuild b/dev-vcs/datalad/datalad-0.18.1.ebuild
index 7ad3e0a43..69b1a5cb5 100644
--- a/dev-vcs/datalad/datalad-0.17.0.ebuild
+++ b/dev-vcs/datalad/datalad-0.18.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
@@ -18,17 +18,19 @@ IUSE="test +downloaders +metadata +publish misc"
RESTRICT="!test? ( test )"
RDEPEND="
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
app-arch/p7zip
app-arch/patool[${PYTHON_USEDEP}]
dev-python/annexremote[${PYTHON_USEDEP}]
- >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
dev-python/distro[${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[${PYTHON_USEDEP}]
@@ -49,27 +51,24 @@ RDEPEND="
dev-vcs/python-gitlab[${PYTHON_USEDEP}]
)
"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
+ ${RDEPEND}
dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/mypy[${PYTHON_USEDEP}]
dev-python/vcrpy[${PYTHON_USEDEP}]
)
"
-
-# Noticed by upstream:
-# https://github.com/datalad/datalad/issues/6623
-PATCHES=( "${FILESDIR}/${PN}-0.17.0-skip.patch" )
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
distutils_enable_tests pytest
python_test() {
local -x DATALAD_TESTS_NONETWORK=1
- #export DATALAD_TESTS_NONETWORK=1
+ # see test groups in "tox.ini"
epytest -k "not turtle and not slow and not usecase"
- #epytest -k "not turtle"
- #${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
- # Full test suite takes for ever:
- # ${EPYTHON} -m nose -s -v datalad || die
}
diff --git a/dev-vcs/datalad/files/datalad-0.16.1-input.patch b/dev-vcs/datalad/files/datalad-0.16.1-input.patch
deleted file mode 100644
index beb539b5d..000000000
--- a/dev-vcs/datalad/files/datalad-0.16.1-input.patch
+++ /dev/null
@@ -1,94 +0,0 @@
-diff --git a/datalad/local/tests/test_gitcredential.py b/datalad/local/tests/test_gitcredential.py
-index 09387a70d..6dc0e0be4 100644
---- a/datalad/local/tests/test_gitcredential.py
-+++ b/datalad/local/tests/test_gitcredential.py
-@@ -70,89 +70,6 @@ def test_gitcredential_interface(path):
- assert_false(cred['password'])
-
-
--@with_tempfile
--def test_datalad_credential_helper(path):
--
-- ds = Dataset(path).create()
--
-- # tell git to use git-credential-datalad
-- ds.config.add('credential.helper', 'datalad', where='local')
-- ds.config.add('datalad.credentials.githelper.noninteractive', 'true',
-- where='global')
--
-- from datalad.downloaders.providers import Providers
--
-- url1 = "https://datalad-test.org/some"
-- url2 = "https://datalad-test.org/other"
-- provider_name = "datalad-test.org"
--
-- # `Providers` code is old and only considers a dataset root based on PWD
-- # for config lookup. contextmanager below can be removed once the
-- # provider/credential system is redesigned.
-- with chpwd(ds.path):
--
-- gitcred = GitCredentialInterface(url=url1, repo=ds)
--
-- # There's nothing set up yet, helper should return empty
-- gitcred.fill()
-- eq_(gitcred['username'], '')
-- eq_(gitcred['password'], '')
--
-- # store new credentials
-- # Note, that `Providers.enter_new()` currently uses user-level config
-- # files for storage only. TODO: make that an option!
-- # To not mess with existing ones, fail if it already exists:
--
-- cfg_file = Path(Providers._get_providers_dirs()['user']) \
-- / f"{provider_name}.cfg"
-- assert_false(cfg_file.exists())
--
-- # Make sure we clean up
-- from datalad.tests import _TEMP_PATHS_GENERATED
-- _TEMP_PATHS_GENERATED.append(str(cfg_file))
--
-- # Give credentials to git and ask it to store them:
-- gitcred = GitCredentialInterface(url=url1, username="dl-user",
-- password="dl-pwd", repo=ds)
-- gitcred.approve()
--
-- assert_true(cfg_file.exists())
-- providers = Providers.from_config_files()
-- p1 = providers.get_provider(url=url1, only_nondefault=True)
-- assert_is_instance(p1.credential, UserPassword)
-- eq_(p1.credential.get('user'), 'dl-user')
-- eq_(p1.credential.get('password'), 'dl-pwd')
--
-- # default regex should be host only, so matching url2, too
-- p2 = providers.get_provider(url=url2, only_nondefault=True)
-- assert_is_instance(p1.credential, UserPassword)
-- eq_(p1.credential.get('user'), 'dl-user')
-- eq_(p1.credential.get('password'), 'dl-pwd')
--
-- # git, too, should now find it for both URLs
-- gitcred = GitCredentialInterface(url=url1, repo=ds)
-- gitcred.fill()
-- eq_(gitcred['username'], 'dl-user')
-- eq_(gitcred['password'], 'dl-pwd')
--
-- gitcred = GitCredentialInterface(url=url2, repo=ds)
-- gitcred.fill()
-- eq_(gitcred['username'], 'dl-user')
-- eq_(gitcred['password'], 'dl-pwd')
--
-- # Rejection must not currently lead to deleting anything, since we would
-- # delete too broadly.
-- gitcred.reject()
-- assert_true(cfg_file.exists())
-- gitcred = GitCredentialInterface(url=url1, repo=ds)
-- gitcred.fill()
-- eq_(gitcred['username'], 'dl-user')
-- eq_(gitcred['password'], 'dl-pwd')
-- dlcred = UserPassword(name=provider_name)
-- eq_(dlcred.get('user'), 'dl-user')
-- eq_(dlcred.get('password'), 'dl-pwd')
--
--
- @with_tempfile
- def test_credential_cycle(path):
-
diff --git a/dev-vcs/datalad/files/datalad-0.17.0-skip.patch b/dev-vcs/datalad/files/datalad-0.17.0-skip.patch
deleted file mode 100644
index 33b2d6f63..000000000
--- a/dev-vcs/datalad/files/datalad-0.17.0-skip.patch
+++ /dev/null
@@ -1,162 +0,0 @@
---- a/datalad/tests/utils_pytest.py 2022-07-08 01:32:06.000000000 -0400
-+++ b/datalad/tests/utils_pytest.py 2022-07-21 05:07:09.341386460 -0400
-@@ -209,7 +209,7 @@
- try:
- imp = __import__(module)
- except Exception as exc:
-- pytest.skip("Module %s fails to load" % module)
-+ pytest.skip("Module %s fails to load" % module, allow_module_level=True)
-
-
- def skip_if_scrapy_without_selector():
-@@ -220,7 +220,9 @@
- except ImportError:
- pytest.skip(
- "scrapy misses Selector (too old? version: %s)"
-- % getattr(scrapy, '__version__'))
-+ % getattr(scrapy, '__version__'),
-+ allow_module_level=True,
-+ )
-
-
- def skip_if_url_is_not_available(url, regex=None):
-@@ -231,9 +233,11 @@
- try:
- content = providers.fetch(url)
- if regex and re.search(regex, content):
-- pytest.skip("%s matched %r -- skipping the test" % (url, regex))
-+ pytest.skip("%s matched %r -- skipping the test" % (url, regex),
-+ allow_module_level=True,
-+ )
- except DownloadError:
-- pytest.skip("%s failed to download" % url)
-+ pytest.skip("%s failed to download" % url, allow_module_level=True)
-
-
- def check_not_generatorfunction(func):
-@@ -252,7 +256,9 @@
-
- def check_and_raise():
- if dl_cfg.get('datalad.tests.nonetwork'):
-- pytest.skip("Skipping since no network settings")
-+ pytest.skip("Skipping since no network settings",
-+ allow_module_level=True,
-+ )
-
- if func:
- @wraps(func)
-@@ -273,7 +279,7 @@
-
- def check_and_raise():
- if on_windows:
-- pytest.skip("Skipping on Windows")
-+ pytest.skip("Skipping on Windows", allow_module_level=True)
-
- if func:
- @wraps(func)
-@@ -296,7 +302,9 @@
-
- def check_and_raise():
- if hasattr(os, "geteuid") and os.geteuid() == 0:
-- pytest.skip("Skipping: test assumptions fail under root")
-+ pytest.skip("Skipping: test assumptions fail under root",
-+ allow_module_level=True,
-+ )
-
- if func:
- @wraps(func)
-@@ -333,7 +341,9 @@
- def _wrap_skip_if(*args, **kwargs):
- if cond:
- if method == 'raise':
-- pytest.skip(msg if msg else "condition was True")
-+ pytest.skip(msg if msg else "condition was True",
-+ allow_module_level=True,
-+ )
- elif method == 'pass':
- print(msg if msg else "condition was True")
- return
-@@ -375,7 +385,7 @@
- @skip_ssh
- def _wrap_skip_nomultiplex_ssh(*args, **kwargs):
- if SSHManager is not MultiplexSSHManager:
-- pytest.skip("SSH without multiplexing is used")
-+ pytest.skip("SSH without multiplexing is used", allow_module_level=True)
- return func(*args, **kwargs)
- return _wrap_skip_nomultiplex_ssh
-
-@@ -784,7 +794,7 @@
- port = queue.get(timeout=300)
- except multiprocessing.queues.Empty as e:
- if self.use_ssl:
-- pytest.skip('No working SSL support')
-+ pytest.skip('No working SSL support', allow_module_level=True)
- else:
- raise
- self.url = 'http{}://{}:{}/'.format(
-@@ -822,7 +832,7 @@
- #except requests.exceptions.SSLError as e:
- except Exception as e:
- self.stop()
-- pytest.skip('No working HTTPS setup')
-+ pytest.skip('No working HTTPS setup', allow_module_level=True)
- # now verify that the stdlib tooling also works
- # if this fails, check datalad/tests/ca/prov.sh
- # for info on deploying a datalad-root.crt
-@@ -843,7 +853,7 @@
- #except URLError as e:
- except Exception as e:
- self.stop()
-- pytest.skip('No working HTTPS setup')
-+ pytest.skip('No working HTTPS setup', allow_module_level=True)
-
- def stop(self):
- """Stop serving `path`.
-@@ -911,7 +921,7 @@
- @attr('without_http_proxy')
- def _wrap_without_http_proxy(*args, **kwargs):
- if on_windows:
-- pytest.skip('Unclear why this is not working on windows')
-+ pytest.skip('Unclear why this is not working on windows', allow_module_level=True)
- # Such tests don't require real network so if http_proxy settings were
- # provided, we remove them from the env for the duration of this run
- env = os.environ.copy()
-@@ -1246,7 +1256,9 @@
- assert(testrepos_uris)
- else:
- if not testrepos_uris:
-- pytest.skip("No non-networked repos to test on")
-+ pytest.skip("No non-networked repos to test on",
-+ allow_module_level=True,
-+ )
-
- fake_dates = dl_cfg.get("datalad.fake-dates")
- ntested = 0
-@@ -1298,7 +1310,7 @@
- # https://git-annex.branchable.com/bugs/Recent_hang_with_rsync_remote_with_older_systems___40__Xenial__44___Jessie__41__/
- if external_versions['cmd:system-ssh'] < '7.4' and \
- '8.20200522' < external_versions['cmd:annex'] < '8.20200720':
-- pytest.skip("Test known to hang")
-+ pytest.skip("Test known to hang", allow_module_level=True)
-
- sr_path, repo_path = args[-2:]
- fn_args = args[:-2]
-@@ -2089,7 +2101,7 @@
- _TESTS_ADJUSTED_TMPDIR = _check()
-
- if _TESTS_ADJUSTED_TMPDIR:
-- pytest.skip("Test incompatible with adjusted branch default")
-+ pytest.skip("Test incompatible with adjusted branch default", allow_module_level=True)
- return func(*args, **kwargs)
- return _wrap_skip_if_adjusted_branch
-
-@@ -2134,7 +2146,9 @@
-
- if port is None:
- pytest.skip("port for {} could not be determined: {}"
-- .format(host, err))
-+ .format(host, err),
-+ allow_module_level=True,
-+ )
- return port
-
diff --git a/eclass/intel-sdp-r1.eclass b/eclass/intel-sdp-r1.eclass
deleted file mode 100644
index 9d902395f..000000000
--- a/eclass/intel-sdp-r1.eclass
+++ /dev/null
@@ -1,571 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: intel-sdp-r1.eclass
-# @MAINTAINER:
-# Justin Lecher <jlec@gentoo.org>
-# David Seifert <soap@gentoo.org>
-# Sci Team <sci@gentoo.org>
-# @BLURB: Handling of Intel's Software Development Products package management
-
-MULTILIB_COMPAT=( abi_x86_{32,64} )
-
-inherit check-reqs eutils multilib-build
-
-EXPORT_FUNCTIONS src_unpack src_install pkg_postinst pkg_postrm pkg_pretend
-
-if [[ ! ${_INTEL_SDP_R1_ECLASS_} ]]; then
-
-case "${EAPI}" in
- 7) ;;
- *) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-# @ECLASS-VARIABLE: INTEL_DIST_NAME
-# @DESCRIPTION:
-# The package name to download from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. parallel_studio_xe
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_NAME:=parallel_studio_xe}
-
-# @ECLASS-VARIABLE: INTEL_DIST_PV
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# The package download version from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. 2016_update1
-#
-# Must be defined before inheriting the eclass.
-
-# @ECLASS-VARIABLE: INTEL_DIST_TARX
-# @DESCRIPTION:
-# The package distfile suffix.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. tgz
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_TARX:=tgz}
-
-# @ECLASS-VARIABLE: INTEL_SUBDIR
-# @DESCRIPTION:
-# The package sub-directory (without version numbers) where it will end-up in /opt/intel
-#
-# e.g. compilers_and_libraries
-#
-# To determine its value, you have to do a raw install from the Intel tarball.
-: ${INTEL_SUBDIR:=compilers_and_libraries}
-
-# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# Possibility to skip the mandatory check for licenses. Only set this if there
-# is really no fix.
-
-# @ECLASS-VARIABLE: INTEL_RPMS_DIR
-# @DESCRIPTION:
-# Main subdirectory which contains the rpms to extract.
-: ${INTEL_RPMS_DIR:=rpm}
-
-# @ECLASS-VARIABLE: INTEL_DIST_BIN_RPMS
-# @DESCRIPTION:
-# Functional name of rpm without any version/arch tag.
-# Has to be a bash array
-#
-# e.g. ("icc-l-all-devel")
-#
-# if the rpm is located in a directory other than INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli")
-[[ ${INTEL_DIST_BIN_RPMS[@]} ]] || INTEL_DIST_BIN_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_AMD64_RPMS
-# @DESCRIPTION:
-# AMD64 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_AMD64_RPMS[@]} ]] || INTEL_DIST_AMD64_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_X86_RPMS
-# @DESCRIPTION:
-# X86 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_X86_RPMS[@]} ]] || INTEL_DIST_X86_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_DAT_RPMS
-# @DESCRIPTION:
-# Functional name of rpm of common data which are arch free
-# without any version tag. Has to be a bash array.
-#
-# e.g. ("openmp-l-all-devel")
-#
-# if the rpm is located in a directory different to INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli-common")
-[[ ${INTEL_DIST_DAT_RPMS[@]} ]] || INTEL_DIST_DAT_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_SPLIT_ARCH
-# @DESCRIPTION:
-# Set to "true" if arches are to be fetched separately, instead of using
-# the combined tarball.
-: ${INTEL_DIST_SPLIT_ARCH:=false}
-
-# @FUNCTION: _isdp_path_exists
-# @INTERNAL
-# @USAGE: [-a|-o] <paths>
-# @DESCRIPTION:
-# Check if the specified paths exist. Works for all types of paths
-# (files/dirs/etc...). The -a and -o flags control the requirements
-# of the paths. They correspond to "and" and "or" logic. So the -a
-# flag means all the paths must exist while the -o flag means at least
-# one of the paths must exist. The default behavior is "and". If no
-# paths are specified, then the return value is "false".
-_isdp_path_exists() {
- local opt=$1
- [[ ${opt} == -[ao] ]] && shift || opt="-a"
-
- # no paths -> return false
- # same behavior as: [[ -e "" ]]
- [[ $# -eq 0 ]] && return 1
-
- local p r=0
- for p in "$@" ; do
- [[ -e ${p} ]]
- : $(( r += $? ))
- done
-
- case ${opt} in
- -a) return $(( r != 0 )) ;;
- -o) return $(( r == $# )) ;;
- esac
- eerror "path_exists has been removed. Please see the following post"
- eerror "for a replacement snippet:"
- eerror "https://blogs.gentoo.org/mgorny/2018/08/09/inlining-path_exists/"
- die "path_exists is banned"
-}
-
-# @FUNCTION: _isdp_get-sdp-year
-# @INTERNAL
-# @DESCRIPTION:
-# Gets the year component from INTEL_DIST_PV
-_isdp_get-sdp-year() {
- local _intel_sdp_year
- _intel_sdp_year=${INTEL_DIST_PV}
- _intel_sdp_year=${_intel_sdp_year%_sp*}
- _intel_sdp_year=${_intel_sdp_year%_update*}
- echo "${_intel_sdp_year}"
-}
-
-# @FUNCTION: isdp_get-sdp-dir
-# @DESCRIPTION:
-# Gets the full rootless path to the installation directory
-#
-# e.g. opt/intel/compilers_and_libraries_2016.1.150
-# opt/intel/vtune_amplifier_2018.2.0.551022
-isdp_get-sdp-dir() {
- local _intel_sdp_dir="opt/intel/${INTEL_SUBDIR}_$(_isdp_get-sdp-year).$(ver_cut 3-)"
- echo "${_intel_sdp_dir}"
-}
-
-# @FUNCTION: isdp_get-sdp-edir
-# @DESCRIPTION:
-# Gets the full rooted/prefixed path to the installation directory
-#
-# e.g. /opt/intel/compilers_and_libraries_2016.1.150
-isdp_get-sdp-edir() {
- local _intel_sdp_edir="${EPREFIX%/}/$(isdp_get-sdp-dir)"
- echo "${_intel_sdp_edir}"
-}
-
-SRC_URI="${INTEL_DIST_NAME}_${INTEL_DIST_PV}.${INTEL_DIST_TARX}"
-LICENSE="Intel-SDP"
-# TODO: Proper slotting
-# Future work, #394411
-SLOT="0"
-
-RESTRICT="bindist mirror fetch"
-
-RDEPEND=""
-DEPEND="app-arch/rpm2targz"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="$(isdp_get-sdp-dir)/*"
-
-# @FUNCTION: isdp_convert2intel-arch
-# @USAGE: <arch>
-# @DESCRIPTION:
-# Convert between portage arch (e.g. amd64, x86) and intel installed arch
-# nomenclature (e.g. intel64, ia32)
-isdp_convert2intel-arch() {
- debug-print-function ${FUNCNAME} "${@}"
-
- case $1 in
- *amd64*|abi_x86_64)
- echo "intel64"
- ;;
- *x86*)
- echo "ia32"
- ;;
- *)
- die "Abi \'$1\' is unsupported"
- ;;
- esac
-}
-
-# @FUNCTION: isdp_get-native-abi-arch
-# @DESCRIPTION:
-# Determine the the intel arch string of the native ABI
-isdp_get-native-abi-arch() {
- debug-print-function ${FUNCNAME} "${@}"
-
- use amd64 && echo "$(isdp_convert2intel-arch abi_x86_64)"
- use x86 && echo "$(isdp_convert2intel-arch abi_x86_32)"
-}
-
-# @FUNCTION: isdp_get-sdp-installed-arches
-# @DESCRIPTION:
-# Returns a space separated list of the arch suffixes used in directory
-# names for enabled ABIs. Intel uses "ia32" for x86 and "intel64" for
-# amd64. The result would be "ia32 intel64" if both ABIs were enabled.
-isdp_get-sdp-installed-arches() {
- local arch=()
- use abi_x86_64 && arch+=($(isdp_convert2intel-arch abi_x86_64))
- use abi_x86_32 && arch+=($(isdp_convert2intel-arch abi_x86_32))
- echo "${arch[*]}"
-}
-
-# @FUNCTION: _isdp_generate-list-install-rpms
-# @INTERNAL
-# @DESCRIPTION:
-# Generates the list of fully expanded RPMs to be extracted.
-_isdp_generate-list-install-rpms() {
- debug-print-function ${FUNCNAME} "${@}"
-
- # Expand components into full RPM filenames
- expand_component_into_full_rpm() {
- local deref_var="${1}[@]"
- local p rpm_prefix expanded_full_rpms=()
-
- for p in "${!deref_var}"; do
- # check if a directory is prefixed
- if [[ "${p}" == "${p##*/}" ]]; then
- rpm_prefix="${INTEL_RPMS_DIR}/intel-"
- else
- rpm_prefix=""
- fi
- expanded_full_rpms+=( "${rpm_prefix}${p}" )
- done
- echo ${expanded_full_rpms[*]}
- }
-
- local vars_to_expand=("INTEL_DIST_BIN_RPMS" "INTEL_DIST_DAT_RPMS")
- if use abi_x86_32; then
- vars_to_expand+=("INTEL_DIST_X86_RPMS")
- fi
- if use abi_x86_64; then
- vars_to_expand+=("INTEL_DIST_AMD64_RPMS")
- fi
-
- local i fully_expanded_intel_rpms=()
- for ((i=0; i<${#vars_to_expand[@]}; i++)); do
- fully_expanded_intel_rpms+=($(expand_component_into_full_rpm "${vars_to_expand[i]}"))
- done
- echo ${fully_expanded_intel_rpms[*]}
-}
-
-# @FUNCTION: _isdp_big-warning
-# @USAGE: [pre-check | test-failed]
-# @INTERNAL
-# @DESCRIPTION:
-# warn user that we really require a license
-_isdp_big-warning() {
- debug-print-function ${FUNCNAME} "${@}"
-
- case ${1} in
- pre-check )
- ewarn "License file not found!"
- ;;
-
- test-failed )
- ewarn "Function test failed. Most probably due to an invalid license."
- ewarn "This means you already tried to bypass the license check once."
- ;;
- esac
-
- ewarn
- ewarn "Make sure you have received an Intel license."
- ewarn "To receive a non-commercial license, you need to register at:"
- ewarn "https://software.intel.com/en-us/qualify-for-free-software"
- ewarn "Install the license file into ${EPREFIX}/opt/intel/licenses"
-
- case ${1} in
- pre-check )
- ewarn "before proceeding with installation of ${P}"
- ;;
- * )
- ;;
- esac
-}
-
-# @FUNCTION: _isdp_version_test
-# @INTERNAL
-# @DESCRIPTION:
-# Testing for valid license by asking for version information of the compiler.
-_isdp_version_test() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local comp
- case ${PN} in
- ifc )
- debug-print "Testing ifort"
- comp=ifort
- ;;
- icc )
- debug-print "Testing icc"
- comp=icc
- ;;
- *)
- die "${PN} is not supported for testing"
- ;;
- esac
-
- local comp_full arch warn
- for arch in $(isdp_get-sdp-installed-arches); do
- case ${EBUILD_PHASE} in
- install )
- comp_full="${ED%/}/$(isdp_get-sdp-dir)/linux/bin/${arch}/${comp}"
- ;;
- postinst )
- comp_full="$(isdp_get-sdp-edir)/linux/bin/${arch}/${comp}"
- ;;
- * )
- die "Compile test not supported in ${EBUILD_PHASE}"
- ;;
- esac
-
- debug-print "LD_LIBRARY_PATH=\"$(isdp_get-sdp-edir)/linux/bin/${arch}/\" \"${comp_full}\" -V"
-
- LD_LIBRARY_PATH="$(isdp_get-sdp-edir)/linux/bin/${arch}/" "${comp_full}" -V &>/dev/null || warn=yes
- done
- [[ ${warn} == yes ]] && _isdp_big-warning test-failed
-}
-
-# @FUNCTION: _isdp_run-test
-# @INTERNAL
-# @DESCRIPTION:
-# Test if installed compiler is working.
-_isdp_run-test() {
- debug-print-function ${FUNCNAME} "${@}"
-
- if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
- case ${PN} in
- ifc | icc )
- _isdp_version_test
- ;;
- * )
- debug-print "No test available for ${PN}"
- ;;
- esac
- fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_pretend
-# @DESCRIPTION:
-#
-# * Check for a (valid) license before proceeding.
-#
-# * Check for space requirements being fulfilled.
-#
-intel-sdp-r1_pkg_pretend() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local warn=1 dir dirs ret arch a p
-
- : ${CHECKREQS_DISK_BUILD:=256M}
- check-reqs_pkg_pretend
-
- if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
- if [[ ${INTEL_LICENSE_FILE} == *@* ]]; then
- einfo "Looks like you are using following license server:"
- einfo " ${INTEL_LICENSE_FILE}"
- return 0
- fi
-
- dirs=(
- "${EPREFIX}/opt/intel/licenses"
- "$(isdp_get-sdp-edir)/licenses"
- "$(isdp_get-sdp-edir)/Licenses"
- )
- for dir in "${dirs[@]}" ; do
- ebegin "Checking for a license in: ${dir}"
- _isdp_path_exists "${dir}"/*lic && warn=0
- eend ${warn} && break
- done
- if [[ ${warn} == 1 ]]; then
- _isdp_big-warning pre-check
- die "Could not find license file"
- fi
- else
- eqawarn "The ebuild doesn't check for presence of a proper intel license!"
- eqawarn "This shouldn't be done unless there is a very good reason."
- fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_nofetch
-# @DESCRIPTION:
-# Advice user to download the parallel studio tarball
-pkg_nofetch() {
- einfo "Please download"
- einfo " ${SRC_URI}"
- einfo "from"
- einfo " https://registrationcenter.intel.com/RegCenter/MyProducts.aspx"
- einfo "and place the tarball in your DISTDIR directory."
-}
-
-# @FUNCTION: intel-sdp-r1_src_unpack
-# @DESCRIPTION:
-# Unpacking necessary rpms from tarball, extract them and rearrange the output.
-intel-sdp-r1_src_unpack() {
- local t
- for t in ${A}; do
- local r list=() source_rpms=($(_isdp_generate-list-install-rpms))
- for r in "${source_rpms[@]}"; do
- list+=( ${t%%.*}/${r} )
- done
-
- local debug_list
- debug_list="$(IFS=$'\n'; echo ${list[@]} )"
-
- debug-print "Adding to decompression list:"
- debug-print ${debug_list}
-
- tar -xvf "${DISTDIR}"/${t} ${list[@]} &> "${T}"/rpm-extraction.log
-
- for r in ${list[@]}; do
- einfo "Unpacking ${r}"
- printf "\nUnpacking %s\n" "${r}" >> "${T}"/rpm-extraction.log
- rpm2tar -O ${r} | tar -xvf - &>> "${T}"/rpm-extraction.log; assert "Unpacking ${r} failed"
- done
- done
-}
-
-# @FUNCTION: intel-sdp-r1_src_install
-# @DESCRIPTION:
-# Install everything
-intel-sdp-r1_src_install() {
- debug-print-function ${FUNCNAME} "${@}"
-
- local i
- # remove uninstall information
- ebegin "Cleaning out uninstall"
- while IFS='\n' read -r -d '' i; do
- rm -r "${i}" || die
- done < <(find opt -regextype posix-extended -regex '.*(uninstall|uninstall.sh)$' -print0)
- eend
-
- # handle documentation
- if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)"; then
- # normal man pages
- if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)/en/man/common/man1"; then
- doman opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man/common/man1/*
- rm -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man || die
- fi
-
- use doc && dodoc -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/*
-
- ebegin "Cleaning out documentation"
- rm -r "opt/intel/documentation_$(_isdp_get-sdp-year)" || die
- rm -rf "$(isdp_get-sdp-dir)"/linux/{documentation,man} || die
- eend
- fi
-
- # MPI man pages
- if _isdp_path_exists "$(isdp_get-sdp-dir)/linux/mpi/man/man3"; then
- doman "$(isdp_get-sdp-dir)"/linux/mpi/man/man3/*
- rm -r "$(isdp_get-sdp-dir)"/linux/mpi/man || die
- fi
-
- # licensing docs
- if _isdp_path_exists "$(isdp_get-sdp-dir)/licensing/documentation"; then
- dodoc -r "$(isdp_get-sdp-dir)/licensing/documentation"/*
- rm -rf "$(isdp_get-sdp-dir)/licensing/documentation" || die
- fi
-
- if _isdp_path_exists opt/intel/"${INTEL_DIST_NAME}"*/licensing; then
- dodoc -r opt/intel/"${INTEL_DIST_NAME}"*/licensing
- rm -rf opt/intel/"${INTEL_DIST_NAME}"* || die
- fi
-
- # handle examples
- if _isdp_path_exists "opt/intel/samples_$(_isdp_get-sdp-year)"; then
- use examples && dodoc -r opt/intel/samples_"$(_isdp_get-sdp-year)"/*
-
- ebegin "Cleaning out examples"
- rm -r "opt/intel/samples_$(_isdp_get-sdp-year)" || die
- eend
- fi
-
- # remove eclipse unconditionally
- ebegin "Cleaning out eclipse files"
- rm -rf opt/intel/ide_support_* || die
- eend
-
- # repair shell scripts used for sourcing PATH (iccvars.sh and such)
- ebegin "Tagging ${PN}"
- find opt -name \*sh -type f -exec sed -i \
- -e "s:<.*DIR>:$(isdp_get-sdp-edir)/linux:g" \
- '{}' + || die
- eend
-
- ebegin "Removing broken symlinks"
- while IFS='\n' read -r -d '' i; do
- rm "${i}" || die
- done < <(find opt -xtype l -print0)
- eend
-
- mv opt "${ED%/}"/ || die "moving files failed"
-
- keepdir "$(isdp_get-sdp-dir)"/licenses /opt/intel/ism/rm
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postinst
-# @DESCRIPTION:
-# Test for all things working
-intel-sdp-r1_pkg_postinst() {
- debug-print-function ${FUNCNAME} "${@}"
-
- _isdp_run-test
-
- if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" ; then
- #add ccache links as icc might get installed after ccache
- "${EROOT}"/usr/bin/ccache-config --install-links
- fi
-
- elog "Beginning with the 2016 suite of Intel tools, Gentoo has removed"
- elog "support for the eclipse plugin. If you require the IDE support,"
- elog "you will have to install the suite on your own, outside portage."
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postrm
-# @DESCRIPTION:
-# Sanitize cache links
-intel-sdp-r1_pkg_postrm() {
- debug-print-function ${FUNCNAME} "${@}"
-
- if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" && [[ -z ${REPLACED_BY_VERSION} ]]; then
- # --remove-links would remove all links, --install-links updates them
- "${EROOT}"/usr/bin/ccache-config --install-links
- fi
-}
-
-_INTEL_SDP_R1_ECLASS_=1
-fi
diff --git a/licenses/estscan b/licenses/estscan
deleted file mode 100644
index 46089aab6..000000000
--- a/licenses/estscan
+++ /dev/null
@@ -1,88 +0,0 @@
- ESTScan license
- ---------------
-
-Copyright (c) Swiss Institute of Bioinformatics, Ludwig Institute for
-Cancer Research (LICR), and Swiss Institute for Experimental Cancer
-Research (ISREC), 1999, 2004. For the purposes of this copyright, the
-Swiss Institute of Bioinformatics acts on behalf of its partners, LICR
-and ISREC.
-
-The ESTScan software is the exclusive property of the copyright
-owners, at UNIL - BEP, CH-1015 LAUSANNE, Switzerland. The Swiss
-Institute of Bioinformatics provides the ESTScan program WITHOUT ANY
-WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR
-ANY OTHER WARRANTY, EXPRESS OR IMPLIED.
-
-
-License Terms:
-
-Use, Modification and Redistribution (including distribution of any
-modified or derived work) in source and binary forms is permitted only
-if each of the following conditions is met:
-
-1. Redistributions qualify as "freeware" or "Open Source Software" under
- one of the following terms:
-
- (a) Redistributions are made at no charge beyond the reasonable cost of
- materials and delivery.
-
- (b) Redistributions are accompanied by a copy of the Source Code or by an
- irrevocable offer to provide a copy of the Source Code for up to three
- years at the cost of materials and delivery. Such redistributions
- must allow further use, modification, and redistribution of the Source
- Code under substantially the same terms as this license. For the
- purposes of redistribution "Source Code" means the complete source
- code of ESTScan including all modifications.
-
- Other forms of redistribution are allowed only under a separate royalty-
- free agreement permitting such redistribution subject to standard
- commercial terms and conditions. A copy of such agreement may be
- obtained from the Swiss Institute of Bioinformatics at the above address.
-
-2. Redistributions of source code must retain the copyright notices as they
- appear in each source code file, these license terms, and the
- disclaimer/limitation of liability set forth in the introductory paragraph.
-
-3. Redistributions in binary form must reproduce the Copyright Notice,
- these license terms, and the disclaimer/limitation of liability set
- forth as above, in the documentation and/or other materials
- provided with the distribution. For the purposes of binary distribution
- the "Copyright Notice" refers to the following language:
- "Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
- All rights reserved."
-
-4. Neither the name of the Swiss Institute of Bioinformatics nor
- the names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written
- permission.
-
-5. All redistributions must comply with the conditions imposed by the
- Swiss Institute of Bioinformatics on certain embedded code, whose copyright
- notice and conditions for redistribution are as follows:
-
- (a) Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
- All rights reserved.
-
- (b) Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- (i) Redistributions of source code must retain the above copyright
- notice, this list of conditions and the above disclaimer.
-
- (ii) Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- (iii) All advertising materials mentioning features or use of this
- software must display the following acknowledgement: "This
- product includes software developed by the Swiss Institute of
- Bioinformatics and its contributors."
-
- (iv) Neither the name of the Institute nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
-($Id: COPYRIGHT,v 1.1.1.1 2004/12/16 12:44:29 c4chris Exp $
-Version 1.1, last updated 9 December 2004)
diff --git a/licenses/mRNAmarkup b/licenses/mRNAmarkup
deleted file mode 100644
index 884ed1bd3..000000000
--- a/licenses/mRNAmarkup
+++ /dev/null
@@ -1,25 +0,0 @@
-Copyright (c) 2000 Volker Brendel
-All Rights Reserved. E-mail: vbrendel@iastate.edu
-
-Permission to use, copy, modify, and distribute this software and its
-documentation for educational, research and non-profit purposes, without fee,
-and without a written agreement is hereby granted, provided that the above
-copyright notice, this paragraph and the following three paragraphs appear in
-all copies. If you modify this file or included files you must cause the
-modified files to carry prominent notices stating that you changed the files.
-
-Inqueries for permission to incorporate this software into commercial products
-should be directed to the Office of Intellectual Property and Technology
-Transfer, 310 Lab of Mechanics, Iowa State University, Ames, IA 50011, phone:
-(515) 294-4740, E-mail: Licensing@iastate.edu.
-
-IN NO EVENT SHALL THE AUTHOR OR IOWA STATE UNIVERSITY BE LIABLE TO ANY PARTY FOR
-DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST
-PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
-IOWA STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-IOWA STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
-AND IOWA STATE UNIVERSITY HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
diff --git a/licenses/staden b/licenses/staden
deleted file mode 100644
index f2e77291a..000000000
--- a/licenses/staden
+++ /dev/null
@@ -1,76 +0,0 @@
-=============================================================================
-
-The Staden Package
-
-Copyright (c) 2003 MEDICAL RESEARCH COUNCIL
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- . Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
- . Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-
- . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
-MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
-
-Portions of this code have been modified by the Wellcome Trust Sanger
-Institute (Genome Research Limited). In some cases entirely new
-programs and/or source files have been created. These are licenced
-under essentially the same conditions as the MRC code (with just name
-changes).
-
-The following licence only applies to files bearing the Genome
-Research Limited copyright notice:
-
-
-
-Copyright (c) 2004 GENOME RESEARCH LIMITED
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- . Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
- . Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-
- . Neither the name of the GENOME RESEARCH LIMITED, the WELLCOME TRUST
-SANGER INSTITUTE nor the names of its contributors may be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
diff --git a/media-gfx/netgen/Manifest b/media-gfx/netgen/Manifest
new file mode 100644
index 000000000..51e722f4d
--- /dev/null
+++ b/media-gfx/netgen/Manifest
@@ -0,0 +1 @@
+DIST netgen-6.2.2204.tar.gz 3394806 BLAKE2B 2b99854cab0890662f1ab7ffee6fb444b60a28ba0bfe9970a89c80c0e4c930c40b8034f9c600ddd61c9b60f542d1cae758a8c220a1ba76949bf9f97fb2fe9020 SHA512 964c40753613c111b0372b0e403b19734cc0c559d1e7e45bbe6b452f4daba10c6bde8abaa5c9541c92b4bccff02d32ea6ba8e8e06ba64f11fec1733f2e374cbf
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-disable-failing-tests.patch b/media-gfx/netgen/files/netgen-6.2.2204-disable-failing-tests.patch
new file mode 100644
index 000000000..a11df8e3d
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-disable-failing-tests.patch
@@ -0,0 +1,19 @@
+From 21bfc56e76a448170dc4bb305c97b8f957b6e75d Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Wed, 14 Dec 2022 07:12:04 +0100
+Subject: [PATCH] disable failing tests
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/tests/catch/CMakeLists.txt
++++ b/tests/catch/CMakeLists.txt
+@@ -34,7 +34,6 @@ add_unit_test(archive archive.cpp)
+ target_link_libraries(test_archive netgen_python)
+ add_unit_test(array array.cpp)
+ add_unit_test(ranges ranges.cpp)
+-add_unit_test(symboltable symboltable.cpp)
+ add_unit_test(utils utils.cpp)
+ add_unit_test(version version.cpp)
+
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-disable-python-tests.patch b/media-gfx/netgen/files/netgen-6.2.2204-disable-python-tests.patch
new file mode 100644
index 000000000..7a6def418
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-disable-python-tests.patch
@@ -0,0 +1,17 @@
+From 2c402f3b552ce18483119de1d3a91fd457c9c170 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Wed, 14 Dec 2022 08:50:07 +0100
+Subject: [PATCH] disable python tests
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/tests/CMakeLists.txt
++++ b/tests/CMakeLists.txt
+@@ -1,5 +1,4 @@
+ add_subdirectory(catch)
+-add_subdirectory(pytest)
+
+ # this code goes here, because tests is the last add_subdirectory (otherwise it gets executed too early)
+ if(APPLE AND BUILD_FOR_CONDA)
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch b/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch
new file mode 100644
index 000000000..cf7b9d31e
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-find-Tk-include-directories.patch
@@ -0,0 +1,21 @@
+From 53c45343f5a26841be10d930467e215da4a779f2 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 15:17:55 +0100
+Subject: [PATCH] find Tk include directories
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -270,6 +270,9 @@ if (USE_GUI)
+ endif(APPLE)
+ find_package(OpenGL REQUIRED)
+
++ include_directories(${TK_INCLUDE_PATH}/generic)
++ include_directories(${TK_INCLUDE_PATH}/unix)
++
+ target_compile_definitions(netgen_gui INTERFACE -DTCL -DOPENGL -DUSE_TOGL_2 -DUSE_TCL_STUBS -DUSE_TK_STUBS)
+ target_include_directories(netgen_gui INTERFACE ${TCL_INCLUDE_PATH} ${TK_INCLUDE_PATH})
+ target_link_libraries(netgen_gui INTERFACE ${TCL_STUB_LIBRARY} ${TK_STUB_LIBRARY})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch b/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch
new file mode 100644
index 000000000..c45f5a4e4
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-find-libjpeg-turbo-library.patch
@@ -0,0 +1,34 @@
+From 39160b692fd051f2638f1a6e1df38eb616b6d6cb Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 16:09:43 +0100
+Subject: [PATCH] find libjpeg-turbo library
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/libsrc/visualization/CMakeLists.txt
++++ b/libsrc/visualization/CMakeLists.txt
+@@ -7,7 +7,7 @@ target_sources(nggui PRIVATE
+ vssolution.cpp
+ visualpkg.cpp
+ )
+-target_link_libraries( nggui PUBLIC "$<BUILD_INTERFACE:netgen_python>" ${MPI_CXX_LIBRARIES} ${OPENGL_LIBRARIES} )
++target_link_libraries( nggui PUBLIC "$<BUILD_INTERFACE:netgen_python>" ${MPI_CXX_LIBRARIES} ${OPENGL_LIBRARIES} ${JPEG_LIBRARIES} )
+
+ install(FILES
+ meshdoc.hpp mvdraw.hpp visual_api.hpp
+--- a/nglib/CMakeLists.txt
++++ b/nglib/CMakeLists.txt
+@@ -7,6 +7,11 @@ endif(USE_OCC)
+
+ target_link_libraries(nglib PUBLIC ngcore)
+
++if(TARGET JPEG::JPEG)
++ get_target_property(JPEG_LIBRARIES JPEG::JPEG IMPORTED_LOCATION_RELEASE)
++else()
++ set(JPEG_LIBRARIES ${JPEG_LIBRARY_RELEASE})
++endif()
+ target_link_libraries( nglib PRIVATE ${MPI_CXX_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${JPEG_LIBRARIES} ${MKL_LIBRARIES} ${ZLIB_LIBRARIES} ${OCC_LIBRARIES} netgen_cgns )
+
+ install(TARGETS nglib netgen_cgns ${NG_INSTALL_DIR})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch b/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch
new file mode 100644
index 000000000..6f7a8bc3c
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-link-against-ffmpeg.patch
@@ -0,0 +1,20 @@
+From 69d9c2da29adc9b7a209e78aae950d9834683f58 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Mon, 31 Oct 2022 13:07:05 +0100
+Subject: [PATCH] link against ffmpeg
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/ng/CMakeLists.txt
++++ b/ng/CMakeLists.txt
+@@ -28,7 +28,7 @@ if(USE_GUI)
+ if(APPLE)
+ set_target_properties(netgen PROPERTIES OUTPUT_NAME netgen)
+ endif(APPLE)
+- target_link_libraries( netgen ${PYTHON_LIBRARIES} ${TCL_LIBRARY} ${TK_LIBRARY})
++ target_link_libraries( netgen ${PYTHON_LIBRARIES} ${TCL_LIBRARY} ${TK_LIBRARY} ${FFMPEG_LIBRARIES})
+ endif(NOT BUILD_FOR_CONDA)
+
+ install(TARGETS nggui ${NG_INSTALL_DIR})
+--
+2.38.1
+
diff --git a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch b/media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch
index c638d83a7..ef11c8b08 100644
--- a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch
+++ b/media-gfx/netgen/files/netgen-6.2.2204-use-external-pybind11.patch
@@ -1,18 +1,12 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index dcc24af..24f444e 100644
+From c3c55fe646ad6934e429edd080aceae54260551c Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Sun, 30 Oct 2022 14:50:48 +0100
+Subject: [PATCH] use external pybind11
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -246,7 +246,8 @@ if (USE_GUI)
-
- add_definitions(-DTCL -DOPENGL -DUSE_TOGL_2)
- include_directories(${TCL_INCLUDE_PATH})
-- include_directories(${TK_INCLUDE_PATH})
-+ include_directories(${TK_INCLUDE_PATH}/generic)
-+ include_directories(${TK_INCLUDE_PATH}/unix)
- set(LIBTOGL togl)
-
- if(WIN32)
-@@ -268,7 +269,7 @@ else()
+@@ -302,7 +302,7 @@ else()
endif()
if (USE_PYTHON)
@@ -21,11 +15,9 @@ index dcc24af..24f444e 100644
find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h HINTS ${PYTHON_INCLUDE_DIR})
if( PYBIND_INCLUDE_DIR )
message(STATUS "Found Pybind11: ${PYBIND_INCLUDE_DIR}")
-diff --git a/cmake/SuperBuild.cmake b/cmake/SuperBuild.cmake
-index c24b631..2354a09 100644
--- a/cmake/SuperBuild.cmake
+++ b/cmake/SuperBuild.cmake
-@@ -39,7 +39,6 @@ endif(NOT WIN32)
+@@ -154,7 +154,6 @@ endif()
#######################################################################
if (USE_PYTHON)
find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h PATHS ${CMAKE_CURRENT_SOURCE_DIR}/external_dependencies/pybind11/include NO_DEFAULT_PATH)
@@ -33,3 +25,6 @@ index c24b631..2354a09 100644
if( NOT PYBIND_INCLUDE_DIR )
# if the pybind submodule is missing, try to initialize and update all submodules
execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-use-system-catch.patch b/media-gfx/netgen/files/netgen-6.2.2204-use-system-catch.patch
new file mode 100644
index 000000000..1c08e49e7
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-use-system-catch.patch
@@ -0,0 +1,40 @@
+From 6eaa13cc02ccd5f1bfa448fbcff3a1d9af8ba90a Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Wed, 14 Dec 2022 07:04:29 +0100
+Subject: [PATCH] use system catch
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -474,7 +474,7 @@ enable_testing()
+ include(CTest)
+
+ if(ENABLE_UNIT_TESTS)
+- include(${CMAKE_CURRENT_LIST_DIR}/cmake/external_projects/catch.cmake)
++ find_package(Catch2 REQUIRED)
+ endif(ENABLE_UNIT_TESTS)
+
+
+--- a/tests/catch/CMakeLists.txt
++++ b/tests/catch/CMakeLists.txt
+@@ -3,11 +3,15 @@ if(ENABLE_UNIT_TESTS)
+ add_custom_target(unit_tests)
+
+ # Build catch_main test object
+-include_directories(${CATCH_INCLUDE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../../libsrc/include ${SPDLOG_INCLUDE_DIR})
++if(TARGET Catch2::Catch2)
++ get_target_property(CATCH_INCLUDE_DIR Catch2::Catch2 INTERFACE_INCLUDE_DIRECTORIES)
++ include_directories(${CATCH_INCLUDE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../../libsrc/include ${SPDLOG_INCLUDE_DIR})
++else()
++ message(SEND_ERROR "Catch header files couldn't be found.")
++endif()
+ add_library(catch_main STATIC main.cpp)
+ set_target_properties(catch_main PROPERTIES CXX_STANDARD 17)
+ add_dependencies(unit_tests catch_main)
+-add_dependencies(catch_main project_catch)
+
+ # ensure the test targets are built before testing
+ add_test(NAME unit_tests_built COMMAND ${CMAKE_COMMAND} --build . --target unit_tests --config ${CMAKE_BUILD_TYPE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../.. )
+--
+2.38.1
+
diff --git a/media-gfx/netgen/files/netgen-6.2.2204-use-system-spdlog.patch b/media-gfx/netgen/files/netgen-6.2.2204-use-system-spdlog.patch
new file mode 100644
index 000000000..cbd45ca07
--- /dev/null
+++ b/media-gfx/netgen/files/netgen-6.2.2204-use-system-spdlog.patch
@@ -0,0 +1,40 @@
+From e20e1e2e2109f1ce6580587f63ad000ac6bdd877 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Tue, 13 Dec 2022 08:14:12 +0100
+Subject: [PATCH] use system spdlog
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -481,8 +481,13 @@ endif(ENABLE_UNIT_TESTS)
+ #######################################################################
+
+ if(USE_SPDLOG)
+- include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/external_projects/spdlog.cmake)
+- include_directories(${SPDLOG_INCLUDE_DIR})
++ find_package(spdlog REQUIRED CONFIG)
++ if(TARGET spdlog::spdlog)
++ get_target_property(SPDLOG_INCLUDE_DIR spdlog::spdlog INTERFACE_INCLUDE_DIRECTORIES)
++ include_directories(${SPDLOG_INCLUDE_DIR})
++ else()
++ message(SEND_ERROR "You enabled USE_SPDLOG, but the spdlog package could not be found.")
++ endif()
+ endif(USE_SPDLOG)
+
+ if(ENABLE_CPP_CORE_GUIDELINES_CHECK)
+--- a/libsrc/core/CMakeLists.txt
++++ b/libsrc/core/CMakeLists.txt
+@@ -50,10 +50,6 @@ endif(TRACE_MEMORY)
+
+ if(USE_SPDLOG)
+ include_directories(${SPDLOG_INCLUDE_DIR})
+- install(DIRECTORY ${SPDLOG_INCLUDE_DIR}
+- DESTINATION ${NG_INSTALL_DIR_INCLUDE}
+- )
+- add_dependencies(ngcore project_spdlog)
+ target_compile_definitions(ngcore PUBLIC NETGEN_USE_SPDLOG)
+ if(DEBUG_LOG)
+ target_compile_definitions(ngcore PUBLIC NETGEN_LOG_DEBUG)
+--
+2.38.1
+
diff --git a/sci-mathematics/netgen/files/netgen.desktop b/media-gfx/netgen/files/netgen.desktop
index 714ba53c4..714ba53c4 100644
--- a/sci-mathematics/netgen/files/netgen.desktop
+++ b/media-gfx/netgen/files/netgen.desktop
diff --git a/sci-mathematics/netgen/files/netgen.png b/media-gfx/netgen/files/netgen.png
index cb2fd8466..cb2fd8466 100644
--- a/sci-mathematics/netgen/files/netgen.png
+++ b/media-gfx/netgen/files/netgen.png
Binary files differ
diff --git a/sci-mathematics/netgen/metadata.xml b/media-gfx/netgen/metadata.xml
index cb94caeca..f19c0cf6e 100644
--- a/sci-mathematics/netgen/metadata.xml
+++ b/media-gfx/netgen/metadata.xml
@@ -6,7 +6,8 @@
<name>Gentoo Mathematics Project</name>
</maintainer>
<use>
- <flag name="opencascade"> Enable OpenCASCADE support</flag>
+ <flag name="logging">Enable logging through <pkg>dev-libs/spdlog</pkg></flag>
+ <flag name="opencascade">Enable OpenCASCADE support</flag>
</use>
<upstream>
<remote-id type="github">NGSolve/netgen</remote-id>
diff --git a/media-gfx/netgen/netgen-6.2.2204.ebuild b/media-gfx/netgen/netgen-6.2.2204.ebuild
new file mode 100644
index 000000000..1d119aaeb
--- /dev/null
+++ b/media-gfx/netgen/netgen-6.2.2204.ebuild
@@ -0,0 +1,152 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit cmake desktop python-single-r1 xdg
+
+DESCRIPTION="Automatic 3d tetrahedral mesh generator"
+HOMEPAGE="https://ngsolve.org/ https://github.com/NGSolve/netgen"
+SRC_URI="https://github.com/NGSolve/netgen/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="ffmpeg gui jpeg logging mpi opencascade python test"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="
+ ${PYTHON_REQUIRED_USE}
+ ffmpeg? ( gui )
+ jpeg? ( gui )
+ python? ( gui )
+"
+
+DEPEND="
+ sys-libs/zlib
+ ffmpeg? ( media-video/ffmpeg:= )
+ gui? (
+ dev-lang/tcl:0/8.6
+ dev-lang/tk:0/8.6
+ media-libs/glu
+ virtual/opengl
+ x11-libs/libX11
+ x11-libs/libXmu
+ x11-libs/libxcb:=
+ )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
+ logging? ( dev-libs/spdlog:= )
+ mpi? (
+ sci-libs/metis
+ virtual/mpi
+ )
+ opencascade? ( sci-libs/opencascade:= )
+ python? (
+ ${PYTHON_DEPS}
+ $(python_gen_cond_dep '
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ '
+ )
+ mpi? (
+ $(python_gen_cond_dep 'dev-python/mpi4py[${PYTHON_USEDEP}]' )
+ )
+ )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ sys-apps/lsb-release
+ virtual/pkgconfig
+ test? (
+ <dev-cpp/catch-3:0
+ python? ( $(python_gen_cond_dep 'dev-python/pytest[${PYTHON_USEDEP}]') )
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-6.2.2204-use-external-pybind11.patch"
+ "${FILESDIR}/${PN}-6.2.2204-find-Tk-include-directories.patch"
+ "${FILESDIR}/${PN}-6.2.2204-find-libjpeg-turbo-library.patch"
+ "${FILESDIR}/${PN}-6.2.2204-link-against-ffmpeg.patch"
+ "${FILESDIR}/${PN}-6.2.2204-use-system-spdlog.patch"
+ "${FILESDIR}/${PN}-6.2.2204-use-system-catch.patch"
+ "${FILESDIR}/${PN}-6.2.2204-disable-failing-tests.patch"
+ "${FILESDIR}/${PN}-6.2.2204-disable-python-tests.patch"
+)
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ # NOTE: need to manually check and update this string on version bumps!
+ cat <<- EOF > "${S}/version.txt" || die
+ v${PV}-0-gde0d706e
+ EOF
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ # currently not working in a sandbox, expects netgen to be installed
+ # see https://github.com/NGSolve/netgen/issues/132
+ -DBUILD_STUB_FILES=OFF
+ -DENABLE_UNIT_TESTS=$(usex test)
+ -DINSTALL_PROFILES=OFF
+ -DNG_INSTALL_DIR_CMAKE="$(get_libdir)/cmake/${PN}"
+ -DNG_INSTALL_DIR_INCLUDE="include/${PN}"
+ -DNG_INSTALL_DIR_LIB="$(get_libdir)"
+ -DUSE_CCACHE=OFF
+ # doesn't build with this version
+ -DUSE_CGNS=OFF
+ -DUSE_GUI=$(usex gui)
+ -DUSE_INTERNAL_TCL=OFF
+ -DUSE_JPEG=$(usex jpeg)
+ -DUSE_MPEG=$(usex ffmpeg)
+ # respect users -march= choice
+ -DUSE_NATIVE_ARCH=OFF
+ -DUSE_MPI=$(usex mpi)
+ -DUSE_OCC=$(usex opencascade)
+ -DUSE_PYTHON=$(usex python)
+ -DUSE_SPDLOG=$(usex logging)
+ -DUSE_SUPERBUILD=OFF
+ )
+ # no need to set this, if we only build the library
+ if use gui; then
+ mycmakeargs+=( -DTK_INCLUDE_PATH="/usr/$(get_libdir)/tk8.6/include" )
+ fi
+ if use python; then
+ mycmakeargs+=(
+ -DPYBIND_INCLUDE_DIR="/usr/lib/${EPYTHON}/site-packages/pybind11/include/"
+ -DNG_INSTALL_PYBIND=OFF
+ )
+ fi
+ if use mpi && use python; then
+ mycmakeargs+=( -DUSE_MPI4PY=ON )
+ else
+ mycmakeargs+=( -DUSE_MPI4PY=OFF )
+ fi
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ use python && python_optimize
+
+ local NETGENDIR="/usr/share/${PN}"
+ echo -e "NETGENDIR=${NETGENDIR}" > ./99netgen || die
+ doenvd 99netgen
+
+ if use gui; then
+ mv "${ED}"/usr/bin/{*.tcl,*.ocf} "${ED}${NETGENDIR}" || die
+
+ doicon "${FILESDIR}"/${PN}.png
+ domenu "${FILESDIR}"/${PN}.desktop
+ fi
+
+ mv "${ED}"/usr/share/${PN}/doc/ng4.pdf "${ED}"/usr/share/doc/${PF} || die
+ dosym -r /usr/share/doc/${PF}/ng4.pdf /usr/share/${PN}/doc/ng4.pdf
+
+ use python || rm -r "${ED}${NETGENDIR}"/py_tutorials || die
+}
diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml
index ae9640ffb..2103548da 100644
--- a/media-libs/libgfx/metadata.xml
+++ b/media-libs/libgfx/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mjgarland/libgfx</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/media-libs/mmg/metadata.xml b/media-libs/mmg/metadata.xml
index 2b9123050..bd7221f19 100644
--- a/media-libs/mmg/metadata.xml
+++ b/media-libs/mmg/metadata.xml
@@ -13,4 +13,7 @@
<flag name="scotch">Use SCOTCH TOOL for renumbering</flag>
<flag name="vtk">Use VTK I/O</flag>
</use>
+ <upstream>
+ <remote-id type="github">MmgTools/mmg</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/metadata/pkgcheck.conf b/metadata/pkgcheck.conf
new file mode 100644
index 000000000..b39b6e490
--- /dev/null
+++ b/metadata/pkgcheck.conf
@@ -0,0 +1,2 @@
+[DEFAULT]
+profiles = stable,dev,-default/linux/amd64/17.0/musl,-default/linux/amd64/17.0/x32
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index af2fbf942..d117605d1 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -2,3 +2,4 @@ DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6b
DIST cernbox-client-2.9.2-6339.src.rpm 6243132 BLAKE2B c73c3c338f9d3fb7fa7b22efe9b6ff1380d80f3804e2e732873f5804ed31d98fb04f9dbcdc0f614136c08081bea825d70948f94a6c0c9dddfe20eca66e41c4c1 SHA512 ec0edff177a5b77144eef173e4e3f5d549762faa6682618124f5c64e37f657c3aa00f639723cf2c48b6c4d1049373cd24b41d347cd9bf3c7bb291ab3340d6b2a
DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
DIST ownCloud-2.11.1.8438.tar.xz 5655380 BLAKE2B da34adafabfc8c2b0bbfdff99a81b56f2d2639b5168b2165a847a6d5a4efe4e86578984c0f0c20564d0978aab18bb1a62330539bdd137f608a5cfc3ff8d84cf0 SHA512 fe38471f62e7233a7ba04f7fd2c7c7231957e6927c39d0bcf3f6f77fd6cbb1223618bbf6a8cc5fa15de10a35c7f07f2f5df0e49acbc2af5fe9333cda2eb41c92
+DIST ownCloud-2.11.1.8946.tar.xz 5654496 BLAKE2B 6b5b82730460071ae590b35d653824f4e56d506d87929c5d4ebb31eef921d0cb0141a44d7f0c996b8d1afffa5874d3e4dda75feaba740e652df2939633475fcd SHA512 b44f72e22c539a731901d9c146f00edbf0a4dabb992d6cde06be1b50506d5bc4a8aa861c6ea0207eed72aaea8c8af8651ce07f9e9154e6e44ccdecdd27e35b75
diff --git a/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild b/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild
new file mode 100644
index 000000000..c698f7562
--- /dev/null
+++ b/net-misc/cernbox-client/cernbox-client-2.11.1.8946.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake rpm xdg
+
+DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
+
+# Origin is classic owncloud-client, branded for CERN during compilation.
+ORIGIN_PN="ownCloud"
+BRANDED_P="cernbox"
+BRANDED_PV="2.9.2"
+BRANDED_REL="6339"
+HOMEPAGE="https://cernbox.cern.ch/"
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+ https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+ https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
+
+LICENSE="CC-BY-3.0 GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dolphin gnome-keyring nautilus test"
+RESTRICT="!test? ( test )"
+
+RDEPEND=">=dev-db/sqlite-3.4:3
+ dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
+ dev-qt/qtconcurrent:5
+ dev-qt/qtcore:5
+ dev-qt/qtdbus:5
+ dev-qt/qtgui:5
+ dev-qt/qtnetwork:5[ssl]
+ dev-qt/qtsql:5
+ dev-qt/qtwidgets:5
+ dev-qt/qtxml:5
+ sys-fs/inotify-tools
+ dolphin? (
+ kde-frameworks/kcoreaddons:5
+ kde-frameworks/kio:5
+ )
+ nautilus? ( dev-python/nautilus-python )"
+
+DEPEND="${RDEPEND}
+ test? (
+ dev-util/cmocka
+ dev-qt/qttest:5
+ )"
+
+BDEPEND="
+ dev-qt/linguist-tools:5
+ kde-frameworks/extra-cmake-modules"
+
+S=${WORKDIR}/${ORIGIN_PN}-${PV}
+
+src_unpack() {
+ rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
+ mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
+}
+
+src_prepare() {
+ # Keep tests in ${T}
+ sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
+
+ if ! use nautilus; then
+ pushd shell_integration > /dev/null || die
+ cmake_comment_add_subdirectory nautilus
+ popd > /dev/null || die
+ fi
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+ -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
+ -DBUILD_TESTING=$(usex test)
+ )
+
+ cmake_src_configure
+}
diff --git a/profiles/default/linux/amd64/17.0/x32/package.mask b/profiles/default/linux/amd64/17.0/x32/package.mask
deleted file mode 100644
index 4f9228f91..000000000
--- a/profiles/default/linux/amd64/17.0/x32/package.mask
+++ /dev/null
@@ -1,3 +0,0 @@
-# Cecil Curry <leycec@gmail.com> (2021-10-07)
-# Panel requires Node.js, which fails to support the x32 ABI.
-dev-python/panel
diff --git a/profiles/package.mask b/profiles/package.mask
index a21bb9773..a0d859d7f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,26 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2022-08-22)
-# Depends on removed sci-libs/io_lib. removal in 30 days
-sci-biology/caftools
-sci-biology/salmon
-sci-biology/staden
-sci-biology/staden_doc
-sci-biology/roche454ace2caf
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
+# Needs bump of PYTHON_COMPAT to at least python3_10
+sci-biology/gffutils
+sci-biology/chiron
+dev-python/snakemake
+dev-python/specutils
+dev-python/regions
+dev-python/pyzo
+dev-python/kmapper
+dev-python/photutils
+dev-python/gammapy
+dev-python/astroquery
+# Reverse deps of above
+dev-python/ripser
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
+# Depends on dev-python/nose, needs porting to pytest
+sci-biology/pyfaidx
+sci-biology/gffutils
+sci-biology/RSeQC
+dev-python/hdf5storage
+dev-python/transforms3d
+dev-python/pysolar
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 8aff1df94..79c0fcb5c 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -19,14 +19,6 @@
# vtk<9 no longer available in ::gentoo
sci-libs/gdcm python
-# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
-# doesn't link with plotutils-2.6
-sci-physics/qcl plotutils
-
-# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
-
# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
diff --git a/profiles/updates/4Q-2022 b/profiles/updates/4Q-2022
new file mode 100644
index 000000000..b80d5a910
--- /dev/null
+++ b/profiles/updates/4Q-2022
@@ -0,0 +1 @@
+move sci-mathematics/netgen media-gfx/netgen
diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml
index 138cb7705..aa4766e73 100644
--- a/sci-biology/BRAKER/metadata.xml
+++ b/sci-biology/BRAKER/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">Gaius-Augustus/BRAKER</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild
index 28ff526f6..443fb3342 100644
--- a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild
+++ b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild
@@ -1,9 +1,10 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -15,4 +16,6 @@ LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
-distutils_enable_tests nose
+distutils_enable_tests pytest
+# Nominally upstream still uses nose, though it does not encumber us, and tests pass:
+# https://github.com/sanger-pathogens/Fastaq/issues/84
diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml
index 138cb7705..480ba370b 100644
--- a/sci-biology/GAL/metadata.xml
+++ b/sci-biology/GAL/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">The-Sequence-Ontology/GAL</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml
index 138cb7705..a3f152e56 100644
--- a/sci-biology/RAILS/metadata.xml
+++ b/sci-biology/RAILS/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/RAILS</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
index 553c21e21..002004bca 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit python-single-r1
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml
index 138cb7705..cc34f33b5 100644
--- a/sci-biology/VelvetOptimiser/metadata.xml
+++ b/sci-biology/VelvetOptimiser/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/VelvetOptimiser</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
index acf637dca..cbb8a4299 100644
--- a/sci-biology/afni/metadata.xml
+++ b/sci-biology/afni/metadata.xml
@@ -13,4 +13,7 @@
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
functional MRI data—a technique for mapping human brain activity.
</longdescription>
+ <upstream>
+ <remote-id type="github">afni/afni</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
index 138cb7705..ed9e5b12d 100644
--- a/sci-biology/angsd/metadata.xml
+++ b/sci-biology/angsd/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ANGSD/angsd</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml
index 9f969ddf9..e8372d21b 100644
--- a/sci-biology/ants/metadata.xml
+++ b/sci-biology/ants/metadata.xml
@@ -21,4 +21,7 @@
<use>
<flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag>
</use>
+ <upstream>
+ <remote-id type="github">ANTsX/ANTs</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml
index 138cb7705..927a160ba 100644
--- a/sci-biology/bamql/metadata.xml
+++ b/sci-biology/bamql/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">BoutrosLaboratory/bamql</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml
index 138cb7705..9183ef1ec 100644
--- a/sci-biology/barrnap/metadata.xml
+++ b/sci-biology/barrnap/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/barrnap</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild
index ca6700729..dc875e7a5 100644
--- a/sci-biology/behaviopy/behaviopy-0.2.ebuild
+++ b/sci-biology/behaviopy/behaviopy-0.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest
index 18637621d..ab53258d3 100644
--- a/sci-biology/bidsschematools/Manifest
+++ b/sci-biology/bidsschematools/Manifest
@@ -1,2 +1,3 @@
DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd
DIST bidsschematools-0.5.1.tar.gz 1159308 BLAKE2B a53355b24e87ea7008fa64ca4f7e71c7bf29effc52f4aa3f855af633ce83817d5551eead4224d39f8cd46693dc48a7d9325a7ad8698e159b468e902982c5a940 SHA512 f1d9ab6b37c8fd4fd6a6aa821ef718c1af7f3d453d44c2c76c104f5601d40e5a328b0332255a591d8431e8c0ca3406dccd852c6c1fc8d832657b27a6b0076adc
+DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1
diff --git a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
index 735f130e9..0e62efa42 100644
--- a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
+++ b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -20,8 +20,8 @@ IUSE="render"
RDEPEND="
dev-python/pyyaml[${PYTHON_USEDEP}]
render? (
- dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
)
"
DEPEND=""
diff --git a/sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild
index 735f130e9..13aabaa37 100644
--- a/sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild
+++ b/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -20,8 +20,9 @@ IUSE="render"
RDEPEND="
dev-python/pyyaml[${PYTHON_USEDEP}]
render? (
- dev-python/tabulate[${PYTHON_USEDEP}]
+ dev-python/markdown-it-py[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
)
"
DEPEND=""
diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
new file mode 100644
index 000000000..13aabaa37
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
@@ -0,0 +1,38 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/markdown-it-py[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml
index 4c433a8ca..4ee13c559 100644
--- a/sci-biology/bismark/metadata.xml
+++ b/sci-biology/bismark/metadata.xml
@@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
and CHH context.
</longdescription>
+ <upstream>
+ <remote-id type="github">FelixKrueger/Bismark</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
index 9550415b1..a94c2be48 100644
--- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
+++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_SETUPTOOLS="rdepend"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml
index 138cb7705..1e02bb596 100644
--- a/sci-biology/btl_bloomfilter/metadata.xml
+++ b/sci-biology/btl_bloomfilter/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/btl_bloomfilter</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest
index 80552af85..90147dff7 100644
--- a/sci-biology/bx-python/Manifest
+++ b/sci-biology/bx-python/Manifest
@@ -1 +1,2 @@
-DIST bx-python-0.8.9.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea
+DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea
+DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc
diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index a0d3ae3df..6cffba1be 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -1,28 +1,35 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
DESCRIPTION="Library for rapid implementation of genome scale analyses"
HOMEPAGE="https://github.com/bxlab/bx-python"
-SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/six[${PYTHON_USEDEP}]
"
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+"
# has file collision with sci-biology/RSeQC
# ToDo: fix doc building:
# Reason: TemplateNotFound('i')
#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
new file mode 100644
index 000000000..6cffba1be
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+"
+
+# has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 6f0b1c9ca..b29975b58 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1 git-r3
@@ -14,15 +14,22 @@ EGIT_REPO_URI="https://github.com/bxlab/bx-python"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/six[${PYTHON_USEDEP}]
"
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+"
# has file collision with sci-biology/RSeQC
# ToDo: fix doc building:
# Reason: TemplateNotFound('i')
#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index 3e13342e3..80a22b44a 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -12,5 +12,6 @@
<upstream>
<remote-id type="bitbucket">james_taylor/bx-python</remote-id>
<remote-id type="pypi">bx-python</remote-id>
+ <remote-id type="github">bxlab/bx-python</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
deleted file mode 100644
index 761665281..000000000
--- a/sci-biology/caftools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d
-DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
deleted file mode 100644
index 7d58f3375..000000000
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/"
-SRC_URI="
- ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
- ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- sci-libs/io_lib
- dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/Makefile.in-"${PV}".patch
-)
-
-src_prepare(){
- default
- mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
-}
-
-src_configure(){
- default
- sed \
- -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
- -i Makefile src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
- default
- doman man/*.[1-5] || die
- elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
- elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
-}
diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch
deleted file mode 100644
index 1e5160487..000000000
--- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- src/Makefile.in.ori 2010-12-05 22:59:40.000000000 +0100
-+++ src/Makefile.in 2010-12-05 23:01:19.000000000 +0100
-@@ -32,8 +32,6 @@
- includedir = @includedir@
- oldincludedir = /usr/include
-
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
- pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
-@@ -323,18 +321,18 @@
-
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- if test -f $$p; then \
-- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+ echo " $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-+ $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- else :; fi; \
- done
-
- uninstall-binPROGRAMS:
- @$(NORMAL_UNINSTALL)
- list='$(bin_PROGRAMS)'; for p in $$list; do \
-- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+ rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- done
-
- .c.o:
-@@ -579,7 +577,7 @@
- $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
- installdirs: installdirs-recursive
- installdirs-am:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
-
-
- mostlyclean-generic:
diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch
deleted file mode 100644
index 4ddd9f628..000000000
--- a/sci-biology/caftools/files/Makefile.in.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100
-+++ src/Makefile.in 2010-12-05 22:10:07.000000000 +0100
-@@ -18,7 +18,7 @@
- srcdir = @srcdir@
- top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
-+prefix = $(DESTDIR)/@prefix@
- exec_prefix = @exec_prefix@
-
- bindir = @bindir@
-@@ -394,14 +394,14 @@
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
- install-binPROGRAMS: $(bin_PROGRAMS)
- @$(NORMAL_INSTALL)
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- if test -f $$p \
- ; then \
- f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
-- echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
-- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
-+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \
-+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \
- else :; fi; \
- done
-
-@@ -409,8 +409,8 @@
- @$(NORMAL_UNINSTALL)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
-- echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
-- rm -f $(DESTDIR)$(bindir)/$$f; \
-+ echo " rm -f $(bindir)/$$f"; \
-+ rm -f $(bindir)/$$f; \
- done
-
- clean-binPROGRAMS:
-@@ -663,7 +663,7 @@
- all-am: Makefile $(PROGRAMS) config.h
- installdirs: installdirs-recursive
- installdirs-am:
-- $(mkinstalldirs) $(DESTDIR)$(bindir)
-+ $(mkinstalldirs) $(bindir)
-
- install: install-recursive
- install-exec: install-exec-recursive
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
deleted file mode 100644
index 224641279..000000000
--- a/sci-biology/caftools/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <longdescription>
-CAF is a text format for describing sequence assemblies. It is acedb-compliant
-and is an extension of the ace-file format used earlier, but with support for
-base quality measures and a more extensive description of the Sequence data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
index 9c9e19081..773e706a6 100644
--- a/sci-biology/dcm2niix/metadata.xml
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -19,4 +19,7 @@
format to the NIfTI format. ICOM provides many ways to store/compress
image data, known as transfer syntaxes.
</longdescription>
+ <upstream>
+ <remote-id type="github">rordenlab/dcm2niix</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/dcmstack/dcmstack-0.8.ebuild b/sci-biology/dcmstack/dcmstack-0.8.ebuild
index 0ac8519b7..8ec65b7b8 100644
--- a/sci-biology/dcmstack/dcmstack-0.8.ebuild
+++ b/sci-biology/dcmstack/dcmstack-0.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml
index ae9640ffb..0272cf14e 100644
--- a/sci-biology/dcmstack/metadata.xml
+++ b/sci-biology/dcmstack/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">moloney/dcmstack</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
index 1eecdd1b9..38f9aea0f 100644
--- a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
+++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest
index 31a5bdb90..649a31cdf 100644
--- a/sci-biology/deeptools/Manifest
+++ b/sci-biology/deeptools/Manifest
@@ -1 +1,2 @@
DIST deeptools-3.5.0.tar.gz 62553343 BLAKE2B a8cd1520b96c50ad36667405677cf422a74376d88f0716f83cc0c6f58d01aefcf47ac1b862aa98b8801e61445d59831dbc9246660e2f41a5b3e0ed3d6573ad50 SHA512 699734c8a863ec76dfead728e3227bbe3ec04d62e91f447269a6aa8406d627ff618837b85ab2e31cc635c671e1d62230c4db0992106bbe921281b81164387b38
+DIST deeptools-3.5.1.tar.gz 62552044 BLAKE2B 3c785ba478b88fbbe7ba2617e2d05984b8a897f787e85d6f8f144f596af07b9e16ba920c8adee35efc4b1b067f255e81f66cf746aaea43e5ee61c23c4d15c9c3 SHA512 f7618f1a51b975d42712a38e13e9ab2ddfeafffe24d81fdab41f1ef7c2e44fd09da0351210670b0036bf72e7af11b679417275adce300ae9fabe4b5339ee9810
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index f53a19bcb..fc48e2224 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
@@ -23,7 +23,7 @@ RDEPEND="
>=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
>=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
>=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
- >=dev-python/plotly-2.0.0[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
>=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
>=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
>=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
@@ -33,4 +33,4 @@ RDEPEND="
S="${WORKDIR}/deepTools-${PV}"
distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse
-distutils_enable_tests nose
+#distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild
new file mode 100644
index 000000000..fc48e2224
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
+HOMEPAGE="https://github.com/deeptools/deepTools"
+SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+ >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
+ >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
+ >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
+ >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
+ >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/deepTools-${PV}"
+
+distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse
+#distutils_enable_tests nose
diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml
index 138cb7705..ac7dfc24a 100644
--- a/sci-biology/diamond/metadata.xml
+++ b/sci-biology/diamond/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bbuchfink/diamond</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild
index 15b986afe..3656d6dc8 100644
--- a/sci-biology/dipy/dipy-1.1.1.ebuild
+++ b/sci-biology/dipy/dipy-1.1.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest
deleted file mode 100644
index 79281bc74..000000000
--- a/sci-biology/estscan/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09
-DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2
-DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4
-DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de
-DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447
-DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5
-DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43
-DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c
-DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1
diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild
deleted file mode 100644
index a0992b76b..000000000
--- a/sci-biology/estscan/estscan-3.0.3.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2 perl-module toolchain-funcs
-
-DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
-HOMEPAGE="https://sourceforge.net/projects/estscan/"
-SRC_URI="
- https://downloads.sourceforge.net/${PN}/${P}.tar.gz
- https://downloads.sourceforge.net/${PN}/At.smat.gz
- https://downloads.sourceforge.net/${PN}/Dm.smat.gz
- https://downloads.sourceforge.net/${PN}/Dr.smat.gz
- https://downloads.sourceforge.net/${PN}/Hs.smat.gz
- https://downloads.sourceforge.net/${PN}/Mm.smat.gz
- https://downloads.sourceforge.net/${PN}/Rn.smat.gz
- https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
- https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"
-
-SLOT="0"
-LICENSE="estscan"
-KEYWORDS="~amd64 ~x86"
-IUSE="icc ifc"
-
-DEPEND="
- dev-perl/BTLib
- icc? ( dev-lang/icc )
- ifc? ( dev-lang/ifc )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
- default
- sed \
- -e 's/\\rm -f/rm -rf/' \
- -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
- -i "${P}"/Makefile || die "failed to edit Makefile"
-
- # fix hard-coded paths
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die
-
- if ! use icc; then
- sed \
- -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die
- fi
-
- if ! use ifc; then
- sed \
- -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
- -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \
- || die
- fi
-
- if use icc; then
- # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives
- # me gcc instead, same for $(tc-getF77)
- # Moreover, the if/else logic here should separate users having only icc
- # while not ifort (and vice-versa) from those having only
- # gcc/gfortran/g77
- #
- # FIXME: below as a dirty hack I force gfortran instead of ifort for
- # my testing purposes. Didn't ebuild contain "PROVIDES" line?
- # Same for FFLAGS.
- sed \
- -e "s:^# CC = icc:CC = icc:" \
- -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \
- -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
- -e "s/^ CC = gcc/# CC = gcc/" \
- -i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC"
-
- fi
-
- if use ifc; then
- sed \
- -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \
- -e "s/^# F77 = ifort/F77 = gfortran/" \
- -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
- -e "s/^ F77 = g77/# F77 = g77/" \
- -i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77"
- fi
-}
-
-src_compile() {
- emake -C ${P}
-}
-
-src_install() {
- # FIXME: Some kind of documentation is in {P}/${PN}.spec
- cd ${P} || die "Failed to chdir to ${P}"
- dobin \
- build_model ${PN} evaluate_model extract_EST extract_UG_EST \
- extract_mRNA makesmat maskred prepare_data winsegshuffle
- # the file build_model_utils.pl should go into some PERL site-packages dir
- # see {P}/${PN}.spec
-
- # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension
- insinto /usr/share/doc/${PN}
- # grab the file directly from ../distdir/
- doins "${DISTDIR}"/user_guide_fev_07.pdf
-
- # install the default precomputed matrices
- cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}"
- insinto /usr/share/${PN}
- doins *.smat
-
- # install BTlib (in perl)
- # dobin fetch indexer netfetch
- insinto /usr/share/${PN}/
- # install the config file which is packed inside the BTLib tarball while is not
- # being installed by dev-perl/BTLib
- doins "${WORKDIR}"/BTLib-0.19/fetch.conf
-
- # FIXME: install the *.pm files from BTLib-0.19
- # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19
- # myinst="DESTDIR=${D}"
- # perl-module_src_install
-
- einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout."
- einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/."
- einfo "You may follow the hints from http://${PN}.sourceforge.net/"
-}
diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml
deleted file mode 100644
index c79c2d1b5..000000000
--- a/sci-biology/estscan/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <use>
- <flag name="icc">Undocumented USE</flag>
- <flag name="ifc">Undocumented USE</flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml
index 7c86089a2..f13c6ccba 100644
--- a/sci-biology/fastqc/metadata.xml
+++ b/sci-biology/fastqc/metadata.xml
@@ -13,4 +13,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">s-andrews/FastQC</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml
index 138cb7705..a9577a9c3 100644
--- a/sci-biology/ffindex/metadata.xml
+++ b/sci-biology/ffindex/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ahcm/ffindex</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild
index f041c2c48..25ec22946 100644
--- a/sci-biology/gemini/gemini-0.30.2.ebuild
+++ b/sci-biology/gemini/gemini-0.30.2.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml
index 138cb7705..b25087121 100644
--- a/sci-biology/longstitch/metadata.xml
+++ b/sci-biology/longstitch/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/LongStitch</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest
deleted file mode 100644
index fb61347b3..000000000
--- a/sci-biology/mRNAmarkup/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
deleted file mode 100644
index fb37b69f9..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Transcript annotation workflow"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB
-
-LICENSE="mRNAmarkup"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- sci-biology/ncbi-tools++
- sci-biology/estscan"
-# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
-# but, mRNAmarkup/INSTALL says:
-# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
-#
-# has a slightly modified estscan copy in src/contributed
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare(){
- default
- sed -e \
- "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
- -i bin/mRNAmarkup.orig || die
- sed -e \
- "s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
- -i bin/mRNAmarkup.orig
-}
-
-src_compile(){
- cd src
- emake
-}
-
-src_install(){
- mv bin/mRNAmarkup.orig bin/mRNAmarkup
- sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
- dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
- # TODO: there are some more files in bin/ , sigh!
- insinto /usr/share/mRNAmarkup/etc
- mv mRNAmarkup.conf.orig mRNAmarkup.conf
- doins mRNAmarkup.conf
- doins bin/ESTScan.conf
- dodoc 0README INSTALL
-}
-
-pkg_postinst(){
- einfo "Please obtain a local copy of NCBI CDD dastabase"
-}
diff --git a/sci-biology/mappy/mappy-2.24.ebuild b/sci-biology/mappy/mappy-2.24.ebuild
index 3e25ed1eb..f8d964df4 100644
--- a/sci-biology/mappy/mappy-2.24.ebuild
+++ b/sci-biology/mappy/mappy-2.24.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild
index f39de8ead..6934f2a74 100644
--- a/sci-biology/minimap2/minimap2-2.24.ebuild
+++ b/sci-biology/minimap2/minimap2-2.24.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
DISTUTILS_OPTIONAL=1
inherit distutils-r1
diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml
index 8417d1580..a60e8c1b5 100644
--- a/sci-biology/mreps/metadata.xml
+++ b/sci-biology/mreps/metadata.xml
@@ -5,4 +5,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">gregorykucherov/mreps</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
index 167e2a8c3..15f83b00c 100644
--- a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
+++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit python-single-r1
DESCRIPTION=" NCBI SRA ( Sequence Read Archive )"
diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml
index 138cb7705..b0874714e 100644
--- a/sci-biology/nextclip/metadata.xml
+++ b/sci-biology/nextclip/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">richardmleggett/nextclip</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
index 138cb7705..f165e6cbc 100644
--- a/sci-biology/ngs/metadata.xml
+++ b/sci-biology/ngs/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ncbi/ngs</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
index 8675ae22a..0574c5076 100644
--- a/sci-biology/ngs/ngs-2.11.2.ebuild
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit python-single-r1 java-pkg-2
DESCRIPTION="NGS Language Bindings "
diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index 166b45466..2592a63fb 100644
--- a/sci-biology/nilearn/nilearn-0.8.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild
index 14f931258..c14c8f665 100644
--- a/sci-biology/nilearn/nilearn-0.9.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild
index 90cb4ff6a..7a767390a 100644
--- a/sci-biology/nitime/nitime-0.9.ebuild
+++ b/sci-biology/nitime/nitime-0.9.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1 virtualx
diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild
index c46edf3c1..3e0894c90 100644
--- a/sci-biology/nitime/nitime-9999.ebuild
+++ b/sci-biology/nitime/nitime-9999.ebuild
@@ -1,9 +1,9 @@
-# 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
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1 git-r3 virtualx
diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml
index 138cb7705..fb03df79c 100644
--- a/sci-biology/ntCard/metadata.xml
+++ b/sci-biology/ntCard/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/ntCard</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
index 2ea281d41..8c90b0a8f 100644
--- a/sci-biology/phusion2/phusion2-3.0.ebuild
+++ b/sci-biology/phusion2/phusion2-3.0.ebuild
@@ -12,7 +12,9 @@ LICENSE="all-rights-reserved" # temporarily placed value
# Availability
# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
SLOT="0"
-KEYWORDS="~amd64"
+#KEYWORDS="~amd64"
+# dependency sci-biology/phrap removed from ::gentoo in f3cfb83adfc5dd1b85d0c9dce5ffbf166b25f4e4
+KEYWORDS=""
DEPEND="app-shells/tcsh
sys-cluster/openmpi"
diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml
index 138cb7705..9272f0d9c 100644
--- a/sci-biology/prokka/metadata.xml
+++ b/sci-biology/prokka/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">tseemann/prokka</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index 95bee9be2..8f4ae591f 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml
index fd0f24633..47cc39d79 100644
--- a/sci-biology/pyfaidx/metadata.xml
+++ b/sci-biology/pyfaidx/metadata.xml
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">pyfaidx</remote-id>
+ <remote-id type="github">mdshw5/pyfaidx</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml
index 8417d1580..e3ce321ed 100644
--- a/sci-biology/quicktree/metadata.xml
+++ b/sci-biology/quicktree/metadata.xml
@@ -5,4 +5,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">khowe/quicktree</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest
deleted file mode 100644
index 6711cecd3..000000000
--- a/sci-biology/roche454ace2caf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732
diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
deleted file mode 100644
index a3c4eee39..000000000
--- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="ace to gap4 converter"
-HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/"
-SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"
-
-LICENSE="FLI-Jena"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/align_to_scf
- sci-biology/sff_dump
- sci-biology/caftools
- sci-biology/staden
- dev-lang/perl
- app-shells/ksh"
-
-S="${WORKDIR}/roche2gap"
-
-src_install(){
- dobin bin/*.pl bin/roche454ace2gap
- einstalldocs
-}
diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml
index 138cb7705..026053b60 100644
--- a/sci-biology/rtg-tools/metadata.xml
+++ b/sci-biology/rtg-tools/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">RealTimeGenomics/rtg-tools</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
deleted file mode 100644
index 37410d297..000000000
--- a/sci-biology/salmon/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
-DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
-DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
-DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2
-DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d
-DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
-DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6
-DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
-DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
deleted file mode 100644
index ac561d793..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200
-+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200
-@@ -213,15 +213,6 @@
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--if(CONDA_BUILD)
-- set (Boost_USE_STATIC_LIBS OFF)
--else ()
-- set (Boost_USE_STATIC_LIBS ON)
--endif(CONDA_BUILD)
--
- set (Boost_USE_MULTITHREADED ON)
- #set (Boost_USE_STATIC_RUNTIME OFF)
-
diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
deleted file mode 100644
index 81edf96f5..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200
-+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200
-@@ -5,7 +5,7 @@
- )
-
- if (SALMON_QUASI_INDEX_RESULT)
-- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}")
-+ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}")
- endif()
-
- set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant)
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
deleted file mode 100644
index eb606c00c..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200
-@@ -296,6 +296,8 @@
- )
- ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-
-+include(GNUInstallDirs)
-+
- set(INSTALL_LIB_DIR lib )
- set(INSTALL_BIN_DIR bin )
- set(INSTALL_INCLUDE_DIR include )
-@@ -311,8 +313,8 @@
-
- install(TARGETS salmon salmon_core
- RUNTIME DESTINATION bin
-- LIBRARY DESTINATION lib
-- ARCHIVE DESTINATION lib
-+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
- )
-
- add_custom_command(TARGET unitTests POST_BUILD
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
deleted file mode 100644
index 0a95757a8..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200
-@@ -335,6 +335,6 @@
- )
-
- include(InstallRequiredSystemLibraries)
--add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
-+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
- add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake )
- add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake )
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
deleted file mode 100644
index 8eddc6e3a..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200
-+++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200
-@@ -29,7 +29,8 @@
- EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
-
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
-
- hashcheck=""
- if exists sha256sum; then
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
deleted file mode 100644
index 438763960..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
+++ /dev/null
@@ -1,200 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200
-+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200
-@@ -235,31 +235,7 @@
-
- find_package (LibLZMA)
- if (NOT LIBLZMA_FOUND)
-- message ("Will attempt to fetch and build liblzma")
-- message ("=======================================")
--ExternalProject_Add(liblzma
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- ##
-- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
-- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
-- tar -xzvf xz-5.2.2.tar.gz
-- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
-- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
-- ##
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- BUILD_IN_SOURCE TRUE
-- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
-- BUILD_COMMAND make ${QUIET_MAKE}
-- INSTALL_COMMAND make ${QUIET_MAKE} install
--)
--
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBLZMA TRUE)
-+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
- else()
- message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
- message("===========================================")
-@@ -267,28 +243,7 @@
-
- find_package (BZip2)
- if (NOT BZIP2_FOUND)
-- message ("Will attempt to fetch and build libbz2")
-- message ("=======================================")
--ExternalProject_Add(libbz2
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
-- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
-- tar -xzvf bzip2-1.0.6.tar.gz
-- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
-- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- BUILD_IN_SOURCE TRUE
-- CONFIGURE_COMMAND ""
-- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
--)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBBZ2 TRUE)
-+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
- else()
- message("Found libbz2 library: ${BZIP2_LIBRARIES}")
- message("===========================================")
-@@ -333,61 +288,15 @@
- # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
- # option, go and grab it for them.
- ##
--if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
-+if (NOT Boost_FOUND)
- message(FATAL_ERROR
- "Salmon cannot be compiled without Boost.\n"
- "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
- "This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
- "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
- )
--elseif(FETCH_BOOST)
-- ## Let the rest of the build process know we're going to be fetching boost
-- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
-- --with-filesystem --with-graph --with-graph_parallel --with-math
-- --with-program_options --with-system --with-thread
-- --with-timer)
-- set (BOOST_WILL_RECONFIGURE TRUE)
-- set (FETCH_BOOST FALSE)
-- message("Build system will fetch and build Boost")
-- message("==================================================================")
-- ExternalProject_Add(libboost
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
-- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
-- tar xzf boost_1_66_0.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
-- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
-- BUILD_IN_SOURCE 1
-- INSTALL_COMMAND ""
-- )
--
-- ##
-- # After we've installed boost,
-- ##
-- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
-- ExternalProject_Add_Step(libboost reconfigure
-- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
-- DEPENDEES install
-- )
-- set (FETCHED_BOOST TRUE)
- endif()
-
--##
--# If we're fetching boost and we need to have dummy paths for these variables
--# so that CMake won't complain
--##
--if (BOOST_WILL_RECONFIGURE)
-- message("Setting Temporary Boost paths")
-- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
-- set(Boost_FOUND TRUE)
--endif()
--
--
- message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
- message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
- message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
-@@ -422,9 +331,9 @@
- include(ExternalProject)
- ExternalProject_Add(libcereal
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&
-- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz &&
-- tar -xzvf cereal-v1.2.2.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&
-+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz &&
-+ tar -xzvf cereal-1.2.2.tar.gz
-
- ##
- #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
-@@ -455,12 +364,12 @@
- ExternalProject_Add(libbwa
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
-- #DOWNLOAD_NAME bwa-master.tar.gz
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
-- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
-- mkdir -p bwa-master &&
-- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
-+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
-+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
-+ mkdir -p bwa-0.7.12.5 &&
-+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
-+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
- BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
-@@ -562,9 +471,9 @@
- message("==================================================================")
- ExternalProject_Add(libgff
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
-- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz &&
-- tar -xzvf libgff.tgz
-+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
-+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
-+ tar -xzvf libgff-1.1.tgz
- ##
- #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
- #DOWNLOAD_NAME libff.tgz
-@@ -600,10 +509,10 @@
- message("==================================================================")
- ExternalProject_Add(libstadenio
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
-- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
-+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
-+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
- mkdir -p staden-io_lib-1.14.8 &&
-- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
- rm -fr staden-io_lib &&
- mv -f staden-io_lib-1.14.8 staden-io_lib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
-@@ -620,9 +529,9 @@
- message("==================================================================")
- ExternalProject_Add(libspdlog
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
-- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
-- tar -xzf spdlog-v0.16.1.tar.gz
-+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
-+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
-+ tar -xzf spdlog-0.16.1.tar.gz
- ##
- #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
- #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
deleted file mode 100644
index 76ef25547..000000000
--- a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be02ab..48ffda2 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -428,9 +428,9 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
-+set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
- if (NOT BOOST_RECONFIGURE)
--find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
-+find_package(Boost 1.59.0 COMPONENTS ALL)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
-@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
- endif()
-
- ## Try and find TBB first
--find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
-+find_package(TBB)
-
- ## NOTE: we actually require at least 2019 U4 or greater
- ## since we are using tbb::global_control. However, they
-@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
- ## source. Check before release if we can bump to the 2020
- ## version (requires having tbb 2020 for OSX).
- if (${TBB_FOUND})
-- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
- message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
- set(TBB_TARGET_EXISTED TRUE)
-- else()
-- set(TBB_TARGET_EXISTED FALSE)
-- endif()
- else()
- set(TBB_TARGET_EXISTED FALSE)
- endif()
-@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
- message("Build system will compile libgff")
- message("==================================================================")
- externalproject_add(libgff
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
-- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
-- tar -xzvf libgff.tgz
- ##
- #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
- #DOWNLOAD_NAME libff.tgz
-diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
-index c8b3eb5..b4c23da 100644
---- a/cmake/Modules/FindTBB.cmake
-+++ b/cmake/Modules/FindTBB.cmake
-@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
- ##################################
-
- if(TBB_INCLUDE_DIRS)
-- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
- string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
- TBB_VERSION_MAJOR "${_tbb_version_file}")
- string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
-diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
-index d32e131..1b5cbf2 100755
---- a/scripts/fetchPufferfish.sh
-+++ b/scripts/fetchPufferfish.sh
-@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
- EXTERNAL_DIR=${CURR_DIR}/../external
- INSTALL_DIR=${CURR_DIR}/../external/install
-
--if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
-- rm -fr ${EXTERNAL_DIR}/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
-- rm -fr ${INSTALL_DIR}/include/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
-- rm -fr ${INSTALL_DIR}/src/pufferfish
--fi
--
- SVER=salmon-v1.6.0
- #SVER=develop
- #SVER=sketch-mode
-@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
- EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
-
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
--
--hashcheck=""
--if exists sha256sum; then
-- hashcheck="sha256sum"
--elif exists shasum; then
-- hashcheck="shasum -a256"
--else
-- unset hashcheck
--fi
--
--if [ -z "${hashcheck-}" ]; then
-- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
--else
-- if [[ $SVER != develop ]]; then
-- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
-- else
-- echo "not testing sha since pulling from develop"
-- fi
--fi
--
--
--rm -fr ${EXTERNAL_DIR}/pufferfish
--unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
-
- mkdir -p ${INSTALL_DIR}/include/pufferfish
-
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
deleted file mode 100644
index 1907254d6..000000000
--- a/sci-biology/salmon/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
- <upstream>
- <remote-id type="github">COMBINE-lab/salmon</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
deleted file mode 100644
index c3ef9e50a..000000000
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
- https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
- https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
- https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
- https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
- https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
- "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
- "${FILESDIR}"/salmon-0.10.2_fix_tests.patch
- "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-RDEPEND="${DEPEND}"
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-# https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
-#
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- app-arch/xz-utils
- dev-libs/boost:0=
- dev-libs/libdivsufsort
- sci-biology/bwa
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
-"
-RDEPEND="${DEPEND}"
-BDEPEND="
- net-misc/curl
- app-arch/unzip
-"
-
-src_prepare() {
- # use system libs
- sed -i \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \
- -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \
- src/CMakeLists.txt || die
-
- cmake_src_prepare
-}
diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
deleted file mode 100644
index 6c19ff58f..000000000
--- a/sci-biology/salmon/salmon-1.6.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="
- https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
- https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
-"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-libs/boost:=
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- dev-libs/cereal
- sci-libs/io_lib[static-libs]
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
-
-PATCHES=(
- "${FILESDIR}/${P}-find-boost.patch"
-)
-
-src_unpack() {
- default
- mkdir -p "${S}/external/install/lib" || die
- mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
- mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
- ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
- ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
- ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
- -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
- -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DFETCH_BOOST=FALSE
- -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
- -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
- -DBoost_ALL_FOUND=TRUE
- -Dboost_headers_FOUND=TRUE
- -DBoost_FOUND=TRUE
- )
- cmake_src_configure
-}
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index aed6061e7..a20c63f61 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1 prefix
diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml
index 138cb7705..a2d91d1c4 100644
--- a/sci-biology/seqtk/metadata.xml
+++ b/sci-biology/seqtk/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">lh3/seqtk</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml
index ae9640ffb..d888971d1 100644
--- a/sci-biology/spm/metadata.xml
+++ b/sci-biology/spm/metadata.xml
@@ -5,4 +5,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">spm/spm12</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
deleted file mode 100644
index 13f7d3536..000000000
--- a/sci-biology/staden/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a
diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
-
- getABIdate: $(OBJSD)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-
- getABIcomment: $(OBJSC)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
-
- alfsplit: $(ALFOBJ)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-
- RSOBJ = $(ALFBIN)/2rs.o
-
diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">staden</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
deleted file mode 100644
index a0f91720b..000000000
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
- app-arch/xz-utils
- dev-lang/tk:0=
- dev-tcltk/tklib
- media-libs/libpng:0
- sci-biology/samtools:0
- >=sci-libs/io_lib-1.13.8
- sys-libs/zlib"
-RDEPEND="${DEPEND}
- >=dev-tcltk/iwidgets-4.0
- tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )
- net-misc/curl
- doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
-
-PATCHES=(
- "${FILESDIR}/${P}-ldflags.patch"
-)
-
-src_prepare() {
- default
- sed \
- -e 's:svnversion:false:' \
- -i configure.in || die
-}
-
-src_configure(){
- use debug && append-cflags "-DCACHE_REF_DEBUG"
- econf \
- $(use_enable X x) \
- $(use_enable amd64 64bit) \
- --with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-src_install() {
- default
- # install the LDPATH so that it appears in /etc/ld.so.conf after env-update
- # subsequently, apps linked against /usr/lib/staden can be run because
- # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
- # somehow for gap2caf, for example
- cat >> "${T}"/99staden <<- EOF
- STADENROOT="${EPREFIX}"/usr/share/staden
- LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
- EOF
- doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
- einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest
deleted file mode 100644
index 108aad2fe..000000000
--- a/sci-biology/staden_doc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden_doc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">staden</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
deleted file mode 100644
index 5a70701b0..000000000
--- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Documentation files for the staden package"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- dev-lang/perl
- app-text/texlive
- app-text/texi2html"
-BDEPEND="app-editors/emacs"
-RDEPEND="${DEPEND} ${BDEPEND}"
-
-S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
-
-# do not use texi2html-5 because it fails with:
-# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
-# Unknown option: index_char
-# src_prepare(){
-# default
-# # avoid running bundled texi2html code
-# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
-# }
-
-src_compile(){
- cd manual || die
- emake -j1 spotless || die
- cd .. || die
- emake -j1 unix PAPER=A4
-}
-
-src_install(){
- emake -j1 install prefix="${D}"/usr
- dodoc gkb547_gml.pdf
-}
diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 84b582151..c5f630a96 100644
--- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{10..10} )
DISTUTILS_USE_SETUPTOOLS=no
inherit distutils-r1
diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml
index 138cb7705..079fb5aae 100644
--- a/sci-biology/trans-abyss/metadata.xml
+++ b/sci-biology/trans-abyss/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">bcgsc/transabyss</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml
index 138cb7705..ac0e44aa7 100644
--- a/sci-biology/trim_galore/metadata.xml
+++ b/sci-biology/trim_galore/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">FelixKrueger/TrimGalore</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml
index a3daeebd2..36e8936e5 100644
--- a/sci-biology/ugene/metadata.xml
+++ b/sci-biology/ugene/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">ugeneunipro/ugene</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml
index eea62e858..996e48735 100644
--- a/sci-chemistry/erkale/metadata.xml
+++ b/sci-chemistry/erkale/metadata.xml
@@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core
(x-ray absorption and x-ray Raman scattering) and valence electron
excitation spectra of atoms and molecules.
</longdescription>
+ <upstream>
+ <remote-id type="github">susilehtola/erkale</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest
index 6aa383614..058ff2285 100644
--- a/sci-chemistry/relion/Manifest
+++ b/sci-chemistry/relion/Manifest
@@ -1 +1 @@
-DIST relion-3.1.1.tar.gz 2340685 BLAKE2B 0e98db3af7ceb312111260d8af51225d9a6b82314f1f066fe52464b533e59f44f5487ba66110708d661506074be4d52eeb7e04d88344a939bbd33139a33f6dec SHA512 fddf6f8a3d63e4f73aa1f529e4fa8fa7da98d9226b6539530c83496b94793ceef27d013a2d902a794993ab994f8d6467569ea4b681b4dd948654acf482529b22
+DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209
diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch
new file mode 100644
index 000000000..d7cb7bf2e
--- /dev/null
+++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch
@@ -0,0 +1,39 @@
+From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001
+From: Takanori Nakane <nakane.t@gmail.com>
+Date: Fri, 28 Oct 2022 19:51:29 +0900
+Subject: [PATCH] Repaired the build failure reported in #826 (by
+ @prehensilecode and @acaprez)
+
+---
+ src/apps/CMakeLists.txt | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt
+index 9870b735..30985aa7 100644
+--- a/src/apps/CMakeLists.txt
++++ b/src/apps/CMakeLists.txt
+@@ -273,16 +273,16 @@ if (CUDA_FOUND)
+
+
+
+- file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" )
++ file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu")
+ cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC})
+
+- #list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
+- #if(BUILD_SHARED_LIBS)
+- # install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
+- #else()
+- # target_link_libraries(relion_jaz_gpu_util relion_lib)
+- # target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+- #endif()
++ list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
++ if(BUILD_SHARED_LIBS)
++ install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
++ else()
++ target_link_libraries(relion_jaz_gpu_util relion_lib)
++ target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
++ endif()
+
+ target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+ target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY})
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
index cdabe7f2c..33e6e7e5d 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -12,4 +12,7 @@
<use>
<flag name="gui">Enable relion gui</flag>
</use>
+ <upstream>
+ <remote-id type="github">3dem/relion</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild
index 39e4ab229..a40375f64 100644
--- a/sci-chemistry/relion/relion-3.1.1.ebuild
+++ b/sci-chemistry/relion/relion-4.0.0.ebuild
@@ -1,7 +1,7 @@
# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake
@@ -12,10 +12,11 @@ SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+gui"
+IUSE="+gui cuda"
DEPEND="
gui? ( x11-libs/fltk )
+ cuda? ( dev-util/nvidia-cuda-toolkit )
dev-cpp/tbb
sci-libs/fftw:3.0
media-libs/tiff
@@ -27,6 +28,8 @@ RDEPEND="
"
BDEPEND="${DEPEND}"
+PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" )
+
src_configure() {
CMAKE_BUILD_TYPE=Release
mycmakeargs=(
@@ -35,7 +38,7 @@ src_configure() {
-DFORCE_OWN_FFTW=OFF
-DFORCE_OWN_FLTK=OFF
-DFORCE_OWN_TBB=OFF
- -DCUDA=OFF
+ -DCUDA=$(usex cuda)
-DGUI=$(usex gui)
)
cmake_src_configure
diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
index 753464ee5..a171606a6 100644
--- a/sci-libs/HDF5Plugin-Zstandard/metadata.xml
+++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
@@ -5,4 +5,7 @@
<email>xgreenlandforwyy@gmail.com</email>
<name>Yiyang Wu</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
index b7a989641..1eb6c5de7 100644
--- a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
+++ b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
@@ -4,7 +4,7 @@
EAPI=8
COMMIT="5eafea4328f1631eab28b1a20e757d1f0e21f8a6"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit cmake flag-o-matic fortran-2 python-single-r1
diff --git a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
index c47095d79..98d68d25d 100644
--- a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
+++ b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_10 )
inherit distutils-r1
diff --git a/sci-libs/daal4py/Manifest b/sci-libs/daal4py/Manifest
new file mode 100644
index 000000000..411db4215
--- /dev/null
+++ b/sci-libs/daal4py/Manifest
@@ -0,0 +1,2 @@
+DIST daal4py-2021.7.1.tar.gz 13813511 BLAKE2B 2dfc04063974654295a51ca9b6ff2b03435e0346320d9db3b7b1cd7e23a983c91b02ac1e3d8e23f8bd04add2817f7765efb8728d2dc9433db9d4073a512ab2b1 SHA512 352ded5c6c1beacd55fac82cd1a2627b3adbf0de991f1ff57e7b8826a4f9ab6219c5bfe3ec558deb748766fb2ba00988919a40c0d50d37b18a7fe9053d422890
+DIST daal4py-2021.7.1_p20221209.tar.gz 13816841 BLAKE2B 276de5650ce94f253ef749da785406365da9b0fab030dc3edeeef242e8d254889e515420c0b466fd2f5af579ca44ed0b826c4fad1370724533dbbc2b5b0d70cc SHA512 7a6a5b14454e793a17e3b894c5c9c3524b5d1ac330a9f08dd94fc991258675b70e7cff63967b7030c0a2052cf80b7b0d228ea51c74181d424168c44dab0dbc03
diff --git a/sci-libs/daal4py/daal4py-2021.7.1.ebuild b/sci-libs/daal4py/daal4py-2021.7.1.ebuild
new file mode 100644
index 000000000..927e08437
--- /dev/null
+++ b/sci-libs/daal4py/daal4py-2021.7.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Python API to the oneAPI Data Analytics Library"
+HOMEPAGE="https://github.com/intel/scikit-learn-intelex"
+SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/scikit-learn-intelex-${PV}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-util/cmake
+ sys-devel/DPC++
+ test? (
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+
+DEPEND="
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/dpctl[${PYTHON_USEDEP}]
+ sci-libs/oneDAL
+ virtual/mpi
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${P}-dont-use-entire-include.patch"
+)
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl"
+ export MPIROOT="${ESYSROOT}/usr"
+ export DALROOT="${ESYSROOT}/usr"
+ # Parallel build is broken
+ export MAKEOPTS="-j1"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/sci-libs/daal4py/daal4py-2021.7.1_p20221209.ebuild b/sci-libs/daal4py/daal4py-2021.7.1_p20221209.ebuild
new file mode 100644
index 000000000..5e9722b4e
--- /dev/null
+++ b/sci-libs/daal4py/daal4py-2021.7.1_p20221209.ebuild
@@ -0,0 +1,59 @@
+# 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
+
+COMMIT="b25ec56dad5672484334ceba9c0ef57fab26b406"
+
+DESCRIPTION="Python API to the oneAPI Data Analytics Library"
+HOMEPAGE="https://github.com/intel/scikit-learn-intelex"
+SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/scikit-learn-intelex-${COMMIT}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-util/cmake
+ sys-devel/DPC++
+ test? (
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+
+DEPEND="
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/dpctl[${PYTHON_USEDEP}]
+ sci-libs/oneDAL
+ virtual/mpi
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${P}-dont-use-entire-include.patch"
+)
+
+python_prepare_all() {
+ # DPC++ compiler required for full functionality
+ export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+ export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+ export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+ export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl:${ESYSROOT}/usr/lib/llvm/intel/include/sycl/CL/sycl"
+ export MPIROOT="${ESYSROOT}/usr"
+ export DALROOT="${ESYSROOT}/usr"
+ # Parallel build is broken
+ export MAKEOPTS="-j1"
+
+ distutils-r1_python_prepare_all
+}
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
new file mode 100644
index 000000000..5d3754d56
--- /dev/null
+++ b/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
@@ -0,0 +1,69 @@
+diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
+index 203c870..7fdac1e 100755
+--- a/generator/gen_daal4py.py
++++ b/generator/gen_daal4py.py
+@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
+ enum_maps, enum_params, wrap_algo, result_to_compute)
+ from .wrapper_gen import wrapper_gen
+ from .format import mk_var
+-from shutil import copytree, rmtree
++from shutil import copytree, copyfile, rmtree
+ from subprocess import call
+
+ try:
+@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
+ head_path = jp("build", "include")
+ algo_path = jp(head_path, "algorithms")
+ rmtree(head_path, ignore_errors=True)
+- copytree(orig_path, head_path)
++ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
++ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
++ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
++ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
++ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
++ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
++ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
+ for (dirpath, dirnames, filenames) in os.walk(algo_path):
+ for filename in filenames:
+ call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
+diff --git a/scripts/build_backend.py b/scripts/build_backend.py
+index a252a1d..c36a312 100755
+--- a/scripts/build_backend.py
++++ b/scripts/build_backend.py
+@@ -116,10 +116,8 @@ def custom_build_cmake_clib(iface, cxx=None):
+ python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
+ numpy_include = np.get_include()
+
+- if iface == 'dpc':
+- cxx = 'dpcpp'
+- elif cxx is None:
+- raise RuntimeError('CXX compiler shall be specified')
++ if cxx is None:
++ cxx=os.environ.get('CXX')
+
+ cmake_args = [
+ "cmake",
+diff --git a/setup.py b/setup.py
+index 864ab5d..7eaa52f 100755
+--- a/setup.py
++++ b/setup.py
+@@ -47,7 +47,7 @@ if dal_root is None:
+
+ if 'linux' in sys.platform:
+ IS_LIN = True
+- lib_dir = jp(dal_root, 'lib', 'intel64')
++ lib_dir = jp(dal_root, 'lib64')
+ elif sys.platform == 'darwin':
+ IS_MAC = True
+ lib_dir = jp(dal_root, 'lib')
+@@ -306,8 +306,8 @@ def build_oneapi_backend():
+ eca, ela, includes = get_build_options()
+
+ return build_backend.build_cpp(
+- cc='dpcpp',
+- cxx='dpcpp',
++ cc=os.environ.get('CC'),
++ cxx=os.environ.get('CXX'),
+ sources=['src/oneapi/oneapi_backend.cpp'],
+ targetname='oneapi_backend',
+ targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
new file mode 100644
index 000000000..9ccf0f156
--- /dev/null
+++ b/