diff options
131 files changed, 1552 insertions, 329 deletions
diff --git a/.mailmap b/.mailmap new file mode 100644 index 000000000..b69b86f7c --- /dev/null +++ b/.mailmap @@ -0,0 +1,8 @@ +# See gitmailmap(5) for format details. +# Please keep this list sorted. +# Use "grep -v '^#' .mailmap | LC_ALL=en_US.utf-8 sort". +Nowa Ammerlaan <nowa@gentoo.org> <aammerlaan@science.ru.nl> +Nowa Ammerlaan <nowa@gentoo.org> <andrewammerlaan@gentoo.org> +Nowa Ammerlaan <nowa@gentoo.org> <andrewammerlaan@riseup.net> +Nowa Ammerlaan <nowa@gentoo.org> <andrew.ammerlaan@ru.nl> +Nowa Ammerlaan <nowa@gentoo.org> <nowa-ammerlaan@riseup.net> diff --git a/dev-python/MagnetoResistance-tool/metadata.xml b/dev-python/MagnetoResistance-tool/metadata.xml index aed122741..74aaa636f 100644 --- a/dev-python/MagnetoResistance-tool/metadata.xml +++ b/dev-python/MagnetoResistance-tool/metadata.xml @@ -2,8 +2,8 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>andrewammerlaan@gentoo.org</email> - <name>Andrew Ammerlaan</name> + <email>nowa@gentoo.org</email> + <name>Nowa Ammerlaan</name> </maintainer> <upstream> <remote-id type="pypi">MagnetoResistance-tool</remote-id> diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest index c3dd31924..3262809c8 100644 --- a/dev-python/archspec/Manifest +++ b/dev-python/archspec/Manifest @@ -1 +1,2 @@ DIST archspec-0.2.4.tar.gz 52834 BLAKE2B cb8b9fce38b44783a361568667d5690e5c5169149ebdd3d4bf0943c056a4c8c9e2cb3a13a0b9b39e07f9b907b8f5ec4d1552a925d2e9bee76acf858d1a3f3ed5 SHA512 40a83854982670cb5cf77aab496198b3c6723a5cc386f05b8a020d9e94834d4109436cade9b9c89abac909c17b912f00aab8df2d6b05251c0afba9cee1932a62 +DIST archspec-0.2.5.tar.gz 53848 BLAKE2B 429c39494d046b3e95a67e58b4f165445ff44a4615f02b1c655a1f57331a8ffae7342b360b1a5560fd99271682b826d0c49710e33e2c93f9e1204f1fe1a8f581 SHA512 583b3cd7442d2392516ddd4fcaf363ff70ef9e5ee4c72089d21f4ea3e7dfff72e22b24a475ab5c00e9baf7789df65a272b894e241bb5ae7c91cf1e3a71bb83bb diff --git a/dev-python/archspec/archspec-0.2.5.ebuild b/dev-python/archspec/archspec-0.2.5.ebuild new file mode 100644 index 000000000..002a57ba1 --- /dev/null +++ b/dev-python/archspec/archspec-0.2.5.ebuild @@ -0,0 +1,21 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=poetry +inherit distutils-r1 pypi + +DESCRIPTION="Labels for various aspects of a system architecture like CPU, etc." +HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/asdf-standard/Manifest b/dev-python/asdf-standard/Manifest new file mode 100644 index 000000000..d297ed333 --- /dev/null +++ b/dev-python/asdf-standard/Manifest @@ -0,0 +1 @@ +DIST asdf_standard-1.1.1.tar.gz 114823 BLAKE2B ae5f85be22fc895f44b77007a02a12a214de1e3a60da9728fe5eb8e56e32f220aa45898eeedef3942821b45d8a58e2f7d16850c2e1958ad02ce22df6bdb62ab1 SHA512 c1b5b40841a8ff6115d8642993a664b9646474d5e4c50ce78e15be9bf49704f598238c523a1b1d7ca18d5390b5166c97311231837ac4efa12179d2a92c905886 diff --git a/dev-python/asdf-standard/asdf-standard-1.1.1.ebuild b/dev-python/asdf-standard/asdf-standard-1.1.1.ebuild new file mode 100644 index 000000000..55db6e6d0 --- /dev/null +++ b/dev-python/asdf-standard/asdf-standard-1.1.1.ebuild @@ -0,0 +1,29 @@ +# Copyright 2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{11..13} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Standards document describing ASDF, Advanced Scientific Data Format." +HOMEPAGE=" + https://github.com/asdf-format/asdf-standard/ + https://pypi.org/project/asdf-standard/ +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/pyyaml[${PYTHON_USEDEP}] + >=dev-python/asdf-3.0.0[${PYTHON_USEDEP}] + >=dev-python/packaging-16.0[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/asdf-standard/metadata.xml b/dev-python/asdf-standard/metadata.xml new file mode 100644 index 000000000..a4ca24b83 --- /dev/null +++ b/dev-python/asdf-standard/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">asdf-standard</remote-id> + <remote-id type="github">asdf-format/asdf-standard</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/asdf-transform-schemas/Manifest b/dev-python/asdf-transform-schemas/Manifest new file mode 100644 index 000000000..9f26dca78 --- /dev/null +++ b/dev-python/asdf-transform-schemas/Manifest @@ -0,0 +1 @@ +DIST asdf_transform_schemas-0.5.0.tar.gz 109226 BLAKE2B 89ee5beb21d7d0ca8ba388bb55eab8cbde68a0b8922e9ce060c48a3659d68f070c65adf5847d86e295f31bc9b785abae0a68f71b5757581017a0c94d9d6f5d38 SHA512 29c803ee8a3b5e3526191c503ff15309aab8e7dcee3df16dc2032156f725dd672862540a25a48f217a644701208ba01c9085f3d5b67f9a8dc68d0a732cfbde8a diff --git a/dev-python/asdf-transform-schemas/asdf-transform-schemas-0.5.0.ebuild b/dev-python/asdf-transform-schemas/asdf-transform-schemas-0.5.0.ebuild new file mode 100644 index 000000000..95c94a662 --- /dev/null +++ b/dev-python/asdf-transform-schemas/asdf-transform-schemas-0.5.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{11..13} ) + +inherit distutils-r1 pypi + +DESCRIPTION="ASDF schemas for validating transform tags." +HOMEPAGE=" + https://github.com/asdf-format/asdf-transform-schemas/ + https://pypi.org/project/asdf-transform-schemas/ +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="test" # needs asdf-astropy + +RDEPEND=" + >=dev-python/asdf-standard-1.1.0[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/asdf-transform-schemas/metadata.xml b/dev-python/asdf-transform-schemas/metadata.xml new file mode 100644 index 000000000..00a47f858 --- /dev/null +++ b/dev-python/asdf-transform-schemas/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">asdf-transform-schemas</remote-id> + <remote-id type="github">asdf-format/asdf-transform-schemas</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest index ac7f18004..46e6164e0 100644 --- a/dev-python/asdf/Manifest +++ b/dev-python/asdf/Manifest @@ -1 +1,2 @@ DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655 +DIST asdf-3.5.0.tar.gz 804561 BLAKE2B b500afe7c95ec4863279246cc233355ae1c120fb57dda3b9e663115ff05cce505b1110de2fb53278d4341ccd9fc99ec9f875cf0553302905640d02dc6d6a511e SHA512 e389b33ee5144596456c6f1ca376b1719343f7b58c00aedbd4fd983bb807c3cff3e5dd469b197ec9ee7b7e2739be4f01b72a6306a10617710438e3a947da3650 diff --git a/dev-python/asdf/asdf-3.5.0.ebuild b/dev-python/asdf/asdf-3.5.0.ebuild new file mode 100644 index 000000000..2e9a29391 --- /dev/null +++ b/dev-python/asdf/asdf-3.5.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Python library for the Advanced Scientific Data Format" +HOMEPAGE="https://asdf.readthedocs.io/en/latest/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/asdf-standard[${PYTHON_USEDEP}] + dev-python/asdf-transform-schemas[${PYTHON_USEDEP}] + >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.22[${PYTHON_USEDEP}] + >=dev-python/packaging-19[${PYTHON_USEDEP}] + >=dev-python/pyyaml-5.4.1[${PYTHON_USEDEP}] + >=dev-python/semantic-version-2.8[${PYTHON_USEDEP}] + >=dev-python/attrs-22.1.0[${PYTHON_USEDEP}] +" + +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + >=dev-python/fsspec-2022.8.2[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/aiohttp[${PYTHON_USEDEP}] + >=dev-python/lz4-0.10[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + >=dev-python/pytest-8[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest index 4c59bb8cb..84a9f541c 100644 --- a/dev-python/awkward-cpp/Manifest +++ b/dev-python/awkward-cpp/Manifest @@ -1,2 +1,3 @@ DIST awkward-cpp-28.tar.gz 1422514 BLAKE2B ec87c37a37e3aceb0a35b580122a8c632070dc9fd284e34de66db2611cf1024dbd7ec8a355f52349783258cdaa91e0f966156689c82427f72574230c8b6ae6e1 SHA512 bbe0df527a7863b192c3c85a90c1295d2eb788eb7670a04a001838294dcdd434b49bdc2b4c3f71e34f5f160b4b9cafdea1cf290206fdcb14c0555005797a666d DIST awkward-cpp-35.tar.gz 1591781 BLAKE2B 4218f3a9e5e9c267135508a39303d2c44d5ce2f9ee94d7c034fb117b8833e7cea5ee16f8acbba464a3e61c5baf92b7f9e1f16d22a36478da3e44d2b33d837a3c SHA512 31ed7b99ee51407db0b76d9876a425863948a45fe9c3df61090fd679739af4091837436a14f54cad54f05c472b09a9130d1626f745d476a59baed627293000e7 +DIST awkward_cpp-39.tar.gz 1588054 BLAKE2B 8bb960a7b9ebcc86dcd8906cad29e9cd5554220eb30e404e9c3d91da7445dedccbddb41a5f06fee2d828e8432cbd76b5582a16a3c9f9abdb3fbe7a494164b99e SHA512 ca1d37406dc845e76805b0abc689e3aa5bc712246f83872318d58413602538575f2ccb1017731bdca5e107019e111a9b4f769e7d3242403164904e58a61b3dcc diff --git a/dev-python/awkward-cpp/awkward-cpp-39.ebuild b/dev-python/awkward-cpp/awkward-cpp-39.ebuild new file mode 100644 index 000000000..2477e97b0 --- /dev/null +++ b/dev-python/awkward-cpp/awkward-cpp-39.ebuild @@ -0,0 +1,33 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +CMAKE_MAKEFILE_GENERATOR="emake" +DISTUTILS_USE_PEP517=scikit-build-core +DISTUTILS_EXT=1 + +inherit pypi distutils-r1 + +DESCRIPTION="awkward-cpp bindings for Python" +HOMEPAGE="https://github.com/scikit-hep/awkward/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=" + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" +BDEPEND=" + >=dev-python/scikit-build-core-0.10[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] +" + +src_prepare() { + default + # https://github.com/scikit-build/scikit-build-core/issues/912 + sed -i -e '/scikit-build-core/s:0\.10:0.8:' pyproject.toml || die +} + +distutils_enable_tests pytest diff --git a/dev-python/awkward/Manifest b/dev-python/awkward/Manifest index 3f4ebd5df..94246b3ae 100644 --- a/dev-python/awkward/Manifest +++ b/dev-python/awkward/Manifest @@ -1,2 +1,3 @@ DIST awkward-2.5.2.tar.gz 5561040 BLAKE2B 4799eeb25fa7433b4889328f9f147b435024c3f507ce66b5cbfcfc5b9c50e63f77131a43b8acd3d9f22d20915eaeb129162e26ffa83fd2071b9a393fbc441e7e SHA512 b6f4f2841e642bfc17aaf40779030d125e9737ef0ded20cc8a898c4b8c15c2932f12c8a0bda3e8c48bb8d13729cf97e181866f15913317bd2dba13b0dad6b929 DIST awkward-2.6.6.tar.gz 6088969 BLAKE2B a2b1db5fe9daae32272348b7bf92894fd805806bcec66ef57acf51af9bc99f033723c637515530a2867ec4bafa51bce5d90ad2b651ed008790ae8f7bee3e73f7 SHA512 2b7c0f1c1f3bd06f1b9fc06ca7cd482b136986d7b5f1648c45627083df5042668d122db7f93e9dbe606630270e577bc53472b9fdca837b12b390ef5c86e8fe48 +DIST awkward-2.6.9.tar.gz 6120280 BLAKE2B f6eb34920d208034be29bd1359e951fb7aa2f9b882b417b895fdb3d34e028c1aa6d6c3e265c41cf95c56acf28b0aa35fa8feec01f49241d79e7bf18323d0b23f SHA512 32996de956fbfc70f338a80788aadb0b75028509e8cc13014ed9ea34326f146da5662a2c7c870c14e9af059678a81153cc2b1096a9a5e202290cd6e7f1aa7f5c diff --git a/dev-python/awkward/awkward-2.6.9.ebuild b/dev-python/awkward/awkward-2.6.9.ebuild new file mode 100644 index 000000000..854349168 --- /dev/null +++ b/dev-python/awkward/awkward-2.6.9.ebuild @@ -0,0 +1,46 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=hatchling +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms." +HOMEPAGE="https://github.com/scikit-hep/awkward" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + ~dev-python/awkward-cpp-39[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/importlib-metadata-4.13.0[${PYTHON_USEDEP}] + ' python3_{10..11}) + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/typing-extensions-4.1.0[${PYTHON_USEDEP}] + ' python3_10) + >=dev-python/fsspec-2022.11.0[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/hatch-vcs[${PYTHON_USEDEP}] + dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}] + test? ( + dev-libs/apache-arrow[zstd] + dev-python/pyarrow[${PYTHON_USEDEP}] + dev-python/numexpr[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + ) +" + +EPYTEST_IGNORE=( + tests-cuda/ + tests-cuda-kernels/ + tests/test_3259_to_torch_from_torch.py # fails if just caffe2 but not pytorch is installed + tests/test_0119_numexpr_and_broadcast_arrays.py # no idea why it fails, seems to be a numexpr error +) + +distutils_enable_tests pytest diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild index ab2084b9c..d8f9779fe 100644 --- a/dev-python/bokeh/bokeh-2.4.2.ebuild +++ b/dev-python/bokeh/bokeh-2.4.2.ebuild @@ -18,7 +18,7 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND=" - >=dev-python/jinja-2.9[${PYTHON_USEDEP}] + >=dev-python/jinja2-2.9[${PYTHON_USEDEP}] >=dev-python/numpy-1.11.3[${PYTHON_USEDEP}] >=dev-python/packaging-16.8[${PYTHON_USEDEP}] >=dev-python/pillow-7.1.0[${PYTHON_USEDEP}] diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest index 78bf6ae03..5f9267a4b 100644 --- a/dev-python/boost-histogram/Manifest +++ b/dev-python/boost-histogram/Manifest @@ -1 +1,2 @@ DIST boost_histogram-1.4.1.tar.gz 1337723 BLAKE2B 42087abfd34471f42b06571ab4e701e7fbc071a5b9f3133f6f80831a0fd01ef95f65cae7bdcc6892674a415fd9b48a20bb0ecd5fd294a4880a6f5e3922e60a09 SHA512 fda8085929677a1664030fd29beb01caf37b42413fe941c2760fed17325301c4bf6b8ec5fa3b0e128558a52dee3245ec3a3fc2f4ca145dd09dea0b88fcfa33d4 +DIST boost_histogram-1.5.0.tar.gz 1181192 BLAKE2B b25e20b9440849d9cd4837b762bcc7a9625e69fec60dbe4a975b0329678e0035d5d29d8ea5a7a35b1b78ee00b1c8941361774f0dcd069da04f67632b98af5783 SHA512 5c107f69514fbbad013e2e2a265537c55f4500b61bbb6a37cfb3a69fcf92d4cfba333ba27b43df444cf6120768d5a324822019dcccac58ce0ae127630f8bf999 diff --git a/dev-python/boost-histogram/boost-histogram-1.5.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.5.0.ebuild new file mode 100644 index 000000000..7bee5b066 --- /dev/null +++ b/dev-python/boost-histogram/boost-histogram-1.5.0.ebuild @@ -0,0 +1,43 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=scikit-build-core +DISTUTILS_EXT=1 +inherit cmake distutils-r1 pypi + +DESCRIPTION="Python bindings for the C++14 Boost::Histogram library" +HOMEPAGE="https://github.com/scikit-hep/boost-histogram" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-libs/boost:=[python,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + >=dev-python/pybind11-2.13.3[${PYTHON_USEDEP}] + test? ( + dev-python/cloudpickle[${PYTHON_USEDEP}] + dev-python/hypothesis[${PYTHON_USEDEP}] + ) +" + +src_prepare() { + default + sed -i 's/\["pytest-benchmark"\]/[]/g' pyproject.toml || die + # https://github.com/scikit-build/scikit-build-core/issues/912 + sed -i -e '/scikit-build-core/s:0\.10:0.8:' pyproject.toml || die +} + +distutils_enable_tests pytest + +EPYTEST_IGNORE=( + tests/test_benchmark_1d.py + tests/test_benchmark_2d.py + tests/test_benchmark_category_axis.py + tests/test_pickle.py + tests/test_threaded_fill.py +) diff --git a/dev-python/cligj/Manifest b/dev-python/cligj/Manifest index b3e1ca5dd..a9253fd62 100644 --- a/dev-python/cligj/Manifest +++ b/dev-python/cligj/Manifest @@ -1 +1 @@ -DIST cligj-0.7.2.tar.gz 9894 BLAKE2B ebd187a6a7108a8d0a7d348fcb1d617402041d050a89209cb6c242bc47a87be953b679101656af9af31fd40947f1a5b3ded567dce9f3e64f425cce7f0f3036c1 SHA512 292c1a6de4ed5d4926ccd71802d369db383d310a3a8590729233448cebe5e9ad9dd6bff0d0c861890102bc9f23e90fe1b9db62275a9263765e3d77436a0b38b4 +DIST cligj-0.7.2.gh.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 index 28e7f5510..3175d457f 100644 --- a/dev-python/cligj/cligj-0.7.2.ebuild +++ b/dev-python/cligj/cligj-0.7.2.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) 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 -> ${P}.tar.gz" +SRC_URI="https://github.com/mapbox/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/cligj/metadata.xml b/dev-python/cligj/metadata.xml index 9afaefe0d..9957eb81e 100644 --- a/dev-python/cligj/metadata.xml +++ b/dev-python/cligj/metadata.xml @@ -6,11 +6,13 @@ <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> + 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> + <bugs-to>https://github.com/mapbox/cligj/issues</bugs-to> + <changelog>https://raw.githubusercontent.com/mapbox/cligj/refs/heads/master/CHANGES.txt</changelog> <remote-id type="github">mapbox/cligj</remote-id> <remote-id type="pypi">cligj</remote-id> </upstream> diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest index bed2fa4ce..193923d1a 100644 --- a/dev-python/fiona/Manifest +++ b/dev-python/fiona/Manifest @@ -1 +1,2 @@ -DIST fiona-1.9.0.gh.tar.gz 290797 BLAKE2B 1cd2a4a26d23d057433889937b4fecefb1e1585dc6b507e297ef3bab8cf72f734bc080bab8487d58c636312bca1330960f78fc2916d27c9a7247df087818c9b3 SHA512 f59d148cfc4f1cab6d89660146522920fab8b6fb1120ad8f3d3e8349d5fa823860984f8fd331e2fc3183a4a186a165508db8dcbcbdf4b943a7dad82d8d51d866 +DIST fiona-1.10.1.gh.tar.gz 691246 BLAKE2B 53a6dd4cc36825aa27cff4edb53c36d5a48874ade9038b5a08bd846bda75a41136b39d6e0ffaa0a4e104b16e10af4cc051ab0b2602dfaa552eb3c282a51824ba SHA512 d84e973de81a53da44dd630d88eee0c1a3a8c5bef58ae70aef32ac7cebff590b9244860ee2674f3e97fdfd7a24ad07061355bb2c48d506bec5aec5e90adff87a +DIST fiona-1.9.6.gh.tar.gz 391486 BLAKE2B bdfc3a9ae972a6cc0bd9e6fa79879183bd87bcbdee1a543bd66f624b633d6ad3d1ab2264176a4d7eabc80680377f0438821d36e1fa111210e37f6788a9efe985 SHA512 91899a79b590a985d3cc266d9aeb346659ef531618e0aa099c9aeb589fd4bea912d9b0f9212b35a44d33f70e61efb627b7af7264631807cab77d3968b4464c2f diff --git a/dev-python/fiona/fiona-1.10.1.ebuild b/dev-python/fiona/fiona-1.10.1.ebuild new file mode 100644 index 000000000..f6fde60a3 --- /dev/null +++ b/dev-python/fiona/fiona-1.10.1.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_EXT=1 +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 -> ${P}.gh.tar.gz" +S="${WORKDIR}/Fiona-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-libs/gdal[geos,sqlite] + dev-python/attrs[${PYTHON_USEDEP}] + dev-python/click-plugins[${PYTHON_USEDEP}] + dev-python/cligj[${PYTHON_USEDEP}] + dev-python/munch[${PYTHON_USEDEP}] + dev-python/certifi[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/aiohttp[${PYTHON_USEDEP}] + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + sci-libs/gdal[geos,sqlite] + ) +" + +distutils_enable_tests pytest + +python_test() { + local EPYTEST_DESELECT=( + # disable tests violating network sandbox + 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] + + # OGR silently fails to convert strings + tests/test_unicode.py::TestUnicodeStringField::test_write_mismatch + ) + + mv fiona{,.bak} || die # Avoid non-working local import + epytest + mv fiona{.bak,} || die +} diff --git a/dev-python/fiona/fiona-1.9.0.ebuild b/dev-python/fiona/fiona-1.9.6.ebuild index 7bc415b14..ad73fbbd0 100644 --- a/dev-python/fiona/fiona-1.9.0.ebuild +++ b/dev-python/fiona/fiona-1.9.6.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/fiona/metadata.xml b/dev-python/fiona/metadata.xml index e1e191ee0..413c4e05f 100644 --- a/dev-python/fiona/metadata.xml +++ b/dev-python/fiona/metadata.xml @@ -6,13 +6,16 @@ <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> + 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> + <bugs-to>https://github.com/Toblerity/Fiona/issues</bugs-to> + <changelog>https://raw.githubusercontent.com/Toblerity/Fiona/refs/heads/main/CHANGES.txt</changelog> + <doc>https://fiona.readthedocs.io/</doc> <remote-id type="github">Toblerity/fiona</remote-id> - <remote-id type="pypi">Fiona</remote-id> + <remote-id type="pypi">fiona</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest index 037a125d3..cbe05bdd4 100644 --- a/dev-python/geopandas/Manifest +++ b/dev-python/geopandas/Manifest @@ -1 +1,2 @@ DIST geopandas-0.13.2.gh.tar.gz 6388249 BLAKE2B 910f32ea7d798bbdeee77be190c57daf7bdc719901a2183b5328ec13619ff9b4145d1717afed8fc71da154d84f388ce2bc30c541478f95ed121c7d8681c691ae SHA512 4dff4bfeca2490081c02c41edf92037fa8a8f4b030b6f6a0cdc231b3119f829604af39277125db9535c66aac0698d2d4dcfac2bb58b92d31bea83f0ee296e21a +DIST geopandas-1.0.1.gh.tar.gz 6433127 BLAKE2B 4d96ca174ed5a3bb35088b60d547d42f1a46b0eb4cab8aeaaf4cd74c42c1b134864c3bcd7842ac5e5b58c1a480f290732a4e8da626dcd935bdb4b1e233b2db1d SHA512 41ed79c1c798837b063ee45b1cda677b9f205cbc38e0ead019f86406a626fb8cfaae111ca8cead369c46155102665da094fa6d9ae2588290fa38b546a3875d87 diff --git a/dev-python/geopandas/geopandas-1.0.1.ebuild b/dev-python/geopandas/geopandas-1.0.1.ebuild new file mode 100644 index 000000000..9b440455f --- /dev/null +++ b/dev-python/geopandas/geopandas-1.0.1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 optfeature + +DESCRIPTION="Python tools for geographic data" +HOMEPAGE=" + https://github.com/geopandas/geopandas + https://pypi.org/project/geopandas/ +" +SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +RESTRICT="test" # 10 tests fail for 1.0.1 + +# upstream order +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/pandas-1.4[${PYTHON_USEDEP}] + >=dev-python/shapely-2.0.0[${PYTHON_USEDEP}] + >=dev-python/pyproj-3.3.0[${PYTHON_USEDEP}] + dev-python/fiona[${PYTHON_USEDEP}] +" + +EPYTEST_DESELECT=( + # violates network sandbox + geopandas/io/tests/test_file.py::test_read_file_url + # fails with RuntimeError thrown by matplotlib + geopandas/tests/test_plotting.py::TestGeoplotAccessor::test_pandas_kind + + # rtree results are known to be unordered, see False-expected1 + geopandas/tests/test_sindex.py::TestShapelyInterface::test_query_bulk_sorting + geopandas/tests/test_sindex.py::TestShapelyInterface::test_query_sorting +) +distutils_enable_tests pytest + +pkg_postinst() { + optfeature "plotting" >=dev-python/matplotlib-3.5.0 + optfeature "geocoding" sci-geosciences/geopy + elog "For full optional dependencies list visit" + elog "https://geopandas.org/en/stable/getting_started/install.html#dependencies" +} diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml index a102c7148..9b2145fd3 100644 --- a/dev-python/geopandas/metadata.xml +++ b/dev-python/geopandas/metadata.xml @@ -6,13 +6,16 @@ <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 + 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> + <bugs-to>https://github.com/geopandas/geopandas/issues</bugs-to> + <changelog>https://geopandas.org/en/stable/docs/changelog.html</changelog> + <doc>https://geopandas.org/en/stable/docs.html</doc> <remote-id type="github">geopandas/geopandas</remote-id> <remote-id type="pypi">geopandas</remote-id> </upstream> diff --git a/dev-python/hist/Manifest b/dev-python/hist/Manifest index f9d572709..e859f1eea 100644 --- a/dev-python/hist/Manifest +++ b/dev-python/hist/Manifest @@ -1,2 +1,3 @@ DIST hist-2.7.2.tar.gz 991866 BLAKE2B 6785114e1a5b3e38b9917c5d8b660e6d03dbe56d7a3238c971686ffc03ec1e9c6361ea6ed73ed61b10a4074b13d4ad785b676a61a856069ba23789985949787e SHA512 92a320a80509eaeaa496c2713b349e3b1442c46a7aeda04e362fdd692aea3f43f06e5bdb35293ca70f9b24536c24494fa1c806e9f9e8573559c13abeee22c4ce DIST hist-2.7.3.tar.gz 992241 BLAKE2B 865e4a7d65633c42d114139390040872d630527292f2941eb70732c1456d5f2571026d2a131f0bc09015a5922d6f6557342f4fb00ec91eeb83bb8b2bc25f28fd SHA512 85c7231f2cbc7bd8d7066f664a8fe9cd54092f79a242c353bdf3fad47ae7040f52b836238a92f006cdf30d2a3ae1e3a0c6bc1d8afaf2004f2056f6da5398d2b2 +DIST hist-2.8.0.tar.gz 992225 BLAKE2B d69302a80b7fed28d298b8dc175932632b31936d6e6a9c61830738d14aee5c089be4c23fb3c2bcfa5e941598786d4ee04bfd51bcb78bc98f2c73ef44437749cf SHA512 4deece91ea85a412d3b4bcfb86f20813ecd10f259a71fd3509cf51f99d12640019aee83a2f95b9a039e67121d752e6cbbb7ce55b7c10f9e1b0cd100528e5fa32 diff --git a/dev-python/hist/hist-2.8.0.ebuild b/dev-python/hist/hist-2.8.0.ebuild new file mode 100644 index 000000000..04160951e --- /dev/null +++ b/dev-python/hist/hist-2.8.0.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Histogramming for analysis powered by boost-histogram " +HOMEPAGE="https://github.com/scikit-hep/hist" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/boost-histogram-1.3.1[${PYTHON_USEDEP}] + >=dev-python/histoprint-2.2.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.14.5[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +RESTRICT="test" +# needs mplhep and dask_histogram ... +#distutils_enable_tests pytest diff --git a/dev-python/histoprint/Manifest b/dev-python/histoprint/Manifest index 2914a2419..c08f978b9 100644 --- a/dev-python/histoprint/Manifest +++ b/dev-python/histoprint/Manifest @@ -1 +1,2 @@ DIST histoprint-2.4.0.tar.gz 359154 BLAKE2B f10abcff02875f1a27b31256c5daf00500e0177986052f3fc9b013a0be0f63daf58f9d9b7bf2b6b5510758e080a118c6ad07801b055019e7e226ee631da57154 SHA512 bbf7c90acb66c298588304a15c7ae3ec0536fb01a468b4aa7b944115e242a0ef3e2ef21c181e8476845f5d7611a944f43de0c9cf80faeab2ddbb8422432e2fa6 +DIST histoprint-2.5.0.tar.gz 360296 BLAKE2B 37a40cfea760a08c0dcfc89d51eb526ee4bdb8c01cca18b2450f0f54ae61e051d4d8331227c05b6db85b7cf3553660e17dd68ed95d47021a874614de16958627 SHA512 e08063f58afbae570721ecbb91f772998d374b50d61d9622ef0c6ff96272711c49cb04d1882befba6ed54ce7933c9bb24fc5ac9fd83b16c43bdd96b135b9828e diff --git a/dev-python/histoprint/histoprint-2.5.0.ebuild b/dev-python/histoprint/histoprint-2.5.0.ebuild new file mode 100644 index 000000000..55286dfc5 --- /dev/null +++ b/dev-python/histoprint/histoprint-2.5.0.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Pretty print histograms to the console" +HOMEPAGE="https://github.com/scikit-hep/histoprint" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/click-7.0.0[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/uhi-0.2.1[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + >=dev-python/awkward-1[${PYTHON_USEDEP}] + >=sci-physics/uproot-4[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild index 22f35fbda..408e7be50 100644 --- a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild +++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild @@ -18,7 +18,7 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND="${PYTHON_DEPS} - dev-python/jinja[${PYTHON_USEDEP}] + dev-python/jinja2[${PYTHON_USEDEP}] dev-python/joblib[${PYTHON_USEDEP}] dev-python/markupsafe[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] diff --git a/dev-python/pyfaidx/Manifest b/dev-python/pyfaidx/Manifest index c66bceba8..0d4ae4b79 100644 --- a/dev-python/pyfaidx/Manifest +++ b/dev-python/pyfaidx/Manifest @@ -1 +1 @@ -DIST pyfaidx-0.8.1.1.tar.gz 103060 BLAKE2B 6910b77950a55885d1e0ae9f30172ec5c1d14320fdb2bad264e21d8f2e7f212f725f2608297ac5b6a2ec8d366b1385245694b2a70410deca8be1765db0683835 SHA512 26d130770069aed9bd378e54f338b6c66840114e6cddfdc971b6496fa30ee651181f2225d372499992b63ba8b0c6d0a7ed827a210dc3f78c0c8592bdb73211b3 +DIST pyfaidx-0.8.1.3.tar.gz 103025 BLAKE2B aac8d21583b1235693ddc41d6a5129288c07b062a1993db193d22b84a8c27100c3acc779e4650a9595153bc04f1f9e5667c04e1c080d443b39c39315e68789a8 SHA512 cf665639dd4c49dd98375aa15cdf3d28c5d8eecea970f0d5ea91c409d8df80b2ac5e3444a79fc00c63954505aad8d8810901d75d52d67a0a356f4a9dd97c5cc8 diff --git a/dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild b/dev-python/pyfaidx/pyfaidx-0.8.1.3.ebuild index 86465aecd..86465aecd 100644 --- a/dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild +++ b/dev-python/pyfaidx/pyfaidx-0.8.1.3.ebuild diff --git a/dev-python/resample/Manifest b/dev-python/resample/Manifest new file mode 100644 index 000000000..347f41acf --- /dev/null +++ b/dev-python/resample/Manifest @@ -0,0 +1 @@ +DIST resample-1.10.1.tar.gz 631943 BLAKE2B e76817a4cfc6b1a04a7a601ba8e2c23d5ef38dac815ec244b0ff7af1a470c5a3dc2fbdd51af142443350369fcfb15a492fcfb84f32888097075a15e4d9408c31 SHA512 4e9ce268c375960f75e5e43bd22e304ef33f7ffe7e9ad894bd4f71bace81f1cb81d11e0486a4e09af72fae3106a3a5155be315b6d69a9d28499d39dfe451f053 diff --git a/dev-python/resample/metadata.xml b/dev-python/resample/metadata.xml new file mode 100644 index 000000000..db0565d2f --- /dev/null +++ b/dev-python/resample/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Resampling-based inference in Python based on data resampling and permutation. + </longdescription> + <upstream> + <remote-id type="pypi">resample</remote-id> + <remote-id type="github">scikit-hep/resample</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/resample/resample-1.10.1.ebuild b/dev-python/resample/resample-1.10.1.ebuild new file mode 100644 index 000000000..424c9c537 --- /dev/null +++ b/dev-python/resample/resample-1.10.1.ebuild @@ -0,0 +1,19 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Randomization-based inference in Python" +HOMEPAGE="https://github.com/scikit-hep/resample" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.21[${PYTHON_USEDEP}] + >=dev-python/scipy-1.10[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild index 943af2cfc..4ac42c358 100644 --- a/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild +++ b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild @@ -16,7 +16,7 @@ SLOT="0" KEYWORDS="~amd64" DEPEND="dev-python/argparse-dataclass[${PYTHON_USEDEP}] - dev-python/ConfigArgParse[${PYTHON_USEDEP}]" + dev-python/configargparse[${PYTHON_USEDEP}]" RESTRICT="test" # no tests collected #distutils_enable_tests pytest diff --git a/dev-python/snakemake/snakemake-7.32.4.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild index 8ff44fdb5..912fbbd37 100644 --- a/dev-python/snakemake/snakemake-7.32.4.ebuild +++ b/dev-python/snakemake/snakemake-7.32.4.ebuild @@ -33,13 +33,13 @@ BDEPEND=" RDEPEND=" dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/ConfigArgParse[${PYTHON_USEDEP}] + dev-python/configargparse[${PYTHON_USEDEP}] dev-python/connection_pool[${PYTHON_USEDEP}] dev-python/datrie[${PYTHON_USEDEP}] dev-python/docutils[${PYTHON_USEDEP}] - dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/gitpython[${PYTHON_USEDEP}] dev-python/humanfriendly[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] + dev-python/jinja2[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/nbformat[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] diff --git a/dev-python/snakemake/snakemake-8.16.0.ebuild b/dev-python/snakemake/snakemake-8.16.0.ebuild index f83e8feb9..f204537d1 100644 --- a/dev-python/snakemake/snakemake-8.16.0.ebuild +++ b/dev-python/snakemake/snakemake-8.16.0.ebuild @@ -34,13 +34,13 @@ BDEPEND=" RDEPEND=" dev-python/appdirs[${PYTHON_USEDEP}] dev-python/immutables[${PYTHON_USEDEP}] - dev-python/ConfigArgParse[${PYTHON_USEDEP}] + dev-python/configargparse[${PYTHON_USEDEP}] >=dev-python/connection_pool-0.0.3[${PYTHON_USEDEP}] dev-python/datrie[${PYTHON_USEDEP}] dev-python/docutils[${PYTHON_USEDEP}] - dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/gitpython[${PYTHON_USEDEP}] dev-python/humanfriendly[${PYTHON_USEDEP}] - >=dev-python/jinja-3.0[${PYTHON_USEDEP}] + >=dev-python/jinja2-3.0[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/nbformat[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] diff --git a/dev-python/uhi/Manifest b/dev-python/uhi/Manifest index 199ee2a62..7eeab5dbb 100644 --- a/dev-python/uhi/Manifest +++ b/dev-python/uhi/Manifest @@ -1 +1,2 @@ DIST uhi-0.4.0.tar.gz 52953 BLAKE2B b0c16c58c676f405d7b46398507968e92e4c3939a53224b49cbd935c3473800341903a9e9c5e3c598d68f171a9ec098feedaa774b2bbfe780581a663e99b2592 SHA512 4f7f0bdce3fef14c8789e0860956d6d4d2ab91e48eb95b6bceb67aef47b23a260f0f33a565c052fe48933f108adfe32f4c28c8cf874cc908929d407687bbc385 +DIST uhi-0.5.0.tar.gz 25769 BLAKE2B a920a17671bb98ee809264c762189feefc0eaed8b24b616e726fa646728c9ca8cfa518077d9b6e94c55505ea41d6dcbd7c937fd4407c80e8995df80ccdfeec54 SHA512 97bd42b9135360888488106554c9c3ad042b0e4f7eabc7abf7edadec978261032c40ab43e3e1c4df7aa6b4447f403085767b4d9beb5c9bdc50466e049a9d3080 diff --git a/dev-python/uhi/uhi-0.5.0.ebuild b/dev-python/uhi/uhi-0.5.0.ebuild new file mode 100644 index 000000000..7dee1e062 --- /dev/null +++ b/dev-python/uhi/uhi-0.5.0.ebuild @@ -0,0 +1,27 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Universal Histogram Interface" +HOMEPAGE="https://github.com/scikit-hep/uhi" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/fastjsonschema[${PYTHON_USEDEP}] + >=dev-python/boost-histogram-1.0[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest index a64079e01..f844796a5 100644 --- a/dev-python/vector/Manifest +++ b/dev-python/vector/Manifest @@ -1,3 +1,4 @@ DIST vector-1.1.1.tar.gz 289916 BLAKE2B 35281c498f244b0307d744a20d0364c4cf664d0bd08a4f17d8d3110aa4eae6d7f66e3b51b4e9847f31d3a6ab943248115221dee4dcd3c3f2f8c47842001b553a SHA512 b1e195751de35ca2c67749b6b2b330db8a29e023f42e9b454adc8fc2408c29b5926b39e9ed6dc6a93f97006fbfb286a2217be8b14cb0eb2b96c9538f6c3943e6 DIST vector-1.3.1.tar.gz 299581 BLAKE2B 36e99e814b5e8afc7a0179acce74f399db8f76e3c3c59ebbb5a2616bfa8f34ca2cfabe9e42752226dbabbdcd77fc15a4725c4e296f5329533a85cade8fcfae0c SHA512 524752789f6ea0201e1bb3dc09e7396a8bc64a1ee78ccab383bbe968134783bbf7499948784b141353612649f8188d0cb93147b53afdf37ba26f812d8ebd84b0 DIST vector-1.4.1.tar.gz 374576 BLAKE2B 863984ed98dbe6920380f467931c9b80b3a57934dfcf0de049de77a7d6ec8f9c9335333609ab28b794ed31a2f6a859bd1475b0bb2976fa9c1f4ca1f2aecbfea9 SHA512 5a08c49f6bf09d07768b90d79a9a0b9aa9b1068c6c03be96f960605d2a708cb80f0ff7fc2da807383d1e652bd454c27048702adffa1a55ee3ca9b740c5b0f2f0 +DIST vector-1.5.2.tar.gz 326552 BLAKE2B 8f648f80fd77e660410aad42f37309e8b6a3634671ca507e5acfec5188e70937b3930cec82dc9d910ab24acf7e3cf9b20000bcb92a8a0f89f951d38e09b703b5 SHA512 3d313b83b3d98459d2763987a0347cf5747e19a22bc26f00d3a6c9710019803a01bb047b392b67bc6e0efd7974255f2a7ac5d6daa4ee4ae686d20d97cf043181 diff --git a/dev-python/vector/vector-1.5.2.ebuild b/dev-python/vector/vector-1.5.2.ebuild new file mode 100644 index 000000000..b9c06d278 --- /dev/null +++ b/dev-python/vector/vector-1.5.2.ebuild @@ -0,0 +1,33 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi optfeature + +DESCRIPTION="Vector classes and utilities" +HOMEPAGE=" + https://github.com/scikit-hep/vector + https://vector.readthedocs.io/ + https://doi.org/10.5281/zenodo.7054478 +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +# tests need numba +RESTRICT="test" + +RDEPEND=" + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + >=dev-python/packaging-19[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} + +pkg_postinst() { + optfeature "awkward array support" dev-python/awkward + optfeature "sympy support" dev-python/sympy +} diff --git a/profiles/package.mask b/profiles/package.mask index c184ca27b..5770f4680 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,14 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18) +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2024-11-26) +# Depends on removed version of vtk +sci-biology/ants + +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2024-11-26) +# Depends on masked sci-biology/ants +sci-biology/samri + +# Nowa Ammerlaan <nowa@gentoo.org> (2024-07-18) # Requires java openmpi bindings, no longer packaged. sci-biology/BBmap diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 39a6df0b7..ac0975f0b 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -15,6 +15,6 @@ ## =media-video/mplayer-0.90_pre5-r1 foo # -# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022) +# Nowa Ammerlaan <nowa@gentoo.org> (23 Aug 2022) # vtk<9 no longer available in ::gentoo sci-libs/gdcm python diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild index 7e196a47d..c9ade12fe 100644 --- a/sci-biology/BBmap/BBmap-38.87.ebuild +++ b/sci-biology/BBmap/BBmap-38.87.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" HOMEPAGE="https://sourceforge.net/projects/bbmap/" @@ -32,7 +32,7 @@ src_prepare(){ } src_compile(){ - ant dist || die + eant dist } src_install(){ diff --git a/sci-biology/MeV/MeV-4.8.1.ebuild b/sci-biology/MeV/MeV-4.8.1.ebuild index eb605976e..44d7a56f5 100644 --- a/sci-biology/MeV/MeV-4.8.1.ebuild +++ b/sci-biology/MeV/MeV-4.8.1.ebuild @@ -5,12 +5,13 @@ EAPI=7 MY_PV="${PV//./_}" -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="Multiple experiment Viewer for genomic data analysis" HOMEPAGE="https://sourceforge.net/projects/mev-tm4/" SRC_URI="https://downloads.sourceforge.net/project/mev-tm4/mev-tm4/MeV%20${PV}/MeV_${MY_PV}_r2727_linux.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}_${MY_PV}" LICENSE="Artistic-2" SLOT="0" KEYWORDS="~amd64" @@ -19,11 +20,8 @@ RDEPEND=">=virtual/jre-1.5:* ${DEPEND}" DEPEND="${RDEPEND} >=virtual/jdk-1.5:* - dev-java/ant-core " -S="${WORKDIR}/${PN}_${MY_PV}" - src_install() { dodoc -r documentation/* rm -r documentation diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest index 183a71158..c6ab841fc 100644 --- a/sci-biology/SnpEff/Manifest +++ b/sci-biology/SnpEff/Manifest @@ -1,2 +1 @@ -DIST SnpEff-4.3t.html 10041 BLAKE2B fe3f9b3cf2198af8690bd1f7fdda0a718c354f69343280d29b3021aa00a426653079aec738f8e0d0be0856d789526678481c8a255f0d77463e7e7dc2b4aec7a5 SHA512 fba76ce6e9414a610e2ee4247c6fa34601d0b2925cce1c35ffa7fc865ad80684c28e2a23c0f551cf5ee47057f847c5e2ebfaca18d5c47f41722951b192b1fbfb DIST snpEff_v4_3t_core.zip 69708122 BLAKE2B c64c68c9923951f086df447b93adf55e5555e545c59e30a2ce2fdef7e9690cf5219aaab112a6dce23ce6ea72d80772f686a7eb5f000d11b28503f792e0df09a7 SHA512 dfb48c2ae6b9b6dc07b02d44ae0b6ee09d235f1abce8e4df9e9bafbe8e9cd00f914f6e83dee7e67fcd7db0369e00c9dbb8f39575a956ddf3c611298d9c8e062f diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild index 843c00356..aa6ce5247 100644 --- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild @@ -3,14 +3,15 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF" HOMEPAGE="https://pcingola.github.io/SnpEff/" SRC_URI=" https://downloads.sourceforge.net/project/snpeff/snpEff_v${PV//./_}_core.zip - https://pcingola.github.io/SnpEff/index.html -> ${P}.html" +" +S="${WORKDIR}" LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64" @@ -21,11 +22,9 @@ RDEPEND=" dev-java/antlr:*" DEPEND="${RDEPEND} >=virtual/jdk-1.7:* - dev-java/ant-core" +" BDEPEND="app-arch/unzip" -S="${WORKDIR}" - src_install(){ cd .. || die mkdir -p "${ED}"/usr/share || die diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 69572ef1e..73b861a86 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1 +1 @@ -DIST bx-python-0.12.0.gh.tar.gz 1660806 BLAKE2B 0eddb9b9a93520319d275001067a3518015483605cf4d096729ec92e14c0eb35f2ceb34db964216dd3c6687351a7415c46061960b1f66a7564c90efeba3a587b SHA512 821b33841dd2935485669f6c112277d404475b1cd778deb3eaa1194f3b21594335a219d9345e279e7afc3adb1e347e71e60f0029712fc58e95d1e70f9e8fbb55 +DIST bx-python-0.13.0.gh.tar.gz 1611987 BLAKE2B 138c081c60249e492cbb1474f88a92faadc76c5340555599d93a97a7d8b8e5130e71724f18174262dff3f286678f3d5cac03362aadadf81ecd90a0b6f621927c SHA512 345faf1f42b24ae97216bb9d231e7f97093cd607d51fe51129335e2c077e47dc30a3657b27733674caace5f32eebab8ef64a3f912c585fabf07333722d24317c diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.13.0.ebuild index 1a00b0395..0062da958 100644 --- a/sci-biology/bx-python/bx-python-0.12.0.ebuild +++ b/sci-biology/bx-python/bx-python-0.13.0.ebuild @@ -17,6 +17,7 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" +BDEPEND="test? ( dev-python/python-lzo[${PYTHON_USEDEP}] )" RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="dev-python/cython[${PYTHON_USEDEP}]" @@ -28,11 +29,6 @@ PATCHES=( distutils_enable_tests pytest # https://github.com/bxlab/bx-python/issues/101 -EPYTEST_DESELECT=( - lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo - lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer -) - python_test() { cd "${BUILD_DIR}/build" || die ln -s "${S}/pytest.ini" . || die diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest new file mode 100644 index 000000000..9b1b4fa20 --- /dev/null +++ b/sci-biology/cutadapt/Manifest @@ -0,0 +1 @@ +DIST cutadapt-4.9.tar.gz 248837 BLAKE2B a95e510801572046689899315283d958933b625a10f57177811bbeae020b7a8f09c919cd15adabac64adbf550cdd901e078cd76cebdc0a1bbf80223584291242 SHA512 332de05a0fd11c07749ee58c171d79699776cae4a0338b7586f9e2939fb9f313b1647388bb4f060b7603e80b94b5b0da54a5e825fab862d6bf3c45b0c02fda0b diff --git a/sci-biology/cutadapt/cutadapt-4.9.ebuild b/sci-biology/cutadapt/cutadapt-4.9.ebuild new file mode 100644 index 000000000..cd1a8fe7c --- /dev/null +++ b/sci-biology/cutadapt/cutadapt-4.9.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Adapter trimming and other preprocessing of high-throughput sequencing reads" +HOMEPAGE="https://github.com/marcelm/cutadapt/" +SRC_URI="$(pypi_sdist_url "${PN^}" "${PV}")" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +DEPEND=" + >=dev-python/xopen-1.6.0[${PYTHON_USEDEP}] + >=dev-python/dnaio-1.2.0[${PYTHON_USEDEP}] +" +RDEPEND=" + ${DEPEND} + test? ( dev-python/pytest ) +" +distutils_enable_tests pytest diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml new file mode 100644 index 000000000..028038de8 --- /dev/null +++ b/sci-biology/cutadapt/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science</name> + </maintainer> + <upstream> + <remote-id type="pypi">cutadapt</remote-id> + <remote-id type="github">marcelm/cutadapt</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest index c158050fa..179048852 100644 --- a/sci-biology/fastp/Manifest +++ b/sci-biology/fastp/Manifest @@ -1 +1 @@ -DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76 +DIST fastp-0.24.0.gh.tar.gz 164236 BLAKE2B 456c2c26275185444f140b64c85db6355d124c8a3008932000be2a343671fb2970c856835a7fb45be760312aa591dd0576750b7c6df15b262c55a20d42c3eef2 SHA512 28307d592e677e50187f58c2013af713830d1f2e2753ef220d7162d0657767a92e3ee78e7b6f6fbbed07ae3a3873098cce3ff6f2c642755e4633767b1176ef03 diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.24.0.ebuild index 70d5ce330..4864761eb 100644 --- a/sci-biology/fastp/fastp-0.23.4.ebuild +++ b/sci-biology/fastp/fastp-0.24.0.ebuild @@ -5,7 +5,7 @@ EAPI=8 DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor" HOMEPAGE="https://github.com/OpenGene/fastp" -SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" KEYWORDS="~amd64" LICENSE="MIT" diff --git a/sci-biology/fastqc/fastqc-0.11.9.ebuild b/sci-biology/fastqc/fastqc-0.11.9.ebuild index be2d3b340..5d42f295a 100644 --- a/sci-biology/fastqc/fastqc-0.11.9.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.9.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit desktop java-pkg-2 java-ant-2 xdg +inherit desktop java-pkg-2 xdg DESCRIPTION="Quality control FASTA/FASTQ sequence files" HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" @@ -24,7 +24,19 @@ DEPEND=" " BDEPEND="media-gfx/imagemagick" -EANT_BUILD_TARGET="build" +src_prepare() { + sed -i -E 's/<property name="source" value="[0-9.]+" \/>//g' build.xml || die + sed -i -E 's/<property name="target" value="[0-9.]+" \/>//g' build.xml || die + sed -i 's/source="${source}"//g' build.xml || die + sed -i 's/target="${target}"//g' build.xml || die + default +} + +src_compile() { + eant build \ + -Dant.build.javac.source="$(java-pkg_get-source)" \ + -Dant.build.javac.target="$(java-pkg_get-target)" +} src_install(){ insinto "opt/${PN}" diff --git a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild index 9d4480272..3244e79b5 100644 --- a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild +++ b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-opt-2 java-ant-2 +inherit java-pkg-opt-2 DESCRIPTION="Genome browser and annotation tool" HOMEPAGE="https://genomeview.sourceforge.net" diff --git a/sci-biology/imagej/imagej-1.54i-r1.ebuild b/sci-biology/imagej/imagej-1.54i-r1.ebuild index f95167bcd..92449b368 100644 --- a/sci-biology/imagej/imagej-1.54i-r1.ebuild +++ b/sci-biology/imagej/imagej-1.54i-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit java-pkg-2 java-ant-2 desktop +inherit java-pkg-2 desktop MY_PN="ij" IJ_PV="154" #plugins now available for 154 @@ -65,6 +65,9 @@ src_prepare() { if ! use debug ; then sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die fi + sed -i -E 's/source="[0-9.]+"//g' build.xml || die + sed -i -E 's/target="[0-9.]+"//g' build.xml || die + default } @@ -72,7 +75,9 @@ src_compile() { local antflags="build" use doc && antflags="${antflags} javadocs" - ant ${antflags} || die "ant build failed" + eant ${antflags} \ + -Dant.build.javac.source="$(java-pkg_get-source)" \ + -Dant.build.javac.target="$(java-pkg_get-target)" # Max memory usage depends on available memory and CPU type MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild index f95167bcd..40f04311b 100644 --- a/sci-biology/imagej/imagej-9999.ebuild +++ b/sci-biology/imagej/imagej-9999.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit java-pkg-2 java-ant-2 desktop +inherit java-pkg-2 desktop MY_PN="ij" IJ_PV="154" #plugins now available for 154 @@ -65,6 +65,8 @@ src_prepare() { if ! use debug ; then sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die fi + sed -i -E 's/source="[0-9.]+"//g' build.xml || die + sed -i -E 's/target="[0-9.]+"//g' build.xml || die default } @@ -72,7 +74,9 @@ src_compile() { local antflags="build" use doc && antflags="${antflags} javadocs" - ant ${antflags} || die "ant build failed" + eant ${antflags} \ + -Dant.build.javac.source="$(java-pkg_get-source)" \ + -Dant.build.javac.target="$(java-pkg_get-target)" # Max memory usage depends on available memory and CPU type MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild index 63ec84d2f..d386ca896 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 perl-module +inherit java-pkg-2 perl-module S="${WORKDIR}"/TreeView-1.1.6r4-bin diff --git a/sci-biology/multiqc/multiqc-1.23.ebuild b/sci-biology/multiqc/multiqc-1.23.ebuild index bf45065aa..2ac362503 100644 --- a/sci-biology/multiqc/multiqc-1.23.ebuild +++ b/sci-biology/multiqc/multiqc-1.23.ebuild @@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~amd64-linux" RDEPEND="dev-python/click[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] dev-python/importlib-metadata[${PYTHON_USEDEP}] - >=dev-python/jinja-3.0.0[${PYTHON_USEDEP}] + >=dev-python/jinja2-3.0.0[${PYTHON_USEDEP}] dev-python/markdown[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] diff --git a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild index 331ab5cd8..f48e98b3b 100644 --- a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild +++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="Illumina adapter trimming tool" HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic" @@ -15,16 +15,23 @@ SRC_URI=" LICENSE="GPL-3" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" -DEPEND=">=virtual/jdk-1.6:* - dev-java/ant-core +DEPEND=">=virtual/jdk-1.7:* app-arch/unzip" -RDEPEND=">=virtual/jre-1.6:*" +RDEPEND=">=virtual/jre-1.7:*" -# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works +src_prepare() { + sed -i -E 's/source="[0-9\.]+"//g' build.xml || die + sed -i -E 's/target="[0-9\.]+"//g' build.xml || die + default +} -EANT_BUILD_TARGET="dist" +src_compile() { + eant dist \ + -Dant.build.javac.source="$(java-pkg_get-source)" \ + -Dant.build.javac.target="$(java-pkg_get-target)" +} src_install() { java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar" diff --git a/sci-chemistry/jligand/Manifest b/sci-chemistry/jligand/Manifest deleted file mode 100644 index cbd60dfb1..000000000 --- a/sci-chemistry/jligand/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST JLigand.1.0.40.tar.gz 69101 BLAKE2B 8c1b2c029abd19b04e7ef29774657fb84f63afa98b04afc8bb300b41a50397b5071d974b2f7e674ada9a21b27a3bb01ac410b57f0e3bb44276e54c8af1fbaa40 SHA512 9600e8a18c015e56f8bb9fc272fbdfe77963be0ceb2ea15b0b037452c58c65ac1acc129e54f5cf5531a27f72843cc1368a78a5f4bd6bc8c7e752b8999cc6dbae diff --git a/sci-chemistry/jligand/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild deleted file mode 100644 index 879964bbf..000000000 --- a/sci-chemistry/jligand/jligand-1.0.40.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -MY_PN="JLigand" - -DESCRIPTION="Java interface which allows links descriptions to be created" -HOMEPAGE="http://www.ysbl.york.ac.uk/mxstat/JLigand/" -SRC_URI="http://www.ysbl.york.ac.uk/mxstat/${MY_PN}/${MY_PN}.${PV}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=">=virtual/jre-1.5" -DEPEND=">=virtual/jdk-1.5" - -S="${WORKDIR}/${MY_PN}.${PV}" - -src_compile() { - sed 's:makefile::g' -i Makefile || die - default -} - -src_install() { - java-pkg_newjar JLigand.jar "${PN}.jar" - java-pkg_dolauncher JLigand \ - --jar "${PN}.jar" -} diff --git a/sci-chemistry/jligand/metadata.xml b/sci-chemistry/jligand/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/jligand/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild index f23e1c738..919af1786 100644 --- a/sci-libs/daal4py/daal4py-2023.0.2.ebuild +++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild @@ -29,7 +29,7 @@ BDEPEND=" " DEPEND=" - dev-python/jinja[${PYTHON_USEDEP}] + dev-python/jinja2[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/dpctl[${PYTHON_USEDEP}] sci-libs/oneDAL diff --git a/sci-libs/rdkit/Manifest b/sci-libs/rdkit/Manifest index 50005a850..4704bbc4a 100644 --- a/sci-libs/rdkit/Manifest +++ b/sci-libs/rdkit/Manifest @@ -1 +1 @@ -DIST rdkit-2021.09.4.tar.gz 78474802 BLAKE2B 8c78c787a0e414b5e035998d9575322edca955acecb6d2df173610398f91cffd0b9053e7fc2c9284a2117afd720f313b7a63ed7e9ab67c708f25a5735b838f59 SHA512 c761fd5c3340ec38141165996b8666c3dcd4ed46ab91ca0d5a43ae3daedfc423ae36ec5882f085e1bd0c4c13dfe1f09497d05ec95e4847048c0acff8bcd0b1db +DIST rdkit-2024.09.2.tar.gz 80717308 BLAKE2B 838596a17f1c6185b54e16cf78c51b688c0aa696cccac31e6b7d338e3f8940c240eedddc81f37b307d8dcb567b2a5b45514e16f089cd5a438b0e9468fae4844e SHA512 ba3eee1a15694b5a2996f51f593fc4965af818faa00699055c7bd94015c59d13358a8ccae0d32297b8fdc0e06d1c70992fcf8a4cd61627832cfc95fb7016545f diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch deleted file mode 100644 index 94a209e0f..000000000 --- a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt -index 8027444..6a8c715 100644 ---- a/Code/GraphMol/MolInterchange/CMakeLists.txt -+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt -@@ -1,16 +1,5 @@ - --if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") -- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" -- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" -- "badd12c511e081fec6c89c43a7027bce") -- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf -- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz -- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) --else() -- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") --endif() -- --include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) -+include_directories(/usr/include/rapidjson) - - - rdkit_library(MolInterchange diff --git a/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch new file mode 100644 index 000000000..42d7c5663 --- /dev/null +++ b/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch @@ -0,0 +1,40 @@ +diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt +index 0c1e9a0de..e6f4fe753 100644 +--- a/Code/GraphMol/MolInterchange/CMakeLists.txt ++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt +@@ -1,24 +1,5 @@ + +-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") +- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" +- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" +- "badd12c511e081fec6c89c43a7027bce") +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf +- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) +- # comment out a line which causes a compilation error on some platforms +- # (based on the change which has already been applied to the RapidJSON master branch, see +- # https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414) +- file(READ ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h RAPIDJSON_DOCUMENT_H) +- string(REGEX REPLACE +- "( *)(GenericStringRef& operator=\\(const GenericStringRef& rhs\\) { s = rhs\\.s. length = rhs\\.length. })" "\\1//\\2" +- RAPIDJSON_DOCUMENT_H "${RAPIDJSON_DOCUMENT_H}") +- file(WRITE ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h "${RAPIDJSON_DOCUMENT_H}") +-else() +- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") +-endif() +- +-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) ++include_directories(/usr/include/rapidjson) + + + rdkit_library(MolInterchange +diff --git a/Code/MinimalLib/CMakeLists.txt b/Code/MinimalLib/CMakeLists.txt +index 84808a971..987b155f8 100644 +--- a/Code/MinimalLib/CMakeLists.txt ++++ b/Code/MinimalLib/CMakeLists.txt +@@ -1,5 +1,4 @@ + include_directories(${RDKit_ExternalDir}) +-include_directories(${RDKit_ExternalDir}/rapidjson-1.1.0/include) + + if(RDK_BUILD_MINIMAL_LIB) + set(MINIMAL_LIB_LIBRARIES "MolInterchange_static;Abbreviations_static;" diff --git a/sci-libs/rdkit/metadata.xml b/sci-libs/rdkit/metadata.xml index be6cc7780..3f69d40d1 100644 --- a/sci-libs/rdkit/metadata.xml +++ b/sci-libs/rdkit/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> <upstream> <remote-id type="github">rdkit/rdkit</remote-id> </upstream> diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2024.09.2.ebuild index a1621ea79..2d1c85a97 100644 --- a/sci-libs/rdkit/rdkit-2021.09.4.ebuild +++ b/sci-libs/rdkit/rdkit-2024.09.2.ebuild @@ -1,14 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..12} ) +CMAKE_IN_SOURCE_BUILD=1 inherit cmake python-single-r1 DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" -HOMEPAGE="http://www.rdkit.org/" +HOMEPAGE="https://www.rdkit.org/" SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/rdkit-Release_${PV//./_}" @@ -33,12 +34,11 @@ RDEPEND="dev-libs/boost DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch" + "${FILESDIR}/${PN}-2024.03.4-find-rapidjson.patch" ) src_configure() { local mycmakeargs=( - -DCATCH_DIR="${EPREFIX}/usr/include/catch2" -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr" -DRDK_INSTALL_INTREE=0 -DRDK_BUILD_CPP_TESTS="$(usex test)" @@ -46,13 +46,18 @@ src_configure() { -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)" # Disable things that trigger fetching and are not packaged -DRDK_INSTALL_COMIC_FONTS=OFF + -DRDK_BUILD_AVALON_SUPPORT=OFF -DRDK_BUILD_COORDGEN_SUPPORT=OFF + -DRDK_BUILD_FREESASA_SUPPORT=OFF + -DRDK_BUILD_INCHI_SUPPORT=OFF -DRDK_BUILD_MAEPARSER_SUPPORT=OFF + -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF + -DRDK_BUILD_YAEHMOP_SUPPORT=OFF -DRDK_USE_URF=OFF ) cmake_src_configure } src_test() { - RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test + RDBASE="${S}" cmake_src_test } diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest index 7cf5fa956..d30501570 100644 --- a/sci-libs/torchvision/Manifest +++ b/sci-libs/torchvision/Manifest @@ -1,2 +1 @@ -DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f -DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be +DIST torchvision-0.19.1.tar.gz 13135101 BLAKE2B 1d8ed851750840518dab6ff1153bbdcac723832500c072e78036282ef9396c33862b9f72cfd09456daea89e8c496d04a01e880a533e0f4c01779ed8add30bc55 SHA512 87ba1616ac6ed92851b0908bf7e5a3f840a3de8ab6fa5d7d3b27f9ed37efc5082540a88b4216a4fd91284c27dd69625ea04f2c1b81a6e5149e4ba3bea261b22b diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch deleted file mode 100644 index 7a3637f3a..000000000 --- a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch +++ /dev/null @@ -1,36 +0,0 @@ -From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?= - <zboszor@gmail.com> -Date: Tue, 7 Nov 2023 10:43:11 +0100 -Subject: [PATCH] Fix build with ffmpeg 6.0 -MIME-Version: 1.0 -Content-Type: text/plain; charset=UTF-8 -Content-Transfer-Encoding: 8bit - -Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com> ---- - torchvision/csrc/io/decoder/stream.cpp | 11 ++--------- - 1 file changed, 2 insertions(+), 9 deletions(-) - -diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp -index 0d625ef211c..8c914050587 100644 ---- a/torchvision/csrc/io/decoder/stream.cpp -+++ b/torchvision/csrc/io/decoder/stream.cpp -@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) { - codecCtx_->thread_count = num_threads; - } else { - // otherwise set sensible defaults -- // with the special case for the different MPEG4 codecs -- // that don't have threading context functions -- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) { -- codecCtx_->thread_type = FF_THREAD_FRAME; -- codecCtx_->thread_count = 2; -- } else { -- codecCtx_->thread_count = 8; -- codecCtx_->thread_type = FF_THREAD_SLICE; -- } -+ codecCtx_->thread_count = 8; -+ codecCtx_->thread_type = FF_THREAD_SLICE; - } - - int ret; diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml index 9c4ddaefd..3ba68fb09 100644 --- a/sci-libs/torchvision/metadata.xml +++ b/sci-libs/torchvision/metadata.xml @@ -5,6 +5,9 @@ <email>jpizarrocallejas@gmail.com</email> <name>Jorge Pizarro Callejas</name> </maintainer> + <use> + <flag name="rocm">Enable ROCm gpu computing support</flag> + </use> <upstream> <remote-id type="github">pytorch/vision</remote-id> </upstream> diff --git a/sci-libs/torchvision/torchvision-0.14.1.ebuild b/sci-libs/torchvision/torchvision-0.14.1.ebuild deleted file mode 100644 index 7f40fe556..000000000 --- a/sci-libs/torchvision/torchvision-0.14.1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 2020-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_10 ) -DISTUTILS_SINGLE_IMPL=1 -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="Datasets, transforms and models to specific to computer vision" -HOMEPAGE="https://github.com/pytorch/vision" -SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/vision-${PV}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - $(python_gen_cond_dep ' - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - ') - sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] - media-video/ffmpeg - dev-qt/qtcore:5 -" -DEPEND="${RDEPEND}" -BDEPEND=" - test? ( - $(python_gen_cond_dep ' - dev-python/mock[${PYTHON_USEDEP}] - ') - )" - -distutils_enable_tests pytest diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.19.1.ebuild index e0c72684c..a8fc6f5f7 100644 --- a/sci-libs/torchvision/torchvision-0.17.1.ebuild +++ b/sci-libs/torchvision/torchvision-0.19.1.ebuild @@ -3,11 +3,12 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_SINGLE_IMPL=1 DISTUTILS_USE_PEP517=setuptools DISTUTILS_EXT=1 -inherit distutils-r1 multiprocessing +ROCM_SKIP_GLOBALS=1 +inherit cuda distutils-r1 multiprocessing rocm DESCRIPTION="Datasets, transforms and models to specific to computer vision" HOMEPAGE="https://github.com/pytorch/vision" @@ -17,7 +18,11 @@ S="${WORKDIR}/vision-${PV}" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64" -RESTRICT="test" +IUSE="cuda rocm test" +REQUIRED_USE="?? ( cuda rocm )" +RESTRICT="!test? ( test )" + +distutils_enable_tests pytest RDEPEND=" $(python_gen_cond_dep ' @@ -27,13 +32,12 @@ RDEPEND=" dev-python/requests[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] ') + sci-libs/caffe2[cuda?,rocm?] sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] media-video/ffmpeg:= " DEPEND="${RDEPEND}" -PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" ) - src_compile() { export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS @@ -41,5 +45,17 @@ src_compile() # Ensure some ext_module sources are compiled before linking export MAKEOPTS="-j1" + use cuda && export NVCC_FLAGS="$(cuda_gccdir -f | tr -d \")" + use rocm && addpredict /dev/kfd + distutils-r1_src_compile } + +python_test() { + use rocm && check_amdgpu + + # https://projects.gentoo.org/python/guide/test.html#importerrors-for-c-extensions + rm -rf torchvision || die + + epytest +} diff --git a/sci-mathematics/frama-c/Manifest b/sci-mathematics/frama-c/Manifest deleted file mode 100644 index 9681962f9..000000000 --- a/sci-mathematics/frama-c/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST frama-c-22.0-Titanium.tar.gz 6008520 BLAKE2B 957f1fd383913718598c8d14bd0ff4b6251cc5350633888ca061fa0e44fae17273b379dcc1b70fe8a187975364aee1f255e0df232a4ee349ff29f9cb922a7b60 SHA512 7366127da4726ffec0022adc06fd867b6ea37fc23b6a5ddccbe7562fcaa635abc6894397d0101fcb0afc339c565299c6d637006305c8331aa62a8ce734740a0f diff --git a/sci-mathematics/frama-c/frama-c-22.0.ebuild b/sci-mathematics/frama-c/frama-c-22.0.ebuild deleted file mode 100644 index aaf815f4f..000000000 --- a/sci-mathematics/frama-c/frama-c-22.0.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -NAME="Titanium" - -DESCRIPTION="Framework for analysis of source codes written in C" -HOMEPAGE="https://frama-c.com" -SRC_URI="https://frama-c.com/download/${P}-${NAME}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64" - -IUSE="doc gtk +ocamlopt" -RESTRICT="strip" - -DEPEND=" - >=dev-lang/ocaml-3.12.1[ocamlopt?] - >=dev-ml/ocamlgraph-1.8.5[ocamlopt?] - dev-ml/zarith - dev-ml/yojson - sci-mathematics/coq - sci-mathematics/ltl2ba - sci-mathematics/alt-ergo - gtk? ( - >=x11-libs/gtksourceview-2.8:2.0 - >=gnome-base/libgnomecanvas-2.26 - >=dev-ml/lablgtk-2.14[sourceview,gnomecanvas(-),ocamlopt?] - )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${P}-${NAME}" - -src_prepare(){ - touch config_file || die - rm -f ocamlgraph.tar.gz || die - default - eautoreconf -} - -src_configure(){ - econf "$(use_enable gtk gui )" -} - -src_compile(){ - # dependencies can not be processed in parallel, - # this is the intended behavior. - emake depend - emake all top DESTDIR="/" - - use doc && emake doc -} - -src_install(){ - default - use doc && dodoc -r doc/doxygen/html/* -} diff --git a/sci-mathematics/frama-c/metadata.xml b/sci-mathematics/frama-c/metadata.xml deleted file mode 100644 index 6e6c849a1..000000000 --- a/sci-mathematics/frama-c/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -Frama-C is a suite of tools dedicated to the analysis of the source code -of software written in C. It gathers several static analysis techniques -in a single collaborative framework. The collaborative approach of -Frama-C allows static analyzers to build upon the results already -computed by other analyzers in the framework. Thanks to this approach, -Frama-C provides sophisticated tools, such as a slicer and dependency -analysis. -</longdescription> -</pkgmetadata> diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild index 7c5137bca..5819064e0 100644 --- a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild +++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild @@ -13,7 +13,7 @@ SRC_URI="https://downloads.sourceforge.net/jwordnet/${MY_P//_rc/-rc}.zip" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" COMMON_DEP=" dev-java/commons-logging:0 diff --git a/sci-physics/cernlib/Manifest b/sci-physics/cernlib/Manifest index d8be46729..b49fa508a 100644 --- a/sci-physics/cernlib/Manifest +++ b/sci-physics/cernlib/Manifest @@ -1,2 +1,4 @@ DIST cernlib-2023.10.31.0-free.tar.gz 39191038 BLAKE2B 941592a65f0c8d7d0c6c3907c96d8209568579dac455ed28657a5635677d73e6580f48667a641a6ca9dd296bf82a40f6a75c5fc801fcefb7f8e9101b4dcd3202 SHA512 d015f89942bab695444d37847a8138c3a8736ceeb6f4826c659553bf1ae5eab2a77b2871645a125ea189e62520856955070fbb3ed2d208d35f82ee8b8559d089 DIST cernlib-2023.10.31.0.tar.gz 39547453 BLAKE2B f37686e4a43b969a8cb604874b6181adf8529b9fc383ccd2e42fc369f92d4693ca8db682bc58638cb58e9941cf22551cfec26b33075e15fc6a0b3fab3dcf7d82 SHA512 9bc866d08e3bce2f571f9f4e21e34ca6c99467088d4dce4cbc9b6c62d8ee2b9018668fd66795996a5f6abb1082ac9559cf08bc7f5201421dbffcdd0db9459008 +DIST cernlib-cernlib-2024.06.12.0-free.tar.gz 37622299 BLAKE2B d4f53b9a64a0745519ef2a63f8ea950a08de8177d1e42d4e735cdd96ea57c4d5da91521cc6b9f865f8ebe886188976ddf2319c4b073aa7705d3e344baee691fb SHA512 d461173771b622516c028d82d853d458fa3c50b07b8094cbad1806bb80f5fa1eb98ad15555c8ddb8b2ac5d04eeceeeec69cffb0a1fc4cb99a5a0b2e48abce386 +DIST cernlib-cernlib-2024.06.12.0.tar.gz 37968830 BLAKE2B e6f391f56f72151cda5d07f838bc8d5b31afaa565cdd1128fbf89c2c6c3891d8cdf384eb1d2048572ddf35c08ceaff92c4eac04f182776d8aafb0813d289f994 SHA512 f015bbdc22ad8c1fc6a4eba39fe1f492fa827a81876174d09917bb9037f3bb7749d000425e00fd4436c18900d59a088af2520fc034fc06acf8c6c07b1ce29ca9 diff --git a/sci-physics/cernlib/cernlib-2024.06.12.0.ebuild b/sci-physics/cernlib/cernlib-2024.06.12.0.ebuild new file mode 100644 index 000000000..299399738 --- /dev/null +++ b/sci-physics/cernlib/cernlib-2024.06.12.0.ebuild @@ -0,0 +1,79 @@ +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" +inherit cmake fortran-2 flag-o-matic + +DESCRIPTION="CERN program library for High Energy Physics" +HOMEPAGE="https://cernlib.web.cern.ch/cernlib/" +SRC_URI=" + free? ( https://cernlib.web.cern.ch/download/$(ver_cut 1)_source/tar/${PN}-${P}-free.tar.gz ) + !free? ( https://cernlib.web.cern.ch/download/$(ver_cut 1)_source/tar/${PN}-${P}.tar.gz ) +" +S="${WORKDIR}/${PN}-${P}" +LICENSE=" + free? ( BSD LGPL-2+ GPL-1+ ) + !free? ( all-rights-reserved ) +" +SLOT="0" +KEYWORDS="~amd64" +# static-libs as default since otherwise test fail... +IUSE="+free +static-libs" +RESTRICT="mirror" + +RDEPEND=" + x11-libs/motif:0 + x11-libs/libXaw + x11-libs/libXau + virtual/lapack + dev-lang/cfortran + x11-libs/xbae + net-libs/libnsl + virtual/libcrypt:= +" +DEPEND="${RDEPEND}" +BDEPEND=" + virtual/pkgconfig +" + +PATCHES=( + "${FILESDIR}"/${PN}-2023.10.31.0-cfortran.patch + "${FILESDIR}"/${PN}-2023.10.31.0-man.patch +) + +src_unpack() { + default + if use free; then + mv ${PN}-${P}-free ${PN}-${P} || die + fi +} + +src_prepare() { + cmake_src_prepare + # cfortran.patch + # Remove cfortran.h since it is already installed from dev-lang/cfortran + # thereby we avoid collisions if e.g. sci-physics/root[fortran] is installed. + rm cfortran/cfortran.h || die +} + +src_configure() { + # docs follow rpm like spliting into packages cernlib, cernlib-devel, etc. + # we move them into a folder that agrees with gentoo doc structure. + sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die + # let upstream decide on optimization (-O0) since code is fragile + #filter-flags -O1 -O2 -O3 -Os -Oz -Og -Ofast + # with -O2 some tests fail + append-flags -O0 + local mycmakeargs=( + -DBUILD_SHARED_LIBS=$(usex static-libs OFF ON) + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + # man.patch + # The CMakeLists.txt already compresses the manual before install + # therefore we install it manually and avoid QA problems. + doman contrib/man/man1/*.1 + doman contrib/man/man8/*.8 +} diff --git a/sci-physics/cuttools/Manifest b/sci-physics/cuttools/Manifest index 590c6fd51..bd3e92f61 100644 --- a/sci-physics/cuttools/Manifest +++ b/sci-physics/cuttools/Manifest @@ -1 +1,2 @@ DIST cuttools_v1.8.2.tar.gz 962232 BLAKE2B aaec06cc892577c2e562e8ee07e9863dd42a8bbf878b4e2aee01d2bbf5bb27bb9e4f50ef3c3a66fe00e73cc527e23b0274f9c3df169779c5fb529c9ff5610cb0 SHA512 6f1af82caa2a86669271346fa4a4f1d13b39f1c1ee7562c5fc29f250276d59017722a55256358bd006819a442acd3198901b642039be9f6a78d3cf31fe0ca976 +DIST cuttools_v1.9.3.tar.gz 1007945 BLAKE2B 832643d9bda99cd920ad289c8edc0394ac335d75330a99a5f1b814d62957d54a7c42f0fc861f2cc9389a0c5d94ed2d67cec4698277f14dc5d3cb27ba8c65bc5f SHA512 6574f9928b3c131bdbf9343323d3a5a56e653c9ace37edd047a3e172aaf6ce4fab04eeb3013cc7eb448bd86937326d15f5effe5600a6a743b750a1eaccaa5db2 diff --git a/sci-physics/cuttools/cuttools-1.9.3-r1.ebuild b/sci-physics/cuttools/cuttools-1.9.3-r1.ebuild new file mode 100644 index 000000000..f27b5beb6 --- /dev/null +++ b/sci-physics/cuttools/cuttools-1.9.3-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Computing 1-loop amplitudes at the integrand level" +HOMEPAGE="https://www.ugr.es/~pittau/CutTools/" +SRC_URI="https://www.ugr.es/~pittau/CutTools/${PN}_v${PV}.tar.gz" +S="${WORKDIR}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="+dummy mpfun90" +DEPEND=" + sci-libs/mpfun90 + sci-physics/qcdloop + sci-physics/oneloop[dpkind,qpkind16,-qpkind,-tlevel,mpfun90?] +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-1.9.3-unbundle.patch" +) + +src_prepare() { + default + sed -i 's/^ALL =.*$/ALL = $(CTS)/' src/makefile || die + if use dummy ; then + cp "${FILESDIR}"/mpnumdummy.f90 src/cts/mpnumdummy.f90 || die + fi + if use dummy ; then + sed -i 's/CTS =/CTS = mpnumdummy.o/' src/makefile || die + fi + if use mpfun90; then + sed -i 's/PRECISION=.*$/PRECISION= MP/g' makefile || die + else + sed -i 's/PRECISION=.*$/PRECISION= QP/g' makefile || die + fi +} + +src_compile() { + if use mpfun90; then + emake -j1 FFLAGS="${FFLAGS} -I${ESYSROOT}/usr/include -fPIC -std=legacy" mp + else + emake -j1 FFLAGS="${FFLAGS} -I${ESYSROOT}/usr/include -fPIC -std=legacy" qp + fi + tc-export AR CXX + cd includects || die + ${AR} -x libcts.a || die + ${CXX} ${CXXFLAGS} ${LDFLAGS} -shared *.o -Wl,-soname,libcuttools.so -o lib${PN}.so || die +} + +src_install() { + cd includects || die + dolib.so lib${PN}.so + cd .. || die + mv includects ${PN} || die + rm ${PN}/*.a || die + rm ${PN}/*.so || die + rm ${PN}/*.o || die + doheader -r ${PN} +} diff --git a/sci-physics/cuttools/cuttools-1.9.3.ebuild b/sci-physics/cuttools/cuttools-1.9.3.ebuild new file mode 100644 index 000000000..03f84b63c --- /dev/null +++ b/sci-physics/cuttools/cuttools-1.9.3.ebuild @@ -0,0 +1,52 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Computing 1-loop amplitudes at the integrand level" +HOMEPAGE="https://www.ugr.es/~pittau/CutTools/" +SRC_URI="https://www.ugr.es/~pittau/CutTools/${PN}_v${PV}.tar.gz" +S="${WORKDIR}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="+dummy" +DEPEND=" + sci-physics/qcdloop + sci-physics/oneloop[dpkind,qpkind16,-qpkind,-tlevel] +" +RDEPEND="${DEPEND}" + +src_prepare() { + default + sed -i 's/^ALL =.*$/ALL = $(CTS)/' src/makefile || die + if use dummy ; then + cp "${FILESDIR}"/mpnumdummy.f90 src/cts/mpnumdummy.f90 || die + fi + if use dummy ; then + sed -i 's/CTS =/CTS = mpnumdummy.o/' src/makefile || die + fi +} + +src_compile() { + emake -j1 FFLAGS="${FFLAGS} -I${ESYSROOT}/usr/include -fPIC -std=legacy" + tc-export AR CXX + cd includects || die + ${AR} -x libcts.a || die + ${CXX} ${CXXFLAGS} -shared *.o -o lib${PN}.so || die +} + +src_install() { + cd includects || die + dolib.so lib${PN}.so + cd .. || die + mv includects ${PN} || die + rm ${PN}/*.a || die + rm ${PN}/*.so || die + rm ${PN}/*.o || die + doheader -r ${PN} +} diff --git a/sci-physics/cuttools/files/cuttools-1.9.3-unbundle.patch b/sci-physics/cuttools/files/cuttools-1.9.3-unbundle.patch new file mode 100644 index 000000000..e1fa1a9ea --- /dev/null +++ b/sci-physics/cuttools/files/cuttools-1.9.3-unbundle.patch @@ -0,0 +1,13 @@ +--- a/makefile 2024-11-20 15:50:21.960336440 +0100 ++++ b/makefile 2024-11-20 15:50:51.503676969 +0100 +@@ -51,10 +51,7 @@ + + $(BLD)/version.h: + -mkdir -p $(BLD) +- cp -p ./src/avh/* $(BLD)/ + cp -p ./src/cts/* $(BLD)/ +- cp -p ./src/mpfun90/* $(BLD)/ +- cp -p ./src/qcdloop/* $(BLD)/ + cp -p ./src/makefile $(BLD)/ + + tar: diff --git a/sci-physics/cuttools/metadata.xml b/sci-physics/cuttools/metadata.xml index ceddefcf0..8a4566dbf 100644 --- a/sci-physics/cuttools/metadata.xml +++ b/sci-physics/cuttools/metadata.xml @@ -17,6 +17,7 @@ the 2-, 3-, and 4-point tensor coefficient functions. </longdescription> <use> - <flag name="dummy">Add dummy module for OpenLoops</flag> + <flag name="dummy">Add dummy module for <pkg>sci-physics/openloops</pkg></flag> + <flag name="mpfun90">Use <pkg>sci-libs/mpfun90</pkg></flag> </use> </pkgmetadata> diff --git a/sci-physics/decaylanguage/Manifest b/sci-physics/decaylanguage/Manifest new file mode 100644 index 000000000..dbceca28a --- /dev/null +++ b/sci-physics/decaylanguage/Manifest @@ -0,0 +1 @@ +DIST decaylanguage-0.18.5.tar.gz 407293 BLAKE2B 83b205ed892e500e63124b27882c1d7dff7974cf3f5f63586bfac4544a7609daff2d9a254fa4d5f9a25e0bc629a1148b62a0ab727fef19e28fd8ea4bf8eb20d8 SHA512 7c9d9e613d4a095dfaef9b856cd62b8d9f9827c75ddd756c0fda2cf0b4f0a9e0d88391d6c7f90488d63c11ba00bda5da001dd3a10385d05f05a04a13901ac08e diff --git a/sci-physics/decaylanguage/decaylanguage-0.18.5.ebuild b/sci-physics/decaylanguage/decaylanguage-0.18.5.ebuild new file mode 100644 index 000000000..1dc5173ca --- /dev/null +++ b/sci-physics/decaylanguage/decaylanguage-0.18.5.ebuild @@ -0,0 +1,28 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi + +DESCRIPTION="DecayLanguage: describe, manipulate and convert particle decays" +HOMEPAGE="https://github.com/scikit-hep/decaylanguage" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] + >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}] + >=dev-python/lark-1.0.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.12[${PYTHON_USEDEP}] + >=dev-python/pandas-0.22[${PYTHON_USEDEP}] + >=sci-physics/particle-0.21.0[${PYTHON_USEDEP}] + >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] + >=dev-python/plumbum-1.7.0[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/sci-physics/decaylanguage/metadata.xml b/sci-physics/decaylanguage/metadata.xml new file mode 100644 index 000000000..87babf086 --- /dev/null +++ b/sci-physics/decaylanguage/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + DecayLanguage implements a language to describe and convert particle decays between digital representations, effectively making it possible to interoperate several fitting programs. Particular interest is given to programs dedicated to amplitude analyses. + </longdescription> + <upstream> + <remote-id type="pypi">decaylanguage</remote-id> + <remote-id type="github">scikit-hep/decaylanguage</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/hepstats/Manifest b/sci-physics/hepstats/Manifest new file mode 100644 index 000000000..7a8ff444f --- /dev/null +++ b/sci-physics/hepstats/Manifest @@ -0,0 +1 @@ +DIST hepstats-0.8.1.tar.gz 16653688 BLAKE2B ae7eef481b0e0c2caf6b928b2bdd2c71ec78c6075c13d784ef0cb018ebaefea8f9b3fe42f38aad1453c237d479a5a1184981982d7216550c104a80ac3fd95f68 SHA512 70f922ad0d5bd7f9ef7fc8dff66714ef89c323c2b3176bd979a93ad84c1f9861272a1744467e10b6ed3e32307f732e50dadb13f221ffbc3c63cfc01436a6b159 diff --git a/sci-physics/hepstats/hepstats-0.8.1.ebuild b/sci-physics/hepstats/hepstats-0.8.1.ebuild new file mode 100644 index 000000000..c14199882 --- /dev/null +++ b/sci-physics/hepstats/hepstats-0.8.1.ebuild @@ -0,0 +1,25 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Statistics tools and utilities." +HOMEPAGE=" + https://scikit-hep.org/hepstats/ + https://github.com/scikit-hep/hepstats +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="test" # needs zfit + +RDEPEND=" + dev-python/asdf[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/uhi[${PYTHON_USEDEP}] +" diff --git a/sci-physics/hepstats/metadata.xml b/sci-physics/hepstats/metadata.xml new file mode 100644 index 000000000..5f10b261f --- /dev/null +++ b/sci-physics/hepstats/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + hepstats is a library for statistical inference aiming to cover the needs High Energy Physics. It is part of the Scikit-HEP project. + </longdescription> + <upstream> + <remote-id type="pypi">hepstats</remote-id> + <remote-id type="github">scikit-hep/hepstats</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/hepunits/Manifest b/sci-physics/hepunits/Manifest index 9b6a3c900..4bd461fd8 100644 --- a/sci-physics/hepunits/Manifest +++ b/sci-physics/hepunits/Manifest @@ -1,2 +1,3 @@ DIST hepunits-2.3.2.tar.gz 13327 BLAKE2B 16986f4cf96eb927e5ae7268dc2975957846678bff0569fc5d5b9d36bb5dae251905283a07e5fcdd895b20982e1e2d32bce5048752d654ca085286e89b65837f SHA512 48d0a4939e19fc6f26b3bb5f8515d8e0d9d4cbed172c14ae30609c2039bdb77625dad8e1e628178481ee0f203d7d36cd2e0d3306f3b344fe14cd68827c4d9477 DIST hepunits-2.3.3.tar.gz 13491 BLAKE2B ec212be4e53e7ea5aa195852ea6ad4f3aac8e3eb49676e6bef76d525be861ecd4480821b248d746950b45affccd31bf23d5232aee13058bb48ec8d76c4f70a14 SHA512 7a29dd6220c1fbe610f15ef66f02e499d7e2ade8c39827e3229ae74035d127ca7805b9e32c3859c5af4b001725d21514fd81f0408d7f0dc76e9ee34aa66191e8 +DIST hepunits-2.3.5.tar.gz 13537 BLAKE2B 57a2e06e5619d6ff90f6a29f11359aa36418c959ee336e40b21ad2ce054cbb381ed75da2f4f973439a0306e37a01481b65374c3e24a1b9ba24063e34c5b71aad SHA512 de63fd24a87ca52b74e46ee74638663a8d83ee352aaf7b8bf84710681c3753a741f30ceb683f0d042c6806fb6b48b92fc80c861195ba9685fe9d60784bf94882 diff --git a/sci-physics/hepunits/hepunits-2.3.5.ebuild b/sci-physics/hepunits/hepunits-2.3.5.ebuild new file mode 100644 index 000000000..b2f76d1d1 --- /dev/null +++ b/sci-physics/hepunits/hepunits-2.3.5.ebuild @@ -0,0 +1,23 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="units and constants in the HEP system of units" +HOMEPAGE="https://github.com/scikit-hep/hepunits" + +LICENSE="BSD" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/hepunits" +else + inherit pypi + KEYWORDS="~amd64" +fi + + +BDEPEND="dev-python/hatch-vcs[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest diff --git a/sci-physics/mplhep-data/Manifest b/sci-physics/mplhep-data/Manifest new file mode 100644 index 000000000..d9fcba67e --- /dev/null +++ b/sci-physics/mplhep-data/Manifest @@ -0,0 +1 @@ +DIST mplhep_data-0.0.4.tar.gz 9128420 BLAKE2B f003e0fa551f2c491160d49e78fe07b8bd7411ddf180c9bb67c8f8d14db59ee44924e57fb1196257f22c25bc65d271ed35befee7f2c5c75417b226938179b2e6 SHA512 959f30c196e23b9fee0922343e121b07b4783c431d4179e14eb606a5615e3e0a773c718f6760480c2397ae39c72f1284a7e8ec74fe96146e2d63d310b1d5110c diff --git a/sci-physics/mplhep-data/metadata.xml b/sci-physics/mplhep-data/metadata.xml new file mode 100644 index 000000000..8f6639407 --- /dev/null +++ b/sci-physics/mplhep-data/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Sub-package to hold data (fonts) for the package mplhep. + Fonts distributed in this package have open licenses and can be redistributed. + </longdescription> + <upstream> + <remote-id type="pypi">mplhep-data</remote-id> + <remote-id type="github">scikit-hep/mplhep_data</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/mplhep-data/mplhep-data-0.0.4.ebuild b/sci-physics/mplhep-data/mplhep-data-0.0.4.ebuild new file mode 100644 index 000000000..bc1f3bcb5 --- /dev/null +++ b/sci-physics/mplhep-data/mplhep-data-0.0.4.ebuild @@ -0,0 +1,17 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Data/font package for mplhep." +HOMEPAGE=" + https://mplhep.readthedocs.io + https://github.com/scikit-hep/mplhep_data +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +distutils_enable_tests pytest diff --git a/sci-physics/mplhep/Manifest b/sci-physics/mplhep/Manifest new file mode 100644 index 000000000..3c168c854 --- /dev/null +++ b/sci-physics/mplhep/Manifest @@ -0,0 +1 @@ +DIST mplhep-0.3.55.tar.gz 1540698 BLAKE2B 67dfb17fb64cfb3bc5e22429efd80f232b7e819c2df88d323f6b22f42275ea1ef7ca562773107dd311c523d336bfa97548dc0ca29a0d01d8e644f2751db8425b SHA512 64b08564e39c7972d49a155b786691b614fa23e8c371df0ea5137a6edc6532e10fdcd35b94bc2bdc0ce22091bd2e4ba4c284d35d5b5bd9015c219c63aa9829fc diff --git a/sci-physics/mplhep/metadata.xml b/sci-physics/mplhep/metadata.xml new file mode 100644 index 000000000..e8b27c898 --- /dev/null +++ b/sci-physics/mplhep/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + A set of helpers for matplotlib to more easily produce plots typically needed in HEP as well as style them in way that's compatible with current collaboration requirements (ROOT-like plots for CMS, ATLAS, LHCb, ALICE). + </longdescription> + <upstream> + <remote-id type="pypi">mplhep</remote-id> + <remote-id type="github">scikit-hep/mplhep</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/mplhep/mplhep-0.3.55.ebuild b/sci-physics/mplhep/mplhep-0.3.55.ebuild new file mode 100644 index 000000000..ed147722d --- /dev/null +++ b/sci-physics/mplhep/mplhep-0.3.55.ebuild @@ -0,0 +1,47 @@ +EAPI=8 + +# wait for pytest-mpl before adding 3_13 +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi + +DESCRIPTION="Histogram plots using matplotlib and HEP compatible styling ROOT." +HOMEPAGE=" + https://mplhep.readthedocs.io + https://github.com/scikit-hep/mplhep +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/matplotlib-3.4[${PYTHON_USEDEP}] + >=dev-python/numpy-1.16.0[${PYTHON_USEDEP}] + sci-physics/mplhep-data[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + >=dev-python/uhi-0.2.0[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] + test? ( + dev-python/boost-histogram[${PYTHON_USEDEP}] + dev-python/hist[${PYTHON_USEDEP}] + dev-python/pytest-mock[${PYTHON_USEDEP}] + dev-python/pytest-mpl[${PYTHON_USEDEP}] + >=dev-python/pytest-6.0[${PYTHON_USEDEP}] + sci-physics/scikit-hep-testdata[${PYTHON_USEDEP}] + >=dev-python/scipy-1.1.0[${PYTHON_USEDEP}] + sci-physics/uproot[${PYTHON_USEDEP}] + ) +" + +# we do not want to care about old uproot4 +EPYTEST_DESELECT=( + 'tests/test_inputs.py::test_inputs_uproot' + 'tests/test_inputs.py::test_uproot_versions[png]' + 'tests/test_inputs.py::test_uproot_versions[pdf]' + 'tests/test_inputs.py::test_uproot_versions[svg]' +) + +distutils_enable_tests pytest diff --git a/sci-physics/oneloop/Manifest b/sci-physics/oneloop/Manifest index baeb504b0..a3069fc1f 100644 --- a/sci-physics/oneloop/Manifest +++ b/sci-physics/oneloop/Manifest @@ -1,2 +1,3 @@ DIST OneLOop-3.6.tgz 111734 BLAKE2B 61e1638b17ec356c29d40c2af187464d5499b9172c2858fc47486bd527f0f47e90eba4d836697176a1ecbb01b7344d774bc595c722a92abede143b3df90067d9 SHA512 979981ad5ecdf1f71424c7b8a8d12c7d30aa140c62295a4452d3e5c0e260d42b431c12efcc0d7f0ab55ee2f9af08d4ab204ada5860f65343b24552cbdd3f3cd2 DIST oneloop-3.6_p20200731.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220 +DIST oneloop-3.7.2.zip 707724 BLAKE2B c73ac11a3aa79d5b17bce6e412a7cf8c699f2b057e4aef7493264964ee0ff7239226ec2261ce36743e33adfb58a6a4ffd4b2bab2e5d8e6703ddae1da166671bd SHA512 862e8d75593568e2f156530a0b956093d0bc8d83c40e3f291e10d8e080c9240eee77f9c6ac4ec721738fc1f9ca19d40f7cbd4b685048d6a37f9c35ed8e35ac65 diff --git a/sci-physics/oneloop/files/oneloop-3.6_p20200731-mpfun90.patch b/sci-physics/oneloop/files/oneloop-3.6_p20200731-mpfun90.patch new file mode 100644 index 000000000..2ec32afbd --- /dev/null +++ b/sci-physics/oneloop/files/oneloop-3.6_p20200731-mpfun90.patch @@ -0,0 +1,14 @@ +--- a/src/avh_olo_boxc.f90 2024-11-21 17:54:03.444134677 +0100 ++++ b/src/avh_olo_boxc.f90 2024-11-21 17:55:47.760664651 +0100 +@@ -179,9 +179,9 @@ + aptmp(3) = areal((pp(5)-pp(3)-pp(4))**2-4*pp(3)*pp(4)) + aptmp(4) = areal((pp(6)-pp(4)-pp(1))**2-4*pp(4)*pp(1)) + icase = sort_4(aptmp) +- if (all(aptmp.ge.rZRO)) then ++ if ((aptmp(1).ge.rZRO) .and. (aptmp(2).ge.rZRO) .and. (aptmp(3).ge.rZRO) .and. (aptmp(4).ge.rZRO) ) then + icase = prmB(icase) +- elseif (all(aptmp.le.rZRO)) then ++ elseif ((aptmp(1).le.rZRO) .and. (aptmp(2).le.rZRO) .and.(aptmp(3).le.rZRO) .and.(aptmp(4).le.rZRO) ) then + errorcode = errorcode+1 + if (eunit.ge.0) write(eunit,*) 'ERROR in OneLOop boxc: ' & + ,'no positive lambda, returning 0' diff --git a/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild b/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild index e25833759..b022ed653 100644 --- a/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild +++ b/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild @@ -27,9 +27,9 @@ REQUIRED_USE=" " DEPEND=" - qpkind? ( sci-libs/qd ) - qpkind16? ( sci-libs/qd ) - arprec? ( sci-libs/arprec ) + qpkind? ( sci-libs/qd[fortran] ) + qpkind16? ( sci-libs/qd[fortran] ) + arprec? ( sci-libs/arprec[fortran] ) mpfun90? ( sci-libs/mpfun90 ) " RDEPEND="${DEPEND}" @@ -38,6 +38,10 @@ BDEPEND=" app-arch/unzip " +PATCHES=( + "${FILESDIR}"/${P}-mpfun90.patch +) + src_configure() { tc-export FC # set fortran @@ -92,7 +96,7 @@ src_compile() { ${EPYTHON} ./create.py source || die "Failed to compile" # create.py does not use soname, so we do it ourself #./create.py dynamic || die - ${FC} -O -fPIC -c avh_olo.f90 -o avh_olo.o || die + ${FC} ${FFLAGS} -O -fPIC -I"${ESYSROOT}"/usr/include -I"${ESYSROOT}"/usr/include/qd -c avh_olo.f90 -o avh_olo.o || die ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so *.o || die } diff --git a/sci-physics/oneloop/oneloop-3.7.2.ebuild b/sci-physics/oneloop/oneloop-3.7.2.ebuild new file mode 100644 index 000000000..0edbfc935 --- /dev/null +++ b/sci-physics/oneloop/oneloop-3.7.2.ebuild @@ -0,0 +1,104 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# python only needed for create.py to get binaries +PYTHON_COMPAT=( python3_{10..12} ) +inherit fortran-2 python-any-r1 toolchain-funcs + +DESCRIPTION="Library of one-loop scalar functions" +HOMEPAGE=" + https://helac-phegas.web.cern.ch/OneLOop.html + https://bitbucket.org/hameren/oneloop +" +SRC_URI="https://bitbucket.org/hameren/oneloop/get/v${PV}.zip -> ${P}.zip" +S="${WORKDIR}/hameren-oneloop-4b012d009f22" # bitbucket treats download by tag like sha + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+dpkind +qpkind qpkind16 dpkind16 qdcpp ddcpp mpfun90 arprec tlevel cppintf" +REQUIRED_USE=" + ?? ( dpkind dpkind16 ddcpp ) + ?? ( qpkind qpkind16 qdcpp ) + ?? ( arprec mpfun90 ) + || ( dpkind dpkind16 ddcpp qpkind qpkind16 qdcpp ) +" + +DEPEND=" + qpkind? ( sci-libs/qd[fortran] ) + qpkind16? ( sci-libs/qd[fortran] ) + arprec? ( sci-libs/arprec[fortran] ) + mpfun90? ( sci-libs/mpfun90 ) +" +RDEPEND="${DEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + app-arch/unzip +" + +src_configure() { + tc-export FC + # set fortran + sed -i "/FC = /s/gfortran/${FC}/g" Config || die + sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die + # Clear config + sed -i "s/^DPKIND.*$//g" Config || die + sed -i "s/^QPKIND.*$//g" Config || die + + if use dpkind ; then + echo "DPKIND = kind(1d0)" >> Config || die + fi + if use qpkind ; then + echo "QPKIND = kind(1d0)" >> Config || die + fi + if use dpkind16 ; then + echo "DPKIND = 16" >> Config || die + fi + if use qpkind16 ; then + echo "QPKIND = 16" >> Config || die + fi + + if use qdcpp ; then + echo "QDTYPE = qdcpp" >> Config || die + fi + if use ddcpp ; then + echo "DDTYPE = qdcpp" >> Config || die + fi + + if use mpfun90 ; then + echo "MPTYPE = mpfun90" >> Config || die + fi + if use arprec ; then + echo "MPTYPE = arprec" >> Config || die + fi + + if use tlevel ; then + sed -i "s/^.*TLEVEL.*$/TLEVEL = yes/" Config || die + else + sed -i "s/^.*TLEVEL.*$/TLEVEL = no/" Config || die + fi + if use cppintf ; then + sed -i "s/^.*CPPINTF.*$/CPPINTF = yes/" Config || die + else + sed -i "s/^.*CPPINTF.*$/CPPINTF = no/" Config || die + fi +} + +src_compile() { + tc-export FC + #emake -f make_cuttools + ${EPYTHON} ./create.py source || die "Failed to compile" + # create.py does not use soname, so we do it ourself + #./create.py dynamic || die + ${FC} ${FFLAGS} -O -fPIC -I"${ESYSROOT}"/usr/include -I"${ESYSROOT}"/usr/include/qd -c avh_olo.f90 -o avh_olo.o || die + ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so *.o || die +} + +src_install() { + #dolib.a libavh_olo.a + dolib.so libavh_olo.so + doheader *.mod + dosym libavh_olo.so /usr/$(get_libdir)/liboneloop.so +} diff --git a/sci-physics/particle/Manifest b/sci-physics/particle/Manifest index 2f92c548b..6d914f4f9 100644 --- a/sci-physics/particle/Manifest +++ b/sci-physics/particle/Manifest @@ -1,3 +1,4 @@ DIST particle-0.23.0.tar.gz 313512 BLAKE2B 33a0dc1cf612af8242b5080d0862f3b1e587254b46fa90f235cd6edba3919594c5077733600dfe88ad0959be889271c301324789abf0511a7fbe588942086877 SHA512 582c42beade0b28f28f3ee9f83f6d8cc75558f8a9aa5fbe3679c7aa68af40bd04f374741211d6f214bb828c24a017a89b541f780739a36d61d85a2fd5e00b530 DIST particle-0.23.1.tar.gz 313729 BLAKE2B fc35163955e065b350dfa0825612a64214baeb1f5be41404af259136e6689e23419891513c059ccdfbe2cbf5891596fccd0b0b7f283031bb3352600b5be43441 SHA512 1b4f4516357fd9725d9d5b0a481467896e93e23a8956b2ce321b9cac1d200a8ee8dd9cc1b22d940b4708f29abe3417988677ac685b78287abe10afafa79fb381 DIST particle-0.24.0.tar.gz 314302 BLAKE2B bbb2d52a80b4d9aafaf86a3cc1b28106253bf0edfe5a6127c03242a32973feaefeb32562063e5ff0438f5df946a905d03baa36c445093ce185d3be71c10e5135 SHA512 5a73079d9120ab509162189ba5992c615fc00e00d37a6556338130739bbf53fd5db01e973cb1b509ef7ce569021c0462ac77e5fcafe40df31e5cef0a89923a2a +DIST particle-0.25.2.tar.gz 316882 BLAKE2B def3a11f7396d211ce312473661c25c4ef75b2c7cc5f4394f8ac3c6551674db3ac7308e083401ad29c31d34073e8491da0b6daf26a553a9c64c5757c93c8ac02 SHA512 6ada0742baa82dd85adaf6b281f2573bd6fdaacff655588cec75a6e39a02d3720cb012623690745f2c1a2631da5f54b3882f3461aadd3fd5621f9e15af98807d diff --git a/sci-physics/particle/particle-0.25.2.ebuild b/sci-physics/particle/particle-0.25.2.ebuild new file mode 100644 index 000000000..e5e49ea91 --- /dev/null +++ b/sci-physics/particle/particle-0.25.2.ebuild @@ -0,0 +1,48 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="PDG particle data and identification codes" +HOMEPAGE="https://github.com/scikit-hep/particle" + +LICENSE="BSD" +SLOT="0" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/particle" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] + >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] + dev-python/deprecated[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/typing-extensions-4.5[${PYTHON_USEDEP}] + ' python3_{11..12}) + +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] + test? ( + dev-python/pandas[${PYTHON_USEDEP}] + >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +distutils_enable_tests pytest + +src_prepare() { + default + + sed -i -e 's:--benchmark-disable::' pyproject.toml || die +} + +python_test() { + epytest --ignore tests/particle/test_performance.py +} diff --git a/sci-physics/particle/particle-9999.ebuild b/sci-physics/particle/particle-9999.ebuild index 43f1e67ca..e5e49ea91 100644 --- a/sci-physics/particle/particle-9999.ebuild +++ b/sci-physics/particle/particle-9999.ebuild @@ -1,6 +1,6 @@ EAPI=8 -PYTHON_COMPAT=( python3_{11..12} ) +PYTHON_COMPAT=( python3_{11..13} ) DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 @@ -22,12 +22,16 @@ RDEPEND=" >=dev-python/attrs-19.2[${PYTHON_USEDEP}] >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] dev-python/deprecated[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/typing-extensions-4.5[${PYTHON_USEDEP}] + ' python3_{11..12}) + " -DEPEND="${RDEPEND}" BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] test? ( - >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] + >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] dev-python/tabulate[${PYTHON_USEDEP}] ) " diff --git a/sci-physics/pylhe/Manifest b/sci-physics/pylhe/Manifest index 11dbc6d26..cc103d71e 100644 --- a/sci-physics/pylhe/Manifest +++ b/sci-physics/pylhe/Manifest @@ -1,2 +1,3 @@ DIST pylhe-0.7.0.gh.tar.gz 140203 BLAKE2B 6c167b37bb6c978752de79586e4f655169b5134c6cd7637807e649323ebaca50d8a360b1ca32eeff2cc162efe5e13d7de92f72d5a9263a7b2c48a5b87b7b919c SHA512 1a338ab4e1c5dd1d8d80e4a03ad84eb59f19ebb151a4b1393b68ee6ecade920c88db6cb940d56bd1f238e833f59b266507ab678124ea49b4086fe05b7f9baa88 DIST pylhe-0.8.0.gh.tar.gz 144541 BLAKE2B 5c6a6511acd1adefad6bf3769fdb5ac2a528a8cc939bb1209d7fd4dc31eef9060d129c330b34e3cfc7b640c9b82f68f043e4604f3a535865240ceda0a33dd691 SHA512 6fc3c525cbb5f2ebe8678d1e03940fde8bdc837f1da6a667c70069584de476ea73c72e817cc84637e018ca7cf21e8bb0f7b2721fe54ef78a9b0eee7900ec400e +DIST pylhe-0.9.0.gh.tar.gz 146969 BLAKE2B 09d1395bfb1b802e8e9bdac2aef91757a54ae4a921d90be27604846b990a2fd68341a17acf113f53347f208773e57572b13490750d47f633abf95668e190cef1 SHA512 3adebbdfee40d25dc6e17d9c058375e0741474f54afd120219c12d2b04c84536202e95af70c5dc56335c424303b51cd449fdf832af5434e3ec2ce6b14abee36b diff --git a/sci-physics/pylhe/pylhe-0.9.0.ebuild b/sci-physics/pylhe/pylhe-0.9.0.ebuild new file mode 100644 index 000000000..7f52fa1d9 --- /dev/null +++ b/sci-physics/pylhe/pylhe-0.9.0.ebuild @@ -0,0 +1,34 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi + +DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files" +HOMEPAGE="https://github.com/scikit-hep/pylhe" +# pypi does not include tests +SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +# export is needed here! +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}] + >=sci-physics/particle-0.16[${PYTHON_USEDEP}] + >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}] + >=dev-python/vector-0.8.1[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] + test? ( + >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}] + ) +" +PATCHES=( + "${FILESDIR}/${PN}"-0.7.0-coverage.patch +) + +distutils_enable_tests pytest diff --git a/sci-physics/qcdloop/Manifest b/sci-physics/qcdloop/Manifest index 84ca31226..df26327e6 100644 --- a/sci-physics/qcdloop/Manifest +++ b/sci-physics/qcdloop/Manifest @@ -1,2 +1,2 @@ -DIST qcdloop-2.0.5.tar.gz 199141 BLAKE2B b16c193bd267b838535a572dd3b1cf50ac9af03b65347877b550bcbdcc9cfdd42f08e198732c513cff8298632ea65be82f2986701de75cee80cec2f9c30e3368 SHA512 9bfa3bad7a8c808b2db5eda32a755da4dadf67eba10845eb798d447fd47062bd40aa877929b60d95ec6b4e3b4a2cbba6384a3d1b13f92cfdec06e76177532c0f +DIST qcdloop-2.0.11.tar.gz 215694 BLAKE2B 91d3729d06c6efb4a554c3f4f4936872e1e2545de4730c93ef177e7cf7439f0017f29e7fdf1f5e61125c65102cf275711b7a784b5b364cf6ecfb578f99b7abad SHA512 34f84f38ab4214297f168504e4758b0c862bbfe160d0ac4060dcdb692d3474f0f330949fa7d4e834d5eb8d05899111e4e8c41bea6c193a1887200498f6f4fb4f DIST qcdloop-2.0.9.tar.gz 214697 BLAKE2B 19d426cc61b8a8f08fc56522b5a2d48c7fea7027225e1317c2e2908b8a87367ff69077bfe5508ee50ee585d8d0f68ae4c1fdad312b4cbc73ca4f3fd735fa94c9 SHA512 c8031dbee1c83d2bd0fcca0b1d94f18e7d07b77c247ca7a15cfec9bc402391e89036a64507c48e743eeecb3a19fe25d4e766ff13ede9f042d4d723adc8adb238 diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.11-quadmathpath.patch b/sci-physics/qcdloop/files/qcdloop-2.0.11-quadmathpath.patch new file mode 100644 index 000000000..86275d338 --- /dev/null +++ b/sci-physics/qcdloop/files/qcdloop-2.0.11-quadmathpath.patch @@ -0,0 +1,21 @@ +From 2c316f000e83e56419709fe64b7627d4541ef5aa Mon Sep 17 00:00:00 2001 +From: Alexander Puck Neuwirth <APN-Pucky@users.noreply.github.com> +Date: Fri, 15 Nov 2024 10:19:40 +0100 +Subject: [PATCH] Add one more QUADMATH lookup path + +--- + CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b8820da..64bd4c3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -75,6 +75,7 @@ find_library(QUADMATH_LIBRARY + /usr/local/lib /usr/x86_64-linux-gnu/* + /usr/lib/gcc/x86_64-linux-gnu/* + /usr/lib/gcc/x86_64-redhat-linux/* ++ /usr/lib/gcc/x86_64-pc-linux-gnu/* + "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}" + ) + diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild b/sci-physics/qcdloop/qcdloop-2.0.11.ebuild index 672957c56..f30ea4e12 100644 --- a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild +++ b/sci-physics/qcdloop/qcdloop-2.0.11.ebuild @@ -16,12 +16,29 @@ SLOT="0" KEYWORDS="~amd64" PATCHES=( - "${FILESDIR}"/${P}-cxx.patch + "${FILESDIR}"/${P}-quadmathpath.patch # https://github.com/scarrazza/qcdloop/pull/31 ) +src_prepare() { + cmake_src_prepare + + # gentoo libdir love + sed -i \ + -e '/DESTINATION/s/lib/lib${LIB_SUFFIX}/g' \ + CMakeLists.txt || die + sed -i \ + -e '/libdir.*/s/lib/lib${LIB_SUFFIX}/g' \ + CMakeLists.txt || die + + #sed -i \ + # -e '/qcdloop/s/SHARED/STATIC/g' \ + # CMakeLists.txt || die +} + src_configure() { local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX="${ESYSROOT}/usr/$(get_libdir)" + -DCMAKE_INSTALL_PREFIX="${ESYSROOT}"/usr + -DENABLE_FORTRAN_WRAPPER=ON ) cmake_src_configure } diff --git a/sci-physics/scikit-hep-testdata/Manifest b/sci-physics/scikit-hep-testdata/Manifest index 1051bc85d..7a8a88f93 100644 --- a/sci-physics/scikit-hep-testdata/Manifest +++ b/sci-physics/scikit-hep-testdata/Manifest @@ -1 +1,2 @@ DIST scikit-hep-testdata-0.4.39.gh.tar.gz 340561478 BLAKE2B 9d0fc60c8bd9c11b5cd786389489b095a5498c7e08c744106d3bacd3f203f4b186f50a5e1ef6cbdcb23fc5d975807277cc25397ea8049e2acccbbc06c53f65d2 SHA512 fe31302178b8148b0486fe314a9d40c7a4318e53113878769484cc79dd55e5adb977357a175ffad887a205e1ea3e99a4f5be192581cca61554ba2187daad3bd2 +DIST scikit-hep-testdata-0.4.48.gh.tar.gz 340986304 BLAKE2B 84f4f5d0c3a883bc182f5c547b4a91e8efef478046d16c2199647e6a66b7e7888e06ee8dd8643eaeb05e6106849d0e5215ef450a28b1a4bb6840a7a07c3475f0 SHA512 328f78f501656a684a935ff196d9d184d6d8a9a215d77ac70afbeba33a4716834343569a3b4cea870a4c4ba300a7291a1a07322369b6f0f4f2a57acbd081a34e diff --git a/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.48.ebuild b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.48.ebuild new file mode 100644 index 000000000..873bf6609 --- /dev/null +++ b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.48.ebuild @@ -0,0 +1,37 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A package to provide example files for testing and developing packages against." +HOMEPAGE="https://github.com/scikit-hep/scikit-hep-testdata" +# pypi does not include the data nor tests +SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +# Fails without this +S="${WORKDIR}/${P}" +# export is needed here! +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +# otherwise we don't install the data +export SKHEP_DATA=1 + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] +" + +EPYTEST_IGNORE=( + test_remote_files.py # we are net sandboxed +) +EPYTEST_DESELECT=( + tests/test_local_files.py::test_data_path_cached # https://github.com/scikit-hep/scikit-hep-testdata/issues/161 +) + +distutils_enable_tests pytest diff --git a/sci-physics/sherpa/Manifest b/sci-physics/sherpa/Manifest index 6913c06e1..f62adfe61 100644 --- a/sci-physics/sherpa/Manifest +++ b/sci-physics/sherpa/Manifest @@ -1 +1 @@ -DIST sherpa-v3.0.0beta1.tar.bz2 5836616 BLAKE2B 5347b6a83b80b148740c6fbf44c4d8f547a30eb85ba70ae4ad620cb3cca3f9d8255c45502969a83dca98d2825207a192ac3cae11dc3b914afdaaf9d65f2e6932 SHA512 9c34851193227a233c962b19cdff00302608d1695841d97de09d2bd40b84ccbd2a2a9f3c89e68e288bdf522e9b4c7fb8fc52032f199014898ac6bacbf628c8ce +DIST sherpa-v3.0.1.tar.bz2 5506595 BLAKE2B 9ab272ee14145b028d8c65860394ab981b468d0fd1e0b0c236e1cb6aed668fa6c559dcb13d076d3ec345be25eef50f7e8b0367aff72aadc46904c4719ed378a5 SHA512 4ec1b5704b8b936252121ea52c6c385cef99c003aaff93f685b1ae822012eb633e26949779005546ae6d9b7aaf2f6f5e833f9ef84334598449c951d8aa65c9c5 diff --git a/sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild b/sci-physics/sherpa/sherpa-3.0.1.ebuild index 79f0efccd..79f0efccd 100644 --- a/sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild +++ b/sci-physics/sherpa/sherpa-3.0.1.ebuild diff --git a/sci-physics/uproot/Manifest b/sci-physics/uproot/Manifest index bb52077be..e8cdc29cf 100644 --- a/sci-physics/uproot/Manifest +++ b/sci-physics/uproot/Manifest @@ -1 +1,2 @@ DIST uproot-5.3.1.tar.gz 919910 BLAKE2B 6c138a56ecabb08905e1edde8c776c3dfae6cca3213bbc3546e7241979052178e1c9718c1fcf298573669bcc4c004806cd54ab16050405038f76f3ef356fb184 SHA512 2525f372caa3b25e3a11b170ce981ce253a7b9ca1fdb2c04b6bb1093b166d206a28e9bc22ffa19dead76870f521cee44a812cbf41a087b34fb9a3bc52c210733 +DIST uproot-5.4.1.tar.gz 935958 BLAKE2B bde5d0d5e2cef6ff35cdaea49656d2d30052a9b2f5d576e61e2df82c0a438c192db69aaffb89bd1acdb96df7aa925197ecf52ea6068bdb30d8819615b358cdfe SHA512 dc0b9b9859b7564b2027bb3f013a0fac07c665dcf32c84a3981e3fc27254598126a4bcbfb77863b419e461dec1a8c37c1e3bc181b894ea52fc141144469aedc0 diff --git a/sci-physics/uproot/uproot-5.4.1.ebuild b/sci-physics/uproot/uproot-5.4.1.ebuild new file mode 100644 index 000000000..7d3b910d5 --- /dev/null +++ b/sci-physics/uproot/uproot-5.4.1.ebuild @@ -0,0 +1,30 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="ROOT I/O in pure Python and Numpy." +HOMEPAGE="https://github.com/scikit-hep/uproot" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +# way too many missing packages, isal, deflate, http servers etc +RESTRICT="test" + +RDEPEND=" + >=dev-python/awkward-2.4.6[${PYTHON_USEDEP}] + >=dev-python/cramjam-2.5.0[${PYTHON_USEDEP}] + dev-python/xxhash[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +# distutils_enable_tests pytest diff --git a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild index 2b608c0d0..549f29d7f 100644 --- a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild +++ b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild @@ -20,7 +20,7 @@ KEYWORDS="~amd64" RDEPEND=" >=dev-python/fslpy-3.9[${PYTHON_USEDEP}] - >=dev-python/jinja-2[${PYTHON_USEDEP}] + >=dev-python/jinja2-2[${PYTHON_USEDEP}] >=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}] >=dev-python/numpy-1.14[${PYTHON_USEDEP}] >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}] diff --git a/scripts/check-duplicates.sh b/scripts/check-duplicates.sh index 56c5bf1dd..974f7fb70 100755 --- a/scripts/check-duplicates.sh +++ b/scripts/check-duplicates.sh @@ -1,5 +1,5 @@ #! /usr/bin/env bash -# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org> +# Maintainer: Nowa Ammerlaan <nowa@gentoo.org> # Maintainer: Theo Anderson <telans@posteo.de> # # This checks for potential and exact package matches within an overlay & ::gentoo diff --git a/scripts/setup-master-gentoo.sh b/scripts/setup-master-gentoo.sh index 1a19d18df..c334a40eb 100755 --- a/scripts/setup-master-gentoo.sh +++ b/scripts/setup-master-gentoo.sh @@ -1,5 +1,5 @@ #! /usr/bin/env bash -# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org> +# Maintainer: Nowa Ammerlaan <nowa@gentoo.org> # # Fetch and setup the latest ::gentoo diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild index 0f7421835..9f483acb3 100644 --- a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild +++ b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild @@ -18,7 +18,7 @@ KEYWORDS="~amd64" RDEPEND=" dev-python/flake8[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] -dev-python/GitPython[${PYTHON_USEDEP}] +dev-python/gitpython[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/autopep8[${PYTHON_USEDEP}] dev-python/requests[${PYTHON_USEDEP}] diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild index c88f89f6f..9d76755e9 100644 --- a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild +++ b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild @@ -25,7 +25,7 @@ fi RDEPEND=" dev-python/flake8[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] - dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/gitpython[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/autopep8[${PYTHON_USEDEP}] dev-python/requests[${PYTHON_USEDEP}] diff --git a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild index c88f89f6f..9d76755e9 100644 --- a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild +++ b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild @@ -25,7 +25,7 @@ fi RDEPEND=" dev-python/flake8[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] - dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/gitpython[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/autopep8[${PYTHON_USEDEP}] dev-python/requests[${PYTHON_USEDEP}] diff --git a/sys-cluster/easybuild/easybuild-4.9.0.ebuild b/sys-cluster/easybuild/easybuild-4.9.0.ebuild index 9a38672aa..2cc80daff 100644 --- a/sys-cluster/easybuild/easybuild-4.9.0.ebuild +++ b/sys-cluster/easybuild/easybuild-4.9.0.ebuild @@ -36,5 +36,5 @@ pkg_postinst() { elog "ml use \$installpath/modules/all" elog "where --installpath is passed to eb" - optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython + optfeature "GitHub PR integration" dev-python/keyring dev-python/gitpython } diff --git a/sys-cluster/easybuild/easybuild-9999.ebuild b/sys-cluster/easybuild/easybuild-9999.ebuild index 9a38672aa..2cc80daff 100644 --- a/sys-cluster/easybuild/easybuild-9999.ebuild +++ b/sys-cluster/easybuild/easybuild-9999.ebuild @@ -36,5 +36,5 @@ pkg_postinst() { elog "ml use \$installpath/modules/all" elog "where --installpath is passed to eb" - optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython + optfeature "GitHub PR integration" dev-python/keyring dev-python/gitpython } |