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-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild2
-rw-r--r--dev-java/scijava-common/Manifest2
-rw-r--r--dev-java/scijava-common/scijava-common-2.97.1.ebuild (renamed from dev-java/scijava-common/scijava-common-2.94.2.ebuild)17
-rw-r--r--dev-java/scijava-common/scijava-common-9999.ebuild17
-rw-r--r--dev-libs/simclist/simclist-1.6_p1.ebuild2
-rw-r--r--dev-python/boost-histogram/Manifest1
-rw-r--r--dev-python/boost-histogram/boost-histogram-1.4.0.ebuild39
-rw-r--r--dev-python/boost-histogram/metadata.xml19
-rw-r--r--dev-python/ccdproc/ccdproc-2.3.0.ebuild2
-rw-r--r--dev-python/colormath/Manifest1
-rw-r--r--dev-python/colormath/colormath-3.0.0.ebuild23
-rw-r--r--dev-python/colormath/metadata.xml12
-rw-r--r--dev-python/dandi-schema/Manifest4
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild (renamed from dev-python/dandi-schema/dandi-schema-0.7.1.ebuild)4
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.8.4.ebuild (renamed from dev-python/dandi-schema/dandi-schema-0.8.2.ebuild)4
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.9.1.ebuild (renamed from dev-python/dandi-schema/dandi-schema-0.8.3.ebuild)19
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch10
-rw-r--r--dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch13
-rw-r--r--dev-python/dpctl/dpctl-0.14.1_rc2.ebuild4
-rw-r--r--dev-python/dpctl/dpctl-0.14.5.ebuild4
-rw-r--r--dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch82
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch21
-rw-r--r--dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch47
-rw-r--r--dev-python/dpnp/dpnp-0.11.1_rc1.ebuild4
-rw-r--r--dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch97
-rw-r--r--dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch80
-rw-r--r--dev-python/fslpy/files/fslpy-2.7.0-coverage.patch16
-rw-r--r--dev-python/gammapy/gammapy-1.0.ebuild2
-rw-r--r--dev-python/hdmf-zarr/Manifest1
-rw-r--r--dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch28
-rw-r--r--dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild32
-rw-r--r--dev-python/hdmf-zarr/metadata.xml16
-rw-r--r--dev-python/hdmf/Manifest3
-rw-r--r--dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch10
-rw-r--r--dev-python/hdmf/files/hdmf-3.3.2-versions.patch20
-rw-r--r--dev-python/hdmf/files/hdmf-3.5.0-open_links.patch170
-rw-r--r--dev-python/hdmf/hdmf-3.11.0.ebuild (renamed from dev-python/hdmf/hdmf-3.4.7.ebuild)11
-rw-r--r--dev-python/hdmf/hdmf-3.5.0_p1.ebuild37
-rw-r--r--dev-python/heudiconv/Manifest2
-rw-r--r--dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch24
-rw-r--r--dev-python/heudiconv/heudiconv-1.0.0.ebuild (renamed from dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild)6
-rw-r--r--dev-python/jacobi/Manifest1
-rw-r--r--dev-python/jacobi/jacobi-0.8.1.ebuild24
-rw-r--r--dev-python/jacobi/metadata.xml21
-rw-r--r--dev-python/llvmlite/Manifest1
-rw-r--r--dev-python/llvmlite/llvmlite-0.41.0.ebuild57
-rw-r--r--dev-python/lzstring/Manifest1
-rw-r--r--dev-python/lzstring/lzstring-1.0.4.ebuild16
-rw-r--r--dev-python/lzstring/metadata.xml12
-rw-r--r--dev-python/neo/Manifest1
-rw-r--r--dev-python/neo/neo-0.12.0.ebuild57
-rw-r--r--dev-python/nptyping/Manifest1
-rw-r--r--dev-python/nptyping/metadata.xml15
-rw-r--r--dev-python/nptyping/nptyping-2.5.0.ebuild66
-rw-r--r--dev-python/numcodecs/Manifest1
-rw-r--r--dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild43
-rw-r--r--dev-python/pandas-stubs/Manifest1
-rw-r--r--dev-python/pandas-stubs/metadata.xml16
-rw-r--r--dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild52
-rw-r--r--dev-python/photutils/photutils-1.6.0.ebuild2
-rw-r--r--dev-python/plac/Manifest2
-rw-r--r--dev-python/plac/plac-1.4.2.ebuild (renamed from dev-python/plac/plac-1.3.5.ebuild)7
-rw-r--r--dev-python/probeinterface/Manifest1
-rw-r--r--dev-python/probeinterface/probeinterface-0.2.20.ebuild37
-rw-r--r--dev-python/pyaml-env/Manifest1
-rw-r--r--dev-python/pyaml-env/metadata.xml12
-rw-r--r--dev-python/pyaml-env/pyaml-env-1.2.1.ebuild22
-rw-r--r--dev-python/pynwb/Manifest3
-rw-r--r--dev-python/pynwb/files/pynwb-2.0.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.1.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.2.0-versions.patch21
-rw-r--r--dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch54
-rw-r--r--dev-python/pynwb/files/pynwb-2.3.1-typing.patch13
-rw-r--r--dev-python/pynwb/pynwb-2.2.0-r1.ebuild56
-rw-r--r--dev-python/pynwb/pynwb-2.5.0.ebuild (renamed from dev-python/pynwb/pynwb-2.3.1-r1.ebuild)16
-rw-r--r--dev-python/pyout/Manifest2
-rw-r--r--dev-python/pyout/pyout-0.7.3.ebuild (renamed from dev-python/pyout/pyout-0.7.1-r1.ebuild)12
-rw-r--r--dev-python/rich-click/Manifest1
-rw-r--r--dev-python/rich-click/metadata.xml12
-rw-r--r--dev-python/rich-click/rich-click-1.7.2.ebuild25
-rw-r--r--dev-python/snakemake/Manifest2
-rw-r--r--dev-python/snakemake/snakemake-7.32.4.ebuild (renamed from dev-python/snakemake/snakemake-7.32.3.ebuild)1
-rw-r--r--dev-python/spectra/Manifest1
-rw-r--r--dev-python/spectra/metadata.xml12
-rw-r--r--dev-python/spectra/spectra-0.0.11.ebuild22
-rw-r--r--dev-python/spikeinterface/Manifest1
-rw-r--r--dev-python/spikeinterface/spikeinterface-0.99.1.ebuild53
-rw-r--r--dev-python/typish/typish-1.9.3.ebuild2
-rw-r--r--dev-python/vector/Manifest1
-rw-r--r--dev-python/vector/metadata.xml19
-rw-r--r--dev-python/vector/vector-1.1.1.ebuild20
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-includes.patch16
-rw-r--r--dev-python/xgboost/Manifest1
-rw-r--r--dev-python/xgboost/xgboost-2.0.3.ebuild27
-rw-r--r--dev-python/yte/Manifest2
-rw-r--r--dev-python/yte/yte-1.5.4.ebuild (renamed from dev-python/yte/yte-1.5.1.ebuild)4
-rw-r--r--dev-python/zarr/Manifest3
-rw-r--r--dev-python/zarr/zarr-2.14.2.ebuild (renamed from dev-python/zarr/zarr-2.11.3.ebuild)0
-rw-r--r--dev-python/zarr/zarr-2.16.1.ebuild61
-rw-r--r--dev-vcs/dandi-cli/Manifest4
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild)20
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.59.1.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild)23
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch46
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch13
-rw-r--r--dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch40
-rw-r--r--dev-vcs/datalad/Manifest2
-rw-r--r--dev-vcs/datalad/datalad-0.19.6.ebuild (renamed from dev-vcs/datalad/datalad-0.18.0.ebuild)4
-rw-r--r--dev-vcs/datalad/metadata.xml1
-rw-r--r--licenses/GSL221
-rw-r--r--media-gfx/brlcad/brlcad-7.32.4.ebuild2
-rw-r--r--media-gfx/brlcad/brlcad-9999.ebuild2
-rw-r--r--media-libs/imglib2/Manifest2
-rw-r--r--media-libs/imglib2/imglib2-6.3.0.ebuild (renamed from media-libs/imglib2/imglib2-6.2.0.ebuild)2
-rw-r--r--media-libs/imglib2/imglib2-9999.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.0.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.1.ebuild2
-rw-r--r--media-libs/mmg/mmg-5.5.2.ebuild2
-rw-r--r--profiles/desc/lhapdf_sets.desc17
-rw-r--r--profiles/make.defaults1
-rw-r--r--profiles/package.mask11
-rw-r--r--sci-biology/SPAdes/Manifest8
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.5.ebuild (renamed from sci-biology/SPAdes/SPAdes-3.15.3.ebuild)10
-rw-r--r--sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch49
-rw-r--r--sci-biology/SPAdes/metadata.xml11
-rw-r--r--sci-biology/ants/files/ants-2.4.1-fix-compile.patch13
-rw-r--r--sci-biology/brkraw/Manifest1
-rw-r--r--sci-biology/brkraw/brkraw-0.3.11.ebuild36
-rw-r--r--sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch11
-rw-r--r--sci-biology/brkraw/metadata.xml (renamed from sci-biology/clview/metadata.xml)11
-rw-r--r--sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch30
-rw-r--r--sci-biology/clview/Manifest2
-rw-r--r--sci-biology/clview/clview-0.1.ebuild108
-rw-r--r--sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild5
-rw-r--r--sci-biology/fastp/Manifest1
-rw-r--r--sci-biology/fastp/fastp-0.23.4.ebuild20
-rw-r--r--sci-biology/fastp/metadata.xml11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch12
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch21
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch10
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-setup.patch198
-rw-r--r--sci-biology/gffcompare/files/Makefile.patch79
-rw-r--r--sci-biology/imagej/Manifest5
-rw-r--r--sci-biology/imagej/imagej-1.53t.ebuild122
-rw-r--r--sci-biology/imagej/imagej-1.54h-r1.ebuild (renamed from sci-biology/imagej/imagej-1.54f.ebuild)4
-rw-r--r--sci-biology/imagej/imagej-9999.ebuild4
-rw-r--r--sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild2
-rw-r--r--sci-biology/libBigWig/Manifest1
-rw-r--r--sci-biology/libBigWig/libBigWig-0.4.7.ebuild31
-rw-r--r--sci-biology/multiqc/Manifest1
-rw-r--r--sci-biology/multiqc/metadata.xml12
-rw-r--r--sci-biology/multiqc/multiqc-1.19.ebuild40
-rw-r--r--sci-biology/neuroconv/Manifest1
-rw-r--r--sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild59
-rw-r--r--sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch39
-rw-r--r--sci-biology/nitime/Manifest1
-rw-r--r--sci-biology/nitime/metadata.xml6
-rw-r--r--sci-biology/nitime/nitime-0.10.2.ebuild33
-rw-r--r--sci-biology/nitime/nitime-9999.ebuild10
-rw-r--r--sci-biology/samri/samri-0.5.3.ebuild2
-rw-r--r--sci-biology/samri/samri-0.5.4.ebuild2
-rw-r--r--sci-biology/samri/samri-9999.ebuild2
-rw-r--r--sci-biology/snapgene-viewer/Manifest1
-rw-r--r--sci-biology/snapgene-viewer/metadata.xml12
-rw-r--r--sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild65
-rw-r--r--sci-biology/sra-tools/files/libs_sra_Makefile.patch77
-rw-r--r--sci-biology/sra-tools/files/sra_sdk-destdir.patch76
-rw-r--r--sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch12
-rw-r--r--sci-chemistry/chimera/Manifest1
-rw-r--r--sci-chemistry/chimera/chimera-1.17.3.ebuild93
-rw-r--r--sci-electronics/mpremote/Manifest1
-rw-r--r--sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch12
-rw-r--r--sci-electronics/mpremote/mpremote-1.22.0.ebuild29
-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.2.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.3.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.8.0.ebuild2
-rw-r--r--sci-libs/asl/asl-0.1.7.ebuild2
-rw-r--r--sci-libs/asl/asl-9999.ebuild2
-rw-r--r--sci-libs/daal4py/daal4py-2023.0.2.ebuild2
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch69
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch72
-rw-r--r--sci-libs/gdcm/gdcm-3.0.14.ebuild2
-rw-r--r--sci-libs/handyg/files/handyg-0.1.5-ld.patch22
-rw-r--r--sci-libs/itk/itk-5.2.1-r2.ebuild2
-rw-r--r--sci-libs/itk/itk-5.3.0-r1.ebuild2
-rw-r--r--sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch11
-rw-r--r--sci-libs/nexus/nexus-4.4.3_p20200126.ebuild2
-rw-r--r--sci-libs/nibabel/Manifest2
-rw-r--r--sci-libs/nibabel/nibabel-5.1.0.ebuild (renamed from sci-libs/nibabel/nibabel-4.0.0.ebuild)10
-rw-r--r--sci-libs/nipy/Manifest2
-rw-r--r--sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild52
-rw-r--r--sci-libs/nipy/nipy-0.6.0.ebuild37
-rw-r--r--sci-libs/nipype/Manifest2
-rw-r--r--sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch50
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r1.ebuild1
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r2.ebuild (renamed from sci-libs/nipype/nipype-1.5.0.ebuild)22
-rw-r--r--sci-libs/nipype/nipype-1.8.6.ebuild97
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0001.patch16
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0002.patch105
-rw-r--r--sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch12
-rw-r--r--sci-mathematics/cipi/cipi-1.0-r1.ebuild51
-rw-r--r--sci-mathematics/cipi/files/cipi-1.0-boost.patch11
-rw-r--r--sci-mathematics/frama-c/files/ocamlgraph185_compat.patch254
-rw-r--r--sci-mathematics/ltl2ba/Manifest2
-rw-r--r--sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild31
-rw-r--r--sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild31
-rw-r--r--sci-mathematics/scilab-bin/Manifest1
-rw-r--r--sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild78
-rw-r--r--sci-misc/openfst/Manifest2
-rw-r--r--sci-misc/openfst/files/kaldi-openfst-1.4.1.patch269
-rw-r--r--sci-misc/openfst/files/kaldi.patch599
-rw-r--r--sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch83
-rw-r--r--sci-misc/openfst/metadata.xml4
-rw-r--r--sci-misc/openfst/openfst-1.8.2.ebuild (renamed from sci-misc/openfst/openfst-1.8.1.ebuild)4
-rw-r--r--sci-physics/hoppet/Manifest1
-rw-r--r--sci-physics/hoppet/hoppet-1.2.0.ebuild35
-rw-r--r--sci-physics/hoppet/metadata.xml19
-rw-r--r--sci-physics/lhapdf-sets/Manifest12
-rw-r--r--sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild66
-rw-r--r--sci-physics/lhapdf-sets/metadata.xml12
-rw-r--r--sci-physics/pyhepmc/Manifest1
-rw-r--r--sci-physics/pyhepmc/metadata.xml19
-rw-r--r--sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild20
-rw-r--r--sci-physics/pyhf/Manifest1
-rw-r--r--sci-physics/pyhf/metadata.xml18
-rw-r--r--sci-physics/pyhf/pyhf-0.7.3.ebuild35
-rw-r--r--sci-physics/tauola/tauola-1.1.8.ebuild2
-rw-r--r--sci-visualization/forge/forge-1.0.5.ebuild2
-rw-r--r--sci-visualization/forge/forge-1.0.7.ebuild2
-rw-r--r--sci-visualization/forge/forge-9999.ebuild2
-rw-r--r--sys-cluster/easybuild-easyblocks/Manifest1
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild36
-rw-r--r--sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild37
-rw-r--r--sys-cluster/easybuild-easyconfigs/Manifest1
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild34
-rw-r--r--sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild34
-rw-r--r--sys-cluster/easybuild-framework/Manifest1
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild40
-rw-r--r--sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild40
-rw-r--r--sys-cluster/easybuild/Manifest1
-rw-r--r--sys-cluster/easybuild/easybuild-4.9.0.ebuild40
-rw-r--r--sys-cluster/easybuild/easybuild-9999.ebuild40
-rw-r--r--sys-devel/DPC++/DPC++-2021.12.ebuild4
-rw-r--r--sys-devel/DPC++/DPC++-2022.09.ebuild4
-rw-r--r--sys-devel/DPC++/DPC++-2022.12.ebuild4
245 files changed, 2862 insertions, 3450 deletions
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 38e0dfbd0..e331bc6c9 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -20,7 +20,7 @@ RESTRICT="!test? ( test )"
BDEPEND="
${PYTHON_DEPS}
- doc? ( app-doc/doxygen[dot] )
+ doc? ( app-text/doxygen[dot] )
"
DEPEND="
boost? ( dev-libs/boost:= )
diff --git a/dev-java/scijava-common/Manifest b/dev-java/scijava-common/Manifest
index 093710215..51c68561b 100644
--- a/dev-java/scijava-common/Manifest
+++ b/dev-java/scijava-common/Manifest
@@ -1 +1 @@
-DIST scijava-common-2.94.2-sources.tar.gz 558014 BLAKE2B eb045006f96ee9eddd6413049162c8f99d90cf8c44b0c2bce916423eba6234241b6e8324b8ffc4300e228eb7e337d9b89e8f570bc744078c8e7859c0965dd46a SHA512 a56c0d957307ecd610b3b72dd98481118ca7a380f44662a6d1bae93d5dcd5d1bb55a630d9724403e6d16430d84a7e5452962d9dca06ddd97c30a4414672b2a86
+DIST scijava-common-2.97.1-sources.tar.gz 559336 BLAKE2B 4511202aaa7947a57a8fff6420397c05d5768571045519b9d02aa67a5b3ecefd738418d8412f447678d5133e089fa73bd335543979a58ae55b0e31e53eedc8ae SHA512 cf8e47097f608480c59b24d7487dbf1e138c16a63660aa3b5f5de4c600913e509b64e2d9360f7fdb6e5558a1320fb7d6f09bd3184e5e99da2c5265a91050002b
diff --git a/dev-java/scijava-common/scijava-common-2.94.2.ebuild b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
index f384bf8bd..37a9bca8d 100644
--- a/dev-java/scijava-common/scijava-common-2.94.2.ebuild
+++ b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
@@ -25,7 +25,7 @@ else
https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ MAVEN_ID="org.scijava:scijava-common:2.97.1"
KEYWORDS="~amd64"
fi
@@ -38,20 +38,19 @@ CDEPEND="
dev-java/jaxb-api:2
"
-BDEPEND="
+BDEPEND="${CDEPEND}
>=virtual/jdk-1.8:*
- ${CDEPEND}
+"
+
+DEPEND="${CDEPEND}
test? (
>=dev-java/junit-4.13.2
- >=dev-java/mockito-2.19.0:2
+ >=dev-java/mockito-4.11.0:4
)
"
-DEPEND="${CDEPEND}"
-
-RDEPEND="
+RDEPEND="${CDEPEND}
>=virtual/jre-1.8:*
- ${CDEPEND}
"
JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
@@ -61,7 +60,7 @@ JAVA_RESOURCE_DIRS=(
"src/main/resources"
)
-JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
JAVA_TEST_SRC_DIR="src/test/java"
JAVA_TEST_RESOURCE_DIRS=(
"src/test/resources"
diff --git a/dev-java/scijava-common/scijava-common-9999.ebuild b/dev-java/scijava-common/scijava-common-9999.ebuild
index f384bf8bd..37a9bca8d 100644
--- a/dev-java/scijava-common/scijava-common-9999.ebuild
+++ b/dev-java/scijava-common/scijava-common-9999.ebuild
@@ -25,7 +25,7 @@ else
https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="org.scijava:scijava-common:2.94.2"
+ MAVEN_ID="org.scijava:scijava-common:2.97.1"
KEYWORDS="~amd64"
fi
@@ -38,20 +38,19 @@ CDEPEND="
dev-java/jaxb-api:2
"
-BDEPEND="
+BDEPEND="${CDEPEND}
>=virtual/jdk-1.8:*
- ${CDEPEND}
+"
+
+DEPEND="${CDEPEND}
test? (
>=dev-java/junit-4.13.2
- >=dev-java/mockito-2.19.0:2
+ >=dev-java/mockito-4.11.0:4
)
"
-DEPEND="${CDEPEND}"
-
-RDEPEND="
+RDEPEND="${CDEPEND}
>=virtual/jre-1.8:*
- ${CDEPEND}
"
JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
@@ -61,7 +60,7 @@ JAVA_RESOURCE_DIRS=(
"src/main/resources"
)
-JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-2"
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
JAVA_TEST_SRC_DIR="src/test/java"
JAVA_TEST_RESOURCE_DIRS=(
"src/test/resources"
diff --git a/dev-libs/simclist/simclist-1.6_p1.ebuild b/dev-libs/simclist/simclist-1.6_p1.ebuild
index 2b7eb84f1..41c9151c5 100644
--- a/dev-libs/simclist/simclist-1.6_p1.ebuild
+++ b/dev-libs/simclist/simclist-1.6_p1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug doc dump hash threads"
-BDEPEND="doc? ( app-doc/doxygen )"
+BDEPEND="doc? ( app-text/doxygen )"
CMAKE_IN_SOURCE_BUILD=1
diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest
new file mode 100644
index 000000000..1fb711744
--- /dev/null
+++ b/dev-python/boost-histogram/Manifest
@@ -0,0 +1 @@
+DIST boost_histogram-1.4.0.tar.gz 1329002 BLAKE2B 1636ed04c5df2f6c156468ffc0fed7b82469bb903c316b1b9fd209b7072ebb5b0de9969f4f8b50da69db7ee40009df534959db7734f1161da2c6216bddce858b SHA512 e7f61cc2d013a0664646d9edf1f713eb5f06f000ad2105e90229ef9b01b25a08c8e717a2ac241ed990fa2c082a1bb84af18e17b238640de5679d0ab76ff08af6
diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
new file mode 100644
index 000000000..0336c4e87
--- /dev/null
+++ b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
@@ -0,0 +1,39 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python bindings for the C++14 Boost::Histogram library"
+HOMEPAGE="https://github.com/scikit-hep/boost-histogram"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-libs/boost:=[python,${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ dev-python/cloudpickle[${PYTHON_USEDEP}]
+ dev-python/hypothesis[${PYTHON_USEDEP}]
+ )
+"
+
+src_prepare() {
+ default
+ sed -i 's/"pytest-benchmark"//g' pyproject.toml || die
+}
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ tests/test_benchmark_1d.py
+ tests/test_benchmark_2d.py
+ tests/test_benchmark_category_axis.py
+ tests/test_pickle.py
+ tests/test_threaded_fill.py
+)
diff --git a/dev-python/boost-histogram/metadata.xml b/dev-python/boost-histogram/metadata.xml
new file mode 100644
index 000000000..345502cba
--- /dev/null
+++ b/dev-python/boost-histogram/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Python bindings for Boost::Histogram (source), a C++14 library. This is one of the fastest libraries for histogramming, while still providing the power of a full histogram object. See what's new.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">boost-histogram</remote-id>
+ <remote-id type="github">scikit-hep/boost-histogram</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
index 481ce2e7b..cdbe1c92c 100644
--- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild
+++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
@@ -28,7 +28,7 @@ RDEPEND="
>=dev-python/astropy-4.0.6[${PYTHON_USEDEP}]
>=dev-python/astroscrappy-1.0.8[${PYTHON_USEDEP}]
>=dev-python/reproject-0.7[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
diff --git a/dev-python/colormath/Manifest b/dev-python/colormath/Manifest
new file mode 100644
index 000000000..82abf9e32
--- /dev/null
+++ b/dev-python/colormath/Manifest
@@ -0,0 +1 @@
+DIST colormath-3.0.0.tar.gz 39761 BLAKE2B 3c7cdd08336a3ab35618a79ad31717433c08b23d8ee4fc5484da7305395fce61fa442fc9ff979ff107808c56e809deca9d176677f17106651047be14edc27e9e SHA512 12d1ab931000dadb087fdf7e56280690ff51a299e976347026703eac83373edcacd3310255fd52e05d842aab54d4f7d3ed19deda8db4b78574a7273f1c8cc058
diff --git a/dev-python/colormath/colormath-3.0.0.ebuild b/dev-python/colormath/colormath-3.0.0.ebuild
new file mode 100644
index 000000000..8bd5a2b02
--- /dev/null
+++ b/dev-python/colormath/colormath-3.0.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/colormath/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]"
+
+# Nose test no longer supported
+RESTRICT="test"
+#distutils_enable_tests nose
diff --git a/dev-python/colormath/metadata.xml b/dev-python/colormath/metadata.xml
new file mode 100644
index 000000000..a633acfa0
--- /dev/null
+++ b/dev-python/colormath/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">gtaylor/python-colormath</remote-id>
+ <remote-id type="pypi">colormath</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
index c33eb24f9..73fc34f40 100644
--- a/dev-python/dandi-schema/Manifest
+++ b/dev-python/dandi-schema/Manifest
@@ -1,3 +1,3 @@
-DIST dandi-schema-0.7.1.gh.tar.gz 57312 BLAKE2B 5aa77c4c98633f82511a964f0b202b44acdb63e162cff62785f44fab64fdf97c04f10b10b3c1329ea7176d7ee1b12eeabd64d467d9646550b1db14b2fcc36a2b SHA512 04e0bf6caa9183cdac021430869be884ba8db207e7056a145ecac11858e9ecf051212cee10f5b4d501ca513838edc112dde014e256ab2256729c810d0c2c6cdf
-DIST dandi-schema-0.8.2.gh.tar.gz 57936 BLAKE2B 2ba355137196b805214e6c9321dd0b8dd9f5f1a39cf732aa3733b51a90f043d39a003e46620e1ec4bf77654cf21a7a45e9d888321b2ceb59f33a52c75db11597 SHA512 b792b5bdc6c51dc63ab796997e3b61cbb3ae3b0dbc5d1c55c51e1c879d1a694e3fc6a89640ac26909399bc63a2a3480c7ef630952cac44a3bb5a27d7fe11d09e
DIST dandi-schema-0.8.3.gh.tar.gz 58040 BLAKE2B 03313fa126eb8805b72de6431e7cb1489aeb54f7415c4ee0899f012881147dd612d2736f27df4c4e314951b589d4167bda17a5144d7346b6371ed3e7160aa50f SHA512 4e9ed27a773e8609a16d841c5c3876026fa1ab6fccb688f6477e1c95f3da72bc99f7bb987799da69948036f0922ed33ed7c096bdc5be6c59b9a74a266ffd47b2
+DIST dandi-schema-0.8.4.gh.tar.gz 58421 BLAKE2B e1fa0f0eed0a01c420769bed63ea99f7cf9868f036028e7ee60dcc5425946dad5e06ce99b7cb319bb52bc37fd823433aeef63d9490d573f15d72782e01e00145 SHA512 1fd3ae88c3115bf89e3fddc0c2bb5c283714f0051e8c59620b36291f49dd26e6871c810de8148c8a3b5ba1209bc4d53ef75aa32d338cbe097bb498676551fb73
+DIST dandi-schema-0.9.1.gh.tar.gz 61794 BLAKE2B f18dda919dad9a685793d075e54c798fd9a0d68926b776f1f5617d414554fed7609684dab3311d35056f385443037f03ab16f7edfb7b57c33f9da1aed9c8016c SHA512 c6ed9763a5a77b8741063ef5f311a889e7e0ba2ef02ab97e2912e1a129da503453d9ccb1b9ed13726f071594af42e564986ef9298b21c07cff6ef48eb3f58fc1
diff --git a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild
index 6f026c947..8a2978c99 100644
--- a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.8.3-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1
@@ -19,7 +19,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
+ <dev-python/pydantic-2[${PYTHON_USEDEP}]
dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.4.ebuild
index 6f026c947..8a2978c99 100644
--- a/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.8.4.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1
@@ -19,7 +19,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
+ <dev-python/pydantic-2[${PYTHON_USEDEP}]
dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
diff --git a/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
index 6f026c947..0e7986806 100644
--- a/dev-python/dandi-schema/dandi-schema-0.8.3.ebuild
+++ b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1
@@ -16,27 +16,34 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+# Package has pydantic version restriction (2.4*), which, however, breaks the test suite:
+# https://github.com/dandi/dandi-schema/issues/228
+# Commented failing tests with upstream version restriction listed below.
RDEPEND="
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/pydantic[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-2.5[${PYTHON_USEDEP}]
dev-python/email-validator[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+ "${FILESDIR}/${P}-coverage.patch"
)
src_configure() {
echo "__version__ = '${PV}'" >> dandischema/_version.py
}
+#EPYTEST_DESELECT=(
+# "dandischema/tests/test_metadata.py::test_asset"
+# "dandischema/tests/test_metadata.py::test_aggregate[files1-summary1]"
+# "dandischema/tests/test_metadata.py::test_aggregate[files2-summary2]"
+#)
+
distutils_enable_tests pytest
python_test() {
export DANDI_TESTS_NONETWORK=1
- pushd dandischema || die
- epytest tests
- popd
+ epytest dandischema
}
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
deleted file mode 100644
index 589091756..000000000
--- a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/setup.py 2021-09-22 19:31:20.533576086 -0400
-+++ b/setup.py 2021-09-23 07:42:02.856983656 -0400
-@@ -21,7 +21,7 @@
-
- # Give setuptools a hint to complain if it's too old a version
- # Should match pyproject.toml
--SETUP_REQUIRES = ["setuptools >= 42.0.0", "versioningit ~= 0.1.0"]
-+SETUP_REQUIRES = ["setuptools >= 42.0.0"]
- # This enables setuptools to install wheel on-the-fly
- SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
new file mode 100644
index 000000000..7f9b7dba0
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
@@ -0,0 +1,13 @@
+diff --git a/tox.ini b/tox.ini
+index c32f3b9..d552c6c 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -30,7 +30,7 @@ commands =
+ mypy dandischema
+
+ [pytest]
+-addopts = --cov=dandischema --tb=short --durations=10
++addopts = --tb=short --durations=10
+ filterwarnings =
+ error
+ # <https://github.com/dateutil/dateutil/issues/1284>
diff --git a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
index 65526b110..4ef429b97 100644
--- a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
+++ b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -21,7 +21,7 @@ BDEPEND="
dev-python/scikit-build[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
dev-vcs/git
sys-devel/DPC++
"
diff --git a/dev-python/dpctl/dpctl-0.14.5.ebuild b/dev-python/dpctl/dpctl-0.14.5.ebuild
index 65526b110..4ef429b97 100644
--- a/dev-python/dpctl/dpctl-0.14.5.ebuild
+++ b/dev-python/dpctl/dpctl-0.14.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -21,7 +21,7 @@ BDEPEND="
dev-python/scikit-build[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
dev-python/versioneer[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
dev-vcs/git
sys-devel/DPC++
"
diff --git a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
deleted file mode 100644
index b7dab5c75..000000000
--- a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 23ae1dd..e144e90 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -26,15 +26,7 @@ install(FILES ${_dpctl_capi_headers}
- # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
- include(GNUInstallDirs)
-
--# Fetch pybind11
--include(FetchContent)
--
--FetchContent_Declare(
-- pybind11
-- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.9.2.tar.gz
-- URL_HASH SHA256=6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1
--)
--FetchContent_MakeAvailable(pybind11)
-+include(/usr/share/cmake/pybind11/pybind11Config.cmake)
-
- add_subdirectory(dpctl)
-
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
deleted file mode 100644
index ac0301886..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-index 2929c33..731f054 100644
---- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-+++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
-@@ -26,76 +26,10 @@
-
- function(get_level_zero_headers)
-
-- if(EXISTS level-zero)
-- # Update the checkout
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} fetch
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not update Level Zero sources."
-- )
-- endif()
-- else()
-- # Clone the Level Zero git repo
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero."
-- )
-- endif()
-- endif()
--
-- # Use git describe to get latest tag name
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0
-- RESULT_VARIABLE result
-- OUTPUT_VARIABLE latest_tag
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not get the name for the latest release."
-- )
-- endif()
--
-- # Use git describe to get latest tag name
-- execute_process(
-- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag}
-- RESULT_VARIABLE result
-- ERROR_VARIABLE error
-- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- ERROR_STRIP_TRAILING_WHITESPACE
-- )
--
-- if(NOT result EQUAL 0)
-- message(FATAL_ERROR
-- "Could not checkout the latest release."
-- )
-- endif()
--
- # Populate the path to the headers
- find_path(LEVEL_ZERO_INCLUDE_DIR
- NAMES zet_api.h
-- PATHS ${CMAKE_BINARY_DIR}/level-zero/include
-+ PATHS /usr/include/level_zero
- NO_DEFAULT_PATH
- NO_CMAKE_ENVIRONMENT_PATH
- NO_CMAKE_PATH
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
deleted file mode 100644
index b2b8c5d81..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index da138c1..ecab139 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -28,15 +28,7 @@ install(FILES ${_dpctl_capi_headers}
- # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
- include(GNUInstallDirs)
-
--# Fetch pybind11
--include(FetchContent)
--
--FetchContent_Declare(
-- pybind11
-- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.1.tar.gz
-- URL_HASH SHA256=111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad
--)
--FetchContent_MakeAvailable(pybind11)
-+include(/usr/share/cmake/pybind11/pybind11Config.cmake)
-
- add_subdirectory(dpctl)
-
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
deleted file mode 100644
index 44b950cb6..000000000
--- a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From d0d3e6f1a9ffbac91f24cc06abce6dcad6509a6b Mon Sep 17 00:00:00 2001
-From: Julien Jerphanion <git@jjerphan.xyz>
-Date: Tue, 6 Dec 2022 10:24:26 +0100
-Subject: [PATCH 1/2] MAINT Include tuple in 'utils/strided_iters.hpp'
-
-This include directive seems to have been forgotten and it is impossible
-for me to compile dpctl without it.
----
- dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-index c24ed54941..595ad3f4a7 100644
---- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-+++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-@@ -30,6 +30,7 @@
- #include <array>
- #include <numeric> // std::iota
- #include <vector>
-+#include <tuple>
-
- /* An N-dimensional array can be stored in a single
- * contiguous chunk of memory by contiguously laying
-
-From f75ccd8c8aeaae92f0cb03874f93be5e7a63a6a7 Mon Sep 17 00:00:00 2001
-From: Julien Jerphanion <git@jjerphan.xyz>
-Date: Tue, 6 Dec 2022 14:45:40 +0100
-Subject: [PATCH 2/2] Make clang-format happy
-
----
- dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-index 595ad3f4a7..0abd7f4f2a 100644
---- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-+++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp
-@@ -29,8 +29,8 @@
- #include <algorithm> // sort
- #include <array>
- #include <numeric> // std::iota
--#include <vector>
- #include <tuple>
-+#include <vector>
-
- /* An N-dimensional array can be stored in a single
- * contiguous chunk of memory by contiguously laying
diff --git a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
index 5443b2dfd..5d25d62d1 100644
--- a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
+++ b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
# Breaks library installation
#DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -19,7 +19,7 @@ KEYWORDS="~amd64"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
sys-devel/DPC++
"
diff --git a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
deleted file mode 100644
index deaa95d0b..000000000
--- a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-diff --git a/0.build.sh b/0.build.sh
-index c089b1d..3bb0739 100755
---- a/0.build.sh
-+++ b/0.build.sh
-@@ -10,14 +10,14 @@ python setup.py clean
- DPLROOT=/opt/intel/oneapi/dpl/latest python setup.py build_clib
-
- # inplace build
--CC=dpcpp python setup.py build_ext --inplace
-+CC=${CC} python setup.py build_ext --inplace
-
- # development build. Root privileges needed
- # python setup.py develop
-
- echo
- echo =========example3==============
--dpcpp -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
-+${CXX} -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3
- # LD_DEBUG=libs,bindings,symbols ./example3
- ./example3
-
-diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
-index 81f073c..bcc4ecc 100644
---- a/dpnp/backend/CMakeLists.txt
-+++ b/dpnp/backend/CMakeLists.txt
-@@ -88,24 +88,6 @@ if (CMAKE_VERSION VERSION_EQUAL 3.19.1)
- )
- endif()
-
--if(UNIX)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # add_compile_options(-fPIC)
--elseif(WIN32)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
-- # set(CMAKE_LINKER "lld-link")
-- # include (Platform/Windows-Clang)
-- # set(CMAKE_LINKER "dpcpp")
-- # set(CMAKE_AR "llvm-ar")
-- # set(CMAKE_RANLIB "llvm-ranlib")
-- # set(CMAKE_CXX_FLAGS "/EHsc")
--
-- add_compile_options(/EHsc) # /Ox /W3 /GL /DNDEBUG /MD /EHsc
--else()
-- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
--endif()
--
- # set language version
- set(CMAKE_CXX_STANDARD 17)
- set(CMAKE_CXX_STANDARD_REQUIRED ON)
-@@ -280,6 +262,7 @@ endif()
- # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
-
- install(TARGETS dpnp_backend_c
-+ DESTINATION ${DPNP_INSTALL_PREFIX}
- PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
- )
-
-diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
-index dc9f322..35432fa 100644
---- a/utils/command_build_clib.py
-+++ b/utils/command_build_clib.py
-@@ -60,8 +60,8 @@ else:
- Set compiler for the project
- """
- # default variables (for Linux)
--_project_compiler = "dpcpp"
--_project_linker = "dpcpp"
-+_project_compiler = os.environ.get("CXX")
-+_project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel"]
- _project_cmplr_flag_sycl = ["-fsycl"]
- _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
-@@ -113,8 +113,8 @@ except ImportError:
-
- # other OS specific
- if IS_WIN:
-- _project_compiler = "dpcpp"
-- _project_linker = "lld-link"
-+ _project_compiler = os.environ.get("CXX")
-+ _project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl = []
- _project_cmplr_flag_stdcpp_static = []
- _project_cmplr_flag_compatibility = []
-diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
-index 0ef0e24..84f2469 100644
---- a/utils/command_build_cmake_clib.py
-+++ b/utils/command_build_cmake_clib.py
-@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
- "-S" + backend_directory,
- "-B" + abs_build_temp_path,
- "-DCMAKE_BUILD_TYPE=" + config,
-- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
-+ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
- "-DDPNP_INSTALL_STRUCTURED=OFF",
- # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
- "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
deleted file mode 100644
index 2ccc0a6b8..000000000
--- a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
-index 409a29f..11d21f1 100644
---- a/dpnp/backend/CMakeLists.txt
-+++ b/dpnp/backend/CMakeLists.txt
-@@ -98,30 +98,7 @@ string(CONCAT COMMON_LINK_FLAGS
- "-fsycl "
- "-fsycl-device-code-split=per_kernel "
- )
--if(UNIX)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # add_compile_options(-fPIC)
--elseif(WIN32)
-- set(CMAKE_CXX_COMPILER "dpcpp")
-- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
-- # set(CMAKE_LINKER "lld-link")
-- # include (Platform/Windows-Clang)
-- # set(CMAKE_LINKER "dpcpp")
-- # set(CMAKE_AR "llvm-ar")
-- # set(CMAKE_RANLIB "llvm-ranlib")
-- # set(CMAKE_CXX_FLAGS "/EHsc")
-
-- string(APPEND COMMON_COMPILER_FLAGS
-- "/EHsc "
--# "/Ox "
--# "/W3 "
--# "/GL "
--# "/DNDEBUG "
--# "/MD "
-- )
--else()
-- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
--endif()
-
- # set language version
- set(CMAKE_CXX_STANDARD 17)
-@@ -327,6 +304,7 @@ endif()
- # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
-
- install(TARGETS dpnp_backend_c
-+ DESTINATION ${DPNP_INSTALL_PREFIX}
- PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
- )
-
-diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
-index 3d1177b..d8fbdac 100644
---- a/utils/command_build_clib.py
-+++ b/utils/command_build_clib.py
-@@ -61,8 +61,8 @@ else:
- Set compiler for the project
- """
- # default variables (for Linux)
--_project_compiler = "dpcpp"
--_project_linker = "dpcpp"
-+_project_compiler = os.environ.get("CXX")
-+_project_linker = os.environ.get("CXX")
- _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func"]
- _project_cmplr_flag_sycl = ["-fsycl"]
- _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
-@@ -114,7 +114,7 @@ except ImportError:
-
- # other OS specific
- if IS_WIN:
-- _project_compiler = "dpcpp"
-+ _project_compiler = os.environ.get("CXX")
- _project_linker = "lld-link"
- _project_cmplr_flag_sycl = []
- _project_cmplr_flag_stdcpp_static = []
-diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
-index 0ef0e24..84f2469 100644
---- a/utils/command_build_cmake_clib.py
-+++ b/utils/command_build_cmake_clib.py
-@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
- "-S" + backend_directory,
- "-B" + abs_build_temp_path,
- "-DCMAKE_BUILD_TYPE=" + config,
-- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments
-+ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments
- "-DDPNP_INSTALL_STRUCTURED=OFF",
- # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
- "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch b/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch
deleted file mode 100644
index 3de6d92f1..000000000
--- a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/setup.cfg b/setup.cfg
-index 9ea1ddb..00eb59b 100644
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -18,8 +18,8 @@ markers =
-
-
- testpaths = tests
--addopts = -v --niters=50 --cov=fsl -m "not longtest"
-+addopts = -v --niters=50 -m "not longtest"
-
-
- [flake8]
--ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
-\ No newline at end of file
-+ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
diff --git a/dev-python/gammapy/gammapy-1.0.ebuild b/dev-python/gammapy/gammapy-1.0.ebuild
index ab50e7a85..6357014ed 100644
--- a/dev-python/gammapy/gammapy-1.0.ebuild
+++ b/dev-python/gammapy/gammapy-1.0.ebuild
@@ -47,7 +47,7 @@ pkg_postinst() {
optfeature "Plotting" dev-python/matplotlib
optfeature "Plotting Astronomical Images" dev-python/aplpy
optfeature "Read/write CVS files" dev-python/pandas
- optfeature "Image Processing" sci-libs/scikit-image
+ optfeature "Image Processing" dev-python/scikit-image
optfeature "Conversion helper functions" dev-python/rootpy
# In science overlay:
diff --git a/dev-python/hdmf-zarr/Manifest b/dev-python/hdmf-zarr/Manifest
new file mode 100644
index 000000000..6b7d2418b
--- /dev/null
+++ b/dev-python/hdmf-zarr/Manifest
@@ -0,0 +1 @@
+DIST hdmf_zarr-0.5.0.tar.gz 3095566 BLAKE2B f824b480bb99ffbf495b18505d561a3511af60f654df66f89c2c5c081ba49889512e29cb31b6eb617ef7abac58472fa4b6d9f23cd9c33be436a77ceb2d54130a SHA512 205dd5b2de1a403fc7098e7ba26e4bbba1949b8f50641173ea614011e821a77a461ab255f19afefddcd5fa019ed0e7c047fd7c940a2d09a1f63c5de5f1ac50cb
diff --git a/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
new file mode 100644
index 000000000..d82c30960
--- /dev/null
+++ b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
@@ -0,0 +1,28 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 4008b3b..40e281a 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -62,9 +62,6 @@ exclude = [".git_archival.txt"]
+ [tool.hatch.build.targets.wheel]
+ packages = ["src/hdmf_zarr"]
+
+-[tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+-
+ [tool.codespell]
+ skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
+ ignore-words-list = "datas"
+diff --git a/tox.ini b/tox.ini
+index 720a97f..66d0df3 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -28,8 +28,7 @@ commands =
+ [testenv:localcoverage]
+ basepython = python3.11
+ commands =
+- pytest --cov=hdmf_zarr
+- coverage html -d tests/coverage/htmlcov
++ pytest
+
+ # Test with python 3.11; pinned dev and optional reqs
+ [testenv:py311-optional]
diff --git a/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
new file mode 100644
index 000000000..692197867
--- /dev/null
+++ b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Zarr I/O backend for HDMF"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf-zarr"
+#SRC_URI="https://github.com/hdmf-dev/hdmf-zarr/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/numcodecs[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf-zarr/metadata.xml b/dev-python/hdmf-zarr/metadata.xml
new file mode 100644
index 000000000..1ced471a1
--- /dev/null
+++ b/dev-python/hdmf-zarr/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">hdmf-dev/hdmf-zarr</remote-id>
+ <remote-id type="pypi">hdmf-zarr</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest
index a8bb51f14..b2e716d9d 100644
--- a/dev-python/hdmf/Manifest
+++ b/dev-python/hdmf/Manifest
@@ -1,4 +1,3 @@
-DIST hdmf-3.4.7.tar.gz 319714 BLAKE2B 189b7629b818371bea002f4c340149e5807a5da9e2b27301574b74c50eda575b711ffbffac997ee2c2d25c30c926ada13d84319e054bf796e5bd74516d84be21 SHA512 c5b6b9dfeace0ea140bcd2cf822f9b45007ea7acefd6eca950b4b023731e31b8ebc592da0e3633e41a41e377a33565f6f5c04a88852a190816c95e89b49efa02
-DIST hdmf-3.5.0.tar.gz 324330 BLAKE2B 256fd974230fb750c5329fbf2cece0f151b6d7366aea26ffd08bafff0601ba6fde789dc906f4de5dbb1a02e9a0d21965a17eda76083df03d3a3afdacf9a7ba70 SHA512 8e1244f70c75f01d18d2d09b6c481efcab59bd02e69392f3da46d2e4541073fccaa9606907cee1ca0873221011e9ce8040668f2affd2ef4ee98fd35bd6356ff4
+DIST hdmf-3.11.0.tar.gz 15845296 BLAKE2B 4526496bd8290891a9058397c9916fce82667bc86541d55853525642ecd8a80ca6a60711bc0eb4ad637f2359ae9409f023da45c8e80aba0cbb9d8a4cf9009095 SHA512 1ec59990e30253036d367be0419c7bfd548866d3006cdc23785d01976621a8a4f86f7613d913084b1e12712f3a99b7e2fba80f197f72d9be8fb8e315073db522
DIST hdmf-3.5.1.tar.gz 324778 BLAKE2B b82d2389466be8e8b4acd843beaafe69b731a38045abab0a741fb7a6143e8ed8f60d570603629c7485f7f7a261047bcc9e21ebeb61802e6d81b35aa276d09af0 SHA512 1545f0c1c6b2bac66437941e631adaa45a42c18436ed68d5ee21a7cafe950a85e2843a4b2258b3f5c0ece5fd6d3ef6f0fd596a83bacd208750bfb5b78a1d5815
DIST hdmf-3.5.2.tar.gz 567466 BLAKE2B 99872885aec1b0aff30dfde17cc3c2f5f30e9da7f3ac5aa77dad203fe795ad6c207bdafd6d19548bf8c3f901a1ec8655b048d9ba41be11eaca3a7c55e6de2825 SHA512 47f8de397fe3defe814db3da7f2bf7ec3814bf3a1d9389c6fe823e229ddea441c97122e41a11883f1c7b5968a841d8fdd0c7314e9d82d4e5ea43a713a40afbfa
diff --git a/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
new file mode 100644
index 000000000..e44a68902
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
@@ -0,0 +1,10 @@
+--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml 2023-12-11 12:00:19.368474488 -0500
+@@ -76,7 +76,6 @@
+ # verbose = 1
+
+ [tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+ norecursedirs = "tests/unit/helpers"
+
+ [tool.codespell]
diff --git a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
deleted file mode 100644
index aaf62e115..000000000
--- a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/setup.py 2022-01-31 02:48:24.645837186 -0500
-+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
-@@ -18,12 +18,12 @@
- schema_dir = 'common/hdmf-common-schema/common'
-
- reqs = [
-- 'h5py>=2.10,<4',
-- 'jsonschema>=2.6.0,<5',
-- 'numpy>=1.16,<1.23',
-- 'pandas>=1.0.5,<2',
-- 'ruamel.yaml>=0.16,<1',
-- 'scipy>=1.1,<2',
-+ 'h5py',
-+ 'jsonschema',
-+ 'numpy',
-+ 'pandas',
-+ 'ruamel.yaml',
-+ 'scipy',
- 'setuptools',
- ]
diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
deleted file mode 100644
index 544bf8f4b..000000000
--- a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
+++ /dev/null
@@ -1,170 +0,0 @@
-From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 16:05:57 -0800
-Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to
- clsoe links
-
----
- src/hdmf/backends/hdf5/h5tools.py | 13 +++++++++----
- 1 file changed, 9 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index ba8946c60..acf2061ad 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -746,10 +746,15 @@ def close_linked_files(self):
- not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened,
- linked-to files.
- """
-- for obj in self.__open_links:
-- if obj:
-- obj.file.close()
-- self.__open_links = []
-+ # Make sure
-+ try:
-+ for obj in self.__open_links:
-+ if obj:
-+ obj.file.close()
-+ except AttributeError: # In case that self.__open_links does not exist on delete
-+ pass
-+ finally:
-+ self.__open_links = []
-
- @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the HDF5 file'},
- {'name': 'link_data', 'type': bool,
-
-From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 17:32:20 -0800
-Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error
-
----
- src/hdmf/backends/hdf5/h5tools.py | 19 +++++++++++++++----
- 1 file changed, 15 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index acf2061ad..75044a64a 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -736,8 +736,15 @@ def close(self, close_links=True):
- """
- if close_links:
- self.close_linked_files()
-- if self.__file is not None:
-- self.__file.close()
-+ try:
-+ if self.__file is not None:
-+ self.__file.close()
-+ except AttributeError:
-+ # Do not do anything in case that self._file does not exist. This
-+ # may happen in case that an error occurs before HDF5IO has been fully
-+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
-+ # and error before self.__file has been created
-+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__file")
-
- def close_linked_files(self):
- """Close all opened, linked-to files.
-@@ -751,8 +758,12 @@ def close_linked_files(self):
- for obj in self.__open_links:
- if obj:
- obj.file.close()
-- except AttributeError: # In case that self.__open_links does not exist on delete
-- pass
-+ except AttributeError:
-+ # Do not do anything in case that self.__open_links does not exist. This
-+ # may happen in case that an error occurs before HDF5IO has been fully
-+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
-+ # and error before self.__open_links has been created.
-+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__open_links.")
- finally:
- self.__open_links = []
-
-
-From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Wed, 18 Jan 2023 17:32:55 -0800
-Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called
- before HDF5IO.__init__ is complete
-
----
- tests/unit/test_io_hdf5_h5tools.py | 34 ++++++++++++++++++++++++++++++
- 1 file changed, 34 insertions(+)
-
-diff --git a/tests/unit/test_io_hdf5_h5tools.py b/tests/unit/test_io_hdf5_h5tools.py
-index 8c03e72f8..0f2f81e31 100644
---- a/tests/unit/test_io_hdf5_h5tools.py
-+++ b/tests/unit/test_io_hdf5_h5tools.py
-@@ -826,6 +826,40 @@ def test_constructor(self):
- self.assertEqual(io.manager, self.manager)
- self.assertEqual(io.source, self.path)
-
-+ def test_delete_with_incomplete_construction_missing_file(self):
-+ """
-+ Here we test what happens when close is called before HDF5IO.__init__ has
-+ bee completed. In this case self.__file is missing
-+ """
-+ class MyHDF5IO(HDF5IO):
-+ def __init__(self):
-+ raise ValueError("test error")
-+ with self.assertWarnsWith(warn_type=UserWarning,
-+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__file"):
-+ try:
-+ with MyHDF5IO() as _:
-+ pass
-+ except ValueError:
-+ pass
-+
-+ def test_delete_with_incomplete_construction_missing_open_files(self):
-+ """
-+ Here we test what happens when close is called before HDF5IO.__init__ has
-+ bee completed. In this case self.__open_file is missing
-+ """
-+
-+ class MyHDF5IO(HDF5IO):
-+ def __init__(self):
-+ raise ValueError("test error")
-+
-+ with self.assertWarnsWith(warn_type=UserWarning,
-+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__open_links."):
-+ try:
-+ with MyHDF5IO() as _:
-+ pass
-+ except ValueError:
-+ pass
-+
- def test_set_file_mismatch(self):
- self.file_obj = File(get_temp_filepath(), 'w')
- err_msg = ("You argued %s as this object's path, but supplied a file with filename: %s"
-
-From f79b3a26bdfaee22b8d24bd3094c93be77e5595f Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel <oruebel@lbl.gov>
-Date: Thu, 19 Jan 2023 13:54:33 -0800
-Subject: [PATCH 5/5] Move init of __file and __openlink up to prevent warning
- during close
-
----
- src/hdmf/backends/hdf5/h5tools.py | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
-index 75044a64a..44b9c612c 100644
---- a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -55,6 +55,9 @@ def __init__(self, **kwargs):
- path, manager, mode, comm, file_obj, driver = popargs('path', 'manager', 'mode', 'comm', 'file', 'driver',
- kwargs)
-
-+ self.__open_links = [] # keep track of other files opened from links in this file
-+ self.__file = None # This will be set below, but set to None first in case an error occurs and we need to close
-+
- if path is None and file_obj is None:
- raise ValueError("You must supply either a path or a file.")
-
-@@ -89,7 +92,6 @@ def __init__(self, **kwargs):
- self.__dci_queue = HDF5IODataChunkIteratorQueue() # a queue of DataChunkIterators that need to be exhausted
- ObjectMapper.no_convert(Dataset)
- self._written_builders = WriteStatusTracker() # track which builders were written (or read) by this IO object
-- self.__open_links = [] # keep track of other files opened from links in this file
-
- @property
- def comm(self):
diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild b/dev-python/hdmf/hdmf-3.11.0.ebuild
index 883b5b95b..2463ccc1a 100644
--- a/dev-python/hdmf/hdmf-3.4.7.ebuild
+++ b/dev-python/hdmf/hdmf-3.11.0.ebuild
@@ -3,13 +3,13 @@
EAPI=8
-DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_USE_PEP517=hatchling
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="The Hierarchical Data Modeling Framework"
HOMEPAGE="https://github.com/hdmf-dev/hdmf"
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
+SRC_URI="$(pypi_sdist_url hdmf)"
SLOT="0"
LICENSE="BSD"
@@ -23,6 +23,9 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
"
-BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${P}-no_test_coverage.patch"
+ )
distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
deleted file mode 100644
index 053831f8d..000000000
--- a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-MY_PV="${PV//_p*/}"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf"
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${MY_PV}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${MY_P}-open_links.patch"
-)
-
-distutils_enable_tests pytest
-
-S="${WORKDIR}/${MY_P}"
diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest
index e3afb5ed5..fe38a3307 100644
--- a/dev-python/heudiconv/Manifest
+++ b/dev-python/heudiconv/Manifest
@@ -1,2 +1,2 @@
-DIST heudiconv-0.11.6.tar.gz 9070519 BLAKE2B df6c66080bbaa89f74490f136674eabd64e9b2844ae7daef82ef4b4ef8c42ed16d3ae3b790534cc13ec121e63de8486838eb7e7becbcdbffff2df6e8bd2bd54c SHA512 c4d1f0caaed9713360ad2614bc276f2cc0e356c54b1b37c8912d762db429313c75d0f081886cb6ea0b8fd171bc5fc5a338fd3b670a8b10a3fbed0c6f9dfb7477
DIST heudiconv-0.13.0.tar.gz 9158053 BLAKE2B 9f87fbcd5ea8ccca39cc029f1bdd84906412a22e5d18e2afe280d19737f0dda4c03248ba93f58c06aae4b15366477e8a5d1c41d09d1b1d3a10ff673aaa050e26 SHA512 b867ee0a60ad98099a3802e290ebb24b858befbd45e93772fafe437a87ea867c5076680ea3ed7856272397267c740ef2eade9f64ffc0d4216d4a37be39add158
+DIST heudiconv-1.0.0.tar.gz 9158631 BLAKE2B af5b3dee2448a025a231fad0ac9692b13d431288ea0ca19b4919d9ae83c86a7c72cf11f9bd3a0ec6b18259d2f8e8cecf9372a0fae605ecb5e9cac0bd4975693a SHA512 165bd814e3c7f25b51ed8884bddde45b82dc226ee93af5984b822aa53ad5e7504aae57088cd1f777c62835669e8816d95dbf84de7fb379038308dca7871d8739
diff --git a/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch b/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch
deleted file mode 100644
index 23be6d000..000000000
--- a/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From 0c30781248e0c1f2d437e0dfd923a74d7e647411 Mon Sep 17 00:00:00 2001
-From: Horea Christian <chr@chymera.eu>
-Date: Wed, 1 Feb 2023 21:34:58 -0500
-Subject: [PATCH] Setting git author and email in test environment
-
----
- heudiconv/tests/conftest.py | 3 +++
- 1 file changed, 3 insertions(+)
- create mode 100644 heudiconv/tests/conftest.py
-
-diff --git /dev/null b/heudiconv/tests/conftest.py
-new file mode 100644
-index 00000000..f4f47d16
---- /dev/null
-+++ b/heudiconv/tests/conftest.py
-@@ -0,0 +1,8 @@
-+import os
-+import pytest
-+@pytest.fixture(autouse=True, scope="session")
-+def git_env():
-+ os.environ["GIT_AUTHOR_EMAIL"] = "maxm@example.com"
-+ os.environ["GIT_AUTHOR_NAME"] = "Max Mustermann"
-+ os.environ["GIT_COMMITTER_EMAIL"] = "maxm@example.com"
-+ os.environ["GIT_COMMITTER_NAME"] = "Max Mustermann"
diff --git a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
index 8dbfcfa0f..7f7db0b0e 100644
--- a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild
+++ b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
@@ -33,12 +33,6 @@ BDEPEND="
)
"
-# Patch sumbitted upstream, check if removal possible in next release:
-# https://github.com/nipy/heudiconv/pull/631
-PATCHES=(
- "${FILESDIR}/${P}-gitenv.patch"
-)
-
# Reported upstream:
# https://github.com/nipy/heudiconv/issues/679
EPYTEST_DESELECT=(
diff --git a/dev-python/jacobi/Manifest b/dev-python/jacobi/Manifest
new file mode 100644
index 000000000..984faa790
--- /dev/null
+++ b/dev-python/jacobi/Manifest
@@ -0,0 +1 @@
+DIST jacobi-0.8.1.tar.gz 997020 BLAKE2B ba54654e8a202976242674afa79de06d486d03c6d78b5566711df7df4ddcf5bbaa0e536eb9feeb0b0d6aaa9a444f677dfbbfa9928e38431aa9377c97132d4a26 SHA512 4a9a280cfae81926563c9736bf1805a3fe379809fe51421bdd0659651008d07d9f772df5006a1b796959311956822839791289eacb03af39823dd5a671b3845a
diff --git a/dev-python/jacobi/jacobi-0.8.1.ebuild b/dev-python/jacobi/jacobi-0.8.1.ebuild
new file mode 100644
index 000000000..404e8c2ca
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.8.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ tests/bench.py
+)
+
diff --git a/dev-python/jacobi/metadata.xml b/dev-python/jacobi/metadata.xml
new file mode 100644
index 000000000..ebbabb06c
--- /dev/null
+++ b/dev-python/jacobi/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Robustly compute the generalised Jacobi matrix for an arbitrary real analytic mapping ℝⁿ → ℝⁱ¹ × ... × ℝⁱⁿ
+ Returns error estimates for derivatives
+ Perform statistical error propagation based on numerically computed jacobian
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">jacobi</remote-id>
+ <remote-id type="github">HDembinski/jacobi</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
index ccc9695f0..ee0fc458a 100644
--- a/dev-python/llvmlite/Manifest
+++ b/dev-python/llvmlite/Manifest
@@ -1,2 +1,3 @@
DIST llvmlite-0.39.1.gh.tar.gz 237119 BLAKE2B c2538994a6b9116d9a124ad8b8fff9c06d654bcdd345fb25251505b7577c6dffdfa56c9226250dbc2de6253cf6154523ec0d3cd849697a66cabf5b522c5e76ca SHA512 16b341300e4034aff4ce9553fec6b5923b9f4cb261c1ec0ee2cef6d87addcbebe8f4805dbc2fb30f357800fa029c3b6fc8ed62a5fdaad7c262e723c3b9c4ad32
DIST llvmlite-0.40.1.gh.tar.gz 261765 BLAKE2B f795fc7e0256333a6f6172788fb839b0b3fd304b654baaa58cae53d5e5e145f6e937fcb83ed096a3885c060a03fbf1d8546007ea7fafaa4028cd21b5aee19bd1 SHA512 b88d931cf252169a9246d8c935fe28ad509fe7da1f8b1842c4b4c40808c64b68d47a2387ed4664c0c0812b39cfbfc30ea4f9e702a7cd893c4c61a3596bc2e697
+DIST llvmlite-0.41.0.gh.tar.gz 248547 BLAKE2B 3b5aa6b19e08d300384cedd123024d6c73368db255f2010cfbe4fa04e1e1f2d81e644db8b1c8540a5c1134d36c0fce333940c92f3ec984c239dc8c47537e8dca SHA512 bd84b754f07bfc82f9800e1e0a2bc965cfee0f726b4f06b21b8ca04a46c388bc4c423c4ed5f6e6b14562f5ff97e3f356022ad770ea1d351f0330277a4f350966
diff --git a/dev-python/llvmlite/llvmlite-0.41.0.ebuild b/dev-python/llvmlite/llvmlite-0.41.0.ebuild
new file mode 100644
index 000000000..595218e7c
--- /dev/null
+++ b/dev-python/llvmlite/llvmlite-0.41.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+inherit distutils-r1 llvm
+
+DESCRIPTION="Python wrapper around the llvm C++ library"
+HOMEPAGE="https://llvmlite.pydata.org/"
+SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz"
+S="${WORKDIR}/${P/_/}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="examples"
+
+LLVM_MAX_SLOT=14
+
+RDEPEND="
+ sys-devel/llvm:${LLVM_MAX_SLOT}
+ sys-libs/zlib:0=
+"
+DEPEND="${RDEPEND}"
+
+python_configure_all() {
+ # upstream's build system is just horrible, and they ignored the PR
+ # fixing it, so let's build the shared lib properly using implicit
+ # make rules
+
+ export LDLIBS=$(llvm-config --libs all)
+ export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
+ export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
+
+ local files=( ffi/*.cpp )
+ emake -f - <<EOF
+ffi/libllvmlite.so: ${files[*]/.cpp/.o}
+ \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
+EOF
+
+ export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
+}
+
+python_test() {
+ "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ if use examples; then
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
diff --git a/dev-python/lzstring/Manifest b/dev-python/lzstring/Manifest
new file mode 100644
index 000000000..f44e5e773
--- /dev/null
+++ b/dev-python/lzstring/Manifest
@@ -0,0 +1 @@
+DIST lzstring-1.0.4.tar.gz 4256 BLAKE2B e1a205f980de050635114e26a86d7251e0822a4459c44042291e80d55129d815f0753ff2b45a179fb468e9020a0a6255748566bc4e62fc98e7e041b07ae073f3 SHA512 0d61fe04402aaa5325d3ab555b9b83132048124a2ff11ae3a947a188d5507f1043b0522fcb7024009d75cf3efd3afbb64d24c238c4c2181346a823c77cb4ea02
diff --git a/dev-python/lzstring/lzstring-1.0.4.ebuild b/dev-python/lzstring/lzstring-1.0.4.ebuild
new file mode 100644
index 000000000..bfdb76a67
--- /dev/null
+++ b/dev-python/lzstring/lzstring-1.0.4.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="String encoding/decoding of binary data"
+HOMEPAGE="https://pypi.org/project/lzstring/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
diff --git a/dev-python/lzstring/metadata.xml b/dev-python/lzstring/metadata.xml
new file mode 100644
index 000000000..4dde9fdd9
--- /dev/null
+++ b/dev-python/lzstring/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">gkovacs/lz-string-python</remote-id>
+ <remote-id type="pypi">lzstring</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/neo/Manifest b/dev-python/neo/Manifest
index e3b133b9e..346e022b8 100644
--- a/dev-python/neo/Manifest
+++ b/dev-python/neo/Manifest
@@ -1,2 +1,3 @@
DIST neo-0.11.0.tar.gz 9411608 BLAKE2B 9257fd8ff9eea8ec80b0a4eb701b63a9db10d51e6f145b704eb5e9a394dd13a5c6e567cb3469fa4d86f538637f80e9c660823d358bb7ddfd651291dc5df73450 SHA512 dab4832317c8dc6a794ffc9fb118124734fa2428c0527eb9c86bc3d35195a34bdb162bc0a44a3604cb8067fff7263ab5b106c0f9871007a093e7185df5ba9993
DIST neo-0.11.1.tar.gz 3906151 BLAKE2B 26b60c715d6f3ec017cdb909c1f54b1509db4862f0630ab6d60b4b07153d5cb8512fbf16dd9039d1998b08e0f9e828bb271d4f482cc2d34a5d17a010ef4d203b SHA512 1f93a9eea020ee40f792f038bef76e053ff4f6e05951f78afa70bf4009bac3da8222be57c2cee88ae5e7539c5c8978cf50bf52cce787dbacafe6d5450d5e1aa7
+DIST neo-0.12.0.tar.gz 28377158 BLAKE2B efc6ae96d8cf8325355367af482d4e6dcc0dc3e3c5f3d449076a1c3ef32f530f777a2b125c946360b05a070cd75ae3f04b31a9e63d9bee7fecf437c3a19fc284 SHA512 1849c5074afb71cba7e90a78fa51b9967b27cb3f0b6242cfbadc3c29faf7a4a13da0a15a1c43cf43df810a5c0ed0b45cf60b42f3ed83520689acc27d3bde07b9
diff --git a/dev-python/neo/neo-0.12.0.ebuild b/dev-python/neo/neo-0.12.0.ebuild
new file mode 100644
index 000000000..6e058728e
--- /dev/null
+++ b/dev-python/neo/neo-0.12.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
+HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/quantities[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/probeinterface[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-vcs/datalad[${PYTHON_USEDEP}]
+ )
+"
+# Testing deps also need:
+# igor
+# pyedflib https://github.com/holgern/pyedflib
+# klusta
+# nixio
+# sonpy
+# ipython
+
+distutils_enable_tests pytest
+
+python_test() {
+ # Reported upstream
+ # https://github.com/NeuralEnsemble/python-neo/issues/1037
+ local EPYTEST_IGNORE=(
+ neo/test/iotest/*
+ neo/test/rawiotest/*
+ )
+ # Requires dynamic data download
+ local EPYTEST_DESELECT=(
+ neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset
+ )
+ epytest
+}
diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest
new file mode 100644
index 000000000..8a541f60d
--- /dev/null
+++ b/dev-python/nptyping/Manifest
@@ -0,0 +1 @@
+DIST nptyping-2.5.0.gh.tar.gz 72870 BLAKE2B 16c6cb90c36bbf0b97da5ff74cee7030c641ef76d055cc5691b9d83adab2714d6e3515fd4e8616fece74606e109e6b115348964614b408df06b4f5c3cbccce37 SHA512 2cde9c5f7694d4f916b85c93b86df7f72709a70b2ffa91b7bbc98c5884236f5b36bb545a89c37e8c02a9b460065c97151d77c64f8d93b92fd93bcff406f039d9
diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml
new file mode 100644
index 000000000..8cbc6e175
--- /dev/null
+++ b/dev-python/nptyping/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <remote-id type="pypi">nptyping</remote-id>
+ <remote-id type="github">ramonhagenaars/nptyping</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/nptyping/nptyping-2.5.0.ebuild b/dev-python/nptyping/nptyping-2.5.0.ebuild
new file mode 100644
index 000000000..f6e8864df
--- /dev/null
+++ b/dev-python/nptyping/nptyping-2.5.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Type hints for Numpy"
+HOMEPAGE="
+ https://pypi.org/project/nptyping/
+ https://github.com/ramonhagenaars/nptyping/
+"
+SRC_URI="
+ https://github.com/ramonhagenaars/nptyping/archive/v${PV}.tar.gz
+ -> ${P}.gh.tar.gz
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/mypy[${PYTHON_USEDEP}]
+ dev-python/pandas-stubs[${PYTHON_USEDEP}]
+ dev-python/typeguard[${PYTHON_USEDEP}]
+ dev-python/beartype[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_IGNORE=(
+ # requires pyright, which is not yet packaged
+ tests/test_pyright.py
+ # requires Internet + feedparser, meaningless for users
+ tests/test_package_info.py
+ # relying on Internet access to fetch packages for pip
+ tests/test_wheel.py
+ tests/pandas_/test_fork_sync.py
+)
+
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/ramonhagenaars/nptyping/issues/113
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_any
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_shape
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_structure
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_function_arguments
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_variable_hints
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_nptyping_types
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_numpy_types
+ tests/test_mypy.py::MyPyTest::test_mypy_accepts_recarray_with_structure
+ tests/test_mypy.py::MyPyTest::test_mypy_disapproves_ndarray_with_wrong_function_arguments
+ tests/test_mypy.py::MyPyTest::test_mypy_knows_of_ndarray_methods
+ tests/test_typeguard.py::TypeguardTest::test_success
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_accepts_dataframe
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_disapproves_dataframe_with_wrong_function_arguments
+ tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_knows_of_dataframe_methods
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
index d256ba401..b14e3311b 100644
--- a/dev-python/numcodecs/Manifest
+++ b/dev-python/numcodecs/Manifest
@@ -1 +1,2 @@
DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2
+DIST numcodecs-0.12.1.tar.gz 4091415 BLAKE2B d7fa8cc549495c7c54130898f2047eb409559541b299640fb34a2332d874049afa64d5c14151426b24a1ab04c0e0444245477aa26f9336ce3ba7aefc8043abcf SHA512 716a1144c17b08cc1737bd429517b5434a7e5dbc9626ed613ca9ab4f9cda356ed97cb4ef0e2bba747a7681dc5b43818cb07c6db7f5537b4910790f6ea23c696c
diff --git a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
new file mode 100644
index 000000000..3d20684ba
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+"
+DEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_compile() {
+ local -x DISABLE_NUMCODECS_AVX2=1
+ local -x DISABLE_NUMCODECS_SSE2=1
+ distutils-r1_python_compile
+}
+
+python_test() {
+ cd "${T}" || die
+ epytest --pyargs numcodecs
+}
diff --git a/dev-python/pandas-stubs/Manifest b/dev-python/pandas-stubs/Manifest
new file mode 100644
index 000000000..856ff2fe2
--- /dev/null
+++ b/dev-python/pandas-stubs/Manifest
@@ -0,0 +1 @@
+DIST pandas-stubs-2.1.1.230928.gh.tar.gz 192865 BLAKE2B f3604def27a3ba7444969473c5800f7cc72fd4487f2363f326de6d637f1b6b60d2a8707f6cbb2647389691fbd856a2e7e5cf3710c0ad014ae106472c76dfb1c8 SHA512 5f9e71f187d1532388a98e0139852098c00d44d3ddf32fc3bad1c5199291c7dd4af82b2d73605b1e16b09a79f3b9df02752b37cf87fcb222faee9e704f52dd47
diff --git a/dev-python/pandas-stubs/metadata.xml b/dev-python/pandas-stubs/metadata.xml
new file mode 100644
index 000000000..8cbc804ad
--- /dev/null
+++ b/dev-python/pandas-stubs/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>python@gentoo.org</email>
+ <name>Gentoo Python Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">pandas-dev/pandas-stubs</remote-id>
+ <remote-id type="pypi">pandas-stubs</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
new file mode 100644
index 000000000..e10fd1aca
--- /dev/null
+++ b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
@@ -0,0 +1,52 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Public type stubs for pandas"
+HOMEPAGE="https://github.com/pandas-dev/pandas-stubs"
+SRC_URI="https://github.com/pandas-dev/pandas-stubs/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# Allegedly also needs dev-python/types-pytz (available in ::guru), but somehow works without it...
+# https://github.com/pandas-dev/pandas-stubs/blob/3c2affdaeb1cb03777cc59832dcdd4b030add27d/pyproject.toml#L34
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/xarray[${PYTHON_USEDEP}]
+ dev-python/pyarrow[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Package has a bunch of test deps missing from ::gentoo and ::science
+ tests/test_frame.py::test_to_markdown
+ tests/test_frame.py::test_types_to_feather
+ tests/test_io.py::test_orc
+ tests/test_io.py::test_orc_path
+ tests/test_io.py::test_orc_buffer
+ tests/test_io.py::test_orc_columns
+ tests/test_io.py::test_orc_bytes
+ tests/test_io.py::test_hdf
+ tests/test_io.py::test_hdfstore
+ tests/test_io.py::test_read_hdf_iterator
+ tests/test_io.py::test_hdf_context_manager
+ tests/test_io.py::test_hdf_series
+ tests/test_io.py::test_spss
+ tests/test_io.py::test_parquet
+ tests/test_io.py::test_parquet_options
+ tests/test_io.py::test_excel_writer_engine
+ tests/test_io.py::test_all_read_without_lxml_dtype_backend
+ tests/test_series.py::test_types_agg
+ tests/test_series.py::test_types_aggregate
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/photutils/photutils-1.6.0.ebuild b/dev-python/photutils/photutils-1.6.0.ebuild
index b2ea8d831..a1fa5f2d2 100644
--- a/dev-python/photutils/photutils-1.6.0.ebuild
+++ b/dev-python/photutils/photutils-1.6.0.ebuild
@@ -37,4 +37,4 @@ distutils_enable_tests pytest
# dev-python/scipy \
# dev-python/matplotlib \
# sci-libs/scikit-learn \
-# sci-libs/scikit-image \
+# dev-python/scikit-image \
diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest
index e50aa7618..f50e462dc 100644
--- a/dev-python/plac/Manifest
+++ b/dev-python/plac/Manifest
@@ -1 +1 @@
-DIST plac-1.3.5.tar.gz 38074 BLAKE2B 8c770ea43d94a5fa80fa22f0e1fb6433e7901769315e0ecd9d6889d773e454b428265c3cd43792867dd56757cc6e31dcbda76052b46266878f07e493cf899c14 SHA512 9de705fbcc7585f9be8bb648ca3136cf0f031702e3def3ae069be6cff0e71969fe193e1420bd4018392f4a323cfe9131f86a10a2a2ecd0001fd1e82ad63a0d4a
+DIST plac-1.4.2.tar.gz 37595 BLAKE2B 5205e9d8a5a775eb2e23ea7ad30e576417a8ba944cb196ccb7a16b514b6c4902856a7191b1bbf71ab0176910b5d8dc163ab36fe3fb0c5bb5765c02d16ae347b1 SHA512 c8c320cabda42f33071d7675b64befab8344bde746d0befe661a9bb26f658559435d2895dad0a27dc1d7c2dc59f07a359b529880e115d900b4fca8f245186742
diff --git a/dev-python/plac/plac-1.3.5.ebuild b/dev-python/plac/plac-1.4.2.ebuild
index dcc47aa3d..50b269f42 100644
--- a/dev-python/plac/plac-1.3.5.ebuild
+++ b/dev-python/plac/plac-1.4.2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( pypy3 python3_{10..12} )
inherit pypi distutils-r1
@@ -15,4 +15,9 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+EPYTEST_DESELECT=(
+ # Missing index.rst
+ doc/test_plac.py::test_doctest
+)
+
distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest
index 53fb37ba4..189bbfcaf 100644
--- a/dev-python/probeinterface/Manifest
+++ b/dev-python/probeinterface/Manifest
@@ -1,2 +1,3 @@
DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84
+DIST probeinterface-0.2.20.gh.tar.gz 1930434 BLAKE2B 0087f82f8cea3e1eb225ba188487eb3862de8444cadb0cf76ebba1046f194eb1f369bab7b3ff35eb6b99c054409b902c1907037d42aa84d0d4253a47fa6009ce SHA512 16cee1845d4cd40f1bfdea654fff99ea5949fbd8606ffc038ea0ca27d6a4f3faa65e2dd448bcda1066c0d2984ce7e3995a0ead028ef57ae59743c34c6c5a4c39
diff --git a/dev-python/probeinterface/probeinterface-0.2.20.ebuild b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
new file mode 100644
index 000000000..75dd43bd4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Requires network access:
+ # https://github.com/SpikeInterface/probeinterface/issues/70
+ tests/test_library.py::test_download_probeinterface_file
+ tests/test_library.py::test_get_from_cache
+ tests/test_library.py::test_get_probe
+ tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/pyaml-env/Manifest b/dev-python/pyaml-env/Manifest
new file mode 100644
index 000000000..06b54d70e
--- /dev/null
+++ b/dev-python/pyaml-env/Manifest
@@ -0,0 +1 @@
+DIST pyaml_env-1.2.1.tar.gz 12759 BLAKE2B 5a037ccefaaa3c60ce393dae5847777eb43745549a31b763ef2f50feb3a6e216ef793f9501df9e80cb381f78782e54b888ee4b043736dc05bcd01619d839ff86 SHA512 1ef873fa66660e4949dc1064260405244c8b3a2ee4391831a0a52be30e503e99d0b80b087c78db78683e9fe2fc1fd73f2e30c1eacc4c94a1394000d8526c9d68
diff --git a/dev-python/pyaml-env/metadata.xml b/dev-python/pyaml-env/metadata.xml
new file mode 100644
index 000000000..44769bf23
--- /dev/null
+++ b/dev-python/pyaml-env/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mkaranasou/pyaml_env</remote-id>
+ <remote-id type="pypi">pyaml-env</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
new file mode 100644
index 000000000..a5169040a
--- /dev/null
+++ b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Parse YAML configuration with environment variables in Python"
+HOMEPAGE="https://pypi.org/project/pyaml-env/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]"
+
+# tests not included in pypi tarball
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index d80f44e8e..f31ed56a4 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,3 +1,2 @@
-DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57
-DIST pynwb-2.3.1.tar.gz 617910 BLAKE2B 6f8a965ff077523d043dd20b34ab1c69387b434a2a489a2a9dab718270fe7484cd88df4acce17da2aa513c56afbc75022fed132d157a0c804c6ced84a0bd627b SHA512 795a20b52d7734d2b1d4ba7da0df75d0e8cdbac4f8911a0a8977fd8890751d8c10b58858f2740a73557dc0d8ffa95530437544b71f4bf14ec0cc9e99213afda0
DIST pynwb-2.3.2.tar.gz 618295 BLAKE2B 5a7e96437e0fe6dae2067e11ae4e927dcaa9574ca1d85594ebd2915d166281751808470f97ea8ba5a6df5f0023ed5f316396fe11da768f6197485a36fc497396 SHA512 bf8633275080735b864e28d792672ebda38ed5dd27c8f5eeb714f848447688c2be2d15cca809b97ee545b29833047d2db26a31272c2e9b4e24cef4ac5fe95c00
+DIST pynwb-2.5.0.tar.gz 620770 BLAKE2B 470f5127560bf79f112061e9e8af208051d76833e449a66b03e31bb0828ffbfd6aa0b9efc136ecc0b7efba758334c3f15525a41ec4540c6f55d02f8afbd55ab2 SHA512 cad84e3ac6c3c67c3c28e3c3ec44402bfc94c4cf988fbe64ddfa461a67115398b24bb9bcac1bd00933e1b63d73048d9b20ec6cd736a51d9f2c7bf4d294edb261
diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
deleted file mode 100644
index d09c50594..000000000
--- a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/setup.py b/tmp/setup.py
-index 39e75824..f7948f64 100755
---- a/setup.py
-+++ b/setup.py
-@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
- schema_dir = 'nwb-schema/core'
-
- reqs = [
-- 'h5py>=2.9,<4',
-- 'hdmf>=3.1.1,<4',
-- 'numpy>=1.16,<1.22',
-- 'pandas>=1.0.5,<2',
-- 'python-dateutil>=2.7,<3',
-+ 'h5py',
-+ 'hdmf',
-+ 'numpy',
-+ 'pandas',
-+ 'python-dateutil',
- 'setuptools'
- ]
-
diff --git a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch b/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
deleted file mode 100644
index 8c816d226..000000000
--- a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/setup.py b/tmp/setup.py
-index 39e75824..f7948f64 100755
---- a/setup.py
-+++ b/setup.py
-@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
- schema_dir = 'nwb-schema/core'
-
- reqs = [
-- 'h5py>=2.10,<4',
-- 'hdmf>=3.3.2,<4',
-- 'numpy>=1.16,<1.23',
-- 'pandas>=1.0.5,<2',
-- 'python-dateutil>=2.7,<3',
-+ 'h5py',
-+ 'hdmf',
-+ 'numpy',
-+ 'pandas',
-+ 'python-dateutil',
- 'setuptools'
- ]
-
diff --git a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
deleted file mode 100644
index 6141f629a..000000000
--- a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/setup.py b/tmp/setup.py
-index 39e75824..f7948f64 100755
---- a/setup.py
-+++ b/setup.py
-@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
- schema_dir = 'nwb-schema/core'
-
- reqs = [
-- 'h5py>=2.10,<4',
-- 'hdmf>=3.4.2,<4',
-- 'numpy>=1.16,<1.24',
-- 'pandas>=1.1.5,<2',
-- 'python-dateutil>=2.7.3,<3',
-+ 'h5py',
-+ 'hdmf',
-+ 'numpy',
-+ 'pandas',
-+ 'python-dateutil',
- 'setuptools'
- ]
-
diff --git a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
deleted file mode 100644
index bf496b900..000000000
--- a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
-From: rly <rly@lbl.gov>
-Date: Fri, 24 Mar 2023 10:17:13 -0700
-Subject: [PATCH] Fix deprecation warning with pkg_resources
-
----
- src/pynwb/__init__.py | 14 +++++++++++---
- tests/back_compat/test_import_structure.py | 1 -
- 2 files changed, 11 insertions(+), 4 deletions(-)
-
-diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py
-index 2df273d43..023cda237 100644
---- a/src/pynwb/__init__.py
-+++ b/src/pynwb/__init__.py
-@@ -15,16 +15,24 @@
- import hdmf.common
-
- CORE_NAMESPACE = 'core'
--__core_ns_file_name = 'nwb.namespace.yaml'
-
- from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402
- from .validate import validate # noqa: F401, E402
-
-
- def __get_resources():
-- from pkg_resources import resource_filename
-+ try:
-+ from importlib.resources import files
-+ except ImportError:
-+ # TODO: Remove when python 3.9 becomes the new minimum
-+ from importlib_resources import files
-+
-+ __location_of_this_file = files(__name__)
-+ __core_ns_file_name = 'nwb.namespace.yaml'
-+ __schema_dir = 'nwb-schema/core'
-+
- ret = dict()
-- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)
-+ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name)
- return ret
-
-
-diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py
-index dba11a48a..e5f931f5d 100644
---- a/tests/back_compat/test_import_structure.py
-+++ b/tests/back_compat/test_import_structure.py
-@@ -34,7 +34,6 @@ def test_outer_import_structure(self):
- "__TYPE_MAP",
- "__builtins__",
- "__cached__",
-- "__core_ns_file_name",
- "__doc__",
- "__file__",
- "__get_resources",
diff --git a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
deleted file mode 100644
index e672f243b..000000000
--- a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/pynwb/ophys.py b/src/pynwb/ophys.py
-index b09267ff6..e3d9f8f6d 100644
---- a/src/pynwb/ophys.py
-+++ b/src/pynwb/ophys.py
-@@ -192,7 +192,7 @@ def __init__(self, **kwargs):
- args_to_set = popargs_to_dict(keys_to_set, kwargs)
- super().__init__(**kwargs)
-
-- if args_to_set["binning"] < 0:
-+ if args_to_set["binning"] is not None and args_to_set["binning"] < 0:
- raise ValueError(f"Binning value must be >= 0: {args_to_set['binning']}")
- if isinstance(args_to_set["binning"], int):
- args_to_set["binning"] = np.uint(args_to_set["binning"])
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
deleted file mode 100644
index 5a286c3b6..000000000
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 pypi
-
-DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=sci-libs/hdf5-1.12.2
- >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/python-dateutil[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${P}-versions.patch"
- )
-
-EPYTEST_DESELECT=(
- # Reported upsream:
- # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
- tests/back_compat/test_read.py::TestReadOldVersions::test_read
- tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_non_external_format
- tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_nonmatch_starting_frame
- tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data
- tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data_construct_mode
- tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format
- tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format_construct_mode
- tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_starting_frame
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
- tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild b/dev-python/pynwb/pynwb-2.5.0.ebuild
index 382bfdb60..ca11c3dbe 100644
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.5.0.ebuild
@@ -15,20 +15,14 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
"
-BDEPEND=""
-
-# Remove both in next release
-PATCHES=(
- "${FILESDIR}/${P}-typing.patch"
- "${FILESDIR}/${P}-pkg_resources.patch"
- )
EPYTEST_DESELECT=(
# Reported upsream:
@@ -45,6 +39,12 @@ EPYTEST_DESELECT=(
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
)
distutils_enable_tests pytest
diff --git a/dev-python/pyout/Manifest b/dev-python/pyout/Manifest
index 551424495..5878b2e20 100644
--- a/dev-python/pyout/Manifest
+++ b/dev-python/pyout/Manifest
@@ -1,2 +1,2 @@
-DIST pyout-0.7.1.tar.gz 180439 BLAKE2B b64808edfa013c8460961afacbe70caad4f3c0520d8b87656e909e278534bf111154fd31a186f95246d3084671c841ea421ed52118ddeee3f08f21106f2f80b1 SHA512 66338ce6dbf1e4ee6a187993609f762fcd2f8dddd981bc976b3240b6ecd461ba1fd47b9f08b91fc29853ce88e26158c7047de0adfcf28a0dd66869adfad5ab71
DIST pyout-0.7.2.tar.gz 181753 BLAKE2B 780e536921151f81097e5dee7c74cfa086153f916fc9b9fd684f01008ada34102ba33ee7bdd3dd8cc4ccf89a8d9821ec0aecdbd87bc356abf25c6e4fe32d4c5a SHA512 e7be6f7829f6b09ead64c596cfdecfa45073af0a1da15401702327e141bbfae10e7968ee5e332358aa04bfc7ddf71b7b6caf2d5877aca8514e4ba544d3b1670a
+DIST pyout-0.7.3.tar.gz 45726 BLAKE2B 4c5bc42b835fefd3db5d97db46c086ec2a7ca488a339813937f6e795a5fef699451dd67cd5078737f4f2bc47a36c96e2cb9f0010645fa45ebd288d24b5e0c3ba SHA512 784a7dd5b1eb811073466828f81783f89e3a251e05bc49edf124cdfc916c2447982299c83b087942845b61791481850f8c89379eea920e91d35c8abc2cbeb8ef
diff --git a/dev-python/pyout/pyout-0.7.1-r1.ebuild b/dev-python/pyout/pyout-0.7.3.ebuild
index 9cd796883..7246139ee 100644
--- a/dev-python/pyout/pyout-0.7.1-r1.ebuild
+++ b/dev-python/pyout/pyout-0.7.3.ebuild
@@ -3,17 +3,17 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
DESCRIPTION="Terminal styling for structured data"
HOMEPAGE="https://github.com/pyout/pyout"
-SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
SLOT="0"
LICENSE="MIT"
KEYWORDS="~amd64 ~x86"
-RESTRICT="test"
RDEPEND="
dev-python/jsonschema[${PYTHON_USEDEP}]
@@ -27,9 +27,7 @@ DEPEND="
distutils_enable_tests pytest
-
-PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" )
-
+#PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" )
python_prepare_all() {
sed -i -e '/pytest-runner/d' setup.py || die
diff --git a/dev-python/rich-click/Manifest b/dev-python/rich-click/Manifest
new file mode 100644
index 000000000..ae8d92c2f
--- /dev/null
+++ b/dev-python/rich-click/Manifest
@@ -0,0 +1 @@
+DIST rich-click-1.7.2.tar.gz 39362 BLAKE2B c4ad70d449ce9ceb3d9bbbccf7c7d3cd43386c35061d60c6395ff7845f606558af36a7c465a3393484008ece244f8e684ca9d71cea14463f04cac21803108543 SHA512 f4046e54874c4f3cc4f77651fdeb1f888d9435ff282f54d320c16c7c42f57c48018c0159230e780684336d29edff6e654454b8940b5b8df5a19139d2219c671b
diff --git a/dev-python/rich-click/metadata.xml b/dev-python/rich-click/metadata.xml
new file mode 100644
index 000000000..79a5238bd
--- /dev/null
+++ b/dev-python/rich-click/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">ewels/rich-click</remote-id>
+ <remote-id type="pypi">rich-click</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/rich-click/rich-click-1.7.2.ebuild b/dev-python/rich-click/rich-click-1.7.2.ebuild
new file mode 100644
index 000000000..e642303e2
--- /dev/null
+++ b/dev-python/rich-click/rich-click-1.7.2.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+PYPI_NO_NORMALIZE=1
+inherit pypi distutils-r1
+
+DESCRIPTION="Format click help output nicely with rich"
+HOMEPAGE="https://pypi.org/project/rich-click/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]"
+
+RESTRICT="test"
+# ModuleNotFoundError: No module named 'tests.conftest'
+#distutils_enable_tests pytest
diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest
index 9beeb00c6..eca03bc0e 100644
--- a/dev-python/snakemake/Manifest
+++ b/dev-python/snakemake/Manifest
@@ -1 +1 @@
-DIST snakemake-7.32.3.gh.tar.gz 8886818 BLAKE2B d407e8bf65bacb5a1d3decaa54caee602f6588239c6c42062897bfaee3a13d6afd6d4afcab85a3b1de0994e2d46fcd4851e9dfd500b164a5c05a73aeba38f92a SHA512 675d1206bda44309f38b4cde441584f4c6243c1c63fb3ab07a781e3538c604e66ef013f75a27dd3b11f620611cf583e4e2fca5531a5492cef5cbd85f44f0b77e
+DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
diff --git a/dev-python/snakemake/snakemake-7.32.3.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild
index 94dd9e925..711aac286 100644
--- a/dev-python/snakemake/snakemake-7.32.3.ebuild
+++ b/dev-python/snakemake/snakemake-7.32.4.ebuild
@@ -42,6 +42,7 @@ RDEPEND="
dev-python/jinja[${PYTHON_USEDEP}]
dev-python/jsonschema[${PYTHON_USEDEP}]
dev-python/nbformat[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
dev-python/psutil[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
diff --git a/dev-python/spectra/Manifest b/dev-python/spectra/Manifest
new file mode 100644
index 000000000..97bcfc93a
--- /dev/null
+++ b/dev-python/spectra/Manifest
@@ -0,0 +1 @@
+DIST spectra-0.0.11.tar.gz 18819 BLAKE2B 45ceefa8d2bab051a8fa8ee687f9fa25f6436e66987bb84c6982f64a522fb0b04120e068ef890f4b04f6626a130c5df1e81090913c143df1e82bda5ca3a01d4d SHA512 7b4e244ba200df8c6d7cff19ddf36a5af6cfe8cf6f89283f8dbb64345a3eb85b4f62456e3c75b7c8ce2d24e01c8a123a5763605b1e702903fe16839966e47b32
diff --git a/dev-python/spectra/metadata.xml b/dev-python/spectra/metadata.xml
new file mode 100644
index 000000000..9332eceee
--- /dev/null
+++ b/dev-python/spectra/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">jsvine/spectra</remote-id>
+ <remote-id type="pypi">spectra</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/spectra/spectra-0.0.11.ebuild b/dev-python/spectra/spectra-0.0.11.ebuild
new file mode 100644
index 000000000..d0df23724
--- /dev/null
+++ b/dev-python/spectra/spectra-0.0.11.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/spectra/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/colormath[${PYTHON_USEDEP}]"
+
+# requires nose
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest
index 28ed71b4c..bdf3e4b60 100644
--- a/dev-python/spikeinterface/Manifest
+++ b/dev-python/spikeinterface/Manifest
@@ -1,2 +1,3 @@
DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef
DIST spikeinterface-0.97.0.tar.gz 6735715 BLAKE2B c11bee4306f8d96ae5cd09cf1b852e267c1db6caa13565f6364cd65ee36fe62c04589e8e0657517003ed1dd6d76d25f60bef226820403111db4ed7717e8a20cd SHA512 befdf3382de6aad2ef2c72e3bbdf64fbee1c1f72f83610ca8bba2f8693992c84b515f8c000dc6b3609825347b0bcd85b026747633e90777d7fdd30dc0ae0ef13
+DIST spikeinterface-0.99.1.tar.gz 11475537 BLAKE2B 9427079f70020b882c7bdbaadb9b60508827f1131f3aeb4fa8fdaaada73f2aa2cb3ec018f87467cd2a7505bea435d6bcf04d9784d921829533ebf41d686d72bb SHA512 4dd513aa6eb8af58fa9d1a80671973b01cb81643588c4522f3f87cfd0ccebcfb7a1f2926e554bc7dadbb2201fc0b2f2873b0003483dd5ca578b5a76d4cce05a2
diff --git a/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
new file mode 100644
index 000000000..a428775eb
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines."
+HOMEPAGE="https://github.com/SpikeInterface/spikeinterface"
+SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+# Reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/2339
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/neo[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ extractors? (
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+ full? (
+ dev-python/distinctipy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/xarray[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+ )
+"
+# Also wants:
+# # Extractors:
+# MEArec
+# pyedflib
+# sonpy
+# dev-python/hdf5storage (in ::science, masked)
+
+distutils_enable_tests pytest
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
index f597d0175..a4ecbb65f 100644
--- a/dev-python/typish/typish-1.9.3.ebuild
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -17,7 +17,7 @@ SRC_URI="
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+KEYWORDS="~amd64"
BDEPEND="
test? (
diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest
new file mode 100644
index 000000000..0ced19d13
--- /dev/null
+++ b/dev-python/vector/Manifest
@@ -0,0 +1 @@
+DIST vector-1.1.1.tar.gz 289916 BLAKE2B 35281c498f244b0307d744a20d0364c4cf664d0bd08a4f17d8d3110aa4eae6d7f66e3b51b4e9847f31d3a6ab943248115221dee4dcd3c3f2f8c47842001b553a SHA512 b1e195751de35ca2c67749b6b2b330db8a29e023f42e9b454adc8fc2408c29b5926b39e9ed6dc6a93f97006fbfb286a2217be8b14cb0eb2b96c9538f6c3943e6
diff --git a/dev-python/vector/metadata.xml b/dev-python/vector/metadata.xml
new file mode 100644
index 000000000..b6aaa9af7
--- /dev/null
+++ b/dev-python/vector/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ Vector is a Python 3.8+ library (Python 3.6 and 3.7 supported till v0.9.0 and v1.0.0, respectively) for 2D, 3D, and Lorentz vectors, especially arrays of vectors, to solve common physics problems in a NumPy-like way.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">vector</remote-id>
+ <remote-id type="github">scikit-hep/vector</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/vector/vector-1.1.1.ebuild b/dev-python/vector/vector-1.1.1.ebuild
new file mode 100644
index 000000000..936578e50
--- /dev/null
+++ b/dev-python/vector/vector-1.1.1.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
diff --git a/dev-python/wraps/files/wraps-0.1.0-includes.patch b/dev-python/wraps/files/wraps-0.1.0-includes.patch
deleted file mode 100644
index a5184e52e..000000000
--- a/dev-python/wraps/files/wraps-0.1.0-includes.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
-+++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
-@@ -20,8 +20,11 @@
- "Topic :: Utilities",
- "Typing :: Typed",
- ]
--
--include = ["CHANGELOG.md", "tests"]
-+include = [
-+ { path = "LICENSE", format = "sdist" },
-+ { path = "README.md", format = "sdist" },
-+ { path = "CHANGELOG.md", format = "sdist" },
-+]
-
- [tool.poetry.urls]
- Discord = "https://nekit.dev/discord"
diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest
index 7c74e59be..b76de8dcc 100644
--- a/dev-python/xgboost/Manifest
+++ b/dev-python/xgboost/Manifest
@@ -1 +1,2 @@
DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b
+DIST xgboost-2.0.3.tar.gz 1048322 BLAKE2B 2140b805aaed441da956e47cbfe08d84db1b0af96844771f4912480b05346b18632051886b237bef3e2b55a80f09c1db996be4dfeff48c942220079c4a4a149c SHA512 93614a9ad9d0a256cc31586b701c46eef4353df76c3eac26f39df23c8c02fa9ec95e72a0cea0b51bc3e416b81b3ac557ed361afeda246376a7b561bb6f7da579
diff --git a/dev-python/xgboost/xgboost-2.0.3.ebuild b/dev-python/xgboost/xgboost-2.0.3.ebuild
new file mode 100644
index 000000000..60302a1cb
--- /dev/null
+++ b/dev-python/xgboost/xgboost-2.0.3.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517="standalone"
+inherit distutils-r1 pypi
+
+DESCRIPTION="XGBoost Python Package"
+HOMEPAGE="
+ https://xgboost.readthedocs.io
+ https://github.com/dmlc/xgboost/
+"
+
+REQUIRED_USE="
+ ${PYTHON_REQUIRED_USE}
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/yte/Manifest b/dev-python/yte/Manifest
index e0bd09674..2ad6d3366 100644
--- a/dev-python/yte/Manifest
+++ b/dev-python/yte/Manifest
@@ -1 +1 @@
-DIST yte-1.5.1.tar.gz 6764 BLAKE2B ebe65bf961e028cb87ec0c7f8e552bcd5890329c0e66b9227becc21480a3b3ce5734090acc3fe32d44efcf2ecc7a2456f7056e75eccf7def75781910bef7dbc5 SHA512 5012e47d1ad8c20cb755b9c605d866d56850f0d16381f74c8d405232de95f43a6ea9ab65eb07cf23a14eeaa18e9105e0f0642a54f2847584bfffe432ce909267
+DIST yte-1.5.4.tar.gz 6352 BLAKE2B f304d1846c0f54949397570564f6bf9d048cd26a99a87feb62f8944403fd0f619546ed0989a2f9fda381c0f39adaa4d987ff66eb4e3bcbce107a460091c1b775 SHA512 eb61553d4c17f6d39f954ea5ab1a09a83009ab8f6f653afbf780b7a30f355e149b4508f8e3755a804f245246e0a1184c74be995f1477e1d2d27bc536bc1ff1f7
diff --git a/dev-python/yte/yte-1.5.1.ebuild b/dev-python/yte/yte-1.5.4.ebuild
index bb3b6354a..ad7b669b1 100644
--- a/dev-python/yte/yte-1.5.1.ebuild
+++ b/dev-python/yte/yte-1.5.4.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=poetry
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit pypi distutils-r1
@@ -20,5 +20,3 @@ RDEPEND="
dev-python/plac[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
"
-
-distutils_enable_tests pytest
diff --git a/dev-python/zarr/Manifest b/dev-python/zarr/Manifest
index 87617bcb1..bb2213da1 100644
--- a/dev-python/zarr/Manifest
+++ b/dev-python/zarr/Manifest
@@ -1,2 +1,3 @@
-DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65
DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
+DIST zarr-2.14.2.tar.gz 3589944 BLAKE2B 5e7de6c3a2bd9bd970b07bdfe1d51f14ad0e50bac37f2fbad91d98066d5239d237fa5af8cfef2f0a1ab4461dba4eeaed1db9fa0a4a1bfcd1757d54da4bbb15f7 SHA512 cc1eb40cd3723e87916e84f958d26df6353fc1e767e33a986068e182ad2a83c2dd7eb4939bf12ff45d4de49d822a0e6cb0afb5a5f1292d4c196f812d48939191
+DIST zarr-2.16.1.tar.gz 3597771 BLAKE2B 459f8022b3a4e3298b0f9650738713f6c13bb474ae50005b9387fefc87360f6358e4899037b26b9893d87298b14606d7b29bc1539fc8fa1479a08b30f2c8323b SHA512 e3b7c234c6376bea535d47304d83ee5b4d8b4bfc6952dde5e0bf1276833c1f427c98a7af0867f351e0139404d3729024b591a1f9b2242e219846a994e0762ee5
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.14.2.ebuild
index f18e92d44..f18e92d44 100644
--- a/dev-python/zarr/zarr-2.11.3.ebuild
+++ b/dev-python/zarr/zarr-2.14.2.ebuild
diff --git a/dev-python/zarr/zarr-2.16.1.ebuild b/dev-python/zarr/zarr-2.16.1.ebuild
new file mode 100644
index 000000000..f18e92d44
--- /dev/null
+++ b/dev-python/zarr/zarr-2.16.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/asciitree[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ )
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+ zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index d249e7c33..170fc436c 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,3 +1,3 @@
-DIST dandi-0.51.0.tar.gz 233955 BLAKE2B 500a6290cba32f413610879357c0ee525d877575c4ad520818a556ae7f58f90c2aec88387dbb0ca78e7906b48673c2c2d3c9c457833727fb312e5ca6d75ce088 SHA512 e77fa803dd2707df8cab2318377a71c28abb8bdc6e2d086cb43daf24512f361e533d249dabd88bfc6c0de06e6332606ac2f3c57482ae9717fedb66da4e2e8d89
-DIST dandi-0.55.0.tar.gz 292471 BLAKE2B 2ccdba123c61025894a327d56163fd71cd0294b315b83396688903d969ba243fe2bb3ad9d2db5cf24d36254395a7de452d6e4ff4a65cf264f001a0cda527cd08 SHA512 e41f699a55cd75161048dd0e0334b84527ae0f4e02c81eedf7c8811b8bc50229488599f9601263e65a97fd815ce1d2cb41c94968fcc9ffde7726b72fe4e0180c
DIST dandi-0.55.1.tar.gz 296372 BLAKE2B 06d1b020bc3362f64779da8a4d229c9919c1edee83b530bf248c7dfa591f97c10b08eb1e9cb2f54ec30d8e7a1bcc0ffe9ee8f925e0a51fb0ba3882699a605a33 SHA512 341f82b8b59ececf8addbb0a9087e2a5ace3b0c452d4da1d94c413daef594590d8350ba4421a077865a4eafbcefe4189478f385e8cfe0dd53a9e46c7782b3ce5
+DIST dandi-0.59.0.tar.gz 304436 BLAKE2B 7a2736cb8cebfc97ff3fe94414cd93652039803b15d87e1d9ac2b1c3f9650152ed56fbf787382977bb8c65d25f8ed02a7bd694dd92f20e55d737fb0572a33bed SHA512 79b650fe6d812244244522eed7bb2fe7d3ed67e953d67548ae5e538b70d431899b7b5254978890ddc60ca3a2f5c87f726f3f776019182abd4b30cc917e3b337e
+DIST dandi-0.59.1.tar.gz 304723 BLAKE2B 564525e8616bbf6fce09f2102ec5951c2d155625674f7d66e48d8c4b33178e329be7805d8afab37b9c1c639ef4a4618453e20fcd2babe763039e01d5263468b9 SHA512 8fe34053ee80bb7ae2c09dbb8c0b34bc2c68a4cec01e9718e0d5d72bf1564e5a4c101b890e39455d1ec034cd07699aec4ef6716e646e8541227c9904b7af9774
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild
index c626dbe8b..df160ad23 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.51.0-r1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.59.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -21,10 +21,9 @@ KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- <sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
=dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
+ >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
@@ -36,6 +35,7 @@ RDEPEND="
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyout[${PYTHON_USEDEP}]
@@ -44,6 +44,7 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
dev-python/zarr_checksum[${PYTHON_USEDEP}]
@@ -52,9 +53,11 @@ RDEPEND="
BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
- dev-python/responses[${PYTHON_USEDEP}]
dev-python/pyfakefs[${PYTHON_USEDEP}]
dev-python/pytest-mock[${PYTHON_USEDEP}]
+ dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
)
"
@@ -63,15 +66,20 @@ BDEPEND="
S="${WORKDIR}/${MY_P}"
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/dandi/dandi-cli/issues/1394
+ dandi/cli/tests/test_command.py::test_no_heavy_imports
+)
+
distutils_enable_tests pytest
src_prepare() {
if use etelemetry; then
default
else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
+ eapply "${FILESDIR}/${P}-no-etelemetry.patch"
default
- sed -i "/etelemetry/d" setup.cfg
fi
}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.59.1.ebuild
index 060424cdb..fa0643648 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.55.0-r1.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.59.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -21,10 +21,9 @@ KEYWORDS="~amd64"
IUSE="test etelemetry"
RDEPEND="
- <sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
=dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
- dev-python/appdirs[${PYTHON_USEDEP}]
+ >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
@@ -36,6 +35,7 @@ RDEPEND="
dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyout[${PYTHON_USEDEP}]
@@ -44,6 +44,7 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/semantic-version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
dev-python/zarr_checksum[${PYTHON_USEDEP}]
@@ -65,22 +66,14 @@ BDEPEND="
S="${WORKDIR}/${MY_P}"
-PATCHES=(
- "${FILESDIR}/${PN}-0.55.0-hdf5.patch"
+EPYTEST_DESELECT=(
+ # Reported upstream:
+ # https://github.com/dandi/dandi-cli/issues/1394
+ dandi/cli/tests/test_command.py::test_no_heavy_imports
)
distutils_enable_tests pytest
-src_prepare() {
- if use etelemetry; then
- default
- else
- eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
- default
- sed -i "/etelemetry/d" setup.cfg
- fi
-}
-
python_test() {
export DANDI_TESTS_NONETWORK=1
epytest
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
deleted file mode 100644
index 4d4715f95..000000000
--- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-From a363b68b79b3dd2004912640c90958882a918537 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
-Date: Wed, 4 May 2022 19:49:37 +0200
-Subject: [PATCH] Prepend to sys.path to fix versioneer in PEP517 mode
-
-Prepend the current directory to sys.path rather than appending it
-in order to fix the build in PEP517 mode properly. If the path
-is appended and versioneer is installed on the system, the system
-versioneer.py (i.e. the module used to install versioneer into projects)
-is imported rather than the local file, and the build fails:
-
-```
-Traceback (most recent call last):
- File "/usr/lib/python-exec/python3.10/gpep517", line 4, in <module>
- sys.exit(main())
- File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 136, in main
- return func(args)
- File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 44, in build_wheel
- wheel_name = backend.build_wheel(args.wheel_dir, args.config_json)
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel
- return self._build_with_temp_dir(['bdist_wheel'], '.whl',
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir
- self.run_setup()
- File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
- exec(compile(code, __file__, 'exec'), locals())
- File "setup.py", line 32, in <module>
- "version": versioneer.get_version(),
-AttributeError: module 'versioneer' has no attribute 'get_version'
-```
----
- setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index e8dddc985..05765009c 100755
---- a/setup.py
-+++ b/setup.py
-@@ -23,7 +23,7 @@
- # This is needed for versioneer to be importable when building with PEP 517.
- # See <https://github.com/warner/python-versioneer/issues/193> and links
- # therein for more information.
--sys.path.append(os.path.dirname(__file__))
-+sys.path.insert(0, os.path.dirname(__file__))
-
- try:
- import versioneer
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
deleted file mode 100644
index bcc3853d3..000000000
--- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/setup.cfg 2021-10-06 11:44:40.549337707 -0400
-+++ b/dsetup.cfg 2021-10-06 11:45:10.236935245 -0400
-@@ -30,8 +30,8 @@
- appdirs
- click
- click-didyoumean
-- dandischema ~= 0.6.0
-- etelemetry >= 0.2.2
-+ dandischema
-+ etelemetry
- fasteners
- fscacher
- # Specifying != might be what causes pip 19.3.1 first to install hdmf 1.5.1
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
new file mode 100644
index 000000000..4d4f42a03
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
@@ -0,0 +1,40 @@
+diff --git a/dandi/files/bases.py b/dandi/files/bases.py
+index 45f5929f..38bde34f 100644
+--- a/dandi/files/bases.py
++++ b/dandi/files/bases.py
+@@ -18,7 +18,6 @@ from dandischema.digests.dandietag import DandiETag
+ from dandischema.models import BareAsset, CommonModel
+ from dandischema.models import Dandiset as DandisetMeta
+ from dandischema.models import get_schema_version
+-from etelemetry import get_project
+ from packaging.version import Version
+ from pydantic import ValidationError
+ import requests
+@@ -737,6 +736,7 @@ def _get_nwb_inspector_version():
+ _current_nwbinspector_version = get_package_version(name="nwbinspector")
+ # Ensure latest version of NWB Inspector is installed and used client-side
+ try:
++ from etelemetry import get_project
+ max_version = Version(
+ get_project(repo="NeurodataWithoutBorders/nwbinspector")["version"]
+ )
+diff --git a/setup.cfg b/setup.cfg
+--- a/setup.cfg 2024-01-09 14:08:33.952653200 -0500
++++ b/setup.cfg 2024-01-25 01:45:34.594335960 -0500
+@@ -34,7 +34,6 @@
+ click >= 7.1
+ click-didyoumean
+ dandischema ~= 0.8.0
+- etelemetry >= 0.2.2
+ fasteners
+ fscacher >= 0.3.0
+ hdmf != 3.5.0
+@@ -147,9 +146,6 @@
+ [mypy-click_didyoumean.*]
+ ignore_missing_imports = True
+
+-[mypy-etelemetry.*]
+-ignore_missing_imports = True
+-
+ [mypy-fasteners.*]
+ ignore_missing_imports = True
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
index 78bcf187d..2e465fff7 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,3 +1,3 @@
-DIST datalad-0.18.0.tar.gz 1425155 BLAKE2B 8d7cbf7f56b1de82c74fa823b2d4512112f1b4c4be106cac433c8db696b2e7f77da758c0bb62b7cb9fe0fbb08d49431dda2818d08d5c60b5052154895c335b33 SHA512 0df8276edc3872c73fee7286ea4e578648a6fb2a630fa49a4f8945e0d6ff88353d9b11d29d942c0ce22ed17a8223e71f99d8b519a6a8afbc2ac9e6da89d95ee5
DIST datalad-0.18.1.tar.gz 1425820 BLAKE2B 574e864feb500062f829dfea3f9c8c51f9ad2e0e68e70966c2a5ea315fafffb259de9a0f57427c0aae1ee93c24ec9a3a91ef42637d109d912cf5b6c41ac07b11 SHA512 19f011428fe66d9f21410ae33276133f26cf2b1a367c23a83c56ab48a0e038837ba18163e12ab2d74eba7d0ec9ce2e660a21494ddba0da3a2df6da2c043c4aad
DIST datalad-0.18.3.tar.gz 1435282 BLAKE2B 8077c0a639920e914b30598ded435ad74564f3947a187f5d57752cd22e0d435838db9bdd797a6d8d8cc54282e1303f5ca5d673d3674da09c678a47f35e8ef3f6 SHA512 06f5a73caaacffb35f11852f69ee48c485ebd1cce55e1440eb8686d8614a29809b01de2d129a48591fd66c02a59af9dcd064b0e7ead698842cc7f79d12af729c
+DIST datalad-0.19.6.tar.gz 1420979 BLAKE2B 49d8e19449652f284f89f99e6696c6d1abf7ddcc58a8eb00004c657be38ce2532ed9c11855dca4a0a8f82c55fbf1633f53ff2bdea063fd18ad946145d27a3404 SHA512 db7cd807a8106727f0b6f587be8c0ce3abcf0dc7cf72b4757e6b44650adca05482e6b0a6c1719050fba37660dcd5de2a6f27df044a8db180ac6855ee7ff8cbda
diff --git a/dev-vcs/datalad/datalad-0.18.0.ebuild b/dev-vcs/datalad/datalad-0.19.6.ebuild
index cd90c1db2..3416c0485 100644
--- a/dev-vcs/datalad/datalad-0.18.0.ebuild
+++ b/dev-vcs/datalad/datalad-0.19.6.ebuild
@@ -5,11 +5,11 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
HOMEPAGE="https://github.com/datalad/datalad"
-SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
diff --git a/dev-vcs/datalad/metadata.xml b/dev-vcs/datalad/metadata.xml
index 8a6c00a2d..9c40d4f36 100644
--- a/dev-vcs/datalad/metadata.xml
+++ b/dev-vcs/datalad/metadata.xml
@@ -26,5 +26,6 @@
</use>
<upstream>
<remote-id type="github">datalad/datalad</remote-id>
+ <remote-id type="pypi">datalad</remote-id>
</upstream>
</pkgmetadata>
diff --git a/licenses/GSL b/licenses/GSL
new file mode 100644
index 000000000..38014b153
--- /dev/null
+++ b/licenses/GSL
@@ -0,0 +1,221 @@
+ END USER LICENSE AGREEMENT
+
+ NOTICE: THIS SOFTWARE END USER LICENSE AGREEMENT ("EULA") IS A LEGAL
+ AGREEMENT BETWEEN YOU (EITHER AS AN INDIVIDUAL OR AN ENTITY) AND GSL
+ BIOTECH LLC ("GSL"). PLEASE READ IT CAREFULLY BEFORE COMPLETING THE
+ INSTALLATION PROCESS AND USING THE SOFTWARE. THIS AGREEMENT PROVIDES A
+ LICENSE TO USE THE SOFTWARE AND CONTAINS WARRANTY INFORMATION AND
+ LIABILITY DISCLAIMERS. BY INSTALLING AND USING THE SOFTWARE, YOU ARE
+ CONFIRMING YOUR ACCEPTANCE OF THE SOFTWARE AND AGREEING TO BECOME BOUND BY
+ THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO BE BOUND BY THESE
+ TERMS, THEN DO NOT INSTALL THE SOFTWARE, AND RETURN THE SOFTWARE TO GSL.
+
+ 1. Recitals
+
+ 1. This End User License Agreement ("EULA") is a legal agreement
+ between you (either an individual person or a single legal
+ entity, who will be referred to in this EULA as "End User", and
+ GSL Biotech LLC ("GSL") for the SnapGene software product
+ ("Software") or SnapGene Viewer software product ("Freeware")
+ that accompanies this EULA, including any associated media,
+ printed materials and electronic documentation.
+ 2. The Software or Freeware also includes any software updates,
+ add-on components, web services and/or supplements that GSL may
+ provide to End User or make available to End User after the date
+ End User obtains the initial copy of the Software or Freeware, to
+ the extent that such items are not accompanied by a separate
+ license agreement or terms of use. By installing, copying,
+ downloading, accessing or otherwise using the Software or
+ Freeware, End User agrees to be bound by the terms of this EULA.
+ If End User does not agree to the terms of this EULA, End User
+ should not install, access or use the Software or Freeware.
+
+ 2. License Grants
+
+ 1. Freeware License. GSL grants End User an unlimited license to use
+ the Freeware. The install packages for the Freeware can be
+ redistributed without restriction, and can be used for both
+ commercial and non-commercial purposes.
+ 2. Trial Period License. End User may download and use the Software
+ for free for thirty (30) days after installation ("Trial
+ Period"). During the Trial Period, GSL grants End User a limited,
+ non-exclusive, non-transferable, non-renewable license to copy
+ and use the Software for evaluation purposes only. At GSL's
+ discretion, GSL may provide limited support through email or
+ discussion forums at GSL's website. The evaluation copy of the
+ Software contains a feature that will automatically disable
+ certain features of the Software at the end of Trial Period. GSL
+ will have no liability to End User if this feature disables the
+ Software.
+ 3. License After Trial Period. This Software is licensed, not sold.
+ End User has the option of paying a license fee in order to use
+ the Software after the expiration of the Trial Period. Upon
+ payment of the license fee, GSL provides End User with a
+ registration number, and grants End User a limited,
+ non-exclusive, non-transferable license as outlined in Sections
+ 2.d through Section 2.g and in Section 3.
+ 4. Computer-Specific License. Under the terms of a Computer-Specific
+ License for the Software, End User may activate each license only
+ on a single computer, and may use the Software only on that
+ computer. The Software may not be accessed remotely.
+ 5. Floating License. Under the terms of a Floating License for the
+ Software, End User may install the Software on an unlimited
+ number of computers. All computers using the Software must have
+ the ability to communicate with a license server. The number of
+ users who may run the Software concurrently must not at any time
+ exceed the number of Floating Licenses purchased.
+ 6. Unlimited License. Under the terms of an Unlimited License for
+ the Software, End User may install and use the Software on an
+ unlimited number of computers with IP addresses in a specified IP
+ range as agreed to by GSL and End User.
+ 7. The Software or Freeware is for educational and non-commercial or
+ commercial research purposes only. GSL makes no representation
+ that the Software or Freeware is a clinically approved medical
+ device, and End User understands and accepts that any result or
+ its display presented in whatever form obtained using the
+ Software or Freeware must not be used for any purpose other than
+ education or research.
+
+ 3. License Restrictions
+
+ 1. End User may use the Software only on the permitted number of
+ computers.
+ 2. End User may make one copy of the Software solely for backup
+ purposes. Any backup copy must contain all copyright notices and
+ any other proprietary legends on the original copy of the
+ Software. End User may not sell or transfer any copy of the
+ Software made for backup purposes.
+ 3. End User's license rights under this EULA are non-exclusive and
+ non-assignable.
+ 4. Other than as set forth in Section 3.b, End User may not make
+ copies of the Software or electronically transfer the Software
+ from one computer to another.
+ 5. End User may not alter, merge, modify, adapt, translate,
+ decompile, reverse engineer, disassemble, or otherwise reduce the
+ Software to a human-perceivable form.
+ 6. End User may not rent, lease, or sublicense the Software.
+ 7. End User may not create derivative works based upon the Software.
+ 8. End User may not export the Software into any country to which
+ such export is prohibited by the United States Export
+ Administration Act.
+ 9. In the event that End User fails to comply with this EULA, GSL
+ and its distributors may, in addition to seeking any damages,
+ terminate the license. Upon termination, End User must destroy
+ all copies of the Software (with all other rights of both parties
+ and all other provisions of this EULA surviving any such
+ termination).
+
+ 4. Ownership
+
+ The foregoing license gives End User a limited license to use the
+ Software. GSL retains all rights, title and interest, including all
+ copyright and intellectual property rights, in and to the Software and
+ all copies thereof. The Software is protected by the copyright laws of
+ the United States and other countries. All rights not expressly
+ granted in this EULA are reserved by GSL.
+
+ 5. LIMITED WARRANTY AND DISCLAIMER
+
+ 1. GSL warrants that, for a period of ninety (90) days, the Software
+ will perform in substantial conformance with published
+ specifications for the Software.
+ 2. EXCEPT AS SET FORTH IN THE FOREGOING LIMITED WARRANTY WITH
+ RESPECT TO THE SOFTWARE, GSL DISCLAIMS ALL OTHER WARRANTIES AND
+ REPRESENTATIONS, WHETHER EXPRESS, IMPLIED, OR OTHERWISE,
+ INCLUDING THE WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
+ PARTICULAR PURPOSE. ALSO, THERE IS NO WARRANTY OF
+ NON-INFRINGEMENT AND TITLE OR QUIET ENJOYMENT. GSL DOES NOT
+ WARRANT THAT THE SOFTWARE IS ERROR-FREE OR WILL OPERATE WITHOUT
+ INTERRUPTION. THE SOFTWARE IS NOT DESIGNED, INTENDED OR LICENSED
+ FOR USE IN HAZARDOUS ENVIRONMENTS REQUIRING FAIL-SAFE CONTROLS.
+ 3. IF APPLICABLE LAW REQUIRES ANY WARRANTIES WITH RESPECT TO THE
+ SOFTWARE, ALL SUCH WARRANTIES ARE LIMITED IN DURATION TO NINETY
+ (90) DAYS FROM THE DATE OF DELIVERY.
+ 4. NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY GSL SHALL
+ CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF ANY
+ WARRANTY PROVIDED HEREIN.
+ 5. (USA only) SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED
+ WARRANTIES, SO THE ABOVE EXCLUSION MAY NOT APPLY TO END USER.
+ THIS WARRANTY GIVES END USER SPECIFIC LEGAL RIGHTS AND END USER
+ MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO STATE.
+
+ 6. Exclusive Remedy
+
+ End User's exclusive remedy is to return the Software to GSL. Provided
+ that any non-compliance with the above warranty is reported in writing
+ to GSL no more than ninety (90) days following delivery to End User,
+ GSL will use reasonable commercial efforts to supply End User with a
+ replacement copy of the Software that substantially conforms to
+ published specifications, provide a replacement for defective media,
+ or refund to End User the purchase price for the Software, at its
+ option. GSL shall have no responsibility if the Software has been
+ altered in any way, or if the media has been damaged by misuse,
+ accident, abuse, modification or misapplication. Any such misuse,
+ accident, abuse, modification or misapplication of the Software will
+ void the warranty above. THIS REMEDY IS THE SOLE AND EXCLUSIVE REMEDY
+ AVAILABLE TO END USER FOR BREACH OF EXPRESS OR IMPLIED WARRANTIES WITH
+ RESPECT TO THE SOFTWARE.
+
+ 7. LIMITATION OF LIABILITY
+
+ 1. GSL SHALL NOT BE LIABLE TO END USER OR ANY THIRD PARTY FOR ANY
+ INDIRECT, SPECIAL, INCIDENTAL, PUNITIVE, COVER OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, DAMAGES FOR THE INABILITY
+ TO USE EQUIPMENT OR ACCESS DATA, LOSS OF BUSINESS, LOSS OF
+ PROFITS, BUSINESS INTERRUPTION OR THE LIKE), ARISING OUT OF THE
+ USE OF, OR INABILITY TO USE, THE SOFTWARE AND BASED ON ANY THEORY
+ OF LIABILITY INCLUDING BREACH OF CONTRACT, BREACH OF WARRANTY,
+ TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY OR OTHERWISE, EVEN
+ IF GSL OR ITS REPRESENTATIVES HAVE BEEN ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGES AND EVEN IF A REMEDY SET FORTH HEREIN
+ IS FOUND TO HAVE FAILED IN ITS ESSENTIAL PURPOSE.
+ 2. GSL'S TOTAL LIABILITY TO END USER FOR ACTUAL DAMAGES FOR ANY
+ CAUSE WHATSOEVER WILL BE LIMITED TO THE AMOUNT END USER PAID FOR
+ THE SOFTWARE.
+ 3. (USA only) SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION
+ OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THE
+ ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO END USER AND END
+ USER MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO
+ STATE.
+ 4. THE FOREGOING LIMITATIONS ON LIABILITY ARE INTENDED TO APPLY TO
+ THE WARRANTIES AND DISCLAIMERS ABOVE AND ALL OTHER ASPECTS OF
+ THIS EULA.
+
+ 8. U.S. GOVERNMENT RESTRICTED RIGHTS LEGEND
+
+ This Software and the documentation are provided with "RESTRICTED
+ RIGHTS" applicable to private and public licenses alike. Without
+ limiting the foregoing, use, duplication, or disclosure by the U.S.
+ Government is subject to restrictions as set forth in this EULA and as
+ provided in DFARS 227.7202-1(a) and 227.7202-3(a) (1995), DFARS
+ 252.227-7013 (c)(1)(ii)(OCT 1988), FAR 12.212(a)(1995), FAR 52.227-19,
+ or FAR 52.227-14, as applicable. Manufacturer: GSL Biotech LLC
+
+ 9. General
+
+ This EULA shall be governed by the internal laws of the State of
+ Illinois, USA. In each case this EULA shall be construed and enforced
+ without regard to the United Nations Convention on the International
+ Sale of Goods.
+
+ This EULA contains the complete agreement between the parties with
+ respect to the subject matter hereof, and supersedes all prior or
+ contemporaneous agreements or understandings, whether oral or written.
+ End User agrees that any varying or additional terms contained in any
+ purchase order or other written notification or document issued by End
+ User in relation to the Software licensed hereunder shall be of no
+ effect. The failure or delay of GSL to exercise any of its rights
+ under this EULA or upon any breach of this EULA shall not be deemed a
+ waiver of those rights or of the breach.
+
+ If any provision of this EULA shall be held by a court of competent
+ jurisdiction to be contrary to law, then that provision will be
+ enforced to the maximum extent permissible and the remaining
+ provisions of this EULA will remain in full force and effect.
+
+ All questions concerning this EULA shall be directed to GSL. This EULA
+ does not authorize End User to use the trademarks of GSL or its
+ suppliers.
+
+ GSL Biotech LLC
+ July 18th, 2017
diff --git a/media-gfx/brlcad/brlcad-7.32.4.ebuild b/media-gfx/brlcad/brlcad-7.32.4.ebuild
index aa70351e9..180542cac 100644
--- a/media-gfx/brlcad/brlcad-7.32.4.ebuild
+++ b/media-gfx/brlcad/brlcad-7.32.4.ebuild
@@ -43,7 +43,7 @@ DEPEND="${RDEPEND}
)
doc? (
dev-libs/libxslt
- app-doc/doxygen
+ app-text/doxygen
)"
# Install into /usr/ not recommended by upstream due to possible file conflicts
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index 5d6a345ce..5f7c0ad4c 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -41,7 +41,7 @@ DEPEND="${RDEPEND}
)
doc? (
dev-libs/libxslt
- app-doc/doxygen
+ app-text/doxygen
)"
# Install into /usr/ not recommended by upstream due to possible file conflicts
diff --git a/media-libs/imglib2/Manifest b/media-libs/imglib2/Manifest
index 3ce824e00..eaae671d4 100644
--- a/media-libs/imglib2/Manifest
+++ b/media-libs/imglib2/Manifest
@@ -1 +1 @@
-DIST imglib2-6.2.0-sources.tar.gz 1088844 BLAKE2B 919b4261199415e0e575bba297900e5dc177785b70511d797a7f962675adaa61f19467d37d664c12a4dc91df3f1f6cd575309c7f508c4792706942670c6946c0 SHA512 e3381979884dac13d051f1754be0837049e430b71c382666d036fa1d3403bc233a7b39c3b0c587852b08d7d12851043111a1ab206e4049d117dedf847da687e9
+DIST imglib2-6.3.0-sources.tar.gz 1100228 BLAKE2B 65aba1c43980e98018154972bc143093d25e000148805d8ee75459f43dbe301cb0ae10463585fccc51dab28c926900e7c43df13696d408e79d2b4cb55ffadfc6 SHA512 9f6159379d1be6478a9cd53ee88241277761a5e569cd2042e26363f43394abc85d3ea2f72e592a57cff6f8b5f8f4cd46821a4168bf76939f7f77680844231748
diff --git a/media-libs/imglib2/imglib2-6.2.0.ebuild b/media-libs/imglib2/imglib2-6.3.0.ebuild
index d024676c7..4233e6795 100644
--- a/media-libs/imglib2/imglib2-6.2.0.ebuild
+++ b/media-libs/imglib2/imglib2-6.3.0.ebuild
@@ -24,7 +24,7 @@ else
https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ MAVEN_ID="net.imglib2:imglib2:6.3.0"
KEYWORDS="~amd64"
fi
diff --git a/media-libs/imglib2/imglib2-9999.ebuild b/media-libs/imglib2/imglib2-9999.ebuild
index d024676c7..4233e6795 100644
--- a/media-libs/imglib2/imglib2-9999.ebuild
+++ b/media-libs/imglib2/imglib2-9999.ebuild
@@ -24,7 +24,7 @@ else
https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
"
S="${WORKDIR}/${PN}-${P}"
- MAVEN_ID="net.imglib2:imglib2:6.2.0"
+ MAVEN_ID="net.imglib2:imglib2:6.3.0"
KEYWORDS="~amd64"
fi
diff --git a/media-libs/mmg/mmg-5.5.0.ebuild b/media-libs/mmg/mmg-5.5.0.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.0.ebuild
+++ b/media-libs/mmg/mmg-5.5.0.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/media-libs/mmg/mmg-5.5.1.ebuild b/media-libs/mmg/mmg-5.5.1.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.1.ebuild
+++ b/media-libs/mmg/mmg-5.5.1.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/media-libs/mmg/mmg-5.5.2.ebuild b/media-libs/mmg/mmg-5.5.2.ebuild
index e5fa82146..1e8e4d8cb 100644
--- a/media-libs/mmg/mmg-5.5.2.ebuild
+++ b/media-libs/mmg/mmg-5.5.2.ebuild
@@ -22,7 +22,7 @@ DEPEND="
"
RDEPEND="${DEPEND}"
BDEPEND="
- app-doc/doxygen
+ app-text/doxygen
"
src_configure() {
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
new file mode 100644
index 000000000..7270fbee7
--- /dev/null
+++ b/profiles/desc/lhapdf_sets.desc
@@ -0,0 +1,17 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# This file contains descriptions of LHAPDF_SETS USE_EXPAND flags.
+
+nnpdf31_nnlo_as_0118_luxqed - NNPDF31_nnlo_as_0118_luxqed LHAPDF grid
+pdf4lhc15_nlo_asvar - PDF4LHC15_nlo_asvar LHAPDF grid
+ct14qed_proton - CT14qed_proton LHAPDF grid
+ct14lo - CT14lo LHAPDF grid
+ct14nlo - CT14nlo LHAPDF grid
+ct10 - CT10 LHAPDF grid
+mrst2007lomod - MRST2007lomod LHAPDF grid
+nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid
+nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
+cteq66 - CTEQ66 LHAPDF grid
+cteq6l1 - CTEQ6L1 LHAPDF grid
+mrst2004qed - MRST2004qed LHAPDF grid \ No newline at end of file
diff --git a/profiles/make.defaults b/profiles/make.defaults
new file mode 100644
index 000000000..88d3fe603
--- /dev/null
+++ b/profiles/make.defaults
@@ -0,0 +1 @@
+USE_EXPAND="LHAPDF_SETS" \ No newline at end of file
diff --git a/profiles/package.mask b/profiles/package.mask
index 9f3b8e7f5..527c834e4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,17 @@
#--- END OF EXAMPLES ---
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (29 Dec 2023)
+# Depends on removed llvm:14, at the time of writing no llvm:15
+# update available.
+dev-python/llvmlite
+dev-python/numba
+dev-python/numba-dpex
+dev-python/pynndescent
+# Reverse dep of numba
+dev-python/tridesclous
+dev-python/umap-learn
+
# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
# Depends on removed dev-python/toml.
# Alternatives are tomli or tomlkit
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index 57f4fc569..cf724a82a 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,4 +1,4 @@
-DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4
-DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b
-DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
-DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
+DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd
+DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa
+DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
index 002004bca..026dd0476 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..12} )
inherit python-single-r1
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
@@ -27,7 +27,13 @@ DEPEND="
${PYTHON_DEPS}
"
RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
+BDEPEND="dev-build/cmake"
+
+# Remove for next release:
+# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831
+PATCHES=(
+ "${FILESDIR}/${P}-gcc13.patch"
+)
src_install(){
einstalldocs
diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
new file mode 100644
index 000000000..3dd3f8c02
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
@@ -0,0 +1,49 @@
+From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001
+From: Bo YU <tsu.yubo@gmail.com>
+Date: Wed, 19 Jul 2023 18:42:04 +0800
+Subject: [PATCH] fix build issues due to gcc-13
+
+Signed-off-by: Bo YU <tsu.yubo@gmail.com>
+---
+ ext/include/llvm/Support/Signals.h | 1 +
+ src/common/pipeline/library_data.hpp | 1 +
+ src/common/sequence/nucl.hpp | 2 ++
+ 3 files changed, 4 insertions(+)
+
+diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h
+index e0a18e72f..148216b8f 100644
+--- a/ext/include/llvm/Support/Signals.h
++++ b/ext/include/llvm/Support/Signals.h
+@@ -14,6 +14,7 @@
+ #ifndef LLVM_SUPPORT_SIGNALS_H
+ #define LLVM_SUPPORT_SIGNALS_H
+
++#include <cstdint>
+ #include <string>
+
+ namespace llvm {
+diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp
+index 3cbaf0adb..1ffaa7b37 100644
+--- a/src/common/pipeline/library_data.hpp
++++ b/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+
+ #include <map>
+ #include <string>
++#include <cstdint>
+
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } }
+diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp
+index 9c7d6de13..e10e7f583 100755
+--- a/src/common/sequence/nucl.hpp
++++ b/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+
++#include <cstdint>
++
+ #include "utils/verify.hpp"
+
+ /**
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 0845ad7a4..5f573393e 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -10,8 +10,11 @@
<name>Gentoo Biology Project</name>
</maintainer>
<longdescription>
-truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
-hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
-dipspades is assembly module for highly polymorphic diploid genomes
-</longdescription>
+ truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+ hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+ dipspades is assembly module for highly polymorphic diploid genomes
+ </longdescription>
+ <upstream>
+ <remote-id type="github">ablab/spades</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
deleted file mode 100644
index bd7eecbcf..000000000
--- a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx
-index d1e7586..048d934 100644
---- a/Examples/PrintHeader.cxx
-+++ b/Examples/PrintHeader.cxx
-@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[])
- // Get the metadata as a generic object
- string key = itMeta->first, v_string;
- itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags =
-- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID;
-+ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID;
-
- if (itk::ExposeMetaData<string>(mdd, key, v_string))
- {
diff --git a/sci-biology/brkraw/Manifest b/sci-biology/brkraw/Manifest
new file mode 100644
index 000000000..6bc79d823
--- /dev/null
+++ b/sci-biology/brkraw/Manifest
@@ -0,0 +1 @@
+DIST brkraw-0.3.11.gh.tar.gz 3919122 BLAKE2B 9881f53bb3fef038385eab4043f76d21c2e5391131c80daa49c909e7882359ed9d0b41b84fc82acd0432f4bac820a75061842de85b75cceff6f33d6f14988aea SHA512 a1e2725b6f50ff82ea6c4f9eacbd044ccb1c966aa26f2753c0872e3ee5e6469821dad336c9ef221dc6e15df2bed537ed9d31d5b09ff432694b757ab30af53631
diff --git a/sci-biology/brkraw/brkraw-0.3.11.ebuild b/sci-biology/brkraw/brkraw-0.3.11.ebuild
new file mode 100644
index 000000000..60a7767b1
--- /dev/null
+++ b/sci-biology/brkraw/brkraw-0.3.11.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} )
+
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="https://github.com/BrkRaw/brkraw"
+SRC_URI="https://github.com/BrkRaw/brkraw/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Strange test infrastructure involving dynamic download via make:
+# https://github.com/BrkRaw/brkraw/blob/main/.github/workflows/test.yml
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+ >=dev-python/pillow-7.1.1[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.45.0[${PYTHON_USEDEP}]
+ >=dev-python/openpyxl-3.0.3[${PYTHON_USEDEP}]
+ >=dev-python/xlrd-1.1.0[${PYTHON_USEDEP}]
+ >=dev-python/pandas-1[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-3.0.2[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-testexclusion.patch" )
+
+distutils_enable_tests pytest
diff --git a/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch
new file mode 100644
index 000000000..40cc8fc4a
--- /dev/null
+++ b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch
@@ -0,0 +1,11 @@
+--- a/setup.py 2023-07-05 17:09:42.000000000 -0400
++++ b/setup.py 2023-11-28 12:38:07.726369571 -0500
+@@ -24,7 +24,7 @@
+ author_email=__email__,
+ url=__url__,
+ license='GNLv3',
+- packages=find_packages(),
++ packages=find_packages(exclude=["tests", "tests.*"]),
+ install_requires=['nibabel>=3.0.2',
+ 'numpy>=1.18.0',
+ 'pandas>=1.0.0',
diff --git a/sci-biology/clview/metadata.xml b/sci-biology/brkraw/metadata.xml
index 7adf609cd..5c436db45 100644
--- a/sci-biology/clview/metadata.xml
+++ b/sci-biology/brkraw/metadata.xml
@@ -2,14 +2,15 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
</maintainer>
<maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="sourceforge">clview</remote-id>
+ <remote-id type="github">BrkRaw/brkraw</remote-id>
+ <remote-id type="pypi">brkraw</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
deleted file mode 100644
index 69f3a963e..000000000
--- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500
-+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500
-@@ -1786,15 +1786,15 @@
- { int item_no = (int) client_data;
- switch (item_no)
- { case CMD_HELP_HTMLHELP:
-- { system("netscape "PREFIX"/cluster/html/index.html &");
-+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &");
- break;
- }
- case CMD_HELP_MANUAL:
-- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &");
-+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &");
- break;
- }
- case CMD_HELP_DOWNLOAD:
-- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
-+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
- break;
- }
- case CMD_HELP_FILEFORMAT:
-@@ -1852,7 +1852,7 @@
- XtManageChild(widget);
- free(helptext);
- n = 0;
-- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0);
-+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0);
- XtSetArg(args[n], XmNx, 10); n++;
- XtSetArg(args[n], XmNy, 410); n++;
- XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++;
diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest
deleted file mode 100644
index 271e4eb76..000000000
--- a/sci-biology/clview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1
-DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9
diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
deleted file mode 100644
index 2f200426d..000000000
--- a/sci-biology/clview/clview-0.1.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools"
-HOMEPAGE="https://sourceforge.net/projects/clview"
-SRC_URI="
- https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz"
-
-# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz
-# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/
-# contents. clview compiles against both versions with same warning messages from g++.
-#
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/
-# total 188
-# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Dec 2 22:23 .
-# drwx------ 5 mmokrejs portage 4096 Dec 2 22:23 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17 2008 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 906 Sep 14 2008 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec 2 22:23 AceParser.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22 2009 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 9200 Dec 16 2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 8844 Dec 2 22:23 GBase.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29 2008 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10 2008 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22 2009 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6246 Sep 14 2008 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec 2 22:23 LayoutParser.o
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/
-# total 268
-# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Nov 18 2008 .
-# drwxr-xr-x 3 mmokrejs mmokrejs 4096 Oct 18 2006 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs 9515 Nov 7 2005 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 886 Nov 7 2005 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov 7 2005 BitHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 7250 Nov 7 2005 GArgs.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 2507 Nov 7 2005 GArgs.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18 2008 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 8142 Nov 18 2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov 7 2005 GCdbYank.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 1831 Nov 7 2005 GCdbYank.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov 7 2005 GFastaFile.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov 7 2005 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov 7 2005 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 28 Nov 7 2005 GReadBuf.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 4022 Nov 7 2005 GReadBuf.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 48 Nov 7 2005 GShMem.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 4012 Nov 7 2005 GShMem.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov 7 2005 GString.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 8453 Nov 7 2005 GString.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov 7 2005 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6063 Nov 7 2005 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov 7 2005 gcdb.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 6941 Nov 7 2005 gcdb.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 8998 Nov 7 2005 gcompress.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs 3670 Nov 7 2005 gcompress.h
-#
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="=x11-libs/fox-1.6*"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_unpack() {
- unpack clview_src.tar.gz
-}
-
-src_prepare() {
- default
- # FIXME: we have to run `/usr/bin/fox-config --cflags' to yield
- # `-I/usr/include/fox-1.6'
- # similarly `fox-config --libs' to yield e.g.
- # `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11
- # -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm
- # -lcups -lnsl -lGLU -lGL'
- FOXVERSION=`WANT_FOX="1.6" fox-config --version`
- FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix`
- FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags`
- FOXLIBS=`WANT_FOX="1.6" fox-config --libs`
- einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}"
-
- sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile"
- sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile"
- sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile"
- sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile"
- sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile"
- sed -i "s#-I-#-I #" clview/Makefile || die
-
- # see tgi_cl/gcl/
- sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die
-}
-
-src_compile(){
- cd "${S}"/clview || die
- default
-}
-
-src_install() {
- # install at least the binaries for clview when we cannot compile it
- dobin clview/clview
-}
diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
index 86304f4f3..8ddd4007e 100644
--- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
+++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit check-reqs
DESCRIPTION="BIDS data files released with the DRLFOM publication"
-HOMEPAGE="http://chymera.eu/docs/focus/open-science/"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
SRC_URI="
https://zenodo.org/record/3598424/files/${P}.tar.xz
"
@@ -15,9 +15,6 @@ LICENSE="CC-BY-SA-4.0"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-RDEPEND=""
-DEPEND=""
-
pkg_pretend() {
CHECKREQS_DISK_BUILD="21G"
check-reqs_pkg_pretend
diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest
new file mode 100644
index 000000000..c158050fa
--- /dev/null
+++ b/sci-biology/fastp/Manifest
@@ -0,0 +1 @@
+DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76
diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild
new file mode 100644
index 000000000..70d5ce330
--- /dev/null
+++ b/sci-biology/fastp/fastp-0.23.4.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor"
+HOMEPAGE="https://github.com/OpenGene/fastp"
+SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="app-arch/libdeflate
+ dev-libs/isa-l"
+
+src_install() {
+ dodir /usr/bin
+ emake PREFIX="${ED}"/usr install
+}
diff --git a/sci-biology/fastp/metadata.xml b/sci-biology/fastp/metadata.xml
new file mode 100644
index 000000000..d51d87c5a
--- /dev/null
+++ b/sci-biology/fastp/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">OpenGene/fastp</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
deleted file mode 100644
index a3872acf0..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400
-+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400
-@@ -141,7 +141,7 @@
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
- #$(info $$CUDAVER is [${CUDAVER}])
--CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
-+CUDA_INSTALLATION = /opt/cuda
- GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION})
- LIB_CUDA = ${CUDA_INSTALLATION}/lib64
- INC_CUDA = ${CUDA_INSTALLATION}/include
diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
deleted file mode 100644
index 40409ec08..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400
-+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400
-@@ -29,6 +29,8 @@
- TMPCXXFLAGS_2=
- TMPNAME_1=
- TMPNAME_2=
-+cuda=1
-+cpu=1
-
- ifndef cuda
- ifndef cpu #Default single cpu, no threading
-@@ -74,7 +75,7 @@
- ifdef NVCC11
- NVCC=${NVCC11}
- endif
--NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
-+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
- ifeq ($(CLOBBER_CLANG),1)
- NVCCFLAGS+= -DCLOBBER_CLANG
- endif
diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
deleted file mode 100644
index 9ddb11a2b..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400
-+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400
-@@ -75,6 +75,7 @@
- #include <iostream>
- #include <fstream>
- #include <sstream>
-+#include <stdexcept>
- #include "NewNifti/NewNifti.h"
- #include "newmatio.h"
- #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
deleted file mode 100644
index 39737fd85..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch
+++ /dev/null
@@ -1,198 +0,0 @@
-From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:54:37 +1300
-Subject: [PATCH] Adjust the build system so it doesnt build packages
- externally provided by portage. Make the compilation flags more generic and
- easily adjustable. Make the build system stop at the first fault.
-
----
- build | 6 +++---
- config/buildSettings.mk | 20 ++++++++++----------
- config/common/buildproj | 8 +++++---
- config/common/vars.mk | 10 +++++-----
- extras/build | 8 ++++----
- src/mist-clean/Makefile | 2 +-
- 6 files changed, 28 insertions(+), 26 deletions(-)
-
-diff --git a/build b/build
-index 05dac06c..d90e407b 100755
---- a/build
-+++ b/build
-@@ -3,7 +3,7 @@
- if [ $# -ge 1 ] ; then
- PROJECTS="$@";
- else
-- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
-+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
- meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
- DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
- asl_mfree \
-@@ -80,8 +80,8 @@ xtract";
- done
- fi
-
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
- finalStatus=$?
- if [ $finalStatus -eq 0 ]; then
- echo "Build completed successfully.";
-diff --git a/config/buildSettings.mk b/config/buildSettings.mk
-index b2e1f150..04532fc2 100644
---- a/config/buildSettings.mk
-+++ b/config/buildSettings.mk
-@@ -18,7 +18,7 @@ MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
- INSTALL = install -p
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- DEPENDFLAGS = -MM
- MACHDBGFLAGS = -g
- #####################################################################
-@@ -124,19 +124,19 @@ endif # if Darwin
- #####################################################################
- ifeq ($(SYSTYPE), Linux)
- ############### System Vars #####################################
--CC = gcc
--CXX = c++
--CXX11 = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
-+CXX11 = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
--ARCHFLAGS = -m64
--ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
-+ARCHFLAGS =
-+ARCHLDFLAGS =
- PARALLELFLAGS = -fopenmp
--OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
- SGI_ANSI_FLAGS = -ansi -fullwarn
- ANSI_FLAGS = ${GNU_ANSI_FLAGS}
--RANLIB = echo
-+RANLIB = @@GENTOO_RANLIB@@
- FSLML = ${FSLDIR}/bin/fslml
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
-@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
- NVCC = ${CUDA_INSTALLATION}/bin/nvcc
- ############### External Libs #####################################
- # ZLIB library
--LIB_ZLIB = /lib64
--INC_ZLIB = /usr/include
-+#LIB_ZLIB = /lib64
-+#INC_ZLIB = /usr/include
- # QT library
- QTDIR = /usr/lib/qt3
- LIB_QT = ${QTDIR}/lib
-diff --git a/config/common/buildproj b/config/common/buildproj
-index 2f0f2b8f..48624a1f 100755
---- a/config/common/buildproj
-+++ b/config/common/buildproj
-@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
- fi
- PROJECTS="$@" ; export PROJECTS ;
-
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- FSLMASTERBUILD=1
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
-
-@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
- if [ -x ./fslconfig ] ; then
- . ./fslconfig ;
- fi
-- if ${MAKE} -k ${MAKEOPTIONS} ; then
-+ if ${MAKE} ${MAKEOPTIONS} ; then
- if ${MAKE} ${MAKEOPTIONS} install ; then
- installok=true;
- # Clean up after ourselves
-@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
- if [ $installok = false ] ; then
- echo " "
- echo "ERROR::Could not install $projname successfully" ;
-+ exit 1
- fi
- else
- echo " "
-@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
- echo " "
- echo " "
- errorprojs="$errorprojs $projname" ; export errorprojs ;
-+ exit 1
- fi
- fi
- done
-diff --git a/config/common/vars.mk b/config/common/vars.mk
-index b027b010..aeeae67c 100755
---- a/config/common/vars.mk
-+++ b/config/common/vars.mk
-@@ -24,15 +24,15 @@ USRINCFLAGS =
- USRCFLAGS =
- USRCXXFLAGS =
-
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
-
--AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
-
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCFLAGS}
-
--CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
-
- HFILES = *.h
- AFILES = *.a
-diff --git a/extras/build b/extras/build
-index 59e7a2ed..0d68232e 100755
---- a/extras/build
-+++ b/extras/build
-@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
- BUILDICONV=1
- fi
- fi
--PROJECTS="tcl tk"
-+#PROJECTS="tcl tk"
- if [ ${BUILDZLIB} -eq 1 ]; then
- PROJECTS="${PROJECTS} zlib"
- fi
--PROJECTS="${PROJECTS} libpng"
-+#PROJECTS="${PROJECTS} libpng"
- if [ ${BUILDICONV} -eq 1 ]; then
- PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
--PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
-+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
- for projname in $PROJECTS; do
- if [ -d $FSLESRCDIR/$projname ] ; then
- buildIt $FSLESRCDIR $projname 1
-diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
-index 20402cca..6918bee4 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,6 +52,6 @@ installpython:
- cp -r python/* ${DESTDIR}/python/mist
-
- clean:
-- rm -f ${OBJS} mist/mist.o mist/mist
-+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
-
- .PHONY: all clean installdata
---
-2.24.1
-
diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch
deleted file mode 100644
index afb52b2e1..000000000
--- a/sci-biology/gffcompare/files/Makefile.patch
+++ /dev/null
@@ -1,79 +0,0 @@
---- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200
-+++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200
-@@ -16,7 +16,7 @@
- endif
-
- # CVS checked in
--CC := g++
-+CXX ?= g++
- BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \
- -fno-exceptions -fno-rtti -D_REENTRANT
-
-@@ -24,7 +24,8 @@
-
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
- # -- release build
-- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS)
-+ CXXFLAGS ?= -O3 -g
-+ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- LDFLAGS =
- LIBS =
- ifneq (,$(findstring static,$(MAKECMDGOALS)))
-@@ -37,16 +38,16 @@
- ifeq "$(GCCVER49)" "0"
- $(error gcc version 4.9 or greater is required for this build target)
- endif
-- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
-+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
- GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
- ifeq "$(GCCVER5)" "1"
-- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-- #CFLAGS += -fcheck-pointer-bounds -mmpx
-+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx
- endif
-- CFLAGS += $(BASEFLAGS)
-- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS)
-- LDFLAGS := -g
-+ CXXFLAGS += $(BASEFLAGS)
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
-+ LDFLAGS ?= -g
- #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
- LIBS := -lasan -lubsan -ldl $(LIBS)
- else
-@@ -55,26 +56,26 @@
- # GMEMTRACE=1
- #endif
- #--- just plain debug build ---
-- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-- LDFLAGS = -g
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-+ LDFLAGS += -g
- LIBS =
- endif
- endif
-
- %.o : %.c
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest
index bd58b4117..4c5068f0a 100644
--- a/sci-biology/imagej/Manifest
+++ b/sci-biology/imagej/Manifest
@@ -1,4 +1,3 @@
DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
-DIST ij153.zip 6503763 BLAKE2B 7b3b30b55fe844e110f3e85eab7790376fc2d62300312c0b9037726758fcbfd5c4a6072842aa09e6ed08a2d593c2b1966d985de5972d801cf01638b41134325e SHA512 788003b35f7c3dd6f9bcda298637a3de78d745de8dd685cf88d8cc6ae22e142b07620c1e47a182d1e87178d68d591e381813f40cedc59f08d21af317065d7de0
-DIST ij153t-src.zip 1549329 BLAKE2B 7e43b759b96c8683be2175348a88080cdd4f038153a937717ebb0f480f9c8fb83d15184f8bf25060dc395ac3b13fd57f905621e680e481ad7dfdc090bbefb323 SHA512 861ecba6a20835566ec4038ffa30211308d37c41cecdfb97ea33d963c0ac2f1dbec0679c014335f89df24317334aeb30350dd09ee5f0fa33990f5355dd2fd06f
-DIST imagej-1.54f.gh.tar.gz 5768851 BLAKE2B a3c04ec949937e01ccf9b2a3a8432206c30833fc1f26a8ff0f487dece26c35a315b3c72cf88fec63ba090c5da6db51795c471b85d43f017f676c9f557f802cfc SHA512 a46deeec0e43c56598a0950393e6d72f866c9026434fb87fd5e4a604efcd13f3e50332b3893ba9cf443dd73fdfab9ddbcbf90604d7acfba7d1a1b72d7d1c916b
+DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9
+DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615
diff --git a/sci-biology/imagej/imagej-1.53t.ebuild b/sci-biology/imagej/imagej-1.53t.ebuild
deleted file mode 100644
index 952eff08b..000000000
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit java-pkg-2 java-ant-2 desktop
-
-MY_PN="ij"
-MY_PV=${PV//.}
-IJ_PV=${MY_PV::-1}
-
-DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="https://imagej.nih.gov/ij/"
-
-SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
- https://imagej.nih.gov/ij/images/ImageJ.png
- plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
-# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
-# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
-
-LICENSE="public-domain" # http://imagej.net/disclaimer.html
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-IUSE="doc plugins debug"
-
-RDEPEND="
- >=virtual/jre-1.7:*
- dev-java/java-config
-"
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.7:*
-"
-BDEPEND="
- dev-java/ant-core
- app-arch/unzip
-"
-
-S="${WORKDIR}/source"
-IJ_S=${WORKDIR}/ImageJ
-
-src_prepare() {
- cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
-
- if ! use debug ; then
- sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
- fi
- default
-}
-
-src_compile() {
- local antflags="build"
- use doc && antflags="${antflags} javadocs"
-
- ant ${antflags} || die "ant build failed"
-
- # Max memory usage depends on available memory and CPU type
- MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
- IJ_MAX_MEM=$(expr ${MEM} / 1024)
- if use x86 && $IJ_MAX_MEM -gt 2048 ; then
- IJ_MAX_MEM=2048
- fi
- # build finished, generate startup wrapper
- cat <<EOF > "${T}/${PN}"
-#!${EPREFIX}/bin/bash
-IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
-if !([ "\${IJ_HOME}" ]) ; then
- IJ_HOME=\${HOME}/.imagej
-fi
-if [ -d \${IJ_HOME}/plugins ] ; then
- IJ_PLG=\${IJ_HOME}
-else
- IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
-fi
-if !([ "\$IJ_MEM" ]) ; then
- IJ_MEM=${IJ_MAX_MEM}
-fi
-if !([ "\$IJ_CP" ]) ; then
- IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
-else
- IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
-fi
-\$(java-config --java) \\
- -Xmx\${IJ_MEM}m -Dswing.aatext=true \\
- -Dawt.useSystemAAFontSettings=on\\
- -cp \${IJ_CP} \\
- -Duser.home=\${IJ_HOME} \\
- -Dplugins.dir=\${IJ_PLG} \\
- ij.ImageJ "\$@"
-EOF
-}
-
-src_install() {
- java-pkg_dojar *.jar
- dobin "${T}/${PN}"
-
- if use plugins ; then
- cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
- cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
- fi
-
- use doc && java-pkg_dohtml -r "${WORKDIR}"/api
-
- insinto /usr/share/pixmaps
- doins "${WORKDIR}/${PN}".png
- make_desktop_entry "${PN}" ImageJ "${PN}" Graphics
-}
-
-pkg_postinst() {
- einfo ""
- einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
- einfo "by setting the environmental variable, \$IJ_HOME."
- einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
- einfo ""
- einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
- einfo "and the class path by setting the environmental variable, \$IJ_CP."
- einfo ""
- einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
- einfo "and add *.class files to \$IJ_HOME/plugins folder"
- einfo ""
-}
diff --git a/sci-biology/imagej/imagej-1.54f.ebuild b/sci-biology/imagej/imagej-1.54h-r1.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-1.54f.ebuild
+++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit java-pkg-2 java-ant-2 desktop
MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
@@ -59,7 +59,7 @@ src_prepare() {
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
fi
fi
diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=8
inherit java-pkg-2 java-ant-2 desktop
MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
@@ -59,7 +59,7 @@ src_prepare() {
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
fi
fi
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
index 3faf27a11..021929bad 100644
--- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
+++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit check-reqs
DESCRIPTION="BIDS data files released with the IRSABI publication"
-HOMEPAGE="http://chymera.eu/docs/focus/open-science/"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
SRC_URI="
https://zenodo.org/record/3601531/files/${P}.tar.xz
"
diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest
index 4a1880c5f..249395f6f 100644
--- a/sci-biology/libBigWig/Manifest
+++ b/sci-biology/libBigWig/Manifest
@@ -1 +1,2 @@
DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71
+DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40
diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
new file mode 100644
index 000000000..7dc83ceed
--- /dev/null
+++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
+HOMEPAGE="https://github.com/dpryan79/libBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/dpryan79/libBigWig"
+else
+ SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="net-misc/curl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ default
+ sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
+ sed -e "s:/lib:/$(get_libdir):" -i Makefile || die
+}
+
+src_install(){
+ emake install DESTDIR="${ED}"
+}
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
new file mode 100644
index 000000000..3585038a3
--- /dev/null
+++ b/sci-biology/multiqc/Manifest
@@ -0,0 +1 @@
+DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml
new file mode 100644
index 000000000..09bd2b6e6
--- /dev/null
+++ b/sci-biology/multiqc/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">ewels/MultiQC</remote-id>
+ <remote-id type="pypi">multiqc</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
new file mode 100644
index 000000000..187f06c22
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.19.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
+HOMEPAGE="https://multiqc.info/"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/coloredlogs[${PYTHON_USEDEP}]
+ dev-python/future[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/lzstring[${PYTHON_USEDEP}]
+ dev-python/markdown[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+ dev-python/rich-click[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/spectra[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[$PYTHON_USEDEP]
+ dev-python/humanize[$PYTHON_USEDEP]
+ dev-python/pyaml-env[$PYTHON_USEDEP]"
+
+# pypi tarball does not include tests
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest
index 54770b3ae..1963b7225 100644
--- a/sci-biology/neuroconv/Manifest
+++ b/sci-biology/neuroconv/Manifest
@@ -1 +1,2 @@
DIST neuroconv-0.2.4.gh.tar.gz 757136 BLAKE2B a3a21b3a00667bde4461d91ade514891c8710f309413b100e1cccfd2684dfcbf9b21feaf4f58b3c5ff845aa08e69bf47467b411926eeb7d3b2862753302b1d9b SHA512 293038feae2704442b81ba0f012d775ba96d7bdffb6aaacaaebd09ca2f8b39e91ef4ea69c972abf060f0f9ab8cb76fedb77dda67455fa992edd52f0e6e504b0d
+DIST neuroconv-0.4.6.gh.tar.gz 1000357 BLAKE2B 24fc43a4c7c1cb588b5af49c1da2348f775506efd0c36b838b7882cf4a03520dac6e0fe6fd17310c17ae84371d3eeb8e3aec4b16fc3b07c10bec2e3c46e51dff SHA512 eeccc6900b6ae9f053f67503a93c4040033afc8b056b8869ad562f7cd2dd802cce2b7a467b5ccaa20fe84a188697821c328043b6177302d1913a30a5a789ae15
diff --git a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
new file mode 100644
index 000000000..1676aa6b7
--- /dev/null
+++ b/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Create NWB files from proprietary formats."
+HOMEPAGE="https://github.com/catalystneuro/neuroconv"
+SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+ecephys +icephys +ophys"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/hdmf-zarr[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/parse[${PYTHON_USEDEP}]
+ dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ ecephys? (
+ dev-python/spikeinterface[${PYTHON_USEDEP}]
+ )
+ icephys? (
+ dev-python/neo[${PYTHON_USEDEP}]
+ )
+ ophys? (
+ sci-biology/roiextractors[${PYTHON_USEDEP}]
+ )
+"
+BDEPEND="
+ test? (
+ dev-python/parameterized[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+ # Additional tests require complex data getting infrastructure, ophys tests still have issues:
+ # https://github.com/catalystneuro/neuroconv/issues/305
+ local my_tests=( "tests/test_minimal" )
+ use ecephys && my_tests+=( "tests/test_ecephys" )
+ #use ophys && my_tests+=( "tests/test_ophys" )
+ epytest ${my_tests[*]// /|}
+}
diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
deleted file mode 100644
index e229d25fb..000000000
--- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- a/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:07.700111595 +0200
-+++ b/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:29.453556439 +0200
-@@ -219,36 +219,6 @@
- assert_raises(ValueError, masker.fit_transform, data_img)
-
-
--def test_joblib_cache():
-- from sklearn.externals.joblib import hash, Memory
-- mask = np.zeros((40, 40, 40))
-- mask[20, 20, 20] = 1
-- mask_img = Nifti1Image(mask, np.eye(4))
--
-- with testing.write_tmp_imgs(mask_img, create_files=True) as filename:
-- masker = NiftiMasker(mask_img=filename)
-- masker.fit()
-- mask_hash = hash(masker.mask_img_)
-- masker.mask_img_.get_data()
-- assert_true(mask_hash == hash(masker.mask_img_))
--
-- # Test a tricky issue with memmapped joblib.memory that makes
-- # imgs return by inverse_transform impossible to save
-- cachedir = mkdtemp()
-- try:
-- masker.memory = Memory(cachedir=cachedir, mmap_mode='r',
-- verbose=0)
-- X = masker.transform(mask_img)
-- # inverse_transform a first time, so that the result is cached
-- out_img = masker.inverse_transform(X)
-- out_img = masker.inverse_transform(X)
-- out_img.to_filename(os.path.join(cachedir, 'test.nii'))
-- finally:
-- # enables to delete "filename" on windows
-- del masker
-- shutil.rmtree(cachedir, ignore_errors=True)
--
--
- def test_mask_init_errors():
- # Errors that are caught in init
- mask = NiftiMasker(mask_strategy='oops')
diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest
index 2ba87b1bb..4a9a85cc0 100644
--- a/sci-biology/nitime/Manifest
+++ b/sci-biology/nitime/Manifest
@@ -1 +1,2 @@
+DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21
DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406
diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml
index 041507ac7..606822ddb 100644
--- a/sci-biology/nitime/metadata.xml
+++ b/sci-biology/nitime/metadata.xml
@@ -10,9 +10,9 @@
<name>Gentoo Science Project</name>
</maintainer>
<longdescription lang="en">
-Nitime is a library for time-series analysis of data from neuroscience experiments
-in both the time and spectral domains.
-</longdescription>
+ Nitime is a library for time-series analysis of data from neuroscience experiments
+ in both the time and spectral domains.
+ </longdescription>
<upstream>
<remote-id type="github">nipy/nitime</remote-id>
<remote-id type="pypi">nitime</remote-id>
diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild
new file mode 100644
index 000000000..7e47d7288
--- /dev/null
+++ b/sci-biology/nitime/nitime-0.10.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Time-series analysis of neuroscience data"
+HOMEPAGE="http://nipy.org/nitime/index.html"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND="${COMMON_DEPEND}
+ dev-python/cython[${PYTHON_USEDEP}]
+ "
+RDEPEND="
+ ${COMMON_DEPEND}
+ dev-python/networkx[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ "
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild
index f297c85f0..ee81c01dc 100644
--- a/sci-biology/nitime/nitime-9999.ebuild
+++ b/sci-biology/nitime/nitime-9999.ebuild
@@ -3,9 +3,10 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 git-r3 virtualx
+inherit distutils-r1 git-r3
DESCRIPTION="Time-series analysis of neuroscience data"
HOMEPAGE="http://nipy.org/nitime/index.html"
@@ -16,9 +17,6 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS=""
-# import file mismatch:
-RESTRICT="test"
-
COMMON_DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
@@ -35,7 +33,3 @@ RDEPEND="
distutils_enable_tests pytest
distutils_enable_sphinx doc
-
-python_test() {
- virtx pytest -v || die
-}
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.4.ebuild
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest
new file mode 100644
index 000000000..2e6582002
--- /dev/null
+++ b/sci-biology/snapgene-viewer/Manifest
@@ -0,0 +1 @@
+DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f
diff --git a/sci-biology/snapgene-viewer/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml
new file mode 100644
index 000000000..5c83ce208
--- /dev/null
+++ b/sci-biology/snapgene-viewer/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>pacho@gentoo.org</email>
+ <name>Pacho Ramos</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-chemistry@gentoo.org</email>
+ <name>Gentoo Chemistry Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
new file mode 100644
index 000000000..d117fbc14
--- /dev/null
+++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
@@ -0,0 +1,65 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit unpacker wrapper xdg
+
+DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis"
+HOMEPAGE="https://www.snapgene.com/features"
+SRC_URI="snapgene_${PV}_linux.deb"
+SNAPGENE_DOWNLOAD="https://www.snapgene.com/local/targets/download.php?os=linux_deb&variant=paid&release=${PV}"
+RESTRICT="fetch"
+
+LICENSE="GSL"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+# ldd /opt/gslbiotech/snapgene/snapgene
+RDEPEND="${DEPEND}
+ app-arch/bzip2
+ app-arch/xz-utils
+ app-crypt/qca[qt6]
+ dev-libs/openssl-compat:1.1.1
+ dev-qt/qt5compat:6
+ dev-qt/qtbase:6[concurrent,gui,network,opengl,sql,widgets,xml]
+ dev-qt/qtdeclarative:6
+ dev-qt/qtpositioning:6
+ dev-qt/qtwebchannel:6
+ dev-qt/qtwebengine:6
+ media-libs/libglvnd
+ media-libs/tiff-compat:4
+ sci-libs/htslib:0/3
+ sys-devel/gcc
+ sys-libs/glibc
+ sys-libs/libcxx[libcxxabi]
+ sys-libs/libunwind:0/8
+ x11-libs/libX11
+ x11-libs/libXau
+ x11-libs/libXdmcp
+ x11-libs/libxcb
+"
+BDEPEND=">=dev-util/patchelf-0.10"
+
+S="${WORKDIR}"
+QA_PREBUILT="*"
+
+pkg_nofetch() {
+ elog "Please download ${SRC_URI} from"
+ elog "${SNAPGENE_DOWNLOAD}"
+ elog "and place it into your DISTDIR directory."
+}
+
+src_install() {
+ patchelf --replace-needed libunwind.so.1 libunwind.so.8 \
+ opt/gslbiotech/snapgene/snapgene || die
+
+ mv usr/share/doc/snapgene usr/share/doc/${PF} || die
+ gzip -d usr/share/doc/${PF}/changelog.Debian.gz || die
+
+ insinto /
+ doins -r *
+
+ fperms +x /opt/gslbiotech/snapgene/snapgene{,.sh}
+ make_wrapper ${PN} ./snapgene.sh /opt/gslbiotech/snapgene/
+}
diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch
deleted file mode 100644
index 44acc42b0..000000000
--- a/sci-biology/sra-tools/files/libs_sra_Makefile.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100
-@@ -100,7 +100,7 @@
- $(addsuffix .$(LOBX),$(SRAPATH_SRC))
-
- $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ)
-- $(LD) --slib -o $@ $^
-+ $(LD) --slib -o $(DESTDIR)$@ $^
-
- libsrapath.vers.h:
- @ true
-@@ -138,10 +138,10 @@
- -dklib
-
- $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB)
-
- $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB)
-
- SRASCHEMA_SRC = \
- sraschema-stub
-@@ -168,10 +168,10 @@
- $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC))
-
- $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS)
-- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
-+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
-
- $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS)
-- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
-+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
-
- libsraschema_tag:
- @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ)
-@@ -205,10 +205,10 @@
- -dklib
-
- $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
-
- $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
-
- libsradb_tag: $(SRADB_TAGS)
- @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ)
-@@ -236,10 +236,10 @@
- -dklib
-
- $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
-
- $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
-
- libwsradb_tag: $(WSRADB_TAGS)
- @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ)
-@@ -266,10 +266,10 @@
- -dklib
-
- $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ)
-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
-
- $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ)
-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
-
- libsrareader_tag:
- @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ)
diff --git a/sci-biology/sra-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch
deleted file mode 100644
index bf66c6e46..000000000
--- a/sci-biology/sra-tools/files/sra_sdk-destdir.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100
-@@ -141,7 +141,7 @@
-
- # create all required output directories
- makedirs:
-- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
-+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR)
-
- ifeq (win,$(OS))
-
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100
-@@ -38,10 +38,10 @@
- # versioned output
- if [ "$VERS" = "" ]
- then
-- DLIB_CMD="$DLIB_CMD -o $TARG"
-- EXE_CMD="$EXE_CMD -o $TARG"
-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG"
-+ EXE_CMD="$EXE_CMD -o $TARG"
- else
- set-vers $(echo $VERS | tr '.' ' ')
-- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS"
- fi
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100
-@@ -52,12 +52,12 @@
-
- set-vers $(echo $VERS | tr '.' ' ')
-
--cd "$OUTDIR" || exit 5
-+cd $DESTDIR$OUTDIR || exit 5
-
- # create link
- create-link ()
- {
-- rm -f "$2"
-+ rm -f $DESTDIR"$2"
- local CMD="ln -s $1 $2"
- echo $CMD
- $CMD
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100
-@@ -77,7 +77,7 @@
- CMD="$CMD $TARG"
- else
- set-vers $(echo $VERS | tr '.' ' ')
-- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
-+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS"
- fi
-
- # tack on object files
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100
-@@ -36,12 +36,12 @@
- LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
-
- LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
-
- # tool options
- WARN = -Wall -Wno-variadic-macros # -Wconversion
diff --git a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
deleted file mode 100644
index 738d67cbd..000000000
--- a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100
-@@ -89,7 +89,7 @@
- $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg
-
- $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg
-- cp $^ $@
-+ cp $^ $(DESTDIR)$@
-
- VDB_COPY_SRC = \
- num-gen \
diff --git a/sci-chemistry/chimera/Manifest b/sci-chemistry/chimera/Manifest
index c6bfe04fd..953fae5f9 100644
--- a/sci-chemistry/chimera/Manifest
+++ b/sci-chemistry/chimera/Manifest
@@ -1,2 +1,3 @@
DIST Chimera512.png 68464 BLAKE2B 51797728b8b9421ab6e42e57bb60881a706d17eed09cbef57506f706b7ebab6511397f90834d15efaea5e86a22fc2ff9e55cf42c7a87d6166716444252d18f49 SHA512 6ed0dd8bd1b5a6b164f80acc1d7e1a91629513b147d37472e1831b657201a3f25c1c0c9a1b44bf565afaa4aa99469910d1ac307a45a80b9a12d0554e1812e2c5
DIST chimera-1.17.1-linux_x86_64.bin 149832020 BLAKE2B 01e78d09a3373a3d927c93daa03d0c17473c18079afd989a29afaad5c56aa57bbfeb968bcef42eb50924e1cde67e939c92a545080c0e7b55549c30e43aae564d SHA512 f6df3ad320f09b3f8d918660a4a7596505c2a97ac0d60a4f6ef9c414851a90bb59ccba9728d5a71df93404b8c6ecf99ab9dca84befcfa10e60285f3a33e3c3bc
+DIST chimera-1.17.3-linux_x86_64.bin 155528316 BLAKE2B 09caddbac9a518606b8065a19840fd2f5e3a57cbb529bea2e4b63cb83ecd91105c1de34dc3f1139382fc80f14e69b28c39152d9b15e16c39a08732ebcd374c51 SHA512 cfbf42dd3aa030db0619bf5750d08ba94acc53f54a890109d422a675394616afba9c85779e5d62bcd4ad83db4a7cfcf8190c2c42c84719c991061859c87288b7
diff --git a/sci-chemistry/chimera/chimera-1.17.3.ebuild b/sci-chemistry/chimera/chimera-1.17.3.ebuild
new file mode 100644
index 000000000..4fdafd361
--- /dev/null
+++ b/sci-chemistry/chimera/chimera-1.17.3.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit desktop xdg
+
+DESCRIPTION="Next generation molecular visualization program from RBVI"
+HOMEPAGE="https://www.cgl.ucsf.edu/chimera/"
+SRC_URI="${P}-linux_x86_64.bin
+ mirror+https://dev.gentoo.org/~pacho/${PN}/Chimera512.png"
+
+SLOT="0"
+LICENSE="chimera"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="fetch mirror strip"
+QA_PREBUILT="*"
+
+DEPEND=""
+BDEPEND=""
+RDEPEND="
+ dev-lang/tcl
+ dev-lang/tk
+ dev-libs/expat
+ dev-libs/libotf
+ dev-libs/openssl:0
+ dev-libs/libpcre
+ sys-libs/zlib
+ media-libs/fontconfig
+ media-libs/freetype
+ media-libs/ftgl
+ media-libs/libpng
+ media-libs/tiff
+ sci-libs/hdf5
+ sys-devel/gcc[openmp,fortran]
+ media-libs/libjpeg-turbo
+ virtual/glu
+ virtual/opengl
+ x11-libs/libX11
+ x11-libs/libICE
+ x11-libs/libXext
+ x11-libs/libXft
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXrender
+ x11-libs/libSM
+ x11-libs/libXt
+ x11-libs/libGLw
+ virtual/libcrypt:=
+"
+
+S="${WORKDIR}"
+
+pkg_nofetch() {
+ elog "Please visit"
+ elog "https://www.cgl.ucsf.edu/chimera/download.html"
+ elog "and download ${P}-linux_x86_64.bin into your DISTDIR"
+}
+
+src_unpack() {
+ cp "${DISTDIR}"/${P}-linux_x86_64.bin ${P}-linux_x86_64.bin.zip
+ unzip ${P}-linux_x86_64.bin.zip || die
+}
+
+src_install() {
+ chmod +x ./chimera.bin
+ dodir /opt/
+ ./chimera.bin -d foo || die
+ newicon "${DISTDIR}"/Chimera512.png Chimera.png
+ make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera
+ mv foo "${ED}/opt/${PN}" || die
+
+ cat >> "${T}"/chimera <<- EOF
+ #!${EPREFX}/bin/bash
+
+ export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
+ "${EPREFIX}/opt/${PN}/bin/chimera" \$@
+ EOF
+
+ exeinto /opt/bin/
+ doexe "${T}"/chimera
+
+ # point the symlink to the correct location
+ rm "${ED}/opt/chimera/include/ft2build.h" || die
+ dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h
+
+ if use prefix; then
+ local i
+ for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
+ patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
+ done
+ fi
+}
diff --git a/sci-electronics/mpremote/Manifest b/sci-electronics/mpremote/Manifest
index a23fad530..1e55b52d3 100644
--- a/sci-electronics/mpremote/Manifest
+++ b/sci-electronics/mpremote/Manifest
@@ -1 +1,2 @@
DIST mpremote-0.4.0.tar.gz 27266 BLAKE2B b31b6184d0f4fc5c525ea7d5d8d2722404e9ce82ce143ea9a14b8bdef28af3260514dd25ec756a0ac2507d5b206fa9d07ce67bd2228b1568d9495c9082bdace8 SHA512 580f0286d8973a93105a04c681428f798e0d72b4b75debbc43f8e49ea7a81da849987aeab795baff66c9cf40607fde27fb54b7b32ab311ae5e9fb3b8f8f976fc
+DIST mpremote-1.22.0.tar.gz 24042 BLAKE2B 8bd6df4b9a46c10a93d42974a569adb42577d2783cb78b5b76ac6a6750f8219611ca49106ed91cb7f69910e3dfb28bb07a4522dbd721af0baac94d3e793c0576 SHA512 a3135e3be347370c967b7dc936f112e1ed5898288fa2dda4c485d216ebf432cb9706e539299d6769c1982ac02e456e9594ed2a7a86cbac2a1c7d08f2ff8a980b
diff --git a/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
new file mode 100644
index 000000000..4d06c25aa
--- /dev/null
+++ b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
@@ -0,0 +1,12 @@
+--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml 2024-01-22 03:59:19.414593373 -0500
+@@ -33,9 +33,6 @@
+ [project.scripts]
+ mpremote = "mpremote.main:main"
+
+-[tool.hatch.metadata.hooks.requirements_txt]
+-files = ["requirements.txt"]
+-
+ # This will be PEP-440 normalised into either:
+ # mpremote-X.Y.Z (on vX.Y.Z release tag)
+ # mpremote-X.Y.Zrc0 (on vX.Y.Z-preview tag, i.e. first commit in the cycle)
diff --git a/sci-electronics/mpremote/mpremote-1.22.0.ebuild b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
new file mode 100644
index 000000000..741478265
--- /dev/null
+++ b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="MicroPython remote control"
+HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/pyserial[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-requirements_txt.patch"
+)
+
+# The package might not have a test suite:
+# https://github.com/orgs/micropython/discussions/11308
+#distutils_enable_tests pytest
diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild
index 50eaeea5d..cbfbde5c6 100644
--- a/sci-libs/asl/asl-0.1.7.ebuild
+++ b/sci-libs/asl/asl-0.1.7.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
S="${WORKDIR}/${MY_PN}-${PV}"
diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild
index 82b464f7f..905c8813a 100644
--- a/sci-libs/asl/asl-9999.ebuild
+++ b/sci-libs/asl/asl-9999.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
src_prepare() {
cmake_src_prepare
diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
index 09fc690fd..f23e1c738 100644
--- a/sci-libs/daal4py/daal4py-2023.0.2.ebuild
+++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
@@ -19,7 +19,7 @@ KEYWORDS="~amd64"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
sys-devel/DPC++
test? (
sci-libs/scikit-learn[${PYTHON_USEDEP}]
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
deleted file mode 100644
index 5d3754d56..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index a252a1d..c36a312 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -116,10 +116,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- cxx = 'dpcpp'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 864ab5d..7eaa52f 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -306,8 +306,8 @@ def build_oneapi_backend():
- eca, ela, includes = get_build_options()
-
- return build_backend.build_cpp(
-- cc='dpcpp',
-- cxx='dpcpp',
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
deleted file mode 100644
index 9ccf0f156..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index bb38056..7216983 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -115,13 +115,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- if IS_WIN:
-- cxx = 'icx'
-- else:
-- cxx = 'icpx'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 00b4f43..76857a2 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -313,8 +313,8 @@ def build_oneapi_backend():
- eca += ['-fsycl']
-
- return build_backend.build_cpp(
-- cc=cc,
-- cxx=cxx,
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
index 10f1d3b50..c1000fea9 100644
--- a/sci-libs/gdcm/gdcm-3.0.14.ebuild
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -40,7 +40,7 @@ RDEPEND="${DEPEND}"
BDEPEND="
dev-libs/libxslt
app-text/docbook-xsl-ns-stylesheets
- doc? ( app-doc/doxygen[dot] )
+ doc? ( app-text/doxygen[dot] )
python? (
${PYTHON_DEPS}
>=dev-lang/swig-3.0.7
diff --git a/sci-libs/handyg/files/handyg-0.1.5-ld.patch b/sci-libs/handyg/files/handyg-0.1.5-ld.patch
deleted file mode 100644
index f3f06cd91..000000000
--- a/sci-libs/handyg/files/handyg-0.1.5-ld.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/configure 2022-09-19 01:59:40.382091704 +0200
-+++ b/configure 2022-09-19 02:00:00.734380534 +0200
-@@ -358,7 +358,7 @@
- FLDFLAGS+=" $1" ;;
- -Bstatic | -Bdynamic | *.ld)
- echo "Found linker flag $1" 1>&2
-- FLDFLAGS+=" -Wl,$1" ;;
-+ FLDFLAGS+=" $1" ;;
- /*)
- echo "Found linker flag $1" 1>&2
- FLDFLAGS+=" -L$1" ;;
---- a/configure 2022-09-19 02:02:18.064324729 +0200
-+++ b/configure 2022-09-19 02:02:22.935393539 +0200
-@@ -364,7 +364,7 @@
- FLDFLAGS+=" -L$1" ;;
- -rpath*)
- echo "Found linker flag $1" 1>&2
-- FLDFLAGS+=" -Wl,$1,$2"
-+ FLDFLAGS+=" $1,$2"
- shift ;;
- -dynamic-linker)
- shift ;;
diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 1aa0dc43a..0b1f25860 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -71,7 +71,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 29a3da5d0..b2c3af801 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -79,7 +79,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
deleted file mode 100644
index 0f64b325f..000000000
--- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib2bit-0.2.1/Makefile.ori 2017-03-31 22:09:48.387098439 +0200
-+++ lib2bit-0.2.1/Makefile 2017-03-31 22:10:29.889020564 +0200
-@@ -8,7 +8,7 @@
- LDLIBS =
- INCLUDES =
-
--prefix = /usr/local
-+prefix = $(DESTDIR)/usr/local
- includedir = $(prefix)/include
- libdir = $(exec_prefix)/lib
-
diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
index b19a65fbe..58d8264cf 100644
--- a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
+++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
@@ -29,7 +29,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- app-doc/doxygen[dot]
+ app-text/doxygen[dot]
"
pkg_setup() {
diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest
index 4bc4a8fd6..d50b1b3b7 100644
--- a/sci-libs/nibabel/Manifest
+++ b/sci-libs/nibabel/Manifest
@@ -1,2 +1,2 @@
-DIST nibabel-4.0.0.tar.gz 4505565 BLAKE2B 5efee05adbb0ff9204218060f75acdf6b5b77a1a7cc9b884d122f4a95805f6110a0d9433946d4a53d3aa615932012effe35b4ffa9773fb992da8ff273bf3cfd7 SHA512 1b34901e69ff7aaabfb94e49199de761eb7e397a0a7360c2077935d250368cd061cf1fa9c6ef561fa7707e4853c421b039818bfa4b32fc4792555f3d6235eeb7
DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4
+DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e
diff --git a/sci-libs/nibabel/nibabel-4.0.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild
index 4a24fb940..0fec805b1 100644
--- a/sci-libs/nibabel/nibabel-4.0.0.ebuild
+++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -27,11 +27,9 @@ RDEPEND="
)
"
-EPYTEST_DESELECT=(
- # Rported upstream:
- # https://github.com/nipy/nibabel/issues/1191
- nibabel/tests/test_volumeutils.py::test_a2f_nan2zero_range
-)
+BDEPEND="test? (
+ dev-python/pytest-httpserver[${PYTHON_USEDEP}]
+)"
distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
distutils_enable_tests pytest
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
index 362628814..9444a9dd3 100644
--- a/sci-libs/nipy/Manifest
+++ b/sci-libs/nipy/Manifest
@@ -1 +1 @@
-DIST nipy-0.5.1_pre20230103.gh.tar.gz 2462662 BLAKE2B 0e6aa24875e514bf16280e20bb3059027ad30c3d510db62b0ed80b33724aacb0a20260f7cf9d87858a9da5d07fab58535cee1306fe2b7be7a72364156197aeab SHA512 7ed89b5e637159c90893a02dd9481a662f7e589fc6fe76c3e7919231144a56668815edc0f57a77728a9c95c7640e474563e922609c56cd0ad0fcfbd3c5bdb6bd
+DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f
diff --git a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild b/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
deleted file mode 100644
index 25bdee0b8..000000000
--- a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-MY_HASH="35a5f5205ba2aa54f1f0524564a6f1f8dafb237f"
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://nipy.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- "
-DEPEND=""
-
-S="${WORKDIR}/${PN}-${MY_HASH}"
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # bug #397605
- [[ ${CHOST} == *-darwin* ]] \
- && append-ldflags -bundle "-undefined dynamic_lookup" \
- || append-ldflags -shared
-
- # nipy uses the horrible numpy.distutils automagic
-}
-
-#python_test() {
-# distutils-r1_install_for_testing
-# cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
-# cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
-# cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
-# cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
-# mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cd "${BUILD_DIR}" || die
-# echo "backend : agg" > matplotlibrc
-# nosetests || die
-#}
diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild
new file mode 100644
index 000000000..8f8ea83e8
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.6.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=meson-python
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_EXT=1
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="https://nipy.org/"
+SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Test data unavailable:
+# https://github.com/nipy/nipy/issues/561#event-11866547632
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/sympy[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ "
+DEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ rm -rf nipy || die
+ epytest
+}
diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest
index a2ffd1d7a..6c9059e1c 100644
--- a/sci-libs/nipype/Manifest
+++ b/sci-libs/nipype/Manifest
@@ -1,2 +1,2 @@
-DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85
DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b
+DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec
diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
new file mode 100644
index 000000000..b5c223422
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
@@ -0,0 +1,50 @@
+diff --git a/nipype/__init__.py b/nipype/__init__.py
+index 06084e823..2e42dcbce 100644
+--- a/nipype/__init__.py
++++ b/nipype/__init__.py
+@@ -73,23 +73,6 @@ from .interfaces import (
+ )
+
+
+-def check_latest_version(raise_exception=False):
+- """
+- Check for the latest version of the library.
+-
+- Parameters
+- ----------
+- raise_exception: bool
+- Raise a RuntimeError if a bad version is being used
+- """
+- import etelemetry
+-
+- logger = logging.getLogger("nipype.utils")
+- return etelemetry.check_available_version(
+- "nipy/nipype", __version__, logger, raise_exception
+- )
+-
+-
+ # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
+ if config.getboolean("execution", "check_version"):
+ import __main__
+@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"):
+ from .interfaces.base import BaseInterface
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index c8099be63..f7770dbfc 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -183,10 +183,9 @@ class BaseInterface(Interface):
+ config.getboolean("execution", "check_version")
+ and "NIPYPE_NO_ET" not in os.environ
+ ):
+- from ... import check_latest_version
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+
+ if not self.input_spec:
+ raise Exception("No input_spec in class: %s" % self.__class__.__name__)
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
index 8214ccff4..7c2e801ff 100644
--- a/sci-libs/nipype/nipype-1.8.4-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
index 750c3ba05..4c3da70b3 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
@@ -28,30 +29,29 @@ DEPEND="
${RDEPEND}
)
"
-# Dependency disabled as upstream test configuration which requires it fails
-#dev-python/pytest-xdist[${PYTHON_USEDEP}]
RDEPEND="
- >=dev-python/click-6.6[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pydotplus[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
- >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/traits[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${P}"-version_check.patch
- "${FILESDIR}/${P}"-collections.patch
+ "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
)
src_prepare() {
# Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
@@ -69,12 +69,10 @@ python_install_all() {
doenvd "${FILESDIR}/98nipype"
}
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
EPYTEST_DESELECT=(
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor_variance_threshold_and_metadata
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor
nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
- nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help
)
python_test() {
diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild
new file mode 100644
index 000000000..88bc23395
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.6.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Tests fail with numpy import error:
+# https://github.com/nipy/nipype/issues/3626
+RESTRICT="test"
+
+DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/prov[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ test? (
+ dev-python/mock[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ ${RDEPEND}
+ )
+"
+
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pydot[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+ # Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
+ sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+ # Mark failing tests
+ sed -i \
+ -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+ nipype/tests/test_nipype.py || die
+ sed -i \
+ -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+ nipype/interfaces/fsl/tests/test_base.py || die
+ default
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+ nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+ # Setting environment variable to disable etelemetry version check:
+ # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+ NIPYPE_NO_ET=1 epytest
+ # Upstream test configuration fails
+ #-c nipype/pytest.ini\
+ #--doctest-modules nipype\
+ #--cov nipype\
+ #--cov-config .coveragerc\
+ #--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use nipype from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch
deleted file mode 100644
index e68c5f4fe..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90
---- wannier90-1.1.old/src/wannier_lib.F90 2007-12-20 10:58:37.000000000 +0100
-+++ wannier90-1.1.new/src/wannier_lib.F90 2008-04-28 17:27:19.000000000 +0200
-@@ -166,6 +166,12 @@
- exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands)
- end if
-
-+ if (postproc_setup) then
-+ call kmesh_write()
-+ write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh ',io_time(),' (sec)'
-+ write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.'
-+ endif
-+
-
- call kmesh_dealloc()
- call param_dealloc()
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch
deleted file mode 100644
index 391a34ca2..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90
---- wannier90-1.1.old/src/disentangle.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/disentangle.F90 2009-03-07 15:48:05.000000000 +0100
-@@ -1784,9 +1784,9 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
-+ write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
- if (icompflag.eq.1) then
-@@ -2551,8 +2551,8 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
-diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90
---- wannier90-1.1.old/src/overlap.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/overlap.F90 2009-03-07 15:48:36.000000000 +0100
-@@ -141,8 +141,8 @@
- nn_found=.true.
- nn=inn
- else
-- call io_error('Error reading '//trim(seedname)//'.mmn.&
-- & More than one matching nearest neighbour found')
-+ call io_error('Error reading '//trim(seedname)// &
-+ '.mmn. More than one matching nearest neighbour found')
- endif
- endif
- end do
-diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90
---- wannier90-1.1.old/src/parameters.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/parameters.F90 2009-03-07 15:50:46.000000000 +0100
-@@ -1054,8 +1054,9 @@
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_species
- do nat=1,atoms_species_num(nsp)
-- write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-- '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
-+ write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') &
-+& '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-+& '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
- end do
- end do
- write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*'
-@@ -1073,8 +1074,8 @@
- write(stdout,'(1x,a)') '| Frac. Coord. l mr r z-axis x-axis Z/a |'
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_proj
-- write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),&
-- & 2x,f4.1,1x,a1)') '|',proj_site(1,nsp),proj_site(2,nsp),&
-+ write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')&
-+& '|',proj_site(1,nsp),proj_site(2,nsp),&
- proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),&
- proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),&
- proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|'
-@@ -2738,8 +2739,8 @@
- dummy=utility_strip(in_data(line))
- dummy=adjustl(dummy)
- pos1=index(dummy,':')
-- if(pos1==0) call io_error('param_read_projection: malformed projection &
-- &definition: '//trim(dummy))
-+ if(pos1==0) &
-+ call io_error('param_read_projection: malformed projection definition: '//trim(dummy))
- sites=0
- ctemp=dummy(:pos1-1)
- ! Read the atomic site
-@@ -2980,11 +2981,11 @@
- endif
- end if
- if(sites==-1) then
-- if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: &
-- &too many projections defined')
-+ if(counter+sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- else
-- if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:&
-- & too many projections defined')
-+ if(counter+sites*sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- end if
- !
- if(sites==-1) then
-@@ -3025,8 +3026,8 @@
-
- ! check there are enough projections and add random projections if required
- if (.not. lpartrandom) then
-- if (counter.ne.num_proj) call io_error('param_get_projections:&
-- & Fewer projections defined than the number of Wannier functions requested')
-+ if (counter.ne.num_proj) call io_error(&
-+ 'param_get_projections: Fewer projections defined than the number of Wannier functions requested')
- else
- call random_seed()
- do loop=counter+1,num_proj
diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
deleted file mode 100644
index c9656ac31..000000000
--- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl
---- wannier90-2.0.1.1.orig/tests/run_test.pl 2016-02-08 11:51:52.000000000 +0000
-+++ wannier90-2.0.1.1/tests/run_test.pl 2017-01-05 12:10:29.584850729 +0000
-@@ -2,7 +2,7 @@
- #
- use Cwd;
- my $cwd = cwd();
--$wanex="../wannier90.x" ;
-+$wanex="../src/wannier90.x" ;
- $wanex=$cwd."/".$wanex ;
- print " Running test set of inputs\n";
- @tests_found = <./test*>;
diff --git a/sci-mathematics/cipi/cipi-1.0-r1.ebuild b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
new file mode 100644
index 000000000..6cd189e33
--- /dev/null
+++ b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake flag-o-matic
+
+DESCRIPTION="Computing information projections iteratively"
+HOMEPAGE="https://github.com/tom111/cipi"
+SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="doc"
+
+DEPEND="
+ dev-libs/boost:=
+ doc? ( virtual/latex-base )"
+RDEPEND="${DEPEND}"
+
+DOCS="AUTHORS README"
+
+CMAKE_IN_SOURCE_BUILD="yes"
+
+PATCHES=(
+ "${FILESDIR}/${P}-boost.patch"
+)
+
+src_prepare() {
+ cmake_src_prepare
+ append-ldflags -Wl,--copy-dt-needed-entries
+}
+
+src_configure() {
+ mycmakeargs=(
+ -DENABLE_DOC=$(usex doc ON OFF)
+ )
+
+ cmake_src_configure
+}
+
+pkg_postinst() {
+ elog
+ elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}"
+ elog
+ if use doc; then
+ elog "A pdf manual has been installed to /usr/share/${PN}-${PV}"
+ fi
+}
diff --git a/sci-mathematics/cipi/files/cipi-1.0-boost.patch b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
new file mode 100644
index 000000000..66aa9fd3f
--- /dev/null
+++ b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
@@ -0,0 +1,11 @@
+--- a/src/CMakeLists.txt 2024-02-16 21:36:58.808186061 +0100
++++ b/src/CMakeLists.txt 2024-02-16 21:36:55.288131610 +0100
+@@ -8,7 +8,7 @@
+ Message("Boost found" ${Boost_LIBRARY_DIR})
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR})
+ #MESSAGE("Boost was found" ${Boost_INCLUDE_DIR})
+- TARGET_LINK_LIBRARIES (cipi boost_thread-mt)
++ TARGET_LINK_LIBRARIES (cipi boost_thread)
+ ENDIF (Boost_FOUND)
+
+ INSTALL(PROGRAMS cipi DESTINATION bin)
diff --git a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch b/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
deleted file mode 100644
index 798d17fd3..000000000
--- a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
+++ /dev/null
@@ -1,254 +0,0 @@
-From: Mehdi Dogguy <mehdi@debian.org>
-Date: Sun, 27 Apr 2014 13:46:16 +0200
-Subject: Port to OCamlgraph 1.8.5
-
----
- src/impact/reason_graph.ml | 2 +-
- src/kernel/stmts_graph.ml | 10 +++++-----
- src/logic/property_status.ml | 8 ++++----
- src/misc/service_graph.ml | 4 ++--
- src/pdg_types/pdgTypes.ml | 6 +++---
- src/postdominators/print.ml | 2 +-
- src/semantic_callgraph/register.ml | 4 ++--
- src/slicing/printSlice.ml | 10 +++++-----
- src/syntactic_callgraph/register.ml | 4 ++--
- src/wp/cil2cfg.ml | 12 ++++++------
- 10 files changed, 31 insertions(+), 31 deletions(-)
-
-diff --git a/src/impact/reason_graph.ml b/src/impact/reason_graph.ml
-index eabacb0..ce19b4a 100644
---- a/src/impact/reason_graph.ml
-+++ b/src/impact/reason_graph.ml
-@@ -139,7 +139,7 @@ module Printer (X: AdditionalInfo) = struct
-
- let graph_attributes _ = [`Label "Impact graph"]
-
-- let default_vertex_attributes _g = [`Style [`Filled]; `Shape `Box]
-+ let default_vertex_attributes _g = [`Style `Filled; `Shape `Box]
- let default_edge_attributes _g = []
-
- let vertex_attributes v =
-diff --git a/src/kernel/stmts_graph.ml b/src/kernel/stmts_graph.ml
-index a8fe121..16059c3 100644
---- a/src/kernel/stmts_graph.ml
-+++ b/src/kernel/stmts_graph.ml
-@@ -157,12 +157,12 @@ module TP = struct
-
- let vertex_attributes s =
- match s.skind with
-- | Loop _ -> [`Color 0xFF0000; `Style [`Filled]]
-- | If _ -> [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
-- | Return _ -> [`Color 0x0000FF; `Style [`Filled]]
-+ | Loop _ -> [`Color 0xFF0000; `Style `Filled]
-+ | If _ -> [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
-+ | Return _ -> [`Color 0x0000FF; `Style `Filled]
- | Block _ -> [`Shape `Box; `Fontsize 8]
-- | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style [`Filled]]
-- | Instr (Skip _) -> [`Color 0x00FFFF ; `Style [`Filled]]
-+ | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style `Filled]
-+ | Instr (Skip _) -> [`Color 0x00FFFF ; `Style `Filled]
- | _ -> []
- let default_vertex_attributes _ = []
-
-diff --git a/src/logic/property_status.ml b/src/logic/property_status.ml
-index f7c278d..47485f6 100644
---- a/src/logic/property_status.ml
-+++ b/src/logic/property_status.ml
-@@ -1481,12 +1481,12 @@ module Consolidation_graph = struct
- let s = get_status p in
- let color = status_color p s in
- let style = match s with
-- | Never_tried -> [`Style [`Bold]; `Width 0.8 ]
-- | _ -> [`Style [`Filled]]
-+ | Never_tried -> [`Style `Bold; `Width 0.8 ]
-+ | _ -> [`Style `Filled]
- in
- style @ [ label v; `Color color; `Shape `Box ]
- | Emitter _ as v ->
-- [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style [`Filled] ]
-+ [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style `Filled ]
- | Tuning_parameter _ as v ->
- [ label v; (*`Style `Dotted;*) `Color 0xb0c4de; ]
- (*| Correctness_parameter _ (*as v*) -> assert false (*[ label v; `Color 0xb0c4de ]*)*)
-@@ -1495,7 +1495,7 @@ module Consolidation_graph = struct
- | None -> []
- | Some s ->
- let c = emitted_status_color s in
-- [ `Color c; `Fontcolor c; `Style [`Bold] ]
-+ [ `Color c; `Fontcolor c; `Style `Bold ]
-
- let default_vertex_attributes _ = []
- let default_edge_attributes _ = []
-diff --git a/src/misc/service_graph.ml b/src/misc/service_graph.ml
-index 4f866c5..d158028 100644
---- a/src/misc/service_graph.ml
-+++ b/src/misc/service_graph.ml
-@@ -289,7 +289,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
- color e
- else
- match CallG.E.label e with
-- | Inter_services -> [ `Style [`Invis] ]
-+ | Inter_services -> [ `Style `Invis ]
- | Inter_functions | Both -> color e
-
- let default_edge_attributes _ = []
-@@ -303,7 +303,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
- sg_attributes =
- [ `Label ("S " ^ cs);
- `Color (Extlib.number_to_color id);
-- `Style [`Bold] ] }
-+ `Style `Bold ] }
-
- end
-
-diff --git a/src/pdg_types/pdgTypes.ml b/src/pdg_types/pdgTypes.ml
-index 05754e4..74cdebf 100644
---- a/src/pdg_types/pdgTypes.ml
-+++ b/src/pdg_types/pdgTypes.ml
-@@ -626,7 +626,7 @@ module Pdg = struct
-
- let graph_attributes _ = [`Rankdir `TopToBottom ]
-
-- let default_vertex_attributes _ = [`Style [`Filled]]
-+ let default_vertex_attributes _ = [`Style `Filled]
- let vertex_name v = string_of_int (Node.id v)
-
- let vertex_attributes v =
-@@ -711,13 +711,13 @@ module Pdg = struct
- if Dpd.is_ctrl d then (`Arrowtail `Odot)::attrib else attrib
- in
- let attrib =
-- if Dpd.is_addr d then (`Style [`Dotted])::attrib else attrib
-+ if Dpd.is_addr d then (`Style `Dotted)::attrib else attrib
- in
- attrib
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (`Style [`Filled]) :: attrib in
-+ let attrib = (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
-diff --git a/src/postdominators/print.ml b/src/postdominators/print.ml
-index f2e3a25..15f4ff2 100644
---- a/src/postdominators/print.ml
-+++ b/src/postdominators/print.ml
-@@ -63,7 +63,7 @@ module Printer = struct
-
- let graph_attributes (title, _) = [`Label title]
-
-- let default_vertex_attributes _g = [`Style [`Filled]]
-+ let default_vertex_attributes _g = [`Style `Filled]
- let default_edge_attributes _g = []
-
- let vertex_attributes (s, has_postdom) =
-diff --git a/src/semantic_callgraph/register.ml b/src/semantic_callgraph/register.ml
-index 1c79dcc..071f061 100644
---- a/src/semantic_callgraph/register.ml
-+++ b/src/semantic_callgraph/register.ml
-@@ -102,8 +102,8 @@ module Service =
- let name = Kernel_function.get_name
- let attributes v =
- [ `Style
-- [if Kernel_function.is_definition v then `Bold
-- else `Dotted] ]
-+ (if Kernel_function.is_definition v then `Bold
-+ else `Dotted) ]
- let entry_point () =
- try Some (fst (Globals.entry_point ()))
- with Globals.No_such_entry_point _ -> None
-diff --git a/src/slicing/printSlice.ml b/src/slicing/printSlice.ml
-index c5363f9..211e0bb 100644
---- a/src/slicing/printSlice.ml
-+++ b/src/slicing/printSlice.ml
-@@ -227,7 +227,7 @@ module PrintProject = struct
-
- let graph_attributes (name, _) = [`Label name]
-
-- let default_vertex_attributes _ = [`Style [`Filled]]
-+ let default_vertex_attributes _ = [`Style `Filled]
-
- let vertex_name v = match v with
- | Src fi -> SlicingMacros.fi_name fi
-@@ -280,16 +280,16 @@ module PrintProject = struct
-
- let edge_attributes (e, call) =
- let attrib = match e with
-- | (Src _, Src _) -> [`Style [`Invis]]
-- | (OptSliceCallers _, _) -> [`Style [`Invis]]
-- | (_, OptSliceCallers _) -> [`Style [`Invis]]
-+ | (Src _, Src _) -> [`Style `Invis]
-+ | (OptSliceCallers _, _) -> [`Style `Invis]
-+ | (_, OptSliceCallers _) -> [`Style `Invis]
- | _ -> []
- in match call with None -> attrib
- | Some call -> (`Label (string_of_int call.sid)):: attrib
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (*(`Label name) ::*) (`Style [`Filled]) :: attrib in
-+ let attrib = (*(`Label name) ::*) (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
-diff --git a/src/syntactic_callgraph/register.ml b/src/syntactic_callgraph/register.ml
-index d4669c4..d41980e 100644
---- a/src/syntactic_callgraph/register.ml
-+++ b/src/syntactic_callgraph/register.ml
-@@ -37,8 +37,8 @@ module Service =
- let name v = nodeName v.cnInfo
- let attributes v =
- [ match v.cnInfo with
-- | NIVar (_,b) when not !b -> `Style [`Dotted]
-- | _ -> `Style [`Bold] ]
-+ | NIVar (_,b) when not !b -> `Style `Dotted
-+ | _ -> `Style `Bold ]
- let equal v1 v2 = id v1 = id v2
- let compare v1 v2 =
- let i1 = id v1 in
-diff --git a/src/wp/cil2cfg.ml b/src/wp/cil2cfg.ml
-index 6d8cf09..ba5f410 100644
---- a/src/wp/cil2cfg.ml
-+++ b/src/wp/cil2cfg.ml
-@@ -1278,9 +1278,9 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
- | Vstart | Vend | Vexit -> [`Color 0x0000FF; `Shape `Doublecircle]
- | VfctIn | VfctOut -> [`Color 0x0000FF; `Shape `Box]
- | VblkIn _ | VblkOut _ -> [`Shape `Box]
-- | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style [`Filled]]
-+ | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style `Filled]
- | Vtest _ | Vswitch _ ->
-- [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
-+ [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
- | Vcall _ | Vstmt _ -> []
- in (`Label (String.escaped label))::attr
-
-@@ -1290,15 +1290,15 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
- let attr = [] in
- let attr = (`Label (String.escaped (PE.edge_txt e)))::attr in
- let attr =
-- if is_back_edge e then (`Constraint false)::(`Style [`Bold])::attr
-+ if is_back_edge e then (`Constraint false)::(`Style `Bold)::attr
- else attr
- in
- let attr = match (edge_type e) with
- | Ethen | EbackThen -> (`Color 0x00FF00)::attr
- | Eelse | EbackElse -> (`Color 0xFF0000)::attr
-- | Ecase [] -> (`Color 0x0000FF)::(`Style [`Dashed])::attr
-+ | Ecase [] -> (`Color 0x0000FF)::(`Style `Dashed)::attr
- | Ecase _ -> (`Color 0x0000FF)::attr
-- | Enext -> (`Style [`Dotted])::attr
-+ | Enext -> (`Style `Dotted)::attr
- | Eback -> attr (* see is_back_edge above *)
- | Enone -> attr
- in
-@@ -1308,7 +1308,7 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
-
- let get_subgraph v =
- let mk_subgraph name attrib =
-- let attrib = (`Style [`Filled]) :: attrib in
-+ let attrib = (`Style `Filled) :: attrib in
- Some { Graph.Graphviz.DotAttributes.sg_name= name;
- sg_parent = None;
- sg_attributes = attrib }
---
diff --git a/sci-mathematics/ltl2ba/Manifest b/sci-mathematics/ltl2ba/Manifest
index 4d6528d6b..659c1c6e6 100644
--- a/sci-mathematics/ltl2ba/Manifest
+++ b/sci-mathematics/ltl2ba/Manifest
@@ -1 +1,3 @@
DIST ltl2ba-1.1.tar.gz 29629 BLAKE2B 06ba7f7b5e3c6b72d2f0ea3b991346c803669e24d66dc38e311109ee08ed6dcc72bfd9f2ebe0f8864b0f80f010a4438029f4f5dbbf0087469ca2d07cdfce6b3f SHA512 8d010e2bb59fa5d682a56a50133865da938fd3bfcde6386184880eec6989bc1b694d6af9146b4b708cefdcdbcf98248f87074b8c973ea8cab65d658b394ccf69
+DIST ltl2ba-1.2.tar.gz 33026 BLAKE2B f19359e33d4eeb4dde75425ed03d940c08f46dd265b1b9c6773807e7dca67fd44f694f685d4153ca786118e336fab736104a865c5d0e9883390fca694f72b492 SHA512 148ffb1b4dbe134b69c6e946a4a9f1a95a809bf36ef3533117eedeceb721dd4c8a3238bbda2de5782a79b7aee70e33adf6ff193917441092a1ccb4e56a53a655
+DIST ltl2ba-1.3.tar.gz 38265 BLAKE2B bd74d9b9e22589ac00fbaa15f745dd6371894f68b50f85507694648274d9391ad3a90cdf1ee6c342abbceb04d0e2eb5d71473d43969b469a933517cfcd1e16c1 SHA512 1bcef13d98879c083dc907939c652e694802ed91c33a5d90bbeb6fc22d6265a0b153932c5fb3f8557aad30582322c16d0be822bf4208f40faf9384b367a84aa6
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+ default
+ sed -i Makefile \
+ -e "s/CC=gcc/#CC=gcc/g" \
+ -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+ append-cflags -fcommon
+ default
+}
+
+src_install() {
+ dobin ltl2ba
+ dodoc README
+}
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+ default
+ sed -i Makefile \
+ -e "s/CC=gcc/#CC=gcc/g" \
+ -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+ append-cflags -fcommon
+ default
+}
+
+src_install() {
+ dobin ltl2ba
+ dodoc README
+}
diff --git a/sci-mathematics/scilab-bin/Manifest b/sci-mathematics/scilab-bin/Manifest
index d4c0e32f7..6029dc30e 100644
--- a/sci-mathematics/scilab-bin/Manifest
+++ b/sci-mathematics/scilab-bin/Manifest
@@ -1 +1,2 @@
+DIST scilab-2023.1.0.bin.x86_64-linux-gnu.tar.xz 182801620 BLAKE2B 19847145a8d70550afa77591854aa651ee5fe23f9998eee21c11acdd4112397fb5e2e82c6bc7edbc2f808048f70905dc0df37db00c43b5794bf304e9a0807ca4 SHA512 af0f71d270513f283ac732e2004094854a117ce4550c5ab579eda5c5ec52bde76a8fa5dd7649db84d68d43124524342f2fdc5f1ba269a60a3930c578ef3391f8
DIST scilab-6.1.1.bin.linux-x86_64.tar.gz 215840619 BLAKE2B dcfb88f2488cf26371c5beee1e905a33e4c6fc343bb490bb43a73334960f0c13df7d372841949a46d7dc5b6c0a404e6648828104717274518a8ff905a0ae15ad SHA512 ed386e01869cfac3d12881ddb4ae0258bb02e1d4a919a82405dbedce77406c04269883b6e1456dbad52551217307a7baebbb355a699168b77810263f5e357895
diff --git a/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild
new file mode 100644
index 000000000..83d189b8a
--- /dev/null
+++ b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit xdg
+
+MY_PN="${PN//-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Scientific software package for numerical computations"
+HOMEPAGE="https://www.scilab.org/"
+SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.x86_64-linux-gnu.tar.xz"
+S="${WORKDIR}/${P//-bin}"
+
+LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT"
+SLOT="0"
+KEYWORDS="-* ~amd64"
+
+# Bundled dependencies not packaged in ::gentoo
+# sci-libs/hdf5[cxx]:0/9
+# libgluegen.so (in ::sci)
+# libjogl_desktop.so (in ::sci)
+# libOpenXLSX.so (in ::sci)
+#
+# Bundled dependencies in ::gentoo
+# dev-lang/tcl
+# dev-libs/openssl:0/1.1
+# dev-libs/newt
+# dev-libs/libpcre
+# net-misc/curl
+# sci-libs/amd
+# sci-libs/arpack
+# sci-libs/camd
+# sci-libs/ccolamd
+# sci-libs/cholmod
+# sci-libs/colamd
+# sci-libs/fftw:3.0/3
+# sci-libs/lapack
+# sci-libs/matio
+# sci-libs/openblas
+# sci-libs/umfpack
+
+RDEPEND="
+ sys-libs/ncurses-compat
+ virtual/jre:1.8
+"
+
+QA_PREBUILT=( "opt/${MY_PN}/*" )
+
+src_prepare() {
+ default
+ local SCILAB_HOME="/opt/${MY_PN}"
+ # fix the .pc file to reflect the dirs where we are installing stuff
+ sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die
+
+ # move appdata to metainfo
+ mv share/appdata share/metainfo || die
+}
+
+src_install() {
+ local SCILAB_HOME="/opt/${MY_PN}"
+ dodir "${SCILAB_HOME}"
+
+ # make convenience symlinks in PATH
+ for file in bin/*; do
+ dosym "../${MY_PN}/${file}" "/opt/${file}"
+ done
+
+ # copy all the things
+ cp -r "${S}/"* "${ED}/${SCILAB_HOME}" || die
+
+ # move out dekstop, icons etc
+ dodir /usr/share
+ mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die
+ dodir /usr/lib64/pkgconfig
+ mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die
+}
diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest
index 3f2abd738..f89088f0a 100644
--- a/sci-misc/openfst/Manifest
+++ b/sci-misc/openfst/Manifest
@@ -1 +1 @@
-DIST openfst-1.8.1.tar.gz 1333532 BLAKE2B 5cc6d222a91c774edde869246fc8ae27ce1975632ac17d3b28236e63c65b6d7f637c1e88c54378b63ef66d59a29acc528a4c3ccc66ec3d7e20100f990cb1d67c SHA512 4c350a3f47de33d134536ac70a906cabf7d3641527c6823d378c4dd8651082dd9246343a233ad7c4c25a42905315441a6528e3e3c3730bfd17da320098e94b59
+DIST openfst-1.8.2.tar.gz 1342793 BLAKE2B bae3ff40e1234a5c2a9bbd642ba5a7e29b0ecef2e304b2a952d1ebb354c3fb4d772dfdf85710fcd4940e01798ac4064226377e59f1a3f46b2331219e1bd3f8cf SHA512 ca7f9f19e24141e1f1d0bbabf43795e6e278bce3887c14261d9ce204a0e01b1588eaf982755a9105247510a19f67da2f566e9b14b1d869497148f95b55606d5c
diff --git a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch b/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch
deleted file mode 100644
index 140ea4e24..000000000
--- a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch
+++ /dev/null
@@ -1,269 +0,0 @@
-diff -crB openfst-1.4.1.orig/src/include/fst/lock.h openfst-1.4.1/src/include/fst/lock.h
-*** openfst-1.4.1.orig/src/include/fst/lock.h 2012-04-25 19:43:47.000000000 -0400
---- openfst-1.4.1/src/include/fst/lock.h 2015-02-28 14:12:29.009385600 -0400
-***************
-*** 78,85 ****
- RefCounter() : count_(1) {}
-
- int count() const { return count_; }
-! int Incr() const { return ++count_; }
-! int Decr() const { return --count_; }
-
- private:
- mutable int count_;
---- 78,93 ----
- RefCounter() : count_(1) {}
-
- int count() const { return count_; }
-!
-! // below lines are modifications of openfst for multi-thrads support,
-! // from tools/extras/openfst_gcc41up.patch, applied by tools/Makefile,
-! // applicable to gcc 4.1 or above
-! // int Incr() const { return ++count_; }
-! // int Decr() const { return --count_; }
-!
-! int Incr() const { return __sync_add_and_fetch(&count_, 1); }
-! int Decr() const { return __sync_sub_and_fetch(&count_, 1); }
-! // end modifications
-
- private:
- mutable int count_;
-diff -crB openfst-1.4.1.orig/src/include/fst/minimize.h openfst-1.4.1/src/include/fst/minimize.h
-*** openfst-1.4.1.orig/src/include/fst/minimize.h 2014-04-29 18:15:17.000000000 -0400
---- openfst-1.4.1/src/include/fst/minimize.h 2015-02-28 14:11:39.270566070 -0400
-***************
-*** 134,140 ****
- typedef typename A::Weight Weight;
- typedef ReverseArc<A> RevA;
-
-! CyclicMinimizer(const ExpandedFst<A>& fst) {
- Initialize(fst);
- Compute(fst);
- }
---- 134,147 ----
- typedef typename A::Weight Weight;
- typedef ReverseArc<A> RevA;
-
-! CyclicMinimizer(const ExpandedFst<A>& fst):
-! // tell the Partition data-member to expect multiple repeated
-! // calls to SplitOn with the same element if we are non-deterministic.
-! P_(fst.Properties(kIDeterministic, true) == 0) {
-! if(fst.Properties(kIDeterministic, true) == 0)
-! CHECK(Weight::Properties() & kIdempotent); // this minimization
-! // algorithm for non-deterministic FSTs can only work with idempotent
-! // semirings.
- Initialize(fst);
- Compute(fst);
- }
-***************
-*** 315,321 ****
- typedef typename A::StateId ClassId;
- typedef typename A::Weight Weight;
-
-! AcyclicMinimizer(const ExpandedFst<A>& fst) {
- Initialize(fst);
- Refine(fst);
- }
---- 322,334 ----
- typedef typename A::StateId ClassId;
- typedef typename A::Weight Weight;
-
-! AcyclicMinimizer(const ExpandedFst<A>& fst):
-! // tell the Partition data-member to expect multiple repeated
-! // calls to SplitOn with the same element if we are non-deterministic.
-! partition_(fst.Properties(kIDeterministic, true) == 0) {
-! if(fst.Properties(kIDeterministic, true) == 0)
-! CHECK(Weight::Properties() & kIdempotent); // minimization for
-! // non-deterministic FSTs can only work with idempotent semirings.
- Initialize(fst);
- Refine(fst);
- }
-***************
-*** 531,543 ****
- void Minimize(MutableFst<A>* fst,
- MutableFst<A>* sfst = 0,
- float delta = kDelta) {
-! uint64 props = fst->Properties(kAcceptor | kIDeterministic|
-! kWeighted | kUnweighted, true);
-! if (!(props & kIDeterministic)) {
-! FSTERROR() << "FST is not deterministic";
-! fst->SetProperties(kError, kError);
-! return;
-! }
-
- if (!(props & kAcceptor)) { // weighted transducer
- VectorFst< GallicArc<A, GALLIC_LEFT> > gfst;
---- 544,550 ----
- void Minimize(MutableFst<A>* fst,
- MutableFst<A>* sfst = 0,
- float delta = kDelta) {
-! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true);
-
- if (!(props & kAcceptor)) { // weighted transducer
- VectorFst< GallicArc<A, GALLIC_LEFT> > gfst;
-diff -crB openfst-1.4.1.orig/src/include/fst/partition.h openfst-1.4.1/src/include/fst/partition.h
-*** openfst-1.4.1.orig/src/include/fst/partition.h 2014-04-29 18:15:17.000000000 -0400
---- openfst-1.4.1/src/include/fst/partition.h 2015-02-28 14:11:39.271566087 -0400
-***************
-*** 43,50 ****
- friend class PartitionIterator<T>;
-
- struct Element {
-! Element() : value(0), next(0), prev(0) {}
-! Element(T v) : value(v), next(0), prev(0) {}
-
- T value;
- Element* next;
---- 43,50 ----
- friend class PartitionIterator<T>;
-
- struct Element {
-! Element() : value(0), next(0), prev(0) {}
-! Element(T v) : value(v), next(0), prev(0) {}
-
- T value;
- Element* next;
-***************
-*** 52,60 ****
- };
-
- public:
-! Partition() {}
-
-! Partition(T num_states) {
- Initialize(num_states);
- }
-
---- 52,62 ----
- };
-
- public:
-! Partition(bool allow_repeated_split):
-! allow_repeated_split_(allow_repeated_split) {}
-
-! Partition(bool allow_repeated_split, T num_states):
-! allow_repeated_split_(allow_repeated_split) {
- Initialize(num_states);
- }
-
-***************
-*** 137,152 ****
- if (class_size_[class_id] == 1) return;
-
- // first time class is split
-! if (split_size_[class_id] == 0)
- visited_classes_.push_back(class_id);
-!
- // increment size of split (set of element at head of chain)
- split_size_[class_id]++;
-!
- // update split point
-! if (class_split_[class_id] == 0)
-! class_split_[class_id] = classes_[class_id];
-! if (class_split_[class_id] == elements_[element_id])
- class_split_[class_id] = elements_[element_id]->next;
-
- // move to head of chain in same class
---- 139,154 ----
- if (class_size_[class_id] == 1) return;
-
- // first time class is split
-! if (split_size_[class_id] == 0) {
- visited_classes_.push_back(class_id);
-! class_split_[class_id] = classes_[class_id];
-! }
- // increment size of split (set of element at head of chain)
- split_size_[class_id]++;
-!
- // update split point
-! if (class_split_[class_id] != 0
-! && class_split_[class_id] == elements_[element_id])
- class_split_[class_id] = elements_[element_id]->next;
-
- // move to head of chain in same class
-***************
-*** 157,165 ****
- // class indices of the newly created class. Returns the new_class id
- // or -1 if no new class was created.
- T SplitRefine(T class_id) {
- // only split if necessary
-! if (class_size_[class_id] == split_size_[class_id]) {
-! class_split_[class_id] = 0;
- split_size_[class_id] = 0;
- return -1;
- } else {
---- 159,169 ----
- // class indices of the newly created class. Returns the new_class id
- // or -1 if no new class was created.
- T SplitRefine(T class_id) {
-+
-+ Element* split_el = class_split_[class_id];
- // only split if necessary
-! //if (class_size_[class_id] == split_size_[class_id]) {
-! if(split_el == NULL) { // we split on everything...
- split_size_[class_id] = 0;
- return -1;
- } else {
-***************
-*** 163,180 ****
- split_size_[class_id] = 0;
- return -1;
- } else {
--
- T new_class = AddClass();
- size_t remainder = class_size_[class_id] - split_size_[class_id];
- if (remainder < split_size_[class_id]) { // add smaller
-- Element* split_el = class_split_[class_id];
- classes_[new_class] = split_el;
-- class_size_[class_id] = split_size_[class_id];
-- class_size_[new_class] = remainder;
- split_el->prev->next = 0;
- split_el->prev = 0;
- } else {
-- Element* split_el = class_split_[class_id];
- classes_[new_class] = classes_[class_id];
- class_size_[class_id] = remainder;
- class_size_[new_class] = split_size_[class_id];
---- 167,189 ----
- split_size_[class_id] = 0;
- return -1;
- } else {
- T new_class = AddClass();
-+
-+ if(allow_repeated_split_) { // split_size_ is possibly
-+ // inaccurate, so work it out exactly.
-+ size_t split_count; Element *e;
-+ for(split_count=0,e=classes_[class_id];
-+ e != split_el; split_count++, e=e->next);
-+ split_size_[class_id] = split_count;
-+ }
- size_t remainder = class_size_[class_id] - split_size_[class_id];
- if (remainder < split_size_[class_id]) { // add smaller
- classes_[new_class] = split_el;
- split_el->prev->next = 0;
- split_el->prev = 0;
-+ class_size_[class_id] = split_size_[class_id];
-+ class_size_[new_class] = remainder;
- } else {
- classes_[new_class] = classes_[class_id];
- class_size_[class_id] = remainder;
- class_size_[new_class] = split_size_[class_id];
-***************
-*** 245,254 ****
---- 254,269 ----
- vector<T> class_size_;
-
- // size of split for each class
-+ // in the nondeterministic case, split_size_ is actually an upper
-+ // bound on the size of split for each class.
- vector<T> split_size_;
-
- // set of visited classes to be used in split refine
- vector<T> visited_classes_;
-+
-+ // true if input fst was deterministic: we can make
-+ // certain assumptions in this case that speed up the algorithm.
-+ bool allow_repeated_split_;
- };
-
-
diff --git a/sci-misc/openfst/files/kaldi.patch b/sci-misc/openfst/files/kaldi.patch
deleted file mode 100644
index 3a3854eff..000000000
--- a/sci-misc/openfst/files/kaldi.patch
+++ /dev/null
@@ -1,599 +0,0 @@
-diff -crB openfst-1.3.4.orig/src/include/fst/interval-set.h openfst-1.3.4/src/include/fst/interval-set.h
-*** openfst-1.3.4.orig/src/include/fst/interval-set.h 2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/interval-set.h 2013-11-21 15:59:08.541136087 +0400
-***************
-*** 37,74 ****
- class IntervalSet {
- public:
- struct Interval {
-! T begin;
-! T end;
-
-! Interval() : begin(-1), end(-1) {}
-
-! Interval(T b, T e) : begin(b), end(e) {}
-
- bool operator<(const Interval &i) const {
-! return begin < i.begin || (begin == i.begin && end > i.end);
- }
-
- bool operator==(const Interval &i) const {
-! return begin == i.begin && end == i.end;
- }
-
- bool operator!=(const Interval &i) const {
-! return begin != i.begin || end != i.end;
- }
-
- istream &Read(istream &strm) {
- T n;
- ReadType(strm, &n);
-! begin = n;
- ReadType(strm, &n);
-! end = n;
- return strm;
- }
-
- ostream &Write(ostream &strm) const {
-! T n = begin;
- WriteType(strm, n);
-! n = end;
- WriteType(strm, n);
- return strm;
- }
---- 37,74 ----
- class IntervalSet {
- public:
- struct Interval {
-! T begin_;
-! T end_;
-
-! Interval() : begin_(-1), end_(-1) {}
-
-! Interval(T b, T e) : begin_(b), end_(e) {}
-
- bool operator<(const Interval &i) const {
-! return begin_ < i.begin_ || (begin_ == i.begin_ && end_ > i.end_);
- }
-
- bool operator==(const Interval &i) const {
-! return begin_ == i.begin_ && end_ == i.end_;
- }
-
- bool operator!=(const Interval &i) const {
-! return begin_ != i.begin_ || end_ != i.end_;
- }
-
- istream &Read(istream &strm) {
- T n;
- ReadType(strm, &n);
-! begin_ = n;
- ReadType(strm, &n);
-! end_ = n;
- return strm;
- }
-
- ostream &Write(ostream &strm) const {
-! T n = begin_;
- WriteType(strm, n);
-! n = end_;
- WriteType(strm, n);
- return strm;
- }
-***************
-*** 108,114 ****
- lower_bound(intervals_.begin(), intervals_.end(), interval);
- if (lb == intervals_.begin())
- return false;
-! return (--lb)->end > value;
- }
-
- // Requires intervals be normalized.
---- 108,114 ----
- lower_bound(intervals_.begin(), intervals_.end(), interval);
- if (lb == intervals_.begin())
- return false;
-! return (--lb)->end_ > value;
- }
-
- // Requires intervals be normalized.
-***************
-*** 123,129 ****
-
- bool Singleton() const {
- return intervals_.size() == 1 &&
-! intervals_[0].begin + 1 == intervals_[0].end;
- }
-
-
---- 123,129 ----
-
- bool Singleton() const {
- return intervals_.size() == 1 &&
-! intervals_[0].begin_ + 1 == intervals_[0].end_;
- }
-
-
-***************
-*** 178,194 ****
- T size = 0;
- for (T i = 0; i < intervals_.size(); ++i) {
- Interval &inti = intervals_[i];
-! if (inti.begin == inti.end)
- continue;
- for (T j = i + 1; j < intervals_.size(); ++j) {
- Interval &intj = intervals_[j];
-! if (intj.begin > inti.end)
- break;
-! if (intj.end > inti.end)
-! inti.end = intj.end;
- ++i;
- }
-! count_ += inti.end - inti.begin;
- intervals_[size++] = inti;
- }
- intervals_.resize(size);
---- 178,194 ----
- T size = 0;
- for (T i = 0; i < intervals_.size(); ++i) {
- Interval &inti = intervals_[i];
-! if (inti.begin_ == inti.end_)
- continue;
- for (T j = i + 1; j < intervals_.size(); ++j) {
- Interval &intj = intervals_[j];
-! if (intj.begin_ > inti.end_)
- break;
-! if (intj.end_ > inti.end_)
-! inti.end_ = intj.end_;
- ++i;
- }
-! count_ += inti.end_ - inti.begin_;
- intervals_[size++] = inti;
- }
- intervals_.resize(size);
-***************
-*** 208,224 ****
- oset->count_ = 0;
-
- while (it1 != intervals_.end() && it2 != iintervals->end()) {
-! if (it1->end <= it2->begin) {
- ++it1;
-! } else if (it2->end <= it1->begin) {
- ++it2;
- } else {
- Interval interval;
-! interval.begin = max(it1->begin, it2->begin);
-! interval.end = min(it1->end, it2->end);
- ointervals->push_back(interval);
-! oset->count_ += interval.end - interval.begin;
-! if (it1->end < it2->end)
- ++it1;
- else
- ++it2;
---- 208,224 ----
- oset->count_ = 0;
-
- while (it1 != intervals_.end() && it2 != iintervals->end()) {
-! if (it1->end_ <= it2->begin_) {
- ++it1;
-! } else if (it2->end_ <= it1->begin_) {
- ++it2;
- } else {
- Interval interval;
-! interval.begin_ = max(it1->begin_, it2->begin_);
-! interval.end_ = min(it1->end_, it2->end_);
- ointervals->push_back(interval);
-! oset->count_ += interval.end_ - interval.begin_;
-! if (it1->end_ < it2->end_)
- ++it1;
- else
- ++it2;
-***************
-*** 235,255 ****
- oset->count_ = 0;
-
- Interval interval;
-! interval.begin = 0;
- for (typename vector<Interval>::const_iterator it = intervals_.begin();
- it != intervals_.end();
- ++it) {
-! interval.end = min(it->begin, maxval);
-! if (interval.begin < interval.end) {
- ointervals->push_back(interval);
-! oset->count_ += interval.end - interval.begin;
- }
-! interval.begin = it->end;
- }
-! interval.end = maxval;
-! if (interval.begin < interval.end) {
- ointervals->push_back(interval);
-! oset->count_ += interval.end - interval.begin;
- }
- }
-
---- 235,255 ----
- oset->count_ = 0;
-
- Interval interval;
-! interval.begin_ = 0;
- for (typename vector<Interval>::const_iterator it = intervals_.begin();
- it != intervals_.end();
- ++it) {
-! interval.end_ = min(it->begin_, maxval);
-! if (interval.begin_ < interval.end_) {
- ointervals->push_back(interval);
-! oset->count_ += interval.end_ - interval.begin_;
- }
-! interval.begin_ = it->end_;
- }
-! interval.end_ = maxval;
-! if (interval.begin_ < interval.end_) {
- ointervals->push_back(interval);
-! oset->count_ += interval.end_ - interval.begin_;
- }
- }
-
-***************
-*** 263,269 ****
- oset->count_ = 0;
- } else {
- IntervalSet<T> cset;
-! iset.Complement(intervals_.back().end, &cset);
- Intersect(cset, oset);
- }
- }
---- 263,269 ----
- oset->count_ = 0;
- } else {
- IntervalSet<T> cset;
-! iset.Complement(intervals_.back().end_, &cset);
- Intersect(cset, oset);
- }
- }
-***************
-*** 277,285 ****
- typename vector<Interval>::const_iterator it2 = intervals->begin();
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end <= it2->begin) {
- ++it1;
-! } else if (it2->end <= it1->begin) {
- ++it2;
- } else {
- return true;
---- 277,285 ----
- typename vector<Interval>::const_iterator it2 = intervals->begin();
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end_ <= it2->begin_) {
- ++it1;
-! } else if (it2->end_ <= it1->begin_) {
- ++it2;
- } else {
- return true;
-***************
-*** 300,320 ****
- bool overlap = false; // point in both intervals_ and intervals
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end <= it2->begin) { // no overlap - it1 first
- only1 = true;
- ++it1;
-! } else if (it2->end <= it1->begin) { // no overlap - it2 first
- only2 = true;
- ++it2;
-! } else if (it2->begin == it1->begin && it2->end == it1->end) { // equals
- overlap = true;
- ++it1;
- ++it2;
-! } else if (it2->begin <= it1->begin && it2->end >= it1->end) { // 1 c 2
- only2 = true;
- overlap = true;
- ++it1;
-! } else if (it1->begin <= it2->begin && it1->end >= it2->end) { // 2 c 1
- only1 = true;
- overlap = true;
- ++it2;
---- 300,320 ----
- bool overlap = false; // point in both intervals_ and intervals
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end_ <= it2->begin_) { // no overlap - it1 first
- only1 = true;
- ++it1;
-! } else if (it2->end_ <= it1->begin_) { // no overlap - it2 first
- only2 = true;
- ++it2;
-! } else if (it2->begin_ == it1->begin_ && it2->end_ == it1->end_) { // equals
- overlap = true;
- ++it1;
- ++it2;
-! } else if (it2->begin_ <= it1->begin_ && it2->end_ >= it1->end_) { // 1 c 2
- only2 = true;
- overlap = true;
- ++it1;
-! } else if (it1->begin_ <= it2->begin_ && it1->end_ >= it2->end_) { // 2 c 1
- only1 = true;
- overlap = true;
- ++it2;
-***************
-*** 346,356 ****
- typename vector<Interval>::const_iterator it2 = intervals->begin();
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end <= it2->begin) { // no overlap - it1 first
- ++it1;
-! } else if (it2->begin < it1->begin || it2->end > it1->end) { // no C
- return false;
-! } else if (it2->end == it1->end) {
- ++it1;
- ++it2;
- } else {
---- 346,356 ----
- typename vector<Interval>::const_iterator it2 = intervals->begin();
-
- while (it1 != intervals_.end() && it2 != intervals->end()) {
-! if (it1->end_ <= it2->begin_) { // no overlap - it1 first
- ++it1;
-! } else if (it2->begin_ < it1->begin_ || it2->end_ > it1->end_) { // no C
- return false;
-! } else if (it2->end_ == it1->end_) {
- ++it1;
- ++it2;
- } else {
-***************
-*** 370,376 ****
- ++it) {
- if (it != intervals->begin())
- strm << ",";
-! strm << "[" << it->begin << "," << it->end << ")";
- }
- strm << "}";
- return strm;
---- 370,376 ----
- ++it) {
- if (it != intervals->begin())
- strm << ",";
-! strm << "[" << it->begin_ << "," << it->end_ << ")";
- }
- strm << "}";
- return strm;
-diff -crB openfst-1.3.4.orig/src/include/fst/minimize.h openfst-1.3.4/src/include/fst/minimize.h
-*** openfst-1.3.4.orig/src/include/fst/minimize.h 2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/minimize.h 2013-11-21 15:59:08.539136087 +0400
-***************
-*** 134,140 ****
- typedef typename A::Weight Weight;
- typedef ReverseArc<A> RevA;
-
-! CyclicMinimizer(const ExpandedFst<A>& fst) {
- Initialize(fst);
- Compute(fst);
- }
---- 134,147 ----
- typedef typename A::Weight Weight;
- typedef ReverseArc<A> RevA;
-
-! CyclicMinimizer(const ExpandedFst<A>& fst):
-! // tell the Partition data-member to expect multiple repeated
-! // calls to SplitOn with the same element if we are non-deterministic.
-! P_(fst.Properties(kIDeterministic, true) == 0) {
-! if(fst.Properties(kIDeterministic, true) == 0)
-! CHECK(Weight::Properties() & kIdempotent); // this minimization
-! // algorithm for non-deterministic FSTs can only work with idempotent
-! // semirings.
- Initialize(fst);
- Compute(fst);
- }
-***************
-*** 315,321 ****
- typedef typename A::StateId ClassId;
- typedef typename A::Weight Weight;
-
-! AcyclicMinimizer(const ExpandedFst<A>& fst) {
- Initialize(fst);
- Refine(fst);
- }
---- 322,334 ----
- typedef typename A::StateId ClassId;
- typedef typename A::Weight Weight;
-
-! AcyclicMinimizer(const ExpandedFst<A>& fst):
-! // tell the Partition data-member to expect multiple repeated
-! // calls to SplitOn with the same element if we are non-deterministic.
-! partition_(fst.Properties(kIDeterministic, true) == 0) {
-! if(fst.Properties(kIDeterministic, true) == 0)
-! CHECK(Weight::Properties() & kIdempotent); // minimization for
-! // non-deterministic FSTs can only work with idempotent semirings.
- Initialize(fst);
- Refine(fst);
- }
-***************
-*** 531,543 ****
- void Minimize(MutableFst<A>* fst,
- MutableFst<A>* sfst = 0,
- float delta = kDelta) {
-! uint64 props = fst->Properties(kAcceptor | kIDeterministic|
-! kWeighted | kUnweighted, true);
-! if (!(props & kIDeterministic)) {
-! FSTERROR() << "FST is not deterministic";
-! fst->SetProperties(kError, kError);
-! return;
-! }
-
- if (!(props & kAcceptor)) { // weighted transducer
- VectorFst< GallicArc<A, STRING_LEFT> > gfst;
---- 544,550 ----
- void Minimize(MutableFst<A>* fst,
- MutableFst<A>* sfst = 0,
- float delta = kDelta) {
-! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true);
-
- if (!(props & kAcceptor)) { // weighted transducer
- VectorFst< GallicArc<A, STRING_LEFT> > gfst;
-diff -crB openfst-1.3.4.orig/src/include/fst/partition.h openfst-1.3.4/src/include/fst/partition.h
-*** openfst-1.3.4.orig/src/include/fst/partition.h 2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/partition.h 2013-11-21 15:59:08.539136087 +0400
-***************
-*** 43,50 ****
- friend class PartitionIterator<T>;
-
- struct Element {
-! Element() : value(0), next(0), prev(0) {}
-! Element(T v) : value(v), next(0), prev(0) {}
-
- T value;
- Element* next;
---- 43,50 ----
- friend class PartitionIterator<T>;
-
- struct Element {
-! Element() : value(0), next(0), prev(0) {}
-! Element(T v) : value(v), next(0), prev(0) {}
-
- T value;
- Element* next;
-***************
-*** 52,60 ****
- };
-
- public:
-! Partition() {}
-
-! Partition(T num_states) {
- Initialize(num_states);
- }
-
---- 52,62 ----
- };
-
- public:
-! Partition(bool allow_repeated_split):
-! allow_repeated_split_(allow_repeated_split) {}
-
-! Partition(bool allow_repeated_split, T num_states):
-! allow_repeated_split_(allow_repeated_split) {
- Initialize(num_states);
- }
-
-***************
-*** 137,152 ****
- if (class_size_[class_id] == 1) return;
-
- // first time class is split
-! if (split_size_[class_id] == 0)
- visited_classes_.push_back(class_id);
-!
- // increment size of split (set of element at head of chain)
- split_size_[class_id]++;
-!
- // update split point
-! if (class_split_[class_id] == 0)
-! class_split_[class_id] = classes_[class_id];
-! if (class_split_[class_id] == elements_[element_id])
- class_split_[class_id] = elements_[element_id]->next;
-
- // move to head of chain in same class
---- 139,154 ----
- if (class_size_[class_id] == 1) return;
-
- // first time class is split
-! if (split_size_[class_id] == 0) {
- visited_classes_.push_back(class_id);
-! class_split_[class_id] = classes_[class_id];
-! }
- // increment size of split (set of element at head of chain)
- split_size_[class_id]++;
-!
- // update split point
-! if (class_split_[class_id] != 0
-! && class_split_[class_id] == elements_[element_id])
- class_split_[class_id] = elements_[element_id]->next;
-
- // move to head of chain in same class
-***************
-*** 157,165 ****
- // class indices of the newly created class. Returns the new_class id
- // or -1 if no new class was created.
- T SplitRefine(T class_id) {
- // only split if necessary
-! if (class_size_[class_id] == split_size_[class_id]) {
-! class_split_[class_id] = 0;
- split_size_[class_id] = 0;
- return -1;
- } else {
---- 159,169 ----
- // class indices of the newly created class. Returns the new_class id
- // or -1 if no new class was created.
- T SplitRefine(T class_id) {
-+
-+ Element* split_el = class_split_[class_id];
- // only split if necessary
-! //if (class_size_[class_id] == split_size_[class_id]) {
-! if(split_el == NULL) { // we split on everything...
- split_size_[class_id] = 0;
- return -1;
- } else {
-***************
-*** 163,180 ****
- split_size_[class_id] = 0;
- return -1;
- } else {
--
- T new_class = AddClass();
- size_t remainder = class_size_[class_id] - split_size_[class_id];
- if (remainder < split_size_[class_id]) { // add smaller
-- Element* split_el = class_split_[class_id];
- classes_[new_class] = split_el;
-- class_size_[class_id] = split_size_[class_id];
-- class_size_[new_class] = remainder;
- split_el->prev->next = 0;
- split_el->prev = 0;
- } else {
-- Element* split_el = class_split_[class_id];
- classes_[new_class] = classes_[class_id];
- class_size_[class_id] = remainder;
- class_size_[new_class] = split_size_[class_id];
---- 167,189 ----
- split_size_[class_id] = 0;
- return -1;
- } else {
- T new_class = AddClass();
-+
-+ if(allow_repeated_split_) { // split_size_ is possibly
-+ // inaccurate, so work it out exactly.
-+ size_t split_count; Element *e;
-+ for(split_count=0,e=classes_[class_id];
-+ e != split_el; split_count++, e=e->next);
-+ split_size_[class_id] = split_count;
-+ }
- size_t remainder = class_size_[class_id] - split_size_[class_id];
- if (remainder < split_size_[class_id]) { // add smaller
- classes_[new_class] = split_el;
- split_el->prev->next = 0;
- split_el->prev = 0;
-+ class_size_[class_id] = split_size_[class_id];
-+ class_size_[new_class] = remainder;
- } else {
- classes_[new_class] = classes_[class_id];
- class_size_[class_id] = remainder;
- class_size_[new_class] = split_size_[class_id];
-***************
-*** 245,254 ****
---- 254,269 ----
- vector<T> class_size_;
-
- // size of split for each class
-+ // in the nondeterministic case, split_size_ is actually an upper
-+ // bound on the size of split for each class.
- vector<T> split_size_;
-
- // set of visited classes to be used in split refine
- vector<T> visited_classes_;
-+
-+ // true if input fst was deterministic: we can make
-+ // certain assumptions in this case that speed up the algorithm.
-+ bool allow_repeated_split_;
- };
-
-
diff --git a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch b/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch
deleted file mode 100644
index 8eb3116d0..000000000
--- a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch
+++ /dev/null
@@ -1,83 +0,0 @@
-diff -Naur -Naur OpenFst/fst/bin/main.cc OpenFst-nu/fst/bin/main.cc
---- OpenFst/fst/bin/main.cc 2008-03-17 17:42:00.000000000 +0200
-+++ OpenFst-nu/fst/bin/main.cc 2008-10-20 16:30:36.000000000 +0300
-@@ -18,6 +18,8 @@
- // Classes and functions for registering and invoking Fst main
- // functions that support multiple and extensible arc types.
-
-+#include <cstring>
-+#include <climits>
- #include <iostream>
-
- #include "fst/bin/main.h"
-diff -Naur -Naur OpenFst/fst/bin/Makefile OpenFst-nu/fst/bin/Makefile
---- OpenFst/fst/bin/Makefile 2008-03-17 17:42:00.000000000 +0200
-+++ OpenFst-nu/fst/bin/Makefile 2008-10-20 16:31:12.000000000 +0300
-@@ -15,7 +15,7 @@
- FSTLIBMAIN=libfstmain.$(LIBTYPE)
- LIBS=-lfstmain -lfst -lm -lpthread -ldl
- CC=g++
--OPT=-O2
-+OPT=-O2 -fPIC
- CFLAGS=-I../.. $(OPT) -DFST_DL
- LDLFLAGS=-Wl,-L$(LIBDIR),-L$(BINDIR)
- LDRFLAGS=-Wl,-rpath,$(LIBDIR),-rpath,$(BINDIR) # empty on macosx
-diff -Naur -Naur OpenFst/fst/lib/compat.h OpenFst-nu/fst/lib/compat.h
---- OpenFst/fst/lib/compat.h 2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/compat.h 2008-10-20 16:25:49.000000000 +0300
-@@ -27,7 +27,7 @@
- #include <map>
- #include <string>
- #include <vector>
--
-+#include <cstring>
- #include <ext/hash_map>
- #include <fcntl.h>
- #include <pthread.h>
-diff -Naur -Naur OpenFst/fst/lib/Makefile OpenFst-nu/fst/lib/Makefile
---- OpenFst/fst/lib/Makefile 2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/Makefile 2008-10-20 16:23:05.000000000 +0300
-@@ -2,7 +2,7 @@
- SRCS=fst.cc properties.cc symbol-table.cc compat.cc
- OBJS=fst.o properties.o symbol-table.o compat.o
- CC=g++
--OPT=-O2
-+OPT=-fPIC -O2
- CFLAGS=$(OPT) -I../.. -DFST_DL
- LIBTYPE=so # "dylib" on macosx
- SOFLAGS=-shared # "-dynamiclib -flat_namespace -undefined suppress" on macosx
-diff -Naur -Naur OpenFst/fst/lib/randgen.h OpenFst-nu/fst/lib/randgen.h
---- OpenFst/fst/lib/randgen.h 2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/randgen.h 2008-10-20 16:44:33.000000000 +0300
-@@ -23,6 +23,7 @@
- #include <cmath>
- #include <cstdlib>
- #include <ctime>
-+#include <climits>
-
- #include "fst/lib/mutable-fst.h"
-
-diff -Naur -Naur OpenFst/fst/lib/symbol-table.cc OpenFst-nu/fst/lib/symbol-table.cc
---- OpenFst/fst/lib/symbol-table.cc 2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/symbol-table.cc 2008-10-20 16:21:16.000000000 +0300
-@@ -17,6 +17,8 @@
- // \file
- // Classes to provide symbol-to-integer and integer-to-symbol mappings.
-
-+#include <cstring>
-+
- #include "fst/lib/symbol-table.h"
- #include "fst/lib/util.h"
-
-diff -Naur -Naur OpenFst/fst/lib/vector-fst.h OpenFst-nu/fst/lib/vector-fst.h
---- OpenFst/fst/lib/vector-fst.h 2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/vector-fst.h 2008-10-20 16:21:25.000000000 +0300
-@@ -21,6 +21,8 @@
- #ifndef FST_LIB_VECTOR_FST_H__
- #define FST_LIB_VECTOR_FST_H__
-
-+#include <cstring>
-+
- #include "fst/lib/mutable-fst.h"
- #include "fst/lib/test-properties.h"
-
diff --git a/sci-misc/openfst/metadata.xml b/sci-misc/openfst/metadata.xml
index 2d4fb61e6..8b44b5491 100644
--- a/sci-misc/openfst/metadata.xml
+++ b/sci-misc/openfst/metadata.xml
@@ -4,4 +4,8 @@
<maintainer type="person">
<email>flammie@gentoo.org</email>
</maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-misc/openfst/openfst-1.8.1.ebuild b/sci-misc/openfst/openfst-1.8.2.ebuild
index 16c275e8e..923a36f64 100644
--- a/sci-misc/openfst/openfst-1.8.1.ebuild
+++ b/sci-misc/openfst/openfst-1.8.2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Finite State Transducer tools by Google et al"
HOMEPAGE="http://www.openfst.org"
diff --git a/sci-physics/hoppet/Manifest b/sci-physics/hoppet/Manifest
new file mode 100644
index 000000000..cc73bfc3b
--- /dev/null
+++ b/sci-physics/hoppet/Manifest
@@ -0,0 +1 @@
+DIST hoppet-1.2.0.tgz 575911 BLAKE2B 4d4dc1874b45b7237384ad3955808b5f4995c86b4d44165ef0c4d8b1da21880cdd1a3f1f1537f02ad7928baef5207e950be411465989ab876bcb806f355725cf SHA512 65ceb170cd417f229f8a974aa995138b8ee7ea5ef04538a5382b353181951e9d4489045234cd45c1ea8f88a5faf4755e3a0e246065711f137676bbf726a29f1f
diff --git a/sci-physics/hoppet/hoppet-1.2.0.ebuild b/sci-physics/hoppet/hoppet-1.2.0.ebuild
new file mode 100644
index 000000000..337881026
--- /dev/null
+++ b/sci-physics/hoppet/hoppet-1.2.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2022-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+DESCRIPTION="Higher Order Perturbative Parton Evolution Toolkit"
+HOMEPAGE="
+ https://hoppet.hepforge.org/
+ https://github.com/gavinsalam/hoppet
+"
+SRC_URI="https://hoppet.hepforge.org/downloads/${P}.tgz"
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64"
+
+
+src_configure() {
+ default
+ # own custom configure
+ ./configure --prefix="${EPREFIX}"/usr FFLAGS="${FFLAGS} -fPIC" || die
+}
+
+src_install() {
+ # Fix install to ED
+ sed -i "s#scripts/install-sh hoppet-config#\##g" Makefile || die
+ sed -i "s#/usr/lib/libhoppet#${ED}/usr/$(get_libdir)/libhoppet#g" src/Makefile || die
+ sed -i "s#/usr/include/hoppet#${ED}/usr/include/hoppet#g" src/Makefile || die
+ emake install
+ emake install-mod
+ dobin hoppet-config
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/hoppet/metadata.xml b/sci-physics/hoppet/metadata.xml
new file mode 100644
index 000000000..37900a238
--- /dev/null
+++ b/sci-physics/hoppet/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+
+ <longdescription lang="en">
+ HOPPET is a Fortran 95 package for carrying out DGLAP evolution and other common manipulations of parton distribution functions (PDFs).
+ </longdescription>
+ <upstream>
+ <remote-id type="github">gavinsalam/hoppet</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/lhapdf-sets/Manifest b/sci-physics/lhapdf-sets/Manifest
new file mode 100644
index 000000000..6b51079a6
--- /dev/null
+++ b/sci-physics/lhapdf-sets/Manifest
@@ -0,0 +1,12 @@
+DIST CT10.tar.gz 10246366 BLAKE2B f0daf0a3ca6cd2f178f993944cdc29de5deb1f441d197e47c8b1c285a56abc0fdb1cd53ec5a8e7736e200397bea9ec9cf4d04420ce206e5c396b85b63f695d00 SHA512 90406bd102ab54b683fa3e6f3fc759febea2454a0b96c6a8d373cdec297f5d652097057a015c7d87241792ed9b5d9ac658a33155cdd7362f59110f8f06ecce73
+DIST CT14lo.tar.gz 474954 BLAKE2B 60e8d3695fa64a997f0431516086f037d8843a9310cb52910c28a8a8960838409bafb280cf776b25fde1b31225743b72a48a3d467b1f7a4ff5478d515607645b SHA512 bc6acfcf522262da227411555f10dd73456fb5d0ab9db334b99cf7953463e1fa3de8c78bbb95269e9a47629860d906d43948e6cf1719b00402645ec18249f959
+DIST CT14nlo.tar.gz 27067462 BLAKE2B b8d46593a62e80c320c76fb89f646ba0f31ab98811076120de1d21ef3b4849ff3d2e7b8d01d01dff5f1ee05a2266d94664e7f4a27347fa32c8ac4c68b0e72acb SHA512 1fcdfd24569966c1bc9c98f8ae2bf7d3a306700387b1351c92bc2b4f061db5d59d048c6cdd25095e1dc58344afa7f65a6526c611d747a5894398754483db77a2
+DIST CT14qed_proton.tar.gz 11064380 BLAKE2B b0b5834473a90d2adfedfa4dd467847349fc1b60907d387d1007387dcf557fac37871ea7430161edc0ecf6f8e8839077283dc8fcad610f03dd192efd70890c3f SHA512 a41f6f82e5505f66014e5523210c272254fb8018bbfac542eb1941e60c1c897ee687bfef1afbd981132cb772240fdd4d19b5dcd2b36b01f8e34ea959d9acd4f7
+DIST MRST2004qed.tar.gz 185079 BLAKE2B 62e0371de965698100755b14b0c282095b84b40800a58cd6776c458b03982f032f3b2464eb76174084dd22de9fd962e202a4896327b0a00579c3a632dac24ccc SHA512 404aacf0e241f572cc42ad4cf963deef1acd3d365fa68cfa3518878f921858046377ea39caf663fdced2cdde07af2f6ce695737f7fea229489df3d3f38283c95
+DIST MRST2007lomod.tar.gz 56685 BLAKE2B 8515b6f77302621f4b37f550840f07f0351e7ea98de16a37ceb4cb0f2ea64aa4b027462ffc442f34d1f4c349d67fac7b35353606d8920f17621c7187e508c689 SHA512 8e55627a01c85d90a62e4fb11b115c2faac2220479b6d558d3d6f1b801fc5c3e88abc377cd5437ccaeedd34b2ca42d6e833014566b796e5e1eebcf4d620e5dc0
+DIST NNPDF23_nlo_as_0119_qed_mc.tar.gz 25223180 BLAKE2B 05dd8772d559e8f08e28dc16da6b256d875563b140e1954cedac9b5f541e9cd325c4dfd5adbb13af434e036cbafa9bfe19325f69ae00ed599cfac6791629d989 SHA512 fc6998d50a61bbe65eef827021c0f453164795c079daef6a4932f825f8db4ae318bbf0e8781b61f1d3ffa9a495b5c4813af3aa31c77694657a44356d93fa970f
+DIST NNPDF23_nnlo_as_0119_qed_mc.tar.gz 28940412 BLAKE2B 57c7c98bb863258f87e236fea2d0233ac61350012aec6ba5cced75de0b4b945a5633d7fd487b0913b822df1c3ef804de2aacf34b1319d6973d959dc02ebbc9b2 SHA512 5088c30acbd1da4e412ba9f6a997ceaa34f426f41c7ebacaf4d2e8aa49b8b45052913e8d873b293d9f140c01e82c05735b66dd527a9aa124b86f73bf5e4d8c53
+DIST NNPDF31_nnlo_as_0118_luxqed.tar.gz 47462442 BLAKE2B 2b473d943ec49e28de63d002e4eadfd3002c63aa6ef9b4e792adf7acf8bb3a771f91298ac6575034407653d15aa4191da6090aaaa34d8a8091cb1a5d4562479a SHA512 5faafc9a2b23dc0a82c7f3ca26a6691cfa476f83741beab2b41a77e63fa5f10428bf43579670636689c0080421f4b08ec058aa63c047f04f6d892b1b848fd702
+DIST PDF4LHC15_nlo_asvar.tar.gz 578871 BLAKE2B a42a24d4af82f892e0dccfeeacedfcbb074be1ddc9649d55ff6c15e3923901173337ba4197248410d2a40e72ab627af9a0cea09e5ee98c37130aceb34402d9d4 SHA512 ef96970050b78f5a5bc54b43ee2d7ed0eb76796ea23ce864f1c8ff6de2d68f99023d5c4530f4e73197948c39886fcb832ed26dfa126ca0396e4fd08e353df8a0
+DIST cteq66.tar.gz 8647237 BLAKE2B 3ac47b6eee434f89ff329cfcb8268782af4ffa552ca4b412a59254e9b10410518f9fe9543b47f193d9cd31b06fc1101556df2be01c25ca17febcb9fb1855e5ca SHA512 25d0fa01dcdb59d71c7092367af8258471a2bc6dfd146766cc79f90ffb0feafa0f2011d0a37a7d75315c10ba7c7a6e3fa583d9c0a28119b072228ac800294e48
+DIST cteq6l1.tar.gz 317834 BLAKE2B eccad131853f9a760d0dfd43a3f8705f8edbac3ec7373de9ef9a8936f13ba06500ba5758cd04649dd1b85ac04fc778e9d96222877e74e9ff02263455b233fa41 SHA512 7177608e97077eaf45a292db4ea74eb9a28b4b500ab8be02098b4837a5583cd397828abc3bf43ead448926eaa75ae3968bd059ecde333d90ed6e4295cbe1873c
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
new file mode 100644
index 000000000..edd3639d2
--- /dev/null
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+LHA_VER="6.2.1"
+
+IUSE_LHAPDF_SETS="
+ lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed
+ lhapdf_sets_pdf4lhc15_nlo_asvar
+ lhapdf_sets_ct14qed_proton
+ lhapdf_sets_ct14lo
+ lhapdf_sets_ct14nlo
+ lhapdf_sets_ct10
+ lhapdf_sets_mrst2007lomod
+ lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc
+ lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc
+ lhapdf_sets_cteq66
+ lhapdf_sets_cteq6l1
+ lhapdf_sets_mrst2004qed
+"
+
+COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current"
+HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_VER}"
+# Alternatively to fetching them here already the user can install them by lhapdf install,
+# BUT some codes need them during test and even compile (Herwig) stage.
+# Also since it belongs to LHAPDF it is better to fetch them here.
+SRC_URI="
+ lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118_luxqed.tar.gz )
+ lhapdf_sets_pdf4lhc15_nlo_asvar? ( ${COMMON_URI}/PDF4LHC15_nlo_asvar.tar.gz )
+ lhapdf_sets_ct14qed_proton? ( ${COMMON_URI}/CT14qed_proton.tar.gz )
+ lhapdf_sets_ct14lo? ( ${COMMON_URI}/CT14lo.tar.gz )
+ lhapdf_sets_ct14nlo? ( ${COMMON_URI}/CT14nlo.tar.gz )
+ lhapdf_sets_ct10? ( ${COMMON_URI}/CT10.tar.gz )
+ lhapdf_sets_mrst2007lomod? ( ${COMMON_URI}/MRST2007lomod.tar.gz )
+ lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nlo_as_0119_qed_mc.tar.gz )
+ lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
+ lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz )
+ lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz )
+ lhapdf_sets_mrst2004qed? ( ${HEPFORGE_URI}/MRST2004qed.tar.gz )
+"
+
+MY_PV=$(ver_cut 1-3)
+MY_PF=LHAPDF-${MY_PV}
+
+DESCRIPTION="LHAPDF data grids"
+HOMEPAGE="https://lhapdf.hepforge.org/"
+KEYWORDS="~amd64 ~x86"
+S="${WORKDIR}"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE="${IUSE_LHAPDF_SETS}"
+SLOT="0"
+RDEPEND="sci-physics/lhapdf"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+ # unpack in destination only to avoid copy
+ return
+}
+
+src_install() {
+ dodir /usr/share/LHAPDF/
+ cd "${ED}/usr/share/LHAPDF/" || die
+ unpack ${A}
+}
diff --git a/sci-physics/lhapdf-sets/metadata.xml b/sci-physics/lhapdf-sets/metadata.xml
new file mode 100644
index 000000000..73a7063eb
--- /dev/null
+++ b/sci-physics/lhapdf-sets/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>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-physics/pyhepmc/Manifest b/sci-physics/pyhepmc/Manifest
new file mode 100644
index 000000000..1351fa866
--- /dev/null
+++ b/sci-physics/pyhepmc/Manifest
@@ -0,0 +1 @@
+DIST pyhepmc-2.11.0.tar.gz 361596 BLAKE2B 18264f61bdef3c27f8aa4d48d25257c03f98cc89745533641119cf7ba6d5fe36c084d25ccaeed6769dc9226fd5f2c27060006030447a8ac8409ff6d752437d2c SHA512 31975d0bee5037c1cc36753ce6324342ed6a48b2d3f91f53d61f445f38f0fa3ecbeb0e29fcbc7f6778bafcc23c1f6a689b9516eae8da4cc620cd7c72b89e0b00
diff --git a/sci-physics/pyhepmc/metadata.xml b/sci-physics/pyhepmc/metadata.xml
new file mode 100644
index 000000000..6f6a9a0bb
--- /dev/null
+++ b/sci-physics/pyhepmc/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ pyhepmc largely mirrors the C++ interface of the HepMC3 library, which is documented here. Parts of the documentation have been copied from HepMC3. Documentation is available as Python docstrings, so you can use Python's help() browser to learn about the API. Alternatively, you can consult the online reference generated from these docstrings which includes some examples.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">pyhepmc</remote-id>
+ <remote-id type="github">scikit-hep/pyhepmc</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
new file mode 100644
index 000000000..c28b094bb
--- /dev/null
+++ b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Pythonic wrapper for the HepMC3 C++ library."
+HOMEPAGE="https://github.com/scikit-hep/pyhepmc"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.0[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ ${RDEPEND}
+ dev-build/cmake
+"
diff --git a/sci-physics/pyhf/Manifest b/sci-physics/pyhf/Manifest
new file mode 100644
index 000000000..756bfb423
--- /dev/null
+++ b/sci-physics/pyhf/Manifest
@@ -0,0 +1 @@
+DIST pyhf-0.7.3.tar.gz 113423 BLAKE2B 216ef186c539481e2819e3f3a198203f085aa99652ab335b1153309a780857c5ad53bc848bb1b12615cfa9b8ee97a67553cef5a0f899bbcf178bfea1b2ca11c5 SHA512 904491f9c161f0231d1e109cfa3a12b31a31b1aa7477752e1eafd1e6c4cec75551e53ce1f6d447bed8f295371dc20b032888a5175af0f2eb808e03c0a8993930
diff --git a/sci-physics/pyhf/metadata.xml b/sci-physics/pyhf/metadata.xml
new file mode 100644
index 000000000..47738d1db
--- /dev/null
+++ b/sci-physics/pyhf/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ The HistFactory p.d.f. template [CERN-OPEN-2012-016] is per-se independent of its implementation in ROOT and sometimes, it’s useful to be able to run statistical analysis outside of ROOT, RooFit, RooStats framework.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">particle</remote-id>
+ <remote-id type="github">scikit-hep/particle</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-physics/pyhf/pyhf-0.7.3.ebuild b/sci-physics/pyhf/pyhf-0.7.3.ebuild
new file mode 100644
index 000000000..8b2d02304
--- /dev/null
+++ b/sci-physics/pyhf/pyhf-0.7.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_11 )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="pure-python fitting/limit-setting/interval estimation HistFactory-style"
+HOMEPAGE="
+ https://github.com/scikit-hep/pyhf
+ https://doi.org/10.5281/zenodo.1169739
+ https://zenodo.org/record/8256635
+ https://doi.org/10.21105/joss.02823
+ https://inspirehep.net/literature/2598491
+ https://arxiv.org/abs/2211.15838
+ https://doi.org/10.22323/1.414.0245
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.5.1[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-5.1[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}]
+ >=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}]
+ >=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}]
+ >=dev-python/click-8.0.0[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
diff --git a/sci-physics/tauola/tauola-1.1.8.ebuild b/sci-physics/tauola/tauola-1.1.8.ebuild
index 61ec51d9f..4d4742dd1 100644
--- a/sci-physics/tauola/tauola-1.1.8.ebuild
+++ b/sci-physics/tauola/tauola-1.1.8.ebuild
@@ -21,7 +21,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}
doc? (
- app-doc/doxygen[dot]
+ app-text/doxygen[dot]
app-text/ghostscript-gpl
app-text/texlive
)
diff --git a/sci-visualization/forge/forge-1.0.5.ebuild b/sci-visualization/forge/forge-1.0.5.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-1.0.5.ebuild
+++ b/sci-visualization/forge/forge-1.0.5.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sci-visualization/forge/forge-1.0.7.ebuild b/sci-visualization/forge/forge-1.0.7.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-1.0.7.ebuild
+++ b/sci-visualization/forge/forge-1.0.7.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sci-visualization/forge/forge-9999.ebuild b/sci-visualization/forge/forge-9999.ebuild
index b222dac0c..dd708d35f 100644
--- a/sci-visualization/forge/forge-9999.ebuild
+++ b/sci-visualization/forge/forge-9999.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="
doc? (
- app-doc/doxygen
+ app-text/doxygen
dev-python/breathe
dev-python/recommonmark
dev-python/sphinx
diff --git a/sys-cluster/easybuild-easyblocks/Manifest b/sys-cluster/easybuild-easyblocks/Manifest
index 2a6fcf00a..955f41791 100644
--- a/sys-cluster/easybuild-easyblocks/Manifest
+++ b/sys-cluster/easybuild-easyblocks/Manifest
@@ -1 +1,2 @@
DIST easybuild-easyblocks-4.6.2.tar.gz 539757 BLAKE2B e33db4b390cdbe11237c5f5750426f15d264cf081e2846c7b9de9254f7a0fbdc1459795920fcc131ceb5681f0acc905a74f96cd841b73b523e030246b78393e8 SHA512 72cb4c057efdfeb4c45fbf1e036a6f231e7f01ad6e593d1c2352b27f002ed4f45cd625c4125b90b708b15f226fb9519a345217f7882c2155b399894986a4505c
+DIST easybuild-easyblocks-4.9.0.tar.gz 574066 BLAKE2B 404ea11287d03edf497c85e9d58eba05d3257aed609eb3f65e3d1543e08e0be27a64fd7459ba30578a3bd2be2051020f711f6598af082d2cdec3fad65116a0ed SHA512 c75695c66f4683128be268471e996abde83fc9cc5f937699b81da5ea94bf02df84bc6b0a88c657a904730afbc4048e3a44cfbc5288a546c1962a51960393d5c7
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
new file mode 100644
index 000000000..d97f48696
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
@@ -0,0 +1,36 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+src_prepare() {
+ # already there from easybuild_framework
+ rm easybuild/__init__.py || die
+ default
+}
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
new file mode 100644
index 000000000..6796cf683
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
@@ -0,0 +1,37 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+ SUB_P=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+src_prepare() {
+ # already there from easybuild_framework
+ rm easybuild/__init__.py || die
+ default
+}
diff --git a/sys-cluster/easybuild-easyconfigs/Manifest b/sys-cluster/easybuild-easyconfigs/Manifest
index c9dfce712..b8328d6aa 100644
--- a/sys-cluster/easybuild-easyconfigs/Manifest
+++ b/sys-cluster/easybuild-easyconfigs/Manifest
@@ -1 +1,2 @@
DIST easybuild-easyconfigs-4.6.2.tar.gz 7991765 BLAKE2B 02e7b629858177db19b7a63fcacd4898805ccfabd7bac343e05015d545d057bb04416b0b89245d3e3c206bc0f129920dda7d7ae1e421e9f7ce690ee6d01acd90 SHA512 4632dc0714b3e070b58a8192cb8054f0e21357701f59df054593ea754f5598c8e6446acd77c0e41f2fb920d31297ea5a5164fd81b26b926835868f24623cdce8
+DIST easybuild-easyconfigs-4.9.0.tar.gz 9636057 BLAKE2B 5b7710c99eb0d728d4df6582db40b7dc72d86cfca32548c79344a2b918e53e56360c97225ab2cf577bf2ba170bf67de211758afb83e696ec157165316b01cf02 SHA512 a39dc1eddc569163b21abdca9633a4c35519f609a03012ef7ec3f58c40a58961450b626c3701c325a2e485e5a00d161d737239c19ea657546b52b2c16de307f5
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
new file mode 100644
index 000000000..ea069535d
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+ SUB_P=9999
+ SUB_PP=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+ >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
new file mode 100644
index 000000000..ea069535d
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+ SUB_P=9999
+ SUB_PP=9999
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+ >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-framework/Manifest b/sys-cluster/easybuild-framework/Manifest
index 633cd3bdc..6845b4e9c 100644
--- a/sys-cluster/easybuild-framework/Manifest
+++ b/sys-cluster/easybuild-framework/Manifest
@@ -1 +1,2 @@
DIST easybuild-framework-4.6.2.tar.gz 2019284 BLAKE2B a32ae1fc43d490b32fc6c44790493204de935d16257846ec46830fc4d18a7343b860317c0ba33a16d89f12f657c33f7bb7359a70bf26a17c4e0dd16b8c78e2cd SHA512 ac8a06301c6c95edded262cb55b02ea8ada9ea14dfb7b7354a3bb29fcd9ad9a8d0011edbf2175085b8cec721f08a2b5f5e74aaa191d381a787eb5438c6c7f8cc
+DIST easybuild-framework-4.9.0.tar.gz 2064113 BLAKE2B 637498e7d52f0e9a6e9bd25c843052d9fc3c730f93b40c37381263b8861b0dd1b8ebf1d13af514d841d43284eb81b7555fcdaacbc1ac2c1bd655748c01540677 SHA512 b7b52d8987f13d9f859df0874adb7b855f8b4961215d9e9cb4a63a15911affe1591d718076277419be0c31e76845cf5cbe4fe553676ac71b8ff33a82d3c17a0e
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
new file mode 100644
index 000000000..56dda1fba
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-python/flake8[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/autopep8[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/archspec[${PYTHON_USEDEP}]
+ dev-python/cryptography[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
new file mode 100644
index 000000000..56dda1fba
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-python/flake8[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/autopep8[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/archspec[${PYTHON_USEDEP}]
+ dev-python/cryptography[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild/Manifest b/sys-cluster/easybuild/Manifest
index 6ae785a0e..b17222baf 100644
--- a/sys-cluster/easybuild/Manifest
+++ b/sys-cluster/easybuild/Manifest
@@ -1 +1,2 @@
DIST easybuild-4.6.2.tar.gz 10680 BLAKE2B ed9dcaf1e138dd0d56fbff51151b5e0a6c0842495a950fe6a37a16435ab679bd0f60d34a703f6791b1486001fa3508e23d8a82ae6cc39f90137f03b5a93f5a0e SHA512 34097122968d31cf7fa8503f1566ff43c4fd34849c02050eb2f7304028479afd224128a0b83c195150b9ff6680b903a6b20fee715c9511bde292e2c4ac88397b
+DIST easybuild-4.9.0.tar.gz 10622 BLAKE2B bf7c69db95d49e2d992541baa145346e173fc35eab6002afd59a62d7c2007fea41672d81a3f1cf0e170f630dcf4bbea957b254fbffd5237738180d2df0976964 SHA512 3a1a4433e58d90f90dd8ba2700f7dcc07a07333d7f103ea23f82145af76a41af436d9e606fbe95fc5cfcf4be07399a3b3d5cc10c57c0bd77ea8018ba4e852c8d
diff --git a/sys-cluster/easybuild/easybuild-4.9.0.ebuild b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
new file mode 100644
index 000000000..c0f284835
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-libs/openssl
+ dev-tcltk/tclx
+ || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+ ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+pkg_postinst() {
+ elog "Remember to set the module install path"
+ elog "ml use \$installpath/modules/all"
+ elog "where --installpath is passed to eb"
+
+ optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-cluster/easybuild/easybuild-9999.ebuild b/sys-cluster/easybuild/easybuild-9999.ebuild
new file mode 100644
index 000000000..c0f284835
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+ https://easybuild.io/
+ https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ dev-libs/openssl
+ dev-tcltk/tclx
+ || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+ ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+ ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+pkg_postinst() {
+ elog "Remember to set the module install path"
+ elog "ml use \$installpath/modules/all"
+ elog "where --installpath is passed to eb"
+
+ optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-devel/DPC++/DPC++-2021.12.ebuild b/sys-devel/DPC++/DPC++-2021.12.ebuild
index 48e7b5d44..348b6f8d6 100644
--- a/sys-devel/DPC++/DPC++-2021.12.ebuild
+++ b/sys-devel/DPC++/DPC++-2021.12.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -62,7 +62,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )
diff --git a/sys-devel/DPC++/DPC++-2022.09.ebuild b/sys-devel/DPC++/DPC++-2022.09.ebuild
index 7532e3c1b..ee2077566 100644
--- a/sys-devel/DPC++/DPC++-2022.09.ebuild
+++ b/sys-devel/DPC++/DPC++-2022.09.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -62,7 +62,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )
diff --git a/sys-devel/DPC++/DPC++-2022.12.ebuild b/sys-devel/DPC++/DPC++-2022.12.ebuild
index 25ac88770..be9a59fec 100644
--- a/sys-devel/DPC++/DPC++-2022.12.ebuild
+++ b/sys-devel/DPC++/DPC++-2022.12.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit cmake python-any-r1
DOCS_BUILDER="doxygen"
DOCS_DIR="build/docs"
@@ -64,7 +64,7 @@ DEPEND="
dev-util/spirv-headers
dev-util/spirv-tools
media-libs/libva
- sys-devel/libtool
+ dev-build/libtool
esimd_emulator? ( dev-libs/libffi:= )
cuda? ( dev-util/nvidia-cuda-toolkit:= )
hip? ( dev-util/hip:= )