diff options
164 files changed, 1327 insertions, 699 deletions
diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.3.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.4.ebuild index 9316ed64e..9316ed64e 100644 --- a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.3.ebuild +++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.4.ebuild diff --git a/dev-python/MagnetoResistance-tool/Manifest b/dev-python/MagnetoResistance-tool/Manifest index 3f0cac0f5..d320ea1e9 100644 --- a/dev-python/MagnetoResistance-tool/Manifest +++ b/dev-python/MagnetoResistance-tool/Manifest @@ -1 +1 @@ -DIST magnetoresistance_tool-0.0.3.tar.gz 21760 BLAKE2B 5549355f56791862ad0aa3496c790b322a54505b8a386e888b435cdf62a945ba1f3d347ce312205c5e472b7c874dc71b3c6d2bf915680ec479264d9d4806132e SHA512 d0034c7b09418765dfc519892af6eb3718511ddee1f4d6bebff2ad7deebaa4b79653b1afa4ff6b7724f37a21a39e354a754e133245355809ed07a724c188544a +DIST magnetoresistance_tool-0.0.4.tar.gz 21686 BLAKE2B 23c7ff69b2998889125f732be7348d2bfd9d70e007fc97c27741362e968ad55d14ced8523197de100384679230080e9b765d807f91ff528fcc856155f061f625 SHA512 ed083d3b051b46514c8aa6c626df19789506cea75d604e0a013bc76225622070274909c5c348b3a4998b10a353aa6746557cd7f9f74691e391046fdc5254eaca diff --git a/dev-python/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest index 84a9f541c..b81bf359c 100644 --- a/dev-python/awkward-cpp/Manifest +++ b/dev-python/awkward-cpp/Manifest @@ -1,3 +1,4 @@ -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 +DIST awkward_cpp-43.tar.gz 1592000 BLAKE2B 9a74c855d7f1af8f1a76c91396869d40d1dfc3257e6ce06eab2c9e2820e1b2ef00da4b3ddda1faa338af27c5d11abb9d82a1828d21f519b871866174728efa5a SHA512 67871fff1247dcd05b6bc2fafee0c7608cc3eae22b1e2be989f55a00bb72e7898890c41454cc7181116e79b1992f11aaf44c1f2747850302ea15ab5dfc318d59 +DIST awkward_cpp-44.tar.gz 1688272 BLAKE2B 0025fb79b91afd0ef6e414abc5c073687d29e2dd13b654f073c8d1abae49b985e17df40027fa528cf9f77d3f3b6e371f9d9a4516d03bf0396e4f1e42f8a837cf SHA512 9fc9850c04b0848bc2ed7252af7eee56c3dbd16b17cb2eb8892e1885d0c897990f42d20e516ca8177c1a8e841241fc0a816e6b7ea3feaa85dd8c81f854255f1d diff --git a/dev-python/awkward-cpp/awkward-cpp-28.ebuild b/dev-python/awkward-cpp/awkward-cpp-43.ebuild index 57634d120..2477e97b0 100644 --- a/dev-python/awkward-cpp/awkward-cpp-28.ebuild +++ b/dev-python/awkward-cpp/awkward-cpp-43.ebuild @@ -1,10 +1,10 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) CMAKE_MAKEFILE_GENERATOR="emake" DISTUTILS_USE_PEP517=scikit-build-core -PYPI_NO_NORMALIZE=1 +DISTUTILS_EXT=1 inherit pypi distutils-r1 @@ -20,7 +20,14 @@ DEPEND=" " RDEPEND="${DEPEND}" BDEPEND=" - >=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}] + >=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-cpp/awkward-cpp-44.ebuild b/dev-python/awkward-cpp/awkward-cpp-44.ebuild new file mode 100644 index 000000000..2477e97b0 --- /dev/null +++ b/dev-python/awkward-cpp/awkward-cpp-44.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 94246b3ae..e57e29363 100644 --- a/dev-python/awkward/Manifest +++ b/dev-python/awkward/Manifest @@ -1,3 +1,4 @@ -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 +DIST awkward-2.7.2.tar.gz 6153396 BLAKE2B a98084b9f7dec9dd584647e21f7629d88ea40cecab714b66fac99adf10ab89032cb9caf73d5699826666871f76ddae22e578f96b8caaf4450f717d67fb294554 SHA512 523ec35e587fdb0f3a3a2b39ab70df80e3e4e9e26a9e67cab144e0af79ce7b26e09dda6a5e2ea2c93175042711e5a98ec58674bb1d4c6d12931e07e1f463e0c9 +DIST awkward-2.7.3.tar.gz 6158785 BLAKE2B 4b656d2f04c842164376c1c181270ab50f975a3ac6239b9e4dc9286ea850c3c1b0ef6e97e2c1492638c832feaf5010d7b6639069aa7043454cd820ffcd84e020 SHA512 4368c185f4405ee1b0f81cf369f42643989a9ef791da172391c01fe780e014bf1751f01701f6fcc8189801eb4511227dda6bacf44f93633216bfddeee96c7770 diff --git a/dev-python/awkward/awkward-2.5.2.ebuild b/dev-python/awkward/awkward-2.7.2.ebuild index c11095214..7448dafe4 100644 --- a/dev-python/awkward/awkward-2.5.2.ebuild +++ b/dev-python/awkward/awkward-2.7.2.ebuild @@ -1,6 +1,6 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) DISTUTILS_USE_PEP517=hatchling export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} inherit distutils-r1 pypi @@ -13,8 +13,16 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND=" + ~dev-python/awkward-cpp-43[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/importlib-metadata-4.13.0[${PYTHON_USEDEP}] + ' python3_{10..11}) >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] - ~dev-python/awkward-cpp-28[${PYTHON_USEDEP}] + dev-python/packaging[${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=" @@ -24,7 +32,6 @@ BDEPEND=" test? ( dev-libs/apache-arrow[zstd] dev-python/pyarrow[${PYTHON_USEDEP}] - dev-python/fsspec[${PYTHON_USEDEP}] dev-python/numexpr[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] ) @@ -33,6 +40,8 @@ BDEPEND=" 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/awkward/awkward-2.7.3.ebuild b/dev-python/awkward/awkward-2.7.3.ebuild new file mode 100644 index 000000000..a0c9c6258 --- /dev/null +++ b/dev-python/awkward/awkward-2.7.3.ebuild @@ -0,0 +1,47 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=hatchling +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms." +HOMEPAGE="https://github.com/scikit-hep/awkward" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + ~dev-python/awkward-cpp-44[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/importlib-metadata-4.13.0[${PYTHON_USEDEP}] + ' python3_{10..11}) + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] + dev-python/packaging[${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/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild index cdbe1c92c..93251b74f 100644 --- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild +++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data" diff --git a/dev-python/colormath2/Manifest b/dev-python/colormath2/Manifest new file mode 100644 index 000000000..1574dbc5f --- /dev/null +++ b/dev-python/colormath2/Manifest @@ -0,0 +1 @@ +DIST colormath2-3.0.3.gh.tar.gz 76925 BLAKE2B 1f6abe88caa0e011f115e73c38e8a4cb00a0880751d841b5c54c4d63c2ff6cc613c4819d2a5ae4da0d6f87e70a7efaae86c8bcd85fc46edb54c1bd12dc0cd322 SHA512 7a026a5589ff20c79dc48a124f18ea522a9a78a8fcac86bc21fb794f50883b620eed865374b6d645586a7c4b922b8eaa568de1c542f8e0fc59da19dad6c2504d diff --git a/dev-python/colormath2/colormath2-3.0.3.ebuild b/dev-python/colormath2/colormath2-3.0.3.ebuild new file mode 100644 index 000000000..87ba7df9b --- /dev/null +++ b/dev-python/colormath2/colormath2-3.0.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) + +inherit distutils-r1 + +DESCRIPTION="Easy color scales and color conversion for Python" +HOMEPAGE="http://python-colormath.readthedocs.org/" +SRC_URI="https://github.com/bkmgit/python-colormath2/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +S="${WORKDIR}/python-colormath2-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/colormath2/metadata.xml b/dev-python/colormath2/metadata.xml new file mode 100644 index 000000000..94e5ba723 --- /dev/null +++ b/dev-python/colormath2/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">bkmgit/python-colormath2</remote-id> + <remote-id type="pypi">colormath2</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpath/dpath-2.2.0.ebuild b/dev-python/dpath/dpath-2.2.0.ebuild index a761ac4ea..ed502bfdb 100644 --- a/dev-python/dpath/dpath-2.2.0.ebuild +++ b/dev-python/dpath/dpath-2.2.0.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2024 Gentoo Foundation +# Copyright 1999-2025 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) inherit pypi distutils-r1 diff --git a/dev-python/expecttest/Manifest b/dev-python/expecttest/Manifest new file mode 100644 index 000000000..3b5dd1136 --- /dev/null +++ b/dev-python/expecttest/Manifest @@ -0,0 +1 @@ +DIST expecttest-0.3.0.gh.tar.gz 16627 BLAKE2B 02a8c41b996dc16d77c711cf023ee18cd97b6a2bb5bd13e80a6c195b18cf8b795a2b71d62b281d62da897d21b61a868f41af17746e849ec3c0f676c13bf7261a SHA512 3627255e9bfd2e2df9cff8026de8d3bf4997a50fc838c09b147b8becbf35f64b97da19e3606b239df4ee2e68018497aa44fef2f02d2cb980ec1d4e38e83f6d50 diff --git a/dev-python/expecttest/expecttest-0.3.0.ebuild b/dev-python/expecttest/expecttest-0.3.0.ebuild new file mode 100644 index 000000000..832ce943e --- /dev/null +++ b/dev-python/expecttest/expecttest-0.3.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=poetry +PYTHON_COMPAT=( python3_{11..12} ) + +inherit distutils-r1 + +DESCRIPTION="This library implements expect tests (also known as \"golden\" tests)" +HOMEPAGE="https://github.com/pytorch/expecttest" +SRC_URI=" + https://github.com/pytorch/expecttest/archive/v${PV}.tar.gz + -> ${P}.gh.tar.gz +" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/flake8-7.0.0[${PYTHON_USEDEP}] + >=dev-python/hypothesis-6.0.0[${PYTHON_USEDEP}] + >=dev-python/mypy-0.910.0[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/fslpy/fslpy-3.10.0.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild index bd802ddf4..52eae04d6 100644 --- a/dev-python/fslpy/fslpy-3.10.0.ebuild +++ b/dev-python/fslpy/fslpy-3.10.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 virtualx diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild index e0fe2f621..b188fe4dc 100644 --- a/dev-python/gffpandas/gffpandas-1.2.0.ebuild +++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/dev-python/heudiconv/heudiconv-0.13.0.ebuild b/dev-python/heudiconv/heudiconv-0.13.0.ebuild index 7f7db0b0e..f3a6721dd 100644 --- a/dev-python/heudiconv/heudiconv-0.13.0.ebuild +++ b/dev-python/heudiconv/heudiconv-0.13.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi DESCRIPTION="Flexible DICOM conversion to structured directory layouts" diff --git a/dev-python/heudiconv/heudiconv-1.0.0.ebuild b/dev-python/heudiconv/heudiconv-1.0.0.ebuild index 7f7db0b0e..f3a6721dd 100644 --- a/dev-python/heudiconv/heudiconv-1.0.0.ebuild +++ b/dev-python/heudiconv/heudiconv-1.0.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi DESCRIPTION="Flexible DICOM conversion to structured directory layouts" diff --git a/dev-python/histoprint/Manifest b/dev-python/histoprint/Manifest index c08f978b9..25424753e 100644 --- a/dev-python/histoprint/Manifest +++ b/dev-python/histoprint/Manifest @@ -1,2 +1,3 @@ DIST histoprint-2.4.0.tar.gz 359154 BLAKE2B f10abcff02875f1a27b31256c5daf00500e0177986052f3fc9b013a0be0f63daf58f9d9b7bf2b6b5510758e080a118c6ad07801b055019e7e226ee631da57154 SHA512 bbf7c90acb66c298588304a15c7ae3ec0536fb01a468b4aa7b944115e242a0ef3e2ef21c181e8476845f5d7611a944f43de0c9cf80faeab2ddbb8422432e2fa6 DIST histoprint-2.5.0.tar.gz 360296 BLAKE2B 37a40cfea760a08c0dcfc89d51eb526ee4bdb8c01cca18b2450f0f54ae61e051d4d8331227c05b6db85b7cf3553660e17dd68ed95d47021a874614de16958627 SHA512 e08063f58afbae570721ecbb91f772998d374b50d61d9622ef0c6ff96272711c49cb04d1882befba6ed54ce7933c9bb24fc5ac9fd83b16c43bdd96b135b9828e +DIST histoprint-2.6.0.tar.gz 353540 BLAKE2B 292722820f2c93c516aeac1c2426c4f6028d2a231c316545d203da3c05b977b4f4b1d66adf7095ab1022bea9969525581ed0ce45a1ed74a7d97cf6a8e5595d00 SHA512 1ae33b017b21afb87cf2043f8ccdf793fa87eef54843640562d254ad7491c9decac274ba328971c63eb34ddea8295e3377b482ea24bda2d2efd3dfe3f7b72121 diff --git a/dev-python/histoprint/histoprint-2.6.0.ebuild b/dev-python/histoprint/histoprint-2.6.0.ebuild new file mode 100644 index 000000000..3b889f55f --- /dev/null +++ b/dev-python/histoprint/histoprint-2.6.0.ebuild @@ -0,0 +1,27 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +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[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] + test? ( + >=dev-python/awkward-1[${PYTHON_USEDEP}] + >=sci-physics/uproot-4[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest new file mode 100644 index 000000000..3ebb51b60 --- /dev/null +++ b/dev-python/llvmlite/Manifest @@ -0,0 +1 @@ +DIST llvmlite-0.44.0.gh.tar.gz 285270 BLAKE2B 701ebb4835b333eeccaf9d74596d394006804b279e03bf8484a06d9333056a02d8128eb615cf1fb56205e387839e14ac91e927cfb7ae5547c57b6946abccc1d4 SHA512 4e4cb492957a853d63204ebed8a4ffb404f973ec373680897ea1ea3abc74caf36821d82c28de0fefce93767b59c55a5aff7bb136f9aa65b0bc4c41054815ec33 diff --git a/dev-python/llvmlite/llvmlite-0.44.0.ebuild b/dev-python/llvmlite/llvmlite-0.44.0.ebuild new file mode 100644 index 000000000..f81f98418 --- /dev/null +++ b/dev-python/llvmlite/llvmlite-0.44.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) +LLVM_COMPAT=( 16 ) +inherit cmake distutils-r1 llvm-r1 + +DESCRIPTION="Python wrapper around the llvm C++ library" +HOMEPAGE="https://github.com/numba/llvmlite" +SRC_URI="https://github.com/numba/llvmlite/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + sys-libs/zlib:0= + $(llvm_gen_dep 'llvm-core/llvm:${LLVM_SLOT}=') +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_compile() { + LLVM_CONFIG="$(get_llvm_prefix)/bin/llvm-config" distutils-r1_python_compile +} + +python_test() { + LD_LIBRARY_PATH="$(get_llvm_prefix)/$(get_libdir)" \ + "${EPYTHON}" runtests.py -v || die "tests failed for ${EPYTHON}" +} + +python_install() { + distutils-r1_python_install + dosym "$(get_llvm_prefix)/$(get_libdir)/libLLVM-${LLVM_SLOT}.so" \ + "$(python_get_sitedir)/llvmlite/binding/libLLVM-${LLVM_SLOT}.so" +} diff --git a/dev-python/llvmlite/metadata.xml b/dev-python/llvmlite/metadata.xml new file mode 100644 index 000000000..22f9bb536 --- /dev/null +++ b/dev-python/llvmlite/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">numba/llvmlite</remote-id> + <remote-id type="pypi">llvmlite</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest new file mode 100644 index 000000000..45d01ba01 --- /dev/null +++ b/dev-python/numba/Manifest @@ -0,0 +1 @@ +DIST numba-0.61.0.gh.tar.gz 2884884 BLAKE2B fecfc6ce22ea2ff58d393410d1bdee6cb39101126e249ccb91bbddc62566667845ed8374450a05f9a761d7c2034de855e2e89668ef1f7602587e3250aa747e17 SHA512 74c12099965b8f2f4782c1fb55383a5867af852833647c6bd772b3f281ad04fcf4622ee9f3afd4535735ee99f16c3ddddfb826184cee8112e33e533b94d8ccef diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml new file mode 100644 index 000000000..aa4ad588e --- /dev/null +++ b/dev-python/numba/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">numba/numba</remote-id> + <remote-id type="pypi">numba</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/numba/numba-0.61.0.ebuild b/dev-python/numba/numba-0.61.0.ebuild new file mode 100644 index 000000000..28d54fb6b --- /dev/null +++ b/dev-python/numba/numba-0.61.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) +inherit distutils-r1 flag-o-matic + +DESCRIPTION="NumPy aware dynamic Python compiler using LLVM" +HOMEPAGE="https://numba.pydata.org/" +SRC_URI="https://github.com/numba/numba/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="debug" + +RDEPEND=" + dev-python/llvmlite[$PYTHON_USEDEP] + <=dev-python/numpy-2.1[$PYTHON_USEDEP] +" +DEPEND="${RDEPEND}" + +RESTRICT="test" # tests need to be run from "${BUILD_DIR}/build/lib.linux-x86_64-cpython-312" +distutils_enable_tests pytest + +python_prepare_all() { + filter-lto + distutils-r1_python_prepare_all +} diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest index b14e3311b..611e6d1be 100644 --- a/dev-python/numcodecs/Manifest +++ b/dev-python/numcodecs/Manifest @@ -1,2 +1 @@ -DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2 -DIST numcodecs-0.12.1.tar.gz 4091415 BLAKE2B d7fa8cc549495c7c54130898f2047eb409559541b299640fb34a2332d874049afa64d5c14151426b24a1ab04c0e0444245477aa26f9336ce3ba7aefc8043abcf SHA512 716a1144c17b08cc1737bd429517b5434a7e5dbc9626ed613ca9ab4f9cda356ed97cb4ef0e2bba747a7681dc5b43818cb07c6db7f5537b4910790f6ea23c696c +DIST numcodecs-0.13.0.tar.gz 5922216 BLAKE2B fbbdce2fdc2d3ae16afa7770c04330f21061436de3f1e09730d481e5bcfd3a2987717e7139049184824c690ff31e701b834a3757dc1b2e7ad62211795618664c SHA512 3a5f5d00374ff7e5efcac35b520ef92ace23f766983ac23e94cf69be0c2583e08849bdebd7f477b758692636ccbddf19cddd6c2462c29bec22f0c15f7341766c diff --git a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild deleted file mode 100644 index 3d20684ba..000000000 --- a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 pypi - -DESCRIPTION="Data storage buffer compression and transformation codecs" -HOMEPAGE="https://github.com/zarr-developers/numcodecs" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -RDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/entrypoints[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/py-cpuinfo[${PYTHON_USEDEP}] -" -DEPEND=" - test? ( - ${RDEPEND} - dev-python/entrypoints[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_compile() { - local -x DISABLE_NUMCODECS_AVX2=1 - local -x DISABLE_NUMCODECS_SSE2=1 - distutils-r1_python_compile -} - -python_test() { - cd "${T}" || die - epytest --pyargs numcodecs -} diff --git a/dev-python/numcodecs/numcodecs-0.11.0.ebuild b/dev-python/numcodecs/numcodecs-0.13.0.ebuild index 500a52b89..758939bd2 100644 --- a/dev-python/numcodecs/numcodecs-0.11.0.ebuild +++ b/dev-python/numcodecs/numcodecs-0.13.0.ebuild @@ -1,11 +1,13 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_EXT=1 DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 pypi + +inherit distutils-r1 pypi flag-o-matic DESCRIPTION="Data storage buffer compression and transformation codecs" HOMEPAGE="https://github.com/zarr-developers/numcodecs" @@ -22,28 +24,26 @@ RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/py-cpuinfo[${PYTHON_USEDEP}] " - DEPEND=" test? ( - ${RDEPEND} dev-python/entrypoints[${PYTHON_USEDEP}] ) " -PATCHES=( - "${FILESDIR}/${P}-nocov.patch" -) - -# Reported upstream: -# https://github.com/zarr-developers/numcodecs/issues/436 EPYTEST_DESELECT=( - tests/test_json.py::test_non_numpy_inputs - tests/test_msgpacks.py::test_non_numpy_inputs + # python segfault + tests/test_blosc.py::test_encode_decode + tests/test_blosc.py::test_partial_decode + tests/test_blosc.py::test_compress_metainfo + tests/test_blosc.py::test_compress_autoshuffle + tests/test_blosc.py::test_multiprocessing + tests/test_blosc.py::test_backwards_compatibility + tests/test_blosc.py::test_max_buffer_size ) distutils_enable_tests pytest -python_test() { - cd "${T}" || die - epytest --pyargs numcodecs +python_prepare_all() { + filter-lto + distutils-r1_python_prepare_all } diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest index ec977e410..2a5423f7e 100644 --- a/dev-python/plac/Manifest +++ b/dev-python/plac/Manifest @@ -1 +1 @@ -DIST plac-1.4.3.tar.gz 38984 BLAKE2B 39ede8377710b1cd3a53d3d1fd2285c2cdb3b9f79c9c11f3b9888a2dc954433488799a4ee31cdcf9b17d15214cc390c424f13504a862136e093842f3a546e416 SHA512 2222657bc524307e342ff21cfbbf0278ac618f2b9db8788362325ad955e5ca5181cf9770564bdef9bbb6acbb52750771593311c0d32aa85f343f51a7b28d0caa +DIST plac-1.4.3.gh.tar.gz 63451 BLAKE2B 32e2d88bc580c6f886982bd673142e34e2203d3eabdb828d84397e842e4fa00a2bb1e02c73134f58c3a5d8edb83496ccd6a7f7791b6a16c494d44c90dced69b0 SHA512 1db76a7e4dd3e965f1217ee88c8558d528a0f77bab463e49a2ff1e96c03477fe265b8c55f20fb846c0b8045db982f24741393deb5d8582d3cb940324830c0efe diff --git a/dev-python/plac/plac-1.4.3.ebuild b/dev-python/plac/plac-1.4.3.ebuild index 8f2be2238..6e997412f 100644 --- a/dev-python/plac/plac-1.4.3.ebuild +++ b/dev-python/plac/plac-1.4.3.ebuild @@ -1,23 +1,19 @@ -# Copyright 1999-2024 Gentoo Foundation +# Copyright 1999-2025 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( pypy3 python3_{10..12} ) +PYTHON_COMPAT=( pypy3 python3_{10..13} ) inherit pypi distutils-r1 DESCRIPTION="Parsing the Command Line the Easy Way" HOMEPAGE="https://pypi.org/project/plac/" +SRC_URI="https://github.com/ialbert/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -EPYTEST_DESELECT=( - # Missing index.rst - doc/test_plac.py::test_doctest -) - distutils_enable_tests pytest diff --git a/dev-python/py2bit/Manifest b/dev-python/py2bit/Manifest index afd79913c..aed695a38 100644 --- a/dev-python/py2bit/Manifest +++ b/dev-python/py2bit/Manifest @@ -1,2 +1 @@ -DIST py2bit-0.3.0.tar.gz 16059 BLAKE2B b66621b91db8c0370933d1531c25e3e9d2cf34cc453e085f5acf92175f16bc4a87368d5b97f4ad1f6b0aeb715ac91e02f752f27d660e733cbcf9788f7fb9ff0b SHA512 914ee4490605a005c5c83e914e5d469dcb860a76cf52dd2337086954d9a37f21addca7a581eb8ff612b77f7969334057de4ab5d5ce2c6e15fb88e56abd36e193 -DIST py2bit-0.3.1.tar.gz 16771 BLAKE2B 044f6c638bc001694a5ee1c0924bebfeccd26616dbeb7f7a692df71dde6937851227d8a4263c9f0c4e44a34d53900340bdf95818aa2c9c699d26b36a75e64158 SHA512 e9cb16e6f617f5f9c4a324abc949562da8aa0b4792e7011148103462ec49f3f38ab29a2c1821a374ec99726c292de2888de506966510a10211ee24295e9f775c +DIST py2bit-0.3.3.gh.tar.gz 17538 BLAKE2B b12675421e3a5acadfa299656630c2eb1dfd6ffa11e9eb0cc648a257dc94cb48da62980f1c9cc89225413af803c5856773da39792065e53f7c2a5f8dbc9accbf SHA512 f1e3752114d0f775c628d05a07074d26f630a4a20bad9752815347d72099611702c361f7b9af081dba9bf557bc21ccf8369105a0d718ad9c2c284f7a5f0fcc46 diff --git a/dev-python/py2bit/py2bit-0.3.0.ebuild b/dev-python/py2bit/py2bit-0.3.0.ebuild deleted file mode 100644 index 4b1c29658..000000000 --- a/dev-python/py2bit/py2bit-0.3.0.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Python library for accessing 2bit files" -HOMEPAGE="https://github.com/dpryan79/py2bit" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/py2bit" -else - SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-libs/lib2bit" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest - -python_test() { - epytest "py2bitTest/test.py" -} diff --git a/dev-python/py2bit/py2bit-0.3.1.ebuild b/dev-python/py2bit/py2bit-0.3.1.ebuild deleted file mode 100644 index 4b1c29658..000000000 --- a/dev-python/py2bit/py2bit-0.3.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Python library for accessing 2bit files" -HOMEPAGE="https://github.com/dpryan79/py2bit" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/py2bit" -else - SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-libs/lib2bit" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest - -python_test() { - epytest "py2bitTest/test.py" -} diff --git a/dev-python/py2bit/py2bit-0.3.3.ebuild b/dev-python/py2bit/py2bit-0.3.3.ebuild new file mode 100644 index 000000000..96177adeb --- /dev/null +++ b/dev-python/py2bit/py2bit-0.3.3.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=setuptools +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} + +inherit distutils-r1 + +DESCRIPTION="Python library for accessing 2bit files" +HOMEPAGE="https://github.com/deeptools/py2bit" +SRC_URI="https://github.com/deeptools/py2bit/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="sci-libs/lib2bit" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest py2bitTest/test.py +} diff --git a/dev-python/py2bit/py2bit-9999.ebuild b/dev-python/py2bit/py2bit-9999.ebuild deleted file mode 100644 index 4b1c29658..000000000 --- a/dev-python/py2bit/py2bit-9999.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Python library for accessing 2bit files" -HOMEPAGE="https://github.com/dpryan79/py2bit" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/py2bit" -else - SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-libs/lib2bit" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest - -python_test() { - epytest "py2bitTest/test.py" -} diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest index b27a43a9b..4871f8402 100644 --- a/dev-python/pyBigWig/Manifest +++ b/dev-python/pyBigWig/Manifest @@ -1,2 +1 @@ -DIST pyBigWig-0.3.17.tar.gz 65490 BLAKE2B 5ae3ad5792357ae36082022aa34548fb7ad105909eccc27305064f8f948714f462e1d239c3af7f9b75b84f5658bcb03231d7d1d3b0ebc8025c96d2e7835f1bfb SHA512 b52fec3a85984708660dd454f5569900a5cce7804d02e719bddbdc7ed2f9f4ab1131e55b0a01ae977b18bb0bbd079e13ec887d5df108d8abfebdd04ad56e503f -DIST pyBigWig-0.3.18.tar.gz 66478 BLAKE2B 0d2e20bed5f59fb8c79026f453c4d5c3e4f9b663e96614b3ef8cbb939357c8895edfa92184da018efdd40e14bbf357f13cc32f898d9cf89419382e7be89b01c8 SHA512 e782f059a8c47043498b2c4b1c0b63f3a1863d03f641c469995536bded220714c61fe0a2f1dbe5841152fe54d0d43b544e14ec4999447d4d808e01b452fa5e88 +DIST pyBigWig-0.3.24.tar.gz 67280 BLAKE2B 3c6b0129eaf82d848d6bca9c78966cb106b53b50ee9551f2bef88e775f0b97d80248a6f1cd11a5f96819c836a36078d107d57683dd37a63b2e0ad49e5d52af77 SHA512 ff08fc987e9320b6c33d57da92ec8f5dcede2fbbafb0cb6a03eb0537da7312d8b7a4aabd30c7ae1cc7e6c9554b7d08654444b1141ee1df944e6d6de957e3d6c0 diff --git a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild deleted file mode 100644 index acaca2306..000000000 --- a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="quick access to and creation of bigWig files" -HOMEPAGE="https://github.com/dpryan79/pyBigWig" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig" -else - SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-biology/libBigWig" -RDEPEND="${DEPEND}" diff --git a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild deleted file mode 100644 index acaca2306..000000000 --- a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="quick access to and creation of bigWig files" -HOMEPAGE="https://github.com/dpryan79/pyBigWig" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig" -else - SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-biology/libBigWig" -RDEPEND="${DEPEND}" diff --git a/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild new file mode 100644 index 000000000..2b5bd449d --- /dev/null +++ b/dev-python/pyBigWig/pyBigWig-0.3.24.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 + +DESCRIPTION="quick access to and creation of bigWig files" +HOMEPAGE="https://github.com/deeptools/pyBigWig" +SRC_URI="https://github.com/deeptools/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +REPEND=" + sys-libs/zlib:0= + sci-biology/libBigWig +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_test() { + local pysite="${BUILD_DIR}"/install/${EPREFIX}/usr/lib/${EPYTHON}/site-packages + ln -s "${S}"/pyBigWigTest/test.bigBed "${pysite}"/pyBigWigTest || die + ln -s "${S}"/pyBigWigTest/test.bw "${pysite}"/pyBigWigTest || die + epytest pyBigWigTest/test.py +} diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild deleted file mode 100644 index acaca2306..000000000 --- a/dev-python/pyBigWig/pyBigWig-9999.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="quick access to and creation of bigWig files" -HOMEPAGE="https://github.com/dpryan79/pyBigWig" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig" -else - SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" - -DEPEND="sci-biology/libBigWig" -RDEPEND="${DEPEND}" diff --git a/dev-python/pyaml-env/Manifest b/dev-python/pyaml-env/Manifest index 06b54d70e..6b07301c0 100644 --- a/dev-python/pyaml-env/Manifest +++ b/dev-python/pyaml-env/Manifest @@ -1 +1 @@ -DIST pyaml_env-1.2.1.tar.gz 12759 BLAKE2B 5a037ccefaaa3c60ce393dae5847777eb43745549a31b763ef2f50feb3a6e216ef793f9501df9e80cb381f78782e54b888ee4b043736dc05bcd01619d839ff86 SHA512 1ef873fa66660e4949dc1064260405244c8b3a2ee4391831a0a52be30e503e99d0b80b087c78db78683e9fe2fc1fd73f2e30c1eacc4c94a1394000d8526c9d68 +DIST pyaml-env-1.2.2.gh.tar.gz 13638 BLAKE2B c49f8c6af5fa6b52ad71a8abbd9f272134569ff74601da467521ad57018b26c40093675b4e6b31597195511d231acb15cdcdd92c5471bb66ce6f20ca5c82acc3 SHA512 c495331a07adbada8c93ebfc6a65767643635b28cb6137b5d44d62395b276ce010efa655ed7dd8fa2ce66717eb83a350668dd1b4d92b3a29172fc83f308c3fcb diff --git a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild b/dev-python/pyaml-env/pyaml-env-1.2.2.ebuild index a5169040a..6e8678d01 100644 --- a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild +++ b/dev-python/pyaml-env/pyaml-env-1.2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,10 +6,12 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools PYTHON_COMPAT=( python3_{10..12} ) -inherit pypi distutils-r1 +inherit distutils-r1 DESCRIPTION="Parse YAML configuration with environment variables in Python" HOMEPAGE="https://pypi.org/project/pyaml-env/" +SRC_URI="https://github.com/mkaranasou/pyaml_env/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/pyaml_env-${PV}" LICENSE="MIT" SLOT="0" @@ -17,6 +19,4 @@ KEYWORDS="~amd64 ~amd64-linux" RDEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]" -# tests not included in pypi tarball -RESTRICT="test" -#distutils_enable_tests pytest +distutils_enable_tests pytest diff --git a/dev-python/pybedtools/Manifest b/dev-python/pybedtools/Manifest index 7db62a4c4..b87b0f9e6 100644 --- a/dev-python/pybedtools/Manifest +++ b/dev-python/pybedtools/Manifest @@ -1 +1 @@ -DIST pybedtools-0.10.0.tar.gz 12497095 BLAKE2B d9fb44bd3afcb8748e0cadbe0c4d55c7325911331d0719b79bd04eff264bd6299d407dee7f511bc05a7e12dd46e92a9c25ce0607b8926e6542e4dd652cc9d23f SHA512 cec04464fcfaa12bb660f223d6f656a30ac5822ea9053455dbc5717d2afbc998db9fd4b7424d8458445450a6ce5aafb65463fa1274b2691b26bfda7fe84bef56 +DIST pybedtools-0.11.0.tar.gz 12498434 BLAKE2B c1157e172e94b565234c592e0c8379e46cb7ed4b5659bc6998dda10ee9654d262c60faf0214c5f90236f1c536cd48bc94f78ed6661612c7d84832831c0947861 SHA512 c06eaae64a9d175e434881cfcf084b4a20c488809c7091599b2eaa5113a6c84b59b89f9d3503e3f606856437c77d30d9364271d660bc675bf4c54ffa20bb5368 diff --git a/dev-python/pybedtools/pybedtools-0.10.0.ebuild b/dev-python/pybedtools/pybedtools-0.11.0.ebuild index ae51c24ce..70012c4eb 100644 --- a/dev-python/pybedtools/pybedtools-0.10.0.ebuild +++ b/dev-python/pybedtools/pybedtools-0.11.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,7 +6,7 @@ EAPI=8 PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517=setuptools DISTUTILS_EXT=1 -inherit distutils-r1 +inherit distutils-r1 flag-o-matic DESCRIPTION="Use BED and GFF files from python using BEDtools" HOMEPAGE="https://daler.github.io/pybedtools" @@ -31,6 +31,11 @@ RDEPEND=" #distutils_enable_sphinx docs/source distutils_enable_tests pytest +python_compile() { + filter-lto + distutils-r1_python_compile +} + python_test() { # Requires network local EPYTEST_DESELECT=( diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild index 93efdd361..988cd887b 100644 --- a/dev-python/reproject/reproject-0.8.ebuild +++ b/dev-python/reproject/reproject-0.8.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi DESCRIPTION="Reproject astronomical images" diff --git a/dev-python/rich-click/Manifest b/dev-python/rich-click/Manifest index 4971bebd8..80a6d1979 100644 --- a/dev-python/rich-click/Manifest +++ b/dev-python/rich-click/Manifest @@ -1 +1 @@ -DIST rich_click-1.8.3.tar.gz 38209 BLAKE2B c87386d729585a579ce881f83737427a250a0c56cf7eda832be308de121590d7af17f7672a78aa3f3dc8834720b858ee1f9ac65e1ddf031acac16a791f91f0db SHA512 2410b7e4d69fa79e41f2394fecf1f4809e9eceaf2d463c91914bf27603842b8ba9550c6aaa90812dd725ce0a74f61fb69b35b0b1ccd87b5412b7bd727eeed74c +DIST rich-click-1.8.6.gh.tar.gz 8140359 BLAKE2B ab5ddbad68cae208797a7893fdd8092035d8b4a428926fd55ffb01ebdd1ea83a510c1bf0622f01fd9f84da791425d1ac5647febc16bc55781c28d3fac96c70d3 SHA512 922c0c133104cb1aba9aca439aa81835202bf055c0b652339f3eb0c66bf71e7cb201881e03eb585f3eb1c0dedf1aa943df18917ce86f0d8d607ea7f9208ab0e2 diff --git a/dev-python/rich-click/rich-click-1.8.3.ebuild b/dev-python/rich-click/rich-click-1.8.6.ebuild index 5394cb4e3..033c0f8d6 100644 --- a/dev-python/rich-click/rich-click-1.8.3.ebuild +++ b/dev-python/rich-click/rich-click-1.8.6.ebuild @@ -1,25 +1,26 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) -inherit pypi distutils-r1 +inherit distutils-r1 DESCRIPTION="Format click help output nicely with rich" HOMEPAGE="https://pypi.org/project/rich-click/" +SRC_URI="https://github.com/ewels/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~amd64-linux" -RDEPEND="dev-python/click[${PYTHON_USEDEP}] +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] dev-python/importlib-metadata[${PYTHON_USEDEP}] dev-python/rich[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}]" + dev-python/typing-extensions[${PYTHON_USEDEP}] +" -RESTRICT="test" -# ModuleNotFoundError: No module named 'tests.conftest' -#distutils_enable_tests pytest +distutils_enable_tests pytest diff --git a/dev-python/snakemake-interface-common/Manifest b/dev-python/snakemake-interface-common/Manifest index f83a8f47e..640723c2d 100644 --- a/dev-python/snakemake-interface-common/Manifest +++ b/dev-python/snakemake-interface-common/Manifest @@ -1 +1 @@ -DIST snakemake_interface_common-1.17.2.tar.gz 9928 BLAKE2B 91be90640adb5f19fb97185ef84954cececd9e26e9c64f59b4ff014eca257575c5d5501ea7a8d74d9de2bb3280e88be500d1a2df2ec3296f2ecd30acbda27c87 SHA512 08d1688f70863825e76832250ee9da0be3a8baae9e67eb9bafaab30d862fe33fb9508eb4571f39322579699a4cd98d8878854ad9a94615e3b73255d18fe38c14 +DIST snakemake_interface_common-1.17.4.tar.gz 9897 BLAKE2B d81df168b25f482a02e132a7d2ac34d348dba136509f1ed4f5196fc08454e713c86829e8d48da03e23f472a42a54408022a980508b7fd646c994bd25a9f2f56c SHA512 8af34099f5db0d6c49af2e4da1f9ed1b862ff5dbba2f19e9dc98a93558850ee1cfdd83f83623a677f30d7030bc738fec9da201229d980926404b80fe168c0253 diff --git a/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.4.ebuild index 4ac42c358..b95b16d26 100644 --- a/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild +++ b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2024 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=8 diff --git a/dev-python/snakemake-interface-executor-plugins/Manifest b/dev-python/snakemake-interface-executor-plugins/Manifest index fae5302d8..5c76ebdd7 100644 --- a/dev-python/snakemake-interface-executor-plugins/Manifest +++ b/dev-python/snakemake-interface-executor-plugins/Manifest @@ -1 +1 @@ -DIST snakemake_interface_executor_plugins-9.2.0.tar.gz 16490 BLAKE2B e239c68edbb14c89322a2bd91bb60beb73a939e523e01bec882ee6762412478bc28d856182cf82d62a7879b65797b299cce34aa69cea6d216b6e3bfb3aa59bca SHA512 d6f6ec6cba2649b801bf2352ac60a66bfdc419e53987c77ce64aa37ed08aebec54d07d0e99b1ef212f122b87b40e7f0cb0a0713a2b756e28228dbb9b27b27fce +DIST snakemake_interface_executor_plugins-9.3.2.tar.gz 16714 BLAKE2B 0ae26f520a81fae4a35cddc059bf76da49f558fffda41e1f29db4ab5bc17d6c6f29c3b01961d683b7fc6be05a9e2541a7f6a853f44b94b68ede0033bb9f42a3f SHA512 c516cc2b0aac2fda7f6ae3cd092e626e72591e5810cd11c4f990d297da9407fb98290b8636a7c5ac9e491cb5b89710b03d97746b8d9fd5007fa60b5fcceced8b diff --git a/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.2.0.ebuild b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.3.2.ebuild index 41008ef8b..41008ef8b 100644 --- a/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.2.0.ebuild +++ b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.3.2.ebuild diff --git a/dev-python/snakemake-interface-report-plugins/Manifest b/dev-python/snakemake-interface-report-plugins/Manifest index 4f890f9e6..7de354267 100644 --- a/dev-python/snakemake-interface-report-plugins/Manifest +++ b/dev-python/snakemake-interface-report-plugins/Manifest @@ -1 +1 @@ -DIST snakemake_interface_report_plugins-1.0.0.tar.gz 4239 BLAKE2B efda3664614d123b0cd0f3d246d324ef7a4e67b2a069a5b1dde929921cf7e2251f67d6fcc1806864488dcc9c9b586681908e5a11b13f78206342ff0383efdbdc SHA512 2f5ac7e0ccd02c10aebcbe0eebfdb617cb32f66204e91316e3bc2b0053c3606207baa5de5bdda570f5559db366c637adf614f9ac23c7a33fb06d64560bd780aa +DIST snakemake_interface_report_plugins-1.1.0.tar.gz 4383 BLAKE2B 3e7201d3f0d3b18389838e3f06ff38feca7b710d26a8848b378c2d5f18a93e9e1c7e6cfb771bc644c1193d76836a35531a6f5bafc0d05b03008ce9a69ae667a1 SHA512 0d664bac65c412ab8492b731d5e23cff1c38fceb7a0fde2037d094f4bc451431b8c05f860fc1355e7eb048b89714f86e8cd7cc810e94abc4b7ab0c0c2e8b0f54 diff --git a/dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.0.0.ebuild b/dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.1.0.ebuild index 25f8d53c7..25f8d53c7 100644 --- a/dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.0.0.ebuild +++ b/dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.1.0.ebuild diff --git a/dev-python/snakemake-interface-storage-plugins/Manifest b/dev-python/snakemake-interface-storage-plugins/Manifest index 65939aa80..cc1bb9682 100644 --- a/dev-python/snakemake-interface-storage-plugins/Manifest +++ b/dev-python/snakemake-interface-storage-plugins/Manifest @@ -1 +1 @@ -DIST snakemake_interface_storage_plugins-3.2.3.tar.gz 11930 BLAKE2B 5f46a52d46c11a2feb9840e5a3eb67374ad4a148ff2366953be0285877d1a33c344fcf9930a8145fccd1987995ddaf177997e393a9f21bbd316102d620b4bc9d SHA512 7692c9cacc5ece8e76dab67be3a8ed1a32930b27ce7edaa3998b23305723e7e01b3c04954b61585d876b5410caf3036efd0cb9569e159abcc5a95d9ab2446494 +DIST snakemake_interface_storage_plugins-3.3.0.tar.gz 12244 BLAKE2B 353c247d139e10bfe4a2dbf45a0af1dbea0e545a668f7c47d71f063262e2c1695ed2e33a2eab2d94ea7084b586542674fc4011f16c4e960857e649e7ffbd527f SHA512 54aab99808f8c896d4ddbccc3dd3fd4522ddfbf20f505916e4ae29086af0404178e2733f3b1bebb1eeb7a48ad08046727d954f4cd71ca7d40b9e5f02ccb7e8a6 diff --git a/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.3.ebuild b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.3.0.ebuild index 39c8b08a2..39c8b08a2 100644 --- a/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.3.ebuild +++ b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.3.0.ebuild diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest index de4027537..48490208a 100644 --- a/dev-python/snakemake/Manifest +++ b/dev-python/snakemake/Manifest @@ -1,2 +1,2 @@ DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a -DIST snakemake-8.16.0.gh.tar.gz 8665306 BLAKE2B 76d3455ce9a7ccc749adb5a729ab954d7a3fd97dc2432c3a0e9aba1ace1cb08e377244a2a2527c676b9709f9bb8b5af29948c0385657755bbbc8449b136fc26d SHA512 29b6ba6da5dbbd347dee45114b949c976973555c9234f8a150dcd83e4af1638c1773590320bc44284cf20ea445efb377dcf9199921ed2b4d62bad3a60a41af3c +DIST snakemake-8.25.3.gh.tar.gz 8693083 BLAKE2B 8d5070d5c78f560bc714da189454776ea87a8403075da98b45b021ac304053cb08763c929846d4c8f949c71245566bdb012b78d8807f40a584805cd08917af14 SHA512 f769c89e98130c738bb43931f240eaa93482d19403c6bcda65334910ccf4cac2e11257ed8b133d220d645ea39b0af8aa580fe24c57221478ea7dd0fb4d21d4e7 diff --git a/dev-python/snakemake/snakemake-8.16.0.ebuild b/dev-python/snakemake/snakemake-8.25.3.ebuild index f204537d1..180f32309 100644 --- a/dev-python/snakemake/snakemake-8.16.0.ebuild +++ b/dev-python/snakemake/snakemake-8.25.3.ebuild @@ -16,21 +16,6 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64" -# cannot import name '_helpers' from 'google.cloud' -RESTRICT="test" - -BDEPEND=" - dev-python/tomli[${PYTHON_USEDEP}] - test? ( - dev-python/requests-mock[${PYTHON_USEDEP}] - dev-python/google-api-python-client[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/pygments[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - net-libs/google-cloud-cpp - ) -" - RDEPEND=" dev-python/appdirs[${PYTHON_USEDEP}] dev-python/immutables[${PYTHON_USEDEP}] @@ -50,13 +35,12 @@ RDEPEND=" dev-python/reretry[${PYTHON_USEDEP}] >=dev-python/smart-open-4.0[${PYTHON_USEDEP}] >=dev-python/snakemake-interface-common-1.17.0[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-executor-plugins-9.2.0[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-executor-plugins-9.3.2[${PYTHON_USEDEP}] >=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-report-plugins-1.0.0[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-report-plugins-1.1.0[${PYTHON_USEDEP}] dev-python/stopit[${PYTHON_USEDEP}] dev-python/tabulate[${PYTHON_USEDEP}] dev-python/throttler[${PYTHON_USEDEP}] - >=dev-python/toposort-1.10[${PYTHON_USEDEP}] dev-python/wrapt[${PYTHON_USEDEP}] >=dev-python/yte-1.5.1[${PYTHON_USEDEP}] >=dev-python/dpath-2.1.6[${PYTHON_USEDEP}] @@ -71,4 +55,17 @@ RDEPEND=" # dev-python/docutils \ # dev-python/recommonmark \ # dev-python/myst-parser + +EPYTEST_IGNORE=( + # __file__ attribute does not match test name ('python_3_7') + tests/test_conda_python_3_7_script/test_script.py + # ModuleNotFoundError: No module named 'snakemake_executor_plugin_cluster_generic' + tests/test_executor_test_suite.py + # ImportError: cannot import name 'snakemake' from 'snakemake.script' + tests/test_script_py/scripts/test_explicit_import.py +) +EPYTEST_DESELECT=( + # No module named 'snakemake_storage_plugin_s3' + tests/test_api.py::test_deploy_sources +) distutils_enable_tests pytest diff --git a/dev-python/soundfile/Manifest b/dev-python/soundfile/Manifest new file mode 100644 index 000000000..9451fccc6 --- /dev/null +++ b/dev-python/soundfile/Manifest @@ -0,0 +1 @@ +DIST soundfile-0.12.1.gh.tar.gz 38409 BLAKE2B b6428f2d904c6cd5123e54c22c0a6313e419ca0c19f645efc1efb81c0b9fa8c6317e9490de2634700a1857b3185798035380ef31aeec41ef517b52b10d8ca398 SHA512 91bac4ffee849c9d322494fa411f027571282ce5ea0fbd7dd41f54afa3ef3d86d8aeb674e2a33ac50abb5828de3694863ee7c40fda38860c678260dd614f607b diff --git a/dev-python/soundfile/soundfile-0.12.1.ebuild b/dev-python/soundfile/soundfile-0.12.1.ebuild new file mode 100644 index 000000000..9e77ed61f --- /dev/null +++ b/dev-python/soundfile/soundfile-0.12.1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( pypy3 python3_{10..13} ) + +inherit distutils-r1 + +DESCRIPTION="SoundFile is an audio library based on libsndfile, CFFI, and NumPy" +HOMEPAGE="https://github.com/bastibe/python-soundfile/" +SRC_URI=" + https://github.com/bastibe/python-soundfile/archive/${PV}.tar.gz + -> ${P}.gh.tar.gz +" +S="${WORKDIR}/python-soundfile-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + media-libs/libsndfile + dev-python/numpy[${PYTHON_USEDEP}] + $(python_gen_cond_dep ' + >=dev-python/cffi-1.0.0[${PYTHON_USEDEP}] + ' 'python*') +" + +distutils_enable_tests pytest diff --git a/dev-python/spectra/Manifest b/dev-python/spectra/Manifest index 97bcfc93a..d66c2332e 100644 --- a/dev-python/spectra/Manifest +++ b/dev-python/spectra/Manifest @@ -1 +1 @@ -DIST spectra-0.0.11.tar.gz 18819 BLAKE2B 45ceefa8d2bab051a8fa8ee687f9fa25f6436e66987bb84c6982f64a522fb0b04120e068ef890f4b04f6626a130c5df1e81090913c143df1e82bda5ca3a01d4d SHA512 7b4e244ba200df8c6d7cff19ddf36a5af6cfe8cf6f89283f8dbb64345a3eb85b4f62456e3c75b7c8ce2d24e01c8a123a5763605b1e702903fe16839966e47b32 +DIST spectra-0.1.0.gh.tar.gz 23083 BLAKE2B c6addce33ea1db2b3656f0cf1f631d51cd0969e79b4dedfd73e8f51acf257aa6bd611f4d8a61539f2f527269ce4087681bae73830c5548c28134597f310aacd0 SHA512 79fd3390f0dd03e7df1355498ac2e394aca9bcb970f055e1cb540971e7eec5cae3525f2f637ac8d47db368d6d44e37491af38c13f86d0a1271a86c4825d79cb4 diff --git a/dev-python/spectra/spectra-0.0.11.ebuild b/dev-python/spectra/spectra-0.0.11.ebuild deleted file mode 100644 index d0df23724..000000000 --- a/dev-python/spectra/spectra-0.0.11.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..12} ) - -inherit pypi distutils-r1 - -DESCRIPTION="Easy color scales and color conversion for Python" -HOMEPAGE="https://pypi.org/project/spectra/" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~amd64-linux" - -RDEPEND="dev-python/colormath[${PYTHON_USEDEP}]" - -# requires nose -RESTRICT="test" -#distutils_enable_tests pytest diff --git a/dev-python/spectra/spectra-0.1.0.ebuild b/dev-python/spectra/spectra-0.1.0.ebuild new file mode 100644 index 000000000..7f3a3cfb7 --- /dev/null +++ b/dev-python/spectra/spectra-0.1.0.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) + +inherit distutils-r1 + +DESCRIPTION="Easy color scales and color conversion for Python" +HOMEPAGE="https://pypi.org/project/spectra/" +SRC_URI="https://github.com/jsvine/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND="dev-python/colormath2[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild index 89d58fc6b..069b463b8 100644 --- a/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild +++ b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools PYPI_NO_NORMALIZE=1 diff --git a/dev-python/texext/texext-0.6.7.ebuild b/dev-python/texext/texext-0.6.7.ebuild index fdeb2350a..857ee1028 100644 --- a/dev-python/texext/texext-0.6.7.ebuild +++ b/dev-python/texext/texext-0.6.7.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest index f844796a5..0782b95d6 100644 --- a/dev-python/vector/Manifest +++ b/dev-python/vector/Manifest @@ -1,4 +1,3 @@ -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 +DIST vector-1.6.0.tar.gz 347747 BLAKE2B 905c12e7562b32a263dde2762a87f724947b4e481307d00145286e35cc315cf8be26254e0bcf79e17aefde4d755e0f8a9a8ecfd9b88373b2d52d4d18179ab082 SHA512 e7376e394c2c568b6c07500bc318578befd1717c8ef742d1360a66ecf225e57a814b1e7448fdcc04ac264b83059fa0a155ed5ab1230cf791a762fc07911bc150 diff --git a/dev-python/vector/vector-1.1.1.ebuild b/dev-python/vector/vector-1.1.1.ebuild deleted file mode 100644 index 8b5a45c3d..000000000 --- a/dev-python/vector/vector-1.1.1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -EAPI=8 - -PYTHON_COMPAT=( python3_{10..12} ) -DISTUTILS_USE_PEP517=hatchling -inherit distutils-r1 pypi - -DESCRIPTION="Vector classes and utilities" -HOMEPAGE="https://github.com/scikit-hep/vector" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" -BDEPEND=" - dev-python/hatch-vcs[${PYTHON_USEDEP}] -" - -export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} diff --git a/dev-python/vector/vector-1.3.1.ebuild b/dev-python/vector/vector-1.3.1.ebuild deleted file mode 100644 index 8b5a45c3d..000000000 --- a/dev-python/vector/vector-1.3.1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -EAPI=8 - -PYTHON_COMPAT=( python3_{10..12} ) -DISTUTILS_USE_PEP517=hatchling -inherit distutils-r1 pypi - -DESCRIPTION="Vector classes and utilities" -HOMEPAGE="https://github.com/scikit-hep/vector" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" -BDEPEND=" - dev-python/hatch-vcs[${PYTHON_USEDEP}] -" - -export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} diff --git a/dev-python/vector/vector-1.6.0.ebuild b/dev-python/vector/vector-1.6.0.ebuild new file mode 100644 index 000000000..b9c06d278 --- /dev/null +++ b/dev-python/vector/vector-1.6.0.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/dev-python/yte/Manifest b/dev-python/yte/Manifest index 2ad6d3366..d634cac82 100644 --- a/dev-python/yte/Manifest +++ b/dev-python/yte/Manifest @@ -1 +1 @@ -DIST yte-1.5.4.tar.gz 6352 BLAKE2B f304d1846c0f54949397570564f6bf9d048cd26a99a87feb62f8944403fd0f619546ed0989a2f9fda381c0f39adaa4d987ff66eb4e3bcbce107a460091c1b775 SHA512 eb61553d4c17f6d39f954ea5ab1a09a83009ab8f6f653afbf780b7a30f355e149b4508f8e3755a804f245246e0a1184c74be995f1477e1d2d27bc536bc1ff1f7 +DIST yte-1.7.0.gh.tar.gz 13766 BLAKE2B 047c1d209f2f42d7da40adff6042ee03f2a00dc1cc2d00a892465d8eabcd88713c3f790b110cc8411403b84bc12d4aca00e7ea7ffeb67455920d4e9ad08f0bef SHA512 8c73f5b7c038078f40c0968cc3e16a800cf9974cba17be6a7ec5f45dacd8b9d31e3b0b8e2d0bdac444ff098834878ff5f7c5ef30afcaaa9d037f5d40c5a452d8 diff --git a/dev-python/yte/yte-1.5.4.ebuild b/dev-python/yte/yte-1.7.0.ebuild index ad7b669b1..f6a4cdd81 100644 --- a/dev-python/yte/yte-1.5.4.ebuild +++ b/dev-python/yte/yte-1.7.0.ebuild @@ -1,15 +1,16 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2025 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=poetry -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) -inherit pypi distutils-r1 +inherit distutils-r1 DESCRIPTION="A YAML template engine with Python expressions" HOMEPAGE="https://pypi.org/project/yte/" +SRC_URI="https://github.com/yte-template-engine/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" @@ -20,3 +21,9 @@ RDEPEND=" dev-python/plac[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] " + +distutils_enable_tests pytest + +python_test() { + epytest tests.py +} diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc index 66da0763c..b2c3655cb 100644 --- a/profiles/desc/lhapdf_sets.desc +++ b/profiles/desc/lhapdf_sets.desc @@ -5,15 +5,18 @@ nnpdf31_nnlo_as_0118_luxqed - NNPDF31_nnlo_as_0118_luxqed LHAPDF grid pdf4lhc15_nlo_asvar - PDF4LHC15_nlo_asvar LHAPDF grid +pdf4lhc15_nnlo_100 - PDF4LHC15_nnlo_100 LHAPDF grid ct14qed_proton - CT14qed_proton LHAPDF grid ct14lo - CT14lo LHAPDF grid ct14nlo - CT14nlo LHAPDF grid ct10 - CT10 LHAPDF grid +ct10nnlo - CT10nnlo LHAPDF grid mrst2007lomod - MRST2007lomod LHAPDF grid +nnpdf23_nlo_as_0119_qed - NNPDF23_nlo_as_0119_qed LHAPDF grid nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid cteq66 - CTEQ66 LHAPDF grid cteq6l1 - CTEQ6L1 LHAPDF grid mrst2004qed - MRST2004qed LHAPDF grid nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid -nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid
\ No newline at end of file +nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid diff --git a/profiles/package.mask b/profiles/package.mask index 5770f4680..4be8ad7af 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,12 +30,32 @@ #--- END OF EXAMPLES --- +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2025-01-10) +# Download server is gone since about 2014. +sci-biology/vague-bin + +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2025-01-10) +# Missing packages org.ejml.simple and org.slf4j. +sci-misc/stanford-parser + +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2025-01-10) +# Upstream binary files removed. +sci-biology/NGSEPcore-bin + +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2025-01-10) +# Needs sci-biology/bam-readcount. +sci-biology/VarScan + +# Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2025-01-10) +# Compilation fails. +sci-biology/bam-readcount + # Alexander Puck Neuwirth <alexander@neuwirth-informatik.de> (2024-11-26) -# Depends on removed version of vtk +# 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 +# Depends on masked sci-biology/ants. sci-biology/samri # Nowa Ammerlaan <nowa@gentoo.org> (2024-07-18) diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild index c9ade12fe..a07a04c8c 100644 --- a/sci-biology/BBmap/BBmap-38.87.ebuild +++ b/sci-biology/BBmap/BBmap-38.87.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/MeV/MeV-4.8.1.ebuild b/sci-biology/MeV/MeV-4.8.1.ebuild index 44d7a56f5..41552d8a0 100644 --- a/sci-biology/MeV/MeV-4.8.1.ebuild +++ b/sci-biology/MeV/MeV-4.8.1.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 MY_PV="${PV//./_}" diff --git a/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild index a47524cf8..8901161ed 100644 --- a/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild +++ b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/NGSEPcore/Manifest b/sci-biology/NGSEPcore/Manifest index ef9c10376..db29a5a3e 100644 --- a/sci-biology/NGSEPcore/Manifest +++ b/sci-biology/NGSEPcore/Manifest @@ -1,4 +1 @@ -DIST NGSEPcore-4.0.3_QuickStart.txt 21313 BLAKE2B b897e25945d337f85f0c525ce93221440f6f1577ad1bde6fa3884a74e4366c2e17d7ef1d8603acba02ab21bdaa63fdfcc4d4251273f5e77b938e2318b13bdc19 SHA512 f5d528555c6115cdbddddbfc1c24939d1ca4776b16a5b848b4b9321cb882903d70eeef00c08e032dce4b6fe5551cea881570fc6f5975837e4f9eaf646de0c363 -DIST NGSEPcore-4.0.3_Tutorial.txt 16946 BLAKE2B 0f397c6cd6d0f57f219d3f7963df32263347345a2e6231c7ccbc1a433d8de6350c6653e1a260182aa3ea5fa6a0bf88f47b659df236c78c8289914823b92f5778 SHA512 b110a0058962e1dc899183d3ca73cdfdd5f9b729561d35fe8d25e2fbeaa9b4647cbb768b047fa6df80b7926b1a34e4dc87c13979b66e6e6fe83f6f0c991fe6a8 -DIST NGSEPcore-4.0.3_UserManual.pdf 10516580 BLAKE2B abe69a790413851181cbd210c8389fd302d917a1f6b4d425fbda2389808234290d38f31532933c0fc8505ca8b530f1b778bb58ce041783d184a85c2d5a716cd9 SHA512 cff9176f0a791b5b3e24fdba681bd71a3c39cb4593c01631e722e60e238140c80f292286454b7337a741a2f54fa6d5db30146c5bfdb02d5d5dd8d65322e3dc6e DIST NGSEPcore_4.0.3.tar.gz 11668258 BLAKE2B de8bdeee18c8647e93dcf8adf0751660618bb54208160a15de184680459122ef6fb62ea6c1ae8d3e81b6ada11ab4a1b2f18ee575b4fdc4543f3c30b9077ffc1d SHA512 12c73243cc026fc37424fc8b5112179288bf569c3e06208bfc768420874dc676a23f10a8fd067eb0120fa8f188556e2a91e22fc4e54a8cd3e7851a0b2e32e036 diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild index 49b13a169..1ae0fec8a 100644 --- a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild +++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild @@ -1,18 +1,16 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 DESCRIPTION="NGSEP (CNV and indel discovery)" HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home https://github.com/NGSEP/NGSEPcore" -SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz - https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.pdf -> ${P}_UserManual.pdf - https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt - https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt" +SRC_URI="https://downloads.sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz" +S="${WORKDIR}/${PN}_${PV}" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" @@ -20,8 +18,6 @@ KEYWORDS="~amd64 ~x86" RDEPEND=">=virtual/jdk-1.8:=" DEPEND="${RDEPEND}" -S="${WORKDIR}/${PN}_${PV}" - src_prepare(){ # recent versions of htsjdk now use gradle, # which is not supported by portage @@ -37,8 +33,5 @@ src_compile(){ src_install(){ java-pkg_dojar *.jar lib/*.jar - dodoc "${DISTDIR}"/${P}_UserManual.pdf \ - "${DISTDIR}"/${P}_Tutorial.txt \ - "${DISTDIR}"/${P}_QuickStart.txt \ - README.txt + einstalldocs } diff --git a/sci-biology/NGSEPcore/metadata.xml b/sci-biology/NGSEPcore/metadata.xml index 642261079..6566fb214 100644 --- a/sci-biology/NGSEPcore/metadata.xml +++ b/sci-biology/NGSEPcore/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">ngsep</remote-id> + <remote-id type="github">NGSEP/NGSEPcore</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild index aa6ce5247..c94bd0300 100644 --- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild b/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild index 5b06676c0..6bb3faece 100644 --- a/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild +++ b/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/VarScan/VarScan-2.4.4.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild index 039a68f06..abe631b90 100644 --- a/sci-biology/VarScan/VarScan-2.4.4.ebuild +++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild index 31bad30bb..fb6be79f3 100644 --- a/sci-biology/act-bin/act-bin-17.0.1.ebuild +++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/beagle/beagle-5.1.ebuild b/sci-biology/beagle/beagle-5.1.ebuild index 38b04921c..010ffa6db 100644 --- a/sci-biology/beagle/beagle-5.1.ebuild +++ b/sci-biology/beagle/beagle-5.1.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/beaglecall/Manifest b/sci-biology/beaglecall/Manifest deleted file mode 100644 index 40e4013f6..000000000 --- a/sci-biology/beaglecall/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST beaglecall_1.0.1_15Nov10.src.zip 109726 BLAKE2B 9c6dc1093a295cd96ac1216010eb3295208037f8e69ffc6b6b9f4c52da84222cbf10c71d0f731660955ab1d6cd4a3651e96147c37c426eb1f6d3dcbd53e64a47 SHA512 7a4485ea74f4ca5f00f952aa469d3f551d80a05bb4b0c41d3a9ffa680fac94a9d415595a6a46bc3048372af7de99aa14bc2c85f20d6a470ef2110e3c97d98236 -DIST beaglecall_1.0_15Nov10.pdf 1134881 BLAKE2B da9c4d25bdbc923b18e2cbcc54e7a1a4ba017a8548c99445054aab2eb439c503b52c82fb8f3aa2123fe67f4e41f5ebce96ddfe4943a68818f67ec5c7f5dff857 SHA512 70bc1c9a05bc28941ee0be428929cbf07e602fda0f3afabca383ad5df5461269e4415c3da25a57a6b5072647112464516cc052ef3fa2be3a642b765ba518deac -DIST beaglecall_example.zip 1556387 BLAKE2B 9251766b9e32a4e06ee96987c070b4125a365ce354f3adc3a7e0a86eaf934840d3ed3265fd413857047a360a8ab18099aa49747879c048623f625e4c1ffdfd71 SHA512 35e66ddfa67b13e0f076994773d99de7c0daacf0308204729cb6fefae011e50d3fc65b42205d00f9b82c83be8323b1def8cd3e9ba63b1bee87369f140b717b63 diff --git a/sci-biology/beaglecall/beaglecall-20101115.ebuild b/sci-biology/beaglecall/beaglecall-20101115.ebuild deleted file mode 100644 index e564665b9..000000000 --- a/sci-biology/beaglecall/beaglecall-20101115.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-pkg-simple - -DESCRIPTION="Simultaneous genotype calling and haplotype phasing for unrelated individuals" -HOMEPAGE="https://faculty.washington.edu/browning/beaglecall/beaglecall.html" -SRC_URI="https://faculty.washington.edu/browning/beaglecall/beaglecall_1.0.1_15Nov10.src.zip - https://faculty.washington.edu/browning/beaglecall/beaglecall_1.0_15Nov10.pdf - https://faculty.washington.edu/browning/beaglecall/beaglecall_example.zip" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=">=virtual/jdk-1.5:* - app-arch/unzip" -RDEPEND="${DEPEND} - >=virtual/jre-1.5:*" - -S="${WORKDIR}/src" diff --git a/sci-biology/brkraw/brkraw-0.3.11.ebuild b/sci-biology/brkraw/brkraw-0.3.11.ebuild index 60a7767b1..a7c4756bb 100644 --- a/sci-biology/brkraw/brkraw-0.3.11.ebuild +++ b/sci-biology/brkraw/brkraw-0.3.11.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild index dc0c49e6f..1ebb02183 100644 --- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild +++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_SETUPTOOLS="rdepend" -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-biology/conform-gt/conform-gt-1174.ebuild b/sci-biology/conform-gt/conform-gt-1174.ebuild index edd699ae1..b5b762041 100644 --- a/sci-biology/conform-gt/conform-gt-1174.ebuild +++ b/sci-biology/conform-gt/conform-gt-1174.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/dcmstack/dcmstack-0.9.ebuild b/sci-biology/dcmstack/dcmstack-0.9.ebuild index d207526c0..2fb81546f 100644 --- a/sci-biology/dcmstack/dcmstack-0.9.ebuild +++ b/sci-biology/dcmstack/dcmstack-0.9.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild index 38f9aea0f..5b967300a 100644 --- a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild +++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{11..12} ) inherit distutils-r1 diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest index 649a31cdf..f42ec4469 100644 --- a/sci-biology/deeptools/Manifest +++ b/sci-biology/deeptools/Manifest @@ -1,2 +1 @@ -DIST deeptools-3.5.0.tar.gz 62553343 BLAKE2B a8cd1520b96c50ad36667405677cf422a74376d88f0716f83cc0c6f58d01aefcf47ac1b862aa98b8801e61445d59831dbc9246660e2f41a5b3e0ed3d6573ad50 SHA512 699734c8a863ec76dfead728e3227bbe3ec04d62e91f447269a6aa8406d627ff618837b85ab2e31cc635c671e1d62230c4db0992106bbe921281b81164387b38 -DIST deeptools-3.5.1.tar.gz 62552044 BLAKE2B 3c785ba478b88fbbe7ba2617e2d05984b8a897f787e85d6f8f144f596af07b9e16ba920c8adee35efc4b1b067f255e81f66cf746aaea43e5ee61c23c4d15c9c3 SHA512 f7618f1a51b975d42712a38e13e9ab2ddfeafffe24d81fdab41f1ef7c2e44fd09da0351210670b0036bf72e7af11b679417275adce300ae9fabe4b5339ee9810 +DIST deeptools-3.5.6.tar.gz 62513989 BLAKE2B 089f97bbac4ffcaab24adfa564981f62c470eb498dd3ebab9f4703ff15f0637fce30629d18a8f460c30c8e842f8692ee5e19ff3f04767aa5301b4ee41a671d36 SHA512 88f69253d49912af6344814fb02381274efaf485c29fdb1c99cbeec143a74816224a19d5793b3b92772850d9691e4cba712d2b6e284733cf16fb09ab1896c294 diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild deleted file mode 100644 index 7c2eaa739..000000000 --- a/sci-biology/deeptools/deeptools-3.5.1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) - -inherit distutils-r1 - -DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" -HOMEPAGE="https://github.com/deeptools/deepTools" -SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -# TODO: fix this -RESTRICT="test" - -RDEPEND=" - >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}] - >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] - >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}] - >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}] - dev-python/plotly[${PYTHON_USEDEP}] - >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] - >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] - >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}] -" - -S="${WORKDIR}/deepTools-${PV}" - -distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse -#distutils_enable_tests nose diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.6.ebuild index 7c2eaa739..32a4ca508 100644 --- a/sci-biology/deeptools/deeptools-3.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{11..12} ) inherit distutils-r1 @@ -16,9 +16,6 @@ LICENSE="BSD" SLOT="0" KEYWORDS="~amd64" -# TODO: fix this -RESTRICT="test" - RDEPEND=" >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}] >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] @@ -28,10 +25,11 @@ RDEPEND=" >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.5.0[${PYTHON_USEDEP}] " S="${WORKDIR}/deepTools-${PV}" +PATCHES=( "${FILESDIR}"/${P}-add-build-backend.patch ) distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse -#distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/sci-biology/deeptools/files/deeptools-3.5.6-add-build-backend.patch b/sci-biology/deeptools/files/deeptools-3.5.6-add-build-backend.patch new file mode 100644 index 000000000..cd001df15 --- /dev/null +++ b/sci-biology/deeptools/files/deeptools-3.5.6-add-build-backend.patch @@ -0,0 +1,12 @@ +diff --git a/pyproject.toml b/pyproject.toml +index 2072ec1f52..9b28626680 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -2,6 +2,7 @@ + requires = [ + "setuptools" + ] ++build-backend = "setuptools.build_meta" + + [project] + name = "deepTools" diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild index 3656d6dc8..a20699a67 100644 --- a/sci-biology/dipy/dipy-1.1.1.ebuild +++ b/sci-biology/dipy/dipy-1.1.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild index 1b3a90297..a74402b29 100644 --- a/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild +++ b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 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 d386ca896..3c9412f8c 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 perl-module diff --git a/sci-biology/minced/Manifest b/sci-biology/minced/Manifest deleted file mode 100644 index 1014985f6..000000000 --- a/sci-biology/minced/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST minced-0.4.2.tar.gz 510282 BLAKE2B 4ff935d8d5ecea900f3a702603a5ce83031d99e9c3bef7414307b4d631eef67632bc600a5bd4ed3e750b77a0e952e152ef310746ad79bf66e3b28487bcca7150 SHA512 6e88ecf8ab8af1aeb53582c5e901bc5b890570ec74c9bfdf1b5f6d3e60775ed5e30fd010a6b885a9f1fdd9c3f802c55c535a7e673b23027630711f8d5565a52b diff --git a/sci-biology/minced/metadata.xml b/sci-biology/minced/metadata.xml deleted file mode 100644 index f7601e7b0..000000000 --- a/sci-biology/minced/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ctSkennerton/minced</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/minced/minced-0.4.2.ebuild b/sci-biology/minced/minced-0.4.2.ebuild deleted file mode 100644 index b9845e859..000000000 --- a/sci-biology/minced/minced-0.4.2.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-pkg-simple - -DESCRIPTION="Short Palindromic Repeat finder tool (for CRISPRs)" -HOMEPAGE="https://github.com/ctSkennerton/minced" -SRC_URI="https://github.com/ctSkennerton/minced/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=">=virtual/jdk-1.7" -RDEPEND=">=virtual/jre-1.7" - -src_install(){ - java-pkg_dojar minced.jar - java-pkg_dolauncher - einstalldocs -} diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest index cf36e2eb5..ae9f6f9f3 100644 --- a/sci-biology/multiqc/Manifest +++ b/sci-biology/multiqc/Manifest @@ -1 +1 @@ -DIST multiqc-1.23.gh.tar.gz 5639815 BLAKE2B 1cd02d82d5a1856470777cdd5db48fbf2d86a37e713fa32118edb608703c9fbf1d23af6254a0ed15c47f2c073999a58c53a5a67c6df9a6bfc61cb773fc857bae SHA512 f7d910122ec34373dfa2d60dd7436ec66494980daf7e46729fbae90481bcceb1318c5dbafc64725dca2079deb5fe66834371813aa4dda7e9bf676dff5a043995 +DIST multiqc-1.27.gh.tar.gz 8476481 BLAKE2B 340dd60c194bf0d8c1b5e60eea8c8db070dc0699c8c1e2e9ddf1b204d7712770377232f6ebcf6fe2bf50f28467de2d761ebf94dd07b741f63cee4f0c1ff8c33e SHA512 307f420e7a0ddfcc10d7ccfbeeb22a76bcfa42bdd2d77409af83e77dd10af5671a19549f76dace3176285c17b0508de149c5a0c6c711acd4d00ef21f01b7b9ab diff --git a/sci-biology/multiqc/multiqc-1.23.ebuild b/sci-biology/multiqc/multiqc-1.27.ebuild index 2ac362503..6ba06e001 100644 --- a/sci-biology/multiqc/multiqc-1.23.ebuild +++ b/sci-biology/multiqc/multiqc-1.27.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -10,12 +10,12 @@ inherit distutils-r1 DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" HOMEPAGE="https://multiqc.info/" -SRC_URI="https://github.com/MultiQC/MultiQC/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +SRC_URI="https://github.com/MultiQC/MultiQC/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" S="${WORKDIR}"/MultiQC-${PV} LICENSE="GPL-3" SLOT="0" -KEYWORDS="~amd64 ~amd64-linux" +KEYWORDS="~amd64" RDEPEND="dev-python/click[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] @@ -28,15 +28,18 @@ RDEPEND="dev-python/click[${PYTHON_USEDEP}] >=dev-python/pillow-10[${PYTHON_USEDEP}] >=dev-python/plotly-5.18[${PYTHON_USEDEP}] >=dev-python/pyyaml-4[${PYTHON_USEDEP}] - dev-python/pyaml-env[${PYTHON_USEDEP}] >=dev-python/rich-10[${PYTHON_USEDEP}] dev-python/rich-click[${PYTHON_USEDEP}] dev-python/coloredlogs[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] >=dev-python/spectra-0.0.10[${PYTHON_USEDEP}] >=dev-python/pydantic-2.7.1[${PYTHON_USEDEP}] - dev-python/typeguard[${PYTHON_USEDEP}]" -# dev-python/kaleido[${PYTHON_USEDEP}] # tested and is optional + dev-python/typeguard[${PYTHON_USEDEP}] + dev-python/python-dotenv[${PYTHON_USEDEP}] + dev-python/natsort[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}]" +# dev-python/tiktoken[${PYTHON_USEDEP}] # not strictly required +# dev-python/kaleido[${PYTHON_USEDEP}] # not strictly required -RESTRICT="test" # no items collected -#distutils_enable_tests pytest +RESTRICT="test" # needs external repository with test data +distutils_enable_tests pytest diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index 92c788f28..812828762 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index 4dbe5101e..b29128954 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild index 7e47d7288..44e9173c0 100644 --- a/sci-biology/nitime/nitime-0.10.2.ebuild +++ b/sci-biology/nitime/nitime-0.10.2.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild index cae7fdfea..f972a6fc2 100644 --- a/sci-biology/nitime/nitime-0.9.ebuild +++ b/sci-biology/nitime/nitime-0.9.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 pypi virtualx diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild index ee81c01dc..d7808ffa1 100644 --- a/sci-biology/nitime/nitime-9999.ebuild +++ b/sci-biology/nitime/nitime-9999.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 git-r3 diff --git a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild index f48e98b3b..e6e69eaa5 100644 --- a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild +++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild index 79ed9fc48..1ecbfae64 100644 --- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild +++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-chemistry/chimera/Manifest b/sci-chemistry/chimera/Manifest index 953fae5f9..1d70918c9 100644 --- a/sci-chemistry/chimera/Manifest +++ b/sci-chemistry/chimera/Manifest @@ -1,3 +1,3 @@ DIST Chimera512.png 68464 BLAKE2B 51797728b8b9421ab6e42e57bb60881a706d17eed09cbef57506f706b7ebab6511397f90834d15efaea5e86a22fc2ff9e55cf42c7a87d6166716444252d18f49 SHA512 6ed0dd8bd1b5a6b164f80acc1d7e1a91629513b147d37472e1831b657201a3f25c1c0c9a1b44bf565afaa4aa99469910d1ac307a45a80b9a12d0554e1812e2c5 -DIST chimera-1.17.1-linux_x86_64.bin 149832020 BLAKE2B 01e78d09a3373a3d927c93daa03d0c17473c18079afd989a29afaad5c56aa57bbfeb968bcef42eb50924e1cde67e939c92a545080c0e7b55549c30e43aae564d SHA512 f6df3ad320f09b3f8d918660a4a7596505c2a97ac0d60a4f6ef9c414851a90bb59ccba9728d5a71df93404b8c6ecf99ab9dca84befcfa10e60285f3a33e3c3bc DIST chimera-1.17.3-linux_x86_64.bin 155528316 BLAKE2B 09caddbac9a518606b8065a19840fd2f5e3a57cbb529bea2e4b63cb83ecd91105c1de34dc3f1139382fc80f14e69b28c39152d9b15e16c39a08732ebcd374c51 SHA512 cfbf42dd3aa030db0619bf5750d08ba94acc53f54a890109d422a675394616afba9c85779e5d62bcd4ad83db4a7cfcf8190c2c42c84719c991061859c87288b7 +DIST chimera-1.18-linux_x86_64.bin 155517493 BLAKE2B eb440fcbff972912485f39ebc720d0ef7d2d11827f9d3e730dd2e05f025b75bdf3b48d3c1f2507abb4bc44ad8112e14826ed85de45d08663b48bc57e293dd0c6 SHA512 fe3359d7c397029d73723aaef6d17ac231f7fca149f918be4a9b2b4bcb671df15013ddab66982075d69072df30dcb4e35f804d83bd745f527d76e6b4f7dedb2f diff --git a/sci-chemistry/chimera/chimera-1.17.1.ebuild b/sci-chemistry/chimera/chimera-1.18.ebuild index 919350ac9..b4b3b164e 100644 --- a/sci-chemistry/chimera/chimera-1.17.1.ebuild +++ b/sci-chemistry/chimera/chimera-1.18.ebuild @@ -6,18 +6,17 @@ inherit desktop xdg DESCRIPTION="Next generation molecular visualization program from RBVI" HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" -SRC_URI="chimera-${PV}-linux_x86_64.bin - fetch+http://svn.cgl.ucsf.edu/svn/chimera/trunk/icons/chimera/Chimera512.png" +SRC_URI="${P}-linux_x86_64.bin + mirror+https://dev.gentoo.org/~pacho/${PN}/Chimera512.png" +S="${WORKDIR}" +LICENSE="chimera" SLOT="0" -LICENSE="chimera" KEYWORDS="~amd64 ~x86" RESTRICT="fetch mirror strip" QA_PREBUILT="*" -DEPEND="" -BDEPEND="" RDEPEND=" dev-lang/tcl dev-lang/tk @@ -32,6 +31,7 @@ RDEPEND=" media-libs/libpng media-libs/tiff sci-libs/hdf5 + sys-libs/ncurses-compat sys-devel/gcc[openmp,fortran] media-libs/libjpeg-turbo virtual/glu @@ -49,17 +49,15 @@ RDEPEND=" virtual/libcrypt:= " -S="${WORKDIR}" - pkg_nofetch() { elog "Please visit" elog "https://www.cgl.ucsf.edu/chimera/download.html" - elog "and download chimera-${PV}-linux_x86_64.bin into your DISTDIR" + elog "and download ${P}-linux_x86_64.bin into your DISTDIR" } src_unpack() { - cp "${DISTDIR}"/chimera-${PV}-linux_x86_64.bin chimera-${PV}-linux_x86_64.bin.zip - unzip chimera-${PV}-linux_x86_64.bin.zip || die + cp "${DISTDIR}"/${P}-linux_x86_64.bin ${P}-linux_x86_64.bin.zip + unzip ${P}-linux_x86_64.bin.zip || die } src_install() { diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild index cd315c348..77a01f7ad 100644 --- a/sci-chemistry/panav/panav-0.20130730.ebuild +++ b/sci-chemistry/panav/panav-0.20130730.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest index 64b9caefd..04e6b18d0 100644 --- a/sci-libs/gdcm/Manifest +++ b/sci-libs/gdcm/Manifest @@ -1,2 +1,3 @@ DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220 +DIST gdcm-3.0.24.tar.bz2 3139207 BLAKE2B c18850a55cb591c1dea663e4799c763c2c4a0180ed460538d1cdb721be0fccc8b9a7cf29b4648164c6251b95d59935676a6655e43e25ab7e28d5261d5732dd78 SHA512 727beb50df893bfc1f693da918d9aafe92df0328dd9a80f074dea43c4f82608999f2aea5f970c5410512fd2791a7159762e5e0c83cc6295bd35465b26dd5f376 DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild index 467fa623c..8b2fc2cba 100644 --- a/sci-libs/gdcm/gdcm-3.0.14.ebuild +++ b/sci-libs/gdcm/gdcm-3.0.14-r1.ebuild @@ -3,20 +3,22 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..12} ) -inherit cmake python-single-r1 +inherit cmake flag-o-matic python-single-r1 DESCRIPTION="Cross-platform DICOM implementation" HOMEPAGE="http://gdcm.sourceforge.net/" SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2 - test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release + test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" +# 3.0.14: .bz2 is broken, should be checked in next release LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc python test vtk" -RESTRICT="!test? ( test )" +# Tests fail https://bugs.gentoo.org/948517 +RESTRICT="test" DEPEND=" app-text/poppler:0=[cxx] @@ -80,42 +82,44 @@ src_prepare() { Applications/Cxx/CMakeLists.txt \ || die + append-cxxflags -std=gnu++20 cmake_src_prepare } src_configure() { local mycmakeargs=( + $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "") + $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "") + -DBUILD_SHARED_LIBS=OFF -DCMAKE_SKIP_RPATH=ON + -DGDCM_BUILD_APPLICATIONS=ON + -DGDCM_BUILD_EXAMPLES=OFF -DGDCM_BUILD_SHARED_LIBS=ON + -DGDCM_BUILD_TESTING=$(usex test) -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData" - -DGDCM_INSTALL_LIB_DIR="$(get_libdir)" + -DGDCM_DOCUMENTATION=$(usex doc) -DGDCM_INSTALL_DOC_DIR="share/doc/${P}" + -DGDCM_INSTALL_LIB_DIR="$(get_libdir)" -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages" - -DGDCM_USE_SYSTEM_ZLIB=ON - -DGDCM_USE_SYSTEM_OPENSSL=ON - -DGDCM_USE_SYSTEM_UUID=ON + -DGDCM_USE_SYSTEM_CHARLS=ON -DGDCM_USE_SYSTEM_EXPAT=ON -DGDCM_USE_SYSTEM_JSON=ON - -DGDCM_USE_SYSTEM_PAPYRUS3=OFF - -DGDCM_USE_SYSTEM_SOCKETXX=OFF - -DSOCKETXX_NAMESPACE=GDCMSOCKETXX + -DGDCM_USE_SYSTEM_LIBXML2=ON -DGDCM_USE_SYSTEM_LJPEG=OFF -DGDCM_USE_SYSTEM_OPENJPEG=ON - -DGDCM_USE_SYSTEM_CHARLS=ON + -DGDCM_USE_SYSTEM_OPENSSL=ON + -DGDCM_USE_SYSTEM_PAPYRUS3=OFF -DGDCM_USE_SYSTEM_POPPLER=ON - -DGDCM_USE_SYSTEM_LIBXML2=ON - -DGDCM_BUILD_TESTING=$(usex test) - -DGDCM_WRAP_PYTHON=$(usex python) - $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "") + -DGDCM_USE_SYSTEM_SOCKETXX=OFF + -DGDCM_USE_SYSTEM_UUID=ON + -DGDCM_USE_SYSTEM_ZLIB=ON + -DGDCM_USE_VTK=$(usex vtk) + -DGDCM_WRAP_CSHARP=OFF + -DGDCM_WRAP_JAVA=OFF -DGDCM_WRAP_PERL=OFF -DGDCM_WRAP_PHP=OFF - -DGDCM_WRAP_JAVA=OFF - -DGDCM_WRAP_CSHARP=OFF - -DGDCM_DOCUMENTATION=$(usex doc) - $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "") - -DGDCM_BUILD_EXAMPLES=OFF - -DGDCM_BUILD_APPLICATIONS=ON - -DGDCM_USE_VTK=$(usex vtk) + -DGDCM_WRAP_PYTHON=$(usex python) + -DSOCKETXX_NAMESPACE=GDCMSOCKETXX ) cmake_src_configure } diff --git a/sci-libs/gdcm/gdcm-3.0.24.ebuild b/sci-libs/gdcm/gdcm-3.0.24.ebuild new file mode 100644 index 000000000..2813a8e16 --- /dev/null +++ b/sci-libs/gdcm/gdcm-3.0.24.ebuild @@ -0,0 +1,126 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +inherit cmake flag-o-matic python-single-r1 + +DESCRIPTION="Cross-platform DICOM implementation" +HOMEPAGE="http://gdcm.sourceforge.net/" +SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2 + test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" +# 3.0.24: .bz2 is still broken, should be checked again next release + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc python test vtk" +# Tests fail https://bugs.gentoo.org/948517 +RESTRICT="test" + +DEPEND=" + app-text/poppler:0=[cxx] + dev-libs/expat:0= + dev-libs/json-c:0= + dev-libs/libxml2:2= + dev-libs/openssl:0= + >=media-libs/charls-2.0.0:0= + >=media-libs/openjpeg-2.0.0:2= + sys-apps/util-linux:0= + sys-libs/zlib:0= + python? ( ${PYTHON_DEPS} ) + vtk? ( + sci-libs/vtk[rendering] + python? ( + sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}] + ) + ) +" +RDEPEND="${DEPEND}" +BDEPEND=" + dev-libs/libxslt + app-text/docbook-xsl-ns-stylesheets + doc? ( app-text/doxygen[dot] ) + python? ( + ${PYTHON_DEPS} + dev-lang/swig + )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +#PATCHES=( +# "${FILESDIR}/gdcm_support_vtk9.patch" +# "${FILESDIR}/gdcm-3.0.14-include-math-h.patch" +#) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_prepare() { + # drop unbundled libs + local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x#gdcm}" + rm -r "Utilities/${x}" || die + sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die + eend $? + done + find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \ + -exec ewarn "Using bundled" {} ';' || die + + # fix charls include case + #sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die + #sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die + + # Use prefixed socket++ (to avoid potential conflicts) + sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \ + Source/MessageExchangeDefinition/CMakeLists.txt \ + Applications/Cxx/CMakeLists.txt \ + || die + + append-cxxflags "-std=gnu++20" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "") + $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "") + -DBUILD_SHARED_LIBS=OFF + -DCMAKE_SKIP_RPATH=ON + -DGDCM_BUILD_APPLICATIONS=ON + -DGDCM_BUILD_EXAMPLES=OFF + -DGDCM_BUILD_SHARED_LIBS=ON + -DGDCM_BUILD_TESTING=$(usex test) + -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData" + -DGDCM_DOCUMENTATION=$(usex doc) + -DGDCM_INSTALL_DOC_DIR="share/doc/${P}" + -DGDCM_INSTALL_LIB_DIR="$(get_libdir)" + -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages" + -DGDCM_USE_SYSTEM_CHARLS=ON + -DGDCM_USE_SYSTEM_EXPAT=ON + -DGDCM_USE_SYSTEM_JSON=ON + -DGDCM_USE_SYSTEM_LIBXML2=ON + -DGDCM_USE_SYSTEM_LJPEG=OFF + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DGDCM_USE_SYSTEM_OPENSSL=ON + -DGDCM_USE_SYSTEM_PAPYRUS3=OFF + -DGDCM_USE_SYSTEM_POPPLER=ON + -DGDCM_USE_SYSTEM_SOCKETXX=OFF + -DGDCM_USE_SYSTEM_UUID=ON + -DGDCM_USE_SYSTEM_ZLIB=ON + -DGDCM_USE_VTK=$(usex vtk) + -DGDCM_WRAP_CSHARP=OFF + -DGDCM_WRAP_JAVA=OFF + -DGDCM_WRAP_PERL=OFF + -DGDCM_WRAP_PHP=OFF + -DGDCM_WRAP_PYTHON=$(usex python) + -DSOCKETXX_NAMESPACE=GDCMSOCKETXX + ) + cmake_src_configure +} diff --git a/sci-libs/nibabel/nibabel-5.0.0.ebuild b/sci-libs/nibabel/nibabel-5.0.0.ebuild index 0fec805b1..5619aa4b4 100644 --- a/sci-libs/nibabel/nibabel-5.0.0.ebuild +++ b/sci-libs/nibabel/nibabel-5.0.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 diff --git a/sci-libs/nibabel/nibabel-5.1.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild index 0fec805b1..5619aa4b4 100644 --- a/sci-libs/nibabel/nibabel-5.1.0.ebuild +++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild index 8f8ea83e8..47bfbc559 100644 --- a/sci-libs/nipy/nipy-0.6.0.ebuild +++ b/sci-libs/nipy/nipy-0.6.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=meson-python -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_EXT=1 inherit distutils-r1 diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild index 7c2e801ff..10cd0f32b 100644 --- a/sci-libs/nipype/nipype-1.8.4-r1.ebuild +++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) PYTHON_REQ_USE="threads(+),sqlite" inherit distutils-r1 diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild index 4c3da70b3..41c8d6ba9 100644 --- a/sci-libs/nipype/nipype-1.8.4-r2.ebuild +++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) PYTHON_REQ_USE="threads(+),sqlite" inherit distutils-r1 diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild index 88bc23395..d12d4dcd9 100644 --- a/sci-libs/nipype/nipype-1.8.6.ebuild +++ b/sci-libs/nipype/nipype-1.8.6.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) PYTHON_REQ_USE="threads(+),sqlite" inherit distutils-r1 diff --git a/sci-libs/pybids/pybids-0.10.2.ebuild b/sci-libs/pybids/pybids-0.10.2.ebuild index 5f2776855..bc471429c 100644 --- a/sci-libs/pybids/pybids-0.10.2.ebuild +++ b/sci-libs/pybids/pybids-0.10.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-libs/pybids/pybids-0.12.4.ebuild b/sci-libs/pybids/pybids-0.12.4.ebuild index 7860d69c9..3c0ee420b 100644 --- a/sci-libs/pybids/pybids-0.12.4.ebuild +++ b/sci-libs/pybids/pybids-0.12.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild index 6103c3191..73b5d6891 100644 --- a/sci-libs/pybids/pybids-0.6.5.ebuild +++ b/sci-libs/pybids/pybids-0.6.5.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_11 ) inherit distutils-r1 diff --git a/sci-libs/torchaudio/Manifest b/sci-libs/torchaudio/Manifest new file mode 100644 index 000000000..0059647a6 --- /dev/null +++ b/sci-libs/torchaudio/Manifest @@ -0,0 +1 @@ +DIST torchaudio-2.4.1.tar.gz 4503000 BLAKE2B 85ae91bb564996f95c9116802058968dff191d4771becbb859987afd3b78189980b31281c5c49088fe91a72a02170dafe865f8bbb4168af6aeafe42f4029c09b SHA512 84c196a19bedefd39c7c1bc690705e317aaba9e16aa52a71dfa5688faf50ffa1985008c59007939ad7096c7900c5450659efb12e0a393c4545fe4bd31f294b11 diff --git a/sci-libs/torchaudio/metadata.xml b/sci-libs/torchaudio/metadata.xml new file mode 100644 index 000000000..445ee5c8c --- /dev/null +++ b/sci-libs/torchaudio/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <use> + <flag name="rocm">Enable ROCm gpu computing support</flag> + <flag name="rnnt">Enable custom RNN-T loss function</flag> + </use> + <upstream> + <remote-id type="github">pytorch/vision</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/torchaudio/torchaudio-2.4.1.ebuild b/sci-libs/torchaudio/torchaudio-2.4.1.ebuild new file mode 100644 index 000000000..6e1067764 --- /dev/null +++ b/sci-libs/torchaudio/torchaudio-2.4.1.ebuild @@ -0,0 +1,80 @@ +# Copyright 2020-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +ROCM_SKIP_GLOBALS=1 +inherit cuda distutils-r1 multiprocessing rocm optfeature + +DESCRIPTION="Data manipulation and transformation for audio signal processing" +HOMEPAGE="https://github.com/pytorch/audio" +SRC_URI="https://github.com/pytorch/audio/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/audio-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="cuda rocm ffmpeg openmp +rnnt" +REQUIRED_USE="?? ( cuda rocm )" + +DEPEND=" + ffmpeg? ( <media-video/ffmpeg-7:= ) + sci-libs/caffe2[cuda?,rocm?,openmp?] +" +RDEPEND=" + ${DEPEND} + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] +" +BDEPEND=" + test? ( + $(python_gen_cond_dep ' + dev-python/expecttest[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/parameterized[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/scikit-learn[${PYTHON_USEDEP}] + dev-python/soundfile[${PYTHON_USEDEP}] + ') + ) +" + +distutils_enable_tests pytest + +src_compile() { + export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS + + export USE_CUDA=$(usex cuda 1 0) + export USE_ROCM=$(usex rocm 1 0) + use rocm && addpredict /dev/kfd + export USE_OPENMP=$(usex openmp 1 0) + export USE_FFMPEG=$(usex ffmpeg 1 0) + export BUILD_SOX=0 + export BUILD_RNNT=$(usex rnnt 1 0) + use ffmpeg && export FFMPEG_ROOT=${EPREFIX}/usr + + distutils-r1_src_compile +} + +EPYTEST_IGNORE=( + # librosa + test/torchaudio_unittest/prototype/hifi_gan/hifi_gan_cpu_test.py + test/torchaudio_unittest/prototype/hifi_gan/hifi_gan_gpu_test.py + + # infinite test? + test/torchaudio_unittest/backend/dispatcher/ffmpeg/load_test.py +) + +python_test() { + use rocm && check_amdgpu + + epytest -p expecttest +} + +pkg_postinst() { + optfeature "SoundFile I/O backend" dev-python/soundfile +} diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild index 5819064e0..7a86bcee7 100644 --- a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild +++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 diff --git a/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild b/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild index bb70e918f..e2f16a04c 100644 --- a/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild +++ b/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 JAVA_PKG_IUSE="doc source" diff --git a/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild b/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild index f3e5339dd..2fd90cda6 100644 --- a/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild +++ b/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 JAVA_PKG_IUSE="doc source" diff --git a/sci-physics/cuttools/Manifest b/sci-physics/cuttools/Manifest index bd3e92f61..65776cd87 100644 --- a/sci-physics/cuttools/Manifest +++ b/sci-physics/cuttools/Manifest @@ -1,2 +1,3 @@ DIST cuttools_v1.8.2.tar.gz 962232 BLAKE2B aaec06cc892577c2e562e8ee07e9863dd42a8bbf878b4e2aee01d2bbf5bb27bb9e4f50ef3c3a66fe00e73cc527e23b0274f9c3df169779c5fb529c9ff5610cb0 SHA512 6f1af82caa2a86669271346fa4a4f1d13b39f1c1ee7562c5fc29f250276d59017722a55256358bd006819a442acd3198901b642039be9f6a78d3cf31fe0ca976 DIST cuttools_v1.9.3.tar.gz 1007945 BLAKE2B 832643d9bda99cd920ad289c8edc0394ac335d75330a99a5f1b814d62957d54a7c42f0fc861f2cc9389a0c5d94ed2d67cec4698277f14dc5d3cb27ba8c65bc5f SHA512 6574f9928b3c131bdbf9343323d3a5a56e653c9ace37edd047a3e172aaf6ce4fab04eeb3013cc7eb448bd86937326d15f5effe5600a6a743b750a1eaccaa5db2 +DIST cuttools_v2.0.tar.gz 1008612 BLAKE2B 69f7ad8e5ed3fc3cf1100cc222cc9afa7acbeaad7e00cf28bcd38a566c31b24394f6c2f69207de260b1c0bc212ede254cf918d8b81c29dc2b9209f6dfcfe3767 SHA512 271b0fa518f3a2f251b21c0c9c1c9c687d3a617e8ba2d4ab9fe43c35c5cd6bd5c15b684cb974bfa747e0c13c7afdf626cd4e7cb0cd32c08e1feac005b95fc294 diff --git a/sci-physics/cuttools/cuttools-1.9.3.ebuild b/sci-physics/cuttools/cuttools-2.0.0.ebuild index 03f84b63c..e67589246 100644 --- a/sci-physics/cuttools/cuttools-1.9.3.ebuild +++ b/sci-physics/cuttools/cuttools-2.0.0.ebuild @@ -5,39 +5,55 @@ EAPI=8 inherit fortran-2 toolchain-funcs +MY_V="$(ver_cut 1).$(ver_cut 2)" + DESCRIPTION="Computing 1-loop amplitudes at the integrand level" HOMEPAGE="https://www.ugr.es/~pittau/CutTools/" -SRC_URI="https://www.ugr.es/~pittau/CutTools/${PN}_v${PV}.tar.gz" +SRC_URI="https://www.ugr.es/~pittau/CutTools/${PN}_v${MY_V}.tar.gz" S="${WORKDIR}" -LICENSE="GPL-3" +LICENSE="MIT" SLOT="0" KEYWORDS="~amd64" -IUSE="+dummy" +IUSE="+dummy mpfun90" DEPEND=" + sci-libs/mpfun90 sci-physics/qcdloop - sci-physics/oneloop[dpkind,qpkind16,-qpkind,-tlevel] + 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 = $(CTS)/' src/makefile || die + sed -i 's/^ALL =.*$/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() { - emake -j1 FFLAGS="${FFLAGS} -I${ESYSROOT}/usr/include -fPIC -std=legacy" + 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} ${CXXFLAGS} -shared *.o -o lib${PN}.so || die + ${CXX} ${CXXFLAGS} ${LDFLAGS} -shared *.o -Wl,-soname,libcuttools.so -o lib${PN}.so || die } src_install() { diff --git a/sci-physics/evtgen/Manifest b/sci-physics/evtgen/Manifest index 174d16349..7f76952ab 100644 --- a/sci-physics/evtgen/Manifest +++ b/sci-physics/evtgen/Manifest @@ -1 +1,2 @@ DIST evtgen-02.02.01.tar.gz 2941525 BLAKE2B 8672f2d2e7452ba2330180a7e385d020372bdb436d22b12507ee22344f5013b439f68817e70ed50afbc3585beb15f01b0c29ee35dcbbaac8ec1ee0f8d573b3e2 SHA512 652424dae1d3e3d69c19fa946cd00e61ca5117e38eee20a41a98972374d79261fe7267311c06ecab497729f31e5842e340d6739434f09e5088972c95d2ce9c17 +DIST evtgen-02.02.03.tar.gz 2940937 BLAKE2B e136442f1d41bf528c292d60e1869b38a6569fa8be494d64c7cc2b7916da1b8682622715d755801efb30eeb819479210fa93d250b3b72d67afbbb45251c6d9dc SHA512 761028e0b20dcc1db0eabf212af5c06090b5ea6aa5c69398aacf72099b229f1fbc83b0b197032e157a70fe10affab92f57e8d7926d99d1144f5bfe190ab1d4d8 diff --git a/sci-physics/evtgen/evtgen-02.02.03.ebuild b/sci-physics/evtgen/evtgen-02.02.03.ebuild new file mode 100644 index 000000000..a8ca9fde7 --- /dev/null +++ b/sci-physics/evtgen/evtgen-02.02.03.ebuild @@ -0,0 +1,39 @@ +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit cmake + +MY_PN="EvtGen" +MY_P=${MY_PN}-${PV} + +DESCRIPTION="EvtGen is a Monte Carlo event generator that simulates the decays" +HOMEPAGE="https://evtgen.hepforge.org/" +SRC_URI="https://evtgen.hepforge.org/downloads?f=${MY_P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_PN}/R$(ver_rs 1-2 '-')" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+hepmc3 pythia photos tauola" + +RDEPEND=" + !hepmc3? ( sci-physics/hepmc:2= ) + hepmc3? ( sci-physics/hepmc:3= ) + pythia? ( >=sci-physics/pythia-8.3.0:= ) + photos? ( >=sci-physics/photos-3.64:=[hepmc3?] ) + tauola? ( >=sci-physics/tauola-1.1.8:=[hepmc3?] ) +" +DEPEND="${RDEPEND}" + +src_configure() { + local mycmakeargs=( + -DEVTGEN_HEPMC3=$(usex hepmc3 ON OFF) + -DHEPMC3_ROOT_DIR="${ESYSROOT}/usr" + -DEVTGEN_PYTHIA=$(usex pythia ON OFF) + $(usex pythia -DPYTHIA8_ROOT_DIR="${ESYSROOT}/usr") + -DEVTGEN_PHOTOS=$(usex photos ON OFF) + -DEVTGEN_TAUOLA=$(usex tauola ON OFF) + ) + cmake_src_configure +} diff --git a/sci-physics/lhapdf-sets/Manifest b/sci-physics/lhapdf-sets/Manifest index 6e1d34375..d39e0ff16 100644 --- a/sci-physics/lhapdf-sets/Manifest +++ b/sci-physics/lhapdf-sets/Manifest @@ -1,14 +1,17 @@ DIST CT10.tar.gz 10246366 BLAKE2B f0daf0a3ca6cd2f178f993944cdc29de5deb1f441d197e47c8b1c285a56abc0fdb1cd53ec5a8e7736e200397bea9ec9cf4d04420ce206e5c396b85b63f695d00 SHA512 90406bd102ab54b683fa3e6f3fc759febea2454a0b96c6a8d373cdec297f5d652097057a015c7d87241792ed9b5d9ac658a33155cdd7362f59110f8f06ecce73 +DIST CT10nnlo.tar.gz 14226448 BLAKE2B 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57c7c98bb863258f87e236fea2d0233ac61350012aec6ba5cced75de0b4b945a5633d7fd487b0913b822df1c3ef804de2aacf34b1319d6973d959dc02ebbc9b2 SHA512 5088c30acbd1da4e412ba9f6a997ceaa34f426f41c7ebacaf4d2e8aa49b8b45052913e8d873b293d9f140c01e82c05735b66dd527a9aa124b86f73bf5e4d8c53 DIST NNPDF31_nnlo_as_0118.tar.gz 43193739 BLAKE2B b826eaebb6483b844bc18cfca36be8ead1dc409641e445f8d31db58f31bde623b7e7753a94c0e2ee0dfe24b28909b9d06b17641a783c223d8ab7ce8e55902a5c SHA512 a62330979f4001933b52e2b1bd3142b4dacd27aeed1e49969108a842e00e7db59a7fe8d80b755c283f3bc706b36e3ec4597e124d95ad3a7f334fb956bebe7ae0 DIST NNPDF31_nnlo_as_0118_luxqed.tar.gz 47462442 BLAKE2B 2b473d943ec49e28de63d002e4eadfd3002c63aa6ef9b4e792adf7acf8bb3a771f91298ac6575034407653d15aa4191da6090aaaa34d8a8091cb1a5d4562479a SHA512 5faafc9a2b23dc0a82c7f3ca26a6691cfa476f83741beab2b41a77e63fa5f10428bf43579670636689c0080421f4b08ec058aa63c047f04f6d892b1b848fd702 DIST PDF4LHC15_nlo_asvar.tar.gz 578871 BLAKE2B a42a24d4af82f892e0dccfeeacedfcbb074be1ddc9649d55ff6c15e3923901173337ba4197248410d2a40e72ab627af9a0cea09e5ee98c37130aceb34402d9d4 SHA512 ef96970050b78f5a5bc54b43ee2d7ed0eb76796ea23ce864f1c8ff6de2d68f99023d5c4530f4e73197948c39886fcb832ed26dfa126ca0396e4fd08e353df8a0 +DIST PDF4LHC15_nnlo_100.tar.gz 29962423 BLAKE2B 0ea3e9d44e4a049fad871b66fe473ff51ce23b7957276f1e930796b5c3ca5e292f1faf9aee27b2e7a07c5af0b6762afd970faaa9d5f8b9d14311cef5339ee23f SHA512 b240c053fa6ce438d32c662457bcf20f1767d2b07d0375782c541e18f616e89a5ad27c5bb967f9273d953239d46c9ed64cd5c73467d4dc12e18f88d4853bb00b DIST cteq66.tar.gz 8647237 BLAKE2B 3ac47b6eee434f89ff329cfcb8268782af4ffa552ca4b412a59254e9b10410518f9fe9543b47f193d9cd31b06fc1101556df2be01c25ca17febcb9fb1855e5ca SHA512 25d0fa01dcdb59d71c7092367af8258471a2bc6dfd146766cc79f90ffb0feafa0f2011d0a37a7d75315c10ba7c7a6e3fa583d9c0a28119b072228ac800294e48 DIST cteq6l1.tar.gz 317834 BLAKE2B eccad131853f9a760d0dfd43a3f8705f8edbac3ec7373de9ef9a8936f13ba06500ba5758cd04649dd1b85ac04fc778e9d96222877e74e9ff02263455b233fa41 SHA512 7177608e97077eaf45a292db4ea74eb9a28b4b500ab8be02098b4837a5583cd397828abc3bf43ead448926eaa75ae3968bd059ecde333d90ed6e4295cbe1873c diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild index 784d94f97..84256bbc9 100644 --- a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild +++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild @@ -7,11 +7,14 @@ LHA_VER="6.2.1" IUSE_LHAPDF_SETS=" lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed lhapdf_sets_pdf4lhc15_nlo_asvar + lhapdf_sets_pdf4lhc15_nnlo_100 lhapdf_sets_ct14qed_proton lhapdf_sets_ct14lo lhapdf_sets_ct14nlo lhapdf_sets_ct10 + lhapdf_sets_ct10nnlo lhapdf_sets_mrst2007lomod + lhapdf_sets_nnpdf23_nlo_as_0119_qed lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc lhapdf_sets_cteq66 @@ -21,6 +24,8 @@ IUSE_LHAPDF_SETS=" lhapdf_sets_nnpdf31_nnlo_as_0118 " +DESCRIPTION="LHAPDF data grids" +HOMEPAGE="https://lhapdf.hepforge.org/" COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current" HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_VER}" # Alternatively to fetching them here already the user can install them by lhapdf install, @@ -29,11 +34,14 @@ HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_ SRC_URI=" lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118_luxqed.tar.gz ) lhapdf_sets_pdf4lhc15_nlo_asvar? ( ${COMMON_URI}/PDF4LHC15_nlo_asvar.tar.gz ) + lhapdf_sets_pdf4lhc15_nnlo_100? ( ${COMMON_URI}/PDF4LHC15_nnlo_100.tar.gz ) lhapdf_sets_ct14qed_proton? ( ${COMMON_URI}/CT14qed_proton.tar.gz ) lhapdf_sets_ct14lo? ( ${COMMON_URI}/CT14lo.tar.gz ) lhapdf_sets_ct14nlo? ( ${COMMON_URI}/CT14nlo.tar.gz ) lhapdf_sets_ct10? ( ${COMMON_URI}/CT10.tar.gz ) + lhapdf_sets_ct10nnlo? ( ${COMMON_URI}/CT10nnlo.tar.gz ) lhapdf_sets_mrst2007lomod? ( ${COMMON_URI}/MRST2007lomod.tar.gz ) + lhapdf_sets_nnpdf23_nlo_as_0119_qed? ( ${COMMON_URI}/NNPDF23_nlo_as_0119_qed.tar.gz ) lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nlo_as_0119_qed_mc.tar.gz ) lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz ) lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz ) @@ -46,15 +54,12 @@ SRC_URI=" MY_PV=$(ver_cut 1-3) MY_PF=LHAPDF-${MY_PV} -DESCRIPTION="LHAPDF data grids" -HOMEPAGE="https://lhapdf.hepforge.org/" -KEYWORDS="~amd64 ~x86" S="${WORKDIR}" - LICENSE="public-domain" + SLOT="0" +KEYWORDS="~amd64 ~x86" IUSE="${IUSE_LHAPDF_SETS}" -SLOT="0" RDEPEND="sci-physics/lhapdf" DEPEND="${RDEPEND}" diff --git a/sci-physics/openloops/Manifest b/sci-physics/openloops/Manifest index 9fa410972..d11ce8193 100644 --- a/sci-physics/openloops/Manifest +++ b/sci-physics/openloops/Manifest @@ -1,4 +1,13 @@ DIST OpenLoops-OpenLoops-2.1.3.tar.bz2 3769562 BLAKE2B ddb664a7310662e2d0891e31870d614c191b0248f1b4c8816d4f33b6709005eea7435fda73c354092a28d55a0b106ec9358fb4e4a7a6ed592d61208ff5334e85 SHA512 a5ae2431506f8e169c42dd1d5fa3db70b4e2d62dfa744041fcd61d8554daba0700d453e9198e50a3e85cb3f196277c0f011fb408fd5913cd6a1c42ed71bb9d51 +DIST OpenLoops-OpenLoops-2.1.4.tar.bz2 3779464 BLAKE2B e4ccec44fe42b2b40a37a4367771d36bd9ae328b9dd202da6037f037fe8e63fcbf8492213fed448f8ea8c913dc1dff1331a488d589990f22c66b8563c6923c2e SHA512 282c0389f230c1e8e1c6226c6aa3099ae510c9d095ee2002bafdf14da2b2701e539bc8f347427927a92c769e1d01c123bc62abf57c29e21249576c913db24f48 +DIST ppajj-93a6e3f7.tar.bz2 1531886 BLAKE2B 75bd4fca293a5cdc352ae24f34b7bbd1416d73938638699bb6a24bf06163739d7c3f0f4ee8aed03779c5f5d6147c459c92ea68ccb13f28ed8186fd25339b58fc SHA512 5685c1d07ec44ecca1e2138755234b3c7bcccbf49d8e37117197ac713918e237831770554821ee2872d39d4785385ef4ecdb2b257e02bff1d17d057731f3e7c6 +DIST pphllj_ew-93a6e3f7.tar.bz2 2853671 BLAKE2B 98c8bb6b6ef41308add690d1b7f25c31e1d79005435e7ff472ef937b5718fc049489c95a2a93df8adb934b1101a585754bc57b1448e17116d712a3c3713d6192 SHA512 62977dc67c2d46e7a072605d73bb6ac86ce8eb5c7b7816e4636097853e0fb2203cc40826fe2357a3272207bc3f3f2eb67d0dc2b2a6df15d12dcef2ef46681075 +DIST ppjj-d3d5302.tar.bz2 342377 BLAKE2B 75811ea600ca8a45884d1af8eb99e5f5e5f114009fd7894ac14a454c2f4c395b03a5a6c941c9f4ad63ea1e23a4b76eacc54f0f417c7f5ec9cbde95480134290c SHA512 f31123573a7dd109c1a0edcf7765aaf3d9ffae387e40a3d58b2511a2e251e37dce3b87402ba54353528f63b811a107274ab183544117d8a0845951c6922c700c +DIST ppjjj-93a6e3f7.tar.bz2 2410772 BLAKE2B 51644d9863fc7d82437f001f5cafdd3e42a34d3b4b540d8e269f365b3ff6238ffa7cb51e4460a12f043b970378c4c55b5304aa09207652b84905091aa5bf4152 SHA512 11465f71b039c0a7522e22ec0c77ce24cb12a2666d58999240897c955bc2834f5e3a6cb606147b10f865c41ebcc780fe505b40eba45f436fac00f3ea79ab3faa +DIST pplla-a3a36918.tar.bz2 586129 BLAKE2B 465a7a04f70540d0d9fdde86568ffd1bceec0914753d9129e40199d6a1bfc803802b0721ad1ab964ee4427f60fc6765c0ae2003a4ce225bf91d3ff5274dfcfe1 SHA512 b2a012966fc370625635948d7547982d1d2c9afc27557b07eb4d06214f9c99af5ba9fc05e391e733110cead8d2b6bf515c9d06bba44781fa05fb51b9bddef6ca +DIST pplla_ew-0a26af9a.tar.bz2 1512376 BLAKE2B 363ff99624248ad24824272f6a3ced26b32d597880d70344dce2690a6eaf451e05ca76eeaafa6b36ba1deebe09f429dccdc774b52b778f9c824426d65ed28dfe SHA512 2858ae591eb372a26597f842d0ed3bf90fdb27e883db3a968e7c449fc569ec6fa28ecef11e4a6f9626596d9a391aff7a4f744bf46faa17b146958c3e09cc9a8a +DIST ppllaj-c77e3a3.tar.bz2 2695198 BLAKE2B 1f725da89f693fe0efa113498a2b3c192300c41b8f7b2c09b2ce3f7db930abce3dae8d4af1ff3761e426bb3dd9f81a149edd13f90ac1fd7cbe97d3344e7e5569 SHA512 ec0eeb1b569da1f0cc13782c19f13e3c63fa27ff9a3faa596f7066cbbc8e1214a4ce416ffa1b9ecd6754d721373edce3925b970b1d52866c0c4160e85641744c +DIST ppllajj-4d8743c.tar.bz2 23114828 BLAKE2B 4fc271bc23b65fb69f68559904b44e01fa45849956b81d48b81d0d41023409fd109b3db6d8b1675df6c6311c62a80b9a35054def366171cc64c9db55cb5bda3b SHA512 c30d76e52988b162241935fba033df565673f83114da265acb300ea12436406ac0614d01e64a09c1b0cfeba2f9a27ea9d96d59e0e37d67211655c0a524584e34 DIST ppllj-a3a36918.tar.bz2 475014 BLAKE2B b73022c23c082637eb2658fafab716eb749b87de5304ef6672552e7bbbb637a915d0f29c4dee352d9d6f18af7c4139047405bf031bf3986e7353fe73ac82903c SHA512 7ffb11b8910782a9316b86388a2de2d7ce7b9fdc2742bec8065f22a143cf1c988447480d10a629c4b820d5d8b1248bc10eab78560cd51b22fd3fe4a23b596b99 DIST pplljj-93a6e3f7.tar.bz2 2472469 BLAKE2B e4d22ff93ffcd3eaf2583ddfd107d75ecfca5abbcfc125d305f0a149b11b2c3784be95f3d2b473f7aee6c9819863f01bfbf3cd4b06dae8ed2ec6542f6acb1a62 SHA512 d52ee86f8b7aa5e6a339b82e0e6bd30eff5e6666ad3b1d33bc4c1122ef77dd986836abcc70b7936f10f66bd65e29dc938221da45c9654fcab2340085200c523a DIST pplnj_ckm-4d8743c.tar.bz2 399934 BLAKE2B dbbc0f9d832c9d1758bdf7166b1936c8ecb48053981d2f96fc7ba0bd4a740515863d6b07ab4a1ec1c88cc267787f9ee061ebfc812c4f457fa4a9d135f6df64e2 SHA512 fc4e5797412951a9144bda5856d14aec9d0d4b2f4a89d9afd2d97573149498d76cdc92b9b96915b7ebd318656d44ad9c3bfa0bd14dbb2bb871f665613156075e diff --git a/sci-physics/openloops/metadata.xml b/sci-physics/openloops/metadata.xml index a32ce734b..f88ff31ee 100644 --- a/sci-physics/openloops/metadata.xml +++ b/sci-physics/openloops/metadata.xml @@ -19,9 +19,17 @@ <flag name="collier">Build with collier</flag> <flag name="extra">Build libs with extra</flag> <flag name="cuttools">Build with cuttools</flag> + <flag name="pplla-ew">Build pp to lla process with EW corrections</flag> <flag name="ppllj">Build pp to llj process</flag> <flag name="pplljj">Build pp to lljj process</flag> <flag name="pplnj-ckm">Build pp to lnj process with ckm matrix</flag> <flag name="pplnjj-ckm">Build pp to lljj process with ckm matrix</flag> + <flag name="ppjj">Build pp to jj process</flag> + <flag name="ppjjj">Build pp to jjj process</flag> + <flag name="ppajj">Build pp to ajj process</flag> + <flag name="pphllj-ew">Build pp to hllj process with EW corrections</flag> + <flag name="pplla">Build pp to lla process</flag> + <flag name="ppllaj">Build pp to llaj process</flag> + <flag name="ppllajj">Build pp to llajj process</flag> </use> </pkgmetadata> diff --git a/sci-physics/openloops/openloops-2.1.3-r1.ebuild b/sci-physics/openloops/openloops-2.1.3-r2.ebuild index ebe75037f..af10ffe93 100644 --- a/sci-physics/openloops/openloops-2.1.3-r1.ebuild +++ b/sci-physics/openloops/openloops-2.1.3-r2.ebuild @@ -24,13 +24,14 @@ SRC_URI=" pplljj? ( ${COMMON_URI}/pplljj/-/archive/93a6e3f7/pplljj-93a6e3f7.tar.bz2 ) pplnj-ckm? ( ${COMMON_URI}/pplnj_ckm/-/archive/4d8743c/pplnj_ckm-4d8743c.tar.bz2 ) pplnjj-ckm? ( ${COMMON_URI}/pplnjj_ckm/-/archive/d3d5302/pplnjj_ckm-d3d5302.tar.bz2 ) + pplla-ew? ( ${COMMON_URI}/pplla_ew/-/archive/0a26af9a/pplla_ew-0a26af9a.tar.bz2 ) " S="${WORKDIR}/${MY_PN}-${MY_P}" LICENSE="GPL-3+" SLOT="0" KEYWORDS="~amd64" -IUSE="+collier +cuttools +extra ppllj pplljj pplnj-ckm pplnjj-ckm" +IUSE="+collier +cuttools +extra pplla-ew ppllj pplljj pplnj-ckm pplnjj-ckm" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" @@ -78,7 +79,7 @@ src_prepare() { src_compile() { escons --cache-disable - for OLPROC in ppllj pplljj pplnj_ckm pplnjj_ckm; do + for OLPROC in pplla_ew ppllj pplljj pplnj_ckm pplnjj_ckm; do if use ${OLPROC//_/-}; then # move downloaded files to src mkdir -p "${S}/process_src/${OLPROC}" || die @@ -92,7 +93,7 @@ src_compile() { cat <<-EOF >> openloops.cfg || die process_src_dir = ${EPREFIX}/opt/${MY_P}/process_src/ process_obj_dir = ${EPREFIX}/opt/${MY_P}/process_obj/ - process_lib_dir = ${EPREFIX}/usr/$(get_libdir)/ + process_lib_dir = ${EPREFIX}/opt/${MY_P}/proclib/ EOF } @@ -106,16 +107,14 @@ src_install() { cd ../lib || die dolib.so libolcommon.so* libopenloops.so* librambo.so* libtrred.so* + cd .. || die # install processes - if [ -d "../proclib" ]; then - cd ../proclib || die - dolib.so *.so - # also install the process info files - insinto /usr/$(get_libdir)/ - doins *.info + if [ -d "./proclib" ]; then + dodir "/opt/${MY_P}/proclib" + mv proclib/* "${ED}/opt/${MY_P}/proclib/" || die fi - cd ../lib_src/olcommon/mod || die + cd ./lib_src/olcommon/mod || die doheader *.mod cd ../../openloops/mod || die doheader *.mod @@ -135,5 +134,5 @@ src_install() { pkg_postinst() { elog "Install processes with openloops libinstall." - elog "They are installed in ${EPREFIX}/usr/$(get_libdir)/." + elog "They are installed in ${EPREFIX}/opt/${MY_P}/proclib/." } diff --git a/sci-physics/openloops/openloops-2.1.4.ebuild b/sci-physics/openloops/openloops-2.1.4.ebuild new file mode 100644 index 000000000..a4f2dba56 --- /dev/null +++ b/sci-physics/openloops/openloops-2.1.4.ebuild @@ -0,0 +1,146 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) + +inherit fortran-2 python-single-r1 scons-utils toolchain-funcs + +MY_PN=OpenLoops +MY_P=${MY_PN}-${PV} + +DESCRIPTION="Evaluation of tree and one-loop matrix elements for any Standard Model." +HOMEPAGE="https://openloops.hepforge.org/index.html" +#SRC_URI="https://openloops.hepforge.org/downloads?f=${MY_P}.tar.gz -> ${MY_P}.tar.gz" +#S="${WORKDIR}/${MY_P}" +# since the files are not publicly versioned we mirror them from +# https://www.physik.uzh.ch/data/openloops/repositories/public/processes/2 +COMMON_URI="https://gitlab.com/openloopsmirror/" + +SRC_URI=" + https://gitlab.com/openloops/OpenLoops/-/archive/${MY_P}/${MY_PN}-${MY_P}.tar.bz2 + ppajj? ( ${COMMON_URI}/ppajj/-/archive/93a6e3f7/ppajj-93a6e3f7.tar.bz2 ) + pphllj-ew? ( ${COMMON_URI}/pphllj_ew/-/archive/93a6e3f7/pphllj_ew-93a6e3f7.tar.bz2 ) + ppjj? ( ${COMMON_URI}/ppjj/-/archive/d3d5302/ppjj-d3d5302.tar.bz2 ) + ppjjj? ( ${COMMON_URI}/ppjjj/-/archive/93a6e3f7/ppjjj-93a6e3f7.tar.bz2 ) + pplla? ( ${COMMON_URI}/pplla/-/archive/a3a36918/pplla-a3a36918.tar.bz2 ) + ppllaj? ( ${COMMON_URI}/ppllaj/-/archive/c77e3a3/ppllaj-c77e3a3.tar.bz2 ) + ppllajj? ( ${COMMON_URI}/ppllajj/-/archive/4d8743c/ppllajj-4d8743c.tar.bz2 ) + pplla-ew? ( ${COMMON_URI}/pplla_ew/-/archive/0a26af9a/pplla_ew-0a26af9a.tar.bz2 ) + ppllj? ( ${COMMON_URI}/ppllj/-/archive/a3a36918/ppllj-a3a36918.tar.bz2 ) + pplljj? ( ${COMMON_URI}/pplljj/-/archive/93a6e3f7/pplljj-93a6e3f7.tar.bz2 ) + pplnj-ckm? ( ${COMMON_URI}/pplnj_ckm/-/archive/4d8743c/pplnj_ckm-4d8743c.tar.bz2 ) + pplnjj-ckm? ( ${COMMON_URI}/pplnjj_ckm/-/archive/d3d5302/pplnjj_ckm-d3d5302.tar.bz2 ) + +" +S="${WORKDIR}/${MY_PN}-${MY_P}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+collier +cuttools +extra pplla-ew ppllj pplljj pplnj-ckm pplnjj-ckm ppjj ppjjj ppajj pphllj-ew pplla ppllaj ppllajj" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + sci-physics/qcdloop + sci-physics/oneloop[dpkind,qpkind16,-qpkind,-cppintf] + collier? ( sci-physics/collier[-static-libs] ) + cuttools? ( sci-physics/cuttools[dummy] ) + ${PYTHON_DEPS} +" +DEPEND="${RDEPEND}" + +src_prepare() { + default + mv openloops.cfg.tmpl openloops.cfg || die + sed -i "s|\\\$BASEDIR/scons -Q|scons -Q -C /opt/${MY_P}/|g" openloops || die + if use extra ; then + sed -i "s|#compile_extra.*|compile_extra = 1|" openloops.cfg || die + fi + + cat <<-EOF >> openloops.cfg || die + compile_libraries = rambo trred + link_libraries = $(usev collier) $(usev cuttools) + ccflags = ${CFLAGS} + cxxflags = ${CXXFLAGS} + f_flags = ${FFLAGS} -I${ESYSROOT}/usr/include/ -I${ESYSROOT}/usr/include/cuttools -lcollier + link_flags = ${LDFLAGS} -I${ESYSROOT}/usr/include/ -I${ESYSROOT}/usr/include/cuttools -lcollier + cc = $(tc-getCC) + cxx = $(tc-getCXX) + fortran_compiler = $(tc-getFC) + + release = $PV + import_env = @all + EOF + + # fix rename for py3.12 + sed -i 's/SafeConfigParser/ConfigParser/g' pyol/tools/OLBaseConfig.py || die + # wipe local scons + rm -r scons-local || die + rm scons || die +} + +src_compile() { + escons --cache-disable + for OLPROC in pplla_ew ppllj pplljj pplnj_ckm pplnjj_ckm ppjj ppjjj ppajj pphllj_ew pplla ppllaj ppllajj; do + if use ${OLPROC//_/-}; then + # move downloaded files to src + mkdir -p "${S}/process_src/${OLPROC}" || die + mv "${WORKDIR}/${OLPROC}-"*/* "${S}/process_src/${OLPROC}" || die + # compile it + escons auto=${OLPROC} generator=0 + fi + done + + # insert these later since we are done with compiling in ${S} now + cat <<-EOF >> openloops.cfg || die + process_src_dir = ${EPREFIX}/opt/${MY_P}/process_src/ + process_obj_dir = ${EPREFIX}/opt/${MY_P}/process_obj/ + process_lib_dir = ${EPREFIX}/opt/${MY_P}/proclib/ + EOF +} + +src_install() { + dosym ../opt/${MY_P} /opt/OpenLoops2 + dobin openloops + cd include || die + doheader openloops.h + + newenvd - 99openloops2 <<- _EOF_ + OpenLoopsPath=${EPREFIX}/opt/OpenLoops2 + _EOF_ + + # Also install so.version links + cd ../lib || die + dolib.so libolcommon.so* libopenloops.so* librambo.so* libtrred.so* + + cd .. || die + # install processes + if [ -d "./proclib" ]; then + dodir "/opt/${MY_P}/proclib" + mv proclib/* "${ED}/opt/${MY_P}/proclib/" || die + fi + + cd ./lib_src/olcommon/mod || die + doheader *.mod + cd ../../openloops/mod || die + doheader *.mod + cd ../../rambo/mod || die + doheader *.mod + cd ../../trred/mod || die + doheader *.mod + + cd "${S}" || die "Failed to cd into ${S}" + insinto /opt/${MY_P} + doins openloops.cfg SConstruct + doins -r pyol + + # no need to also install the source code + #doins -r process_src +} + +pkg_postinst() { + elog "Install processes with openloops libinstall." + elog "They are installed in ${EPREFIX}/opt/${MY_P}/proclib/." +} diff --git a/sci-physics/photos/photos-3.64.ebuild b/sci-physics/photos/photos-3.64.ebuild index 32c09af64..5b920400e 100644 --- a/sci-physics/photos/photos-3.64.ebuild +++ b/sci-physics/photos/photos-3.64.ebuild @@ -19,7 +19,7 @@ S="${WORKDIR}/${MY_PN}" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64" -IUSE="doc examples hepmc2 hepmc3 pythia tauola" +IUSE="+hepmc3 doc examples hepmc2 pythia tauola" RDEPEND=" hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] ) diff --git a/sci-physics/pyhepmc/Manifest b/sci-physics/pyhepmc/Manifest index 1351fa866..db277d121 100644 --- a/sci-physics/pyhepmc/Manifest +++ b/sci-physics/pyhepmc/Manifest @@ -1 +1,2 @@ DIST pyhepmc-2.11.0.tar.gz 361596 BLAKE2B 18264f61bdef3c27f8aa4d48d25257c03f98cc89745533641119cf7ba6d5fe36c084d25ccaeed6769dc9226fd5f2c27060006030447a8ac8409ff6d752437d2c SHA512 31975d0bee5037c1cc36753ce6324342ed6a48b2d3f91f53d61f445f38f0fa3ecbeb0e29fcbc7f6778bafcc23c1f6a689b9516eae8da4cc620cd7c72b89e0b00 +DIST pyhepmc-2.14.0.tar.gz 398256 BLAKE2B 3de49a1935c06f562590baf98bd76b49ffd48865d0f2d1674898cc68178304b9978c28079cf6111504a0732913916e9b26725169072b1867e343531568c02e6a SHA512 cb94dc3d306430cefd72b13d01826d56f8547a96da480a51558063126499f351115a0713649c6e3cbea9fc049b5c39368f3ad762e3990a5ea1d4b84e6ee79295 diff --git a/sci-physics/pyhepmc/pyhepmc-2.14.0.ebuild b/sci-physics/pyhepmc/pyhepmc-2.14.0.ebuild new file mode 100644 index 000000000..f99145a7f --- /dev/null +++ b/sci-physics/pyhepmc/pyhepmc-2.14.0.ebuild @@ -0,0 +1,21 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +inherit distutils-r1 pypi + +DESCRIPTION="A Pythonic wrapper for the HepMC3 C++ library." +HOMEPAGE="https://github.com/scikit-hep/pyhepmc" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.2[${PYTHON_USEDEP}] +" +BDEPEND=" + ${RDEPEND} + dev-build/cmake +" diff --git a/sci-physics/pylhe/Manifest b/sci-physics/pylhe/Manifest index cc103d71e..af93fd85b 100644 --- a/sci-physics/pylhe/Manifest +++ b/sci-physics/pylhe/Manifest @@ -1,3 +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 +DIST pylhe-0.9.1.gh.tar.gz 225008 BLAKE2B f18ecc5b3cc1370e8a10db974042ef54364672bc78aabd1f5c259e3cf0259feea5ad860ee9e27e74b0f5cebcc7f2c36bffd970aeeaf27dc957f1aba367d5ceb8 SHA512 ca2a81ad71ad6589e8ab9de9687533dc7209321bbcb44ef7645a67e3ea9805c940c11ecbbb699eb5f46d634fc2d0dbbac1fefc79ab765790e897f454d108c667 diff --git a/sci-physics/pylhe/pylhe-0.7.0.ebuild b/sci-physics/pylhe/pylhe-0.9.1.ebuild index 45ef91695..fa3002e86 100644 --- a/sci-physics/pylhe/pylhe-0.7.0.ebuild +++ b/sci-physics/pylhe/pylhe-0.9.1.ebuild @@ -1,7 +1,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{11..12} ) -DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 pypi DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files" @@ -16,14 +16,13 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND=" + >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}] >=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}] " -DEPEND="${RDEPEND}" BDEPEND=" - dev-python/setuptools-scm[${PYTHON_USEDEP}] + dev-python/hatch-vcs[${PYTHON_USEDEP}] test? ( >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}] ) diff --git a/sci-physics/qgraf/Manifest b/sci-physics/qgraf/Manifest index c633a5b46..9333381da 100644 --- a/sci-physics/qgraf/Manifest +++ b/sci-physics/qgraf/Manifest @@ -1,4 +1,4 @@ DIST qgraf-3.4.2.tgz 358979 BLAKE2B 06c5cf82faab531d6d17387d62e80b2e395ad0ffd80a69dc49608588f4acdf23d226877db047d3906963b5f64d85329665fed0e10359ddbb649122fb328b78f8 SHA512 e86f94480eaf7cd0b4d79b60ec1420c21f0285133f2184d1c0a1d05ec0d9abc3e483d100d43c38fafc06bf8cecea413c0304adcb64d900522e877b1a24e7b61b -DIST qgraf-3.5.2.tgz 426930 BLAKE2B 0bd50cbefee9a91cdfe9a15a53fb018c1b15088b211a03dde63f08410bbac4acd7586ef4cece17debd5197d3d5b7a8c889aeec27d7f3f137df7ef95f1687a709 SHA512 1e1fbafc80c60a663537a5ca555f405ec1517beccf09e2f68fcd9c84963b4b20d3a66e77980c4c4ff68f82950dc41f4492dc0272fdf5e3c105861fcf4c0e8c80 -DIST qgraf-3.6.7.tgz 460592 BLAKE2B d4275d7e5b9138eab3a2848b1e75883a4d52b61bdddd2ecbefe674559a56d9315bb03bd86c5a607f01d708c634f35b180f4cfde99242e65a40bf3f81ce6fa9e3 SHA512 c721eb82975a6077da77a82f7875d0e0346e21932d0312109d1bab68391a0210fc3f7ff79327d515668dedee0c5fce4e01d7433177232c43a4e39d8204f01405 -DIST qgraf-4.0.1.tgz 420190 BLAKE2B 3f13757da764c6b9653e1c3463557223d5e87cc7f376967300c094c8d96942ab807500a0a2d570a66600cb926681bbda5ed6c69c44dbffbba1f481d2eb7f8459 SHA512 e5f3b586b29413c71434ac144dc2355959f4e736aa5ad55fa17f888d4ddc7cc1bf2ff92cc544e538471c13aea95ddd1d9248f71622f84d4daa173abbbbb0dc8a +DIST qgraf-3.5.3.tgz 432499 BLAKE2B 16c851d81743e6be196a9039ff6675d298fd0f127a14f1f968188d4d1e277dd6e25aa445a0ca784032666d12acb443470c8ad8f2fca896e9f524bb080e5bbcc4 SHA512 64dba189e3565794d08cab7835e58e853cfcf2c8ce4f7e401d32ae488a743be57e00a45c88cb235259b687fd58a05adc87c4994ea3e3accf648cc4e6cd3f0faa +DIST qgraf-3.6.9.tgz 461476 BLAKE2B 8f7ddd88e65d9ba58d4930eb1a5fdc048f59b64b0ef6c67e7a920a3f2b9b8e50a9d461029d63b176238ae5c21567170a2ba20d9b5b2b53563e4dc5b3ec4eef7e SHA512 0a9a436e7f95526e3f16e131ea68dcb344310a57e92016428804e7f70538baffa890a9a516f5ec9c5c77d2ef9c9e05e39c21a28cd4c1f0fea56655e9c68ede08 +DIST qgraf-4.0.5.tgz 500340 BLAKE2B c6fa90724e192f57e1ee83e9f12c736884ef870e5844fe630c62e012672156bc24a39335e2f1cd1155b93e9fd92e70d889b71c6671ceb550fb4ee14fb0eb9b2d SHA512 31e10e36e6587a8bc0af371b214b14d36e81b9c909626a620ed24d1e2ffda11f8c0b77a6113e1fadfacd715533b7da89441d19159879d9720cb7f49bbfe7f38d diff --git a/sci-physics/qgraf/qgraf-4.0.1.ebuild b/sci-physics/qgraf/qgraf-3.5.3.ebuild index 942ef732a..942ef732a 100644 --- a/sci-physics/qgraf/qgraf-4.0.1.ebuild +++ b/sci-physics/qgraf/qgraf-3.5.3.ebuild diff --git a/sci-physics/qgraf/qgraf-3.5.2.ebuild b/sci-physics/qgraf/qgraf-3.6.9.ebuild index 4194295a4..942ef732a 100644 --- a/sci-physics/qgraf/qgraf-3.5.2.ebuild +++ b/sci-physics/qgraf/qgraf-3.6.9.ebuild @@ -11,10 +11,10 @@ SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgr S="${WORKDIR}" LICENSE="all-rights-reserved" -RESTRICT="bindist mirror" SLOT="0" KEYWORDS="~amd64" IUSE="doc examples" +RESTRICT="bindist mirror" src_compile() { $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" diff --git a/sci-physics/qgraf/qgraf-3.6.7.ebuild b/sci-physics/qgraf/qgraf-4.0.5.ebuild index 4194295a4..1a2533a2c 100644 --- a/sci-physics/qgraf/qgraf-3.6.7.ebuild +++ b/sci-physics/qgraf/qgraf-4.0.5.ebuild @@ -3,21 +3,22 @@ EAPI=8 -inherit toolchain-funcs fortran-2 +inherit fortran-2 DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models" HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html" SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz" -S="${WORKDIR}" +S="${WORKDIR}/${P}.dir" LICENSE="all-rights-reserved" -RESTRICT="bindist mirror" SLOT="0" KEYWORDS="~amd64" IUSE="doc examples" +RESTRICT="bindist mirror" src_compile() { - $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" + sed -i -e 's:gfortran:$(FC) $(FFLAGS) $(LDFLAGS):' Makefile || die + emake qgraf } src_install() { diff --git a/sci-physics/recola2-SM/Manifest b/sci-physics/recola2-SM/Manifest new file mode 100644 index 000000000..b5d0abd2f --- /dev/null +++ b/sci-physics/recola2-SM/Manifest @@ -0,0 +1 @@ +DIST recola2-SM-2.2.3.tar.gz 252881 BLAKE2B e8ad77ee8800ca910b1e589434b692c2ca2b86c1a92b75ebcb54eb91019f0958258bf3730a15fd6dea757b0495fcbd1590522dd4b09f34803280472c57dd3b6e SHA512 b53aba890c4a231c23e0562c15ea8b6ba6788d7dbdb07a9e594ffe65b8a32e31c0c7341a711ac61ffe1fa9c3d60fb27acbef1dc88aa534579b9e3dda45c722c2 diff --git a/sci-biology/beaglecall/metadata.xml b/sci-physics/recola2-SM/metadata.xml index 138cb7705..bdee6992b 100644 --- a/sci-biology/beaglecall/metadata.xml +++ b/sci-physics/recola2-SM/metadata.xml @@ -2,11 +2,11 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> </maintainer> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> </maintainer> </pkgmetadata> diff --git a/sci-physics/recola2-SM/recola2-SM-2.2.3.ebuild b/sci-physics/recola2-SM/recola2-SM-2.2.3.ebuild new file mode 100644 index 000000000..476311bac --- /dev/null +++ b/sci-physics/recola2-SM/recola2-SM-2.2.3.ebuild @@ -0,0 +1,33 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit fortran-2 cmake + +MY_P="SM_${PV}" + +DESCRIPTION="RECOLA2 Standard Model" +HOMEPAGE="https://recola.gitlab.io/recola2/index.html" +SRC_URI="https://recola.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=" + sci-physics/collier +" +RDEPEND="${DEPEND}" + +src_configure() { + local mycmakeargs=( + -DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir) + -DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake + -DCMAKE_PREFIX_PATH=/usr/$(get_libdir) + ) + cmake_src_configure +} diff --git a/sci-physics/recola2/Manifest b/sci-physics/recola2/Manifest new file mode 100644 index 000000000..7cbcbdf95 --- /dev/null +++ b/sci-physics/recola2/Manifest @@ -0,0 +1 @@ +DIST recola2-2.2.4.tar.gz 266646 BLAKE2B 706a17e0e50b9582151313999677dbf2ed3b675dd96ba721463c503d3acb8b074690987cd729d15d193e851683341178df77793cc984ff8d0b5cd46d49d22d5d SHA512 9d1095de6d1bf6b13b08cd0e3aa3d7a7c2717872d18ef1cddd17801614a9dd24c4540f5e09bebfe4f9ee8f37c9aac6f88e45867b8d84b59ecd5383fe082187ee diff --git a/sci-physics/recola2/metadata.xml b/sci-physics/recola2/metadata.xml new file mode 100644 index 000000000..9b3a974d2 --- /dev/null +++ b/sci-physics/recola2/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + RECOLA is a Fortran95 computer program for the automated generation and numerical computation of tree and one-loop amplitudes at next-to-leading order (EW, QCD) in the Standard Model (SM) and Beyond the SM (BSM). + </longdescription> + <use> + <flag name="SM">Use SM model</flag> + </use> +</pkgmetadata> diff --git a/sci-physics/recola2/recola2-2.2.4.ebuild b/sci-physics/recola2/recola2-2.2.4.ebuild new file mode 100644 index 000000000..1d96f2b4b --- /dev/null +++ b/sci-physics/recola2/recola2-2.2.4.ebuild @@ -0,0 +1,49 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" +PYTHON_COMPAT=( python3_{10..13} ) + +inherit fortran-2 cmake python-single-r1 + +DESCRIPTION="Recursive Computation of 1-Loop Amplitudes." +HOMEPAGE="https://recola.gitlab.io/recola2/index.html" +SRC_URI="https://recola.hepforge.org/downloads/?f=${P}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="+SM" # TODO add more models here and below +REQUIRED_USE="${PYTHON_REQUIRED_USE} || ( SM )" + +DEPEND=" + sci-mathematics/otter + sci-physics/collier + SM? ( sci-physics/recola2-SM ) + ${PYTHON_DEPS} +" +RDEPEND="${DEPEND}" + +src_prepare() { + # CMAKE should look in system install for required libs + sed -e 's/NO_DEFAULT_PATH//g' -i src/CMakeLists.txt || die + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir) + -DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake/recola + -DCMAKE_PREFIX_PATH=/usr/$(get_libdir)/ + -Dwith_python3=ON + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + python_optimize +} diff --git a/sci-physics/tauola/metadata.xml b/sci-physics/tauola/metadata.xml index fcbc9de77..86d6c9418 100644 --- a/sci-physics/tauola/metadata.xml +++ b/sci-physics/tauola/metadata.xml @@ -14,7 +14,6 @@ TAUOLA is a program that simulates the decays of polarized tau leptons, which are elementary particles that belong to the lepton family. Tau leptons are heavier than electrons and muons, and they can decay into various final states, such as hadrons, leptons, and neutrinos. TAUOLA can generate Monte Carlo events for tau lepton decays, taking into account the polarization, spin correlations, and radiative corrections. TAUOLA can also model anomalous and lepton flavor violating decays, which are beyond the standard model of particle physics. </longdescription> <use> - <flag name="hepmc"> Compile with <pkg>sci-physics/hepmc</pkg> version 2 interface </flag> <flag name="hepmc2"> Compile with <pkg>sci-physics/hepmc</pkg> version 2 interface </flag> <flag name="hepmc3"> Compile with <pkg>sci-physics/hepmc</pkg> version 3 interface </flag> <flag name="pythia"> Compile with <pkg>sci-physics/pythia</pkg> connection </flag> diff --git a/sci-physics/tauola/tauola-1.1.8.ebuild b/sci-physics/tauola/tauola-1.1.8.ebuild deleted file mode 100644 index 4d4742dd1..000000000 --- a/sci-physics/tauola/tauola-1.1.8.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -MYPN=TAUOLA - -DESCRIPTION="Tau decay Monte Carlo generator" -HOMEPAGE="https://tauolapp.web.cern.ch/tauolapp/" -SRC_URI="https://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.${PV}/${MYPN}.${PV}.tar.gz" - -#HepMC interface is licensed under GPL, other code under CPC -LICENSE="CPC GPL-2+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples hepmc tau-spinner" - -RDEPEND=" - hepmc? ( sci-physics/hepmc ) - tau-spinner? ( sci-physics/lhapdf ) -" -DEPEND="${RDEPEND} - doc? ( - app-text/doxygen[dot] - app-text/ghostscript-gpl - app-text/texlive - ) -" - -S="${WORKDIR}/${MYPN}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.1.3-tau-spinner-makefile.patch -) - -src_configure() { - econf \ - --without-mc-tester \ - --without-pythia8 \ - $(use_with hepmc hepmc "${EPREFIX}/usr") \ - --without-hepmc3 \ - $(use_with tau-spinner) \ - $(use_with tau-spinner lhapdf "${EPREFIX}/usr") -} - -src_compile() { - emake -j1 - if use doc; then - cd "${S}/documentation/doxy_documentation" || die - default - cd "${S}/documentation/latex_documentation" || die - default - fi -} - -src_install() { - emake DESTDIR="${ED}" install - - if use doc; then - dodoc documentation/doxy_documentation/html/* - dodoc documentation/latex_documentation/Tauola_interface_design.pdf - fi - - if use examples; then - dodoc -r examples - use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples - fi -} diff --git a/sci-physics/uproot/Manifest b/sci-physics/uproot/Manifest index e8cdc29cf..4b1084697 100644 --- a/sci-physics/uproot/Manifest +++ b/sci-physics/uproot/Manifest @@ -1,2 +1,3 @@ DIST uproot-5.3.1.tar.gz 919910 BLAKE2B 6c138a56ecabb08905e1edde8c776c3dfae6cca3213bbc3546e7241979052178e1c9718c1fcf298573669bcc4c004806cd54ab16050405038f76f3ef356fb184 SHA512 2525f372caa3b25e3a11b170ce981ce253a7b9ca1fdb2c04b6bb1093b166d206a28e9bc22ffa19dead76870f521cee44a812cbf41a087b34fb9a3bc52c210733 DIST uproot-5.4.1.tar.gz 935958 BLAKE2B bde5d0d5e2cef6ff35cdaea49656d2d30052a9b2f5d576e61e2df82c0a438c192db69aaffb89bd1acdb96df7aa925197ecf52ea6068bdb30d8819615b358cdfe SHA512 dc0b9b9859b7564b2027bb3f013a0fac07c665dcf32c84a3981e3fc27254598126a4bcbfb77863b419e461dec1a8c37c1e3bc181b894ea52fc141144469aedc0 +DIST uproot-5.5.1.tar.gz 941313 BLAKE2B 067c70a5d3e5c5c3b2021a565437e52e9dcb2a4db4dce780f3fc3f6f58a1b07e1e36f404096d806fb0e96b63a1e5e8fa0a52d18cc0c043b62435b7e22739cf5f SHA512 3eabeaee0d08cbac1df6cf3e705bdbde709e933e271468bdcfe9c58832af5ff2cc88f8bb09321891a3eb55e10160806ddb0beb9377c311c135f124194f04b35c diff --git a/sci-physics/uproot/uproot-5.5.1.ebuild b/sci-physics/uproot/uproot-5.5.1.ebuild new file mode 100644 index 000000000..7d3b910d5 --- /dev/null +++ b/sci-physics/uproot/uproot-5.5.1.ebuild @@ -0,0 +1,30 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${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-props/fsleyes-props-1.8.2.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild index 860a6315b..fb41e5ac4 100644 --- a/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild +++ b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 virtualx diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild index 11f8a76ed..9b7457975 100644 --- a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild +++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 virtualx diff --git a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild index c63c53e6e..ba1589f46 100644 --- a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild +++ b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_11 ) DISTUTILS_USE_PEP517=setuptools inherit xdg distutils-r1 desktop virtualx |