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-rw-r--r--README.md7
-rw-r--r--app-arch/libdeflate/Manifest2
-rw-r--r--app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch2
-rw-r--r--app-arch/libdeflate/libdeflate-1.2.ebuild4
-rw-r--r--app-arch/libdeflate/libdeflate-1.6.ebuild4
-rw-r--r--app-arch/libdeflate/libdeflate-1.8.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.9.ebuild28
-rw-r--r--app-text/noweb/noweb-2.12.ebuild2
-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild4
-rw-r--r--dev-cpp/blitz/blitz-9999.ebuild48
-rw-r--r--dev-java/flexdock/Manifest1
-rw-r--r--dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch12
-rw-r--r--dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch12
-rw-r--r--dev-java/flexdock/flexdock-1.2.4.ebuild46
-rw-r--r--dev-java/flexdock/metadata.xml8
-rw-r--r--dev-java/gluegen/Manifest2
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-copy-jars.patch17
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-strip.patch22
-rw-r--r--dev-java/gluegen/files/2.1.4-dont-test-archive.patch16
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-copy-jars.patch17
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-strip.patch22
-rw-r--r--dev-java/gluegen/files/2.2.4-dont-test-archive.patch16
-rw-r--r--dev-java/gluegen/gluegen-2.1.4.ebuild72
-rw-r--r--dev-java/gluegen/gluegen-2.2.4.ebuild72
-rw-r--r--dev-java/gluegen/metadata.xml22
-rw-r--r--dev-java/htsjdk/Manifest2
-rw-r--r--dev-java/htsjdk/htsjdk-2.19.0.ebuild53
-rw-r--r--dev-java/htsjdk/htsjdk-2.3.0.ebuild47
-rw-r--r--dev-java/htsjdk/htsjdk-9999.ebuild53
-rw-r--r--dev-java/htsjdk/metadata.xml15
-rw-r--r--dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild3
-rw-r--r--dev-java/jgraphx/Manifest1
-rw-r--r--dev-java/jgraphx/jgraphx-4.2.2.ebuild40
-rw-r--r--dev-java/jgraphx/metadata.xml19
-rw-r--r--dev-java/jlatexmath-fop/Manifest1
-rw-r--r--dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch13
-rw-r--r--dev-java/jlatexmath-fop/files/version.xml5
-rw-r--r--dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild48
-rw-r--r--dev-java/jlatexmath-fop/metadata.xml13
-rw-r--r--dev-java/jlatexmath/Manifest1
-rw-r--r--dev-java/jlatexmath/jlatexmath-1.0.3.ebuild30
-rw-r--r--dev-java/jlatexmath/metadata.xml13
-rw-r--r--dev-java/jogl/Manifest1
-rw-r--r--dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch41
-rw-r--r--dev-java/jogl/files/1.1.0/uncouple-gluegen.patch32
-rw-r--r--dev-java/jogl/jogl-2.2.4.ebuild70
-rw-r--r--dev-java/jogl/metadata.xml18
-rw-r--r--dev-java/jrosetta/Manifest1
-rw-r--r--dev-java/jrosetta/files/api-build.xml262
-rw-r--r--dev-java/jrosetta/files/build.xml74
-rw-r--r--dev-java/jrosetta/files/engine-build.xml274
-rw-r--r--dev-java/jrosetta/jrosetta-1.0.4.ebuild39
-rw-r--r--dev-java/jrosetta/metadata.xml8
-rw-r--r--dev-java/lucene/Manifest3
-rw-r--r--dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch24
-rw-r--r--dev-java/lucene/files/lucene_contrib_icu4j_v50.patch20
-rw-r--r--dev-java/lucene/lucene-3.6.2-r2.ebuild162
-rw-r--r--dev-java/lucene/lucene-5.2.1.ebuild211
-rw-r--r--dev-java/lucene/lucene-8.4.0.ebuild223
-rw-r--r--dev-java/lucene/metadata.xml12
-rw-r--r--dev-java/skinlf/Manifest1
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-build.xml276
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-common.xml171
-rw-r--r--dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch77
-rw-r--r--dev-java/skinlf/metadata.xml8
-rw-r--r--dev-java/skinlf/skinlf-6.7.10.ebuild56
-rw-r--r--dev-lang/tcl/Manifest1
-rw-r--r--dev-lang/tcl/files/tcl-8.5.13-multilib.patch11
-rw-r--r--dev-lang/tcl/files/tcl-8.5.14-conf.patch11
-rw-r--r--dev-lang/tcl/files/tcl-8.6.8-libieee.patch15
-rw-r--r--dev-lang/tcl/tcl-8.5.17-r1.ebuild117
-rw-r--r--dev-lang/terra/Manifest1
-rw-r--r--dev-lang/terra/metadata.xml14
-rw-r--r--dev-lang/terra/terra-1.0.0_beta2.ebuild46
-rw-r--r--dev-lang/tk/Manifest1
-rw-r--r--dev-lang/tk/files/tk-8.4.15-aqua.patch11
-rw-r--r--dev-lang/tk/files/tk-8.5.11-fedora-xft.patch13
-rw-r--r--dev-lang/tk/files/tk-8.5.13-multilib.patch12
-rw-r--r--dev-lang/tk/files/tk-8.5.14-conf.patch16
-rw-r--r--dev-lang/tk/files/tk-8.6.8-libieee.patch15
-rw-r--r--dev-lang/tk/metadata.xml11
-rw-r--r--dev-lang/tk/tk-8.5.17-r1.ebuild128
-rw-r--r--dev-libs/boost/Manifest1
-rw-r--r--dev-libs/boost/boost-1.72.0-r2.ebuild356
-rw-r--r--dev-libs/boost/files/boost-1.71.0-build-auto_index-tool.patch13
-rw-r--r--dev-libs/boost/files/boost-1.71.0-context-x32.patch38
-rw-r--r--dev-libs/boost/files/boost-1.71.0-disable_icu_rpath.patch29
-rw-r--r--dev-libs/boost/files/boost-1.72.0-boost-mpi-python.patch50
-rw-r--r--dev-libs/boost/files/boost-1.72.0-missing-serialization-split_member-include.patch29
-rw-r--r--dev-libs/boost/files/boost-1.72.0-revert-cease-dependence-on-range.patch49
-rw-r--r--dev-libs/boost/metadata.xml21
-rw-r--r--dev-libs/half/Manifest2
-rw-r--r--dev-libs/half/half-1.12.0.ebuild17
-rw-r--r--dev-libs/half/half-2.1.0.ebuild20
-rw-r--r--dev-libs/half/metadata.xml11
-rw-r--r--dev-libs/memkind/memkind-1.10.1.ebuild6
-rw-r--r--dev-libs/memkind/memkind-1.11.0.ebuild4
-rw-r--r--dev-libs/memkind/memkind-9999.ebuild6
-rw-r--r--dev-libs/optix/Manifest5
-rw-r--r--dev-libs/optix/optix-6.0.0.ebuild46
-rw-r--r--dev-libs/optix/optix-7.0.0.ebuild37
-rw-r--r--dev-libs/optix/optix-7.1.0.ebuild37
-rw-r--r--dev-libs/optix/optix-7.4.0.ebuild (renamed from dev-libs/optix/optix-7.2.0.ebuild)4
-rw-r--r--dev-libs/protobuf/Manifest1
-rw-r--r--dev-libs/protobuf/files/proto.vim1
-rw-r--r--dev-libs/protobuf/files/protobuf-3.11.0-disable_no-warning-test.patch19
-rw-r--r--dev-libs/protobuf/files/protobuf-3.11.0-protoc_input_output_files.patch262
-rw-r--r--dev-libs/protobuf/files/protobuf-3.11.0-system_libraries.patch121
-rw-r--r--dev-libs/protobuf/metadata.xml8
-rw-r--r--dev-libs/protobuf/protobuf-3.11.4.ebuild117
-rw-r--r--dev-python/affine/Manifest1
-rw-r--r--dev-python/affine/affine-2.3.0.ebuild18
-rw-r--r--dev-python/affine/metadata.xml17
-rw-r--r--dev-python/asdf/Manifest2
-rw-r--r--dev-python/asdf/asdf-2.8.3.ebuild (renamed from dev-python/asdf/asdf-2.7.1.ebuild)10
-rw-r--r--dev-python/astropy-healpix/Manifest2
-rw-r--r--dev-python/astropy-healpix/astropy-healpix-0.6.ebuild (renamed from dev-python/astropy-healpix/astropy-healpix-0.5.ebuild)10
-rw-r--r--dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild6
-rw-r--r--dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild6
-rw-r--r--dev-python/astropy/Manifest2
-rw-r--r--dev-python/astropy/astropy-5.0.ebuild (renamed from dev-python/astropy/astropy-4.2.ebuild)13
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild6
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild2
-rw-r--r--dev-python/cligj/Manifest1
-rw-r--r--dev-python/cligj/cligj-0.7.2.ebuild20
-rw-r--r--dev-python/cligj/metadata.xml17
-rw-r--r--dev-python/extension-helpers/extension-helpers-0.1.ebuild6
-rw-r--r--dev-python/fiona/Manifest1
-rw-r--r--dev-python/fiona/fiona-1.8.20.ebuild74
-rw-r--r--dev-python/fiona/metadata.xml18
-rw-r--r--dev-python/fslpy/Manifest1
-rw-r--r--dev-python/fslpy/fslpy-3.8.1.ebuild39
-rw-r--r--dev-python/geopandas/Manifest1
-rw-r--r--dev-python/geopandas/geopandas-0.10.2.ebuild34
-rw-r--r--dev-python/geopandas/metadata.xml19
-rw-r--r--dev-python/hdmf/Manifest1
-rw-r--r--dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch10
-rw-r--r--dev-python/hdmf/hdmf-3.1.1.ebuild32
-rw-r--r--dev-python/hdmf/metadata.xml18
-rw-r--r--dev-python/llvmlite/Manifest2
-rw-r--r--dev-python/llvmlite/llvmlite-0.37.0.ebuild60
-rw-r--r--dev-python/llvmlite/llvmlite-0.38.0.ebuild60
-rw-r--r--dev-python/llvmlite/metadata.xml18
-rw-r--r--dev-python/numba/Manifest1
-rw-r--r--dev-python/numba/numba-0.55.0.ebuild85
-rw-r--r--dev-python/protobuf-python/Manifest1
-rw-r--r--dev-python/protobuf-python/files/protobuf-python-3.13.0-google.protobuf.pyext._message.PyUnknownFieldRef.patch22
-rw-r--r--dev-python/protobuf-python/metadata.xml8
-rw-r--r--dev-python/protobuf-python/protobuf-python-3.11.4-r1.ebuild59
-rw-r--r--dev-python/pybind11-stubgen/Manifest1
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild19
-rw-r--r--dev-python/pyerfa/Manifest2
-rw-r--r--dev-python/pyerfa/pyerfa-2.0.0.1.ebuild (renamed from dev-python/pyerfa/pyerfa-1.7.1.1.ebuild)10
-rw-r--r--dev-python/pytest-doctestplus/Manifest2
-rw-r--r--dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild (renamed from dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild)7
-rw-r--r--dev-python/pytorch-lightning/Manifest1
-rw-r--r--dev-python/pytorch-lightning/metadata.xml (renamed from dev-lang/tcl/metadata.xml)5
-rw-r--r--dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild32
-rw-r--r--dev-python/rasterio/Manifest1
-rw-r--r--dev-python/rasterio/metadata.xml18
-rw-r--r--dev-python/rasterio/rasterio-1.2.10.ebuild104
-rw-r--r--dev-python/rasterstats/Manifest1
-rw-r--r--dev-python/rasterstats/metadata.xml18
-rw-r--r--dev-python/rasterstats/rasterstats-0.16.0.ebuild30
-rw-r--r--dev-python/snuggs/Manifest1
-rw-r--r--dev-python/snuggs/metadata.xml17
-rw-r--r--dev-python/snuggs/snuggs-1.4.7.ebuild26
-rw-r--r--dev-python/sphinx-astropy/Manifest2
-rw-r--r--dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild (renamed from dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild)9
-rw-r--r--dev-python/sphinx-automodapi/Manifest2
-rw-r--r--dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild (renamed from dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild)8
-rw-r--r--dev-python/traits/traits-6.0.0.ebuild3
-rw-r--r--dev-python/traits/traits-6.1.1.ebuild2
-rw-r--r--dev-python/trimesh/Manifest1
-rw-r--r--dev-python/trimesh/trimesh-3.9.42.ebuild65
-rw-r--r--dev-tcltk/togl/Manifest2
-rw-r--r--dev-tcltk/togl/metadata.xml11
-rw-r--r--dev-tcltk/togl/togl-1.7-r1.ebuild39
-rw-r--r--dev-tcltk/togl/togl-2.0.ebuild41
-rw-r--r--dev-util/bcm/Manifest1
-rw-r--r--dev-util/bcm/bcm-0.0.1_p20191110.ebuild19
-rw-r--r--dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch13
-rw-r--r--dev-util/bcm/metadata.xml7
-rw-r--r--dev-util/boost-build/Manifest1
-rw-r--r--dev-util/boost-build/boost-build-1.72.0.ebuild73
-rw-r--r--dev-util/boost-build/files/boost-build-1.71.0-add-none-feature-options.patch22
-rw-r--r--dev-util/boost-build/files/boost-build-1.71.0-disable_python_rpath.patch11
-rw-r--r--dev-util/boost-build/files/boost-build-1.71.0-fix-test.patch11
-rw-r--r--dev-util/boost-build/files/boost-build-1.71.0-no-implicit-march-flags.patch266
-rw-r--r--dev-util/boost-build/files/boost-build-1.71.0-respect-c_ld-flags.patch9
-rw-r--r--dev-util/boost-build/files/site-config.jam11
-rw-r--r--dev-util/boost-build/metadata.xml11
-rw-r--r--dev-util/f90cache/f90cache-0.99c.ebuild2
-rw-r--r--dev-util/rocm-clang-ocl/Manifest2
-rw-r--r--dev-util/rocm-clang-ocl/metadata.xml11
-rw-r--r--dev-util/rocm-clang-ocl/rocm-clang-ocl-4.0.0-r1.ebuild31
-rw-r--r--dev-util/rocm-clang-ocl/rocm-clang-ocl-4.1.0.ebuild31
-rw-r--r--licenses/CeCILL-2.1519
-rw-r--r--licenses/jing85
-rw-r--r--licenses/sun-bcla-jhall234
-rw-r--r--media-gfx/brlcad/Manifest2
-rw-r--r--media-gfx/brlcad/brlcad-7.32.4.ebuild (renamed from media-gfx/brlcad/brlcad-7.32.0.ebuild)58
-rw-r--r--media-gfx/brlcad/brlcad-9999.ebuild56
-rw-r--r--media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch12
-rw-r--r--media-gfx/brlcad/metadata.xml4
-rw-r--r--media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild29
-rw-r--r--media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch33
-rw-r--r--media-libs/DualContouringSample/metadata.xml7
-rw-r--r--media-libs/imgui/Manifest1
-rw-r--r--media-libs/imgui/files/imgui-1.48-pkgconfig.patch65
-rw-r--r--media-libs/imgui/imgui-1.80.ebuild22
-rw-r--r--media-libs/imgui/metadata.xml7
-rw-r--r--media-libs/implicitmesher/Manifest1
-rw-r--r--media-libs/implicitmesher/files/implicitmesher-0_glm.patch38
-rw-r--r--media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild31
-rw-r--r--media-libs/implicitmesher/metadata.xml7
-rw-r--r--media-libs/yocto-gl/Manifest1
-rw-r--r--media-libs/yocto-gl/metadata.xml7
-rw-r--r--media-libs/yocto-gl/yocto-gl-3.3.0.ebuild39
-rw-r--r--metadata/layout.conf3
-rw-r--r--net-misc/cernbox-client/Manifest4
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild)26
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.7.6.3261.ebuild)23
-rw-r--r--net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch11
-rw-r--r--profiles/package.use.mask11
-rw-r--r--profiles/updates/1Q-20221
-rw-r--r--profiles/updates/4Q-20211
-rw-r--r--sci-astronomy/erfa/Manifest2
-rw-r--r--sci-astronomy/erfa/erfa-1.7.0.ebuild30
-rw-r--r--sci-astronomy/erfa/erfa-1.7.1.ebuild30
-rw-r--r--sci-astronomy/erfa/metadata.xml21
-rw-r--r--sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild2
-rw-r--r--sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild2
-rw-r--r--sci-biology/LINKS/LINKS-1.8.7.ebuild31
-rw-r--r--sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild2
-rw-r--r--sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild2
-rw-r--r--sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild2
-rw-r--r--sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild2
-rw-r--r--sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild2
-rw-r--r--sci-biology/Trinotate/Trinotate-3.2.1.ebuild2
-rw-r--r--sci-biology/abyss/Manifest3
-rw-r--r--sci-biology/abyss/abyss-2.2.5-r1.ebuild58
-rw-r--r--sci-biology/abyss/abyss-2.3.0-r1.ebuild58
-rw-r--r--sci-biology/abyss/abyss-2.3.1.ebuild58
-rw-r--r--sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch11
-rw-r--r--sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch11
-rw-r--r--sci-biology/abyss/metadata.xml18
-rw-r--r--sci-biology/afni/afni-19.3.12.ebuild4
-rw-r--r--sci-biology/afni/afni-20.1.16.ebuild2
-rw-r--r--sci-biology/afni/afni-20.3.03.ebuild2
-rw-r--r--sci-biology/afni/afni-9999.ebuild4
-rw-r--r--sci-biology/aghermann/aghermann-1.1.2-r2.ebuild2
-rw-r--r--sci-biology/ants/ants-2.3.4.ebuild4
-rw-r--r--sci-biology/bamql/bamql-1.6.1.ebuild4
-rw-r--r--sci-biology/bedops/bedops-2.4.26.ebuild2
-rw-r--r--sci-biology/bedops/bedops-2.4.39.ebuild2
-rw-r--r--sci-biology/biobambam2/biobambam2-2.0.146.ebuild2
-rw-r--r--sci-biology/bismark/bismark-0.23.0.ebuild2
-rw-r--r--sci-biology/blasr/Manifest1
-rw-r--r--sci-biology/blasr/blasr-5.3.5.ebuild (renamed from sci-biology/blasr/blasr-9999.ebuild)14
-rw-r--r--sci-biology/bowtie/Manifest2
-rw-r--r--sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild81
-rw-r--r--sci-biology/bowtie/bowtie-1.3.0.ebuild63
-rw-r--r--sci-biology/bowtie/bowtie-2.4.2.ebuild62
-rw-r--r--sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch17
-rw-r--r--sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch32
-rw-r--r--sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch22
-rw-r--r--sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch14
-rw-r--r--sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch16
-rw-r--r--sci-biology/bowtie/metadata.xml16
-rw-r--r--sci-biology/canu/canu-2.1.1.ebuild2
-rw-r--r--sci-biology/conrad/Manifest1
-rw-r--r--sci-biology/conrad/conrad-1.ebuild52
-rw-r--r--sci-biology/conrad/metadata.xml15
-rw-r--r--sci-biology/cramtools/Manifest1
-rw-r--r--sci-biology/cramtools/cramtools-3.0.ebuild34
-rw-r--r--sci-biology/cramtools/metadata.xml15
-rw-r--r--sci-biology/fastqc/Manifest2
-rw-r--r--sci-biology/fastqc/fastqc-0.11.3.ebuild48
-rw-r--r--sci-biology/fastqc/fastqc-0.11.9.ebuild40
-rw-r--r--sci-biology/fastqc/files/00fastqc1
-rw-r--r--sci-biology/fastqc/files/build.xml59
-rw-r--r--sci-biology/flexbar/flexbar-3.5.0.ebuild2
-rw-r--r--sci-biology/fsl/Manifest2
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519 files changed, 2890 insertions, 13005 deletions
diff --git a/README.md b/README.md
index 99fcfe316..e7618050b 100644
--- a/README.md
+++ b/README.md
@@ -125,12 +125,7 @@ We welcome new contributors and are happy to include new packages.
### Areas to contribute
-- [Current open issues](https://github.com/gentoo/sci/issues)
- [Current open bugs](https://bugs.gentoo.org/buglist.cgi?no_redirect=1&quicksearch=[science+overlay])
-- EAPI 6 (or 5) ebuilds which need updating
-```
-find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done
-```
### Resources
@@ -144,4 +139,4 @@ Additionally, please make sure to add the Science Project as an additional maint
## Support
You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
-Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+Alternatively you can report bugs on the [Gentoo Bugzilla](https://bugs.gentoo.org/).
diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
index 0b3011ce3..f2e2fae94 100644
--- a/app-arch/libdeflate/Manifest
+++ b/app-arch/libdeflate/Manifest
@@ -1,3 +1,5 @@
DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb
DIST libdeflate-1.6.tar.gz 139031 BLAKE2B c9390408322dc71f27d86fb69e0dd47996a725a3f4ddbe1d395e07dcd1b1f2b6fde1a9decfa8d7a0bd841defff67a659b1f2efd2609db7d79626e038cb44e020 SHA512 b7225c7defb3e9b1177c434aa0de80e525de06160894282e9d3e736d6c17d2ee107e321042104a67dfa3649d982a022ee30fe30380259b8aa65ac75d1d02e334
DIST libdeflate-1.7.tar.gz 144143 BLAKE2B 6aa947a4e2489f5a3e5681d56c2272b0a694981ed2607fa4112d90a8b4565ba1066364ffcac2fe8836bacbbad0346bce5efea54b4abae55022a33ee7d983e570 SHA512 82b297af2d3128a244e561893cce1d3664de410469ba6745c3f68fc3a1962c62467c427f3857bb679578e0f704cd0eba1a64b13c30505addd310ff9af1883068
+DIST libdeflate-1.8.tar.gz 145823 BLAKE2B 3597e41cbcae17b5b6b5bbb196af6ea52ac55b279f42e1ca3b12ba45638602e8a3f7520d84d7be637675c04fd82e096cb03d15f5fd742a31db5ba22cbd6e71f4 SHA512 b40caecdf783487488a5bd8213304175348b9db9bc1efdf6d5222fb912f61698b5e196522195a3640d7ff61ba953a93c0c8f75e07f548ac8b9d9c5dd5a787544
+DIST libdeflate-1.9.tar.gz 157565 BLAKE2B a8762bb1c2e73d9f7bf26121ac194362be61fd14a8e2a2a0ca72ffc7c512f5c96b19f3f0c563495e25e849342de26f89260af5e67aa5ec2b37b30da596ec3cdf SHA512 aecfa2414a4d22f5233cbe58385e1637b5cbe252e1d4dc55e20e7769908158190a22af11af175e5dfb376f3b4a90fcee58e25468ccb47a5d5b02ae2b248c58f3
diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
index a583d7d2e..790aa6de9 100644
--- a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
+++ b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
@@ -5,7 +5,7 @@
override CFLAGS := \
- $(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon \
-+ -O2 $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon \
++ $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon \
-Wall -Wundef \
$(call cc-option,-Wpedantic) \
$(call cc-option,-Wdeclaration-after-statement) \
diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild b/app-arch/libdeflate/libdeflate-1.2.ebuild
index 5548ea150..c5924c064 100644
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.2.ebuild
@@ -1,10 +1,8 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit multilib
-
DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
HOMEPAGE="https://github.com/ebiggers/libdeflate"
SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> ${P}.tar.gz"
diff --git a/app-arch/libdeflate/libdeflate-1.6.ebuild b/app-arch/libdeflate/libdeflate-1.6.ebuild
index 5485ad25f..666506943 100644
--- a/app-arch/libdeflate/libdeflate-1.6.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.6.ebuild
@@ -1,10 +1,8 @@
-# Copyright 2019-2020 Gentoo Authors
+# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit multilib
-
DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
HOMEPAGE="https://github.com/ebiggers/libdeflate"
SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
diff --git a/app-arch/libdeflate/libdeflate-1.8.ebuild b/app-arch/libdeflate/libdeflate-1.8.ebuild
new file mode 100644
index 000000000..bfafcfecd
--- /dev/null
+++ b/app-arch/libdeflate/libdeflate-1.8.ebuild
@@ -0,0 +1,28 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
+HOMEPAGE="https://github.com/ebiggers/libdeflate"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
+else
+ SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="static-libs test"
+RESTRICT="!test? ( test )"
+
+src_install() {
+ emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
+ if ! use static-libs; then
+ find "${ED}" -name '*.a' -delete || die
+ fi
+ dodoc NEWS README.md
+}
diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild b/app-arch/libdeflate/libdeflate-1.9.ebuild
new file mode 100644
index 000000000..9f66534f1
--- /dev/null
+++ b/app-arch/libdeflate/libdeflate-1.9.ebuild
@@ -0,0 +1,28 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
+HOMEPAGE="https://github.com/ebiggers/libdeflate"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
+else
+ SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="static-libs test"
+RESTRICT="!test? ( test )"
+
+src_install() {
+ emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
+ if ! use static-libs; then
+ find "${ED}" -name '*.a' -delete || die
+ fi
+ dodoc NEWS README.md
+}
diff --git a/app-text/noweb/noweb-2.12.ebuild b/app-text/noweb/noweb-2.12.ebuild
index e62e7dd59..29fc8cd5a 100644
--- a/app-text/noweb/noweb-2.12.ebuild
+++ b/app-text/noweb/noweb-2.12.ebuild
@@ -3,7 +3,7 @@
EAPI="7"
-inherit eutils toolchain-funcs elisp-common
+inherit toolchain-funcs elisp-common
MYPV="$(ver_rs 1 _)"
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 3c796ab5f..389e5430d 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -25,7 +25,7 @@ BDEPEND="
doc? ( app-doc/doxygen[dot] )
"
DEPEND="
- boost? ( dev-libs/boost:=[static-libs(-)] )
+ boost? ( dev-libs/boost:= )
"
src_configure() {
diff --git a/dev-cpp/blitz/blitz-9999.ebuild b/dev-cpp/blitz/blitz-9999.ebuild
deleted file mode 100644
index cb92e37f0..000000000
--- a/dev-cpp/blitz/blitz-9999.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake git-r3 python-any-r1
-
-DESCRIPTION="Multi-dimensional array library for C++"
-HOMEPAGE="https://github.com/blitzpp/blitz"
-EGIT_REPO_URI="https://github.com/blitzpp/blitz"
-
-LICENSE="BSD LGPL-3+"
-SLOT="0"
-IUSE="boost doc test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="
- ${PYTHON_DEPS}
- doc? ( app-doc/doxygen[dot] )
-"
-DEPEND="
- boost? ( dev-libs/boost:=[static-libs(-)] )
-"
-
-src_configure() {
- local mycmakeargs=(
- -DBUILD_DOC=$(usex doc)
- -DBUILD_TESTING=$(usex test)
- -DENABLE_SERIALISATION=$(usex boost)
- )
- use doc && mycmakeargs+=( -DDISABLE_REFMAN_PDF=ON )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- use doc && cmake_build blitz-doc
- use test && cmake_build testsuite benchmark examples
-}
-
-src_install() {
- cmake_src_install
- if use doc ; then
- find "${D}" -type f \( -name "*.md5" -o -name "*.map" \) -delete || die
- fi
-}
diff --git a/dev-java/flexdock/Manifest b/dev-java/flexdock/Manifest
deleted file mode 100644
index 19976b9ca..000000000
--- a/dev-java/flexdock/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST flexdock-1.2.4.tar.gz 5977054 BLAKE2B f0057d4a09fa994297c437c8ecd3e0f96c922bec5f95b142f19279e154fd352628a342a8dce9dcaab4b5997665b10fc98c8daf59c766a7b83cd7adda50f2b00c SHA512 f20c92d33b0567ed1e779d4c7c843ac9d72e5ae0f0a145d69adf5066bd1dcc426cd8acfe7d0587bd36fc09cab63dd7217f27cd8eee1d5d9b522bec860df9b44f
diff --git a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch b/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml 2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml 2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
- <src path="${java.src.drag}"/>
- <src path="${java.src.perspective}"/>
- </javac>
-- <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
-- <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
- </target>
-
-
diff --git a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch b/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml 2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml 2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
- <src path="${java.src.drag}"/>
- <src path="${java.src.perspective}"/>
- </javac>
-- <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
-- <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
- </target>
-
-
diff --git a/dev-java/flexdock/flexdock-1.2.4.ebuild b/dev-java/flexdock/flexdock-1.2.4.ebuild
deleted file mode 100644
index 64898244e..000000000
--- a/dev-java/flexdock/flexdock-1.2.4.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java docking framework for use in cross-platform Swing applications"
-HOMEPAGE="https://forge.scilab.org/index.php/p/flexdock/"
-SRC_URI="https://forge.scilab.org/index.php/p/flexdock/downloads/get/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=">=virtual/jre-1.5:=
- dev-java/skinlf:0"
-BDEPEND="app-arch/unzip"
-DEPEND="${RDEPEND}"
-
-EANT_BUILD_TARGET="jar"
-EANT_DOC_TARGET="doc"
-
-PATCHES=(
- "${FILESDIR}/${P}-nodemo.patch"
-)
-
-src_prepare() {
- default
-
- #some cleanups
- find . -name '*.so' -exec rm -v {} \;|| die
- find . -name '*.dll' -exec rm -v {} \;|| die
-
- #remove built-in jars and use the system ones
- cd lib || die
- rm -rvf *.jar jmf|| die
- java-pkg_jar-from skinlf
-}
-
-src_install() {
- java-pkg_newjar "build/${P}.jar" "${PN}.jar"
- use doc && java-pkg_dojavadoc build/docs/api
- use source && java-pkg_dosrc src
-}
diff --git a/dev-java/flexdock/metadata.xml b/dev-java/flexdock/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-java/flexdock/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-java/gluegen/Manifest b/dev-java/gluegen/Manifest
deleted file mode 100644
index 4e44921ef..000000000
--- a/dev-java/gluegen/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gluegen-2.1.4.tar.gz 42235490 BLAKE2B 31e5a55c9cc983d0e1c7f53988b7cc0779e01d1c4c0df8a33ca817acd51d0d28e453e6a84e1be65ecfb62883e8900c62a2219f78035dc7a68c26412e7c2b5135 SHA512 196478de92686b168d6f35e2e7141a31f682d22a7f96b5bc84d46905c42eb5bf25bacd74ccc51975fc7894e2e0ba2e236a4a68c101bbabaaa5193e4bdc50f607
-DIST gluegen-2.2.4.tar.gz 43113191 BLAKE2B 8908cff19b4eeaac01eb91ecf51005433c60acbf35a2922e09f7bfe3d11dee46296b466ea22cf570cae5a1013ea6dd9b375fbaa5b0723509d0bad0926014b9fb SHA512 53e973ca8478f4513f9662d1375406af95f2181dae3fb3e3247e4752960e60e741f7eae36981967dba10ac7bc3dc0e85c159c193323c177ce733a9eb0540b98b
diff --git a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
deleted file mode 100644
index 6f51d6811..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/make/build.xml b/make/build.xml
-index 55ef270..bce6d12 100644
---- a/make/build.xml
-+++ b/make/build.xml
-@@ -806,12 +806,6 @@
- </fileset>
- </jar>
-
-- <!-- Copy antlr.jar into build directory for convenience so
-- gluegen.jar can be run via "java -jar". antlr.jar is
-- referenced via a Class-Path entry in the Manifest of
-- gluegen.jar. -->
-- <copy file="${antlr.jar}" todir="${build}" />
--
- <!-- copy a jnlp with empty codebase into build folder for local testing
- overwrite property in gluegen.proerpties if desired -->
- <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.1.4-dont-strip.patch b/dev-java/gluegen/files/2.1.4-dont-strip.patch
deleted file mode 100644
index d64c742cd..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/make/gluegen-cpptasks-base.xml b/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/make/gluegen-cpptasks-base.xml
-+++ b/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
- - Helper strip.libraries for stripping off debug information
- -->
- <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
-- <echo message="Strip symbols from libs in ${libdir}" />
-- <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false"
-- failonerror="true">
-- <arg line="${c.strip.args}"/>
-- <fileset dir="${libdir}">
-- <include name="**/*.so"/> <!-- unix -->
-- <include name="**/*.dll"/> <!-- windows -->
-- <include name="**/*.dylib"/> <!-- macosx -->
-- <include name="**/*.jnilib"/> <!-- macosx -->
-- </fileset>
-- </apply>
- </target>
-
- <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch b/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
deleted file mode 100644
index f03a28399..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/make/build-test.xml b/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/make/build-test.xml
-+++ b/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
-
- <!-- updates / create the test results zip file -->
- <target name="test-zip-archive" depends="init">
-+ <!--
- <archive.7z destfile="${build}/${test.archive.name}.7z"
- basedir="${project.root}"
- includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+ -->
- </target>
-
-
diff --git a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
deleted file mode 100644
index 6f51d6811..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/make/build.xml b/make/build.xml
-index 55ef270..bce6d12 100644
---- a/make/build.xml
-+++ b/make/build.xml
-@@ -806,12 +806,6 @@
- </fileset>
- </jar>
-
-- <!-- Copy antlr.jar into build directory for convenience so
-- gluegen.jar can be run via "java -jar". antlr.jar is
-- referenced via a Class-Path entry in the Manifest of
-- gluegen.jar. -->
-- <copy file="${antlr.jar}" todir="${build}" />
--
- <!-- copy a jnlp with empty codebase into build folder for local testing
- overwrite property in gluegen.proerpties if desired -->
- <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.2.4-dont-strip.patch b/dev-java/gluegen/files/2.2.4-dont-strip.patch
deleted file mode 100644
index d64c742cd..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/make/gluegen-cpptasks-base.xml b/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/make/gluegen-cpptasks-base.xml
-+++ b/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
- - Helper strip.libraries for stripping off debug information
- -->
- <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
-- <echo message="Strip symbols from libs in ${libdir}" />
-- <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false"
-- failonerror="true">
-- <arg line="${c.strip.args}"/>
-- <fileset dir="${libdir}">
-- <include name="**/*.so"/> <!-- unix -->
-- <include name="**/*.dll"/> <!-- windows -->
-- <include name="**/*.dylib"/> <!-- macosx -->
-- <include name="**/*.jnilib"/> <!-- macosx -->
-- </fileset>
-- </apply>
- </target>
-
- <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch b/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
deleted file mode 100644
index f03a28399..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/make/build-test.xml b/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/make/build-test.xml
-+++ b/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
-
- <!-- updates / create the test results zip file -->
- <target name="test-zip-archive" depends="init">
-+ <!--
- <archive.7z destfile="${build}/${test.archive.name}.7z"
- basedir="${project.root}"
- includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+ -->
- </target>
-
-
diff --git a/dev-java/gluegen/gluegen-2.1.4.ebuild b/dev-java/gluegen/gluegen-2.1.4.ebuild
deleted file mode 100644
index e98823dba..000000000
--- a/dev-java/gluegen/gluegen-2.1.4.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="https://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.1"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEP="
- dev-java/ant-core:0
- dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
- >=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
- >=virtual/jdk-1.5
- dev-java/cpptasks:0
- test? (
- dev-java/junit:4
- dev-java/ant-junit4
- )"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-PATCHES=(
- "${FILESDIR}/${PV}-dont-copy-jars.patch"
- "${FILESDIR}/${PV}-dont-strip.patch"
- "${FILESDIR}/${PV}-dont-test-archive.patch"
-)
-
-src_prepare() {
- rm -rf make/lib
- default
- java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
- EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
- java-pkg_dojar build/${PN}{,-rt}.jar
- java-pkg_doso build/obj/*.so
-
- use doc && dodoc -r doc/manual
- use source && java-pkg_dosrc src/java/*
-
- # for building jogl
- insinto /usr/share/${PN}-${SLOT}/make
- doins -r make/*
- insinto /usr/share/${PN}-${SLOT}/build
- doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/gluegen-2.2.4.ebuild b/dev-java/gluegen/gluegen-2.2.4.ebuild
deleted file mode 100644
index cd15a0c2a..000000000
--- a/dev-java/gluegen/gluegen-2.2.4.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="https://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEP="
- dev-java/ant-core:0
- dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
- >=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
- >=virtual/jdk-1.5
- dev-java/cpptasks:0
- test? (
- dev-java/junit:4
- dev-java/ant-junit4
- )"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-PATCHES=(
- "${FILESDIR}/${PV}-dont-copy-jars.patch"
- "${FILESDIR}/${PV}-dont-strip.patch"
- "${FILESDIR}/${PV}-dont-test-archive.patch"
-)
-
-src_prepare() {
- rm -rf make/lib
- default
- java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
- EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
- java-pkg_dojar build/${PN}{,-rt}.jar
- java-pkg_doso build/obj/*.so
-
- use doc && dodoc -r doc/manual
- use source && java-pkg_dosrc src/java/*
-
- # for building jogl
- insinto /usr/share/${PN}-${SLOT}/make
- doins -r make/*
- insinto /usr/share/${PN}-${SLOT}/build
- doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml
deleted file mode 100644
index b81144d5f..000000000
--- a/dev-java/gluegen/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-GlueGen is a tool which automatically generates the Java and JNI code necessary
-to call C libraries. It reads as input ANSI C header files and separate
-configuration files which provide control over many aspects of the glue code
-generation. GlueGen uses a complete ANSI C parser and an internal representation
-(IR) capable of representing all C types to represent the APIs for which it
-generates interfaces. It has the ability to perform significant transformations
-on the IR before glue code emission. GlueGen is currently powerful enough to
-bind even low-level APIs such as the Java Native Interface (JNI) and the AWT
-Native Interface (JAWT) back up to the Java programming language.
-</longdescription>
- <upstream>
- <remote-id type="github">sgothel/gluegen</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/htsjdk/Manifest b/dev-java/htsjdk/Manifest
deleted file mode 100644
index ee5ea5e79..000000000
--- a/dev-java/htsjdk/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST htsjdk-2.19.0.tar.gz 15602200 BLAKE2B eee9e4cbed27122020b7ec9de50c301c3078cc995a9aa6f89061518f9fab823054759dc17c16fb71da231b7e19876743146116ee7398af04a8e65b7781c62924 SHA512 07af3f5a592ab519349bd8a47dc336fe8673232daeb1d4c1a120dd4dde1c42db443998948185e2b18f27a5ac578b0afa0d7d09b36a66f69eba156ac0912d96b5
-DIST htsjdk-2.3.0.tar.gz 11466439 BLAKE2B 5bdfb89f99767335c3e3e45b43a237d8e050c68f02f4816d9cb23d2fce78ec133a1c29ea297eba0224ec11a162d2b40b3ea486d834488b4369d24931fbcb72b6 SHA512 43029b59c039accd5ae5d7631d72a11bfab80c38fcbfb3fa02e9bc9e9b795ca86f048a34a7182325c4d7123a82d2b6c5094e11f7118c09fca222b3b2327f6249
diff --git a/dev-java/htsjdk/htsjdk-2.19.0.ebuild b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
deleted file mode 100644
index 349e56673..000000000
--- a/dev-java/htsjdk/htsjdk-2.19.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0
- dev-java/gradle-bin:*"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
- default
-}
-
-src_compile(){
- # work around gradle writing $HOME/.gradle and $HOME/.git
- # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
- GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
-}
-
-src_install() {
- cd dist || die
-
- for i in *.jar; do
- java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- done
-
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-2.3.0.ebuild b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
deleted file mode 100644
index c94f79781..000000000
--- a/dev-java/htsjdk/htsjdk-2.3.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
- default
- rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
- cd dist || die
-
- for i in *.jar; do
- java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- done
-
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-9999.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
deleted file mode 100644
index 2123bbc55..000000000
--- a/dev-java/htsjdk/htsjdk-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit git-r3 java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
- dev-java/commons-compress:0
- dev-java/commons-logging:0
- dev-java/gradle-bin:*"
-
-DEPEND=">=virtual/jdk-1.8
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
- default
-}
-
-src_compile(){
- # work around gradle writing $HOME/.gradle and $HOME/.git
- # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
- GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
-src_install() {
- cd build/libs || die
-
- #for i in *-SNAPSHOT.jar; do
- # java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
- #done
- java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar
- use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar
- use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar
-}
diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml
deleted file mode 100644
index e18a4898a..000000000
--- a/dev-java/htsjdk/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>ercpe@gentoo.org</email>
- <name>Johann Schmitz (ercpe)</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">samtools/htsjdk</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild b/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild
index 81910f356..a64ebcd74 100644
--- a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild
+++ b/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild
@@ -3,7 +3,8 @@
EAPI=7
JAVA_PKG_IUSE="source"
-inherit eutils java-pkg-2 java-ant-2
+
+inherit java-pkg-2 java-ant-2
DESCRIPTION="Core module of MathML rendering solution"
HOMEPAGE="https://github.com/rototor/jeuclid"
diff --git a/dev-java/jgraphx/Manifest b/dev-java/jgraphx/Manifest
deleted file mode 100644
index 421fe6919..000000000
--- a/dev-java/jgraphx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jgraphx-4.2.2.tar.gz 3525225 BLAKE2B a716df6d843fdc3b0ef32ba9549701d658f1daa104fd90df00137753d837756a2008129cb449771ec8dac3731b3033b429a7758f7f2e3ca58f27b93c88732b5c SHA512 767c0972100c8ed41561304367cba4574d1ba1bcd5c5d57fa869dd0a1bc1b2d6d70253577a4d2a2f03641afec5bd0d4e81e52a13529681737de7918c0c24cee7
diff --git a/dev-java/jgraphx/jgraphx-4.2.2.ebuild b/dev-java/jgraphx/jgraphx-4.2.2.ebuild
deleted file mode 100644
index de4e6ab36..000000000
--- a/dev-java/jgraphx/jgraphx-4.2.2.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Open-source graph component for Java"
-HOMEPAGE="https://github.com/jgraph"
-SRC_URI="https://github.com/jgraph/jgraphx/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="doc examples source"
-
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
-
-src_prepare() {
- default
- # don't do javadoc always
- sed -i \
- -e 's/depends="doc"/depends="compile"/' \
- build.xml || die "sed failed"
- rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
- java-pkg_dojar lib/${PN}.jar
-
- use doc && java-pkg_dojavadoc docs/api
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/metadata.xml b/dev-java/jgraphx/metadata.xml
deleted file mode 100644
index 2a4062ae5..000000000
--- a/dev-java/jgraphx/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-JGraph X is based on the mxGraph architecture, a re-designed core
-based on JGraph experience.
-Overall, JGraph X provides more features that JGraph, with a far
-smaller code size and complexity. Redesigning the codebase from
-scratch now means implementing common feature extensions are easier
-and require less coding. A number of new loosely coupled
-application-centric features have been added, making prototyping
-even faster, without their usage restricting application
-flexibility.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath-fop/Manifest b/dev-java/jlatexmath-fop/Manifest
deleted file mode 100644
index d92e07cb2..000000000
--- a/dev-java/jlatexmath-fop/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-fop-src-1.0.3.zip 115024 BLAKE2B c45d79c3b57c5439ab0f39fd17926e0cdb8bae4d5ef5bcec476c1daefefecbd197663beded3202dd53f25a3dee71c096f536b0c52b8d366c557c5ed89897abfe SHA512 92e81ab2c2a14cd9ac935028f6cd4370de5925f919e41fb94290a331660e2ea983ab3ca7a5fe7e5fd7c6a2caf34a4bae7ee45c0efc33b4ac0f154f16465c37f8
diff --git a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch b/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
deleted file mode 100644
index 1cd5b69eb..000000000
--- a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -urN a/build.xml b/build.xml
---- a/build.xml 2013-04-23 20:42:19.776644942 -0400
-+++ b/build.xml 2013-04-23 20:42:36.821646638 -0400
-@@ -1,7 +1,7 @@
- <?xml version="1.0" encoding="ISO-8859-1"?>
- <project name="jlatexmath-fop" basedir="." default="buildJar">
-- <import file="${basedir}/../../version.xml"/>
-- <property file="../../fop.properties"/>
-+ <import file="${basedir}/version.xml"/>
-+ <property file="fop.properties"/>
-
- <path id="libs-build-classpath">
- <pathelement location="${fop.jar}"/>
diff --git a/dev-java/jlatexmath-fop/files/version.xml b/dev-java/jlatexmath-fop/files/version.xml
deleted file mode 100644
index b538b79a3..000000000
--- a/dev-java/jlatexmath-fop/files/version.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project name="version_jlm">
- <property name="version" value="1.0.3" />
- <property name="java_version" value="5" />
-</project>
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
deleted file mode 100644
index 1782fb0b1..000000000
--- a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="jlatexmath plugin for dev-java/fop"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/jlatexmath:1
- dev-java/xmlgraphics-commons:2
- >=dev-java/fop-2.0-r1:0"
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.5"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5
- ${CDEPEND}"
-
-EANT_BUILD_TARGET="buildJar"
-
-S="${WORKDIR}"
-
-PATCHES=(
- "${FILESDIR}/${P}-fixpaths.patch"
-)
-
-src_prepare() {
- default
- cp "${FILESDIR}/version.xml" "${S}" || die
- echo "fop.jar=$(java-pkg_getjar fop fop.jar)
-xmlgraphics-commons.jar=$(java-pkg_getjar xmlgraphics-commons-2 xmlgraphics-commons.jar)
-jlatexmath.jar=$(java-pkg_getjar jlatexmath-1 jlatexmath.jar)" \
- >>fop.properties || die
-}
-
-src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath-fop/metadata.xml b/dev-java/jlatexmath-fop/metadata.xml
deleted file mode 100644
index 9ded36c47..000000000
--- a/dev-java/jlatexmath-fop/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style. This package installs the plugin for dev-java/fop.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath/Manifest b/dev-java/jlatexmath/Manifest
deleted file mode 100644
index 44a2a7205..000000000
--- a/dev-java/jlatexmath/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-src-1.0.3.zip 1086238 BLAKE2B 16e420326f5387bb6bae251032d6c3e262334adfa23083e38fc4d5e7552b415c03761172decc0c2a205d9fc3cd63190b949c44a32fa983f964d8a4557be82702 SHA512 85c71568b5bffd897338e7c3fd03be0c0f52fc0543b5d91f54453f20f3f4ec41225cb356667dbaca86df673db1b7ac8afc2b16e57db981ec8037143e26521e82
diff --git a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
deleted file mode 100644
index a9945c021..000000000
--- a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java API to render LaTeX"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=virtual/jdk-1.5"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-EANT_BUILD_TARGET="buildJar"
-EANT_DOC_TARGET="doc"
-
-src_install() {
- java-pkg_newjar dist/"${P}.jar" "${PN}.jar"
- use doc && java-pkg_dojavadoc doc
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath/metadata.xml b/dev-java/jlatexmath/metadata.xml
deleted file mode 100644
index 7ad985657..000000000
--- a/dev-java/jlatexmath/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jogl/Manifest b/dev-java/jogl/Manifest
deleted file mode 100644
index 09b10e415..000000000
--- a/dev-java/jogl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jogl-2.2.4.tar.gz 50214295 BLAKE2B 984d32e4bd43e33807dca1d0222aae9a9ca453d616002865d4a6b80ec9a8f3e8f833669067daa545103a391af8db6e5c75cfc45501053b3d850c5a28ac311a7e SHA512 79fb054d65e8aa532a75e8c8911f43987d877f7b71584ea24cc0f9152f8aaaddabd4afef7f7504b3df73c4d240bedc123bb8aeb8670d9ae2bd165bd0490e420e
diff --git a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch b/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
deleted file mode 100644
index 6d77bc3fe..000000000
--- a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff -Naur gluegen.orig/make/gluegen-cpptasks.xml gluegen/make/gluegen-cpptasks.xml
---- gluegen.orig/make/gluegen-cpptasks.xml 2007-03-14 23:09:20.000000000 +1300
-+++ gluegen/make/gluegen-cpptasks.xml 2007-03-14 23:09:40.000000000 +1300
-@@ -397,16 +397,16 @@
- <compilerarg value="-fPIC"/>
- </compiler>
-
-- <compiler id="compiler.cfg.solaris" name="suncc">
-+ <compiler id="compiler.cfg.solaris" name="gcc">
- </compiler>
-
-- <compiler id="compiler.cfg.solaris.sparcv9" name="suncc">
-+ <compiler id="compiler.cfg.solaris.sparcv9" name="gcc">
- <compilerarg value="-fast" />
- <compilerarg value="-xchip=ultra" />
- <compilerarg value="-xarch=v9a" />
- </compiler>
-
-- <compiler id="compiler.cfg.solaris.amd64" name="suncc">
-+ <compiler id="compiler.cfg.solaris.amd64" name="gcc">
- <compilerarg value="-fast" />
- <compilerarg value="-xchip=opteron" />
- <compilerarg value="-xarch=amd64" />
-@@ -492,14 +492,14 @@
- <linker id="linker.cfg.linux.amd64" name="gcc">
- </linker>
-
-- <linker id="linker.cfg.solaris" name="suncc">
-+ <linker id="linker.cfg.solaris" name="gcc">
- </linker>
-
-- <linker id="linker.cfg.solaris.sparcv9" name="suncc">
-+ <linker id="linker.cfg.solaris.sparcv9" name="gcc">
- <linkerarg value="-xarch=v9a" />
- </linker>
-
-- <linker id="linker.cfg.solaris.amd64" name="suncc">
-+ <linker id="linker.cfg.solaris.amd64" name="gcc">
- <linkerarg value="-xarch=amd64" />
- </linker>
-
diff --git a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch b/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
deleted file mode 100644
index a508c610f..000000000
--- a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-diff -Naur jogl.orig/make/build.xml jogl/make/build.xml
---- jogl.orig/make/build.xml 2007-02-13 17:45:16.000000000 +1300
-+++ jogl/make/build.xml 2007-03-14 22:55:50.000000000 +1300
-@@ -127,7 +127,18 @@
- <property name="gluegen.build.xml" value="${gluegen.make.dir}/build.xml" />
- <property name="gluegen.jar" value="../../gluegen/build/gluegen.jar" />
- <property name="gluegen-rt.jar" value="../../gluegen/build/gluegen-rt.jar" />
--
-+ <!-- This property is used to skip building gluegen if the jar files
-+ - are already available on the system and have been overridden
-+ - by the user. The purpose is to allow linux distro's to uncouple
-+ - gluegen from jogl.
-+ -->
-+ <condition property="gluegen.prebuilt" >
-+ <and>
-+ <available file="${gluegen.jar}" />
-+ <available file="${gluegen-rt.jar}" />
-+ </and>
-+ </condition>
-+
- <!-- Names of directories relative to the project root.
- Some of these are used in FileMappers later for dependence information
- and need exact string matching, which is why they use file.separator
-@@ -479,7 +490,7 @@
- <!--
- - Build GlueGen
- -->
-- <target name="build.gluegen" depends="init">
-+ <target name="build.gluegen" depends="init" unless="gluegen.prebuilt">
- <!-- Run the GlueGen build to ensure that the GlueGen ANT task
- - has been built. -->
- <!-- FIXME: remove passing down of antlr.jar when gluegen.properties is on all
diff --git a/dev-java/jogl/jogl-2.2.4.ebuild b/dev-java/jogl/jogl-2.2.4.ebuild
deleted file mode 100644
index 9d2345b53..000000000
--- a/dev-java/jogl/jogl-2.2.4.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="https://jogamp.org/jogl/www/"
-SRC_URI="https://github.com/sgothel/jogl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cg"
-
-CDEPEND="
- ~dev-java/gluegen-${PV}:${SLOT}
- dev-java/antlr:0
- dev-java/ant-core:0
- x11-libs/libX11
- x11-libs/libXxf86vm
- dev-java/swt:3.7
- virtual/opengl
- cg? ( media-gfx/nvidia-cg-toolkit )"
-
-RDEPEND="${CDEPEND}
- >=virtual/jre-1.5"
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.5"
-
-# upstream has a crude way to call the junit tests, which cause a lot of trouble to pass
-# our test classpath...
-RESTRICT="test"
-
-JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="init build.nativewindow build.jogl build.newt build.oculusvr one.dir tag.build"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="gluegen-${SLOT},antlr,ant-core,swt-3.7"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}/*.jar:${S}/build/nativewindow/*.jar"
-EANT_NEEDS_TOOLS="yes"
-
-src_prepare() {
- default
- #we keep make/lib/plugin3/puglin3-public.jar
- find -name 'make/lib/swt/*.jar' -delete -print || die
-
- # Empty filesets are never out of date!
- sed -i -e 's/<outofdate>/<outofdate force="true">/' make/build*xml || die
-
- EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true"
- EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/"
- EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)"
- EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)"
-
- use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-}
-
-src_install() {
- java-pkg_dojar build/jar/*.jar
- java-pkg_doso build/lib/*.so
-
- use doc && dodoc -r doc
- use source && java-pkg_dosrc src/jogl/classes/*
-}
diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml
deleted file mode 100644
index 7751e096e..000000000
--- a/dev-java/jogl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-JOGL provides Java with a Binding for the OpenGL® API (JSR-231), and is designed
-to provide hardware-supported 3D graphics to applications written in Java.
-</longdescription>
- <use>
- <flag name="cg">Enable NVidia Cg binding.</flag>
- </use>
- <upstream>
- <remote-id type="github">sgothel/jogl</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-java/jrosetta/Manifest b/dev-java/jrosetta/Manifest
deleted file mode 100644
index 3cb51fd1d..000000000
--- a/dev-java/jrosetta/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jrosetta-1.0.4-sources.jar 94931 BLAKE2B 205a3bf9c9be9f361902f59f7f1756161ba436a29cf5650bf7173f8e431818cab235754cbbc031eb69604bf8857150a17df069bc3f87fff8a1f5f75c2d136f4d SHA512 84b613a0dc6e3ca80414aba8f7c8cf044f013d27ed27c0f18fdbea056a6358c849ee193e3ab7320ffa7368fa17f255d4390fc306e8aa2c0ad70de51f36b6e878
diff --git a/dev-java/jrosetta/files/api-build.xml b/dev-java/jrosetta/files/api-build.xml
deleted file mode 100644
index 6627122ab..000000000
--- a/dev-java/jrosetta/files/api-build.xml
+++ /dev/null
@@ -1,262 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-api-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Build environment properties -->
- <!-- ====================================================================== -->
-
- <property file="${user.home}/.m2/maven.properties"/>
- <property file="maven-build.properties"/>
-
- <property name="maven.build.finalName" value="jrosetta-api-1.0.4"/>
- <property name="maven.build.dir" value="target"/>
- <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
- <property name="maven.build.srcDir.0" value="src/main/java"/>
- <property name="maven.build.resourceDir.0" value="src/main/resources"/>
- <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
- <property name="maven.build.testDir.0" value="src/test/java"/>
- <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
- <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
- <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
- <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
- <property name="maven.settings.offline" value="true"/>
- <property name="maven.settings.interactiveMode" value="true"/>
-
- <!-- ====================================================================== -->
- <!-- Defining classpaths -->
- <!-- ====================================================================== -->
-
- <path id="build.classpath"/>
- <path id="build.test.classpath">
- <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
- <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
- </path>
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <delete dir="${maven.build.dir}"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" depends="get-deps" description="Compile the code">
- <mkdir dir="${maven.build.outputDir}"/>
- <javac destdir="${maven.build.outputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.srcDir.0}"/>
- </src>
- <classpath refid="build.classpath"/>
- </javac>
- <copy todir="${maven.build.outputDir}">
- <fileset dir="${maven.build.resourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests"
- depends="compile"
- description="Compile the test code"
- unless="maven.test.skip">
- <mkdir dir="${maven.build.testOutputDir}"/>
- <javac destdir="${maven.build.testOutputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.testDir.0}"/>
- </src>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- </classpath>
- </javac>
- <copy todir="${maven.build.testOutputDir}">
- <fileset dir="${maven.build.testResourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test"
- depends="compile-tests, junit-missing"
- unless="junit.skipped"
- description="Run the test cases">
- <mkdir dir="${maven.test.reports}"/>
- <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
- <sysproperty key="basedir" value="."/>
- <formatter type="xml"/>
- <formatter type="plain" usefile="false"/>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- <pathelement location="${maven.build.testOutputDir}"/>
- </classpath>
- <batchtest todir="${maven.test.reports}" unless="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/Test*.java"/>
- <include name="**/*Test.java"/>
- <include name="**/*TestCase.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- <batchtest todir="${maven.test.reports}" if="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/${test}.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- </junit>
- </target>
-
- <target name="test-junit-present">
- <available classname="junit.framework.Test" property="junit.present"/>
- </target>
-
- <target name="test-junit-status"
- depends="test-junit-present">
- <condition property="junit.missing">
- <and>
- <isfalse value="${junit.present}"/>
- <isfalse value="${maven.test.skip}"/>
- </and>
- </condition>
- <condition property="junit.skipped">
- <or>
- <isfalse value="${junit.present}"/>
- <istrue value="${maven.test.skip}"/>
- </or>
- </condition>
- </target>
-
- <target name="junit-missing"
- depends="test-junit-status"
- if="junit.missing">
- <echo>=================================== WARNING ===================================</echo>
- <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
- <echo>===============================================================================</echo>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <javadoc sourcepath="${maven.build.srcDir.0}"
- packagenames="*"
- destdir="${maven.reporting.outputDirectory}/apidocs"
- access="protected"
- old="false"
- verbose="false"
- version="true"
- use="true"
- author="true"
- splitindex="false"
- nodeprecated="false"
- nodeprecatedlist="false"
- notree="false"
- noindex="false"
- nohelp="false"
- nonavbar="false"
- serialwarn="false"
- charset="ISO-8859-1"
- linksource="false"
- breakiterator="false"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" depends="compile,test" description="Package the application">
- <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar"
- compress="true"
- index="false"
- basedir="${maven.build.outputDir}"
- excludes="**/package.html">
- <manifest>
- </manifest>
- </jar>
- </target>
-
- <!-- ====================================================================== -->
- <!-- A dummy target for the package named after the type it creates -->
- <!-- ====================================================================== -->
-
- <target name="jar" depends="package" description="Builds the jar for the application"/>
-
- <!-- ====================================================================== -->
- <!-- Download dependencies target -->
- <!-- ====================================================================== -->
-
- <target name="test-offline">
- <condition property="maven.mode.offline">
- <equals arg1="${maven.settings.offline}" arg2="true"/>
- </condition>
- </target>
-
- <target name="get-deps"
- depends="test-offline"
- description="Download all dependencies"
- unless="maven.mode.offline">
- <mkdir dir="${maven.repo.local}"/>
- <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
- <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
- <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/build.xml b/dev-java/jrosetta/files/build.xml
deleted file mode 100644
index c6959deb0..000000000
--- a/dev-java/jrosetta/files/build.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="clean"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="clean"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" description="Compile the code">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests" description="Compile the test code">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile-tests"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile-tests"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test" description="Run the test cases">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="test"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="test"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="javadoc"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="javadoc"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" description="Package the application">
- <ant antfile="build.xml" dir="modules/jrosetta-api" target="package"/>
- <ant antfile="build.xml" dir="modules/jrosetta-engine" target="package"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/engine-build.xml b/dev-java/jrosetta/files/engine-build.xml
deleted file mode 100644
index 9ee8429f4..000000000
--- a/dev-java/jrosetta/files/engine-build.xml
+++ /dev/null
@@ -1,274 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above. -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!-- -->
-<!-- Any modifications will be overwritten. -->
-<!-- -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/ -->
-<!-- -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-engine-from-maven" default="package" basedir=".">
-
- <!-- ====================================================================== -->
- <!-- Build environment properties -->
- <!-- ====================================================================== -->
-
- <property file="${user.home}/.m2/maven.properties"/>
- <property file="maven-build.properties"/>
-
- <property name="maven.build.finalName" value="jrosetta-engine-1.0.4"/>
- <property name="maven.build.dir" value="target"/>
- <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
- <property name="maven.build.srcDir.0" value="src/main/java"/>
- <property name="maven.build.resourceDir.0" value="src/main/resources"/>
- <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
- <property name="maven.build.testDir.0" value="src/test/java"/>
- <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
- <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
- <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
- <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
- <property name="maven.settings.offline" value="true"/>
- <property name="maven.settings.interactiveMode" value="true"/>
-
- <!-- ====================================================================== -->
- <!-- Defining classpaths -->
- <!-- ====================================================================== -->
-
- <path id="build.classpath">
- <pathelement location="../jrosetta-api/target/classes"/>
- </path>
- <path id="build.test.classpath">
- <pathelement location="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"/>
- <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
- <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
- </path>
-
- <!-- ====================================================================== -->
- <!-- Cleaning up target -->
- <!-- ====================================================================== -->
-
- <target name="clean" description="Clean the output directory">
- <delete dir="${maven.build.dir}"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile" depends="get-deps" description="Compile the code">
- <mkdir dir="${maven.build.outputDir}"/>
- <javac destdir="${maven.build.outputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.srcDir.0}"/>
- </src>
- <classpath refid="build.classpath"/>
- </javac>
- <copy todir="${maven.build.outputDir}">
- <fileset dir="${maven.build.resourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Test-compilation target -->
- <!-- ====================================================================== -->
-
- <target name="compile-tests"
- depends="compile"
- description="Compile the test code"
- unless="maven.test.skip">
- <mkdir dir="${maven.build.testOutputDir}"/>
- <javac destdir="${maven.build.testOutputDir}"
- nowarn="false"
- debug="true"
- optimize="false"
- deprecation="true"
- target="1.6"
- verbose="false"
- fork="false"
- source="1.6">
- <src>
- <pathelement location="${maven.build.testDir.0}"/>
- </src>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- </classpath>
- </javac>
- <copy todir="${maven.build.testOutputDir}">
- <fileset dir="${maven.build.testResourceDir.0}"/>
- </copy>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Run all tests -->
- <!-- ====================================================================== -->
-
- <target name="test"
- depends="compile-tests, junit-missing"
- unless="junit.skipped"
- description="Run the test cases">
- <mkdir dir="${maven.test.reports}"/>
- <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
- <sysproperty key="basedir" value="."/>
- <formatter type="xml"/>
- <formatter type="plain" usefile="false"/>
- <classpath>
- <path refid="build.test.classpath"/>
- <pathelement location="${maven.build.outputDir}"/>
- <pathelement location="${maven.build.testOutputDir}"/>
- </classpath>
- <batchtest todir="${maven.test.reports}" unless="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/Test*.java"/>
- <include name="**/*Test.java"/>
- <include name="**/*TestCase.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- <batchtest todir="${maven.test.reports}" if="test">
- <fileset dir="${maven.build.testDir.0}">
- <include name="**/${test}.java"/>
- <exclude name="**/*Abstract*Test.java"/>
- </fileset>
- </batchtest>
- </junit>
- </target>
-
- <target name="test-junit-present">
- <available classname="junit.framework.Test" property="junit.present"/>
- </target>
-
- <target name="test-junit-status"
- depends="test-junit-present">
- <condition property="junit.missing">
- <and>
- <isfalse value="${junit.present}"/>
- <isfalse value="${maven.test.skip}"/>
- </and>
- </condition>
- <condition property="junit.skipped">
- <or>
- <isfalse value="${junit.present}"/>
- <istrue value="${maven.test.skip}"/>
- </or>
- </condition>
- </target>
-
- <target name="junit-missing"
- depends="test-junit-status"
- if="junit.missing">
- <echo>=================================== WARNING ===================================</echo>
- <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
- <echo>===============================================================================</echo>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Javadoc target -->
- <!-- ====================================================================== -->
-
- <target name="javadoc" description="Generates the Javadoc of the application">
- <javadoc sourcepath="${maven.build.srcDir.0}"
- packagenames="*"
- destdir="${maven.reporting.outputDirectory}/apidocs"
- access="protected"
- old="false"
- verbose="false"
- version="true"
- use="true"
- author="true"
- splitindex="false"
- nodeprecated="false"
- nodeprecatedlist="false"
- notree="false"
- noindex="false"
- nohelp="false"
- nonavbar="false"
- serialwarn="false"
- charset="ISO-8859-1"
- linksource="false"
- breakiterator="false"/>
- </target>
-
- <!-- ====================================================================== -->
- <!-- Package target -->
- <!-- ====================================================================== -->
-
- <target name="package" depends="compile,test" description="Package the application">
- <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar"
- compress="true"
- index="false"
- basedir="${maven.build.outputDir}"
- excludes="**/package.html">
- <manifest>
- </manifest>
- </jar>
- </target>
-
- <!-- ====================================================================== -->
- <!-- A dummy target for the package named after the type it creates -->
- <!-- ====================================================================== -->
-
- <target name="jar" depends="package" description="Builds the jar for the application"/>
-
- <!-- ====================================================================== -->
- <!-- Download dependencies target -->
- <!-- ====================================================================== -->
-
- <target name="test-offline">
- <condition property="maven.mode.offline">
- <equals arg1="${maven.settings.offline}" arg2="true"/>
- </condition>
- </target>
-
- <target name="get-deps"
- depends="test-offline"
- description="Download all dependencies"
- unless="maven.mode.offline">
- <mkdir dir="${maven.repo.local}"/>
- <mkdir dir="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4"/>
- <get src="http://maven.artenum.com/content/groups/public/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
- <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar"
- dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
- <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"
- usetimestamp="false"
- ignoreerrors="true"/>
- </target>
-
-</project>
diff --git a/dev-java/jrosetta/jrosetta-1.0.4.ebuild b/dev-java/jrosetta/jrosetta-1.0.4.ebuild
deleted file mode 100644
index bf0f72e79..000000000
--- a/dev-java/jrosetta/jrosetta-1.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Common base for graphical component to build a graphical console"
-HOMEPAGE="http://dev.artenum.com/projects/JRosetta"
-#currently down
-#SRC_URI="http://maven.artenum.com/content/groups/public/com/artenum/${PN}/${PV}/${P}-sources.jar"
-SRC_URI="http://pkgs.fedoraproject.org/repo/pkgs/${PN}/${P}-sources.jar/5c3589d4207f71bad6eeefd4857bce50/${P}-sources.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=virtual/jdk-1.5:*"
-BDEPEND="app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5:*"
-
-EANT_BUILD_TARGET="compile package"
-JAVA_ANT_BSFIX_EXTRA_ARGS="--maven-cleaning"
-
-src_prepare () {
- default
- cp "${FILESDIR}/api-build.xml" modules/jrosetta-api/build.xml || die
- cp "${FILESDIR}/engine-build.xml" modules/jrosetta-engine/build.xml || die
- cp "${FILESDIR}/build.xml" . || die
- echo "${PV}" > modules/jrosetta-engine/src/main/resources/version.txt || die
-}
-
-src_install () {
- java-pkg_newjar "modules/jrosetta-api/target/jrosetta-api-${PV}.jar" \
- jrosetta-api.jar
- java-pkg_newjar "modules/jrosetta-engine/target/jrosetta-engine-${PV}.jar" \
- jrosetta-engine.jar
-}
diff --git a/dev-java/jrosetta/metadata.xml b/dev-java/jrosetta/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-java/jrosetta/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-java/lucene/Manifest b/dev-java/lucene/Manifest
deleted file mode 100644
index 514721f91..000000000
--- a/dev-java/lucene/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST lucene-3.6.2-src.tgz 32139784 BLAKE2B 48fe88efeae8396e084f827aa66530480f40aee3a2e59c8524420059f004a73be4c1e50c98345ad0ad4808ff8a0a996f9406523bf5c124616657ec91f9797f70 SHA512 e9a08a1b5303c44e4feecc0bb6e7013e4a9420517ae4e98999bd318ec25b5b2ff3b6de8b51db8f68afc0fdc3149829297023a95b103d4f99e7db68deee4c3965
-DIST lucene-5.2.1-src.tgz 29669184 BLAKE2B ec69a85ddf7870c760aedf9e79d93dad623d3dd759b1b6d992f64a169a86ff5f7992c0af9bd1692b78bb2c9d2abd7ca57d7c43bd507dfd0a672d31db06a30514 SHA512 294f4a0b2d1d11a8da6db0b577b962037beb4331c1ddee3e65a54e9f3155e44c3aa945b8b8f04631eb42d9bee94c1bcc468d12278fd06f2740512b9375880a02
-DIST lucene-8.4.0-src.tgz 43420829 BLAKE2B df9f34ece8d6b477950ba22d3883d81652f0a6b43adcd55152d465fa99679520314edd61500dedc3ecab85ea8410948d91c37e27bfd774dce9b6281c782b5ff0 SHA512 3848372cc0ef914502bff8f139fdd3f3c2dda68ed69492b1b189ebdc734a9a14f2b1d9f00273f7794368ccc13be304c083029d2333cc2cf61e568f04d8e91936
diff --git a/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch b/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch
deleted file mode 100644
index 8d70c406f..000000000
--- a/dev-java/lucene/files/lucene-3.6.2-ant-1.10.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/lucene/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java b/lucene/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-index 5a9509c..beecebe 100644
---- a/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-+++ b/test-framework/src/java/org/apache/lucene/util/LuceneJUnitDividingSelector.java
-@@ -21,6 +21,7 @@ import java.io.File;
- import org.apache.tools.ant.BuildException;
- import org.apache.tools.ant.types.Parameter;
- import org.apache.tools.ant.types.selectors.BaseExtendSelector;
-+import org.apache.tools.ant.types.Resource;
-
- /** Divides filesets into equal groups */
- public class LuceneJUnitDividingSelector extends BaseExtendSelector {
-@@ -30,6 +31,11 @@ public class LuceneJUnitDividingSelector extends BaseExtendSelector {
- /** Current part to accept. */
- private int part;
-
-+ @Override
-+ public boolean isSelected(Resource r) {
-+ return false;
-+ }
-+
- @Override
- public void setParameters(Parameter[] pParameters) {
- super.setParameters(pParameters);
diff --git a/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch b/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch
deleted file mode 100644
index 8c3dd8a01..000000000
--- a/dev-java/lucene/files/lucene_contrib_icu4j_v50.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/contrib/icu/src/java/org/apache/lucene/analysis/icu/segmentation/BreakIteratorWrapper.java
-+++ b/contrib/icu/src/java/org/apache/lucene/analysis/icu/segmentation/BreakIteratorWrapper.java
-@@ -21,7 +21,6 @@ import java.text.CharacterIterator;
-
- import com.ibm.icu.lang.UCharacter;
- import com.ibm.icu.text.BreakIterator;
--import com.ibm.icu.text.DictionaryBasedBreakIterator;
- import com.ibm.icu.text.RuleBasedBreakIterator;
- import com.ibm.icu.text.UTF16;
-
-@@ -67,8 +66,7 @@ abstract class BreakIteratorWrapper {
- * it like a generic BreakIterator.
- */
- static BreakIteratorWrapper wrap(BreakIterator breakIterator) {
-- if (breakIterator instanceof RuleBasedBreakIterator
-- && !(breakIterator instanceof DictionaryBasedBreakIterator))
-+ if (breakIterator instanceof RuleBasedBreakIterator)
- return new RBBIWrapper((RuleBasedBreakIterator) breakIterator);
- else
- return new BIWrapper(breakIterator);
diff --git a/dev-java/lucene/lucene-3.6.2-r2.ebuild b/dev-java/lucene/lucene-3.6.2-r2.ebuild
deleted file mode 100644
index 97e5c8d6e..000000000
--- a/dev-java/lucene/lucene-3.6.2-r2.ebuild
+++ /dev/null
@@ -1,162 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test contrib"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml contrib-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="mirror://apache/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="3.6"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- contrib? (
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:56
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.6"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.6"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-# [0]: Patch so that we can compile the package against ICU 50 and above
-PATCHES=(
- "${FILESDIR}"/lucene_contrib_icu4j_v50.patch
- "${FILESDIR}"/${P}-ant-1.10.patch
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- common-build.xml || die
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use contrib; then
- EANT_GENTOO_CLASSPATH+="
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-56
- "
- EANT_BUILD_TARGET+=" build-contrib"
- EANT_DOC_TARGET+=" javadocs-all"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use contrib; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-contrib"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- java-pkg_newjar build/core/${PN}-core-${PV}.jar ${PN}-core.jar
-
- if use contrib; then
- local i j
- for i in $(find build/contrib -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- fi
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs/api
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use contrib && java-pkg_dosrc contrib
- fi
-}
diff --git a/dev-java/lucene/lucene-5.2.1.ebuild b/dev-java/lucene/lucene-5.2.1.ebuild
deleted file mode 100644
index 8038db195..000000000
--- a/dev-java/lucene/lucene-5.2.1.ebuild
+++ /dev/null
@@ -1,211 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test modules"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="https://archive.apache.org/dist/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="5.2"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- modules? (
- dev-java/ant-apache-log4j:0
- dev-java/antlr:3.5
- dev-java/asm:9
- dev-java/asm-commons:9
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:56
- dev-java/log4j:0
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.7"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.7"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-lucene-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- -e '/conf="${ivy.default.configuration}" sync="${ivy.sync}"/d' \
- -e '/<fail>Ivy is not available<\/fail>/d' \
- -e '/ivy:configure/d' \
- -e '/svnversion.exe/d' \
- common-build.xml || die
-
- # do not build tests if modules enabled, we are missing a dependency
- sed -i \
- -e 's/<target name="build-modules" depends="compile-test"/<target name="build-modules"/g' \
- build.xml
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- if use modules; then
- mkdir -p analysis/icu/lib
- java-pkg_jar-from --into analysis/icu/lib icu4j-56
- # disable morfologik, dependency does not build
- # disable uima, dependency does not build
- # disable phonetic, dependency does not exist
- sed -i \
- -e 's/morfologik,//g' \
- -e 's/,uima//g' \
- -e 's/phonetic,//g' \
- -e 's/,compile-test//g' \
- analysis/build.xml || die
- rm -r analysis/morfologik || die
- rm -r analysis/uima || die
- rm -r analysis/phonetic || die
- # do not compile all the tests just because we want the modules
- sed -i \
- -e 's/name="build-modules" depends="compile-test"/name="build-modules"/g' \
- build.xml || die
- sed -i \
- -e 's/, compile-test//g' \
- module-build.xml || die
- mkdir -p expressions/lib
- # facet requires hppc which does not compile
- sed -i \
- -e '/<ant dir="${common.dir}\/facet" target="jar-core" inheritall="false">/,+2d' \
- module-build.xml || die
- rm -r facet || die
- # requires spatial4j, which does not exist
- sed -i \
- -e '/<ant dir="${common.dir}\/spatial" target="jar-core" inheritAll="false">/,+2d' \
- module-build.xml || die
- rm -r spatial || die
- # these require modules which we have disabled
- rm -r benchmark || die
- rm -r demo || die
- # fails to build for unknown reasons
- rm -r replicator || die
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use modules; then
- EANT_GENTOO_CLASSPATH+="
- ant-apache-log4j
- antlr-3.5
- asm-9
- asm-commons-9
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-56
- log4j
- "
- EANT_BUILD_TARGET+=" build-modules"
- EANT_DOC_TARGET+=" javadocs-modules"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use modules; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-modules"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- local i j
- for i in $(find build -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use modules && java-pkg_dosrc */src */*/src
- fi
-}
diff --git a/dev-java/lucene/lucene-8.4.0.ebuild b/dev-java/lucene/lucene-8.4.0.ebuild
deleted file mode 100644
index b9967b3e5..000000000
--- a/dev-java/lucene/lucene-8.4.0.ebuild
+++ /dev/null
@@ -1,223 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source test modules"
-JAVA_PKG_BSFIX_ALL="no"
-JAVA_PKG_BSFIX_NAME="build.xml common-build.xml"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="High-performance, full-featured text search engine written entirely in Java"
-HOMEPAGE="https://lucene.apache.org"
-SRC_URI="https://archive.apache.org/dist/lucene/java/${PV}/${P}-src.tgz"
-
-LICENSE="Apache-2.0"
-SLOT="8.4"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/ant-core:0
- dev-java/ant-junit:0
- dev-java/hamcrest-core:0
- dev-java/jflex:0
- modules? (
- dev-java/ant-apache-log4j:0
- dev-java/antlr:4
- dev-java/asm:9
- dev-java/asm-commons:9
- dev-java/junit:4
- dev-java/jakarta-regexp:1.4
- dev-java/commons-compress:0
- dev-java/commons-collections:0
- dev-java/commons-digester:0
- dev-java/commons-logging:0
- dev-java/commons-beanutils:1.7
- dev-java/commons-codec:0
- dev-java/icu4j:56
- dev-java/log4j:0
- )"
-
-DEPEND="
- ${CDEPEND}
- >=virtual/jdk-1.8"
-
-RDEPEND="
- ${CDEPEND}
- >=virtual/jre-1.8"
-
-DOCS=(
- CHANGES.txt README.txt
- NOTICE.txt CHANGES.txt
- JRE_VERSION_MIGRATION.txt
-)
-
-EANT_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- hamcrest-core
- jflex
- "
-EANT_EXTRA_ARGS="-Dversion=${PV} -Dfailonjavadocwarning=false"
-EANT_DOC_TARGET="javadocs-lucene-core"
-
-EANT_TEST_TARGET="test-core"
-EANT_TEST_EXTRA_ARGS="-Dheadless=true -Djava.io.tmpdir=${T}"
-EANT_TEST_GENTOO_CLASSPATH="
- ant-core
- ant-junit
- junit-4
- "
-EANT_TEST_ANT_TASKS="ant-junit"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-# All tests in contrib/icu/test fail.
-RESTRICT="test"
-
-src_prepare() {
- default
-
- sed -i \
- -e '/-Xmax/ d' \
- -e '/property="ivy.available"/s,resource="${ivy.resource}",file="." type="dir",g' \
- -e '/<ivy:retrieve/d' \
- -e '/conf="${ivy.default.configuration}" sync="${ivy.sync}"/d' \
- -e '/<fail>Ivy is not available<\/fail>/d' \
- -e '/ivy:configure/d' \
- -e '/<groovy /d' \
- -e '/svnversion.exe/d' \
- -e 's/depends="ivy-availability-check,/depends="/g' \
- -e 's/ivy-availability-check,//g' \
- -e 's/resolve-groovy,//g' \
- -e 's/depends="resolve-groovy"//g' \
- -e '/<ivy:cachepath/,/\/>/d' \
- -e '/<ivy:cachepath/,/\/ivy:cachepath>/d' \
- -e '/<ivy:dependency/d' \
- -e '/<\/ivy:cachepath>/d' \
- -e '/<taskdef name="groovy"/,/\/>/d' \
- common-build.xml || die
-
- # do not build tests if modules enabled, we are missing a dependency
- sed -i \
- -e 's/<target name="build-modules" depends="compile-test"/<target name="build-modules"/g' \
- build.xml
-
- # FIXME: docs do not build if behind a proxy, -autoproxy does not work
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a failonerror \
- -v "false" \
- -a additionalparam \
- -v "-Xdoclint:none"
-
- # There are some JS in the javadocs's bootom and in VM >= 1.8 the --allow-script-in-comments
- # is needed so docs could be built
- if java-pkg_is-vm-version-ge "1.8" ; then
- java-ant_xml-rewrite -f common-build.xml \
- -c -e javadoc \
- -a additionalparam \
- -v "-Xdoclint:none --allow-script-in-comments"
- fi
-
- if use modules; then
- mkdir -p analysis/icu/lib
- java-pkg_jar-from --into analysis/icu/lib icu4j-56
- # disable morfologik, dependency does not build
- # disable opennlp, dependency does not exist
- # disable phonetic, dependency does not exist
- sed -i \
- -e 's/morfologik,//g' \
- -e 's/opennlp,//g' \
- -e 's/phonetic,//g' \
- -e 's/,compile-test//g' \
- analysis/build.xml || die
- rm -r analysis/morfologik || die
- rm -r analysis/opennlp || die
- rm -r analysis/phonetic || die
- # do not compile all the tests just because we want the modules
- sed -i \
- -e 's/name="build-modules" depends="compile-test"/name="build-modules"/g' \
- build.xml || die
- sed -i \
- -e 's/, compile-test//g' \
- module-build.xml || die
- mkdir -p expressions/lib
- # facet requires hppc which does not compile
- sed -i \
- -e '/<ant dir="${common.dir}\/facet" target="jar-core" inheritall="false">/,+2d' \
- module-build.xml || die
- rm -r facet || die
- # requires spatial4j, which does not exist
- sed -i \
- -e '/<ant dir="${common.dir}\/spatial-extras" target="jar-core" inheritAll="false">/,+2d' \
- module-build.xml || die
- rm -r spatial-extras || die
- # these require modules which we have disabled
- rm -r benchmark || die
- rm -r demo || die
- # this fails due to missing log4j, even though it is included in classpath
- rm -r luke || die
- # fails to build for unknown reasons
- rm -r replicator || die
- fi
-
- java-pkg-2_src_prepare
-}
-
-src_compile() {
- EANT_BUILD_TARGET="jar-core"
-
- if use modules; then
- EANT_GENTOO_CLASSPATH+="
- ant-apache-log4j
- antlr-4
- asm-9
- asm-commons-9
- jakarta-regexp-1.4
- commons-compress
- commons-collections
- commons-digester
- commons-logging
- commons-beanutils-1.7
- commons-codec
- icu4j-56
- log4j
- "
- EANT_BUILD_TARGET+=" build-modules"
- EANT_DOC_TARGET+=" javadocs-modules"
- fi
-
- java-ant_rewrite-classpath common-build.xml
-
- default
- java-pkg-2_src_compile
-}
-
-src_test() {
- if use modules; then
- EANT_TEST_GENTOO_CLASSPATH+=" commons-codec ${EANT_GENTOO_CLASSPATH}"
- EANT_TEST_TARGET+=" test-modules"
- fi
-
- java-pkg-2_src_test
-}
-
-src_install() {
- einstalldocs
- local i j
- for i in $(find build -name \*-${PV}.jar); do
- j=${i##*/}
- java-pkg_newjar $i ${j%%-${PV}.jar}.jar
- done
- if use doc; then
- dodoc -r docs
- java-pkg_dohtml -r build/docs
- fi
- if use source; then
- java-pkg_dosrc core/src/java/org
- use modules && java-pkg_dosrc */src */*/src
- fi
-}
diff --git a/dev-java/lucene/metadata.xml b/dev-java/lucene/metadata.xml
deleted file mode 100644
index 8bfdfa59a..000000000
--- a/dev-java/lucene/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <use>
- <flag name="contrib">Include extra functionality from contrib/</flag>
- <flag name="modules">Also build optional modules</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-java/skinlf/Manifest b/dev-java/skinlf/Manifest
deleted file mode 100644
index 725284f44..000000000
--- a/dev-java/skinlf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST skinlf-6.7.10.tar.gz 185870 BLAKE2B 4534f4d463ad3c9604d21a7113c12b5bbe1aecd7cdd80610644ce668821cd2bd1e47d0b926550014301f84e20d52f63f16bee817c339fbdc1631f57f2d74a082 SHA512 24cb44f709c5202fff1a9ca58e8cdda4de0d5e9bad8c2a7579694eabcd590993ebd5d60e200a3ff67078627502c592da2e8a021faff8f95de4ab4f8bf4945899
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-build.xml b/dev-java/skinlf/files/skinlf-6.7.10-build.xml
deleted file mode 100644
index 42b4c1145..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-build.xml
+++ /dev/null
@@ -1,276 +0,0 @@
-<!DOCTYPE project [
- <!ENTITY build-COMMON SYSTEM "common.xml">
-]>
-
-<!--
- Skin Look And Feel Build
--->
-<project name="skinlf" default="compile.java" basedir=".">
-
- <!-- Allow user to override settings -->
- <property file="${user.home}/skinlf-ant.properties" />
- <property file="build.properties" />
-
- <!-- Project Identification -->
- <property name="project" value="skinlf"/>
- <property name="version" value="6.7"/>
- <property name="year" value="2000-2006"/>
- <property name="project.fullname" value="Skin Look And Feel"/>
- <property name="project.nativeskin" value="nativeskin"/>
-
- <property name="javadoc.packagenames" value="com.l2fprod.gui,com.l2fprod.gui.plaf.skin,com.l2fprod.gui.region,com.l2fprod.gui.nativeskin"/>
-
-
-
- <path id="classpath">
- <fileset dir="lib" includes="**/*.jar"/>
- </path>
-
- <property name="classpath.asprop" refid="classpath"/>
-
- &build-COMMON;
-
- <target name="compile.javacc" depends="init">
- <javacc target="src/com/l2fprod/gui/plaf/skin/impl/gtk/parser/GtkParser.jj"
- outputdirectory="src/com/l2fprod/gui/plaf/skin/impl/gtk/parser"
- javacchome="lib"
- static="false"
- javaunicodeescape="true" />
- </target>
-
- <target name="compile" depends="init">
- </target>
-
- <!--
- Utility targets to use the style converters
- -->
- <target name="convert.msstyles">
- <fail unless="msstyle" message="Specify path to msstyle xml -Dmsstyle=pathtoxml"/>
- <fail unless="skin" message="Specify themepack folder -Dskin=pathtothemepackdir"/>
- <java classname="com.l2fprod.tools.msstyles.MsStylesToSkinLF"
- classpath="${classpath.asprop}:${java.src.dir}:${build.classes}"
- fork="yes">
- <arg value="${msstyle}" />
- <arg value="${msstyle}.xml" />
- <arg value="${skin}" />
- </java>
- <copy todir="${skin}">
- <fileset dir="src/themepacks/skeletonthemepack" includes="**"/>
- </copy>
- </target>
-
- <!--
- Start Demos
- -->
- <target name="demo">
- <java classname="examples.demo"
- classpath="${classpath.asprop}:${java.src.dir}:${build.classes}"
- fork="yes">
- <arg value="${skin}" />
- </java>
- </target>
-
- <!-- Dist targets -->
- <target name="jar" depends="compile.java">
- <jar destfile="${build.dir}/${project}.jar">
- <fileset dir="${build.classes}" includes="*.class,com/**/*.class" excludes="**/region/**,**/nativeskin/**"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.properties"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.template"/>
- <fileset dir="${java.src.dir}" includes="com/**/*.gif"/>
- <manifest>
- <attribute name="Built-by" value="${user.name}"/>
- <attribute name="Main-Class" value="com.l2fprod.gui.plaf.skin.Skinit"/>
- <attribute name="Class-Path" value="laf-plugin.jar"/>
- <section name="com/l2fprod/gui/plaf/skin">
- <attribute name="Specification-Title" value="${project.fullname}"/>
- <attribute name="Specification-Version" value="${version}"/>
- <attribute name="Specification-Vendor" value="L2FProd.com"/>
- <attribute name="Implementation-Title" value="${project.fullname}"/>
- <attribute name="Implementation-Version" value="${version}"/>
- <attribute name="Implementation-Vendor" value="L2FProd.com"/>
- </section>
- </manifest>
- </jar>
- </target>
-
- <target name="obfuscate" depends="jar">
- <taskdef name="proguard"
- classname="proguard.ant.ProGuardTask"
- classpath="lib/proguard.jar"/>
- <move file="${build.dir}/${project}.jar"
- tofile="${build.dir}/${project}-toobfuscate.jar"/>
- <proguard
- outjar="${build.dir}/${project}.jar"
- obfuscate="yes"
- usemixedclassnames="no"
- overloadaggressively="yes"
- printmapping="obfuscatemapping.txt"
- printusage="obfuscateusage.txt">
- <libraryjar name="${java.home}/lib/rt.jar"/>
- <injar name="${build.dir}/${project}-toobfuscate.jar"/>
- <keep access="public" type="class" name="Skinit">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.SkinApplet">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.SkinChooser">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.WindowSnapping">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.nativeskin.**">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.CompoundSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.IncorrectVersionException">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.LinuxLookAndFeel">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.Skin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinButton">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinFrame">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.Skinit">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinLookAndFeel">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinPersonality">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinPreviewWindow">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinProgress">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinScrollbar">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSeparator">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSlider">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinSplitPane">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.SkinTab">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.*">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.gtk.GtkSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.plaf.skin.impl.kde.KdeSkin">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.gui.region.*">
- <method name="*"/>
- </keep>
- <keep access="public" type="class" name="com.l2fprod.tools.**">
- <method name="*"/>
- </keep>
- <keep type="class" name="com.l2fprod.util.**">
- <method name="*"/>
- </keep>
- </proguard>
- </target>
-
- <target name="dist.pre" depends="jar">
- <!-- examples.jar -->
- <jar destfile="${build.dist.lib}/examples.jar">
- <fileset dir="${build.classes}" includes="examples/**.class"/>
- <fileset dir="${java.src.dir}" includes="examples/**.properties,examples/**.gif,examples/**.jpg"/>
- </jar>
- <!-- nativeskin.jar -->
- <jar jarfile="${build.dist.lib}/nativeskin.jar">
- <fileset dir="${build.classes}"
- includes="com/l2fprod/gui/region/**,com/l2fprod/gui/nativeskin/**,com/l2fprod/util/OS**,,com/l2fprod/util/Access**"
- excludes="**/*.html"/>
- </jar>
- <!-- batch files -->
- <copy todir="${build.dist.bin}"
- flatten="yes"
- preservelastmodified="yes">
- <fileset dir="src" includes="**/*.bat"/>
- </copy>
- <!-- dlls -->
- <copy todir="${build.dist.lib}">
- <fileset dir="src/native/win32" includes="*.dll"/>
- </copy>
- <!-- default theme -->
- <zip destfile="${build.dist.lib}/themepack.zip">
- <zipfileset dir="src/themepacks/whistlerthemepack"/>
- </zip>
- </target>
-
- <!--
- Publish the new version of SKinLF
- -->
- <target name="publish" depends="init">
- <!-- copy zip to dist folder -->
- <copy todir="${publish.download.dir}"
- file="${project}-${version}-${build.version}.zip"/>
-
- <filter token="WEB" value="${publish.web.url}"/>
- <!-- update the jnlp website with the new release -->
- <!-- put skinlf.jar in jnlp folder -->
- <copy todir="${publish.skinlf.home}/jnlp/" filtering="on" overwrite="yes">
- <fileset dir="src/jnlp" includes="*.jnlp"/>
- </copy>
- <copy file="${build.dist.lib}/${project}.jar" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/examples.jar" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/themepack.zip" todir="${publish.skinlf.home}/jnlp/"/>
- <copy file="${build.dist.lib}/nativeskin.jar" todir="${publish.skinlf.home}/jnlp"/>
- <jar destfile="${publish.skinlf.home}/jnlp/nativeskinlibs.jar"
- basedir="${build.dist.lib}" includes="*.dll"/>
-
- <!-- copy the documentation
- <copy todir="${web.skinlf.home}/documentation">
- <fileset dir="${javadoc.destdir}"/>
- </copy>
- -->
- <!-- Sign all Jars -->
- <signjar keystore="../common/keystore" alias="L2FProd.com" storepass="L2FProd.com">
- <fileset dir="${publish.skinlf.home}/jnlp" includes="*.jar"/>
- </signjar>
-
- </target>
-
- <target name="themes">
- <zip destfile="${build.www.themedir}/cellshadedthemepack.zip"
- basedir="src/themepacks/cellshadedthemepack"/>
- <zip destfile="${build.www.themedir}/whistlerthemepack.zip"
- basedir="src/themepacks/whistlerthemepack"/>
- <zip destfile="${build.www.themedir}/xplunathemepack.zip"
- basedir="src/themepacks/xplunathemepack"/>
- <zip destfile="${build.www.themedir}/toxicthemepack.zip"
- basedir="src/themepacks/toxicthemepack"/>
- <zip destfile="${build.www.themedir}/beigeazulthemepack.zip"
- basedir="src/themepacks/beigeazulthemepack"/>
-
-
- <!-- png for these themepacks are not in cvs -->
- <zip destfile="${build.www.themedir}/aquathemepack.zip"
- basedir="src/themepacks/aquathemepack"/>
- <zip destfile="${build.www.themedir}/alloythemepack.zip"
- basedir="src/themepacks/alloythemepack"/>
- </target>
-
-</project>
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-common.xml b/dev-java/skinlf/files/skinlf-6.7.10-common.xml
deleted file mode 100644
index c2803acc5..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-common.xml
+++ /dev/null
@@ -1,171 +0,0 @@
-<!--
- Common Target which could be reused by other projects later.
--->
-
-<!-- COMMON PROPERTIES -->
-
- <property name="debug" value="true"/>
- <property name="optimize" value="false"/>
-
- <!-- Java Related -->
- <property name="java.src.dir" value="src"/>
- <property name="javac.compiler" value="modern"/>
-
- <!-- Destination Directory for the build -->
- <property name="build.dir" value="build"/>
- <property name="build.classes" value="${build.dir}/classes"/>
- <property name="build.src" value="${build.dir}/src"/>
- <property name="build.dist.dir" value="${project}-${version}"/>
- <property name="build.dist.src" value="${build.dist.dir}/src"/>
- <property name="build.dist.lib" value="${build.dist.dir}/lib"/>
- <property name="build.dist.bin" value="${build.dist.dir}/bin"/>
- <property name="build.www.dir" value="${build.dir}/www"/>
-
-<!-- COMMON TARGETS -->
-
- <target name="init.properties">
- <tstamp>
- <format property="build.time" pattern="MM/dd/yyyy hh:mm aa" locale="en"/>
- <format property="build.version" pattern="yyyyMMdd" locale="en"/>
- </tstamp>
- <filter token="VERSION" value="${version}"/>
- <filter token="PROJECT.FULLNAME" value="${project.fullname}"/>
- <filter token="DATE" value="${build.time}"/>
- <filter token="YEAR" value="${year}"/>
- </target>
-
- <target name="init.directories">
- <mkdir dir="${build.dir}"/>
- <mkdir dir="${build.classes}"/>
- <mkdir dir="${build.dist.dir}"/>
- <mkdir dir="${build.dist.src}"/>
- <mkdir dir="${build.dist.lib}"/>
- <mkdir dir="${build.dist.bin}"/>
- </target>
-
- <target name="init" depends="init.properties,init.directories">
- </target>
-
- <target name="clean">
- <delete dir="${build.dir}"/>
- <delete dir="${build.dist.dir}"/>
- </target>
-
- <target name="fixcrlf">
- <fixcrlf srcdir="${basedir}" eol="cr">
- <include name="AUTHORS,LICENSE*,README,THANKS" />
- <include name="**/*.java" />
- </fixcrlf>
- </target>
-
-<!-- Java Related Targets -->
-
- <target name="compile.java" depends="init">
- <depend srcdir="${java.src.dir}"
- destdir="${build.classes}"
- cache="${build.dir}/dependcache"
- closure="yes"/>
-
- <copy todir="${build.src}" filtering="yes">
- <fileset dir="${java.src.dir}">
- <include name="**/*.java"/>
- </fileset>
- </copy>
- <javac srcdir="${build.src}"
- destdir="${build.classes}"
- classpathref="classpath"
- compiler="${javac.compiler}"
- includeAntRuntime="false"
- includeJavaRuntime="false"
- debug="${debug}"
- optimize="${optimize}"
- target="1.3" source="1.3">
- </javac>
- </target>
-
-<!-- Distribution Target -->
-
- <target name="dist" depends="jar,dist.pre">
- <!-- project.jar -->
- <copy todir="${build.dist.lib}"
- file="${build.dir}/${project}.jar"
- preservelastmodified="yes"/>
- <!-- source code -->
- <copy todir="${build.dist.src}"
- preservelastmodified="yes">
- <fileset dir="${build.src}" includes="**/*.java"/>
- <fileset dir="${java.src.dir}" includes="**/*.properties"/>
- </copy>
- <!-- regular files -->
- <copy todir="${build.dist.dir}"
- filtering="yes"
- preservelastmodified="yes">
- <fileset dir="${basedir}">
- <include name="AUTHORS"/>
- <include name="INSTALL"/>
- <include name="README"/>
- <include name="THANKS"/>
- <include name="LICENSE"/>
- <include name="LICENSE_*"/>
- </fileset>
- </copy>
- <xslt in="xdocs/CHANGES.xml"
- out="${build.dist.dir}/CHANGES"
- style="xdocs/xsl/text.xsl"/>
- <!-- zip file -->
- <zip destfile="${project}-${version}-${build.version}.zip">
- <zipfileset dir="${build.dist.dir}"
- prefix="${project}-${version}" />
- </zip>
- </target>
-
-<!-- Source code formatting -->
-
- <target name="jalopy" depends="init">
- </target>
-
-<!-- Project Web Documentation -->
-
- <target name="www" depends="init">
- <mkdir dir="${build.www.dir}"/>
- <xslt in="xdocs/www.xml"
- out="${build.www.dir}/empty.html"
- style="xdocs/xsl/tohtml.xsl">
- <param name="output.dir" expression="${build.www.dir}"/>
- <param name="timestamp" expression="${build.time}"/>
- </xslt>
- <copy todir="${build.www.dir}">
- <fileset dir="xdocs">
- <include name="images/**"/>
- <include name="**.java"/>
- </fileset>
- </copy>
- <mkdir dir="${build.www.dir}/javadoc"/>
- <javadoc sourcepath="${java.src.dir}"
- classpath="${classpath}"
- destdir="${build.www.dir}/javadoc"
- packagenames="${javadoc.packagenames}"
- private="false" protected="true"
- windowtitle="${project.fullname} ${version} API"
- doctitle="${project.fullname} ${version}"
- version="false" author="false" use="false"
- stylesheetfile="xdocs/javadoc.css"
- splitindex="true"
- bottom="Copyright &#169; ${year} L2FProd.com. All Rights Reserved."/>
- <delete file="${build.www.dir}/empty.html"/>
- </target>
-
- <target name="www.sync" depends="init">
- <ftp server="${build.www.server}"
- userid="${build.www.userid}"
- password="${build.www.password}"
- remotedir="${build.www.remotedir}"
- action="put"
- verbose="yes"
- depends="yes">
- <fileset dir="${build.www.dir}">
- <include name="**/**"/>
- </fileset>
- </ftp>
- </target>
-
diff --git a/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch b/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch
deleted file mode 100644
index 123335241..000000000
--- a/dev-java/skinlf/files/skinlf-6.7.10-image-utils-without-jimi.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff -ru skinlf-1.2.12-orig/src/com/l2fprod/tools/ImageUtils.java skinlf-1.2.12/src/com/l2fprod/tools/ImageUtils.java
---- a/src/com/l2fprod/tools/ImageUtils.java 2006-01-24 20:09:36.000000000 +0100
-+++ b/src/com/l2fprod/tools/ImageUtils.java 2006-01-24 20:19:19.000000000 +0100
-@@ -6,15 +6,12 @@
-
- import javax.swing.ImageIcon;
-
--import com.ibm.imageconversion.*;
--import com.sun.jimi.core.*;
-+import javax.imageio.*;
-
- public class ImageUtils {
-
- public static Component bitmapCreator = new javax.swing.JLabel();
-
-- static BMPDecoder decoder = new BMPDecoder();
-- static BMPEncoder encoder = new BMPEncoder();
-
- public static Image loadPng(String pathToImage) throws Exception {
- ImageIcon icon = new ImageIcon(new File(pathToImage).toURL());
-@@ -22,29 +19,33 @@
- }
-
- public static void savePng(Image image, String pathToImage) throws Exception {
-- Jimi.putImage(image, pathToImage);
-+ ImageIO.write((RenderedImage)image, "png", new File(pathToImage));
- }
-
-+ private static String getFileFmt(String pathToImage) throws Exception {
-+ String fmt;
-+ if (pathToImage.toLowerCase().endsWith(".png")) {
-+ return "png";
-+ }
-+ if (pathToImage.toLowerCase().endsWith(".gif")) {
-+ return "gif";
-+ }
-+ if (pathToImage.toLowerCase().endsWith(".bmp")) {
-+ return "bmp";
-+ }
-+ return "";
-+ }
-+
- public static void createPicture(String pathToImage, int index, int maxParts,
- String filename, boolean horizontal) {
- try {
- System.out.println("working with " + pathToImage);
- Image image = null;
--
-- if (pathToImage.toLowerCase().endsWith(".png") ||
-- pathToImage.toLowerCase().endsWith(".gif")) {
-- image = loadPng(pathToImage);
-- } else if (pathToImage.toLowerCase().endsWith(".bmp")) {
-- decoder.setInputFilename(pathToImage);
-- decoder.triggerAction();
-- image = decoder.getResult();
-- } else {
-- throw new Error("do not know how to load " + pathToImage);
-- }
-+ image = Toolkit.getDefaultToolkit().getImage(pathToImage);
-
- // if only one image, dump it as it
-- if (index == 0 && maxParts == 1) {
-- Jimi.putImage(image, filename);
-+ if (index == 0 && maxParts == 1) {
-+ ImageIO.write((RenderedImage)image, getFileFmt(pathToImage), new File(pathToImage));
- } else {
- if (horizontal) {
- int partHeight = image.getHeight(bitmapCreator) / maxParts;
-@@ -55,7 +56,7 @@
- image = grab(image, partWidth * index, 0,
- partWidth, image.getHeight(bitmapCreator));
- }
-- Jimi.putImage(image, filename);
-+ ImageIO.write((RenderedImage)image, getFileFmt(pathToImage), new File(pathToImage));
- }
- } catch (Exception e) {
- System.out.println("error while working with " + pathToImage);
diff --git a/dev-java/skinlf/metadata.xml b/dev-java/skinlf/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/dev-java/skinlf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-java/skinlf/skinlf-6.7.10.ebuild b/dev-java/skinlf/skinlf-6.7.10.ebuild
deleted file mode 100644
index a63320a6d..000000000
--- a/dev-java/skinlf/skinlf-6.7.10.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Skin Look and Feel - Skinning Engine for the Swing toolkit"
-HOMEPAGE="http://skinlf.l2fprod.com/"
-# Upstream is gone, use this url from ubuntu/debian instead
-SRC_URI="https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/libskinlf-java/$(ver_rs 2 -)/libskinlf-java_$(ver_cut 1-2).orig.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/laf-plugin:0
- dev-java/xalan:0"
-
-RDEPEND=">=virtual/jre-1.4
- ${CDEPEND}"
-
-DEPEND=">=virtual/jdk-1.4
- ${CDEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-image-utils-without-jimi.patch"
-)
-
-S="${WORKDIR}/${PN}-$(ver_cut 1-2)"
-
-src_prepare() {
- default
-
- cp "${FILESDIR}/${P}-build.xml" build.xml || die
- cp "${FILESDIR}/${P}-common.xml" common.xml || die
-
- cd lib || die
-
- java-pkg_jar-from xalan,laf-plugin
-}
-
-src_install() {
- java-pkg_dojar build/${PN}.jar
-
- # laf-plugin.jar is referenced in manifest's Class-Path
- # doesn't work without it due to class loader trickery
- # upstream solved this by absorbing laf-plugin in own jar...
- java-pkg_dojar lib/laf-plugin.jar
-
- use examples && java-pkg_doexamples src/examples
- use source && java-pkg_dosrc src/com src/*.java
-
- dodoc CHANGES README
-}
diff --git a/dev-lang/tcl/Manifest b/dev-lang/tcl/Manifest
deleted file mode 100644
index 10e9ca415..000000000
--- a/dev-lang/tcl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tcl8.5.17-src.tar.gz 4546317 BLAKE2B 27031dd3bd5790d03692e77edf91eb7fae8a40d8d193d8c8ce4e79b21f90e683bfc9d5b71764760223987fb163be844e6096d0aea1058b8ce255731d97e2a0ea SHA512 ad5ddb4cd6378fd6bbea8cd85ceb1cf90392b2e8c49fbfb3e4b35c81d3ae3e3f087697c41fcba8c8e06de1d9e7539397e26d58b864dc01ba65abe4ba4efa9568
diff --git a/dev-lang/tcl/files/tcl-8.5.13-multilib.patch b/dev-lang/tcl/files/tcl-8.5.13-multilib.patch
deleted file mode 100644
index 82f5fa031..000000000
--- a/dev-lang/tcl/files/tcl-8.5.13-multilib.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -645,7 +645,7 @@
-
- eval "TCL_LIB_FILE=${TCL_LIB_FILE}"
-
--TCL_LIBRARY='$(prefix)/lib/tcl$(VERSION)'
-+TCL_LIBRARY='$(libdir)/tcl$(VERSION)'
- PRIVATE_INCLUDE_DIR='$(includedir)'
- HTML_DIR='$(DISTDIR)/html'
-
diff --git a/dev-lang/tcl/files/tcl-8.5.14-conf.patch b/dev-lang/tcl/files/tcl-8.5.14-conf.patch
deleted file mode 100644
index ffd9f6fea..000000000
--- a/dev-lang/tcl/files/tcl-8.5.14-conf.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/tcl.m4
-+++ b/tcl.m4
-@@ -1427,7 +1427,7 @@ dnl AC_CHECK_TOOL(AR, ar)
- # get rid of the warnings.
- #CFLAGS_OPTIMIZE="${CFLAGS_OPTIMIZE} -D__NO_STRING_INLINES -D__NO_MATH_INLINES"
-
-- SHLIB_LD='${CC} -shared ${CFLAGS} ${LDFLAGS}'
-+ SHLIB_LD='${CC} -shared ${CFLAGS} ${LDFLAGS} -fPIC -Wl,-soname,${@}'
- DL_OBJS="tclLoadDl.o"
- DL_LIBS="-ldl"
- LDFLAGS="$LDFLAGS -Wl,--export-dynamic"
diff --git a/dev-lang/tcl/files/tcl-8.6.8-libieee.patch b/dev-lang/tcl/files/tcl-8.6.8-libieee.patch
deleted file mode 100644
index e7c1f5aae..000000000
--- a/dev-lang/tcl/files/tcl-8.6.8-libieee.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- a/tcl.m4
-+++ b/tcl.m4
-@@ -2470,12 +2470,9 @@
- #--------------------------------------------------------------------
- # On a few very rare systems, all of the libm.a stuff is
- # already in libc.a. Set compiler flags accordingly.
-- # Also, Linux requires the "ieee" library for math to work
-- # right (and it must appear before "-lm").
- #--------------------------------------------------------------------
-
- AC_CHECK_FUNC(sin, MATH_LIBS="", MATH_LIBS="-lm")
-- AC_CHECK_LIB(ieee, main, [MATH_LIBS="-lieee $MATH_LIBS"])
-
- #--------------------------------------------------------------------
- # Interactive UNIX requires -linet instead of -lsocket, plus it
diff --git a/dev-lang/tcl/tcl-8.5.17-r1.ebuild b/dev-lang/tcl/tcl-8.5.17-r1.ebuild
deleted file mode 100644
index 9b2e9fa61..000000000
--- a/dev-lang/tcl/tcl-8.5.17-r1.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools flag-o-matic multilib toolchain-funcs multilib-minimal
-
-MY_P="${PN}${PV/_beta/b}"
-
-DESCRIPTION="Tool Command Language"
-HOMEPAGE="http://www.tcl.tk/"
-SRC_URI="mirror://sourceforge/tcl/${MY_P}-src.tar.gz"
-
-LICENSE="tcltk"
-SLOT="0/8.5"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x86-solaris"
-IUSE="debug threads"
-
-RDEPEND=">=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-SPARENT="${WORKDIR}/${MY_P}"
-S="${SPARENT}"/unix
-
-PATCHES=(
- "${FILESDIR}"/${PN}-8.5.13-multilib.patch
- "${FILESDIR}"/${PN}-8.5.14-conf.patch
- "${FILESDIR}"/${PN}-8.6.8-libieee.patch
-)
-
-src_prepare() {
- default
-
- # workaround stack check issues, bug #280934
- use hppa && append-cflags "-DTCL_NO_STACK_CHECK=1"
-
- tc-export CC
-
- sed \
- -e '/chmod/s:555:755:g' \
- -i Makefile.in || die
-
- eautoconf
- multilib_copy_sources
-}
-
-multilib_src_configure() {
- # We went ahead and deleted the whole compat/ subdir which means
- # the configure tests to detect broken versions need to pass (else
- # we'll fail to build). This comes up when cross-compiling, but
- # might as well get a minor configure speed up normally.
- export ac_cv_func_memcmp_working="yes"
- export tcl_cv_str{str,toul,tod}_unbroken="ok"
- export tcl_cv_strtod_buggy="no"
-
- econf \
- $(use_enable threads) \
- $(use_enable debug symbols)
-}
-
-multilib_src_install() {
- #short version number
- local v1=$(ver_cut 1-2)
- local mylibdir=$(get_libdir)
-
- S= default
-
- # fix the tclConfig.sh to eliminate refs to the build directory
- # and drop unnecessary -L inclusion to default system libdir
-
- sed \
- -e "/^TCL_BUILD_LIB_SPEC=/s:-L$(pwd) *::g" \
- -e "/^TCL_LIB_SPEC=/s:-L${EPREFIX}/usr/${mylibdir} *::g" \
- -e "/^TCL_SRC_DIR=/s:${SPARENT}:${EPREFIX}/usr/${mylibdir}/tcl${v1}/include:g" \
- -e "/^TCL_BUILD_STUB_LIB_SPEC=/s:-L$(pwd) *::g" \
- -e "/^TCL_STUB_LIB_SPEC=/s:-L${EPREFIX}/usr/${mylibdir} *::g" \
- -e "/^TCL_BUILD_STUB_LIB_PATH=/s:$(pwd):${EPREFIX}/usr/${mylibdir}:g" \
- -e "/^TCL_LIB_FILE=/s:'libtcl${v1}..TCL_DBGX..so':\"libtcl${v1}\$\{TCL_DBGX\}.so\":g" \
- -i "${ED}"/usr/${mylibdir}/tclConfig.sh || die
- if use prefix && [[ ${CHOST} != *-darwin* && ${CHOST} != *-mint* ]] ; then
- sed \
- -e "/^TCL_CC_SEARCH_FLAGS=/s|'$|:${EPREFIX}/usr/${mylibdir}'|g" \
- -e "/^TCL_LD_SEARCH_FLAGS=/s|'$|:${EPREFIX}/usr/${mylibdir}'|" \
- -i "${ED}"/usr/${mylibdir}/tclConfig.sh || die
- fi
-
- # install private headers
- insinto /usr/${mylibdir}/tcl${v1}/include/unix
- doins *.h
- insinto /usr/${mylibdir}/tcl${v1}/include/generic
- doins "${SPARENT}"/generic/*.h
- rm -f "${ED}"/usr/${mylibdir}/tcl${v1}/include/generic/{tcl,tclDecls,tclPlatDecls}.h || die
-
- # install symlink for libraries
- dosym libtcl${v1}$(get_libname) /usr/${mylibdir}/libtcl$(get_libname)
- dosym libtclstub${v1}.a /usr/${mylibdir}/libtclstub.a
-
- if multilib_is_native_abi; then
- dosym tclsh${v1} /usr/bin/tclsh
- dodoc "${SPARENT}"/{ChangeLog*,README,changes}
- fi
-}
-
-pkg_postinst() {
- for version in ${REPLACING_VERSIONS}; do
- if ! ver_test 8.5 -ge ${version}; then
- echo
- ewarn "You're upgrading from <${P}, you must recompile the other"
- ewarn "packages on your system that link with tcl after the upgrade"
- ewarn "completes. To perform this action, please run revdep-rebuild"
- ewarn "in package app-portage/gentoolkit."
- ewarn "If you have dev-lang/tk and dev-tcltk/tclx installed you should"
- ewarn "upgrade them before this recompilation, too,"
- echo
- fi
- done
-}
diff --git a/dev-lang/terra/Manifest b/dev-lang/terra/Manifest
deleted file mode 100644
index 79c86caf5..000000000
--- a/dev-lang/terra/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST terra-1.0.0_beta2.tar.gz 1418736 BLAKE2B 6910e56afd863e2449902b17fa7b368458d75fce8c5f18b1424ed69e3fe563fdb910f682b8e0880d75d1ff2c6c49c54f063c2e226f01d8eb073693fd62f66c4d SHA512 0084cdd9d018f9b175a756587f122650c16af16195eef1271a5748f9bef6fcdcec4046bf9f753977eae5474212a7ba5abb62b2a19d6123170f90015a17df6a3c
diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml
deleted file mode 100644
index 5f4b89aee..000000000
--- a/dev-lang/terra/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>ottxor@gentoo.org</email>
- <name>Christoph Junghans</name>
- </maintainer>
- <upstream>
- <remote-id type="github">zdevito/terra</remote-id>
- </upstream>
- <use>
- <flag name="cuda">Enable CUDA</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-lang/terra/terra-1.0.0_beta2.ebuild b/dev-lang/terra/terra-1.0.0_beta2.ebuild
deleted file mode 100644
index d9b087cf9..000000000
--- a/dev-lang/terra/terra-1.0.0_beta2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV="${PV//_/-}"
-
-LUA_COMPAT=( lua5-{1..4} )
-
-inherit cmake llvm lua-single
-
-DESCRIPTION="A low-level counterpart to Lua"
-HOMEPAGE="http://terralang.org/"
-SRC_URI="https://github.com/zdevito/terra/archive/release-${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="cuda"
-
-REQUIRED_USE="${LUA_REQUIRED_USE}"
-
-DEPEND="${LUA_DEPS}
- cuda? ( dev-util/nvidia-cuda-toolkit )"
-RDEPEND="${DEPEND}"
-BDEPEND="
- sys-devel/clang:*
- sys-devel/llvm:=
- dev-lang/luajit:=
-"
-
-S="${WORKDIR}/${PN}-release-${MY_PV}"
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_PREFIX_PATH="$(get_llvm_prefix)"
- -DTERRA_ENABLE_CUDA="$(usex cuda ON OFF)"
- -DTERRA_STATIC_LINK_LLVM=OFF
- -DTERRA_SLIB_INCLUDE_LLVM=OFF
- -DTERRA_STATIC_LINK_LUAJIT=OFF
- -DTERRA_SLIB_INCLUDE_LUAJIT=OFF
- )
-
- cmake_src_configure
-}
diff --git a/dev-lang/tk/Manifest b/dev-lang/tk/Manifest
deleted file mode 100644
index 68d0a397e..000000000
--- a/dev-lang/tk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tk8.5.17-src.tar.gz 4095985 BLAKE2B 4cbb140c30ca717ee499b9ad9e1a3df27a470a78613edbaec425c39afaa41d59276bbe487933a4e77a9722fcafa9113b203cf5c828660bdeb38f667c3263c3cd SHA512 ddadc738c2567e35d1257b59212c8a0eb70a1bf041d986bc6df3b841b51d934d79a0ef389c928223a64516a92cae3357b2c789edca9c8a626ff4c1cf320c4f4f
diff --git a/dev-lang/tk/files/tk-8.4.15-aqua.patch b/dev-lang/tk/files/tk-8.4.15-aqua.patch
deleted file mode 100644
index 9e6f59d12..000000000
--- a/dev-lang/tk/files/tk-8.4.15-aqua.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- unix/Makefile.in
-+++ unix/Makefile.in
-@@ -468,7 +468,7 @@
-
- AQUA_HDRS = $(MAC_OSX_DIR)/tkMacOSX.h $(GENERIC_DIR)/tkIntXlibDecls.h
-
--AQUA_XLIB_HDRS = $(XLIB_DIR)/X11/*.h $(XLIB_DIR)/xbytes.h
-+AQUA_XLIB_HDRS =
-
- AQUA_PRIVATE_HDRS = $(MAC_OSX_DIR)/tkMacOSXPort.h $(MAC_OSX_DIR)/tkMacOSXInt.h
-
diff --git a/dev-lang/tk/files/tk-8.5.11-fedora-xft.patch b/dev-lang/tk/files/tk-8.5.11-fedora-xft.patch
deleted file mode 100644
index 08bfbf759..000000000
--- a/dev-lang/tk/files/tk-8.5.11-fedora-xft.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- unix/configure.in.old 2010-09-02 20:12:14.000000000 +0200
-+++ unix/configure.in 2011-02-17 13:32:22.719116636 +0100
-@@ -530,8 +530,8 @@
- XFT_LIBS=`xft-config --libs 2>/dev/null` || found_xft="no"
- if test "$found_xft" = "no" ; then
- found_xft=yes
-- XFT_CFLAGS=`pkg-config --cflags xft 2>/dev/null` || found_xft="no"
-- XFT_LIBS=`pkg-config --libs xft 2>/dev/null` || found_xft="no"
-+ XFT_CFLAGS=`pkg-config --cflags xft freetype2 2>/dev/null` || found_xft="no"
-+ XFT_LIBS=`pkg-config --libs xft freetype2 2>/dev/null` || found_xft="no"
- fi
- AC_MSG_RESULT([$found_xft])
- dnl make sure that compiling against Xft header file doesn't bomb
diff --git a/dev-lang/tk/files/tk-8.5.13-multilib.patch b/dev-lang/tk/files/tk-8.5.13-multilib.patch
deleted file mode 100644
index 5ba9c19c9..000000000
--- a/dev-lang/tk/files/tk-8.5.13-multilib.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur unix/configure.in unix/configure.in
---- unix/configure.in 2005-06-30 01:43:10.000000000 +0900
-+++ unix/configure.in 2005-07-02 23:22:16.000000000 +0900
-@@ -393,7 +393,7 @@
- TCL_STUB_FLAGS="-DUSE_TCL_STUBS"
- fi
-
--TK_LIBRARY='$(prefix)/lib/tk$(VERSION)'
-+TK_LIBRARY='$(libdir)/tk$(VERSION)'
- PRIVATE_INCLUDE_DIR='$(includedir)'
- HTML_DIR='$(DISTDIR)/html'
- TK_PKG_DIR='tk$(VERSION)$(TK_DBGX)'
diff --git a/dev-lang/tk/files/tk-8.5.14-conf.patch b/dev-lang/tk/files/tk-8.5.14-conf.patch
deleted file mode 100644
index 5f8274f9e..000000000
--- a/dev-lang/tk/files/tk-8.5.14-conf.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- unix/tcl.m4 | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/unix/tcl.m4 b/unix/tcl.m4
-index 3974753..9c36eb5 100644
---- unix/tcl.m4
-+++ unix/tcl.m4
-@@ -1420,7 +1420,7 @@ AC_DEFUN([SC_CONFIG_CFLAGS], [
- # get rid of the warnings.
- #CFLAGS_OPTIMIZE="${CFLAGS_OPTIMIZE} -D__NO_STRING_INLINES -D__NO_MATH_INLINES"
-
-- SHLIB_LD='${CC} -shared ${CFLAGS} ${LDFLAGS}'
-+ SHLIB_LD='${CC} -shared ${CFLAGS} ${LDFLAGS} -Wl,-soname,${@}'
- DL_OBJS="tclLoadDl.o"
- DL_LIBS="-ldl"
- LDFLAGS="$LDFLAGS -Wl,--export-dynamic"
diff --git a/dev-lang/tk/files/tk-8.6.8-libieee.patch b/dev-lang/tk/files/tk-8.6.8-libieee.patch
deleted file mode 100644
index 6bc8fa11a..000000000
--- a/dev-lang/tk/files/tk-8.6.8-libieee.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- unix/tcl.m4
-+++ unix/tcl.m4
-@@ -2470,12 +2470,9 @@
- #--------------------------------------------------------------------
- # On a few very rare systems, all of the libm.a stuff is
- # already in libc.a. Set compiler flags accordingly.
-- # Also, Linux requires the "ieee" library for math to work
-- # right (and it must appear before "-lm").
- #--------------------------------------------------------------------
-
- AC_CHECK_FUNC(sin, MATH_LIBS="", MATH_LIBS="-lm")
-- AC_CHECK_LIB(ieee, main, [MATH_LIBS="-lieee $MATH_LIBS"])
-
- #--------------------------------------------------------------------
- # Interactive UNIX requires -linet instead of -lsocket, plus it
diff --git a/dev-lang/tk/metadata.xml b/dev-lang/tk/metadata.xml
deleted file mode 100644
index 354c72665..000000000
--- a/dev-lang/tk/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">tcl</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-lang/tk/tk-8.5.17-r1.ebuild b/dev-lang/tk/tk-8.5.17-r1.ebuild
deleted file mode 100644
index 8f7e78d7f..000000000
--- a/dev-lang/tk/tk-8.5.17-r1.ebuild
+++ /dev/null
@@ -1,128 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools multilib prefix toolchain-funcs virtualx
-
-MY_P="${PN}${PV/_beta/b}"
-
-DESCRIPTION="Tk Widget Set"
-HOMEPAGE="http://www.tcl.tk/"
-SRC_URI="mirror://sourceforge/tcl/${MY_P}-src.tar.gz"
-
-LICENSE="tcltk"
-SLOT="0/8.5"
-KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris"
-IUSE="debug threads truetype aqua xscreensaver"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- !aqua? (
- media-libs/fontconfig
- media-libs/freetype:2
- x11-libs/libX11
- x11-libs/libXt
- truetype? ( x11-libs/libXft )
- xscreensaver? ( x11-libs/libXScrnSaver )
- )
- ~dev-lang/tcl-${PV}:0="
-DEPEND="${RDEPEND}
- !aqua? ( x11-base/xorg-proto )"
-
-SPARENT="${WORKDIR}/${MY_P}"
-S="${SPARENT}"/unix
-
-src_prepare() {
- eapply \
- "${FILESDIR}"/${PN}-8.5.11-fedora-xft.patch \
- "${FILESDIR}"/${PN}-8.5.13-multilib.patch
-
- eapply "${FILESDIR}"/${PN}-8.4.15-aqua.patch
- eprefixify Makefile.in
-
- # Bug 125971
- eapply "${FILESDIR}"/${PN}-8.5.14-conf.patch
-
- # Bug 648570
- eapply "${FILESDIR}"/${PN}-8.6.8-libieee.patch
-
- # Make sure we use the right pkg-config, and link against fontconfig
- # (since the code base uses Fc* functions).
- sed \
- -e 's/FT_New_Face/XftFontOpen/g' \
- -e "s:\<pkg-config\>:$(tc-getPKG_CONFIG):" \
- -e 's:xft freetype2:xft freetype2 fontconfig:' \
- -i configure.in || die
- rm -f configure || die
-
- sed \
- -e '/chmod/s:555:755:g' \
- -i Makefile.in || die
-
- tc-export CC
-
- default
- eautoconf
-}
-
-src_configure() {
- local mylibdir=$(get_libdir)
-
- econf \
- --with-tcl="${EPREFIX}/usr/${mylibdir}" \
- $(use_enable threads) \
- $(use_enable aqua) \
- $(use_enable truetype xft) \
- $(use_enable xscreensaver xss) \
- $(use_enable debug symbols)
-}
-
-src_test() {
- virtx emake test
-}
-
-src_install() {
- #short version number
- local v1=$(ver_cut 1-2)
- local mylibdir=$(get_libdir)
-
- S= default
-
- # normalize $S path, bug #280766 (pkgcore)
- local nS="$(cd "${S}"; pwd)"
-
- # fix the tkConfig.sh to eliminate refs to the build directory
- # and drop unnecessary -L inclusion to default system libdir
-
- sed \
- -e "/^TK_BUILD_LIB_SPEC=/s:-L${SPARENT}.*unix *::g" \
- -e "/^TK_LIB_SPEC=/s:-L${EPREFIX}/usr/${mylibdir} *::g" \
- -e "/^TK_SRC_DIR=/s:${SPARENT}:${EPREFIX}/usr/${mylibdir}/tk${v1}/include:g" \
- -e "/^TK_BUILD_STUB_LIB_SPEC=/s:-L${SPARENT}.*unix *::g" \
- -e "/^TK_STUB_LIB_SPEC=/s:-L${EPREFIX}/usr/${mylibdir} *::g" \
- -e "/^TK_BUILD_STUB_LIB_PATH=/s:${SPARENT}.*unix:${EPREFIX}/usr/${mylibdir}:g" \
- -e "/^TK_LIB_FILE=/s:'libtk${v1}..TK_DBGX..so':\"libk${v1}\$\{TK_DBGX\}.so\":g" \
- -i "${ED}"/usr/${mylibdir}/tkConfig.sh || die
- if use prefix && [[ ${CHOST} != *-darwin* && ${CHOST} != *-mint* ]] ; then
- sed \
- -e "/^TK_CC_SEARCH_FLAGS=/s|'$|:${EPREFIX}/usr/${mylibdir}'|g" \
- -e "/^TK_LD_SEARCH_FLAGS=/s|'$|:${EPREFIX}/usr/${mylibdir}'|" \
- -i "${ED}"/usr/${mylibdir}/tkConfig.sh || die
- fi
-
- # install private headers
- insinto /usr/${mylibdir}/tk${v1}/include/unix
- doins "${S}"/*.h
- insinto /usr/${mylibdir}/tk${v1}/include/generic
- doins "${SPARENT}"/generic/*.h
- rm -f "${ED}"/usr/${mylibdir}/tk${v1}/include/generic/{tk,tkDecls,tkPlatDecls}.h || die
-
- # install symlink for libraries
- dosym libtk${v1}$(get_libname) /usr/${mylibdir}/libtk$(get_libname)
- dosym libtkstub${v1}.a /usr/${mylibdir}/libtkstub.a
-
- dosym wish${v1} /usr/bin/wish
-
- dodoc "${SPARENT}"/{ChangeLog*,README,changes}
-}
diff --git a/dev-libs/boost/Manifest b/dev-libs/boost/Manifest
deleted file mode 100644
index 34653ed7e..000000000
--- a/dev-libs/boost/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST boost_1_72_0.tar.bz2 106907358 BLAKE2B ab270a0e3cb24da687d86785e2d2e6d7731b4dbc07bd839eadb642dfa5a428ad584acb1f3529661a8de9a986008ff3427491041059ea2b742348d02e00761cd8 SHA512 63bbd1743e7c904b2e69fdc2eafd1c2a8a30fd70d960dcd366059d0100f000cb605d56cbd9397bb18421631f1c9552a772c434d0f0caddbe56302273f51fd1f6
diff --git a/dev-libs/boost/boost-1.72.0-r2.ebuild b/dev-libs/boost/boost-1.72.0-r2.ebuild
deleted file mode 100644
index dffb3e5f9..000000000
--- a/dev-libs/boost/boost-1.72.0-r2.ebuild
+++ /dev/null
@@ -1,356 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit flag-o-matic multiprocessing python-r1 toolchain-funcs multilib-minimal
-
-MY_PV="$(ver_rs 1- _)"
-MAJOR_V="$(ver_cut 1-2)"
-
-DESCRIPTION="Boost Libraries for C++"
-HOMEPAGE="https://www.boost.org/"
-SRC_URI="https://dl.bintray.com/boostorg/release/${PV}/source/boost_${MY_PV}.tar.bz2"
-
-LICENSE="Boost-1.0"
-SLOT="0/${PV}" # ${PV} instead ${MAJOR_V} due to bug 486122
-KEYWORDS="~amd64"
-IUSE="bzip2 context debug doc icu lzma +nls mpi numpy python static-libs +threads tools zlib zstd"
-REQUIRED_USE="
- mpi? ( threads )
- python? ( ${PYTHON_REQUIRED_USE} )"
-
-# the tests will never fail because these are not intended as sanity
-# tests at all. They are more a way for upstream to check their own code
-# on new compilers. Since they would either be completely unreliable
-# (failing for no good reason) or completely useless (never failing)
-# there is no point in having them in the ebuild to begin with.
-RESTRICT="test"
-
-RDEPEND="
- bzip2? ( app-arch/bzip2:=[${MULTILIB_USEDEP}] )
- icu? ( >=dev-libs/icu-3.6:=[${MULTILIB_USEDEP}] )
- !icu? ( virtual/libiconv[${MULTILIB_USEDEP}] )
- lzma? ( app-arch/xz-utils:=[${MULTILIB_USEDEP}] )
- mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP},cxx,threads] )
- python? (
- ${PYTHON_DEPS}
- numpy? ( $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]' -3) )
- )
- zlib? ( sys-libs/zlib:=[${MULTILIB_USEDEP}] )
- zstd? ( app-arch/zstd:=[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}"
-BDEPEND="=dev-util/boost-build-${MAJOR_V}*"
-
-S="${WORKDIR}/${PN}_${MY_PV}"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-1.71.0-disable_icu_rpath.patch
- "${FILESDIR}"/${PN}-1.71.0-context-x32.patch
- "${FILESDIR}"/${PN}-1.71.0-build-auto_index-tool.patch
- # Bug 703294, incomplete Boost.Serialization refactoring
- "${FILESDIR}"/${PN}-1.72.0-missing-serialization-split_member-include.patch
- # Bug 703036, per python-impl Boost.MPI
- "${FILESDIR}"/${PN}-1.72.0-boost-mpi-python.patch
- # Bug 704128, missing include on Boost.Ranges
- "${FILESDIR}"/${PN}-1.72.0-revert-cease-dependence-on-range.patch
-)
-
-python_bindings_needed() {
- multilib_is_native_abi && use python
-}
-
-tools_needed() {
- multilib_is_native_abi && use tools
-}
-
-create_user-config.jam() {
- local user_config_jam="${BUILD_DIR}"/user-config.jam
- if [[ -s ${user_config_jam} ]]; then
- einfo "${user_config_jam} already exists, skipping configuration"
- return
- else
- einfo "Creating configuration in ${user_config_jam}"
- fi
-
- local compiler compiler_version compiler_executable="$(tc-getCXX)"
- if [[ ${CHOST} == *-darwin* ]]; then
- compiler="darwin"
- compiler_version="$(gcc-fullversion)"
- else
- compiler="gcc"
- compiler_version="$(gcc-version)"
- fi
-
- if use mpi; then
- local mpi_configuration="using mpi ;"
- fi
-
- cat > "${user_config_jam}" <<- __EOF__ || die
- using ${compiler} : ${compiler_version} : ${compiler_executable} : <cflags>"${CFLAGS}" <cxxflags>"${CXXFLAGS}" <linkflags>"${LDFLAGS}" ;
- ${mpi_configuration}
- __EOF__
-
- if python_bindings_needed; then
- append_to_user_config() {
- local py_config
- if tc-is-cross-compiler; then
- py_config="using python : ${EPYTHON#python} : : ${ESYSROOT}/usr/include/${EPYTHON} : ${ESYSROOT}/usr/$(get_libdir) ;"
- else
- py_config="using python : ${EPYTHON#python} : ${PYTHON} : $(python_get_includedir) ;"
- fi
- echo "${py_config}" >> "${user_config_jam}" || die
- }
- python_foreach_impl append_to_user_config
- fi
-
- if python_bindings_needed && use numpy; then
- einfo "Enabling support for NumPy extensions in Boost.Python"
- else
- einfo "Disabling support for NumPy extensions in Boost.Python"
-
- # Boost.Build does not allow for disabling of numpy
- # extensions, thereby leading to automagic numpy
- # https://github.com/boostorg/python/issues/111#issuecomment-280447482
- sed \
- -e 's/\[ unless \[ python\.numpy \] : <build>no \]/<build>no/g' \
- -i "${BUILD_DIR}"/libs/python/build/Jamfile || die
- fi
-}
-
-pkg_setup() {
- # Bail out on unsupported build configuration, bug #456792
- if [[ -f "${EROOT}"/etc/site-config.jam ]]; then
- if ! grep -q 'gentoo\(debug\|release\)' "${EROOT}"/etc/site-config.jam; then
- eerror "You are using custom ${EROOT}/etc/site-config.jam without defined gentoorelease/gentoodebug targets."
- eerror "Boost can not be built in such configuration."
- eerror "Please, either remove this file or add targets from ${EROOT}/usr/share/boost-build/site-config.jam to it."
- die "Unsupported target in ${EROOT}/etc/site-config.jam"
- fi
- fi
-}
-
-src_prepare() {
- default
- multilib_copy_sources
-}
-
-ejam() {
- create_user-config.jam
-
- local b2_opts=( "--user-config=${BUILD_DIR}/user-config.jam" )
- if python_bindings_needed; then
- append_to_b2_opts() {
- b2_opts+=( python="${EPYTHON#python}" )
- }
- python_foreach_impl append_to_b2_opts
- else
- b2_opts+=( --without-python )
- fi
- b2_opts+=( "$@" )
-
- echo b2 "${b2_opts[@]}" >&2
- b2 "${b2_opts[@]}"
-}
-
-src_configure() {
- # Workaround for too many parallel processes requested, bug #506064
- [[ "$(makeopts_jobs)" -gt 64 ]] && MAKEOPTS="${MAKEOPTS} -j64"
-
- OPTIONS=(
- $(usex debug gentoodebug gentoorelease)
- "-j$(makeopts_jobs)"
- -q
- -d+2
- pch=off
- $(usex icu "-sICU_PATH=${ESYSROOT}/usr" '--disable-icu boost.locale.icu=off')
- $(usex mpi '' '--without-mpi')
- $(usex nls '' '--without-locale')
- $(usex context '' '--without-context --without-coroutine --without-fiber')
- $(usex threads '' '--without-thread')
- --without-stacktrace
- --boost-build="${BROOT}"/usr/share/boost-build
- --prefix="${ED}/usr"
- --layout=system
- # CMake has issues working with multiple python impls,
- # disable cmake config generation for the time being
- # https://github.com/boostorg/python/issues/262#issuecomment-483069294
- --no-cmake-config
- # building with threading=single is currently not possible
- # https://svn.boost.org/trac/boost/ticket/7105
- threading=multi
- link=$(usex static-libs shared,static shared)
- # this seems to be the only way to disable compression algorithms
- # https://www.boost.org/doc/libs/1_70_0/libs/iostreams/doc/installation.html#boost-build
- -sNO_BZIP2=$(usex bzip2 0 1)
- -sNO_LZMA=$(usex lzma 0 1)
- -sNO_ZLIB=$(usex zlib 0 1)
- -sNO_ZSTD=$(usex zstd 0 1)
- )
-
- if [[ ${CHOST} == *-darwin* ]]; then
- # We need to add the prefix, and in two cases this exceeds, so prepare
- # for the largest possible space allocation.
- append-ldflags -Wl,-headerpad_max_install_names
- fi
-
- # Use C++14 globally as of 1.62
- append-cxxflags -std=c++14
-}
-
-multilib_src_compile() {
- ejam "${OPTIONS[@]}" || die
-
- if tools_needed; then
- pushd tools >/dev/null || die
- ejam \
- "${OPTIONS[@]}" \
- || die "Building of Boost tools failed"
- popd >/dev/null || die
- fi
-}
-
-multilib_src_install_all() {
- if ! use numpy; then
- rm -r "${ED}"/usr/include/boost/python/numpy* || die
- fi
-
- if use python; then
- if use mpi; then
- move_mpi_py_into_sitedir() {
- local pyver="${EPYTHON#python}"
- python_moduleinto boost
- python_domodule "${ED}"/usr/$(get_libdir)/mpi${pyver/./}.so
- rm "${ED}"/usr/$(get_libdir)/mpi${pyver/./}* || die
- dosym mpi${pyver/./}.so $(python_get_sitedir)/boost/mpi.so
-
- # create a proper python package
- touch "${D}"/$(python_get_sitedir)/boost/__init__.py || die
- python_optimize
- }
- python_foreach_impl move_mpi_py_into_sitedir
- else
- rm -r "${ED}"/usr/include/boost/mpi/python* || die
- fi
- else
- rm -r "${ED}"/usr/include/boost/{python*,mpi/python*,parameter/aux_/python,parameter/python*} || die
- fi
-
- if ! use nls; then
- rm -r "${ED}"/usr/include/boost/locale || die
- fi
-
- if ! use context; then
- rm -r "${ED}"/usr/include/boost/context || die
- rm -r "${ED}"/usr/include/boost/coroutine{,2} || die
- rm "${ED}"/usr/include/boost/asio/spawn.hpp || die
- fi
-
- if use doc; then
- # find extraneous files that shouldn't be installed
- # as part of the documentation and remove them.
- find libs/*/* \( -iname 'test' -o -iname 'src' \) -exec rm -rf '{}' + || die
- find doc \( -name 'Jamfile.v2' -o -name 'build' -o -name '*.manifest' \) -exec rm -rf '{}' + || die
- find tools \( -name 'Jamfile.v2' -o -name 'src' -o -name '*.cpp' -o -name '*.hpp' \) -exec rm -rf '{}' + || die
-
- docinto html
- dodoc *.{htm,html,png,css}
- dodoc -r doc libs more tools
-
- # To avoid broken links
- dodoc LICENSE_1_0.txt
-
- dosym ../../../../include/boost /usr/share/doc/${PF}/html/boost
- fi
-}
-
-multilib_src_install() {
- ejam \
- "${OPTIONS[@]}" \
- --includedir="${ED}/usr/include" \
- --libdir="${ED}/usr/$(get_libdir)" \
- install || die "Installation of Boost libraries failed"
-
- pushd "${ED}/usr/$(get_libdir)" >/dev/null || die
-
- local ext=$(get_libname)
- if use threads; then
- local f
- for f in *${ext}; do
- dosym ${f} /usr/$(get_libdir)/${f/${ext}/-mt${ext}}
- done
- fi
-
- popd >/dev/null || die
-
- if tools_needed; then
- dobin dist/bin/*
-
- insinto /usr/share
- doins -r dist/share/boostbook
- fi
-
- # boost's build system truely sucks for not having a destdir. Because for
- # this reason we are forced to build with a prefix that includes the
- # DESTROOT, dynamic libraries on Darwin end messed up, referencing the
- # DESTROOT instread of the actual EPREFIX. There is no way out of here
- # but to do it the dirty way of manually setting the right install_names.
- if [[ ${CHOST} == *-darwin* ]]; then
- einfo "Working around completely broken build-system(tm)"
- local d
- for d in "${ED}"/usr/lib/*.dylib; do
- if [[ -f ${d} ]]; then
- # fix the "soname"
- ebegin " correcting install_name of ${d#${ED}}"
- install_name_tool -id "/${d#${D}}" "${d}"
- eend $?
- # fix references to other libs
- refs=$(otool -XL "${d}" | \
- sed -e '1d' -e 's/^\t//' | \
- grep "^libboost_" | \
- cut -f1 -d' ')
- local r
- for r in ${refs}; do
- ebegin " correcting reference to ${r}"
- install_name_tool -change \
- "${r}" \
- "${EPREFIX}/usr/lib/${r}" \
- "${d}"
- eend $?
- done
- fi
- done
- fi
-}
-
-pkg_preinst() {
- # Yai for having symlinks that are nigh-impossible to remove without
- # resorting to dirty hacks like these. Removes lingering symlinks
- # from the slotted versions.
- local symlink
- for symlink in "${EROOT}"/usr/include/boost "${EROOT}"/usr/share/boostbook; do
- if [[ -L ${symlink} ]]; then
- rm -f "${symlink}" || die
- fi
- done
-
- # some ancient installs still have boost cruft lying around
- # for unknown reasons, causing havoc for reverse dependencies
- # Bug: 607734
- rm -rf "${EROOT}"/usr/include/boost-1_[3-5]? || die
-}
-
-pkg_postinst() {
- elog "Boost.Regex is *extremely* ABI sensitive. If you get errors such as"
- elog
- elog " undefined reference to \`boost::re_detail_$(ver_cut 1)0$(ver_cut 2)00::cpp_regex_traits_implementation"
- elog " <char>::transform_primary[abi:cxx11](char const*, char const*) const'"
- elog
- elog "Then you need to recompile Boost and all its reverse dependencies"
- elog "using the same toolchain. In general, *every* change of the C++ toolchain"
- elog "requires a complete rebuild of the boost-dependent ecosystem."
- elog
- elog "See for instance https://bugs.gentoo.org/638138"
-}
diff --git a/dev-libs/boost/files/boost-1.71.0-build-auto_index-tool.patch b/dev-libs/boost/files/boost-1.71.0-build-auto_index-tool.patch
deleted file mode 100644
index ca793b9d0..000000000
--- a/dev-libs/boost/files/boost-1.71.0-build-auto_index-tool.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Build auto_index tool with USE="tools"
-See also: https://bugs.gentoo.org/529066
-
---- a/tools/Jamfile.v2
-+++ b/tools/Jamfile.v2
-@@ -18,6 +18,7 @@
- ;
-
- TOOLS =
-+ auto_index/build//auto_index
- bcp//bcp
- inspect/build//inspect
- quickbook//quickbook
diff --git a/dev-libs/boost/files/boost-1.71.0-context-x32.patch b/dev-libs/boost/files/boost-1.71.0-context-x32.patch
deleted file mode 100644
index 9ee3d545d..000000000
--- a/dev-libs/boost/files/boost-1.71.0-context-x32.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- a/libs/context/src/asm/jump_i386_sysv_elf_gas.S
-+++ b/libs/context/src/asm/jump_i386_sysv_elf_gas.S
-@@ -24,6 +24,10 @@
- * *
- ****************************************************************************************/
-
-+#ifdef __x86_64__
-+#include "jump_x86_64_sysv_elf_gas.S"
-+#else
-+
- .file "jump_i386_sysv_elf_gas.S"
- .text
- .globl jump_fcontext
-@@ -81,3 +85,5 @@
-
- /* Mark that we don't need executable stack. */
- .section .note.GNU-stack,"",%progbits
-+
-+#endif
---- a/libs/context/src/asm/make_i386_sysv_elf_gas.S
-+++ b/libs/context/src/asm/make_i386_sysv_elf_gas.S
-@@ -24,6 +24,10 @@
- * *
- ****************************************************************************************/
-
-+#ifdef __x86_64__
-+#include "make_x86_64_sysv_elf_gas.S"
-+#else
-+
- .file "make_i386_sysv_elf_gas.S"
- .text
- .globl make_fcontext
-@@ -105,3 +109,5 @@
-
- /* Mark that we don't need executable stack. */
- .section .note.GNU-stack,"",%progbits
-+
-+#endif
diff --git a/dev-libs/boost/files/boost-1.71.0-disable_icu_rpath.patch b/dev-libs/boost/files/boost-1.71.0-disable_icu_rpath.patch
deleted file mode 100644
index 32faf8d0e..000000000
--- a/dev-libs/boost/files/boost-1.71.0-disable_icu_rpath.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- a/libs/locale/build/Jamfile.v2
-+++ b/libs/locale/build/Jamfile.v2
-@@ -65,8 +65,8 @@
-
- if $(ICU_LINK)
- {
-- ICU_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <dll-path>$(ICU_PATH)/bin <runtime-link>shared ;
-- ICU64_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <dll-path>$(ICU_PATH)/bin64 <runtime-link>shared ;
-+ ICU_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <runtime-link>shared ;
-+ ICU64_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <runtime-link>shared ;
- }
- else
- {
-@@ -124,7 +124,6 @@
- <library>icuuc/<link>shared/<runtime-link>shared
- <library>icudt/<link>shared/<runtime-link>shared
- <library>icuin/<link>shared/<runtime-link>shared
-- <dll-path>$(ICU_PATH)/bin
- <runtime-link>shared ;
-
-
-@@ -183,7 +182,6 @@
- <library>icuuc_64/<link>shared/<runtime-link>shared
- <library>icudt_64/<link>shared/<runtime-link>shared
- <library>icuin_64/<link>shared/<runtime-link>shared
-- <dll-path>$(ICU_PATH)/bin64
- <runtime-link>shared ;
-
-
diff --git a/dev-libs/boost/files/boost-1.72.0-boost-mpi-python.patch b/dev-libs/boost/files/boost-1.72.0-boost-mpi-python.patch
deleted file mode 100644
index 8fb164a62..000000000
--- a/dev-libs/boost/files/boost-1.72.0-boost-mpi-python.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-Tag Boost.MPI python impls properly to avoid name clash
-https://github.com/boostorg/mpi/issues/112
-
---- a/boostcpp.jam
-+++ b/boostcpp.jam
-@@ -185,7 +185,7 @@
-
- rule tag ( name : type ? : property-set )
- {
-- if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB
-+ if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB PYTHON_EXTENSION
- {
- local args = $(.format-name-args) ;
- if $(layout) = versioned
-@@ -223,7 +223,7 @@
- {
- local result = $(name) ;
-
-- if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB
-+ if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB PYTHON_EXTENSION
- {
- # Add Python version suffix
-
---- a/libs/mpi/build/Jamfile.v2
-+++ b/libs/mpi/build/Jamfile.v2
-@@ -58,13 +58,13 @@
- rule python-tag ( name : type ? : property-set )
- {
- local result = $(name) ;
-- if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB
-+ if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB PYTHON_EXTENSION
- {
- local version = [ $(property-set).get <python> ] ;
- local lib-suffix = [ version-suffix $(version) ] ;
- result = $(result)$(lib-suffix) ;
- }
-- if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB && $(PYTHON_ID)
-+ if $(type) in STATIC_LIB SHARED_LIB IMPORT_LIB PYTHON_EXTENSION && $(PYTHON_ID)
- {
- result = $(result)-$(PYTHON_ID) ;
- }
-@@ -168,6 +168,8 @@
- <link>shared:<define>BOOST_PYTHON_DYN_LINK=1
- <link>shared <runtime-link>shared
- <python-debugging>on:<define>BOOST_DEBUG_PYTHON
-+ -<tag>@$(BOOST_JAMROOT_MODULE)%$(BOOST_JAMROOT_MODULE).tag
-+ <tag>@$(__name__).python-tag
- ;
-
- mpi_python_libs = boost_mpi_python mpi ;
diff --git a/dev-libs/boost/files/boost-1.72.0-missing-serialization-split_member-include.patch b/dev-libs/boost/files/boost-1.72.0-missing-serialization-split_member-include.patch
deleted file mode 100644
index 0c9f72583..000000000
--- a/dev-libs/boost/files/boost-1.72.0-missing-serialization-split_member-include.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Missing #include, as the split_member.hpp include is not
-part of the nvp.hpp interface, and hence cannot be relied
-upon to be included transitively.
-
-Confirmed on
-https://github.com/boostorg/serialization/commit/c32a663c9963385430abc563f9c85f94d8da43a9#r36528430
-
-Bug: https://bugs.gentoo.org/703294
-
---- a/boost/bimap/detail/map_view_iterator.hpp
-+++ b/boost/bimap/detail/map_view_iterator.hpp
-@@ -22,6 +22,7 @@
-
- #ifndef BOOST_BIMAP_DISABLE_SERIALIZATION
- #include <boost/serialization/nvp.hpp>
-+ #include <boost/serialization/split_member.hpp>
- #endif // BOOST_BIMAP_DISABLE_SERIALIZATION
-
- #include <boost/iterator/detail/enable_if.hpp>
---- a/boost/bimap/detail/set_view_iterator.hpp
-+++ b/boost/bimap/detail/set_view_iterator.hpp
-@@ -22,6 +22,7 @@
-
- #ifndef BOOST_BIMAP_DISABLE_SERIALIZATION
- #include <boost/serialization/nvp.hpp>
-+ #include <boost/serialization/split_member.hpp>
- #endif // BOOST_BIMAP_DISABLE_SERIALIZATION
-
- #include <boost/iterator/detail/enable_if.hpp>
diff --git a/dev-libs/boost/files/boost-1.72.0-revert-cease-dependence-on-range.patch b/dev-libs/boost/files/boost-1.72.0-revert-cease-dependence-on-range.patch
deleted file mode 100644
index a6002074a..000000000
--- a/dev-libs/boost/files/boost-1.72.0-revert-cease-dependence-on-range.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-From 436e1dbe6fcd31523d261d18ad011392f1d6fbbc Mon Sep 17 00:00:00 2001
-From: Oliver Kowalke <oliver.kowalke@gmail.com>
-Date: Sun, 1 Dec 2019 20:40:28 +0100
-Subject: [PATCH] Revert "Cease dependence on Range"
-
-This reverts commit 0c556bb59241e682bbcd3f572815149c5a9b17db.
-
-see #44 (One test fails to compile after boostorg/coroutine submodule updated)
----
- boost/coroutine/asymmetric_coroutine.hpp | 12 +++---------
- 1 file changed, 3 insertions(+), 9 deletions(-)
-
-diff --git a/boost/coroutine/asymmetric_coroutine.hpp b/boost/coroutine/asymmetric_coroutine.hpp
-index ea96981..640896f 100644
---- a/boost/coroutine/asymmetric_coroutine.hpp
-+++ b/boost/coroutine/asymmetric_coroutine.hpp
-@@ -14,6 +14,7 @@
- #include <boost/assert.hpp>
- #include <boost/config.hpp>
- #include <boost/move/move.hpp>
-+#include <boost/range.hpp>
- #include <boost/throw_exception.hpp>
- #include <boost/utility/explicit_operator_bool.hpp>
-
-@@ -2354,19 +2355,12 @@ end( push_coroutine< R > & c)
-
- }
-
--// forward declaration of Boost.Range traits to break dependency on it
--template<typename C, typename Enabler>
--struct range_mutable_iterator;
--
--template<typename C, typename Enabler>
--struct range_const_iterator;
--
- template< typename Arg >
--struct range_mutable_iterator< coroutines::push_coroutine< Arg >, void >
-+struct range_mutable_iterator< coroutines::push_coroutine< Arg > >
- { typedef typename coroutines::push_coroutine< Arg >::iterator type; };
-
- template< typename R >
--struct range_mutable_iterator< coroutines::pull_coroutine< R >, void >
-+struct range_mutable_iterator< coroutines::pull_coroutine< R > >
- { typedef typename coroutines::pull_coroutine< R >::iterator type; };
-
- }
---
-2.24.1
-
diff --git a/dev-libs/boost/metadata.xml b/dev-libs/boost/metadata.xml
deleted file mode 100644
index 4f031402a..000000000
--- a/dev-libs/boost/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <description>Gentoo Science Project</description>
- </maintainer>
- <use>
- <flag name="context">Build and install the Boost.Context (and Boost.Fiber) library and all other Boost libraries that depend on it</flag>
- <flag name="debug">Build and install only the debug version of the Boost libraries. Only enable this flag if you're developing against boost.</flag>
- <flag name="doc">Install the full API documentation documentation. This takes over 200MB of extra disk space.</flag>
- <flag name="nls">Build libboost_locale. This library requires compatible C library interfaces, which might not be provided by uClibc or other embedded libraries.</flag>
- <flag name="numpy">Optionally build NumPy extensions when Boost.Python is enabled</flag>
- <flag name="threads">Build multi-thread-compatible libraries instead of single-threaded only.</flag>
- <flag name="tools">Build and install the boost tools (bcp, quickbook, inspect, wave)</flag>
- </use>
- <upstream>
- <remote-id type="cpe">cpe:/a:boost:boost</remote-id>
- <remote-id type="sourceforge">boost</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-libs/half/Manifest b/dev-libs/half/Manifest
deleted file mode 100644
index 13b3240b2..000000000
--- a/dev-libs/half/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST half-1.12.0.tar.gz 108704 BLAKE2B f0084f380b10485b30da3ff38c5e3098044cc21fe00b084b2b9dd69b9a5c06b2ddedae1cefa61197d74a14552da2e5648db3e3108044b5fc5f7975fa1e10c6d4 SHA512 152f9c08a4493662aed96ddce5d45ece94836727766a66060640f8f1f43ee6ecdb174e7e17421ba83f2a01ba836bb1cba9fe60d83aea517f4772b9038173274b
-DIST half-2.1.0.zip 47043 BLAKE2B 53d42c48b9a39bbbdace0442e876373cb8c76d395b7cdc04db2d7beca27c507a10c094ea705a94384fbaa0d2bdca6a82977738ec8bfbe47fc12f82c0ce74c6db SHA512 fc81a1b58862eb4570f18b5c82ca66eb9e6cf697801ef5686dc36950d149adaa8e6c2543a1b698e983e29253da5137e6b565a69991d4924598f0a10a8ba52142
diff --git a/dev-libs/half/half-1.12.0.ebuild b/dev-libs/half/half-1.12.0.ebuild
deleted file mode 100644
index 5df7cc0cc..000000000
--- a/dev-libs/half/half-1.12.0.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Half-precision floating-point library"
-HOMEPAGE="http://half.sourceforge.net/"
-SRC_URI="https://github.com/ROCmSoftwarePlatform/half/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-
-src_install() {
- cd include
- doheader half.hpp
-}
diff --git a/dev-libs/half/half-2.1.0.ebuild b/dev-libs/half/half-2.1.0.ebuild
deleted file mode 100644
index 023316aab..000000000
--- a/dev-libs/half/half-2.1.0.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Half-precision floating-point library"
-HOMEPAGE="http://half.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/project/half/half/${PV}/${P}.zip"
-S="${WORKDIR}"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-
-BDEPEND="app-arch/unzip"
-
-src_install() {
- cd include
- doheader half.hpp
-}
diff --git a/dev-libs/half/metadata.xml b/dev-libs/half/metadata.xml
deleted file mode 100644
index 336bdb639..000000000
--- a/dev-libs/half/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>gentoo@holzke.net</email>
- <name>Wilfried Holzke</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-libs/memkind/memkind-1.10.1.ebuild b/dev-libs/memkind/memkind-1.10.1.ebuild
index 7aa39135a..df6efc9e4 100644
--- a/dev-libs/memkind/memkind-1.10.1.ebuild
+++ b/dev-libs/memkind/memkind-1.10.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,7 +13,7 @@ if [[ ${PV} == 9999 ]]; then
EGIT_REPO_URI="https://github.com/memkind/memkind"
else
SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~arm64 ~ppc ~ppc64 ~x86"
+ KEYWORDS="~amd64 ~x86"
fi
LICENSE="BSD"
@@ -22,7 +22,7 @@ IUSE="+heap-manager openmp secure +tls"
RESTRICT="test"
DEPEND="
- sys-apps/ndctl
+ sys-block/ndctl
sys-process/numactl
"
RDEPEND="${DEPEND}"
diff --git a/dev-libs/memkind/memkind-1.11.0.ebuild b/dev-libs/memkind/memkind-1.11.0.ebuild
index 047d3b9cd..df6efc9e4 100644
--- a/dev-libs/memkind/memkind-1.11.0.ebuild
+++ b/dev-libs/memkind/memkind-1.11.0.ebuild
@@ -13,7 +13,7 @@ if [[ ${PV} == 9999 ]]; then
EGIT_REPO_URI="https://github.com/memkind/memkind"
else
SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~arm64 ~ppc ~ppc64 ~x86"
+ KEYWORDS="~amd64 ~x86"
fi
LICENSE="BSD"
@@ -22,7 +22,7 @@ IUSE="+heap-manager openmp secure +tls"
RESTRICT="test"
DEPEND="
- sys-apps/ndctl
+ sys-block/ndctl
sys-process/numactl
"
RDEPEND="${DEPEND}"
diff --git a/dev-libs/memkind/memkind-9999.ebuild b/dev-libs/memkind/memkind-9999.ebuild
index 7aa39135a..df6efc9e4 100644
--- a/dev-libs/memkind/memkind-9999.ebuild
+++ b/dev-libs/memkind/memkind-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,7 +13,7 @@ if [[ ${PV} == 9999 ]]; then
EGIT_REPO_URI="https://github.com/memkind/memkind"
else
SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~arm64 ~ppc ~ppc64 ~x86"
+ KEYWORDS="~amd64 ~x86"
fi
LICENSE="BSD"
@@ -22,7 +22,7 @@ IUSE="+heap-manager openmp secure +tls"
RESTRICT="test"
DEPEND="
- sys-apps/ndctl
+ sys-block/ndctl
sys-process/numactl
"
RDEPEND="${DEPEND}"
diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest
index 11e08c79f..0a6859644 100644
--- a/dev-libs/optix/Manifest
+++ b/dev-libs/optix/Manifest
@@ -1,4 +1 @@
-DIST NVIDIA-OptiX-SDK-6.0.0-linux64-25650775.sh 642319364 BLAKE2B 5dc6e23d606ca9f947aff046d20592729e562c66c475d47aa0cda8d3e7361cabbe102b5b0e125744d27e25321d4ac8486a55bc145c54c96c719de6e821744ba9 SHA512 33fbb312c47174a9ddb26bd4b1a1e5089b70eaebdecd80561c91c1926fba2fb8c94ec39b4c2dc8f0ccbb5e27bbd38ad8fb08df1d605ed1ec5b3fd34ecca908b7
-DIST NVIDIA-OptiX-SDK-7.0.0-linux64.sh 28930132 BLAKE2B ae09bc862ccd39c25d5cc103d97b5587e21638079905e5811528b3d59deb7fd546034f24f73696c212274c0613f5b1dca7508bff696f5fec535dda7351166d7e SHA512 349baf367af7890afac87a879c8f7360cc9c93e984cf234216062af0a3cedce8fc6f3fd74240897d4b3854622ce1976a78433cbeadf6fa89c8e84d24e26eef89
-DIST NVIDIA-OptiX-SDK-7.1.0-linux64-x86_64.sh 45564234 BLAKE2B 374bdbe5045ff36b71da8200ad29189cc3afba9783a38a74515caafeb90176eec5bf7a7d5e2045e47c399aa226a61fd12e6e7dd6c034b8a0f260a5850f775e47 SHA512 808a45e2007d8081de21fe15cad4577ba9fe10fc3612486b1230e03b7f17de91902dc773d1f3fef2b89398f230448d9522a03e19d4e6fa12aa4ffd78f1a4f9dc
-DIST NVIDIA-OptiX-SDK-7.2.0-linux64-x86_64.sh 44573802 BLAKE2B 546f2f02336d7487e2aab3f348290aaf9bdac153a3fe161b48ad8a897f5d14f6126e06d3b8b4c301f8a6df5735d951dcf544795b2668bc42116bd909e032b18d SHA512 c37f36e2c0d5dbf151a03513e9dc82c21c46f1a88b123153647f44f4305367d1021e522236dda97ab9c641db006242507ae323d668cf2186cf04a83a54b5707f
+DIST NVIDIA-OptiX-SDK-7.4.0-linux64-x86_64.sh 57923655 BLAKE2B c3e159106ec6c8c446090ebd182fd3b0a75ec48b62e6984ae6559578688fd9a6cb29ea6065cb89aecdeb02247acbf3fb3bb0cbf69b10c29c222eb9fcbb0c6d90 SHA512 04f50c49d08c5e4e9be73ee322c4bff4f10a5e30445bc431e213c879a35cc5e36e0ceb8c864313f417628575a3c71593e65467ea13dd111b432fdf1db9383ae0
diff --git a/dev-libs/optix/optix-6.0.0.ebuild b/dev-libs/optix/optix-6.0.0.ebuild
deleted file mode 100644
index d0cb4c078..000000000
--- a/dev-libs/optix/optix-6.0.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake cuda
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-25650775.sh"
-
-SLOT="0/6"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="dev-util/nvidia-cuda-toolkit
- virtual/opengl
- media-libs/freeglut"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-CMAKE_USE_DIR=${S}/SDK
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +218 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_prepare() {
- cmake_src_prepare
- rm -rf SDK-precompiled-samples
- export PATH=$(cuda_gccdir):${PATH}
-}
-
-src_install() {
- insinto /opt/${PN}
- doins -r doc include lib64
-}
diff --git a/dev-libs/optix/optix-7.0.0.ebuild b/dev-libs/optix/optix-7.0.0.ebuild
deleted file mode 100644
index c419a9cee..000000000
--- a/dev-libs/optix/optix-7.0.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64.sh"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit
- media-libs/freeglut
- virtual/opengl
-"
-S="${WORKDIR}"
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_install() {
- insinto /opt/${PN}
- dodoc -r doc
- doins -r include SDK
-}
diff --git a/dev-libs/optix/optix-7.1.0.ebuild b/dev-libs/optix/optix-7.1.0.ebuild
deleted file mode 100644
index afeda2b32..000000000
--- a/dev-libs/optix/optix-7.1.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit
- media-libs/freeglut
- virtual/opengl
-"
-S="${WORKDIR}"
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_install() {
- insinto /opt/${PN}
- dodoc -r doc
- doins -r include SDK
-}
diff --git a/dev-libs/optix/optix-7.2.0.ebuild b/dev-libs/optix/optix-7.4.0.ebuild
index 34dcf66c4..a3f61205e 100644
--- a/dev-libs/optix/optix-7.2.0.ebuild
+++ b/dev-libs/optix/optix-7.4.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2021 Gentoo Authors
+# Copyright 2021-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="NVIDIA Ray Tracing Engine"
HOMEPAGE="https://developer.nvidia.com/optix"
diff --git a/dev-libs/protobuf/Manifest b/dev-libs/protobuf/Manifest
deleted file mode 100644
index 81632cac5..000000000
--- a/dev-libs/protobuf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST protobuf-3.11.4.tar.gz 5140799 BLAKE2B 97b450c0623593efe6a42b66582ff183344b8831689e6a5b4d36096dbd57c33da9569bbf26578536aaf73ecd866ac0588b6cb7d55a6a9b9a6e840d4c57099001 SHA512 777bbb0e9e2375eaebe6b8c87abd660bac70ee469c9ad00dd25917b82d7fb5bbe33cf87f0d69c90e19d55c07a7285ec20974ba4768623ce9ccfadf147fd5e261
diff --git a/dev-libs/protobuf/files/proto.vim b/dev-libs/protobuf/files/proto.vim
deleted file mode 100644
index 6d26809ef..000000000
--- a/dev-libs/protobuf/files/proto.vim
+++ /dev/null
@@ -1 +0,0 @@
-au BufRead,BufNewFile *.proto set filetype=proto
diff --git a/dev-libs/protobuf/files/protobuf-3.11.0-disable_no-warning-test.patch b/dev-libs/protobuf/files/protobuf-3.11.0-disable_no-warning-test.patch
deleted file mode 100644
index ec043e386..000000000
--- a/dev-libs/protobuf/files/protobuf-3.11.0-disable_no-warning-test.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Disable no-warning-test which is compiled with -Werror option and whose only purpose is checking if compilation results in any warnings.
-
---- /src/Makefile.am
-+++ /src/Makefile.am
-@@ -714,7 +714,7 @@
- GOOGLEMOCK_SRC_DIR=$(srcdir)/../third_party/googletest/googlemock
- check_PROGRAMS = protoc protobuf-test protobuf-lazy-descriptor-test \
- protobuf-lite-test test_plugin protobuf-lite-arena-test \
-- no-warning-test $(GZCHECKPROGRAMS)
-+ $(GZCHECKPROGRAMS)
- protobuf_test_LDADD = $(PTHREAD_LIBS) libprotobuf.la libprotoc.la \
- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la \
- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock.la \
-@@ -901,4 +901,4 @@
-
- TESTS = protobuf-test protobuf-lazy-descriptor-test protobuf-lite-test \
- google/protobuf/compiler/zip_output_unittest.sh $(GZTESTS) \
-- protobuf-lite-arena-test no-warning-test
-+ protobuf-lite-arena-test
diff --git a/dev-libs/protobuf/files/protobuf-3.11.0-protoc_input_output_files.patch b/dev-libs/protobuf/files/protobuf-3.11.0-protoc_input_output_files.patch
deleted file mode 100644
index 0e22b34ef..000000000
--- a/dev-libs/protobuf/files/protobuf-3.11.0-protoc_input_output_files.patch
+++ /dev/null
@@ -1,262 +0,0 @@
-https://github.com/protocolbuffers/protobuf/pull/235
-
---- /src/google/protobuf/compiler/command_line_interface.cc
-+++ /src/google/protobuf/compiler/command_line_interface.cc
-@@ -938,6 +938,28 @@
- }
-
- if (mode_ == MODE_ENCODE || mode_ == MODE_DECODE) {
-+ bool success = false;
-+ int in_fd = STDIN_FILENO;
-+ int out_fd = STDOUT_FILENO;
-+
-+ if (!protobuf_in_path_.empty()) {
-+ in_fd = open(protobuf_in_path_.c_str(), O_RDONLY);
-+ if (in_fd == -1) {
-+ std::cerr << protobuf_in_path_ << ": error: failed to open file." << std::endl;
-+ return 1;
-+ }
-+ }
-+ if (!protobuf_out_path_.empty()) {
-+ out_fd = open(protobuf_out_path_.c_str(),
-+ O_WRONLY | O_CREAT | O_TRUNC,
-+ 0644);
-+ if (out_fd == -1) {
-+ std::cerr << protobuf_out_path_ << ": error: failed to open file." << std::endl;
-+ close(in_fd);
-+ return 1;
-+ }
-+ }
-+
- if (codec_type_.empty()) {
- // HACK: Define an EmptyMessage type to use for decoding.
- DescriptorPool pool;
-@@ -946,13 +968,20 @@
- file.add_message_type()->set_name("EmptyMessage");
- GOOGLE_CHECK(pool.BuildFile(file) != NULL);
- codec_type_ = "EmptyMessage";
-- if (!EncodeOrDecode(&pool)) {
-- return 1;
-- }
-+ success = EncodeOrDecode(&pool, in_fd, out_fd);
- } else {
-- if (!EncodeOrDecode(descriptor_pool.get())) {
-- return 1;
-- }
-+ success = EncodeOrDecode(descriptor_pool.get(), in_fd, out_fd);
-+ }
-+
-+ if (in_fd != STDIN_FILENO) {
-+ close(in_fd);
-+ }
-+ if (out_fd != STDOUT_FILENO) {
-+ close(out_fd);
-+ }
-+
-+ if (!success) {
-+ return 1;
- }
- }
-
-@@ -990,6 +1019,11 @@
- for (int i = 0; i < proto_path_.size(); i++) {
- source_tree->MapPath(proto_path_[i].first, proto_path_[i].second);
- }
-+ if (mode_ == MODE_COMPILE &&
-+ (!protobuf_in_path_.empty() || !protobuf_out_path_.empty())) {
-+ std::cerr << "--protobuf_in and --protobuf_out are only valid with "
-+ << "decode operations. Ignoring.";
-+ }
-
- // Map input files to virtual paths if possible.
- if (!MakeInputsBeProtoPathRelative(source_tree, fallback_database)) {
-@@ -1650,6 +1684,12 @@
-
- codec_type_ = value;
-
-+ } else if (name == "--protobuf_in") {
-+ protobuf_in_path_ = value;
-+
-+ } else if (name == "--protobuf_out") {
-+ protobuf_out_path_ = value;
-+
- } else if (name == "--error_format") {
- if (value == "gcc") {
- error_format_ = ERROR_FORMAT_GCC;
-@@ -1786,29 +1826,50 @@
- " -h, --help Show this text and exit.\n"
- " --encode=MESSAGE_TYPE Read a text-format message of the "
- "given type\n"
-- " from standard input and write it in "
-- "binary\n"
-- " to standard output. The message type "
-- "must\n"
-+ " and write it in binary. The message "
-+ "type must\n"
- " be defined in PROTO_FILES or their "
- "imports.\n"
-+ " The input/output protobuf files are "
-+ "specified\n"
-+ " using the --protobuf_in and "
-+ "--protobuf_out\n"
-+ " command line flags.\n"
- " --decode=MESSAGE_TYPE Read a binary message of the given "
-- "type from\n"
-- " standard input and write it in text "
-- "format\n"
-- " to standard output. The message type "
-- "must\n"
-- " be defined in PROTO_FILES or their "
-- "imports.\n"
-+ "type and\n"
-+ " write it in text format. The message "
-+ "type\n"
-+ " must be defined in PROTO_FILES or "
-+ "their imports.\n"
-+ " The input/output protobuf files are "
-+ "specified\n"
-+ " using the --protobuf_in and "
-+ "--protobuf_out\n"
-+ " command line flags.\n"
- " --decode_raw Read an arbitrary protocol message "
-- "from\n"
-- " standard input and write the raw "
-- "tag/value\n"
-- " pairs in text format to standard "
-- "output. No\n"
-+ "and write\n"
-+ " the raw tag/value pairs in text format."
-+ " No\n"
- " PROTO_FILES should be given when using "
- "this\n"
-- " flag.\n"
-+ " flag. The input/output protobuf files "
-+ "are\n"
-+ " specified using the --protobuf_in and\n"
-+ " --protobuf_out command line flags.\n"
-+ " --protobuf_in=FILE Absolute path to the protobuf file "
-+ "from which\n"
-+ " input of encoding/decoding operation "
-+ "will be\n"
-+ " read. If omitted, input will be read "
-+ "from\n"
-+ " standard input.\n"
-+ " --protobuf_out=FILE Absolute path to the protobuf file "
-+ "to which\n"
-+ " output of encoding/decoding operation "
-+ "will be\n"
-+ " written. If omitted, output will be "
-+ "written to\n"
-+ " standard output.\n"
- " --descriptor_set_in=FILES Specifies a delimited list of FILES\n"
- " each containing a FileDescriptorSet "
- "(a\n"
-@@ -2123,7 +2184,9 @@
- return true;
- }
-
--bool CommandLineInterface::EncodeOrDecode(const DescriptorPool* pool) {
-+bool CommandLineInterface::EncodeOrDecode(const DescriptorPool* pool,
-+ int in_fd,
-+ int out_fd) {
- // Look up the type.
- const Descriptor* type = pool->FindMessageTypeByName(codec_type_);
- if (type == NULL) {
-@@ -2135,15 +2198,15 @@
- std::unique_ptr<Message> message(dynamic_factory.GetPrototype(type)->New());
-
- if (mode_ == MODE_ENCODE) {
-- SetFdToTextMode(STDIN_FILENO);
-- SetFdToBinaryMode(STDOUT_FILENO);
-+ SetFdToTextMode(in_fd);
-+ SetFdToBinaryMode(out_fd);
- } else {
-- SetFdToBinaryMode(STDIN_FILENO);
-- SetFdToTextMode(STDOUT_FILENO);
-+ SetFdToBinaryMode(in_fd);
-+ SetFdToTextMode(out_fd);
- }
-
-- io::FileInputStream in(STDIN_FILENO);
-- io::FileOutputStream out(STDOUT_FILENO);
-+ io::FileInputStream in(in_fd);
-+ io::FileOutputStream out(out_fd);
-
- if (mode_ == MODE_ENCODE) {
- // Input is text.
---- /src/google/protobuf/compiler/command_line_interface.h
-+++ /src/google/protobuf/compiler/command_line_interface.h
-@@ -288,7 +288,9 @@
- GeneratorContext* generator_context, std::string* error);
-
- // Implements --encode and --decode.
-- bool EncodeOrDecode(const DescriptorPool* pool);
-+ bool EncodeOrDecode(const DescriptorPool* pool,
-+ int in_fd,
-+ int out_fd);
-
- // Implements the --descriptor_set_out option.
- bool WriteDescriptorSet(
-@@ -420,6 +422,13 @@
- // parsed FileDescriptorSets to be used for loading protos. Otherwise, empty.
- std::vector<std::string> descriptor_set_in_names_;
-
-+ // When using --encode / --decode / --decode_raw absolute path to the output
-+ // file. (Empty string indicates write to STDOUT).
-+ std::string protobuf_out_path_;
-+ // When using --encode / --decode / --decode_raw, absolute path to the input
-+ // file. (Empty string indicates read from STDIN).
-+ std::string protobuf_in_path_;
-+
- // If --descriptor_set_out was given, this is the filename to which the
- // FileDescriptorSet should be written. Otherwise, empty.
- std::string descriptor_set_out_name_;
---- /src/google/protobuf/compiler/command_line_interface_unittest.cc
-+++ /src/google/protobuf/compiler/command_line_interface_unittest.cc
-@@ -95,7 +95,7 @@
- virtual void SetUp();
- virtual void TearDown();
-
-- // Runs the CommandLineInterface with the given command line. The
-+ // Run the CommandLineInterface with the given command line. The
- // command is automatically split on spaces, and the string "$tmpdir"
- // is replaced with TestTempDir().
- void Run(const std::string& command);
-@@ -2491,6 +2491,17 @@
- std::string::npos);
- }
-
-+ void ExpectBinaryFilesMatch(const string &expected_file,
-+ const string &actual_file) {
-+ string expected_output, actual_output;
-+ ASSERT_TRUE(File::ReadFileToString(expected_file, &expected_output));
-+ ASSERT_TRUE(File::ReadFileToString(actual_file, &actual_output));
-+
-+ // Don't use EXPECT_EQ because we don't want to print raw binary data to
-+ // stdout on failure.
-+ EXPECT_TRUE(expected_output == actual_output);
-+ }
-+
- private:
- void WriteUnittestProtoDescriptorSet() {
- unittest_proto_descriptor_set_filename_ =
-@@ -2585,6 +2596,19 @@
- "net/proto2/internal/no_such_file.proto: No such file or directory\n");
- }
-
-+TEST_P(EncodeDecodeTest, RedirectInputOutput) {
-+ string out_file = TestTempDir() + "/golden_message_out.pbf";
-+ EXPECT_TRUE(
-+ Run(TestUtil::MaybeTranslatePath("net/proto2/internal/unittest.proto") +
-+ " --encode=protobuf_unittest.TestAllTypes" +
-+ " --protobuf_in=" + TestUtil::GetTestDataPath(
-+ "net/proto2/internal/"
-+ "testdata/text_format_unittest_data_oneof_implemented.txt") +
-+ " --protobuf_out=" + out_file));
-+ ExpectBinaryFilesMatch(out_file, TestUtil::GetTestDataPath(
-+ "net/proto2/internal/testdata/golden_message_oneof_implemented"));
-+}
-+
- INSTANTIATE_TEST_SUITE_P(FileDescriptorSetSource, EncodeDecodeTest,
- testing::Values(PROTO_PATH, DESCRIPTOR_SET_IN));
- } // anonymous namespace
diff --git a/dev-libs/protobuf/files/protobuf-3.11.0-system_libraries.patch b/dev-libs/protobuf/files/protobuf-3.11.0-system_libraries.patch
deleted file mode 100644
index 8311ce8b2..000000000
--- a/dev-libs/protobuf/files/protobuf-3.11.0-system_libraries.patch
+++ /dev/null
@@ -1,121 +0,0 @@
---- /Makefile.am
-+++ /Makefile.am
-@@ -11,28 +11,10 @@
- # Always include third_party directories in distributions.
- DIST_SUBDIRS = src conformance benchmarks third_party/googletest
-
--# Build gmock before we build protobuf tests. We don't add gmock to SUBDIRS
--# because then "make check" would also build and run all of gmock's own tests,
--# which takes a lot of time and is generally not useful to us. Also, we don't
--# want "make install" to recurse into gmock since we don't want to overwrite
--# the installed version of gmock if there is one.
- check-local:
-- @echo "Making lib/libgmock.a lib/libgmock_main.a in gmock"
-- @cd third_party/googletest/googletest && $(MAKE) $(AM_MAKEFLAGS) lib/libgtest.la lib/libgtest_main.la
-- @cd third_party/googletest/googlemock && $(MAKE) $(AM_MAKEFLAGS) lib/libgmock.la lib/libgmock_main.la
-
--# We would like to clean gmock when "make clean" is invoked. But we have to
--# be careful because clean-local is also invoked during "make distclean", but
--# "make distclean" already recurses into gmock because it's listed among the
--# DIST_SUBDIRS. distclean will delete gmock/Makefile, so if we then try to
--# cd to the directory again and "make clean" it will fail. So, check that the
--# Makefile exists before recursing.
- clean-local:
-- @if test -e third_party/googletest/Makefile; then \
-- echo "Making clean in googletest"; \
-- cd third_party/googletest && $(MAKE) $(AM_MAKEFLAGS) clean; \
-- fi; \
-- if test -e conformance/Makefile; then \
-+ @if test -e conformance/Makefile; then \
- echo "Making clean in conformance"; \
- cd conformance && $(MAKE) $(AM_MAKEFLAGS) clean; \
- fi; \
---- /configure.ac
-+++ /configure.ac
-@@ -223,12 +223,5 @@
- esac
- AM_CONDITIONAL([OBJC_CONFORMANCE_TEST], [test $OBJC_CONFORMANCE_TEST = 1])
-
--# HACK: Make gmock's configure script pick up our copy of CFLAGS and CXXFLAGS,
--# since the flags added by ACX_CHECK_SUNCC must be used when compiling gmock
--# too.
--export CFLAGS
--export CXXFLAGS
--AC_CONFIG_SUBDIRS([third_party/googletest])
--
- AC_CONFIG_FILES([Makefile src/Makefile benchmarks/Makefile conformance/Makefile protobuf.pc protobuf-lite.pc])
- AC_OUTPUT
---- /src/Makefile.am
-+++ /src/Makefile.am
-@@ -708,19 +708,11 @@
- google/protobuf/testing/file.cc \
- google/protobuf/testing/file.h
-
--GOOGLETEST_BUILD_DIR=../third_party/googletest/googletest
--GOOGLEMOCK_BUILD_DIR=../third_party/googletest/googlemock
--GOOGLETEST_SRC_DIR=$(srcdir)/../third_party/googletest/googletest
--GOOGLEMOCK_SRC_DIR=$(srcdir)/../third_party/googletest/googlemock
- check_PROGRAMS = protoc protobuf-test protobuf-lazy-descriptor-test \
- protobuf-lite-test test_plugin protobuf-lite-arena-test \
- $(GZCHECKPROGRAMS)
- protobuf_test_LDADD = $(PTHREAD_LIBS) libprotobuf.la libprotoc.la \
-- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock_main.la
--protobuf_test_CPPFLAGS = -I$(GOOGLETEST_SRC_DIR)/include \
-- -I$(GOOGLEMOCK_SRC_DIR)/include
-+ -lgtest -lgmock -lgmock_main
- # Disable optimization for tests unless the user explicitly asked for it,
- # since test_util.cc takes forever to compile with optimization (with GCC).
- # See configure.ac for more info.
-@@ -812,12 +804,8 @@
- # Run cpp_unittest again with PROTOBUF_TEST_NO_DESCRIPTORS defined.
- protobuf_lazy_descriptor_test_LDADD = $(PTHREAD_LIBS) libprotobuf.la \
- libprotoc.la \
-- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock_main.la
--protobuf_lazy_descriptor_test_CPPFLAGS = -I$(GOOGLEMOCK_SRC_DIR)/include \
-- -I$(GOOGLETEST_SRC_DIR)/include \
-- -DPROTOBUF_TEST_NO_DESCRIPTORS
-+ -lgtest -lgmock -lgmock_main
-+protobuf_lazy_descriptor_test_CPPFLAGS = -DPROTOBUF_TEST_NO_DESCRIPTORS
- protobuf_lazy_descriptor_test_CXXFLAGS = $(NO_OPT_CXXFLAGS)
- protobuf_lazy_descriptor_test_SOURCES = \
- google/protobuf/compiler/cpp/cpp_unittest.cc \
-@@ -838,11 +826,7 @@
- # full runtime and we want to make sure this test builds without full
- # runtime.
- protobuf_lite_test_LDADD = $(PTHREAD_LIBS) libprotobuf-lite.la \
-- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock_main.la
--protobuf_lite_test_CPPFLAGS= -I$(GOOGLEMOCK_SRC_DIR)/include \
-- -I$(GOOGLETEST_SRC_DIR)/include
-+ -lgtest -lgmock -lgmock_main
- protobuf_lite_test_CXXFLAGS = $(NO_OPT_CXXFLAGS)
- protobuf_lite_test_SOURCES = \
- google/protobuf/lite_unittest.cc \
-@@ -854,11 +838,7 @@
- # gtest when building the test internally our memory sanitizer doesn't detect
- # memory leaks (don't know why).
- protobuf_lite_arena_test_LDADD = $(PTHREAD_LIBS) libprotobuf-lite.la \
-- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock.la \
-- $(GOOGLEMOCK_BUILD_DIR)/lib/libgmock_main.la
--protobuf_lite_arena_test_CPPFLAGS = -I$(GOOGLEMOCK_SRC_DIR)/include \
-- -I$(GOOGLETEST_SRC_DIR)/include
-+ -lgtest -lgmock -lgmock_main
- protobuf_lite_arena_test_CXXFLAGS = $(NO_OPT_CXXFLAGS)
- protobuf_lite_arena_test_SOURCES = \
- google/protobuf/lite_arena_unittest.cc \
-@@ -868,8 +848,7 @@
-
- # Test plugin binary.
- test_plugin_LDADD = $(PTHREAD_LIBS) libprotobuf.la libprotoc.la \
-- $(GOOGLETEST_BUILD_DIR)/lib/libgtest.la
--test_plugin_CPPFLAGS = -I$(GOOGLETEST_SRC_DIR)/include
-+ -lgtest
- test_plugin_SOURCES = \
- google/protobuf/compiler/mock_code_generator.cc \
- google/protobuf/testing/file.cc \
diff --git a/dev-libs/protobuf/metadata.xml b/dev-libs/protobuf/metadata.xml
deleted file mode 100644
index 0d125ed97..000000000
--- a/dev-libs/protobuf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <description>Gentoo Science Project</description>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-libs/protobuf/protobuf-3.11.4.ebuild b/dev-libs/protobuf/protobuf-3.11.4.ebuild
deleted file mode 100644
index 8e2342b29..000000000
--- a/dev-libs/protobuf/protobuf-3.11.4.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 2008-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="7"
-
-inherit autotools elisp-common flag-o-matic multilib-minimal toolchain-funcs
-
-DESCRIPTION="Google's Protocol Buffers - Extensible mechanism for serializing structured data"
-HOMEPAGE="https://developers.google.com/protocol-buffers/ https://github.com/protocolbuffers/protobuf"
-SRC_URI="https://github.com/protocolbuffers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/22"
-KEYWORDS="~amd64"
-IUSE="emacs examples static-libs test zlib"
-RESTRICT="!test? ( test )"
-
-BDEPEND="emacs? ( app-editors/emacs:* )"
-DEPEND="test? ( >=dev-cpp/gtest-1.9[${MULTILIB_USEDEP}] )
- zlib? ( sys-libs/zlib[${MULTILIB_USEDEP}] )"
-RDEPEND="emacs? ( app-editors/emacs:* )
- zlib? ( sys-libs/zlib[${MULTILIB_USEDEP}] )"
-
-PATCHES=(
- "${FILESDIR}/${PN}-3.11.0-disable_no-warning-test.patch"
- "${FILESDIR}/${PN}-3.11.0-system_libraries.patch"
- "${FILESDIR}/${PN}-3.11.0-protoc_input_output_files.patch"
-)
-
-DOCS=(CHANGES.txt CONTRIBUTORS.txt README.md)
-
-src_prepare() {
- default
-
- # https://github.com/protocolbuffers/protobuf/issues/7413
- sed -e "/^AC_PROG_CXX_FOR_BUILD$/d" -i configure.ac || die
-
- eautoreconf
-}
-
-src_configure() {
- append-cppflags -DGOOGLE_PROTOBUF_NO_RTTI
-
- if tc-ld-is-gold; then
- # https://sourceware.org/bugzilla/show_bug.cgi?id=24527
- tc-ld-disable-gold
- fi
-
- multilib-minimal_src_configure
-}
-
-multilib_src_configure() {
- local options=(
- $(use_enable static-libs static)
- $(use_with zlib)
- )
-
- if tc-is-cross-compiler; then
- # Build system uses protoc when building, so protoc copy runnable on host is needed.
- mkdir -p "${WORKDIR}/build" || die
- pushd "${WORKDIR}/build" > /dev/null || die
- ECONF_SOURCE="${S}" econf_build "${options[@]}"
- options+=(--with-protoc="$(pwd)/src/protoc")
- popd > /dev/null || die
- fi
-
- ECONF_SOURCE="${S}" econf "${options[@]}"
-}
-
-src_compile() {
- multilib-minimal_src_compile
-
- if use emacs; then
- elisp-compile editors/protobuf-mode.el
- fi
-}
-
-multilib_src_compile() {
- if tc-is-cross-compiler; then
- emake -C "${WORKDIR}/build/src" protoc
- fi
-
- default
-}
-
-multilib_src_test() {
- emake check
-}
-
-multilib_src_install_all() {
- find "${D}" -name "*.la" -type f -delete || die
-
- insinto /usr/share/vim/vimfiles/syntax
- doins editors/proto.vim
- insinto /usr/share/vim/vimfiles/ftdetect
- doins "${FILESDIR}/proto.vim"
-
- if use emacs; then
- elisp-install ${PN} editors/protobuf-mode.el*
- elisp-site-file-install "${FILESDIR}/70${PN}-gentoo.el"
- fi
-
- if use examples; then
- DOCS+=(examples)
- docompress -x /usr/share/doc/${PF}/examples
- fi
-
- einstalldocs
-}
-
-pkg_postinst() {
- use emacs && elisp-site-regen
-}
-
-pkg_postrm() {
- use emacs && elisp-site-regen
-}
diff --git a/dev-python/affine/Manifest b/dev-python/affine/Manifest
new file mode 100644
index 000000000..519703c98
--- /dev/null
+++ b/dev-python/affine/Manifest
@@ -0,0 +1 @@
+DIST affine-2.3.0.tar.gz 14860 BLAKE2B 3f1f2bf69e26bc7c73ad7d4fc2fa0a51b3cb5ccea3e88982dd682f377df0c6fde00e037893aa466d89955e7800fa99580b02108ce7acb68fb1b38cb67e4753e6 SHA512 25e3671542a4bcb45c04a3e4a1c312f7e427091470b30b115dd8d0c7a1f3ac008e1b1f9222ca60b08b4717cab90fc224f2e70fc0184ca371ccf918f8c04a23ce
diff --git a/dev-python/affine/affine-2.3.0.ebuild b/dev-python/affine/affine-2.3.0.ebuild
new file mode 100644
index 000000000..a298cec26
--- /dev/null
+++ b/dev-python/affine/affine-2.3.0.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Library for handling affine transformations of the plane"
+HOMEPAGE="https://github.com/rasterio/affine"
+SRC_URI="https://github.com/rasterio/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/affine/metadata.xml b/dev-python/affine/metadata.xml
new file mode 100644
index 000000000..298f9156d
--- /dev/null
+++ b/dev-python/affine/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Affine is a python library for handling affine transformations of the plane.
+ Georeferenced raster datasets use affine transformations to map from image
+ coordinates to world coordinates.
+</longdescription>
+ <upstream>
+ <remote-id type="github">rasterio/affine</remote-id>
+ <remote-id type="pypi">affine</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest
index ed535128d..3b2cf6ef8 100644
--- a/dev-python/asdf/Manifest
+++ b/dev-python/asdf/Manifest
@@ -1 +1 @@
-DIST asdf-2.7.1.tar.gz 494491 BLAKE2B 7ff36829626972e85362cb364bdf5ced4745a592c7229b70584ef36722935959a21c6cc11a37ea58c625c1aefdee96d72d5edfef67e5a7975c653f70ed9689c1 SHA512 dc807013d7dbf67c8cb269398d0b7ff56b1c5212d2cfbb768b7844979951c56b9263327cba3a3db32b65ac9de2ede94731823b4d7f120a4306efc203cfc75266
+DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df
diff --git a/dev-python/asdf/asdf-2.7.1.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild
index ddace4966..96663e49a 100644
--- a/dev-python/asdf/asdf-2.7.1.ebuild
+++ b/dev-python/asdf/asdf-2.8.3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -27,8 +27,8 @@ BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]
"
RDEPEND="
+ >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}]
>=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}]
- <dev-python/jsonschema-4[${PYTHON_USEDEP}]
>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
>=dev-python/semantic_version-2.8[${PYTHON_USEDEP}]
@@ -40,5 +40,5 @@ distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-py
python_test() {
# discovers things in docs dir if we do not
# explicitly set it to run on the tests dir
- pytest -vv asdf/tests || die " Tests failed with ${EPYTHON}"
+ epytest asdf/tests
}
diff --git a/dev-python/astropy-healpix/Manifest b/dev-python/astropy-healpix/Manifest
index 50717914d..0845b8ed4 100644
--- a/dev-python/astropy-healpix/Manifest
+++ b/dev-python/astropy-healpix/Manifest
@@ -1 +1 @@
-DIST astropy-healpix-0.5.tar.gz 163123 BLAKE2B f82d7a7eba168353378eea56f9db4c8a3cae0c33fe504745ab53290ab049a7ebf5907b212b5fb35bfa9560ce0d7cba98b2ba81f75085a03bd2eed937fa6ebdda SHA512 8eb43da00b907de7763143153641117d57bd1ccdb50b57d721b5858fc33e5f4c63348134c2eaa044ee5619ae93cb6436d26565d42e9d9df6bfc515b388833576
+DIST astropy_healpix-0.6.tar.gz 104224 BLAKE2B a06474de29f2848d18dedb45202ea63ba5893d6993ef39ebb91e02b55c0f5e100522c267198a233c8771f3920c620f7eddb83f08c82c3cb4151432e1815b00d8 SHA512 c54a41e50c7eaa51126b20abc88e5fc8f7c02521baeb4a69a5a8eac42f59350273e8f30c17926daf628c7866550eec141980ce0349028ff72a4ac2786275f428
diff --git a/dev-python/astropy-healpix/astropy-healpix-0.5.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
index 6f813524d..ce6ec0cd3 100644
--- a/dev-python/astropy-healpix/astropy-healpix-0.5.ebuild
+++ b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild
@@ -1,15 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="HEALPix for Astropy"
HOMEPAGE="https://github.com/astropy/astropy-healpix"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P/-/_}.tar.gz"
+S="${WORKDIR}/${P/-/_}"
LICENSE="BSD"
SLOT="0"
@@ -27,7 +28,6 @@ RESTRICT="test"
BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]"
RDEPEND="
- sci-astronomy/healpix
>=dev-python/astropy-3.2[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
"
diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
index 51514e535..393066583 100644
--- a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
+++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 xdg-utils
diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
index dae2f430f..844b614bd 100644
--- a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
+++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest
index 0bacc3982..c8278e21a 100644
--- a/dev-python/astropy/Manifest
+++ b/dev-python/astropy/Manifest
@@ -1 +1 @@
-DIST astropy-4.2.tar.gz 7462293 BLAKE2B 47a26cde10e99be3c2ea0e5f2e6fb90afc70a27c53bad63683c0cd6ca7a97ff45542d68c8326bbfcae23135594b1a2533eccdb54aec1e62ddc0ff11cb78aa263 SHA512 14bb90aac13f3fe668114ebe578aac401987e8e2cd2bb9fb0971e5b8e9f8df6a594d454bb53e330807c3854c44d295e2b4dc96b57ccb69e5f53ee11356869d9d
+DIST astropy-5.0.tar.gz 7823746 BLAKE2B e769f9ea26e156a2342dc75b307c16c2c38108adf0dfd931812b2eb3234941055c013378a492306f2247c16b4804fe569ba1cbfd8427df1aac2b808976082cf9 SHA512 3c0b0cdef434f27ee399fbfc3d55b95ce8395624caf8e73a205dba7742c39d8a2bcea9bf61c2c20235da7388d40c657c5474bfc7e3dc3c9e5911e39bab47cdb9
diff --git a/dev-python/astropy/astropy-4.2.ebuild b/dev-python/astropy/astropy-5.0.ebuild
index 9b17173a4..c650533d6 100644
--- a/dev-python/astropy/astropy-4.2.ebuild
+++ b/dev-python/astropy/astropy-5.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,7 +16,6 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
#TODO: Package all these pytest deps:
-# pytest-doctestplus>=0.2.0
# pytest-remotedata>=0.3.1
# pytest-openfiles>=0.3.1
# pytest-astropy-header>=0.1.2
@@ -26,8 +25,10 @@ RESTRICT="test"
RDEPEND="
dev-libs/expat:0=
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pyerfa[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+ >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}]
+ >=dev-python/packaging-19.0[${PYTHON_USEDEP}]
sci-astronomy/wcslib:0=
>=sci-libs/cfitsio-3.350:0=
sys-libs/zlib:0=
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
index 1a638a985..ec0b8526d 100644
--- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
+++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{8..9} )
# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
-inherit check-reqs cmake llvm multiprocessing python-single-r1
+inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
MY_PN=OCP
MY_PV="${PV//_/-}"
@@ -32,7 +32,7 @@ BDEPEND="
"
RDEPEND="
${PYTHON_DEPS}
- sci-libs/opencascade:7.5=[json,tbb,vtk,-gles2]
+ sci-libs/opencascade:0/7.5[json,tbb,vtk]
>=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
"
DEPEND="${RDEPEND}
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
index fc97f9db1..19494930c 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{8..9} )
-inherit llvm toolchain-funcs distutils-r1
+inherit llvm distutils-r1
DESCRIPTION="C++ binding generator based on libclang and pybind11"
HOMEPAGE="https://github.com/CadQuery/pywrap"
diff --git a/dev-python/cligj/Manifest b/dev-python/cligj/Manifest
new file mode 100644
index 000000000..b3e1ca5dd
--- /dev/null
+++ b/dev-python/cligj/Manifest
@@ -0,0 +1 @@
+DIST cligj-0.7.2.tar.gz 9894 BLAKE2B ebd187a6a7108a8d0a7d348fcb1d617402041d050a89209cb6c242bc47a87be953b679101656af9af31fd40947f1a5b3ded567dce9f3e64f425cce7f0f3036c1 SHA512 292c1a6de4ed5d4926ccd71802d369db383d310a3a8590729233448cebe5e9ad9dd6bff0d0c861890102bc9f23e90fe1b9db62275a9263765e3d77436a0b38b4
diff --git a/dev-python/cligj/cligj-0.7.2.ebuild b/dev-python/cligj/cligj-0.7.2.ebuild
new file mode 100644
index 000000000..c90584b75
--- /dev/null
+++ b/dev-python/cligj/cligj-0.7.2.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Library for processing GeoJSON commands"
+HOMEPAGE="https://github.com/mapbox/cligj"
+SRC_URI="https://github.com/mapbox/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
diff --git a/dev-python/cligj/metadata.xml b/dev-python/cligj/metadata.xml
new file mode 100644
index 000000000..9afaefe0d
--- /dev/null
+++ b/dev-python/cligj/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ cligj is for Python developers who create command line interfaces for
+ geospatial data. cligj allows you to quickly build consistent,
+ well-tested and interoperable CLIs for handling GeoJSON.
+</longdescription>
+ <upstream>
+ <remote-id type="github">mapbox/cligj</remote-id>
+ <remote-id type="pypi">cligj</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
index 714cb7123..8119b0206 100644
--- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild
+++ b/dev-python/extension-helpers/extension-helpers-0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest
new file mode 100644
index 000000000..6f48f8721
--- /dev/null
+++ b/dev-python/fiona/Manifest
@@ -0,0 +1 @@
+DIST fiona-1.8.20.tar.gz 269491 BLAKE2B 0778a0824e3ecd70fc7a153a4be4631c04e70dc6218c3c78e7ddffae01db22a081f8f8b7f44cce37f864e32277b88596263d6ac640293c93e6a14ec7a932aa04 SHA512 4864f3c48903b34c6b4d2cf5dcdc5ebb6e155e32e7e138bdf17756a823f36a0985162c211127b283235569235c830e11abd330c229b2bb8de6cee053fe3204d7
diff --git a/dev-python/fiona/fiona-1.8.20.ebuild b/dev-python/fiona/fiona-1.8.20.ebuild
new file mode 100644
index 000000000..1127afa70
--- /dev/null
+++ b/dev-python/fiona/fiona-1.8.20.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="API for reading/writing vector geospatial data"
+HOMEPAGE="https://github.com/Toblerity/fiona"
+SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ dev-python/attrs[${PYTHON_USEDEP}]
+ dev-python/click-plugins[${PYTHON_USEDEP}]
+ dev-python/cligj[${PYTHON_USEDEP}]
+ dev-python/munch[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ dev-python/certifi[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ test? (
+ dev-python/boto3[${PYTHON_USEDEP}]
+ sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ )
+"
+
+S="${WORKDIR}/Fiona-${PV}"
+
+distutils_enable_tests pytest
+
+python_test() {
+ local deselect=(
+ # disable tests due to networking blocked
+ tests/test_vfs.py::test_open_http
+ tests/test_vfs.py::test_open_zip_https
+ tests/test_collection.py::test_collection_http
+ tests/test_collection.py::test_collection_zip_http
+
+ # disable tests failing due to deprecated GDAL features
+ tests/test_data_paths.py::test_gdal_data_wheel
+ tests/test_data_paths.py::test_proj_data_wheel
+ tests/test_data_paths.py::test_env_gdal_data_wheel
+ tests/test_data_paths.py::test_env_proj_data_wheel
+ tests/test_datetime.py::test_datefield[GPSTrackMaker-datetime]
+ tests/test_datetime.py::test_datefield_null[GPSTrackMaker-datetime]
+ tests/test_drvsupport.py::test_write_or_driver_error[GPSTrackMaker]
+ tests/test_drvsupport.py::test_no_append_driver_cannot_append[GPSTrackMaker]
+ tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK]
+ tests/test_drvsupport.py::test_write_or_driver_error[DGN]
+
+ # geos
+ #tests/test_collection.py::test_mask_polygon_triangle
+ #tests/test_collection.py::test_mask_polygon_triangle
+ #tests/test_collection.py::test_mask_polygon_triangle
+
+ # sqlite
+ #tests/test_schema.py::test_geometry_only_schema_write[GPKG]
+ #tests/test_schema.py::test_geometry_only_schema_update[GPKG]
+ #tests/test_schema.py::test_property_only_schema_write[GPKG]
+ #tests/test_schema.py::test_property_only_schema_update[GPKG]
+ )
+
+ mv fiona{,.bak} || die # Avoid non-working local import
+ epytest ${deselect[@]/#/--deselect }
+ mv fiona{.bak,} || die
+}
diff --git a/dev-python/fiona/metadata.xml b/dev-python/fiona/metadata.xml
new file mode 100644
index 000000000..e1e191ee0
--- /dev/null
+++ b/dev-python/fiona/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Fiona reads and writes geographic data files and thereby helps Python
+ programmers integrate geographic information systems with other
+ computer systems. Fiona contains extension modules that link the
+ Geospatial Data Abstraction Library (GDAL).
+</longdescription>
+ <upstream>
+ <remote-id type="github">Toblerity/fiona</remote-id>
+ <remote-id type="pypi">Fiona</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest
index dc2502c8d..895961b9b 100644
--- a/dev-python/fslpy/Manifest
+++ b/dev-python/fslpy/Manifest
@@ -1,2 +1,3 @@
DIST fslpy-2.8.4.tar.gz 4655735 BLAKE2B 3ab673b724c375e2cdc0caf797e1d528381fdfc0cef1e09f8d5348f34502c6da0d311e51172cb7f0402219110d72ab8aa3cfbb3cb108aa894171f4b6d6f4e7e3 SHA512 43acb95fdfc23e1810d372c945a9080e784106f2c1f65c096962681f3e0f6d4b3b7c3b59bb8b4c196cf9df6093ff01e4cce3a50e16e8a64f1f97739ded84c6e5
DIST fslpy-3.4.0.tar.gz 4691622 BLAKE2B 95cb246aafe7210fcaf5dd11336ad1ba9afca27c50fec23a56bbcd5658d6a0f28ef15e71816f1a0d77949d6232f15325b85331a16b50578d8cdeb7f4da94a326 SHA512 4e860e70fc3681c6c7e1869e9b9f8ed7d63fbf9496dd302493670e2aac730cc5ef72e246264b4b8f448a85b0dd78282778fd4516d2751fd1d9b7be0d11db89e9
+DIST fslpy-3.8.1.tar.gz 4698603 BLAKE2B 33740081a065b6684b864eaf50910a38e26ce7aa10d18bf8faaeaf34ee87dfa22e8f2ee3cebc5681f2356cfb519a59ba07232a3cfb81526258ef92f3ced893ea SHA512 1b5d945f6aae6557e892e5700f228170bab8a235c77d06b162fc2afc16663f3bdbe18e54e4e20dad46ac873ccbf0cdc2649e5ac1c53e17b0d78c45e91e8a1896
diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.8.1.ebuild
new file mode 100644
index 000000000..5bff5ed60
--- /dev/null
+++ b/dev-python/fslpy/fslpy-3.8.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1 virtualx
+
+DESCRIPTION="The FSL Python Library"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
+SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-python/h5py-2.9[${PYTHON_USEDEP}]
+ >=dev-python/indexed_gzip-0.7.0[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1[${PYTHON_USEDEP}]
+ >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
+ >=dev-python/trimesh-2.37.29[${PYTHON_USEDEP}]
+ =dev-python/wxpython-4*[${PYTHON_USEDEP}]
+ >=sci-libs/rtree-0.8.3[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-2.4[${PYTHON_USEDEP}]
+ >=dev-python/scipy-0.18[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/fslpy-2.7.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+
+python_test() {
+ virtx epytest --niters=50 -m "not (dicomtest or longtest or fsltest)"
+}
diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest
new file mode 100644
index 000000000..c541ed559
--- /dev/null
+++ b/dev-python/geopandas/Manifest
@@ -0,0 +1 @@
+DIST geopandas-0.10.2.tar.gz 6317604 BLAKE2B 5eb0d84c11eda99b43bc15b179a971c5e56fb36d40c771b523161dd6ddac4faee4bac483ccd1bdb9f10f73dfd2adf6d72703cc180359cd68383bfba9410f4f5b SHA512 339660c423955b9f110eb390c3d1dc88eeb1ed74fa300870ae277d312e9b2e6733463bc45b445c73a9f8b6dee82d82f203c7b75c0a4aad7e36e43e5c7ec78f42
diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.10.2.ebuild
new file mode 100644
index 000000000..6dde1c23f
--- /dev/null
+++ b/dev-python/geopandas/geopandas-0.10.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Python tools for geographic data"
+HOMEPAGE="https://github.com/geopandas/geopandas"
+SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/pandas[${PYTHON_USEDEP}]
+ sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/fiona[${PYTHON_USEDEP}]
+ dev-python/pyproj[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+python_test() {
+ local deselect=(
+ # disable tests due to networking being blocked
+ geopandas/io/tests/test_file.py::test_read_file_remote_zipfile_url
+ geopandas/io/tests/test_file.py::test_read_file_remote_geojson_url
+ )
+
+ epytest ${deselect[@]/#/--deselect }
+}
diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml
new file mode 100644
index 000000000..a9b62a0d8
--- /dev/null
+++ b/dev-python/geopandas/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ GeoPandas is a project to add support for geographic data to pandas
+ objects. It currently implements GeoSeries and GeoDataFrame types
+ which are subclasses of pandas.Series and pandas.DataFrame
+ respectively. GeoPandas objects can act on shapely geometry objects
+ and perform geometric operations.
+</longdescription>
+ <upstream>
+ <remote-id type="github">geopandas/geopandas</remote-id>
+ <remote-id type="pypi">geopandas</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest
new file mode 100644
index 000000000..67e1f4b6c
--- /dev/null
+++ b/dev-python/hdmf/Manifest
@@ -0,0 +1 @@
+DIST hdmf-3.1.1.tar.gz 292419 BLAKE2B eed1b1c282f022f7e1bd3af63c3078563a74895bf177244841ee0cabd3ab391e2d7a48c9a111a909f5982bf1a1c9b44f1b82fd710f9729681bcada396d3c3d7b SHA512 41776932b1150126a162e9f87072d6626a28bb3f0e05f75337e4f6529c27005ca9db932fdff0c45bb16cbebf68388c7cbf575bbd17950c29c300702a37afacf0
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
new file mode 100644
index 000000000..989332bb5
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
@@ -0,0 +1,10 @@
+--- a/setup.py 2021-09-24 00:51:55.892741725 -0400
++++ b/setup.py 2021-10-27 14:33:20.733741241 -0400
+@@ -23,7 +23,7 @@
+ 'scipy>=1.1,<2',
+ 'pandas>=1.0.5,<2',
+ 'ruamel.yaml>=0.16,<1',
+- 'jsonschema>=2.6.0,<4',
++ 'jsonschema>=2.6.0',
+ 'setuptools',
+ ]
diff --git a/dev-python/hdmf/hdmf-3.1.1.ebuild b/dev-python/hdmf/hdmf-3.1.1.ebuild
new file mode 100644
index 000000000..1731b0d90
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.1.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1
+
+DESCRIPTION="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf"
+SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${PN}-3.1.1-new_jsonschema.patch"
+)
diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml
new file mode 100644
index 000000000..82da7c426
--- /dev/null
+++ b/dev-python/hdmf/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The Hierarchical Data Modeling Framework, or HDMF, is a Python package
+ for working with hierarchical data. It provides APIs for specifying
+ data models, reading and writing data to different storage backends,
+ and representing data with Python object.
+ </longdescription>
+</pkgmetadata>
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
new file mode 100644
index 000000000..ea7fa3ead
--- /dev/null
+++ b/dev-python/llvmlite/Manifest
@@ -0,0 +1,2 @@
+DIST llvmlite-0.37.0.gh.tar.gz 223602 BLAKE2B 74f975d5ac1782528f60f1c0d5c6230a02953e0d494d8323e4caa6651f642ad791ad51df44f6593da41edc5c34bd883f144e95b16f9b8962393d16de013fdbc5 SHA512 665f486fd38c9cc4ee91b15fc75f33451ada6391fc9f1b371091ece844693e0cd8e23766400bf76d9879e8f10f53f4e21f8bb19f3ff1e01c4a95ce9004b0884a
+DIST llvmlite-0.38.0.gh.tar.gz 230044 BLAKE2B b027f34a6ba4c6d8a4fe8963501a49b1f87cc86976c131c94c597383ab47aef1faf6bb05f27f148f03b2d6673e12b04fdfbdab20658de32b18c257bb1cd16fee SHA512 014e2ba08a451ff8bb76ea4b25d2d6605bc048cae560ad367a3bb3afd13421aaf151862116e73e7606d800638d2a2df713cc0e187a6acc483b80df1290c81743
diff --git a/dev-python/llvmlite/llvmlite-0.37.0.ebuild b/dev-python/llvmlite/llvmlite-0.37.0.ebuild
new file mode 100644
index 000000000..d76175444
--- /dev/null
+++ b/dev-python/llvmlite/llvmlite-0.37.0.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+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}/${P/_/}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="examples"
+
+LLVM_MAX_SLOT=11
+
+RDEPEND="
+ sys-devel/llvm:${LLVM_MAX_SLOT}
+ sys-libs/zlib:0=
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
+ distutils-r1_src_prepare
+}
+
+python_configure_all() {
+ # upstream's build system is just horrible, and they ignored the PR
+ # fixing it, so let's build the shared lib properly using implicit
+ # make rules
+
+ export LDLIBS=$(llvm-config --libs all)
+ export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
+ export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
+
+ local files=( ffi/*.cpp )
+ emake -f - <<EOF
+ffi/libllvmlite.so: ${files[*]/.cpp/.o}
+ \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
+EOF
+
+ export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
+}
+
+python_test() {
+ "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ if use examples; then
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
diff --git a/dev-python/llvmlite/llvmlite-0.38.0.ebuild b/dev-python/llvmlite/llvmlite-0.38.0.ebuild
new file mode 100644
index 000000000..cadbc5407
--- /dev/null
+++ b/dev-python/llvmlite/llvmlite-0.38.0.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+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}/${P/_/}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="examples"
+
+LLVM_MAX_SLOT=11
+
+RDEPEND="
+ sys-devel/llvm:${LLVM_MAX_SLOT}
+ sys-libs/zlib:0=
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
+ distutils-r1_src_prepare
+}
+
+python_configure_all() {
+ # upstream's build system is just horrible, and they ignored the PR
+ # fixing it, so let's build the shared lib properly using implicit
+ # make rules
+
+ export LDLIBS=$(llvm-config --libs all)
+ export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
+ export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
+
+ local files=( ffi/*.cpp )
+ emake -f - <<EOF
+ffi/libllvmlite.so: ${files[*]/.cpp/.o}
+ \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
+EOF
+
+ export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
+}
+
+python_test() {
+ "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ if use examples; then
+ dodoc -r examples
+ docompress -x /usr/share/doc/${PF}/examples
+ fi
+}
diff --git a/dev-python/llvmlite/metadata.xml b/dev-python/llvmlite/metadata.xml
new file mode 100644
index 000000000..0983f7a41
--- /dev/null
+++ b/dev-python/llvmlite/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription>
+ llvmlite uses the LLVM library for JIT (just-in-time) compilation of
+ Python code into native machine instructions during runtime. Instead
+ of exposing large parts of the LLVM C++ API for direct calls into the
+ LLVM library, llvmlite follows a lightweight multi-layered approach.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">llvmlite</remote-id>
+ <remote-id type="github">numba/llvmlite</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index 04302b8a6..05834c652 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1 +1,2 @@
DIST numba-0.54.0.tar.gz 2263302 BLAKE2B 24747fcf23f686460fdd8df4784a3bccd6c41f07ff7e657f797a2959066254c079b05ec4460a7cbafef9482f463aa000ee28f8f09339cd7568a0c85b52bc4437 SHA512 ad1142e8c772660b7cbbd17566b9dc96784057467b5cc546f88e2215c9428905e1f6da05ffe104f4ad526f5131fedfa9057745d5458c3293a8cd8e01a49d0fad
+DIST numba-0.55.0.tar.gz 2335694 BLAKE2B 38b0b6f1aa0a903db4a3a8185d5e0b81a5eb87be8db3e5f176e3e2dcd0b1777a473826742d975de2ff7cb5acbd7c3fd3c2e8a5a9d1199cb335b95bc5b913b085 SHA512 cbf758c2b928537968dc70e2f6a97ff14ced0954b7b61a091ace921866adaa1ed17a31cc7d27aa43f071b32c473508e13eb56f1cb6473aeaa00c04f5e7484f86
diff --git a/dev-python/numba/numba-0.55.0.ebuild b/dev-python/numba/numba-0.55.0.ebuild
new file mode 100644
index 000000000..c700339ad
--- /dev/null
+++ b/dev-python/numba/numba-0.55.0.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit optfeature multiprocessing distutils-r1
+
+DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
+HOMEPAGE="https://numba.pydata.org/
+ https://github.com/numba"
+SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="openmp threads"
+
+RDEPEND="
+ >=dev-python/llvmlite-0.38.0[${PYTHON_USEDEP}]
+ <=dev-python/llvmlite-0.39.0
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+ <dev-python/numpy-1.22[${PYTHON_USEDEP}]
+ threads? ( >=dev-cpp/tbb-2019.5 )
+"
+BDEPEND="
+ dev-python/pip[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+"
+
+DISTUTILS_IN_SOURCE_BUILD=1
+distutils_enable_tests unittest
+distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
+)
+
+pkg_setup() {
+ if ! use openmp; then
+ export NUMBA_DISABLE_OPENMP=1 || die
+ else
+ unset NUMBA_DISABLE_OPENMP || die
+ fi
+ if ! use threads; then
+ export NUMBA_DISABLE_TBB=1 || die
+ else
+ unset NUMBA_DISABLE_TBB || die
+ export TBBROOT="${EPREFIX}/usr" || die
+ fi
+}
+
+python_prepare_all() {
+ # This conf.py only works in a git repo
+ if use doc; then
+ git init -q || die
+ git config user.email "larry@gentoo.org" || die
+ git config user.name "Larry the Cow" || die
+ git add . || die
+ git commit -m "init" || die
+ fi
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ # FIXME: parallel python building fails. See Portage bug #614464 and
+ # gentoo/sci issue #1080.
+ export MAKEOPTS=-j1 || die
+ distutils-r1_python_compile
+}
+
+# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
+python_test() {
+ distutils_install_for_testing
+ ${EPYTHON} setup.py build_ext --inplace || die \
+ "${EPYTHON} failed to build_ext"
+ ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
+ "${EPYTHON} failed unittests"
+}
+
+pkg_postinst() {
+ optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
+}
diff --git a/dev-python/protobuf-python/Manifest b/dev-python/protobuf-python/Manifest
deleted file mode 100644
index 81632cac5..000000000
--- a/dev-python/protobuf-python/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST protobuf-3.11.4.tar.gz 5140799 BLAKE2B 97b450c0623593efe6a42b66582ff183344b8831689e6a5b4d36096dbd57c33da9569bbf26578536aaf73ecd866ac0588b6cb7d55a6a9b9a6e840d4c57099001 SHA512 777bbb0e9e2375eaebe6b8c87abd660bac70ee469c9ad00dd25917b82d7fb5bbe33cf87f0d69c90e19d55c07a7285ec20974ba4768623ce9ccfadf147fd5e261
diff --git a/dev-python/protobuf-python/files/protobuf-python-3.13.0-google.protobuf.pyext._message.PyUnknownFieldRef.patch b/dev-python/protobuf-python/files/protobuf-python-3.13.0-google.protobuf.pyext._message.PyUnknownFieldRef.patch
deleted file mode 100644
index 68318320b..000000000
--- a/dev-python/protobuf-python/files/protobuf-python-3.13.0-google.protobuf.pyext._message.PyUnknownFieldRef.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-https://github.com/protocolbuffers/protobuf/issues/6205
-https://github.com/protocolbuffers/protobuf/pull/7016
-
---- /python/google/protobuf/pyext/unknown_fields.cc
-+++ /python/google/protobuf/pyext/unknown_fields.cc
-@@ -277,13 +277,13 @@
- PyObject* data = NULL;
- switch (field->type()) {
- case UnknownField::TYPE_VARINT:
-- data = PyInt_FromLong(field->varint());
-+ data = PyLong_FromUnsignedLongLong(field->varint());
- break;
- case UnknownField::TYPE_FIXED32:
-- data = PyInt_FromLong(field->fixed32());
-+ data = PyLong_FromUnsignedLong(field->fixed32());
- break;
- case UnknownField::TYPE_FIXED64:
-- data = PyInt_FromLong(field->fixed64());
-+ data = PyLong_FromUnsignedLongLong(field->fixed64());
- break;
- case UnknownField::TYPE_LENGTH_DELIMITED:
- data = PyBytes_FromStringAndSize(field->length_delimited().data(),
diff --git a/dev-python/protobuf-python/metadata.xml b/dev-python/protobuf-python/metadata.xml
deleted file mode 100644
index 0d125ed97..000000000
--- a/dev-python/protobuf-python/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <description>Gentoo Science Project</description>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-python/protobuf-python/protobuf-python-3.11.4-r1.ebuild b/dev-python/protobuf-python/protobuf-python-3.11.4-r1.ebuild
deleted file mode 100644
index 1d447ef46..000000000
--- a/dev-python/protobuf-python/protobuf-python-3.11.4-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 2008-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="7"
-PYTHON_COMPAT=(python{3_7,3_8})
-DISTUTILS_USE_SETUPTOOLS="rdepend"
-
-inherit distutils-r1
-
-DESCRIPTION="Google's Protocol Buffers - Python bindings"
-HOMEPAGE="https://developers.google.com/protocol-buffers/ https://github.com/protocolbuffers/protobuf"
-SRC_URI="https://github.com/protocolbuffers/protobuf/archive/v${PV}.tar.gz -> protobuf-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/22"
-KEYWORDS="~amd64"
-IUSE=""
-
-BDEPEND="${PYTHON_DEPS}
- ~dev-libs/protobuf-${PV}
- dev-python/namespace-google[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]"
-DEPEND="${PYTHON_DEPS}
- ~dev-libs/protobuf-${PV}"
-RDEPEND="${BDEPEND}"
-
-S="${WORKDIR}/protobuf-${PV}/python"
-
-if [[ "${PV}" == "9999" ]]; then
- EGIT_CHECKOUT_DIR="${WORKDIR}/protobuf-${PV}"
-fi
-
-python_prepare_all() {
- pushd "${WORKDIR}/protobuf-${PV}" > /dev/null || die
- eapply "${FILESDIR}/${PN}-3.13.0-google.protobuf.pyext._message.PyUnknownFieldRef.patch"
- eapply_user
- popd > /dev/null || die
-
- distutils-r1_python_prepare_all
-}
-
-python_configure_all() {
- mydistutilsargs=(--cpp_implementation)
-}
-
-python_compile() {
- python_is_python3 || local -x CXXFLAGS="${CXXFLAGS} -fno-strict-aliasing"
- distutils-r1_python_compile
-}
-
-python_test() {
- esetup.py test
-}
-
-python_install_all() {
- distutils-r1_python_install_all
-
- find "${ED}" -name "*.pth" -type f -delete || die
-}
diff --git a/dev-python/pybind11-stubgen/Manifest b/dev-python/pybind11-stubgen/Manifest
index 57271a3a5..783143fe7 100644
--- a/dev-python/pybind11-stubgen/Manifest
+++ b/dev-python/pybind11-stubgen/Manifest
@@ -1,2 +1,3 @@
+DIST pybind11-stubgen-0.10.4.tar.gz 12605 BLAKE2B 5cb3e4301a896066ac26a7e6b9af83c77fb16fd5a3e48713a597e981a68e41cd90ddf0e351c177b7385966e8720100ef03b0524dfd381f17c87a2016a6eba808 SHA512 b43795c5fef6eee5198ec7590338f8a2dabbc4a2530de49f50a3b1a410da60188da86f7148a74ff014068c8d9ce5b058695902e236407ab221d640ac9b15903d
DIST pybind11-stubgen-0.8.6.tar.gz 10993 BLAKE2B f3073dac1bff941cbf2470d50d11a090a99ff335a08cca3efc217d06c3a0cab266cf9769a1a7bdc5349da7cc3120e8a6b54f60df775ee27fcfbf0b5003867726 SHA512 6a8338f78d636b865bb76a3e769997f1c781acb57a0bb4f68f59ae2d6f3c60efe2b2ec7a9034f4e172b3d4bc4c74c990a4a24c6b2df242573fa7f03b97a84851
DIST pybind11-stubgen-0.8.7.tar.gz 10993 BLAKE2B e672e955535bb7d797a3ee692f3fb13658d589bedc60c207dc094efff2e6281aec81636b0719a61567be46eb2fb27b7235e38cc06c436dea2689ae32b4b53b18 SHA512 56f3d84027d7cb06cce608ac7403a3fea902277d6e44fa3e284227656bca036ba956ef6b51a4f963a0b19e8fe30c0ddfac6670ea338905bf3ac39668748da668
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
new file mode 100644
index 000000000..f73f2dd4b
--- /dev/null
+++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
+HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-python/pybind11[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/pyerfa/Manifest b/dev-python/pyerfa/Manifest
index 1f49a4621..29344f9fb 100644
--- a/dev-python/pyerfa/Manifest
+++ b/dev-python/pyerfa/Manifest
@@ -1 +1 @@
-DIST pyerfa-1.7.1.1.tar.gz 1322843 BLAKE2B 416c357faeb5316a692a214039e0e2792088fc93b26b6a006fc63b6b2fd9443c3399972ab8d12066b19640c8b97b5fdd24f3bd158a92dbf1224bf4a8f1eeb12b SHA512 59c2dceed6ef5b1ece618742dd0084b729cce8eb52f903dff2aad009fa0f495defb4511688da0a5203ed5900d041a552fbe50668ddac0c3a6bb3fd6d34d089bb
+DIST pyerfa-2.0.0.1.tar.gz 808497 BLAKE2B b9c6973330236f4a983fdbb6b0f3faefc3fd8ec8a2187b5cd37d3d4a97ab9aa7da4008c1d77f9b2465282b164cdf338f41e816344f5ba15af3fda48ccb71d3b8 SHA512 420e7bb2d00a9bd7d2290b6b0598b5963404ac021f713ae7bbf607135b9db6605f63dd89694d2cf406eb230b58b1028f2458f96ed834127ce9a398810cfea589
diff --git a/dev-python/pyerfa/pyerfa-1.7.1.1.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
index d8c73e666..2e5bdf3e0 100644
--- a/dev-python/pyerfa/pyerfa-1.7.1.1.ebuild
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,11 +16,11 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
# ImportError: cannot import name 'ufunc' from 'erfa'
-RESTRICT="test"
+#RESTRICT="test"
RDEPEND="
sci-astronomy/erfa:0=
- dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
"
BDEPEND="${RDEPEND}
dev-python/setuptools_scm[${PYTHON_USEDEP}]
diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest
index 4f66e9882..4a1e50d88 100644
--- a/dev-python/pytest-doctestplus/Manifest
+++ b/dev-python/pytest-doctestplus/Manifest
@@ -1 +1 @@
-DIST pytest-doctestplus-0.8.0.tar.gz 27489 BLAKE2B 1377eeadc1c0558c0f0f497aec775f04fc111b7815468c87a48e1abedbb66f648128b10ba050a798232cc63cba1c79e794c4653e51f8ee5a27029a6ed10fb5a6 SHA512 108f6bf2d5d663bfc9c6c50e63633814baf248062b6e2d83ca6e83d1d8db9940251ebbb60cd57b04e8ede20b9511f4c86e4ac618618cb42ccaa68c6c38989f2e
+DIST pytest-doctestplus-0.11.2.tar.gz 34943 BLAKE2B a45779ff3d65e1b920282f400d67b618f620a9a905da69edff96db799f30e1b93562e69bd567a49629194b962a080b1f675619b0c6995227a1391c3d0e74be20 SHA512 fed49a551be78f51db60161ccfa592e461719cca76e2a48e3267e8a22dbec60d02d8fbb757a88cb5cf4dc22143e27d3d20f25b51855be835254c72fd8260abbd
diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
index 05b962262..17b19cbb0 100644
--- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.8.0.ebuild
+++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -16,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
# TODO: fix this
+# AttributeError: type object 'reprec' has no attribute 'assertoutcome'
RESTRICT="test"
RDEPEND="dev-python/pytest[${PYTHON_USEDEP}]"
diff --git a/dev-python/pytorch-lightning/Manifest b/dev-python/pytorch-lightning/Manifest
new file mode 100644
index 000000000..f9f1f6b1d
--- /dev/null
+++ b/dev-python/pytorch-lightning/Manifest
@@ -0,0 +1 @@
+DIST pytorch-lightning-1.5.8.tar.gz 444592 BLAKE2B 7fa8e230811381a0aea43f4d098f9d833350183cfe10ea2f51aa6c4a8c9835ed979d103572b352c2831361d5802caf66a674da0fccf948ba9b14cdb7d77d325e SHA512 e9c08b5614f8041e2511977b0e42be5d209efbf20a80ae8067bf7ac4dedd5d30908a33542fb3f1601814dba769ffeb545ba8a66ff368ff038e8fdc5f630dc808
diff --git a/dev-lang/tcl/metadata.xml b/dev-python/pytorch-lightning/metadata.xml
index 354c72665..2e30eb3db 100644
--- a/dev-lang/tcl/metadata.xml
+++ b/dev-python/pytorch-lightning/metadata.xml
@@ -3,9 +3,10 @@
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
+ <name>Science Project</name>
</maintainer>
<upstream>
- <remote-id type="sourceforge">tcl</remote-id>
+ <remote-id type="github">PyTorchLightning/pytorch-lightning</remote-id>
+ <remote-id type="pypi">pytorch-lightning</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
new file mode 100644
index 000000000..7b3ad5e3f
--- /dev/null
+++ b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_SINGLE_IMPL=1
+
+inherit distutils-r1
+
+DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
+HOMEPAGE="https://github.com/PyTorchLightning/pytorch-lightning"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-libs/pytorch[python,${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/future[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ sci-visualization/tensorboard[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/ratelimit[${PYTHON_USEDEP}]
+ ')
+"
diff --git a/dev-python/rasterio/Manifest b/dev-python/rasterio/Manifest
new file mode 100644
index 000000000..a87aed058
--- /dev/null
+++ b/dev-python/rasterio/Manifest
@@ -0,0 +1 @@
+DIST rasterio-1.2.10.tar.gz 12888995 BLAKE2B e6e4e55ae2fc7c10839625331f52a3366815672412dee7ee2332d32ce842c35ebbbb81e446d03a92a1cb6f877ecc377de1509d2d8c857ab7034dd246996b0318 SHA512 97559778163a36982b733137f6b5a879649c9591583cf80ccb38739f6565bf65c6b198d499242811ebb7342a3a4ef3756451bc3c7d1b431f8d1e568c6bae41d5
diff --git a/dev-python/rasterio/metadata.xml b/dev-python/rasterio/metadata.xml
new file mode 100644
index 000000000..88f92bb1c
--- /dev/null
+++ b/dev-python/rasterio/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Rasterio reads and writes geospatial raster data. Geographic information
+ systems use GeoTIFF and other formats to organize and store gridded,
+ or raster, datasets. Rasterio reads and writes these formats and
+ provides a Python API based on N-D arrays.
+</longdescription>
+ <upstream>
+ <remote-id type="github">rasterio/rasterio</remote-id>
+ <remote-id type="pypi">rasterio</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/rasterio/rasterio-1.2.10.ebuild b/dev-python/rasterio/rasterio-1.2.10.ebuild
new file mode 100644
index 000000000..625e4a7da
--- /dev/null
+++ b/dev-python/rasterio/rasterio-1.2.10.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Command line tool and API for geospatial raster data"
+HOMEPAGE="https://github.com/rasterio/rasterio"
+SRC_URI="https://github.com/rasterio/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ dev-python/affine[${PYTHON_USEDEP}]
+ dev-python/attrs[${PYTHON_USEDEP}]
+ dev-python/certifi[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/cligj[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/click-plugins[${PYTHON_USEDEP}]
+ dev-python/snuggs[${PYTHON_USEDEP}]
+"
+#DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ test? (
+ dev-python/boto3[${PYTHON_USEDEP}]
+ dev-python/hypothesis[${PYTHON_USEDEP}]
+ sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+ local deselect=(
+ # disable tests failing for unknown reason
+ tests/test_env.py::test_rio_env_no_credentials
+ tests/test_rio_info.py::test_info_azure_unsigned
+ tests/test_warp.py::test_reproject_resampling[Resampling.cubic]
+ tests/test_warp.py::test_reproject_resampling[Resampling.lanczos]
+ tests/test_warp.py::test_reproject_resampling_alpha[Resampling.cubic]
+ tests/test_warp.py::test_reproject_resampling_alpha[Resampling.lanczos]
+
+ #tests/test_warp.py::test_warp_from_to_file_multi
+
+ # aux-xml
+ #tests/test_dataset.py::test_files
+ #tests/test_gcps.py::test_write_read_gcps_buffereddatasetwriter
+ #tests/test_rio_edit_info.py::test_delete_nodata
+ #tests/test_update.py::test_update_nodatavals_none
+
+ # curl
+ #tests/test_warp.py::test_reproject_error_propagation
+
+ # geos
+ #tests/test_warp.py::test_transform_geom_polygon_offset
+ #tests/test_warp.py::test_transform_geom_polygon_cutting
+
+ # png
+ #tests/test_colormap.py::test_write_colormap
+ #tests/test_no_georef.py::test_write
+ #tests/test_png.py::test_write_ubyte
+ #tests/test_rio_convert.py::test_autodetect_format
+ #tests/test_rio_merge.py::test_merge_output_dataset
+ #tests/test_shutil.py::test_delete[None-png]
+ #tests/test_shutil.py::test_delete[PNG-png]
+ #tests/test_write.py::test_write__autodetect_driver[png-PNG]
+ #tests/test_write.py::test_issue2088[PNG]
+
+ # jpeg
+ #tests/test_blocks.py::test_block_size_exception
+ #tests/test_crs.py::test_read_no_crs
+ #tests/test_memoryfile.py::test_zip_file_object_read
+ #tests/test_memoryfile.py::test_vrt_memfile
+ #tests/test_memoryfile.py::test_write_plus_model_jpeg
+ #tests/test_rio_convert.py::test_format
+ #tests/test_rio_convert.py::test_format_short
+ #tests/test_rio_convert.py::test_output_opt
+ #tests/test_rio_convert.py::test_convert_overwrite_without_option
+ #tests/test_rio_convert.py::test_convert_overwrite_with_option
+ #tests/test_rio_stack.py::test_format_jpeg
+ #tests/test_rio_warp.py::test_warp_vrt_gcps
+ #tests/test_shutil.py::test_copy_strict_failure
+ #tests/test_shutil.py::test_copy_strict_silent_failure
+ #tests/test_write.py::test_write__autodetect_driver[jpg-JPEG]
+ #tests/test_write.py::test_write__autodetect_driver[jpeg-JPEG]
+ #tests/test_write.py::test_issue2088[JPEG]
+
+ # threads
+ #tests/test_thread_pool_executor.py::test_threads_main_env
+ #tests/test_threading.py::test_child_thread_inherits_env
+ )
+
+ mv rasterio{,.bak} || die # Avoid non-working local import
+ epytest ${deselect[@]/#/--deselect }
+ mv rasterio{.bak,} || die
+}
diff --git a/dev-python/rasterstats/Manifest b/dev-python/rasterstats/Manifest
new file mode 100644
index 000000000..261dbac3d
--- /dev/null
+++ b/dev-python/rasterstats/Manifest
@@ -0,0 +1 @@
+DIST rasterstats-0.16.0.tar.gz 610224 BLAKE2B bc84e93e7aa9d4ca32516d85b6f01d3c1badd42af2a211d6116a78614252b9bd5488a21b3a3a1000f1fd0bd205e2009e598df8953add000f4eee2d572a4d6c61 SHA512 c3174d1a8aa18f663d5bf05beb4f56aeaf768939220b29d26d5b892936309a48b8777ee16a88b009011f718fbd7432056deaffaac917161631532b0670c0263e
diff --git a/dev-python/rasterstats/metadata.xml b/dev-python/rasterstats/metadata.xml
new file mode 100644
index 000000000..ab1322912
--- /dev/null
+++ b/dev-python/rasterstats/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ rasterstats is a Python module for summarizing geospatial raster datasets
+ based on vector geometries. It includes functions for zonal statistics
+ and interpolated point queries. The command-line interface allows for
+ easy interoperability with other GeoJSON tools.
+</longdescription>
+ <upstream>
+ <remote-id type="github">perrygeo/python-rasterstats</remote-id>
+ <remote-id type="pypi">rasterstats</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
new file mode 100644
index 000000000..ccaa17351
--- /dev/null
+++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Python module for summarizing geospatial raster datasets based on vectors"
+HOMEPAGE="https://github.com/perrygeo/python-rasterstats"
+SRC_URI="https://github.com/perrygeo/python-${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/affine[${PYTHON_USEDEP}]
+ sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/rasterio[${PYTHON_USEDEP}]
+ dev-python/cligj[${PYTHON_USEDEP}]
+ dev-python/fiona[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/python-${P}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/snuggs/Manifest b/dev-python/snuggs/Manifest
new file mode 100644
index 000000000..d9ccc74fd
--- /dev/null
+++ b/dev-python/snuggs/Manifest
@@ -0,0 +1 @@
+DIST snuggs-1.4.7.tar.gz 7762 BLAKE2B fae10c4e6f759219cbecdbea4b8f49001980824fe1d43fba9d5b62837a88183d1ecb6f55e191b637048e03856b1c6466cb17a9c38dfa332537d8968c8510fc25 SHA512 c1f40e521d1b0cf15075b22b04000c74ecbd0522cdd820b8c159aac812924d877349b3f3bca93b09eed5b025a34c26665a41c7a52a8145419558b115cf8ef361
diff --git a/dev-python/snuggs/metadata.xml b/dev-python/snuggs/metadata.xml
new file mode 100644
index 000000000..19390156e
--- /dev/null
+++ b/dev-python/snuggs/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Snuggs library parses S-expressions using numpy. Available function
+ include arithmetic and logical operators. Also members of the numpy
+ module such as "asarray()", "mean()" and "where" are available.
+</longdescription>
+ <upstream>
+ <remote-id type="github">mapbox/snuggs</remote-id>
+ <remote-id type="pypi">snuggs</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/snuggs/snuggs-1.4.7.ebuild b/dev-python/snuggs/snuggs-1.4.7.ebuild
new file mode 100644
index 000000000..ebae883ff
--- /dev/null
+++ b/dev-python/snuggs/snuggs-1.4.7.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="S-expressions for numpy"
+HOMEPAGE="https://github.com/mapbox/snuggs"
+SRC_URI="https://github.com/mapbox/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? ( dev-python/hypothesis[${PYTHON_USEDEP}] )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest
index fc19e0aa8..26a909677 100644
--- a/dev-python/sphinx-astropy/Manifest
+++ b/dev-python/sphinx-astropy/Manifest
@@ -1 +1 @@
-DIST sphinx-astropy-1.3.tar.gz 15797 BLAKE2B 737d7a4ae2f7ec6fb382cc8d6fa3de911d13000045e9691f21360b3938e4bebb9b4b70a804deb8bd4343f1bba8e297d8f39fd8ed7787946ba0cb859a4208c980 SHA512 c39df1df90d82e8f67546623fe334ca7d706020f1e00923fcfc41232289aff41d1e697f99ee9b6d43f35f31ef9566be4d9aa99404ee35e1ea85da4b8e30f2ae6
+DIST sphinx-astropy-1.7.0.tar.gz 18266 BLAKE2B 363733c5a3e5974cdf0f62f879babc9a28617ff61d15292649acd189798e24611c2d84e69af5dc05b89241f395cc997233f966bdf8e8a84ccfe235f873d533c2 SHA512 4b9af1528805c5017695be6ad9d0b789437da4ea01080190d5c0e44a76d927098864002cfd2a59529924a8d2844e26d2e7635fb3f0417ed90502e7e47d0239d3
diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
index 4fc2ef799..be4395414 100644
--- a/dev-python/sphinx-astropy/sphinx-astropy-1.3.ebuild
+++ b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -19,9 +19,10 @@ KEYWORDS="~amd64 ~x86"
RESTRICT="test"
RDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}]
dev-python/numpydoc[${PYTHON_USEDEP}]
- dev-python/sphinx[${PYTHON_USEDEP}]
+ >=dev-python/sphinx-1.7[${PYTHON_USEDEP}]
dev-python/sphinx-automodapi[${PYTHON_USEDEP}]
dev-python/sphinx-gallery[${PYTHON_USEDEP}]
dev-python/pillow[${PYTHON_USEDEP}]
diff --git a/dev-python/sphinx-automodapi/Manifest b/dev-python/sphinx-automodapi/Manifest
index 8856f8a59..31e6f3c8b 100644
--- a/dev-python/sphinx-automodapi/Manifest
+++ b/dev-python/sphinx-automodapi/Manifest
@@ -1 +1 @@
-DIST sphinx-automodapi-0.13.tar.gz 38240 BLAKE2B 51eaaebab92881563e0e9df03e2979dbf0d22bf61bd8a7c56198cfbbcf97a17447019296dcee25f3a5dce091efb0c8e0748fb83dd47e93976aa1b01e165cbce7 SHA512 394b45ddeb923248250989271e400586188df973c8b13d551345cd056322de1208a8d7a135c095b2daa7b5b491b77a4077bba2dc450ef718ea5dbe07f7f63d36
+DIST sphinx-automodapi-0.14.1.tar.gz 45504 BLAKE2B 1d6aa247c9991260c0d6421dbeb80adccec72f60e6e0035ef892d6582e62608dd526a77da6c4b5066c9c100228fd6aceb77a9965eab76c0b9117a96d76ee221a SHA512 fae2927f8f9ec29f5e8e945b2902a0fa94231446b514be884ddab1a8644b4e305408e986b74a4506447baf00c4941cf9e7585f0c8e82820935a3d831bcfa6374
diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
index 5c93e04fe..f98b972ae 100644
--- a/dev-python/sphinx-automodapi/sphinx-automodapi-0.13.ebuild
+++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -15,7 +15,7 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-# TODO: fix this
+# Requires network for some reason
RESTRICT="test"
RDEPEND="dev-python/sphinx[${PYTHON_USEDEP}]"
diff --git a/dev-python/traits/traits-6.0.0.ebuild b/dev-python/traits/traits-6.0.0.ebuild
index 0d1a480b1..732c6247a 100644
--- a/dev-python/traits/traits-6.0.0.ebuild
+++ b/dev-python/traits/traits-6.0.0.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit distutils-r1 virtualx
+inherit distutils-r1
DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
HOMEPAGE="https://docs.enthought.com/traits/
@@ -17,6 +17,7 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
IUSE="test"
+RESTRICT="!test? ( test )"
RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild
index ac4465fe9..e0263e441 100644
--- a/dev-python/traits/traits-6.1.1.ebuild
+++ b/dev-python/traits/traits-6.1.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit distutils-r1 virtualx
+inherit distutils-r1
DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
HOMEPAGE="https://docs.enthought.com/traits/
diff --git a/dev-python/trimesh/Manifest b/dev-python/trimesh/Manifest
index 842411fcb..dc63d312d 100644
--- a/dev-python/trimesh/Manifest
+++ b/dev-python/trimesh/Manifest
@@ -1 +1,2 @@
DIST trimesh-3.9.1.tar.gz 10407978 BLAKE2B e16829d9f99d1d88bc924004d7187d086a04d1cc91fefb1e32e1a22d8774469b492d3240b902ec2fbd1f085fa43e2b9196b4d077c8856037cfd0447beaa13c4d SHA512 ef278acf894abff6b64223934d669558a2c0bfaa611607c908810df67597f635d50786b6e18651e30ee70dee88163ec9a624f4d8e13a3a9b171782ee04498bc2
+DIST trimesh-3.9.42.tar.gz 10626604 BLAKE2B 3b6c8caeb50b2fa3f540638f4e9cf228e64e9d8c41b2908689d6122ac1444ecfa67bd622afc9df0c02af3936bfee712aa55a8afb65ba6f0f4711872cbf801e5f SHA512 fa5e048ef5baba51466be1a3c16924fd89ca4047b05e630c2980345c6e8a1bdf7ce5819858dd7ed95e9aef6a0bb6ca4a5ae605e8d0279f5ccd7529c3a143bf18
diff --git a/dev-python/trimesh/trimesh-3.9.42.ebuild b/dev-python/trimesh/trimesh-3.9.42.ebuild
new file mode 100644
index 000000000..3ec15c516
--- /dev/null
+++ b/dev-python/trimesh/trimesh-3.9.42.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="Python library for loading and using triangular meshes."
+HOMEPAGE="https://trimsh.org/"
+SRC_URI="https://github.com/mikedh/trimesh/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="extra"
+
+DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="
+ extra? (
+ dev-libs/xxhash
+ dev-python/colorlog[${PYTHON_USEDEP}]
+ dev-python/chardet[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/pyglet[${PYTHON_USEDEP}]
+ dev-python/pycollada[${PYTHON_USEDEP}]
+ dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/svg-path[${PYTHON_USEDEP}]
+ dev-python/sympy[${PYTHON_USEDEP}]
+ sci-libs/scikit-image[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ sci-libs/shapely[${PYTHON_USEDEP}]
+ sci-libs/rtree[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+# TODO: package pypandoc
+# distutils_enable_sphinx docs \
+# dev-python/sphinx_rtd_theme \
+# dev-python/numpy \
+# dev-python/scipy \
+# dev-python/networkx \
+# dev-python/recommonmark \
+# dev-python/jupyter \
+# dev-python/pyopenssl \
+# dev-python/autodocsumm \
+# dev-python/jinja2 \
+# dev-python/matplotlib
+
+python_test() {
+ if use extra; then
+ epytest
+ else
+ cd tests || die
+ epytest -p no:warnings $(grep -v '^#' basic.list)
+ fi
+}
diff --git a/dev-tcltk/togl/Manifest b/dev-tcltk/togl/Manifest
deleted file mode 100644
index 5621b858f..000000000
--- a/dev-tcltk/togl/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Togl-1.7.tar.gz 205532 BLAKE2B 5a05356d0e3c7655135f0c6ccaa77f61cb38cc1209d9b9d3122591649358c6739b5bef7a9aebd3ffe26c1d450c1eb28470a34ec0b17bfef2b3f5885a6a35112c SHA512 86dccaf1585767fc2e217cee3172619fe08b1d054beb679bd1db140195a100ec90daef02ac9b85d3e6c2b805d0a7668a540b80754023aee85138cefa7275e84a
-DIST togl-2.0.tar.gz 244968 BLAKE2B f094fb4bba7049470d7f61a2748d4a5baaf47c99c766d96ef8061e254673acf7f2a11555e202ec01f5d6b7a00ae7c275a33981fba5df7f1478f69da17f3180b8 SHA512 2be3062baada848d96b2802582bc5590b215f2ab4dc02c91761e72af2bf8c0ba768a71a2ffb8107bca83b63b7d1321ee83de19b97f83b1c2f0962f9288948b0a
diff --git a/dev-tcltk/togl/metadata.xml b/dev-tcltk/togl/metadata.xml
deleted file mode 100644
index c191e6dbe..000000000
--- a/dev-tcltk/togl/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">togl</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-tcltk/togl/togl-1.7-r1.ebuild b/dev-tcltk/togl/togl-1.7-r1.ebuild
deleted file mode 100644
index c847ab287..000000000
--- a/dev-tcltk/togl/togl-1.7-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_P="Togl-${PV}"
-
-DESCRIPTION="A Tk widget for OpenGL rendering"
-HOMEPAGE="http://togl.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="1.7"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +threads"
-
-RDEPEND="
- dev-lang/tk:0
- virtual/opengl"
-DEPEND="${RDEPEND}"
-
-# tests directory is missing
-RESTRICT="test"
-
-S=${WORKDIR}/${MY_P}
-
-src_configure() {
- econf \
- $(use_enable debug symbols) \
- $(use_enable amd64 64bit) \
- $(use_enable threads)
-}
-
-src_install() {
- default
- rm "${D}"/usr/include/* || die
- insinto /usr/include/${PN}-${SLOT}
- doins togl*.h
-}
diff --git a/dev-tcltk/togl/togl-2.0.ebuild b/dev-tcltk/togl/togl-2.0.ebuild
deleted file mode 100644
index 2dba7d44e..000000000
--- a/dev-tcltk/togl/togl-2.0.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_P="Togl${PV}"
-
-DESCRIPTION="Tk widget for OpenGL rendering"
-HOMEPAGE="http://togl.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}-src.tar.gz -> ${P}.tar.gz"
-S=${WORKDIR}/${MY_P}
-
-LICENSE="BSD"
-SLOT="2.0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +threads"
-
-RDEPEND="
- dev-lang/tk:0
- virtual/opengl
-"
-DEPEND="${RDEPEND}"
-
-# tests directory is missing
-RESTRICT="test"
-
-src_configure() {
- local myconf=(
- $(use_enable debug symbols)
- $(use_enable amd64 64bit)
- $(use_enable threads)
- )
- econf ${myconf[@]}
-}
-
-src_install() {
- default
- rm "${ED}"/usr/include/* || die
- insinto /usr/include/${PN}-${SLOT}
- doins togl*.h
-}
diff --git a/dev-util/bcm/Manifest b/dev-util/bcm/Manifest
deleted file mode 100644
index 77dcd235c..000000000
--- a/dev-util/bcm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bcm-0.0.1_p20191110.tar.gz 28708 BLAKE2B 0c97f93607cb947ede7278f91cf64ddeb9ee06fafc19b8cf8df87ea1bcc49a47cba5276bea43cec3cc5fce390d463108561ba978a9ca5bd80a41a5f0ec114c6a SHA512 ce829791752eb7a2d1aa192173532c80a1d0bfc5ab451fdaf09ec926678653d38a4c6aa19c0fdf6c8aa921ce358bb87f367317c2cc54479c845c5741232b220d
diff --git a/dev-util/bcm/bcm-0.0.1_p20191110.ebuild b/dev-util/bcm/bcm-0.0.1_p20191110.ebuild
deleted file mode 100644
index 64611d6e9..000000000
--- a/dev-util/bcm/bcm-0.0.1_p20191110.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Boost cmake modules"
-HOMEPAGE="http://bcm.readthedocs.io"
-
-COMMIT="2045990a6ace40eb4c4a9f6e5cc1aeeaf7a05fc9"
-SRC_URI="https://github.com/simoncblyth/bcm/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${PN}-${COMMIT}
-
-KEYWORDS="~amd64"
-LICENSE="Boost-1.0"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}"/bcm-0.0.1_donot-send-error.patch )
diff --git a/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch b/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch
deleted file mode 100644
index 17c1c51ea..000000000
--- a/dev-util/bcm/files/bcm-0.0.1_donot-send-error.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: bcm-0.0.1_p20191110/share/bcm/cmake/BCMExport.cmake
-===================================================================
---- bcm-0.0.1_p20191110.orig/share/bcm/cmake/BCMExport.cmake
-+++ bcm-0.0.1_p20191110/share/bcm/cmake/BCMExport.cmake
-@@ -12,7 +12,7 @@ function(bcm_get_target_package_source O
- if(TARGET_IMPORTED OR TARGET_ALIAS)
- get_property(TARGET_FIND_PACKAGE_NAME TARGET ${TARGET} PROPERTY INTERFACE_FIND_PACKAGE_NAME)
- if(NOT TARGET_FIND_PACKAGE_NAME)
-- message(SEND_ERROR "The target ${TARGET_FIND_PACKAGE_NAME} does not have information about find_package() call.")
-+ message(AUTHOR_WARNING "The target ${TARGET_FIND_PACKAGE_NAME} does not have information about find_package() call.")
- endif()
- set(PKG_NAME ${TARGET_FIND_PACKAGE_NAME})
- get_property(TARGET_FIND_PACKAGE_VERSION TARGET ${TARGET} PROPERTY INTERFACE_FIND_PACKAGE_VERSION)
diff --git a/dev-util/bcm/metadata.xml b/dev-util/bcm/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/dev-util/bcm/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-util/boost-build/Manifest b/dev-util/boost-build/Manifest
deleted file mode 100644
index 34653ed7e..000000000
--- a/dev-util/boost-build/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST boost_1_72_0.tar.bz2 106907358 BLAKE2B ab270a0e3cb24da687d86785e2d2e6d7731b4dbc07bd839eadb642dfa5a428ad584acb1f3529661a8de9a986008ff3427491041059ea2b742348d02e00761cd8 SHA512 63bbd1743e7c904b2e69fdc2eafd1c2a8a30fd70d960dcd366059d0100f000cb605d56cbd9397bb18421631f1c9552a772c434d0f0caddbe56302273f51fd1f6
diff --git a/dev-util/boost-build/boost-build-1.72.0.ebuild b/dev-util/boost-build/boost-build-1.72.0.ebuild
deleted file mode 100644
index 7b78ca129..000000000
--- a/dev-util/boost-build/boost-build-1.72.0.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic prefix toolchain-funcs
-
-MY_PV="$(ver_rs 1- _)"
-
-DESCRIPTION="A system for large project software construction, simple to use and powerful"
-HOMEPAGE="https://boostorg.github.io/build/"
-SRC_URI="https://dl.bintray.com/boostorg/release/${PV}/source/boost_${MY_PV}.tar.bz2"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples"
-RESTRICT="test"
-
-S="${WORKDIR}/boost_${MY_PV}/tools/build/src"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-1.71.0-disable_python_rpath.patch
- "${FILESDIR}"/${PN}-1.71.0-add-none-feature-options.patch
- "${FILESDIR}"/${PN}-1.71.0-respect-c_ld-flags.patch
- "${FILESDIR}"/${PN}-1.71.0-no-implicit-march-flags.patch
-)
-
-src_unpack() {
- tar xojf "${DISTDIR}/${A}" boost_${MY_PV}/tools/build || die "unpacking tar failed"
-}
-
-src_prepare() {
- default
-
- pushd .. >/dev/null || die
- eapply "${FILESDIR}"/${PN}-1.71.0-fix-test.patch
- popd >/dev/null || die
-}
-
-src_configure() {
- hprefixify engine/Jambase
- tc-export CXX
-}
-
-src_compile() {
- cd engine || die
- ./build.sh cxx -d+2 --without-python || die "building bjam failed"
-}
-
-src_test() {
- # Forget tests, bjam is a lost cause
- :
-}
-
-src_install() {
- dobin engine/{bjam,b2}
-
- insinto /usr/share/boost-build
- doins -r "${FILESDIR}/site-config.jam" \
- ../boost-build.jam bootstrap.jam build-system.jam ../example/user-config.jam *.py \
- build kernel options tools util
-
- find "${ED}"/usr/share/boost-build -iname '*.py' -delete || die
-
- dodoc ../notes/{changes,release_procedure,build_dir_option,relative_source_paths}.txt
-
- if use examples; then
- docinto examples
- dodoc -r ../example/.
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-util/boost-build/files/boost-build-1.71.0-add-none-feature-options.patch b/dev-util/boost-build/files/boost-build-1.71.0-add-none-feature-options.patch
deleted file mode 100644
index ddd1641d1..000000000
--- a/dev-util/boost-build/files/boost-build-1.71.0-add-none-feature-options.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/tools/features/debug-feature.jam
-+++ b/tools/features/debug-feature.jam
-@@ -8,7 +8,7 @@
- import feature ;
-
- feature.feature debug-symbols
-- : on off
-+ : on off none
- : propagated ;
-
- feature.feature profiling
---- a/tools/features/optimization-feature.jam
-+++ b/tools/features/optimization-feature.jam
-@@ -8,7 +8,7 @@
- import feature ;
-
- feature.feature optimization
-- : off speed space
-+ : off none speed space
- : propagated ;
-
- feature.feature inlining
diff --git a/dev-util/boost-build/files/boost-build-1.71.0-disable_python_rpath.patch b/dev-util/boost-build/files/boost-build-1.71.0-disable_python_rpath.patch
deleted file mode 100644
index b7b47cc93..000000000
--- a/dev-util/boost-build/files/boost-build-1.71.0-disable_python_rpath.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/tools/python.jam
-+++ b/tools/python.jam
-@@ -1000,7 +1000,7 @@
- # linux).
- : $(usage-requirements)
- <testing.launcher>$(set-PYTHONPATH)
-- <library-path>$(libraries) <dll-path>$(dll-path) <library>python.lib
-+ <library-path>$(libraries) <library>python.lib
- ;
- }
-
diff --git a/dev-util/boost-build/files/boost-build-1.71.0-fix-test.patch b/dev-util/boost-build/files/boost-build-1.71.0-fix-test.patch
deleted file mode 100644
index 3f8b177c7..000000000
--- a/dev-util/boost-build/files/boost-build-1.71.0-fix-test.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/test/startup_v2.py
-+++ b/test/startup_v2.py
-@@ -50,7 +50,7 @@
- return re.match(expected, actual, re.DOTALL) != None
-
-
--t = BoostBuild.Tester(match=match_re, boost_build_path="", pass_toolset=0)
-+t = BoostBuild.Tester(match=match_re, boost_build_path="/invalid/location", pass_toolset=0)
- t.set_tree("startup")
- check_for_existing_boost_build_jam(t)
-
diff --git a/dev-util/boost-build/files/boost-build-1.71.0-no-implicit-march-flags.patch b/dev-util/boost-build/files/boost-build-1.71.0-no-implicit-march-flags.patch
deleted file mode 100644
index cd184030d..000000000
--- a/dev-util/boost-build/files/boost-build-1.71.0-no-implicit-march-flags.patch
+++ /dev/null
@@ -1,266 +0,0 @@
-Prevent bjam from injecting what it thinks are great -march/-mcpu flags
-in order to optimize code for you. This breaks on 32-bit builds, because
--march=i686 will not work on an i486 CHOST.
-
-See also:
-https://bugs.gentoo.org/624616
-
---- a/tools/gcc.jam
-+++ b/tools/gcc.jam
-@@ -1187,128 +1187,8 @@
- # x86 and compatible
- # The 'native' option appeared in gcc 4.2 so we cannot safely use it as default.
- # Use i686 instead for 32-bit.
--toolset.flags gcc OPTIONS <architecture>x86/<address-model>32/<instruction-set> : -march=i686 ;
--cpu-flags gcc OPTIONS : x86 : native : -march=native ;
--cpu-flags gcc OPTIONS : x86 : i486 : -march=i486 ;
--cpu-flags gcc OPTIONS : x86 : i586 : -march=i586 ;
--cpu-flags gcc OPTIONS : x86 : i686 : -march=i686 ;
--cpu-flags gcc OPTIONS : x86 : pentium : -march=pentium ;
--cpu-flags gcc OPTIONS : x86 : pentium-mmx : -march=pentium-mmx ;
--cpu-flags gcc OPTIONS : x86 : pentiumpro : -march=pentiumpro ;
--cpu-flags gcc OPTIONS : x86 : pentium2 : -march=pentium2 ;
--cpu-flags gcc OPTIONS : x86 : pentium3 : -march=pentium3 ;
--cpu-flags gcc OPTIONS : x86 : pentium3m : -march=pentium3m ;
--cpu-flags gcc OPTIONS : x86 : pentium-m : -march=pentium-m ;
--cpu-flags gcc OPTIONS : x86 : pentium4 : -march=pentium4 ;
--cpu-flags gcc OPTIONS : x86 : pentium4m : -march=pentium4m ;
--cpu-flags gcc OPTIONS : x86 : prescott : -march=prescott ;
--cpu-flags gcc OPTIONS : x86 : nocona : -march=nocona ;
--cpu-flags gcc OPTIONS : x86 : core2 : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : conroe : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : conroe-xe : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : conroe-l : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : allendale : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : wolfdale : -march=core2 -msse4.1 ;
--cpu-flags gcc OPTIONS : x86 : merom : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : merom-xe : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : kentsfield : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : kentsfield-xe : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : yorksfield : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : penryn : -march=core2 ;
--cpu-flags gcc OPTIONS : x86 : corei7 : -march=corei7 ;
--cpu-flags gcc OPTIONS : x86 : nehalem : -march=corei7 ;
--cpu-flags gcc OPTIONS : x86 : corei7-avx : -march=corei7-avx ;
--cpu-flags gcc OPTIONS : x86 : sandy-bridge : -march=corei7-avx ;
--cpu-flags gcc OPTIONS : x86 : core-avx-i : -march=core-avx-i ;
--cpu-flags gcc OPTIONS : x86 : ivy-bridge : -march=core-avx-i ;
--cpu-flags gcc OPTIONS : x86 : haswell : -march=core-avx-i -mavx2 -mfma -mbmi -mbmi2 -mlzcnt ;
--cpu-flags gcc OPTIONS : x86 : broadwell : -march=broadwell ;
--cpu-flags gcc OPTIONS : x86 : skylake : -march=skylake ;
--cpu-flags gcc OPTIONS : x86 : skylake-avx512 : -march=skylake-avx512 ;
--cpu-flags gcc OPTIONS : x86 : cannonlake : -march=skylake-avx512 -mavx512vbmi -mavx512ifma -msha ;
--cpu-flags gcc OPTIONS : x86 : icelake : -march=icelake ;
--cpu-flags gcc OPTIONS : x86 : k6 : -march=k6 ;
--cpu-flags gcc OPTIONS : x86 : k6-2 : -march=k6-2 ;
--cpu-flags gcc OPTIONS : x86 : k6-3 : -march=k6-3 ;
--cpu-flags gcc OPTIONS : x86 : athlon : -march=athlon ;
--cpu-flags gcc OPTIONS : x86 : athlon-tbird : -march=athlon-tbird ;
--cpu-flags gcc OPTIONS : x86 : athlon-4 : -march=athlon-4 ;
--cpu-flags gcc OPTIONS : x86 : athlon-xp : -march=athlon-xp ;
--cpu-flags gcc OPTIONS : x86 : athlon-mp : -march=athlon-mp ;
- ##
--cpu-flags gcc OPTIONS : x86 : k8 : -march=k8 ;
--cpu-flags gcc OPTIONS : x86 : opteron : -march=opteron ;
--cpu-flags gcc OPTIONS : x86 : athlon64 : -march=athlon64 ;
--cpu-flags gcc OPTIONS : x86 : athlon-fx : -march=athlon-fx ;
--cpu-flags gcc OPTIONS : x86 : k8-sse3 : -march=k8-sse3 ;
--cpu-flags gcc OPTIONS : x86 : opteron-sse3 : -march=opteron-sse3 ;
--cpu-flags gcc OPTIONS : x86 : athlon64-sse3 : -march=athlon64-sse3 ;
--cpu-flags gcc OPTIONS : x86 : amdfam10 : -march=amdfam10 ;
--cpu-flags gcc OPTIONS : x86 : barcelona : -march=barcelona ;
--cpu-flags gcc OPTIONS : x86 : bdver1 : -march=bdver1 ;
--cpu-flags gcc OPTIONS : x86 : bdver2 : -march=bdver2 ;
--cpu-flags gcc OPTIONS : x86 : bdver3 : -march=bdver3 ;
--cpu-flags gcc OPTIONS : x86 : bdver4 : -march=bdver4 ;
--cpu-flags gcc OPTIONS : x86 : btver1 : -march=btver1 ;
--cpu-flags gcc OPTIONS : x86 : btver2 : -march=btver2 ;
--cpu-flags gcc OPTIONS : x86 : znver1 : -march=znver1 ;
--cpu-flags gcc OPTIONS : x86 : winchip-c6 : -march=winchip-c6 ;
--cpu-flags gcc OPTIONS : x86 : winchip2 : -march=winchip2 ;
--cpu-flags gcc OPTIONS : x86 : c3 : -march=c3 ;
--cpu-flags gcc OPTIONS : x86 : c3-2 : -march=c3-2 ;
- ##
--cpu-flags gcc OPTIONS : x86 : atom : -march=atom ;
--# Sparc
--cpu-flags gcc OPTIONS : sparc : v7 : -mcpu=v7 : default ;
--cpu-flags gcc OPTIONS : sparc : cypress : -mcpu=cypress ;
--cpu-flags gcc OPTIONS : sparc : v8 : -mcpu=v8 ;
--cpu-flags gcc OPTIONS : sparc : supersparc : -mcpu=supersparc ;
--cpu-flags gcc OPTIONS : sparc : sparclite : -mcpu=sparclite ;
--cpu-flags gcc OPTIONS : sparc : hypersparc : -mcpu=hypersparc ;
--cpu-flags gcc OPTIONS : sparc : sparclite86x : -mcpu=sparclite86x ;
--cpu-flags gcc OPTIONS : sparc : f930 : -mcpu=f930 ;
--cpu-flags gcc OPTIONS : sparc : f934 : -mcpu=f934 ;
--cpu-flags gcc OPTIONS : sparc : sparclet : -mcpu=sparclet ;
--cpu-flags gcc OPTIONS : sparc : tsc701 : -mcpu=tsc701 ;
--cpu-flags gcc OPTIONS : sparc : v9 : -mcpu=v9 ;
--cpu-flags gcc OPTIONS : sparc : ultrasparc : -mcpu=ultrasparc ;
--cpu-flags gcc OPTIONS : sparc : ultrasparc3 : -mcpu=ultrasparc3 ;
- # RS/6000 & PowerPC
--cpu-flags gcc OPTIONS : power : 403 : -mcpu=403 ;
--cpu-flags gcc OPTIONS : power : 505 : -mcpu=505 ;
--cpu-flags gcc OPTIONS : power : 601 : -mcpu=601 ;
--cpu-flags gcc OPTIONS : power : 602 : -mcpu=602 ;
--cpu-flags gcc OPTIONS : power : 603 : -mcpu=603 ;
--cpu-flags gcc OPTIONS : power : 603e : -mcpu=603e ;
--cpu-flags gcc OPTIONS : power : 604 : -mcpu=604 ;
--cpu-flags gcc OPTIONS : power : 604e : -mcpu=604e ;
--cpu-flags gcc OPTIONS : power : 620 : -mcpu=620 ;
--cpu-flags gcc OPTIONS : power : 630 : -mcpu=630 ;
--cpu-flags gcc OPTIONS : power : 740 : -mcpu=740 ;
--cpu-flags gcc OPTIONS : power : 7400 : -mcpu=7400 ;
--cpu-flags gcc OPTIONS : power : 7450 : -mcpu=7450 ;
--cpu-flags gcc OPTIONS : power : 750 : -mcpu=750 ;
--cpu-flags gcc OPTIONS : power : 801 : -mcpu=801 ;
--cpu-flags gcc OPTIONS : power : 821 : -mcpu=821 ;
--cpu-flags gcc OPTIONS : power : 823 : -mcpu=823 ;
--cpu-flags gcc OPTIONS : power : 860 : -mcpu=860 ;
--cpu-flags gcc OPTIONS : power : 970 : -mcpu=970 ;
--cpu-flags gcc OPTIONS : power : 8540 : -mcpu=8540 ;
--cpu-flags gcc OPTIONS : power : power : -mcpu=power ;
--cpu-flags gcc OPTIONS : power : power2 : -mcpu=power2 ;
--cpu-flags gcc OPTIONS : power : power3 : -mcpu=power3 ;
--cpu-flags gcc OPTIONS : power : power4 : -mcpu=power4 ;
--cpu-flags gcc OPTIONS : power : power5 : -mcpu=power5 ;
--cpu-flags gcc OPTIONS : power : powerpc : -mcpu=powerpc ;
--cpu-flags gcc OPTIONS : power : powerpc64 : -mcpu=powerpc64 ;
--cpu-flags gcc OPTIONS : power : rios : -mcpu=rios ;
--cpu-flags gcc OPTIONS : power : rios1 : -mcpu=rios1 ;
--cpu-flags gcc OPTIONS : power : rios2 : -mcpu=rios2 ;
--cpu-flags gcc OPTIONS : power : rsc : -mcpu=rsc ;
--cpu-flags gcc OPTIONS : power : rs64a : -mcpu=rs64 ;
--cpu-flags gcc OPTIONS : s390x : z196 : -march=z196 ;
--cpu-flags gcc OPTIONS : s390x : zEC12 : -march=zEC12 ;
--cpu-flags gcc OPTIONS : s390x : z13 : -march=z13 ;
--cpu-flags gcc OPTIONS : s390x : z14 : -march=z14 ;
- # AIX variant of RS/6000 & PowerPC
- toolset.flags gcc AROPTIONS <address-model>64/<target-os>aix : "-X64" ;
---- a/tools/gcc.py
-+++ b/tools/gcc.py
-@@ -745,125 +745,14 @@
- # x86 and compatible
- flags('gcc', 'OPTIONS', ['<architecture>x86/<address-model>32'], ['-m32'])
- flags('gcc', 'OPTIONS', ['<architecture>x86/<address-model>64'], ['-m64'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'native', ['-march=native'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'i486', ['-march=i486'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'i586', ['-march=i586'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'i686', ['-march=i686'], default=True)
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium', ['-march=pentium'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium-mmx', ['-march=pentium-mmx'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentiumpro', ['-march=pentiumpro'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium2', ['-march=pentium2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium3', ['-march=pentium3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium3m', ['-march=pentium3m'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium-m', ['-march=pentium-m'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium4', ['-march=pentium4'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium4m', ['-march=pentium4m'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'prescott', ['-march=prescott'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'nocona', ['-march=nocona'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'core2', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'conroe', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'conroe-xe', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'conroe-l', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'allendale', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'wolfdale', ['-march=core2', '-msse4.1'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'merom', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'merom-xe', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'kentsfield', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'kentsfield-xe', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'yorksfield', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'penryn', ['-march=core2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'corei7', ['-march=corei7'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'nehalem', ['-march=corei7'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'corei7-avx', ['-march=corei7-avx'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'sandy-bridge', ['-march=corei7-avx'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'core-avx-i', ['-march=core-avx-i'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'ivy-bridge', ['-march=core-avx-i'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'haswell', ['-march=core-avx-i', '-mavx2', '-mfma', '-mbmi', '-mbmi2', '-mlzcnt'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'k6', ['-march=k6'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'k6-2', ['-march=k6-2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'k6-3', ['-march=k6-3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon', ['-march=athlon'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-tbird', ['-march=athlon-tbird'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-4', ['-march=athlon-4'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-xp', ['-march=athlon-xp'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-mp', ['-march=athlon-mp'])
- ##
--cpu_flags('gcc', 'OPTIONS', 'x86', 'k8', ['-march=k8'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'opteron', ['-march=opteron'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon64', ['-march=athlon64'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-fx', ['-march=athlon-fx'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'k8-sse3', ['-march=k8-sse3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'opteron-sse3', ['-march=opteron-sse3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon64-sse3', ['-march=athlon64-sse3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'amdfam10', ['-march=amdfam10'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'barcelona', ['-march=barcelona'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'bdver1', ['-march=bdver1'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'bdver2', ['-march=bdver2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'bdver3', ['-march=bdver3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'btver1', ['-march=btver1'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'btver2', ['-march=btver2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'winchip-c6', ['-march=winchip-c6'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'winchip2', ['-march=winchip2'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'c3', ['-march=c3'])
--cpu_flags('gcc', 'OPTIONS', 'x86', 'c3-2', ['-march=c3-2'])
- ##
--cpu_flags('gcc', 'OPTIONS', 'x86', 'atom', ['-march=atom'])
- # Sparc
- flags('gcc', 'OPTIONS', ['<architecture>sparc/<address-model>32'], ['-m32'])
- flags('gcc', 'OPTIONS', ['<architecture>sparc/<address-model>64'], ['-m64'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'v7', ['-mcpu=v7'], default=True)
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'cypress', ['-mcpu=cypress'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'v8', ['-mcpu=v8'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'supersparc', ['-mcpu=supersparc'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclite', ['-mcpu=sparclite'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'hypersparc', ['-mcpu=hypersparc'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclite86x', ['-mcpu=sparclite86x'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'f930', ['-mcpu=f930'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'f934', ['-mcpu=f934'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclet', ['-mcpu=sparclet'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'tsc701', ['-mcpu=tsc701'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'v9', ['-mcpu=v9'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'ultrasparc', ['-mcpu=ultrasparc'])
--cpu_flags('gcc', 'OPTIONS', 'sparc', 'ultrasparc3', ['-mcpu=ultrasparc3'])
- # RS/6000 & PowerPC
- flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>32'], ['-m32'])
- flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>64'], ['-m64'])
--cpu_flags('gcc', 'OPTIONS', 'power', '403', ['-mcpu=403'])
--cpu_flags('gcc', 'OPTIONS', 'power', '505', ['-mcpu=505'])
--cpu_flags('gcc', 'OPTIONS', 'power', '601', ['-mcpu=601'])
--cpu_flags('gcc', 'OPTIONS', 'power', '602', ['-mcpu=602'])
--cpu_flags('gcc', 'OPTIONS', 'power', '603', ['-mcpu=603'])
--cpu_flags('gcc', 'OPTIONS', 'power', '603e', ['-mcpu=603e'])
--cpu_flags('gcc', 'OPTIONS', 'power', '604', ['-mcpu=604'])
--cpu_flags('gcc', 'OPTIONS', 'power', '604e', ['-mcpu=604e'])
--cpu_flags('gcc', 'OPTIONS', 'power', '620', ['-mcpu=620'])
--cpu_flags('gcc', 'OPTIONS', 'power', '630', ['-mcpu=630'])
--cpu_flags('gcc', 'OPTIONS', 'power', '740', ['-mcpu=740'])
--cpu_flags('gcc', 'OPTIONS', 'power', '7400', ['-mcpu=7400'])
--cpu_flags('gcc', 'OPTIONS', 'power', '7450', ['-mcpu=7450'])
--cpu_flags('gcc', 'OPTIONS', 'power', '750', ['-mcpu=750'])
--cpu_flags('gcc', 'OPTIONS', 'power', '801', ['-mcpu=801'])
--cpu_flags('gcc', 'OPTIONS', 'power', '821', ['-mcpu=821'])
--cpu_flags('gcc', 'OPTIONS', 'power', '823', ['-mcpu=823'])
--cpu_flags('gcc', 'OPTIONS', 'power', '860', ['-mcpu=860'])
--cpu_flags('gcc', 'OPTIONS', 'power', '970', ['-mcpu=970'])
--cpu_flags('gcc', 'OPTIONS', 'power', '8540', ['-mcpu=8540'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'power', ['-mcpu=power'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'power2', ['-mcpu=power2'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'power3', ['-mcpu=power3'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'power4', ['-mcpu=power4'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'power5', ['-mcpu=power5'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'powerpc', ['-mcpu=powerpc'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'powerpc64', ['-mcpu=powerpc64'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'rios', ['-mcpu=rios'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'rios1', ['-mcpu=rios1'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'rios2', ['-mcpu=rios2'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'rsc', ['-mcpu=rsc'])
--cpu_flags('gcc', 'OPTIONS', 'power', 'rs64a', ['-mcpu=rs64'])
--cpu_flags('gcc', 'OPTIONS', 's390x', 'z196', ['-march=z196'])
--cpu_flags('gcc', 'OPTIONS', 's390x', 'zEC12', ['-march=zEC12'])
--cpu_flags('gcc', 'OPTIONS', 's390x', 'z13', ['-march=z13'])
--cpu_flags('gcc', 'OPTIONS', 's390x', 'z14', ['-march=z14'])
- # AIX variant of RS/6000 & PowerPC
- flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>32/<target-os>aix'], ['-maix32'])
- flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>64/<target-os>aix'], ['-maix64'])
diff --git a/dev-util/boost-build/files/boost-build-1.71.0-respect-c_ld-flags.patch b/dev-util/boost-build/files/boost-build-1.71.0-respect-c_ld-flags.patch
deleted file mode 100644
index f51abea61..000000000
--- a/dev-util/boost-build/files/boost-build-1.71.0-respect-c_ld-flags.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- a/engine/build.sh
-+++ b/engine/build.sh
-@@ -439,5 +439,5 @@
- if check_debug_build "$@" ; then B2_CXXFLAGS="${B2_CXXFLAGS_DEBUG}"
- else B2_CXXFLAGS="${B2_CXXFLAGS_RELEASE} -DNDEBUG"
- fi
--echo_run ${B2_CXX} ${CXXFLAGS} ${B2_CXXFLAGS} ${B2_SOURCES} -o b2
-+echo_run ${B2_CXX} ${CPPFLAGS} ${CXXFLAGS} ${LDFLAGS} ${B2_CXXFLAGS} ${B2_SOURCES} -o b2
- echo_run cp b2 bjam
diff --git a/dev-util/boost-build/files/site-config.jam b/dev-util/boost-build/files/site-config.jam
deleted file mode 100644
index 50002cf15..000000000
--- a/dev-util/boost-build/files/site-config.jam
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Define two new variants to be used when building boost (or separate boost-libs)
-# on Gentoo. The two variants make use of Gentoo-specific optimization and debug-symbols
-# values "none" which are not part of the official boost distribution.
-# DO NOT RELY ON THE FOLLOWING VARIANTS TO BE PRESENT ON OTHER OS!
-variant gentoorelease : release : <optimization>none <debug-symbols>none <runtime-link>shared ;
-variant gentoodebug : debug : <optimization>none <debug-symbols>on <runtime-link>shared ;
-
diff --git a/dev-util/boost-build/metadata.xml b/dev-util/boost-build/metadata.xml
deleted file mode 100644
index e63200f91..000000000
--- a/dev-util/boost-build/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <description>Gentoo Science Project</description>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">boost</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-util/f90cache/f90cache-0.99c.ebuild b/dev-util/f90cache/f90cache-0.99c.ebuild
index c3a5b82ec..cc5024c91 100644
--- a/dev-util/f90cache/f90cache-0.99c.ebuild
+++ b/dev-util/f90cache/f90cache-0.99c.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit fortran-2 multilib toolchain-funcs
+inherit fortran-2
DESCRIPTION="Compiler cache for fortran"
HOMEPAGE="https://perso.univ-rennes1.fr/edouard.canot//f90cache/"
diff --git a/dev-util/rocm-clang-ocl/Manifest b/dev-util/rocm-clang-ocl/Manifest
deleted file mode 100644
index 80600df00..000000000
--- a/dev-util/rocm-clang-ocl/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST rocm-clang-ocl-4.0.0.tar.gz 3259 BLAKE2B a3c0237590b662a9298c39da306559c893ca50ff9dcb4a7cb150dcf381db0a9c17da7be553e0e33075a63c7a00c77e9dd30a40ae1ebdee225b0fd9cd199b0c9e SHA512 8d1b3a976fd1995980b524c32345a67eb6876ed76253efe99d55aea8dc07c673d6f84f69bf6379aeba95fd9d49ad745555096fce63300090c7e2868f3eecd261
-DIST rocm-clang-ocl-4.1.0.tar.gz 3238 BLAKE2B 60086022b3edd63ad4a76fc4751256c54db606e1ee915eb2b45dd9122e9aaa8c26192da814da17eccbe05977aa44ea29f3c2e5ccd2aedcfc609c4cc7339c37fb SHA512 685b21821d2a18c40dea41e610c4905916f9dedb80a9c4808c763c8ccbb5f4c473b51ab76da6782c7de985d00bd5b78a63e7cdb025ff74e3c088ab3f273b7e71
diff --git a/dev-util/rocm-clang-ocl/metadata.xml b/dev-util/rocm-clang-ocl/metadata.xml
deleted file mode 100644
index 336bdb639..000000000
--- a/dev-util/rocm-clang-ocl/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>gentoo@holzke.net</email>
- <name>Wilfried Holzke</name>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.0.0-r1.ebuild b/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.0.0-r1.ebuild
deleted file mode 100644
index e153f61d3..000000000
--- a/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.0.0-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="OpenCL compilation with clang compiler"
-HOMEPAGE="https://github.com/RadeonOpenCompute/clang-ocl.git"
-SRC_URI="https://github.com/RadeonOpenCompute/clang-ocl/archive/rocm-${PV}.tar.gz -> rocm-clang-ocl-${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="dev-libs/rocm-opencl-runtime"
-DEPEND="dev-util/cmake
- dev-util/rocm-cmake
- ${RDEPEND}"
-
-S=${WORKDIR}/clang-ocl-rocm-${PV}
-
-src_prepare() {
- sed -e "s:HINTS \${CXX_COMPILER_PATH}/bin:NO_DEFAULT_PATH:" \
- -e "s:/opt/rocm/llvm/bin:${EPREFIX}/usr/lib/llvm/roc/bin:" \
- -e "/AMDDeviceLibs PATHS/s:/opt/rocm:${EPREFIX}/usr/lib/cmake/AMDDeviceLibs:" \
- -e "s:\${AMD_DEVICE_LIBS_PREFIX}/amdgcn/bitcode:${EPREFIX}/usr/lib/amdgcn/bitcode:" \
- -i CMakeLists.txt || die
-
- cmake_src_prepare
-}
diff --git a/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.1.0.ebuild b/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.1.0.ebuild
deleted file mode 100644
index 1429be33c..000000000
--- a/dev-util/rocm-clang-ocl/rocm-clang-ocl-4.1.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="OpenCL compilation with clang compiler"
-HOMEPAGE="https://github.com/RadeonOpenCompute/clang-ocl.git"
-SRC_URI="https://github.com/RadeonOpenCompute/clang-ocl/archive/rocm-${PV}.tar.gz -> rocm-clang-ocl-${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="dev-libs/rocm-opencl-runtime"
-DEPEND="
- dev-util/rocm-cmake
- ${RDEPEND}"
-
-S="${WORKDIR}/clang-ocl-rocm-${PV}"
-
-src_prepare() {
- sed -e "s:HINTS \${CXX_COMPILER_PATH}/bin:NO_DEFAULT_PATH:" \
- -e "s:/opt/rocm/llvm/bin:${EPREFIX}/usr/lib/llvm/roc/bin:" \
- -e "/AMDDeviceLibs PATHS/s:/opt/rocm:${EPREFIX}/usr/lib/cmake/AMDDeviceLibs:" \
- -e "s:\${AMD_DEVICE_LIBS_PREFIX}/amdgcn/bitcode:${EPREFIX}/usr/lib/amdgcn/bitcode:" \
- -i CMakeLists.txt || die
-
- cmake_src_prepare
-}
diff --git a/licenses/CeCILL-2.1 b/licenses/CeCILL-2.1
deleted file mode 100644
index b705f37a2..000000000
--- a/licenses/CeCILL-2.1
+++ /dev/null
@@ -1,519 +0,0 @@
-
- CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-Version 2.1 dated 2013-06-21
-
-
- Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to users,
- * secondly, the election of a governing law, French law, with which it
- is conformant, both as regards the law of torts and intellectual
- property law, and the protection that it offers to both authors and
- holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are:
-
-Commissariat l'nergie atomique et aux nergies alternatives - CEA, a
-public scientific, technical and industrial research establishment,
-having its principal place of business at 25 rue Leblanc, immeuble Le
-Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-Inria, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
- Preamble
-
-The purpose of this Free Software license agreement is to grant users
-the right to modify and redistribute the software governed by this
-license within the framework of an open source distribution model.
-
-The exercising of this right is conditional upon certain obligations for
-users so as to preserve this status for all subsequent redistributions.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-Frequently asked questions can be found on the official website of the
-CeCILL licenses family (http://www.cecill.info/index.en.html) for any
-necessary clarification.
-
-
- Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
-Software.
-
-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-GNU GPL: means the GNU General Public License version 2 or any
-subsequent version, as published by the Free Software Foundation Inc.
-
-GNU Affero GPL: means the GNU Affero General Public License version 3 or
-any subsequent version, as published by the Free Software Foundation Inc.
-
-EUPL: means the European Union Public License version 1.1 or any
-subsequent version, as published by the European Commission.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
- Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 <#scope> hereinafter for the whole
-term of the protection granted by the rights over said Software.
-
-
- Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
- * (i) loading the Software by any or all means, notably, by
- downloading from a remote server, or by loading from a physical medium;
- * (ii) the first time the Licensee exercises any of the rights granted
- hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-<#accepting> hereinabove, and the Licensee hereby acknowledges that it
-has read and understood it.
-
-
- Article 4 - EFFECTIVE DATE AND TERM
-
-
- 4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1 <#accepting>.
-
-
- 4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
- Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
- 5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
- 1. permanent or temporary reproduction of all or part of the Software
- by any or all means and in any or all form.
-
- 2. loading, displaying, running, or storing the Software on any or all
- medium.
-
- 3. entitlement to observe, study or test its operation so as to
- determine the ideas and principles behind any or all constituent
- elements of said Software. This shall apply when the Licensee
- carries out any or all loading, displaying, running, transmission or
- storage operation as regards the Software, that it is entitled to
- carry out hereunder.
-
-
- 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
- 5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
- 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows effective access to the full Source
-Code of the Software for a period of at least three years from the
-distribution of the Software, it being understood that the additional
-acquisition cost of the Source Code shall not exceed the cost of the
-data transfer.
-
-
- 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
-conditions for the distribution of the resulting Modified Software
-become subject to all the provisions of this Agreement.
-
-The Licensee is authorized to distribute the Modified Software, in
-source code or object code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-
-and, in the event that only the object code of the Modified Software is
-redistributed,
-
- 3. a note stating the conditions of effective access to the full source
- code of the Modified Software for a period of at least three years
- from the distribution of the Modified Software, it being understood
- that the additional acquisition cost of the source code shall not
- exceed the cost of the data transfer.
-
-
- 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
-
-
- 5.3.4 COMPATIBILITY WITH OTHER LICENSES
-
-The Licensee can include a code that is subject to the provisions of one
-of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
-Modified or unmodified Software, and distribute that entire code under
-the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-The Licensee can include the Modified or unmodified Software in a code
-that is subject to the provisions of one of the versions of the GNU GPL,
-GNU Affero GPL and/or EUPL and distribute that entire code under the
-terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-
- Article 6 - INTELLECTUAL PROPERTY
-
-
- 6.1 OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or
-all use of the Initial Software is subject to compliance with the terms
-and conditions under which the Holder has elected to distribute its work
-and no one shall be entitled to modify the terms and conditions for the
-distribution of said Initial Software.
-
-The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2 <#term>.
-
-
- 6.2 OVER THE CONTRIBUTIONS
-
-The Licensee who develops a Contribution is the owner of the
-intellectual property rights over this Contribution as defined by
-applicable law.
-
-
- 6.3 OVER THE EXTERNAL MODULES
-
-The Licensee who develops an External Module is the owner of the
-intellectual property rights over this External Module as defined by
-applicable law and is free to choose the type of agreement that shall
-govern its distribution.
-
-
- 6.4 JOINT PROVISIONS
-
-The Licensee expressly undertakes:
-
- 1. not to remove, or modify, in any manner, the intellectual property
- notices attached to the Software;
-
- 2. to reproduce said notices, in an identical manner, in the copies of
- the Software modified or not.
-
-The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights on the Software of the Holder and/or
-Contributors, and to take, where applicable, vis--vis its staff, any
-and all measures required to ensure respect of said intellectual
-property rights of the Holder and/or Contributors.
-
-
- Article 7 - RELATED SERVICES
-
-7.1 Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
- Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
- Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5 <#scope>).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 <#good-faith> and, in particular,
-without any warranty as to its commercial value, its secured, safe,
-innovative or relevant nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-expertise for its defense. Such technical and legal expertise shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
- Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
- Article 11 - MISCELLANEOUS
-
-
- 11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
- 11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
- Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4
-<#compatibility>.
-
-
- Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
diff --git a/licenses/jing b/licenses/jing
new file mode 100644
index 000000000..0833c55c8
--- /dev/null
+++ b/licenses/jing
@@ -0,0 +1,85 @@
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>Jing Copying Conditions</title>
+</head>
+
+<body>
+<h1>Jing Copying Conditions</h1>
+
+<p>Copyright (c) 2001-2003 Thai Open Source Software Center Ltd<br />
+All rights reserved.</p>
+
+<p>Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:</p>
+
+<ul>
+ <li>Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.</li>
+
+ <li>Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.</li>
+
+ <li>Neither the name of the Thai Open Source Software Center Ltd nor
+ the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.</li>
+</ul>
+
+<p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</p>
+
+<h2>Third-party JARs</h2>
+
+<p>This distribution includes some additional JAR files, which have
+their own copying conditions:</p>
+
+<dl>
+
+<dt><code>saxon.jar</code></dt>
+
+<dd>Comes from the <a href="http://saxon.sourceforge.net/">Saxon</a>
+6.5.2 distribution and is covered by these <a
+href="http://saxon.sourceforge.net/saxon6.5.2/conditions.html">conditions</a></dd>
+
+<dt><code>xercesImpl.jar</code></dt>
+<dt><code>xml-apis.jar</code></dt>
+<dd>Come from the <a href="http://xml.apache.org/xerces2-j/">Xerces-J</a> 2.4.0
+distribution and are covered by the <a href="xerces.copying.txt">Apache
+Software License</a></dd>
+
+<dt><code>isorelax.jar</code></dt>
+<dd>Comes from <a href="http://sourceforge.net/projects/iso-relax/">ISO RELAX</a>
+2003/01/08 distribution and is covered by the following license:
+
+<p>Copyright (c) 2001-2002, SourceForge ISO-RELAX Project (ASAMI Tomoharu, Daisuke
+Okajima, Kohsuke Kawaguchi, and MURATA Makoto)</p>
+
+<p>Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the
+Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
+
+<p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
+
+<p>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
+A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
+</dd>
+
+</dl>
+
+</body>
+
+</html>
diff --git a/licenses/sun-bcla-jhall b/licenses/sun-bcla-jhall
new file mode 100644
index 000000000..5dfad9d6e
--- /dev/null
+++ b/licenses/sun-bcla-jhall
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"><html><head>
+ <meta http-equiv="CONTENT-TYPE" content="text/html; charset=iso-8859-1"><title></title>
+
+ <meta name="GENERATOR" content="StarOffice 6.0 (Solaris Sparc)">
+ <meta name="AUTHOR" content="douglass hall">
+ <meta name="CREATED" content="20010118;13284400">
+ <meta name="CHANGED" content="20030905;13512000"></head>
+
+<body lang="en-US">
+<p align="center"><font size="4">Sun Microsystems, Inc.</font> <br><font size="4">Binary
+Code License Agreement</font></p>
+<p>READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL
+LICENSE TERMS (COLLECTIVELY "AGREEMENT") CAREFULLY BEFORE
+OPENING THE SOFTWARE MEDIA PACKAGE. BY OPENING THE SOFTWARE
+MEDIA PACKAGE, YOU AGREE TO THE TERMS OF THIS AGREEMENT. IF YOU
+ARE ACCESSING THE SOFTWARE ELECTRONICALLY, INDICATE YOUR ACCEPTANCE
+OF THESE TERMS BY SELECTING THE "ACCEPT" BUTTON AT THE END
+OF THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL THESE TERMS,
+PROMPTLY RETURN THE UNUSED SOFTWARE TO YOUR PLACE OF PURCHASE FOR A
+REFUND OR, IF THE SOFTWARE IS ACCESSED ELECTRONICALLY, SELECT THE
+"DECLINE" BUTTON AT THE END OF THIS AGREEMENT.
+</p>
+<p><b>1. LICENSE TO USE.</b> Sun grants you a
+non-exclusive and non-transferable license for the internal use only
+of the accompanying software and documentation and any error
+corrections provided by Sun (collectively "Software"), by
+the number of users and the class of computer hardware for which the
+corresponding fee has been paid.
+</p>
+<p><b>2. RESTRICTIONS.</b> Software is confidential and
+copyrighted. Title to Software and all associated intellectual
+property rights is retained by Sun and/or its licensors. Except
+as specifically authorized in any Supplemental License Terms, you may
+not make copies of Software, other than a single copy of Software for
+archival purposes. Unless enforcement is prohibited by
+applicable law, you may not modify, decompile, or reverse engineer
+Software. You acknowledge that Software is not designed,
+licensed or intended for use in the design, construction, operation
+or maintenance of any nuclear facility. Sun disclaims any
+express or implied warranty of fitness for such uses. No right,
+title or interest in or to any trademark, service mark, logo or trade
+name of Sun or its licensors is granted under this Agreement.
+</p>
+<p><b>3. LIMITED WARRANTY.</b> Sun warrants to you that for a
+period of ninety (90) days from the date of purchase, as evidenced by
+a copy of the receipt, the media on which Software is furnished (if
+any) will be free of defects in materials and workmanship under
+normal use. Except for the foregoing, Software is provided "AS
+IS". Your exclusive remedy and Sun's entire liability
+under this limited warranty will be at Sun's option to replace
+Software media or refund the fee paid for Software.
+</p>
+<p><b>4. DISCLAIMER OF WARRANTY.</b> UNLESS SPECIFIED IN
+THIS AGREEMENT, ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS
+AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT ARE DISCLAIMED,
+EXCEPT TO THE EXTENT THAT THESE DISCLAIMERS ARE HELD TO BE LEGALLY
+INVALID.
+</p>
+<p><b>5. LIMITATION OF LIABILITY.</b> TO THE EXTENT NOT
+PROHIBITED BY LAW, IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE
+FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR SPECIAL, INDIRECT,
+CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED
+REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF OR RELATED TO
+THE USE OF OR INABILITY TO USE SOFTWARE, EVEN IF SUN HAS BEEN ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGES. In no event will Sun's
+liability to you, whether in contract, tort (including negligence),
+or otherwise, exceed the amount paid by you for Software under this
+Agreement. The foregoing limitations will apply even if the
+above stated warranty fails of its essential purpose.
+</p>
+<p><b>6. Termination.</b> This Agreement is effective
+until terminated. You may terminate this Agreement at any time
+by destroying all copies of Software. This Agreement will
+terminate immediately without notice from Sun if you fail to comply
+with any provision of this Agreement. Upon Termination, you
+must destroy all copies of Software.
+</p>
+<p><b>7. Export Regulations.</b> All Software and technical data
+delivered under this Agreement are subject to US export control laws
+and may be subject to export or import regulations in other
+countries. You agree to comply strictly with all such laws and
+regulations and acknowledge that you have the responsibility to
+obtain such licenses to export, re-export, or import as may be
+required after delivery to you.
+</p>
+<p><b>8. U.S. Government Restricted Rights.</b> If
+Software is being acquired by or on behalf of the U.S. Government or
+by a U.S. Government prime contractor or subcontractor (at any tier),
+then the Government's rights in Software and accompanying
+documentation will be only as set forth in this Agreement; this is in
+accordance with 48 CFR 227.7201 through 227.7202-4 (for Department of
+Defense (DOD) acquisitions) and with 48 CFR 2.101 and 12.212 (for
+non-DOD acquisitions).
+</p>
+<p><b>9. Governing Law.</b> Any action related to this
+Agreement will be governed by California law and controlling U.S.
+federal law. No choice of law rules of any jurisdiction will
+apply.
+</p>
+<p><b>10. Severability.</b> If any provision of this Agreement
+is held to be unenforceable, this Agreement will remain in effect
+with the provision omitted, unless omission would frustrate the
+intent of the parties, in which case this Agreement will immediately
+terminate.
+</p>
+<p><b>11. Integration.</b> This Agreement is the entire
+agreement between you and Sun relating to its subject matter.
+It supersedes all prior or contemporaneous oral or written
+communications, proposals, representations and warranties and
+prevails over any conflicting or additional terms of any quote,
+order, acknowledgment, or other communication between the parties
+relating to its subject matter during the term of this Agreement.
+No modification of this Agreement will be binding, unless in writing
+and signed by an authorized representative of each party.
+</p>
+<p align="center" style="margin-bottom: 0cm;"><font size="4"><font color="#000000">JAVAHELP</font>(TM)<font color="#000000"><font size="2" style="font-size: 9pt;">
+</font>VERSION 2.0</font></font><br><font size="4">SUPPLEMENTAL LICENSE
+TERMS</font></p>
+<p align="center" style="margin-bottom: 0cm;"><br>
+</p>
+<p>These supplemental license terms ("Supplemental Terms")
+add to or modify the terms of the Binary Code License Agreement
+(collectively, the "Agreement"). Capitalized terms not
+defined in these Supplemental Terms shall have the same meanings
+ascribed to them in the Agreement. These Supplemental Terms shall
+supersede any inconsistent or conflicting terms in the Agreement, or
+in any license contained within the Software.
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>1. Software
+Internal Use and Development License Grant.</b> Subject to the terms
+and conditions of this Agreement, including, but not limited to
+Section 4 (Java(TM) Technology Restrictions) of these Supplemental
+Terms, Sun grants you a non-exclusive, non-transferable, limited
+license to reproduce internally and use internally the binary form of
+the Software complete and unmodified for the sole purpose of
+designing, developing and testing your Java applets and applications
+intended to run on the Java platform ("Programs"). </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>2. License
+to Distribute Software.</b> In addition to the license granted
+in Section 1 (Software Internal Use and Development License Grant) of
+these Supplemental Terms, subject to the terms and conditions of this
+Agreement, including but not limited to Section 4 (Java Technology
+Restrictions), Sun grants you a non-exclusive, non-transferable,
+limited license to reproduce and distribute the Software in binary
+form only, provided that you (i) distribute the Software complete and
+unmodified and only bundled as part of your Programs, (ii) do not
+distribute additional software intended to replace any component(s)
+of the Software, (iii) do not remove or alter any proprietary legends
+or notices contained in the Software, (iv) only distribute the
+Software subject to a license agreement that protects Sun's interests
+consistent with the terms contained in this Agreement, and (v) agree
+to defend and indemnify Sun and its licensors from and against any
+damages, costs, liabilities, settlement amounts and/or expenses
+(including attorneys' fees) incurred in connection with any claim,
+lawsuit or action by any third party that arises or results from the
+use or distribution of any and all Programs and/or Software. </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>3. License
+to Distribute Redistributables.</b> In addition to the license
+granted in Section 1 (Software Internal Use and Development License
+Grant) of these Supplemental Terms, subject to the terms and
+conditions of this Agreement, including but not limited to Section 3
+(Java Technology Restrictions) of these Supplemental Terms, Sun
+grants you a non-exclusive, non-transferable, limited license to
+reproduce and distribute those files specifically identified as
+redistributable in the Software "README" file
+("Redistributables") provided that: (i) you distribute the
+Redistributables complete and unmodified (unless otherwise specified
+in the applicable README file), and only bundled as part of your
+Programs, (ii) you do not distribute additional software intended to
+supersede any component(s) of the Redistributables, (iii) you do not
+remove or alter any proprietary legends or notices contained in or on
+the Redistributables, (iv) you only distribute the Redistributables
+pursuant to a license agreement that protects Sun's interests
+consistent with the terms contained in the Agreement, and (v) you
+agree to defend and indemnify Sun and its licensors from and against
+any damages, costs, liabilities, settlement amounts and/or expenses
+(including attorneys' fees) incurred in connection with any claim,
+lawsuit or action by any third party that arises or results from the
+use or distribution of any and all Programs and/or Software. </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><b><font color="#000000">4. Java
+Techn</font>ology Restrictions.</b> You may not modify the Java
+Platform Interface ("JPI", identified as classes contained
+within the "java" package or any subpackages of the "java"
+package), by creating additional classes within the JPI or otherwise
+causing the addition to or modification of the classes in the JPI.
+In the event that you create an additional class and associated
+API(s) which (i) extends the functionality of the Java platform, and
+(ii) is exposed to third party software developers for the purpose of
+developing additional software which invokes such additional API, you
+must promptly publish broadly an accurate specification for such API
+for free use by all developers. You may not create, or authorize your
+licensees to create, additional classes, interfaces, or subpackages
+that are in any way identified as "java", "javax",
+"sun" or similar convention as specified by Sun in any
+naming convention designation.
+</p>
+<p style="margin-bottom: 0.51cm;"><b>5. Java Runtime Availability.</b>
+Refer to the appropriate version of the Java Runtime Environment
+binary code license (currently located at
+http://www.java.sun.com/jdk/index.html) for the availability of
+runtime code which may be distributed with Java applets and
+applications.
+</p>
+<p style="margin-bottom: 0.51cm;"><b>6. Trademarks and Logos.</b> You
+acknowledge and agree as between you and Sun that Sun owns the SUN,
+SOLARIS, JAVA, JINI, FORTE, and iPLANET trademarks and all SUN,
+SOLARIS, JAVA, JINI, FORTE, and iPLANET-related trademarks, service
+marks, logos and other brand designations ("Sun Marks"),
+and you agree to comply with the Sun Trademark and Logo Usage
+Requirements currently located at
+http://www.sun.com/policies/trademarks. Any use you make of the Sun
+Marks inures to Sun's benefit.
+</p>
+<p style="margin-bottom: 0.51cm;"><b>7. Source Code.</b> Software may
+contain source code that is provided solely for reference purposes
+pursuant to the terms of this Agreement. Source code may not be
+redistributed unless expressly provided for in this Agreement. Some
+source code may contain alternative license terms that apply only to
+that source code file.</p>
+<p style="margin-bottom: 0.51cm;"><b>8. Termination for Infringement.</b>
+Either party may terminate this Agreement immediately should any
+Software become, or in either party's opinion be likely to become,
+the subject of a claim of infringement of any intellectual property
+right.
+</p>
+<p style="margin-bottom: 0.51cm;"><font face="Thorndale"><font color="#000000">For
+inquiries please contact: Sun Microsystems, Inc. 4150 Network Circle,
+Santa Clara, California 95054.</font></font> <br><i>(LFI#135834/Form
+ID#011801)</i></p>
+</body></html> \ No newline at end of file
diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest
index 7a28f3894..0ead205b0 100644
--- a/media-gfx/brlcad/Manifest
+++ b/media-gfx/brlcad/Manifest
@@ -1 +1 @@
-DIST brlcad-7.32.0.tar.gz 134873524 BLAKE2B f7b12dddace34d4de3b9fe87e5ac91131968f10d41bf1a2816d2a8e3fb0c6079b85ea879b6cbf8de5931ea5c410e6cdb544e234673ba51f910e6e05b9b25afa3 SHA512 236f4588e08a076c58e57516d56091f58330e4cfc55fbdc9cb4481e4d0d72f81cb94a6cd76b7e3db051fc5285c69af3ba666a63f04fbeea158b8fe94423562f0
+DIST brlcad-7.32.4.tar.gz 124190135 BLAKE2B 44366199aa5274853d3c8482d6a741e6774a9dc3c8dd8f14ac7c0379c0a776d640d1a48870fdd2c916c6edb2d871f3aacf9402fe73dc64682607b9d998caa02e SHA512 14388ec1a63e70bd5418372711f9231a371de0468bc3d535b772149f910a1825f457810547fdc2cf0efae2236f87edaf49439e209bff2c62f26f3f0cfc097e1a
diff --git a/media-gfx/brlcad/brlcad-7.32.0.ebuild b/media-gfx/brlcad/brlcad-7.32.4.ebuild
index c628aea72..aa70351e9 100644
--- a/media-gfx/brlcad/brlcad-7.32.0.ebuild
+++ b/media-gfx/brlcad/brlcad-7.32.4.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit cmake java-pkg-2 flag-o-matic
+inherit cmake desktop java-pkg-2 flag-o-matic
DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="https://brlcad.org/"
-SRC_URI="https://downloads.sourceforge.net/project/brlcad/BRL-CAD%20Source/${PV}/${P}.tar.gz"
+HOMEPAGE="https://brlcad.org/ https://github.com/BRL-CAD/brlcad"
+SRC_URI="https://github.com/BRL-CAD/${PN}/archive/refs/tags/rel-${PV//./-}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-rel-${PV//./-}"
LICENSE="LGPL-2 BSD"
SLOT="0"
@@ -16,18 +17,21 @@ IUSE="benchmarks debug doc examples java opengl smp"
RDEPEND="
java? (
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
)
"
DEPEND="${RDEPEND}
+ dev-util/astyle
+ dev-util/re2c
>=sci-libs/tnt-3
+ sci-libs/proj
+ sci-libs/lemon
sys-devel/bison
sys-devel/flex
media-libs/libpng:0
- <dev-lang/tcl-8.6:0/8.5
- <dev-lang/tk-8.6:0/8.5
- dev-tcltk/tktable
+ >=dev-lang/tcl-8.6:0/8.6
+ >=dev-lang/tk-8.6:0/8.6
sys-libs/zlib
sys-libs/libtermcap-compat
media-libs/urt
@@ -35,15 +39,19 @@ DEPEND="${RDEPEND}
x11-libs/libXi
java? (
sci-libs/jama
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
)
doc? (
dev-libs/libxslt
app-doc/doxygen
)"
+# Install into /usr/ not recommended by upstream due to possible file conflicts
+# with bundled libraries!
BRLCAD_DIR="${EPREFIX}/usr/${PN}"
+PATCHES=( "${FILESDIR}/${P}-skip-gstep.patch" )
+
src_prepare() {
cmake_src_prepare
}
@@ -52,9 +60,9 @@ src_configure() {
append-cflags "-w"
if use debug; then
CMAKE_BUILD_TYPE=Debug
- else
+ else
CMAKE_BUILD_TYPE=Release
- fi
+ fi
local mycmakeargs=(
-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
-DBRLCAD_ENABLE_STRICT=NO
@@ -63,13 +71,31 @@ src_configure() {
-DBRLCAD_FLAGS_OPTIMIZATION=ON
-DBRLCAD_ENABLE_X11=ON
-DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON
+ -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=ON
+# requires itk/itcl version 3, not packaged, use bundled instead
+# -DBRLCAD_TKTABLE=OFF
+# -DBRLCAD_IWIDGETS=OFF
+# -DBRLCAD_ITCL=OFF
+# -DBRLCAD_ITK=OFF
+# -DBRLCAD_TKPNG=OFF
+# Not packaged, use bundled
+# -DBRLCAD_GDIAM
+# -DBRLCAD_VDS
+# -DBRLCAD_SC
+# -DBRLCAD_OPENNURBS
+# -DBRLCAD_TKHTML
+# -DBRLCAD_UTAHRLE
+# -DBRLCAD_TERMLIB
+# -DBRLCAD_XMLLINT
+# -DBRLCAD_XSLTPROC
+# -DBRLCAD_PERPLEX
)
# use flag triggered options
if use debug; then
- mycmakeargs+="-DCMAKE_BUILD_TYPE=Debug"
+ mycmakeargs+=( -DCMAKE_BUILD_TYPE="Debug" )
else
- mycmakeargs+="-DCMAKE_BUILD_TYPE=Release"
+ mycmakeargs+=( -DCMAKE_BUILD_TYPE="Release" )
fi
mycmakeargs+=(
$(usex opengl BRLCAD_ENABLE_OPENGL)
@@ -104,8 +130,8 @@ src_install() {
echo "PATH=\"${BRLCAD_DIR}/bin\"" > 99brlcad
echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
doenvd 99brlcad
- for size in 16,24,36,48,64,96,128,256; do
- doicon misc/debian/${size}x${Size}/*
+ for size in {16,24,36,48,64,96,128,256}; do
+ doicon misc/debian/icons/${size}x${size}/*
done
domenu misc/debian/*.desktop
}
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index 2a5b83afe..5d6a345ce 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -1,33 +1,35 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit cmake subversion java-pkg-2 flag-o-matic
+inherit cmake desktop git-r3 java-pkg-2 flag-o-matic
DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="https://brlcad.org/"
-ESVN_REPO_URI="https://brlcad.svn.sourceforge.net/svnroot/${PN}/${PN}/trunk"
+HOMEPAGE="https://brlcad.org/ https://github.com/BRL-CAD/brlcad"
+EGIT_REPO_URI="https://github.com/BRL-CAD/brlcad"
LICENSE="LGPL-2 BSD"
SLOT="0"
-KEYWORDS=""
IUSE="benchmarks debug doc examples java opengl smp"
RDEPEND="
java? (
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
)
"
DEPEND="${RDEPEND}
+ dev-util/astyle
+ dev-util/re2c
>=sci-libs/tnt-3
+ sci-libs/proj
+ sci-libs/lemon
sys-devel/bison
sys-devel/flex
media-libs/libpng:0
- <dev-lang/tcl-8.6:0/8.5
- <dev-lang/tk-8.6:0/8.5
- dev-tcltk/tktable
+ >=dev-lang/tcl-8.6:0/8.6
+ >=dev-lang/tk-8.6:0/8.6
sys-libs/zlib
sys-libs/libtermcap-compat
media-libs/urt
@@ -35,13 +37,15 @@ DEPEND="${RDEPEND}
x11-libs/libXi
java? (
sci-libs/jama
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
)
doc? (
dev-libs/libxslt
app-doc/doxygen
)"
+# Install into /usr/ not recommended by upstream due to possible file conflicts
+# with bundled libraries!
BRLCAD_DIR="${EPREFIX}/usr/${PN}"
src_prepare() {
@@ -52,9 +56,9 @@ src_configure() {
append-cflags "-w"
if use debug; then
CMAKE_BUILD_TYPE=Debug
- else
+ else
CMAKE_BUILD_TYPE=Release
- fi
+ fi
local mycmakeargs=(
-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
-DBRLCAD_ENABLE_STRICT=NO
@@ -63,13 +67,31 @@ src_configure() {
-DBRLCAD_FLAGS_OPTIMIZATION=ON
-DBRLCAD_ENABLE_X11=ON
-DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON
+ -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=ON
+# requires itk/itcl version 3, not packaged, use bundled instead
+# -DBRLCAD_TKTABLE=OFF
+# -DBRLCAD_IWIDGETS=OFF
+# -DBRLCAD_ITCL=OFF
+# -DBRLCAD_ITK=OFF
+# -DBRLCAD_TKPNG=OFF
+# Not packaged, use bundled
+# -DBRLCAD_GDIAM
+# -DBRLCAD_VDS
+# -DBRLCAD_SC
+# -DBRLCAD_OPENNURBS
+# -DBRLCAD_TKHTML
+# -DBRLCAD_UTAHRLE
+# -DBRLCAD_TERMLIB
+# -DBRLCAD_XMLLINT
+# -DBRLCAD_XSLTPROC
+# -DBRLCAD_PERPLEX
)
# use flag triggered options
if use debug; then
- mycmakeargs+="-DCMAKE_BUILD_TYPE=Debug"
+ mycmakeargs+=( -DCMAKE_BUILD_TYPE="Debug" )
else
- mycmakeargs+="-DCMAKE_BUILD_TYPE=Release"
+ mycmakeargs+=( -DCMAKE_BUILD_TYPE="Release" )
fi
mycmakeargs+=(
$(usex opengl BRLCAD_ENABLE_OPENGL)
@@ -104,8 +126,8 @@ src_install() {
echo "PATH=\"${BRLCAD_DIR}/bin\"" > 99brlcad
echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
doenvd 99brlcad
- for size in 16,24,36,48,64,96,128,256; do
- doicon misc/debian/${size}x${Size}/*
+ for size in {16,24,36,48,64,96,128,256}; do
+ doicon misc/debian/icons/${size}x${size}/*
done
domenu misc/debian/*.desktop
}
diff --git a/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch b/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch
new file mode 100644
index 000000000..5768ad63a
--- /dev/null
+++ b/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch
@@ -0,0 +1,12 @@
+--- a/db/nist/CMakeLists.txt
++++ b/db/nist/CMakeLists.txt
+@@ -10,7 +10,8 @@ set(NIST_SAMPLE_MODELS
+ )
+
+ foreach(im ${NIST_SAMPLE_MODELS})
+- ADD_G_TARGET(${im} "BRL-CAD Geometry Models/Sample")
++# disabled because this often segfaults
++# ADD_G_TARGET(${im} "BRL-CAD Geometry Models/Sample")
+ endforeach(im ${NIST_SAMPLE_MODELS})
+
+ CMAKEFILES(
diff --git a/media-gfx/brlcad/metadata.xml b/media-gfx/brlcad/metadata.xml
index 5a5505b09..51a1c2468 100644
--- a/media-gfx/brlcad/metadata.xml
+++ b/media-gfx/brlcad/metadata.xml
@@ -32,9 +32,9 @@ photon mapping.
<use>
<flag name="benchmarks">
Run benchmarks during test phase (need test option enabled)
-</flag>
+ </flag>
</use>
<upstream>
- <remote-id type="sourceforge">brlcad</remote-id>
+ <remote-id type="github">BRL-CAD/brlcad</remote-id>
</upstream>
</pkgmetadata>
diff --git a/media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild b/media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild
deleted file mode 100644
index 00eece82f..000000000
--- a/media-libs/DualContouringSample/DualContouringSample-0_p20191111-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="A sample Dual Contouring implementation"
-HOMEPAGE="https://github.com/simoncblyth/DualContouringSample"
-
-EGIT_REPO_URI="https://github.com/simoncblyth/${PN}.git"
-EGIT_COMMIT="d5ed08c21228575f948292422cd8542cbdce255c"
-KEYWORDS="~amd64"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND="dev-util/bcm
- media-libs/glm"
-
-PATCHES=( "${FILESDIR}"/DualContouringSample-0_glm.patch )
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/${PN}
- )
-
- cmake_src_configure
-}
diff --git a/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch b/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch
deleted file mode 100644
index efa40b66e..000000000
--- a/media-libs/DualContouringSample/files/DualContouringSample-0_glm.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Index: DualContouringSample-0_p20191111/CMakeLists.txt
-===================================================================
---- DualContouringSample-0_p20191111.orig/CMakeLists.txt
-+++ DualContouringSample-0_p20191111/CMakeLists.txt
-@@ -3,18 +3,11 @@ set(name DualContouringSample)
- project(${name} VERSION 0.1.0)
-
- include(CTest)
--include(OpticksBuildOptions)
--
--include(GNUInstallDirs)
--set(CMAKE_INSTALL_INCLUDEDIR "externals/include/${name}")
--set(CMAKE_INSTALL_LIBDIR "externals/lib")
--set(CMAKE_INSTALL_BINDIR "lib")
--#set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
-
- find_package(BCM REQUIRED)
- include(BCMDeploy)
-
--find_package(GLM REQUIRED)
-+find_package(glm REQUIRED)
-
-
- set(SOURCES
-@@ -37,7 +30,7 @@ set(HEADERS
- )
-
- add_library(${name} SHARED ${SOURCES})
--target_link_libraries(${name} PUBLIC Opticks::GLM)
-+target_link_libraries(${name} PUBLIC glm)
-
- # needed for tests that use non-installed headers
- target_include_directories(${name} PUBLIC
diff --git a/media-libs/DualContouringSample/metadata.xml b/media-libs/DualContouringSample/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/DualContouringSample/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/imgui/Manifest b/media-libs/imgui/Manifest
deleted file mode 100644
index 27a17860f..000000000
--- a/media-libs/imgui/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST imgui-1.80.tar.gz 1391496 BLAKE2B 34c66bc79396adef4f4ea32255be6a7572106a43eec14f9b3b02d3457924e25be6468580766132ef0876cb69cab7fd3e0289db7bff269bad258b945e41ab324e SHA512 760ba1e434d477677919766893681ff4f3c258f84875f5f9a8ba24f0a60f3dd2a386bc7d082aaf701639c6388eeb31ef571f6a61777f20fb6bb0e6d96ba32777
diff --git a/media-libs/imgui/files/imgui-1.48-pkgconfig.patch b/media-libs/imgui/files/imgui-1.48-pkgconfig.patch
deleted file mode 100644
index 14744138e..000000000
--- a/media-libs/imgui/files/imgui-1.48-pkgconfig.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-Index: imgui-1.73/CMakeLists.txt
-===================================================================
---- imgui-1.73.orig/CMakeLists.txt
-+++ imgui-1.73/CMakeLists.txt
-@@ -7,24 +7,18 @@ but has now been moved into my ImGui for
-
- set(name ImGui)
- project(${name} VERSION 0.1.0)
--include(OpticksBuildOptions)
-+include(FindPkgConfig)
-+pkg_check_modules(OpticksGLEW REQUIRED glew)
-+message(STATUS "ImGui.OpticksGLEW_INCLUDE_DIRS : ${OpticksGLEW_INCLUDE_DIRS}")
-+message(STATUS "ImGui.OpticksGLEW_LIBRARIES : ${OpticksGLEW_LIBRARIES}")
-
--set(OpticksGLEW_VERBOSE ON)
--find_package(OpticksGLEW REQUIRED MODULE)
--message(STATUS "ImGui.OpticksGLEW_INCLUDE_DIR : ${OpticksGLEW_INCLUDE_DIR}")
--message(STATUS "ImGui.OpticksGLEW_LIBRARY : ${OpticksGLEW_LIBRARY}")
-+find_package(glfw3 REQUIRED Config)
-
--find_package(OpticksGLFW REQUIRED MODULE)
--message(STATUS "ImGui.OpticksGLFW_INCLUDE_DIR : ${OpticksGLFW_INCLUDE_DIR}")
--message(STATUS "ImGui.OpticksGLFW_LIBRARY : ${OpticksGLFW_LIBRARY}")
--
--
--set(IMGUI_DEFINITIONS
--)
-+set(IMGUI_DEFINITIONS)
-
- set(LIBRARIES
-- ${OpticksGLEW_LIBRARY}
-- ${OpticksGLFW_LIBRARY}
-+ ${OpticksGLEW_LIBRARIES}
-+ glfw
- )
-
- if(APPLE)
-@@ -92,13 +86,13 @@ set(INCLUDE_DIRS
- ${CMAKE_CURRENT_BINARY_DIR}
-
- ${ImGui_SOURCE_DIR}/examples/opengl3_example
-- ${OpticksGLEW_INCLUDE_DIR}
-- ${OpticksGLFW_INCLUDE_DIR}
-+ ${OpticksGLEW_INCLUDE_DIRS}
-+ ${GLFW_INCLUDE_DIR}
- )
-
- set(DEFINITIONS
- ${OpticksGLEW_DEFINITIONS}
-- ${OpticksGLFW_DEFINITIONS}
-+ ${GLFW_DEFINITIONS}
- ${IMGUI_DEFINITIONS}
- )
-
-@@ -139,8 +133,8 @@ endif(WIN32)
-
- target_link_libraries(${name} ${LIBRARIES})
-
--install(TARGETS ${name} DESTINATION externals/lib)
--install(FILES ${HEADERS} DESTINATION externals/include/${name})
-+install(TARGETS ${name} DESTINATION ${LIBDIR})
-+install(FILES ${HEADERS} DESTINATION include/${name})
-
-
- #[=[
diff --git a/media-libs/imgui/imgui-1.80.ebuild b/media-libs/imgui/imgui-1.80.ebuild
deleted file mode 100644
index 239f915ed..000000000
--- a/media-libs/imgui/imgui-1.80.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Bloat-free graphical user interface library for C++"
-HOMEPAGE="https://github.com/simoncblyth/imgui"
-SRC_URI="https://github.com/ocornut/imgui/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="media-libs/glew:0"
-DEPEND="${RDEPEND}"
-
-src_install() {
- insinto "/usr/include/${PN}"
- doins *.h
- insinto "/usr/include/${PN}/backend"
- doins backends/*.h
-}
diff --git a/media-libs/imgui/metadata.xml b/media-libs/imgui/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/imgui/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/implicitmesher/Manifest b/media-libs/implicitmesher/Manifest
deleted file mode 100644
index 2feca3fdf..000000000
--- a/media-libs/implicitmesher/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST implicitmesher-0_p20200413.tar.gz 23224 BLAKE2B fd7d10406f56c88a42821b5aa9848d228317147e4a7d8283b13719ebd9a6e57fecc5b4fb140c1ae23da16e45f90332d9953d5daa1be80ec633c7c011342f00f5 SHA512 5641a44d8a02ef3868d23e92afb053556e775f5beeb5d618dabf7d3e3f19a0a597693134524be2d92387481306af89d8be54c1677fa61fa111dae72ed25b3ea4
diff --git a/media-libs/implicitmesher/files/implicitmesher-0_glm.patch b/media-libs/implicitmesher/files/implicitmesher-0_glm.patch
deleted file mode 100644
index 2f1841f4d..000000000
--- a/media-libs/implicitmesher/files/implicitmesher-0_glm.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index d1a0cf3..f9013cb 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,7 +1,6 @@
- cmake_minimum_required (VERSION 3.5)
- set(name ImplicitMesher)
- project(${name} VERSION 0.1.0)
--include(OpticksBuildOptions)
-
- #[=[
- Hmm OpticksBuildOptions sets CMAKE_INSTALL_INCLUDEDIR to "include/${name}"
-@@ -14,7 +13,7 @@ set(CMAKE_INSTALL_LIBDIR "externals/lib")
- set(CMAKE_INSTALL_BINDIR "lib")
-
-
--find_package(GLM REQUIRED)
-+find_package(glm REQUIRED)
-
- set(SOURCES
-
-@@ -44,7 +43,7 @@ set(HEADERS
- )
-
- add_library(${name} SHARED ${SOURCES})
--target_link_libraries(${name} PUBLIC Opticks::GLM)
-+target_link_libraries(${name} PUBLIC glm)
-
- if(UNIX AND NOT APPLE)
- message(STATUS "adding stdc++ m for UNIX AND NOT APPLE")
-@@ -74,7 +73,6 @@ if(PC_VERBOSE)
- endif()
-
-
--bcm_deploy(TARGETS ${name} NAMESPACE Opticks:: SKIP_HEADER_INSTALL)
- install(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
-
- add_subdirectory(tests)
diff --git a/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild b/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild
deleted file mode 100644
index e6fae861d..000000000
--- a/media-libs/implicitmesher/implicitmesher-0_p20200413.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-COMMIT="4b7a47056074"
-
-DESCRIPTION="Real-time implicit surface polygonization"
-HOMEPAGE="https://bitbucket.org/simoncblyth/implicitmesher"
-SRC_URI="https://bitbucket.org/simoncblyth/implicitmesher/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="media-libs/glm"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/simoncblyth-${PN}-${COMMIT}"
-
-PATCHES=( "${FILESDIR}"/implicitmesher-0_glm.patch )
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/ImplicitMesher
- )
-
- cmake_src_configure
-}
diff --git a/media-libs/implicitmesher/metadata.xml b/media-libs/implicitmesher/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/implicitmesher/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/yocto-gl/Manifest b/media-libs/yocto-gl/Manifest
deleted file mode 100644
index e1a26da8c..000000000
--- a/media-libs/yocto-gl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST yocto-gl-3.3.0.tar.gz 196860271 BLAKE2B a2b563a16d9b07a1e92fe5f05de56d1cc21abe2dd05b2d72700feba020989c60aa676072e70ebb83cd6cba0ea8dba521d6c8ee2d894a012a070773a715315171 SHA512 f6b824fe1b546a29a093ab7932fb2c5ca4e194813dfcc45e22f0f1532bf0693ef92ebe95eeeba6f02f8a46368925cea2275189ab2c4d022620e8ac4d8d2f4648
diff --git a/media-libs/yocto-gl/metadata.xml b/media-libs/yocto-gl/metadata.xml
deleted file mode 100644
index 7203fb853..000000000
--- a/media-libs/yocto-gl/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
-</pkgmetadata>
diff --git a/media-libs/yocto-gl/yocto-gl-3.3.0.ebuild b/media-libs/yocto-gl/yocto-gl-3.3.0.ebuild
deleted file mode 100644
index e6102dde1..000000000
--- a/media-libs/yocto-gl/yocto-gl-3.3.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DOCS_BUILDER="mkdocs"
-DOCS_DEPEND="dev-python/mkdocs-material"
-
-inherit cmake python-any-r1 docs
-
-DESCRIPTION="Single File Libraries for Physically-Based Graphics"
-HOMEPAGE="https://github.com/simoncblyth/yocto-gl"
-SRC_URI="https://github.com/xelatihy/yocto-gl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="dev-util/bcm"
-
-src_prepare() {
- sed -i -e 's/isnan/std::isnan/g' libs/yocto/yocto_mesh.cpp || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_INCLUDEDIR=include/YoctoGL
- )
-
- cmake_src_configure
-}
-
-src_compile() {
- docs_compile
- cmake_src_compile
-}
diff --git a/metadata/layout.conf b/metadata/layout.conf
index 30d140512..0719596ad 100644
--- a/metadata/layout.conf
+++ b/metadata/layout.conf
@@ -22,8 +22,7 @@ manifest-required-hashes = BLAKE2B
# 2015-10-11 council meeting deprecated EAPI 4.
# 2016-01-10 council meeting banned EAPI 3.
# 2018-05-13 council meeting deprecated EAPI 5 for ebuilds.
-eapis-banned = 0 1 2 3 4 5
-eapis-deprecated = 6
+eapis-banned = 0 1 2 3 4 5 6
# Bug #337853 - gentoo's council says to enable
# --echangelog by default for the "gentoo" repo
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index d826df9fb..05ff69f80 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,3 @@
DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
-DIST ownCloud-2.7.6.3261.tar.xz 14237692 BLAKE2B 914b069b10fa2f169677768e1578c5b8569836eb574889c72c0ea1ca3e16e6b7c65bcdd1f4a5ce4259eab6ec56110e3b45799d010921e47c7f64ccfd0ed545bf SHA512 1f647dd0b33472e31719651fa22b5864867d98fa1e2f11f9eadb6ce15382f5f97ac49d726af079716b6fac573367485a6f11a5b2e5e5c95d4d063f6caab51dcd
-DIST ownCloud-2.8.2.4246.tar.xz 15044652 BLAKE2B ee1ee412667266273a9a9722940559562c6c43213b013fe7c21328e04ac967afb16f460e6fa711f37d1d4ea7d0fc15fc398d835cf6a939f4c8dfd54cd4846fed SHA512 0ab2ef72191cc2d5c2621c97c09cb1d25472a30f511235a190465e246a8312f13a255011abb9690c481887f2f15094414c87ce594252eb8debcb39b9cbc8a178
+DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2
+DIST ownCloud-2.9.2.6206.tar.xz 5759996 BLAKE2B c328ea261a4fddecf93837dbcac01aab0971542d8dfb3f5b0a32a8432ca0e0904c3f4fc81c5c7811da8b3af64b58e929c055e7cec0649f00049e037372948eec SHA512 d075a11ee92aa9771c631a766feddfa1a70907d7d341b58043e1ba96ac52786a6a750b15c2f9b7a0992fe02a45586cc3445755dc9df4cd267e72f070d2222f0f
diff --git a/net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild
index 2eb01cf8e..c4eeaa7be 100644
--- a/net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake rpm xdg
@@ -13,14 +13,14 @@ BRANDED_P="cernbox"
BRANDED_PV="2.7.1"
BRANDED_REL="2596"
HOMEPAGE="https://cernbox.cern.ch/"
-SRC_URI="http://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="doc dolphin gnome-keyring nautilus test"
+IUSE="dolphin gnome-keyring nautilus test"
COMMON_DEPEND=">=dev-db/sqlite-3.4:3
dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
@@ -43,12 +43,6 @@ RDEPEND="${COMMON_DEPEND}"
DEPEND="${COMMON_DEPEND}
dev-qt/linguist-tools:5
kde-frameworks/extra-cmake-modules
- doc? (
- dev-python/sphinx
- dev-tex/latexmk
- dev-texlive/texlive-latexextra
- virtual/latex-base
- )
test? (
dev-util/cmocka
dev-qt/qttest:5
@@ -58,6 +52,8 @@ RESTRICT="!test? ( test )"
S=${WORKDIR}/${ORIGIN_PN}-${PV}
+PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch )
+
src_unpack() {
rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
@@ -77,20 +73,10 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
- -DSYSCONF_INSTALL_DIR="${EPREFIX}"/etc
-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
- -DCMAKE_DISABLE_FIND_PACKAGE_Sphinx=$(usex !doc)
-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
-DBUILD_TESTING=$(usex test)
)
cmake_src_configure
}
-
-pkg_postinst() {
- if ! use doc ; then
- elog "Documentation and man pages not installed"
- elog "Enable doc USE-flag to generate them"
- fi
- xdg_pkg_postinst
-}
diff --git a/net-misc/cernbox-client/cernbox-client-2.7.6.3261.ebuild b/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild
index 2eb01cf8e..27080cd72 100644
--- a/net-misc/cernbox-client/cernbox-client-2.7.6.3261.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake rpm xdg
@@ -13,14 +13,14 @@ BRANDED_P="cernbox"
BRANDED_PV="2.7.1"
BRANDED_REL="2596"
HOMEPAGE="https://cernbox.cern.ch/"
-SRC_URI="http://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="doc dolphin gnome-keyring nautilus test"
+IUSE="dolphin gnome-keyring nautilus test"
COMMON_DEPEND=">=dev-db/sqlite-3.4:3
dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
@@ -43,12 +43,6 @@ RDEPEND="${COMMON_DEPEND}"
DEPEND="${COMMON_DEPEND}
dev-qt/linguist-tools:5
kde-frameworks/extra-cmake-modules
- doc? (
- dev-python/sphinx
- dev-tex/latexmk
- dev-texlive/texlive-latexextra
- virtual/latex-base
- )
test? (
dev-util/cmocka
dev-qt/qttest:5
@@ -58,6 +52,8 @@ RESTRICT="!test? ( test )"
S=${WORKDIR}/${ORIGIN_PN}-${PV}
+PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch )
+
src_unpack() {
rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
@@ -79,18 +75,9 @@ src_configure() {
local mycmakeargs=(
-DSYSCONF_INSTALL_DIR="${EPREFIX}"/etc
-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
- -DCMAKE_DISABLE_FIND_PACKAGE_Sphinx=$(usex !doc)
-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
-DBUILD_TESTING=$(usex test)
)
cmake_src_configure
}
-
-pkg_postinst() {
- if ! use doc ; then
- elog "Documentation and man pages not installed"
- elog "Enable doc USE-flag to generate them"
- fi
- xdg_pkg_postinst
-}
diff --git a/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch b/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch
new file mode 100644
index 000000000..c2ccbcc5e
--- /dev/null
+++ b/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch
@@ -0,0 +1,11 @@
+--- a/branding/cernbox-theme.h 2021-10-21 13:10:22.832842670 +0200
++++ b/branding/cernbox-theme.h 2021-10-21 13:14:57.394479817 +0200
+@@ -62,7 +62,7 @@
+
+
+ QString about() const {
+- QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" MIRALL_STRINGIFY(APPLICATION_DOMAIN))), Utility::escape(QStringLiteral(MIRALL_STRINGIFY(APPLICATION_DOMAIN))));
++ QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" APPLICATION_DOMAIN)), Utility::escape(QStringLiteral(APPLICATION_DOMAIN)));
+
+
+ return devString;
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 3668ef20d..92d1d843a 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,11 +15,6 @@
## =media-video/mplayer-0.90_pre5-r1 foo
#
-# Benda Xu <heroxbd@gentoo.org> (24 Jan 2021)
-# It doesn't work, mask 30 days for removal, unless someone come up
-# with a fix. cf. https://github.com/gentoo/sci/issues/1011
-sci-libs/pytorch mkl
-
# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
# doesn't link with plotutils-2.6
sci-physics/qcl plotutils
@@ -31,3 +26,9 @@ sci-biology/estscan icc ifc
# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Jan 2022)
+# dependencies not available
+# https://github.com/gentoo/sci/issues/1085
+# https://github.com/gentoo/sci/issues/1084
+sci-libs/mlpack go R
diff --git a/profiles/updates/1Q-2022 b/profiles/updates/1Q-2022
new file mode 100644
index 000000000..8b44d82fa
--- /dev/null
+++ b/profiles/updates/1Q-2022
@@ -0,0 +1 @@
+move sci-biology/sra_sdk sci-biology/sra-tools
diff --git a/profiles/updates/4Q-2021 b/profiles/updates/4Q-2021
new file mode 100644
index 000000000..63c17f4be
--- /dev/null
+++ b/profiles/updates/4Q-2021
@@ -0,0 +1 @@
+move sys-apps/ndctl sys-block/ndctl
diff --git a/sci-astronomy/erfa/Manifest b/sci-astronomy/erfa/Manifest
deleted file mode 100644
index 4fa7aee46..000000000
--- a/sci-astronomy/erfa/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST erfa-1.7.0.tar.gz 656949 BLAKE2B 071ae7c5e60a8904b0b93a615c1a23d8db6ea7100e822cfa842f279ce6eed341426d6ef46131dfa92c3ec605c03eeb1c7f204238ad229d4ed524fbc91e58d39c SHA512 0a25faa22cc756776df40cfd927388077f7d253ee89fd4e21c4ddb35198dafd5fd7e9904d00f419675c5f3b26232b5bd04087d4a2f175da1f89179173f98692f
-DIST erfa-1.7.1.tar.gz 720703 BLAKE2B a8299ba397555aa8ac8ad1778171712ec8f5a5a89fcc26a3baa9df24a8c0d4abbf92908c2306777ff57c08cb76fb961f1729125a8777258f909d3c345fa3b983 SHA512 9596696bd34a017537180d29ed15a3562806b7d50a36f06ddc4c49ad9b6b39fbb25d72a03bd97447a78f8031a12a684def703a3463f4379b3863bd4dd0a46d1e
diff --git a/sci-astronomy/erfa/erfa-1.7.0.ebuild b/sci-astronomy/erfa/erfa-1.7.0.ebuild
deleted file mode 100644
index ba7c72781..000000000
--- a/sci-astronomy/erfa/erfa-1.7.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools eutils
-
-DESCRIPTION="Essential Routines for Fundamental Astronomy"
-HOMEPAGE="https://github.com/liberfa/erfa"
-SRC_URI="https://github.com/liberfa/erfa/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="static-libs"
-
-src_prepare() {
- default
- eautoreconf
-}
-
-src_configure() {
- econf $(use_enable static-libs static)
-}
-
-src_install() {
- default
- find "${D}" -name '*.la' -delete || die
-}
diff --git a/sci-astronomy/erfa/erfa-1.7.1.ebuild b/sci-astronomy/erfa/erfa-1.7.1.ebuild
deleted file mode 100644
index ba7c72781..000000000
--- a/sci-astronomy/erfa/erfa-1.7.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools eutils
-
-DESCRIPTION="Essential Routines for Fundamental Astronomy"
-HOMEPAGE="https://github.com/liberfa/erfa"
-SRC_URI="https://github.com/liberfa/erfa/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="static-libs"
-
-src_prepare() {
- default
- eautoreconf
-}
-
-src_configure() {
- econf $(use_enable static-libs static)
-}
-
-src_install() {
- default
- find "${D}" -name '*.la' -delete || die
-}
diff --git a/sci-astronomy/erfa/metadata.xml b/sci-astronomy/erfa/metadata.xml
deleted file mode 100644
index 3d7ebf32a..000000000
--- a/sci-astronomy/erfa/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>davidroman96@gmail.com</email>
- <name>David Roman</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-astronomy@gentoo.org</email>
- <name>Gentoo Astronomy Project</name>
- </maintainer>
- <longdescription lang="en">
- Essential Routines for Fundamental Astronomy is a C
- library containing key algorithms for astronomy, and is based on
- the SOFA library published by the International Astronomical Union
- (IAU).
-</longdescription>
- <upstream>
- <remote-id type="github">liberfa/erfa</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index a731be61c..38383a14d 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
HOMEPAGE="https://bigd.big.ac.cn/tools/kaks"
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 89b4fe03c..c01f01587 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
HOMEPAGE="
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
index 5009e9922..898898b94 100644
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -9,17 +9,42 @@ SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
RESTRICT="test"
RDEPEND="
>=dev-lang/perl-1.6
dev-lang/swig
- sci-biology/btl_bloomfilter
+ dev-util/cppcheck
"
+# sci-biology/btl_bloomfilter
+
+src_compile(){
+ cd btllib | die "Cannot chdir to bundled btllib/"
+ ./compile-wrappers || die "Failed to compile bundled btllib"
+ # baah, this also does some kind of install
+ # SUCCESS: sdsl was installed successfully!
+ # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
+ # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
+ #
+ # Sample programs can be found in the examples-directory.
+ # A program 'example.cpp' can be compiled with the command:
+ # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
+ # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
+ # example.cpp -lsdsl -ldivsufsort -ldivsufsort64
+ #
+ # Tests in the test-directory
+ # A cheat sheet in the extras/cheatsheet-directory.
+ # Have fun!
+ # [2/3] Installing files.
+ # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
+ # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python
+}
src_install(){
- dobin bin/LINKS *.pl releases/links_v1.8.5/tools/*.pl
+ sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
+ sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
+ dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
dodoc README.md
}
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
index 3af0ec3b3..321d3901c 100644
--- a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
+++ b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit toolchain-funcs java-pkg-2
+inherit java-pkg-2
MY_PV="${PV//./_}"
diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild
index 135408288..67423c48c 100644
--- a/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild
+++ b/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild
@@ -5,7 +5,7 @@ EAPI=7
MODULE_AUTHOR=EASR
-inherit multilib perl-module
+inherit perl-module
DESCRIPTION="Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)"
HOMEPAGE="https://metacpan.org/release/ONTO-PERL"
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
index 8ae80d466..33fd4a2a3 100644
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
+++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
diff --git a/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild
index ef0d862ef..81258a0ef 100644
--- a/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild
+++ b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit multilib
-
DESCRIPTION="Analyze and trim single-end and paired-end reads, show quality statistics"
HOMEPAGE="https://sourceforge.net/projects/solexaqa"
SRC_URI="https://sourceforge.net/projects/solexaqa/files/src/SolexaQA++_v${PV}.zip"
diff --git a/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
index ed37d3a05..c9181641f 100644
--- a/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit perl-functions toolchain-funcs
+inherit perl-functions
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="https://github.com/TransDecoder/TransDecoder/wiki"
diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
index 1af77dccd..ca61abdf4 100644
--- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit perl-module toolchain-funcs
+inherit perl-module
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index 1540aba61..000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST abyss-2.2.5.tar.gz 1698962 BLAKE2B cb629242dd25b8ca9f9b3f9d7b7f4211a0791b02a4bbbe9c1b11bb436098d1267f37a15ec7409a62e05fd1b75c8ff2f44be20d4a9788e46dfe8b310737e2e32f SHA512 d7ac857f9a9078357c9b7e509379a8b7e0f2e75fc2495f31e30d9403d20b1129372bd51fb601ea2fa37b52cb2dfa158706c121d15ac1746cd958a09c67204ae7
-DIST abyss-2.3.0.tar.gz 1530977 BLAKE2B feda6dc6b757a9183157b01c44c6ee7ec721e95860f50a8a44d245932622c91d0f21fd347bfacc50b787f766b18e0f94b69407bbed9c771601825e63f65a8320 SHA512 efd0423dfbf4fa6c8b529a43222cdf9421369093b780b1ce9309a0b7a89ae8ccd77645a4790cbfdacb1d40814bb0aa4f5f3b225a1e0c299b9bc913cb34084a33
-DIST abyss-2.3.1.tar.gz 1531044 BLAKE2B 2365080bdcca3a1fc5af91557da0187af7f18b20d1f91111b6818a8f53991337913d8ff8cf264aaac560bfc0e860e99f6833beb0b78a56ace014c96b869bec8a SHA512 c7fb8b0a1a1346d138a0a64d2a2886b7c081ed628011b614e8ff14d1cbf4a992a8acb1cc668640c0c6a9c22802e4b0cb839f136b8e1f12fe76dae3248cec1777
diff --git a/sci-biology/abyss/abyss-2.2.5-r1.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.2.5-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- dev-libs/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
- "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
- )
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/abyss-2.3.0-r1.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.3.0-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- dev-libs/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
- "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
- )
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild b/sci-biology/abyss/abyss-2.3.1.ebuild
deleted file mode 100644
index d9134813b..000000000
--- a/sci-biology/abyss/abyss-2.3.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- dev-libs/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
- "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
- )
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
deleted file mode 100644
index 95181f082..000000000
--- a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.000000000 +0200
-+++ abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000 +0200
-@@ -171,7 +171,7 @@
- template <typename T>
- ContigProperties& operator+=(ContigProperties& a, const T& b)
- {
-- assert((int)a.length + (int)b.distance > 0);
-+ assert((int)a.length + (int)b.distance >= 0);
- a.length += b.distance;
- return a;
- }
diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
deleted file mode 100644
index 754e25acc..000000000
--- a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.000000000 +0200
-+++ abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000 +0200
-@@ -379,7 +379,7 @@
- unsigned overlap, Sequence& seq,
- const Sequence& s, const ContigNode& node, const Path& path)
- {
-- assert(s.length() > overlap);
-+ assert(s.length() >= overlap);
- Sequence ao;
- Sequence bo(s, 0, overlap);
- Sequence o;
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index 47116e507..000000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="project">
- <email>haskell@gentoo.org</email>
- <name>Gentoo Haskell</name>
- </maintainer>
- <use>
- <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
- </use>
- <upstream>
- <remote-id type="github">bcgsc/abyss</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild
index c60a87138..db19930fd 100644
--- a/sci-biology/afni/afni-19.3.12.ebuild
+++ b/sci-biology/afni/afni-19.3.12.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit eutils multilib pax-utils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index da68d2d6d..e2ed432c8 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils multilib pax-utils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
index ed100cb3c..3185a297a 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils multilib pax-utils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
index e30be5542..c6e4c669b 100644
--- a/sci-biology/afni/afni-9999.ebuild
+++ b/sci-biology/afni/afni-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit eutils multilib pax-utils git-r3 toolchain-funcs
+inherit git-r3 toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
diff --git a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
index 10b78c648..4606fa9df 100644
--- a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
+++ b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
@@ -5,7 +5,7 @@ EAPI=7
LUA_COMPAT=( lua5-{1..3} )
-inherit multilib lua
+inherit lua
DESCRIPTION="A sleep-research experiment manager, EDF viewer & Process S simulator"
HOMEPAGE="http://johnhommer.com/academic/code/aghermann"
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
index a457397a9..756fde11d 100644
--- a/sci-biology/ants/ants-2.3.4.ebuild
+++ b/sci-biology/ants/ants-2.3.4.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake multilib
+inherit cmake
MY_PN="ANTs"
diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild b/sci-biology/bamql/bamql-1.6.1.ebuild
index f11a50278..435a7b3a5 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit autotools eutils
+inherit autotools
DESCRIPTION="Extract reads from BAM files"
HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
index 0bdabc617..3746b4b8f 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Manipulate BED file (alternative to bedtools)"
HOMEPAGE="http://bedops.readthedocs.io
https://github.com/bedops/bedops"
diff --git a/sci-biology/bedops/bedops-2.4.39.ebuild b/sci-biology/bedops/bedops-2.4.39.ebuild
index 3f8f956bb..348d53065 100644
--- a/sci-biology/bedops/bedops-2.4.39.ebuild
+++ b/sci-biology/bedops/bedops-2.4.39.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Manipulate BED file (alternative to bedtools)"
HOMEPAGE="http://bedops.readthedocs.io
https://github.com/bedops/bedops"
diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
index 4b1a7873d..ff7768d6d 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit autotools
-
release_data="20191030105216"
DESCRIPTION="Tools for bam file processing (libmaus2)"
diff --git a/sci-biology/bismark/bismark-0.23.0.ebuild b/sci-biology/bismark/bismark-0.23.0.ebuild
index 0a59fbb15..121447992 100644
--- a/sci-biology/bismark/bismark-0.23.0.ebuild
+++ b/sci-biology/bismark/bismark-0.23.0.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Map bisulfite converted sequence reads and cytosine methylation states"
HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/"
SRC_URI="https://github.com/FelixKrueger/Bismark/archive/${PV}.tar.gz -> ${P}.tar.gz"
diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest
new file mode 100644
index 000000000..7819d5a37
--- /dev/null
+++ b/sci-biology/blasr/Manifest
@@ -0,0 +1 @@
+DIST blasr-5.3.5.tar.gz 2709986 BLAKE2B 48a8d12e4a47159c00d5febab4222dec5e2f4e5ce4d7a481243b4b62e0ba693eb9e1aa2a11b5de36606ec977db3947178cfdd0a1a09ccfea213e1a1567402e74 SHA512 79155f29076e4a9fe1d66d9e8310d38d3b6690fe1959be923627607ed4d7dfe97c020ff9f9134a3cffcb8e1cd5eb1b3a861d10cb476f9c3866c87e85e6ae93e7
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
index cbd012727..8552bff9e 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-5.3.5.ebuild
@@ -1,26 +1,24 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit meson git-r3
+inherit meson
DESCRIPTION="The PacBio long read aligner"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
LICENSE="blasr"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
BDEPEND="
dev-util/cmake
virtual/pkgconfig
"
DEPEND="
- sci-biology/pbbam
sci-biology/libblasr
- dev-libs/boost:=[threads(-)]
+ dev-libs/boost:=
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
deleted file mode 100644
index bed47bc41..000000000
--- a/sci-biology/bowtie/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST bowtie-1.3.0.tar.gz 7673510 BLAKE2B 8e4d80d2d6715f659bebae2c488d16b7b513c272996bcdcb5ea9bbfef2d0177a27fe5d7be74595f8e8ec1eb5f0cd3eea12ad7017e1d3e4a846488e85e722963c SHA512 e042d1950a9db1e8c491d39f554d8d8b9fa2e8c8a5ba30a10cfbbe66e1527a3943bae69be085d435569bd7bf589f1c330275162abdd5862eaaf62de0bff4ae06
-DIST bowtie-2.4.2.tar.gz 10590144 BLAKE2B 0cfbf73f826002481ca7e4bbdc061d26e6acbaa25bd11b164e08dd103bf9e995f91011b8fbe5a225da97c4ff43b6d2c8b39abd3d9539937e4d72d948a1941a09 SHA512 f8bb74aaec7557bcd1bc4b5ec5e2a3b141d78c88b04f39cdcc417d15f058bdb48b15d159c4ab569b4d655e3d1bd0cf8152343f05b9a20d5d29680c3e8c2f1a05
diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
deleted file mode 100644
index 857bc9cd1..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs git-r3
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
-EGIT_BRANCH="bug_fixes"
-COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- app-arch/unzip"
-# sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-#PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#
-# still to be considered
-#PATCHES=(
-# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-# "${FILESDIR}/${P}-unbundle-seqan.patch"
-# "${FILESDIR}/${P}-fix-setBegin-call.patch"
-# "${FILESDIR}/${P}-seqan-popcount.patch"
-# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-# "${FILESDIR}/${P}-spelling.patch"
-# "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
- default
-
- # remove bundled library of headers, use system seqan 1.4
- # rm -rf SeqAn-1.1/ third_party/ || die
-
- # innocuous non-security flags, prevent log pollution
- append-cxxflags \
- -Wno-unused-local-typedefs \
- -Wno-unused-but-set-variable \
- -Wno-unused-variable
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN} ${PN}-*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*
-
- newman MANUAL ${PN}.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r genomes indexes
- fi
-}
diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild
deleted file mode 100644
index 118cc1303..000000000
--- a/sci-biology/bowtie/bowtie-1.3.0.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- app-arch/unzip"
-# sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_prepare() {
- default
-
- # remove bundled library of headers, use system seqan 1.4
- # rm -rf SeqAn-1.1/ third_party/ || die
-
- # innocuous non-security flags, prevent log pollution
- append-cxxflags \
- -Wno-unused-local-typedefs \
- -Wno-unused-but-set-variable \
- -Wno-unused-variable
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS}" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN} ${PN}-*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*
-
- newman MANUAL ${PN}.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r genomes indexes
- fi
-}
diff --git a/sci-biology/bowtie/bowtie-2.4.2.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild
deleted file mode 100644
index 03cf3f8a9..000000000
--- a/sci-biology/bowtie/bowtie-2.4.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb" # sra
-# IUSE=sra Use sra-toolkit to download input datasets on the fly.
-
-RDEPEND="dev-lang/perl
- tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- app-arch/unzip
- sys-libs/readline"
-# sra? ( sci-biology/sra_sdk )"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-pkg_pretend() {
- if ! use cpu_flags_x86_sse2 ; then
- eerror "This package requires a CPU supporting the SSE2 instruction set."
- die "SSE2 support missing"
- fi
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS} -msse2" \
- WITH_TBB="$(usex tbb 1 0)"
- # USE_SRA="$(usex sra 1 0)"
-}
-
-src_install() {
- dobin ${PN}2 ${PN}2-*
-
- exeinto /usr/libexec/${PN}2
- doexe scripts/*
-
- newman MANUAL ${PN}2.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}2
- doins -r example
- fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 4bcd61ba3..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class.
-Forwarded: no
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Last-Update: 2014-100-06
-
---- bowtie-1.2.2/diff_sample.h 2017-11-03 01:25:56.000000000 +0100
-+++ bowtie-1.2.2/diff_sample.h 2019-02-18 12:50:37.894674282 +0100
-@@ -979,7 +979,7 @@
- {
- Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose());
- VMSG_NL(" Invoking Larsson-Sadakane on ranks");
-- _Context_LSS<TIndexOff> c;
-+ ContextLss_<TIndexOff> c;
- c.suffixsort(
- (TIndexOff*)begin(_isaPrime, Standard()),
- (TIndexOff*)begin(sPrime, Standard()),
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
deleted file mode 100644
index 75942efb5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-fix compilation errors with Intel compilers:
-error: no operator "=" matches these operands
-author: Ward Poelmans
---- bowtie-1.2.2/hit.h 2018-01-24 12:57:47.135575442 +0100
-+++ bowtie-1.2.2/hit.h 2018-01-24 12:57:58.615869774 +0100
-@@ -640,10 +640,26 @@
- s.moveTo(btString);
- }
-
-+ batch(const batch &other)
-+ {
-+ batchId = other.batchId;
-+ isWritten = other.isWritten;
-+ btString = other.btString;
-+ }
-+
- bool operator<(const batch& other) const {
- return batchId < other.batchId;
- }
-
-+ batch& operator=(batch&& other) {
-+ if (&other != this) {
-+ batchId = other.batchId;
-+ isWritten = other.isWritten;
-+ other.btString.moveTo(btString);
-+ }
-+ return *this;
-+ }
-+
- batch& operator=(batch& other) {
- if (&other != this) {
- batchId = other.batchId;
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
deleted file mode 100644
index de19e42a8..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
-From: Rone Charles <rone_charles@fastmail.com>
-Date: Tue, 4 Sep 2018 21:06:39 -0400
-Subject: [PATCH] Fix isa return type
-
----
- ebwt.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ebwt.h b/ebwt.h
-index fe6300cc..8f886b8d 100644
---- a/ebwt.h
-+++ b/ebwt.h
-@@ -862,7 +862,7 @@ class Ebwt {
- TIndexOffU* ftab() const { return _ftab; }
- TIndexOffU* eftab() const { return _eftab; }
- TIndexOffU* offs() const { return _offs; }
-- uint32_t* isa() const { return _isa; } /* check */
-+ TIndexOffU* isa() const { return _isa; } /* check */
- TIndexOffU* plen() const { return _plen; }
- TIndexOffU* rstarts() const { return _rstarts; }
- uint8_t* ebwt() const { return _ebwt; }
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
deleted file mode 100644
index b1a5f98f5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- bowtie-1.2.2/Makefile 2019-02-18 13:26:29.490835084 +0100
-+++ bowtie-1.2.2/Makefile 2019-02-18 13:28:36.864742545 +0100
-@@ -5,10 +5,7 @@
- prefix = /usr/local
- bindir = $(prefix)/bin
-
--SEQAN_DIR = ./SeqAn-1.1
--# treat SeqAn as a sysdir to suppress warnings
--SEQAN_INC = -isystem $(SEQAN_DIR)
--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
- CPP = g++
- CXX = $(CPP)
- CC = gcc
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
deleted file mode 100644
index 822b673ae..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument
-#being incompatible with parameter of type "int *"
-#M. Fujinaga (fujinaga@ualberta.ca)
---- processor_support.h 2017-02-02 21:48:42.436432756 +0000
-+++ processor_support.h 2017-02-02 21:48:54.419309743 +0000
-@@ -44,8 +44,8 @@
-
- try {
- #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )
-- __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
-- __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
-+ __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
-+ __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
- #elif defined(USING_GCC_COMPILER)
- __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
deleted file mode 100644
index 71e8d3bb8..000000000
--- a/sci-biology/bowtie/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">bowtie-bio</remote-id>
- </upstream>
- <use>
- <flag name="tbb">Enables building bowtie with the Intel
- Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
- flag is recommended.</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index a92b6e581..e14efe3af 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit java-pkg-2 perl-module python-r1 multilib
+inherit java-pkg-2 perl-module python-r1
DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
HOMEPAGE="https://canu.readthedocs.io/en/latest"
diff --git a/sci-biology/conrad/Manifest b/sci-biology/conrad/Manifest
deleted file mode 100644
index 33745ecdd..000000000
--- a/sci-biology/conrad/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conrad-1.zip 13266670 BLAKE2B bd89175dd02541323bfefeed1c0a9691c46f21ed08041b5f89a7424660a4eeeb469e4695f6345a15544b8affb5a5e3879f3551729299802c0e3454624cd85164 SHA512 804b70442437317276dd4757806ce1dec2deb4f3121ef08c981c955dd0e943d135c98727a956f605a6d42a913c9efb2c72c1c2dab4015e8fce925f10f51118f3
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
deleted file mode 100644
index bca495174..000000000
--- a/sci-biology/conrad/conrad-1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor"
-HOMEPAGE="https://sourceforge.net/projects/conradcrf"
-SRC_URI="https://downloads.sourceforge.net/project/conradcrf/conradcrf/Version%201/conradSrc.zip -> ${P}.zip"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- >=virtual/jre-1.5:*
- <virtual/jdk-1.9:*
- dev-java/commons-logging
- >=dev-java/commons-lang-2.1:*
- dev-java/colt
- dev-java/dom4j
- "
- # spring # see bug #97004
- # dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.5:*
- <virtual/jdk-1.9:*
- dev-java/ant-core
- >=dev-java/jfreechart-1.0.3
- >=dev-java/jcommon-1.0.6
- >=dev-java/commons-math-1.1
- "
-BDEPEND="app-arch/unzip"
-S="${WORKDIR}"
-
-src_prepare(){
- default
- sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
-}
-
-src_compile(){
- cd dev || die
- ant compile || die
-}
-
-src_install() {
- dobin bin/conrad.sh
- java-pkg_dojar lib/conrad.jar
- java-pkg_dolauncher conrad --jar conrad.jar
- dodoc -r docs models samples trainingFiles
-}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
deleted file mode 100644
index 814dcabcc..000000000
--- a/sci-biology/conrad/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">conradcrf</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/cramtools/Manifest b/sci-biology/cramtools/Manifest
deleted file mode 100644
index 7d81698d2..000000000
--- a/sci-biology/cramtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cramtools-3.0.tar.gz 7394093 BLAKE2B dc0b21f94b1c3f256a55f4aa324106b6bfb3cd9548ce0aaf589c4da9f95fcbb0007a71c44ed6a915340d86c80555f91ebbf5864e38603f06a73aa132af23772e SHA512 077806ece2e0449f2245e4aefd5ebf5ae91e01f177575a3fed9f7458f8d0ba0a554c368ec56ba305f58ed7f3502a7ac1da1685fb38a19e3230564f4329ecb080
diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild
deleted file mode 100644
index b57f4fb26..000000000
--- a/sci-biology/cramtools/cramtools-3.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java tools and APIs for efficient compression of sequence read data"
-HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit
- https://github.com/enasequence/cramtools"
-SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- >=virtual/jdk-1.7:*
- dev-java/ant-core
- dev-java/htsjdk"
-RDEPEND="
- ${DEPEND}
- >=virtual/jre-1.7:*"
-
-# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk?
-# https://github.com/enasequence/cramtools/issues/58
-# https://github.com/enasequence/cramtools/issues/59
-src_compile(){
- ant -f build/build.xml runnable || die
-}
-
-src_install() {
- java-pkg_newjar "${P}.jar" "${PN}.jar"
-}
diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml
deleted file mode 100644
index 5a55ad312..000000000
--- a/sci-biology/cramtools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">enasequence/cramtools</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/fastqc/Manifest b/sci-biology/fastqc/Manifest
index 470141cc1..91b60dbc9 100644
--- a/sci-biology/fastqc/Manifest
+++ b/sci-biology/fastqc/Manifest
@@ -1 +1 @@
-DIST fastqc_v0.11.3_source.zip 10073593 BLAKE2B 4b72d8c06c7495baa138a39f4f6140022c9d8a954dd284c3e66fdf547411315425995e72005eb6605559197b094ead9aab28918bf0f89b3a1d49fef00b02ce28 SHA512 bab27d6997ad6525b7804ba9a3a54eec1cdb835d548c2840ae882334902d12eea4bbff549370669176ade76633a5f1d7dc6f7ee865a25f1a41b525764660b471
+DIST fastqc-0.11.9.tar.gz 10077703 BLAKE2B 7922effe383801ae30a4f16cca06d893883af48a730f5640926bc83eedae4df78e956973f1985a5ff9bb83ff061314b80eeecaed738f0eafa7feb59ecfad6984 SHA512 20f46fd9b5608565b6da8ec3bedb1f173a3619b0004bc0987147b1e3240813ef6ebbb07b9bcf2c472272dfad8262ad6edf68055ccad3b81b5ffb63ddc5278a4a
diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
deleted file mode 100644
index 4be2ae23b..000000000
--- a/sci-biology/fastqc/fastqc-0.11.3.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 eutils java-ant-2 prefix
-
-DESCRIPTION="Quality control FASTA/FASTQ sequence files"
-HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
-SRC_URI="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND} >=virtual/jdk-1.5:*"
-BDEPEND="app-arch/unzip"
-
-S="${WORKDIR}"/FastQC
-
-src_prepare(){
- cp "${FILESDIR}"/build.xml . || die
- default
-}
-
-src_compile(){
- ant || die
-}
-
-src_install(){
- insinto "opt/${PN}"
- doins -r bin
- chmod a+x "${ED}/opt/${PN}/bin/fastqc"
- # Add the package's bin directory to the PATH.
- doenvd "${FILESDIR}/00fastqc"
- if use prefix ; then
- hprefixify "${ED}/etc/env.d/00fastqc"
- fi
-
- dodoc README.txt RELEASE_NOTES.txt
-}
-
-pkg_postinst() {
- ewarn "Remember to run: env-update && source \"${EPREFIX}/etc/profile\" if you plan"
- ewarn "to use this tool in a shell before logging out (or restarting"
- ewarn "your login manager)"
-}
diff --git a/sci-biology/fastqc/fastqc-0.11.9.ebuild b/sci-biology/fastqc/fastqc-0.11.9.ebuild
new file mode 100644
index 000000000..be2d3b340
--- /dev/null
+++ b/sci-biology/fastqc/fastqc-0.11.9.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit desktop java-pkg-2 java-ant-2 xdg
+
+DESCRIPTION="Quality control FASTA/FASTQ sequence files"
+HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+SRC_URI="https://github.com/s-andrews/FastQC/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/FastQC-${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-lang/perl
+ >=virtual/jre-1.8:*
+"
+DEPEND="
+ dev-lang/perl
+ >=virtual/jdk-1.8:*
+"
+BDEPEND="media-gfx/imagemagick"
+
+EANT_BUILD_TARGET="build"
+
+src_install(){
+ insinto "opt/${PN}"
+ doins -r bin/*
+ chmod a+x "${ED}/opt/${PN}/fastqc"
+ # add convenience symlink
+ dosym ../${PN}/${PN} /opt/bin/${PN}
+
+ convert ${PN}_icon.ico ${PN}.png || die
+ doicon ${PN}.png
+ make_desktop_entry ${PN} FastQC ${PN}
+ einstalldocs
+}
diff --git a/sci-biology/fastqc/files/00fastqc b/sci-biology/fastqc/files/00fastqc
deleted file mode 100644
index 021de8bb0..000000000
--- a/sci-biology/fastqc/files/00fastqc
+++ /dev/null
@@ -1 +0,0 @@
-PATH="/opt/fastqc/bin"
diff --git a/sci-biology/fastqc/files/build.xml b/sci-biology/fastqc/files/build.xml
deleted file mode 100644
index c4a692096..000000000
--- a/sci-biology/fastqc/files/build.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- WARNING: Eclipse auto-generated file.
- Any modifications will be overwritten.
- To include a user specific buildfile here, simply create one in the same
- directory with the processing instruction <?eclipse.ant.import?>
- as the first entry and export the buildfile again. -->
-<project basedir="." default="build" name="FastQC">
- <property environment="env"/>
- <property name="debuglevel" value="source,lines,vars"/>
- <property name="target" value="1.5"/>
- <property name="source" value="1.5"/>
- <path id="FastQC.classpath">
- <pathelement location="bin"/>
- <pathelement location="jbzip2-0.9.jar"/>
- <pathelement location="sam-1.103.jar"/>
- <pathelement location="cisd-jhdf5.jar"/>
- </path>
- <target name="init">
- <mkdir dir="bin"/>
- <copy includeemptydirs="false" todir="bin">
- <fileset dir=".">
- <exclude name="**/*.launch"/>
- <exclude name="**/*.java"/>
- </fileset>
- </copy>
- </target>
- <target name="clean">
- <delete dir="bin"/>
- </target>
- <target depends="clean" name="cleanall"/>
- <target depends="build-subprojects,build-project" name="build"/>
- <target name="build-subprojects"/>
- <target depends="init" name="build-project">
- <echo message="${ant.project.name}: ${ant.file}"/>
- <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
- <src path="."/>
- <classpath refid="FastQC.classpath"/>
- </javac>
- </target>
- <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>
- <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
- <copy todir="${ant.library.dir}">
- <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
- </copy>
- <unzip dest="${ant.library.dir}">
- <patternset includes="jdtCompilerAdapter.jar"/>
- <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
- </unzip>
- </target>
- <target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
- <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
- <antcall target="build"/>
- </target>
- <target name="FastQCApplication">
- <java classname="uk.ac.babraham.FastQC.FastQCApplication" failonerror="true" fork="yes">
- <classpath refid="FastQC.classpath"/>
- </java>
- </target>
-</project>
diff --git a/sci-biology/flexbar/flexbar-3.5.0.ebuild b/sci-biology/flexbar/flexbar-3.5.0.ebuild
index b390f5056..49f67558b 100644
--- a/sci-biology/flexbar/flexbar-3.5.0.ebuild
+++ b/sci-biology/flexbar/flexbar-3.5.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cmake
+inherit cmake flag-o-matic
DESCRIPTION="Barcode, MID tag and adapter sequence removal"
HOMEPAGE="https://github.com/seqan/flexbar"
diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index 868861b84..3a1d5a7d9 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1,2 +1,2 @@
-DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca
DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3
+DIST fsl-6.0.5.tar.gz 2509109593 BLAKE2B d1e5efbb6b73e2b40e7147dc4958584e057311084d2064335aae1c0a36cfab5e12061f3fac4f54118d840e66620b7e64a5dc4c32c0e0e3e6233c25cc3b48e6fd SHA512 e5124ae640f51002692de6ad9fdc3aec0e3caffc94dd18c16fadba686fa2a9bf37c7752e67affca53d9859cbab3e2e62ca28ef43c754c464bab5e182e55b02a1
diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
deleted file mode 100644
index f490b6e7c..000000000
--- a/sci-biology/fsl/fsl-6.0.2.ebuild
+++ /dev/null
@@ -1,167 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
- dev-libs/boost
- <dev-python/fslpy-3
- media-gfx/graphviz
- media-libs/gd
- media-libs/glu
- media-libs/libpng:0=
- sci-libs/ciftilib
- sci-libs/nlopt
- sys-libs/zlib
- dev-lang/tcl:0=
- dev-lang/tk:0=
- >=virtual/lapack-3.8
- >=virtual/blas-3.8
- "
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
- "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
- "${FILESDIR}/${PN}"-6.0.2-setup.patch
- "${FILESDIR}/${PN}"-6.0.2-template.patch
- "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
- "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
- "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
- "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
- "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
- "${FILESDIR}/${PN}"-5.0.9-headers.patch
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
-)
-
-src_prepare(){
- default
-
- sed -i \
- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
- config/buildSettings.mk || die
-
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
- etc/js/label-div.html
-
- # Disable mist-clean the hard way for now.
- rm -rf src/mist-clean
-
- makefilelist=$(find src/ -name Makefile)
-
- sed -i \
- -e "s:-I\${INC_BOOST}::" \
- -e "s:-I\${INC_ZLIB}::" \
- -e "s:-I\${INC_GD}::" \
- -e "s:-I\${INC_PNG}::" \
- -e "s:-L\${LIB_GD}::" \
- -e "s:-L\${LIB_PNG}::" \
- -e "s:-L\${LIB_ZLIB}::" \
- ${makefilelist} || die
-
- sed -e "s:\${FSLDIR}/bin/::g" \
- -e "s:\$FSLDIR/bin/::g" \
- -i $(grep -rl "\${FSLDIR}/bin" src/*) \
- -i $(grep -rl "\$FSLDIR/bin" src/*) \
- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
- $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
-
- sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
- -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
- -i $(grep -rl "\$FSLDIR/data" src/*) \
- $(grep -rl "\${FSLDIR}/data" src/*) || die
-
- sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -i $(grep -rl "\$FSLDIR/doc" src/*) \
- $(grep -rl "\${FSLDIR}/doc" src/*) || die
-
- sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -i $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
- sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
- -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
- -i $(grep -rlI "\$FSLDIR/etc" *) \
- -i $(grep -rlI "\${FSLDIR}/etc" *) || die
-
- # Use generic blas/lapack rather than openblas
- sed -e "s:-lopenblas:-llapack -lblas:g" \
- -i $(grep -rlI lopenblas *) || die
-
- # script wanting to have access to flsversion at buildtime
- sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
- -i ${makefilelist} || die
-}
-
-src_compile() {
- export FSLDIR=${WORKDIR}/${PN}
- export FSLCONDIR=${WORKDIR}/${PN}/config
- export FSLMACHTYPE=generic
-
- export USERLDFLAGS="${LDFLAGS}"
- export USERCFLAGS="${CFLAGS}"
- export USERCXXFLAGS="${CXXFLAGS}"
-
- export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
- export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
-
- ./build || die
-}
-
-src_install() {
- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
- $(grep -lI "\${FSLDIR}/tcl" bin/*) \
- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
- $(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
- dobin bin/*
-
- insinto /usr/share/${PN}
- doins -r data
- dodoc -r doc/. refdoc
-
- insinto /usr/libexec/fsl
- doins -r tcl/*
-
- insinto /etc/fslconf
- doins etc/fslconf/fsl.sh
-
- insinto /etc
- doins etc/fslversion
- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-
- #the following is needed for FSL and depending programs to be able
- #to find its files, since FSL uses an uncommon installation path:
- #https://github.com/gentoo-science/sci/pull/612#r60289295
- dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
- dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
- dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
- doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
- mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
- echo
- einfo "Please run the following commands if you"
- einfo "intend to use fsl from an existing shell:"
- einfo "env-update && source /etc/profile"
- echo
-}
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index e0feb82d9..4797c1298 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cuda flag-o-matic toolchain-funcs prefix
+inherit cuda toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
index ae12098ec..c51a9d30e 100644
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -1,58 +1,66 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit cuda flag-o-matic toolchain-funcs prefix
+inherit cuda toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}"
LICENSE="FSL BSD-2 newmat"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE="cuda"
DEPEND="
+ dev-cpp/libxmlpp:=
+ dev-cpp/tbb
+ dev-db/sqlite
dev-libs/boost
- <dev-python/fslpy-3
+ dev-libs/libfmt
+ dev-libs/libxml2
+ dev-libs/pugixml
+ >=dev-python/fslpy-3.7.0
media-gfx/graphviz
media-libs/gd
media-libs/glu
media-libs/libpng:0=
+ sci-libs/gsl
sci-libs/ciftilib
+ sci-libs/fftw
sci-libs/nlopt
+ sci-libs/vtk
sys-libs/zlib
dev-lang/tcl:0=
dev-lang/tk:0=
>=virtual/lapack-3.8
>=virtual/blas-3.8
-
cuda? (
|| (
- ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
)
)
"
RDEPEND="${DEPEND}"
-S=${WORKDIR}/${PN}
UPSTREAM_FSLDIR="/usr/share/fsl"
PATCHES=(
- "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
- "${FILESDIR}/${PN}"-6.0.2-setup.patch
- "${FILESDIR}/${PN}"-6.0.2-template.patch
- "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
- "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
- "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
- "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
- "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
- "${FILESDIR}/${PN}"-5.0.9-headers.patch
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
+# "${FILESDIR}/${PN}"-6.0.4-gcc10_include.patch
+ "${FILESDIR}/${PN}"-6.0.4-setup.patch
+# "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+# "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+# "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+# "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+# "${FILESDIR}/${PN}"-5.0.9-headers.patch
+ "${FILESDIR}/${PN}"-6.0.4-flameo_std.patch
+ "${FILESDIR}/${PN}"-6.0.4-melodic_std.patch
+ "${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p1.patch
+ "${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p2.patch
+# "${FILESDIR}/${PN}"-6.0.4-fdt_cuda.patch
)
src_prepare() {
@@ -67,20 +75,23 @@ src_prepare() {
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
etc/js/label-div.html
- # Disable mist-clean the hard way for now.
- rm -rf src/mist-clean
-
+# # Disable mist the hard way for now.
+# rm -r src/mist || die
+#
+# # Disable ptx2 for now
+# rm -r src/ptx2 || die
+#
makefilelist=$(find src/ -name Makefile)
- sed -i \
- -e "s:-I\${INC_BOOST}::" \
- -e "s:-I\${INC_ZLIB}::" \
- -e "s:-I\${INC_GD}::" \
- -e "s:-I\${INC_PNG}::" \
- -e "s:-L\${LIB_GD}::" \
- -e "s:-L\${LIB_PNG}::" \
- -e "s:-L\${LIB_ZLIB}::" \
- ${makefilelist} || die
+# sed -i \
+# -e "s:-I\${INC_BOOST}::" \
+# -e "s:-I\${INC_ZLIB}::" \
+# -e "s:-I\${INC_GD}::" \
+# -e "s:-I\${INC_PNG}::" \
+# -e "s:-L\${LIB_GD}::" \
+# -e "s:-L\${LIB_PNG}::" \
+# -e "s:-L\${LIB_ZLIB}::" \
+# ${makefilelist} || die
sed -e "s:\${FSLDIR}/bin/::g" \
-e "s:\$FSLDIR/bin/::g" \
@@ -111,7 +122,7 @@ src_prepare() {
sed -e "s:-lopenblas:-llapack -lblas:g" \
-i $(grep -rlI lopenblas *) || die
- # script wanting to have access to flsversion at buildtime
+ # script wanting to have access to fslversion at buildtime
sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
-i ${makefilelist} || die
@@ -129,8 +140,8 @@ src_prepare() {
CUDA_INSTALLATION="/opt/cuda"
CUDAVER=`cuda_toolkit_version`
- eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch"
- eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch"
+ eapply "${FILESDIR}/${PN}-6.0.4-eddy_cuda.patch"
+ eapply "${FILESDIR}/${PN}-6.0.4-cuda_buildsettings.patch"
sed -i \
-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
@@ -145,8 +156,14 @@ src_compile() {
export FSLCONDIR=${WORKDIR}/${PN}/config
export FSLMACHTYPE=generic
+ # define the default build system to match upstream official standard
+ # -> individual projects may overwrite the '-std=' flag
+ export ANSI_CFLAGS="-std=c99"
+ export ANSI_CXXFLAGS="-std=c++98"
+
export USERLDFLAGS="${LDFLAGS}"
export USERCFLAGS="${CFLAGS}"
+ export USERCPPFLAGS="${CPPFLAGS}"
export USERCXXFLAGS="${CXXFLAGS}"
export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
diff --git a/sci-biology/gffread/gffread-0.11.0.ebuild b/sci-biology/gffread/gffread-0.11.0.ebuild
index bfedb57a5..871d38d03 100644
--- a/sci-biology/gffread/gffread-0.11.0.ebuild
+++ b/sci-biology/gffread/gffread-0.11.0.ebuild
@@ -1,10 +1,8 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
https://github.com/gpertea/gffread"
diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild
index 5aa279af0..d459d664b 100644
--- a/sci-biology/glean/glean-1.0.1.ebuild
+++ b/sci-biology/glean/glean-1.0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit perl-module toolchain-funcs
+inherit perl-module
DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)"
HOMEPAGE="https://sourceforge.net/projects/glean-gene"
diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index 15a2d7bca..b2e6ea25b 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit flag-o-matic
-
DESCRIPTION="k-mer counter within reads for assemblies"
HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index 6bd33a14c..e8e3c8fd0 100644
--- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit flag-o-matic autotools
-
DESCRIPTION="k-mer counter within reads for assemblies"
HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
@@ -16,15 +14,13 @@ SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
-DEPEND=""
+RDEPEND="
+ sci-biology/samtools:0
+ sci-libs/htslib
+"
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
-src_prepare(){
- eautoreconf
- default
-}
-
# TODO: enable compilation of Bindings to Ruby, Python and Perl
# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding', '--enable-swig'
src_configure(){
diff --git a/sci-biology/jigsaw/Manifest b/sci-biology/jigsaw/Manifest
deleted file mode 100644
index 1fcded0c0..000000000
--- a/sci-biology/jigsaw/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jigsaw-3.2.10m.tar.gz 1024885 BLAKE2B 59b98b3e8469b84fcb8bdceadc0cef3a628bf5b1e059af905a07b89de29a686aa66c20c451308bd980b8daba4e9c1ff0ec953b56a58d926ef626e1f4ee8b1a48 SHA512 5d19e933b5c9f2c57cb73a56a9017e5c088ce0135c2899caf21f2b9c0f092c35673b96be918e73f5fdb1c641dce853123e8f9d5592a64ac8704c28314b2d7877
diff --git a/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild b/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild
deleted file mode 100644
index 1a78ae08e..000000000
--- a/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Combine results from external gene predictors into final gene models"
-HOMEPAGE="https://www.cbcb.umd.edu/software/jigsaw"
-SRC_URI="https://www.cbcb.umd.edu/software/jigsaw/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-
-S="${WORKDIR}/${PN}-${PV//m}"
-
-src_compile() {
- cd src/main || die
- emake
- cd ../../lib/oc1
- emake
-}
-
-src_install() {
- cd src/main || die
- emake DESTDIR="${ED}" install
- cd ../../lib/oc1
- emake DESTDIR="${ED}" install
-}
diff --git a/sci-biology/jtreeview/Manifest b/sci-biology/jtreeview/Manifest
deleted file mode 100644
index db64018f4..000000000
--- a/sci-biology/jtreeview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST TreeView-1.2.0-src.tar.gz 3176518 BLAKE2B 0e80c2298236fa064d8a36f5cea71d962f1a1b38bf9128bcc964ad44f5c0502d92008e1f5c70a290522763fff356beb01584b02eea0834392df14196f4313c93 SHA512 b2c2d8c2d2e9201fb9877c7014607bd21a946a57159ebda0fb834563e9a8751298e964bd32474bc6f53303727c2a3d03c72869d1485d9656150591c44c26a9b1
-DIST helper-scripts-0.0.2.tar.gz 18260 BLAKE2B 2f794063fa2f9263b92465b48a891efc5ae65ab3a64ade7250aa3a9f166873d9a6f9c5ad69387caa6d9f15affb907cd2b3587e7c261b862337319c0e7d7be9d6 SHA512 6d335ffa4da7db2d5b2d0009e8db87145cc9b3b85772059f6afde55f544de1ee1348a8450e69393ea59313268549204be3d26931dc43085d843ff3c6c3c27d88
diff --git a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
deleted file mode 100644
index 8f0e777c9..000000000
--- a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module java-pkg-2 java-ant-2
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
-SRC_URI="
- https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-src.tar.gz
- https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
-"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=">virtual/jdk-1.7:*
- dev-java/nanoxml"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/TreeView-${PV}-src"
-JAVA_PKG_BSFIX_NAME="${S}"
-
-# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
deleted file mode 100644
index 316368b4e..000000000
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
-EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=">virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml
deleted file mode 100644
index 5139daeeb..000000000
--- a/sci-biology/jtreeview/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="bitbucket">TreeView3Dev/treeview3</remote-id>
- <remote-id type="sourceforge">jtreeview</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild
index 39c4fc6c1..a915d1491 100644
--- a/sci-biology/kat/kat-2.4.2.ebuild
+++ b/sci-biology/kat/kat-2.4.2.ebuild
@@ -7,7 +7,7 @@ PYTHON_COMPAT=( python3_{7,8,9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-inherit flag-o-matic autotools distutils-r1
+inherit autotools distutils-r1
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 404f0d0c2..acbdac423 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -7,7 +7,7 @@ PYTHON_COMPAT=( python3_{7,8,9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-inherit flag-o-matic autotools distutils-r1 git-r3
+inherit autotools distutils-r1 git-r3
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
diff --git a/sci-biology/libblasr/Manifest b/sci-biology/libblasr/Manifest
new file mode 100644
index 000000000..c575f4081
--- /dev/null
+++ b/sci-biology/libblasr/Manifest
@@ -0,0 +1 @@
+DIST libblasr-5.3.5.tar.gz 3950694 BLAKE2B 879910dbbfc60592528fab4de0e3bd975f8d12b7e68ca80e031577c9b18a6959a95c76186455fbdecbe3d8455320ba5b83db2c88318467d50a2470569860c514 SHA512 45997fce4fba12ff40c4624bc152990a683e4298d898b404f82e645493557a0565476ead2420fd9c28790e1985cdf3a88401c30181fdc57f84bbd61a707a8b5e
diff --git a/sci-biology/libblasr/libblasr-9999.ebuild b/sci-biology/libblasr/libblasr-5.3.5.ebuild
index 5f5ba504c..a12dc25ac 100644
--- a/sci-biology/libblasr/libblasr-9999.ebuild
+++ b/sci-biology/libblasr/libblasr-5.3.5.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit meson git-r3
+inherit meson
DESCRIPTION="Library for blasr"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr_libcpp.git"
-#SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/blasr_libcpp-${PV}"
LICENSE="blasr"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
BDEPEND="
dev-util/cmake
virtual/pkgconfig
"
DEPEND="
+ sci-biology/pbbam
sci-libs/hdf5[cxx]
"
RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/blasr_libcpp-${PV}"
diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild b/sci-biology/longstitch/longstitch-1.0.1.ebuild
index 787c3219b..6cd035d86 100644
--- a/sci-biology/longstitch/longstitch-1.0.1.ebuild
+++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild
@@ -9,7 +9,7 @@ SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz ->
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
RESTRICT="test"
diff --git a/sci-biology/merlin/merlin-1.1.2.ebuild b/sci-biology/merlin/merlin-1.1.2.ebuild
index 678745a24..9151564d5 100644
--- a/sci-biology/merlin/merlin-1.1.2.ebuild
+++ b/sci-biology/merlin/merlin-1.1.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit toolchain-funcs flag-o-matic
+inherit toolchain-funcs
DESCRIPTION="Statistical analysis of gene flow in pedigrees"
HOMEPAGE="https://csg.sph.umich.edu/abecasis/Merlin/"
diff --git a/sci-biology/minimap2/Manifest b/sci-biology/minimap2/Manifest
index bb0d7474b..54585ee56 100644
--- a/sci-biology/minimap2/Manifest
+++ b/sci-biology/minimap2/Manifest
@@ -1 +1 @@
-DIST minimap2-2.17.tar.bz2 152305 BLAKE2B 14e3a5598fda8a63574704c3d9496967bbbf9f56da77fea7dd03c636dc3f5d24df0363cdacefb514206ff2c96abce45439421b7af525cab6f755e57b3a8fe89d SHA512 4a858b842c9eb0fb195ea3d4b579466a914dd81dbc50ec1b761f950a116f008ed26b7ed7608d89ec08ffa2083a2b837973bdb1879cf55c70d6b95474d185165e
+DIST minimap2-2.24.tar.bz2 169939 BLAKE2B 0e16e144b748c291990c1d076157939ec773643659201ba84cf24587b910e8e56d0d90c28bdeccfcfd120c388a3df495282ade0d1454567910471fd897472a34 SHA512 0f16cfbafd7c5aa2e554052d82384aba14dd83cf60fe425526f7e0d093670d105e5c5c1051bc465113202e026bb320bbb36fc174dc50ed15aabf14f7bfa68859
diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild b/sci-biology/minimap2/minimap2-2.17.ebuild
deleted file mode 100644
index e4f51e1d9..000000000
--- a/sci-biology/minimap2/minimap2-2.17.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="splice-aware sequence aligner"
-HOMEPAGE="https://github.com/lh3/minimap2"
-SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-src_install(){
- dobin "${PN}"
-}
diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild
new file mode 100644
index 000000000..f39de8ead
--- /dev/null
+++ b/sci-biology/minimap2/minimap2-2.24.ebuild
@@ -0,0 +1,63 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_OPTIONAL=1
+inherit distutils-r1
+
+DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
+HOMEPAGE="https://github.com/lh3/minimap2"
+SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="python cpu_flags_x86_sse4_1"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="sys-libs/zlib
+ python? (
+ ${PYTHON_DEPS}
+ )"
+RDEPEND="${DEPEND}"
+BDEPEND="python? ( dev-python/cython[${PYTHON_USEDEP}] )"
+
+src_prepare(){
+ sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
+ if ! use cpu_flags_x86_sse4_1; then
+ sed -i -e "/extra_compile_args.append('-msse4.1')/d" setup.py || die
+ fi
+ if use python; then
+ distutils-r1_src_prepare
+ fi
+ default
+}
+
+src_configure() {
+ if use python; then
+ distutils-r1_src_configure
+ fi
+ default
+}
+
+src_compile() {
+ if use python; then
+ distutils-r1_src_compile
+ fi
+ default
+}
+
+src_install() {
+ if use python; then
+ distutils-r1_src_install
+ fi
+ dobin "${PN}"
+ insinto /usr/include
+ doins minimap.h mmpriv.h
+ insinto /usr/share/"${PN}"/examples
+ doins example.c
+ doman minimap2.1
+ einstalldocs
+}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 94c273172..623759901 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 783f3a266..d4ae93742 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils flag-o-matic multilib toolchain-funcs
+inherit toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
@@ -76,6 +76,10 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}/c++"
# ncbi-blast-2.2.30+-src/c++
+PATCHES=(
+ "${FILESDIR}"/"${P}"__fix_lib_deps.patch
+)
+
src_prepare() {
# filter-ldflags -Wl,--as-needed
# append-ldflags -Wl,--no-undefined
@@ -117,7 +121,6 @@ src_prepare() {
## epatch ${PATCHES[@]}
# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 7874c2295..f0269f0b5 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils flag-o-matic multilib toolchain-funcs
+inherit toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index c04fb4cae..b232894b4 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit eutils flag-o-matic multilib toolchain-funcs
+inherit toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 94c273172..623759901 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
MY_P="ncbi-blast-${PV}+-src"
# workdir/ncbi-blast-2.2.30+-src
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index e646cd099..6daf7b3f0 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit flag-o-matic multilib toolchain-funcs
+inherit toolchain-funcs
MY_TAG="Jun_15_2010"
MY_Y="${MY_TAG/*_/}"
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index e6f233bc7..e2db30639 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
MY_TAG="Jun_15_2010"
MY_Y="${MY_TAG/*_/}"
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index f98fd4282..7df161c99 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit python-single-r1 toolchain-funcs
MY_TAG="Mar_28_2019"
MY_Y="${MY_TAG/*_/}"
diff --git a/sci-biology/ncbi-vdb/Manifest b/sci-biology/ncbi-vdb/Manifest
new file mode 100644
index 000000000..6e69589e6
--- /dev/null
+++ b/sci-biology/ncbi-vdb/Manifest
@@ -0,0 +1 @@
+DIST ncbi-vdb-2.11.2.tar.gz 26543426 BLAKE2B a0acdeefa5e4fadfcc304d33b29be5ae937630fb74b13674e1e7ea8dd4cd71048a1374803fcc6e2248fa4ecb9be93945fcd567f40159748eb86f0fdc98bf6aff SHA512 c3b9e582c9faccd637d5718bbaac49603c993be9234c7bd561ab84cabb9a2d60508822211871c9cd2d3bd42fbb059e5f72194d9e28e126c21ccf70ea8ab6b5b0
diff --git a/sci-biology/jigsaw/metadata.xml b/sci-biology/ncbi-vdb/metadata.xml
index 138cb7705..138cb7705 100644
--- a/sci-biology/jigsaw/metadata.xml
+++ b/sci-biology/ncbi-vdb/metadata.xml
diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
new file mode 100644
index 000000000..167e2a8c3
--- /dev/null
+++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION=" NCBI SRA ( Sequence Read Archive )"
+HOMEPAGE="https://github.com/ncbi/ncbi-vdb"
+SRC_URI="https://github.com/ncbi/ncbi-vdb/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+# Sandbox error: tries to access files from within deleted dir in compile phase
+KEYWORDS=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ sci-libs/hdf5
+ sci-biology/ngs
+"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+ # this is some non-standard configure script
+ ./configure \
+ --with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
+ --with-hdf5-prefix=/usr \
+ || die
+}
+
+src_install() {
+ dodir /usr/include
+ dodir /etc/profile.d
+ # Hard way around hard coded paths
+ find . -type f -exec sed -i \
+ -e "s:/usr/local:${ED}/usr:g" \
+ -e "s:/etc:${ED}/etc:g" \
+ -e "s:/usr/lib:${ED}/usr/lib:g" \
+ -e "s:/usr/include:${ED}/usr/include:g" \
+ -e "s:setup.py -q install:setup.py install --root="${D}":g" \
+ {} \; || die
+ default
+}
diff --git a/sci-biology/nextclip/nextclip-1.3.1.ebuild b/sci-biology/nextclip/nextclip-1.3.1.ebuild
index 74b1f78b4..3f0741815 100644
--- a/sci-biology/nextclip/nextclip-1.3.1.ebuild
+++ b/sci-biology/nextclip/nextclip-1.3.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit flag-o-matic toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Split Illumina Nextera long mate-pairs"
HOMEPAGE="https://github.com/richardmleggett/nextclip
diff --git a/sci-biology/ngs/Manifest b/sci-biology/ngs/Manifest
new file mode 100644
index 000000000..1941b3421
--- /dev/null
+++ b/sci-biology/ngs/Manifest
@@ -0,0 +1 @@
+DIST ngs-2.11.2.tar.gz 1101119 BLAKE2B efa877540b8df1fbaad5550ba17ee17bd01a692a30536bd4d172b8189f7e35a88d3cd55050b676653531d1bf4655950a25a3c65a8555ef89fbcb6b503a0d3b21 SHA512 708d3b20d4aa26f44a04e103dc4fd0621acda3c07ff70911aba406e869285612879329ffb06f4f7fa69d5216c503d4118114247c9d5e851a2c400b79a01c5921
diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/ngs/metadata.xml
index 138cb7705..138cb7705 100644
--- a/sci-biology/pilon-bin/metadata.xml
+++ b/sci-biology/ngs/metadata.xml
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
new file mode 100644
index 000000000..8675ae22a
--- /dev/null
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1 java-pkg-2
+
+DESCRIPTION="NGS Language Bindings "
+HOMEPAGE="https://github.com/ncbi/ngs"
+SRC_URI="https://github.com/ncbi/ngs/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ sci-biology/bamtools
+ virtual/jdk:1.8
+"
+RDEPEND="${DEPEND}
+ virtual/jre:1.8
+"
+
+src_configure() {
+ # this is some non-standard configure script
+ ./configure || die
+}
+
+src_install() {
+ dodir /usr/include
+ dodir /etc/profile.d
+ # Hard way around hard coded paths
+ find . -type f -exec sed -i \
+ -e "s:/usr/local:${ED}/usr:g" \
+ -e "s:/etc:${ED}/etc:g" \
+ -e "s:/usr/lib:${ED}/usr/lib:g" \
+ -e "s:/usr/include:${ED}/usr/include:g" \
+ -e "s:setup.py -q install:setup.py install --root="${D}":g" \
+ {} \; || die
+ default
+}
diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild
index d90744bd5..c46edf3c1 100644
--- a/sci-biology/nitime/nitime-9999.ebuild
+++ b/sci-biology/nitime/nitime-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-inherit distutils-r1 git-r3
+inherit distutils-r1 git-r3 virtualx
DESCRIPTION="Time-series analysis of neuroscience data"
HOMEPAGE="http://nipy.org/nitime/index.html"
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index 3e97758a6..71f68463b 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit perl-functions toolchain-funcs
+inherit perl-functions
DESCRIPTION="HMM-based cDNA to genome aligner"
HOMEPAGE="https://mblab.wustl.edu/software.html"
diff --git a/sci-biology/pbbam/Manifest b/sci-biology/pbbam/Manifest
index 28d1a1423..c35432703 100644
--- a/sci-biology/pbbam/Manifest
+++ b/sci-biology/pbbam/Manifest
@@ -1 +1 @@
-DIST pbbam-1.6.0.tar.gz 11037740 BLAKE2B 72bd0b7b427dd9704095c0a5b1763aaf320438b4cbb394cc85fe13b8c2a678191dc55112869fa87a87426e44ce02c492b49f6ef9226331ac2ca379b4f4968c96 SHA512 5d07184aba0dd3873a769376174b5558071c1dbcd8ad140c7c9a9f58cd3825763d3050b971358be0e4916aa8b2b41ee51dc0bf063a78976a92c520b2d40f633f
+DIST pbbam-1.8.1.tar.gz 11069936 BLAKE2B 6ef23c81f4cfbdb060bfc8355ca628024038466482a6cacb3dd162fa58ab1052702e482ab797a60160264fd2cc70fe116dd5385c6094560060adf6fe2cf74d10 SHA512 ea28b4683c72fafb2e459ac1f37a9be258ddc82e059ba9d8b094e8dd6e3a40d3f25d5edcc790c5bd274805190caf1123311199e30166bd4f3e815dcc77929387
diff --git a/sci-biology/pbbam/pbbam-1.6.0.ebuild b/sci-biology/pbbam/pbbam-1.8.1.ebuild
index 98f0089e3..a114da0fc 100644
--- a/sci-biology/pbbam/pbbam-1.6.0.ebuild
+++ b/sci-biology/pbbam/pbbam-1.8.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit meson
@@ -20,7 +20,8 @@ BDEPEND="
"
DEPEND="
sci-biology/pbcopper
+ sci-biology/samtools:0
>=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
+ >=dev-libs/boost-1.55:=
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
deleted file mode 100644
index 1f03ab1a9..000000000
--- a/sci-biology/pbbam/pbbam-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 meson
-
-DESCRIPTION="PacBio modified BAM file format"
-HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
-
-LICENSE="blasr"
-SLOT="0"
-KEYWORDS=""
-
-BDEPEND="
- virtual/pkgconfig
- >=dev-cpp/gtest-1.8.1
- >=dev-lang/swig-3.0.5
-"
-DEPEND="
- sci-biology/pbcopper
- >=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
-"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbcopper/Manifest b/sci-biology/pbcopper/Manifest
index 6c1e6f430..93e0659d5 100644
--- a/sci-biology/pbcopper/Manifest
+++ b/sci-biology/pbcopper/Manifest
@@ -1 +1 @@
-DIST pbcopper-1.9.0.tar.gz 3325390 BLAKE2B be25b28e23bb24d44ea2f42e6efef123ab2e9922987afbb4028a7c401897a8489bc304d9cb742f6606ee1e63ef3244dff0ee2147e955f1c1bfb49d15a2465009 SHA512 20649185f1f85cefad78e984a4e07ace4657fa3ca848049f59b803c32d4d1f90e40580878cfe245496448c3749bcb01edacf30aa397d43008431d2defe05e92e
+DIST pbcopper-1.9.5.tar.gz 3386984 BLAKE2B d38b6dfa7c5f0a9ed7fc9b89f9ee71bcd0e2248a36e593cea82ce214411b0e16bac6aff289805bcafb38ad69abe38805fbd4d7c5c0bdb7b197691ee0514c397b SHA512 006470f318341c311f600e12495b9e72a47a0fb1795dcd4d13b06c02e4872f7cde077d98bebc32ac29bb41d410d0bc7b73eead4da4ac6cf3c110e896c15df8c6
diff --git a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
index 972b98d65..79307d839 100644
--- a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild
+++ b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit meson
@@ -21,6 +21,6 @@ BDEPEND="
DEPEND="
>=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads(-)]
+ >=dev-libs/boost-1.55:=
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/pilon-bin/Manifest b/sci-biology/pilon-bin/Manifest
deleted file mode 100644
index 3f3de6bcc..000000000
--- a/sci-biology/pilon-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pilon-1.24.jar 11034933 BLAKE2B 7c97c8e30a05ad56c8d2830e414c285eb086bc3ccb51ab10af33fe53771287b4c99880930484fe7574dd1f57df5c003af3ceb98b9026d842ee447aecaacb78f8 SHA512 48d3688059f0bcb2055fd9291cd36d282733724f68832633ffc08adb883af4b3146759bb2b13d99f0695b11f283d3bb89a2f8ff18102b1a125e38fb2de0f5461
diff --git a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
deleted file mode 100644
index 49d15366f..000000000
--- a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2
-
-DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
-HOMEPAGE="
- https://github.com/broadinstitute/pilon
- https://github.com/broadinstitute/pilon/wiki"
-SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-# contains bundled sbt-assembly module
-DEPEND=">=virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*
- >=dev-java/htsjdk-1.130"
-
-S="${WORKDIR}"
-
-src_install(){
- cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
- java-pkg_dojar pilon-${PV}.jar
-}
diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest
index 9fa366e93..8cfd1985e 100644
--- a/sci-biology/pybedtools/Manifest
+++ b/sci-biology/pybedtools/Manifest
@@ -1 +1 @@
-DIST pybedtools-0.8.0.tar.gz 12445206 BLAKE2B 036bdd39681634a0292dd527da5db3b19d2df6fbfb006b3d90daeca2d0ffa58553b3a2fb921c67bfa49eacf3f1c9687123274c7642497b5959075fa5b6133b46 SHA512 1ee83c2b9ee1f5cf7f087e54d630f580d09505ab78d94e3b17a9e031f66564408193d33e1f4ac5f3777539182f4a12968ecc4b3c6f1bb350dd19f38a62acee42
+DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe
diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index 6d391b0a8..95bee9be2 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -14,32 +14,23 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="minimal"
+
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
RESTRICT="test"
-# Tests reported to fail on Gentoo:
-# https://github.com/daler/pybedtools/issues/329
-# see requirements.txt
RDEPEND="
sci-biology/bedtools
- sci-biology/pysam
+ sci-biology/pysam[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
- !minimal? ( sci-libs/htslib )"
-# optional-requirements.txt also lists:
-# ucsc-bigwigtobedgraph
-# ucsc-bedgraphtobigwig
-# ucsc-wigtobigwig
-BDEPEND="${RDEPEND}
- dev-python/cython[${PYTHON_USEDEP}]"
-
-# ToDo: fix docs building
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# TODO: fix docs building
# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
# even if pybedtools is installed
#distutils_enable_sphinx docs/source
distutils_enable_tests pytest
-
-src_compile(){
- python setup.py cythonize
- distutils-r1_src_compile
-}
diff --git a/sci-biology/quorum/Manifest b/sci-biology/quorum/Manifest
deleted file mode 100644
index 68b3dd9c6..000000000
--- a/sci-biology/quorum/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST quorum-1.1.1.tar.gz 659218 BLAKE2B 26710674e12115b3d218c113eaa6b36d9694f85c65bb5e1a8b8e2b4405b585115b2e3ded34c84bdb24d680ae5a1d6e4c387689bdde8bc63824d8eb254d0894da SHA512 12d7a03ffa45dd358f52c55226e6888fc92bff8e361e1c5eca7b4f8545d70243793dd963602932b895702284f89cd77361b2b5636c062d86b467b538df0b9f16
diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
deleted file mode 100644
index b5b68a8fb..000000000
--- a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- src/error_correct_reads.cc 2018-04-21 14:25:41.310473159 +0200
-+++ src/error_correct_reads.cc 2018-04-21 14:26:58.262493179 +0200
-@@ -25,9 +25,9 @@
- #endif
-
- //#define DEBUG 1
--#include <jellyfish/dbg.hpp>
--#include <jellyfish/atomic_gcc.hpp>
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/dbg.hpp>
-+#include <jellyfish1/atomic_gcc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-
- #include <jflib/multiplexed_io.hpp>
- #include <gzip_stream.hpp>
---- src/combine_jf_dbs.cc 2018-04-21 14:25:50.220707057 +0200
-+++ src/combine_jf_dbs.cc 2018-04-21 14:27:04.652660923 +0200
-@@ -1,9 +1,9 @@
--#include <jellyfish/err.hpp>
--#include <jellyfish/misc.hpp>
--#include <jellyfish/mer_counting.hpp>
--#include <jellyfish/compacted_hash.hpp>
--#include <jellyfish/thread_exec.hpp>
--#include <jellyfish/misc.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/misc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-+#include <jellyfish1/compacted_hash.hpp>
-+#include <jellyfish1/thread_exec.hpp>
-+#include <jellyfish1/misc.hpp>
- #include <src/combine_jf_dbs.hpp>
-
- int main(int argc, char *argv[])
---- src/error_correct_reads.hpp 2018-04-21 14:26:10.091228666 +0200
-+++ src/error_correct_reads.hpp 2018-04-21 14:27:09.792795853 +0200
-@@ -2,12 +2,12 @@
- #define __ERROR_CORRECT_READS_HPP__
-
- #include <config.h>
--#include <jellyfish/err.hpp>
--#include <jellyfish/mapped_file.hpp>
--#include <jellyfish/invertible_hash_array.hpp>
--#include <jellyfish/allocators_mmap.hpp>
--#include <jellyfish/parse_read.hpp>
--#include <jellyfish/thread_exec.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/mapped_file.hpp>
-+#include <jellyfish1/invertible_hash_array.hpp>
-+#include <jellyfish1/allocators_mmap.hpp>
-+#include <jellyfish1/parse_read.hpp>
-+#include <jellyfish1/thread_exec.hpp>
- #include <iostream>
- #include <fstream>
- #include <assert.h>
---- configure.ac.ori 2018-04-21 15:00:35.225439196 +0200
-+++ configure.ac 2018-04-21 15:01:37.977086449 +0200
-@@ -28,7 +28,7 @@
- JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1)
- AC_SUBST([JELLYFISH_VERSION])
- AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to looking in PATH)])
--AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish], [false])])
-+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1], [false])])
-
- AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum])
-
-@@ -47,7 +47,7 @@
- # --with-relative-jf-path
- AC_ARG_WITH([relative-jf-path],
- [AC_HELP_STRING([--with-relative-jf-path], [relative path from quorum to jellyfish (use an absolute path if not given. default to "." if given with no argument)])],
-- [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;; esac],
-+ [case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;; esac],
- [with_relative_jf_path= ])
- AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
- AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
deleted file mode 100644
index 4af286fcb..000000000
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Correct substitution errors in Illumina reads"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html
- https://github.com/gmarcais/Quorum"
-SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=sci-biology/jellyfish-2.1.4:2"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- default
- # fix jellyfish include path
- find -type f -name "*.cc" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
- find -type f -name "*.hpp" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
-}
-
-src_configure(){
- econf --enable-relative-paths --with-relative-jf-path
- default
-}
diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
index faecd8848..20c923eb0 100644
--- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
+++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
@@ -3,6 +3,8 @@
EAPI=7
+inherit check-reqs
+
DESCRIPTION="A collection of rat brain templates in NIfTI format"
HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator"
SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index 8ba4d0cf7..9fa4060ca 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cmake multilib
+inherit cmake
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index 27d1abdc8..a76e8ee89 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cmake git-r3 multilib
+inherit cmake git-r3
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index b5bd8bdfe..c3ef9e50a 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake multilib
+inherit cmake
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
@@ -48,7 +48,7 @@ DEPEND="
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
- dev-libs/boost:0[threads(-)]
+ dev-libs/boost:0=
dev-libs/libdivsufsort
sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
deleted file mode 100644
index 89ca690c6..000000000
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-RDEPEND="
- dev-libs/boost:=[threads(-)]
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- sci-biology/pufferfish
- dev-libs/cereal
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
index 79c5949de..f94119541 100644
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ b/sci-biology/samri/samri-0.4.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7..8} )
-inherit distutils-r1
+inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 8faa270ab..84161f65f 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7..8} )
-inherit distutils-r1
+inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 507d6a53c..8dba8864c 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=7
PYTHON_COMPAT=( python3_{7..8} )
-inherit distutils-r1 git-r3
+inherit distutils-r1 prefix git-r3
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
diff --git a/sci-biology/sickle/sickle-1.33.ebuild b/sci-biology/sickle/sickle-1.33.ebuild
index 452e27edc..e2ebdb3a3 100644
--- a/sci-biology/sickle/sickle-1.33.ebuild
+++ b/sci-biology/sickle/sickle-1.33.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
HOMEPAGE="https://github.com/najoshi/sickle"
if [ "$PV" == "9999" ]; then
diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild
index 452e27edc..e2ebdb3a3 100644
--- a/sci-biology/sickle/sickle-9999.ebuild
+++ b/sci-biology/sickle/sickle-9999.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs
-
DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
HOMEPAGE="https://github.com/najoshi/sickle"
if [ "$PV" == "9999" ]; then
diff --git a/sci-biology/spm/Manifest b/sci-biology/spm/Manifest
index d1a4c4b07..6d40dd923 100644
--- a/sci-biology/spm/Manifest
+++ b/sci-biology/spm/Manifest
@@ -1,3 +1 @@
-DIST spm-12_p6470.tar.gz 94904848 BLAKE2B 51ba79b721e7a3518b546edd3fca647fd1e12fc80d1bc942d6ca208831ddcf82c2b37b6f2b158978add4e60ddea53eb6d712c6d2817f37b86c3d96c69976ed63 SHA512 7cc2cfed5aa69ea9846cb36f5e489255340e8c27f2e404372a474923d9c4fee6b6ee2dc5dd7f31362b6d2f95eeb281f24008b8b3e174ae3702e6cb040f06c4f2
-DIST spm-12_p7219.tar.gz 97358283 BLAKE2B 70c174f0a7f8f0005f8217d01fb01f45877f7b8d608f5a3ab933b48fae7a7f79d7f4a64f363dae918819688172958e1d503b52408564eb182a5e0dcec155afe4 SHA512 7312c0e74abb65eb211f920f8787e7582fe3269e272920283a5e4ebf6760baf12f2d4223e19696bcf1040c01242513fae2f0ab6241ddcba7de057c2adb33880a
DIST spm-12_p7771.tar.gz 113583785 BLAKE2B e3c011206569ad66af4ca4475a224751622c760760bd02f27ef18b1cbbde63592da633ca6a880a42a7cf22857eb40bf8d8bba6a6cb92ba53cb1b73bec25534af SHA512 063adac233d28d6912ab6e0a1bc4bda56f011bf0349855eb45ae5e2f63ee6b6a459829ed5a7145ee6744d1afa7c7d9ca8acfe8783784876f048e88d7ee287adb
diff --git a/sci-biology/spm/spm-12_p6470.ebuild b/sci-biology/spm/spm-12_p6470.ebuild
deleted file mode 100644
index 86e2d5a0d..000000000
--- a/sci-biology/spm/spm-12_p6470.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV_MAJ=$(ver_cut 1)
-MY_PV_REL=$(ver_cut 3)
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="https://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="https://github.com/${PN}/${PN}${MY_PV_MAJ}/archive/r${MY_PV_REL}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.8"
-DEPEND="${RDEPEND}
- app-arch/unzip
-"
-
-MY_PN="${PN}${MY_PV_MAJ}-r${MY_PV_REL}"
-S="${WORKDIR}/${MY_PN}/src"
-
-src_prepare() {
- default
- emake distclean PLATFORM=octave
-}
-
-src_compile() {
- emake PLATFORM=octave
-}
-
-src_install() {
- emake install PLATFORM=octave
- insinto "$(octave-config --m-site-dir)/${P}"
- doins -r "${WORKDIR}/${MY_PN}"/*
-}
diff --git a/sci-biology/spm/spm-12_p7219.ebuild b/sci-biology/spm/spm-12_p7219.ebuild
deleted file mode 100644
index 86e2d5a0d..000000000
--- a/sci-biology/spm/spm-12_p7219.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV_MAJ=$(ver_cut 1)
-MY_PV_REL=$(ver_cut 3)
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="https://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="https://github.com/${PN}/${PN}${MY_PV_MAJ}/archive/r${MY_PV_REL}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.8"
-DEPEND="${RDEPEND}
- app-arch/unzip
-"
-
-MY_PN="${PN}${MY_PV_MAJ}-r${MY_PV_REL}"
-S="${WORKDIR}/${MY_PN}/src"
-
-src_prepare() {
- default
- emake distclean PLATFORM=octave
-}
-
-src_compile() {
- emake PLATFORM=octave
-}
-
-src_install() {
- emake install PLATFORM=octave
- insinto "$(octave-config --m-site-dir)/${P}"
- doins -r "${WORKDIR}/${MY_PN}"/*
-}
diff --git a/sci-biology/sra-tools/Manifest b/sci-biology/sra-tools/Manifest
new file mode 100644
index 000000000..1ece174af
--- /dev/null
+++ b/sci-biology/sra-tools/Manifest
@@ -0,0 +1 @@
+DIST sra-tools-2.11.3.tar.gz 9098150 BLAKE2B 852db3b1d1409b37e3a8f36d0a64f5480ba8c85b86efa8f1d9524a5a8a4c2763aa6970739aa06a0821be576b920946784ab9a9ce1af3e6ceaa54da9b743a0434 SHA512 070ab552df1789d37e970e1c9ac2ce7ac6b39ce7833a999aabee4baef553a29a4bfcbdb21be00f4b5d8a55013bcf88b46c839a124dde704b4a371b234c05609f
diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch
index 44acc42b0..44acc42b0 100644
--- a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch
+++ b/sci-biology/sra-tools/files/libs_sra_Makefile.patch
diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch
index bf66c6e46..bf66c6e46 100644
--- a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
+++ b/sci-biology/sra-tools/files/sra_sdk-destdir.patch
diff --git a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
index 738d67cbd..738d67cbd 100644
--- a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch
+++ b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch
diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/sra-tools/metadata.xml
index 138cb7705..138cb7705 100644
--- a/sci-biology/quorum/metadata.xml
+++ b/sci-biology/sra-tools/metadata.xml
diff --git a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
new file mode 100644
index 000000000..57c5b881e
--- /dev/null
+++ b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
+HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"
+SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+# Fix ncbi-vdb first
+KEYWORDS=""
+
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ dev-libs/libxml2:2=
+ sci-libs/hdf5
+ sci-biology/ngs
+ sci-biology/ncbi-vdb
+"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/sra-tools-${PV}"
+
+src_configure() {
+ # this is some non-standard configure script
+ ./configure \
+ --with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
+ --with-hdf5-prefix=/usr \
+ || die
+}
+
+src_install() {
+ dodir /usr/include
+ dodir /etc/profile.d
+ # Hard way around hard coded paths
+ find . -type f -exec sed -i \
+ -e "s:/usr/local:${ED}/usr:g" \
+ -e "s:/etc:${ED}/etc:g" \
+ -e "s:/usr/lib:${ED}/usr/lib:g" \
+ -e "s:/usr/include:${ED}/usr/include:g" \
+ -e "s:setup.py -q install:setup.py install --root="${D}":g" \
+ {} \; || die
+ default
+}
diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest
deleted file mode 100644
index 336274f86..000000000
--- a/sci-biology/sra_sdk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sra_sdk-2.10.9.tar.gz 8788975 BLAKE2B f3d84656f53b1667cc2dcf47f35db3b77723631a143b9af9c2f08b238c8b25ec39825a8ef1043c70fbcc2accf2d60bb79a317f838da33e471bf0d4409fda4bca SHA512 d57a05bf761918bad0c932cd7d3957002333807f7bd756cebd7462716aa941cb8e082cfc6344fb3571dd3fb80d87b4172214fac37d7f0d1bbb198903c97be78c
diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/sra_sdk/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
deleted file mode 100644
index ef1c8a5d6..000000000
--- a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
-HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"
-SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-# missing dep ngs-sdk
-KEYWORDS=""
-
-DEPEND="
- app-shells/bash:*
- sys-libs/zlib
- app-arch/bzip2
- dev-libs/libxml2:2="
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/sra-tools-${PV}"
-
-src_configure() {
- # this is some non-standard configure script
- ./configure || die
-}
-
-src_compile(){
- emake OUTDIR="${WORKDIR}"/objdir out
- emake dynamic
- emake release
- default
-}
-
-src_install(){
- rm -rf /var/tmp/portage/sci-biology/"${P}"/image/var
- # BUG: at the moment every binary is installed three times, e.g.:
- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
- if use amd64; then
- builddir="x86_64"
- elif use x86; then
- builddir="i386"
- fi
- dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema
-
- OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel
-
- # BUG: neither 'doins -r' nor cp --preserve=all work
- #insinto /usr/bin
- #doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
- for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
- # install the main libs and the ncbi/vdb-copy.kfg file
- insinto /usr/lib/ncbi
- doins "${OBJDIR}"/lib/ncbi/*
-
- # zap the subdirectory so that copying below does not fail
- rm -rf "${OBJDIR}"/lib/ncbi || die
-
- # BUG: neither the dolib nor cp --preserve=all work
- #insinto /usr/lib64
- #dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
- mkdir -p "${D}"/usr/lib64
- for f in "${OBJDIR}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
-
- insinto /usr/ncbi/schema
- doins \
- "${W}"/interfaces/align/*.vschema \
- "${W}"/interfaces/sra/*.vschema \
- "${W}"/interfaces/vdb/*.vschema \
- "${W}"/interfaces/ncbi/*.vschema \
- "${W}"/interfaces/insdc/*.vschema
-}
diff --git a/sci-biology/stacks/stacks-2.55.ebuild b/sci-biology/stacks/stacks-2.55.ebuild
index 4d7095d4f..becd91a5d 100644
--- a/sci-biology/stacks/stacks-2.55.ebuild
+++ b/sci-biology/stacks/stacks-2.55.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit flag-o-matic perl-module webapp autotools
+inherit perl-module webapp autotools
DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
HOMEPAGE="http://creskolab.uoregon.edu/stacks"
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
index d6b1b8de1..a0f91720b 100644
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit flag-o-matic fortran-2 multilib
+inherit flag-o-matic fortran-2
DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
HOMEPAGE="https://sourceforge.net/projects/staden"
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 7b61a0fa0..b2ed35724 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit flag-o-matic fortran-2 multilib subversion
+inherit flag-o-matic fortran-2 subversion
DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
HOMEPAGE="https://sourceforge.net/projects/staden/"
diff --git a/sci-biology/tabixpp/tabixpp-1.1.0.ebuild b/sci-biology/tabixpp/tabixpp-1.1.0.ebuild
index 9d6192d93..d3e69f914 100644
--- a/sci-biology/tabixpp/tabixpp-1.1.0.ebuild
+++ b/sci-biology/tabixpp/tabixpp-1.1.0.ebuild
@@ -3,8 +3,6 @@
EAPI=7
-inherit toolchain-funcs multilib
-
DESCRIPTION="C++ wrapper to tabix indexer "
HOMEPAGE="https://github.com/ekg/tabixpp"
SRC_URI="https://github.com/ekg/tabixpp/archive/v${PV}.tar.gz -> ${P}.tar.gz"
diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 6900ea7aa..84b582151 100644
--- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -24,6 +24,7 @@ RDEPEND="
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
app-arch/pigz
+ app-shells/zsh
sci-biology/samtools
sci-biology/minimap2
sci-biology/seqtk
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
index 30bd4ca62..9ecaf24f2 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
+++ b/