diff options
65 files changed, 938 insertions, 140 deletions
diff --git a/dev-python/aiohttp-retry/Manifest b/dev-python/aiohttp-retry/Manifest new file mode 100644 index 000000000..f050b37c0 --- /dev/null +++ b/dev-python/aiohttp-retry/Manifest @@ -0,0 +1 @@ +DIST aiohttp-retry-2.8.3.gh.tar.gz 11952 BLAKE2B f2ea6f7b2f13001bd8d49b4529eacb3766cab080ff3a9457e40287bc797afebae10393a628cf78756074ca60a62df78c59c6120f1368316084155f1d7fd7cdfb SHA512 71869c3997e9b5089c298fa6f992b0ed08ca3da0f93c4f37566d8c6b9809bb1873a629cc47f1ffaeccac112d96036851794ee564b11c0f4f1eec00f49413358d diff --git a/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild new file mode 100644 index 000000000..25df27ba6 --- /dev/null +++ b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Simple retry client for aiohttp" +HOMEPAGE="https://github.com/inyutin/aiohttp_retry" +# Test suite missing from PyPI tarball, reported upstream: +# https://github.com/inyutin/aiohttp_retry/issues/94 +SRC_URI="https://github.com/inyutin/aiohttp_retry/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~arm ~arm64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND="dev-python/aiohttp[${PYTHON_USEDEP}]" + +BDEPEND=" + test? ( + dev-python/pytest-aiohttp[${PYTHON_USEDEP}] + dev-python/pytest-asyncio[${PYTHON_USEDEP}] + dev-python/pytest-tornasync[${PYTHON_USEDEP}] + )" + +distutils_enable_tests pytest diff --git a/dev-python/aiohttp-retry/metadata.xml b/dev-python/aiohttp-retry/metadata.xml new file mode 100644 index 000000000..900a7e9f8 --- /dev/null +++ b/dev-python/aiohttp-retry/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">inyutin/aiohttp_retry</remote-id> + <remote-id type="pypi">aiohttp-retry</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/fusepy/Manifest b/dev-python/fusepy/Manifest new file mode 100644 index 000000000..1654ec369 --- /dev/null +++ b/dev-python/fusepy/Manifest @@ -0,0 +1 @@ +DIST fusepy-3.0.1.tar.gz 11519 BLAKE2B c76319b0d0b64a8dc674b803551f32352fed9a1e6e050110963a159259c3fed8fefbb63cfe6dda689738f07cb796c6b9da14e3070c4a1cf5b70892a6ebe52cc2 SHA512 f913dfd9f29412daa8239548c8ad8bcc64f8fc7be1425bf34cd40a5c4d22faae67c5d5575c187395d911f64ad0dda186614ada598b38b9557e18794639d43767 diff --git a/dev-python/fusepy/fusepy-3.0.1.ebuild b/dev-python/fusepy/fusepy-3.0.1.ebuild new file mode 100644 index 000000000..6e9b3de3c --- /dev/null +++ b/dev-python/fusepy/fusepy-3.0.1.ebuild @@ -0,0 +1,20 @@ +# Copyright 2022-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Simple ctypes bindings for FUSE" +HOMEPAGE="https://github.com/fusepy/fusepy" + +LICENSE="ISC" +SLOT="0" +KEYWORDS="~amd64 ~x86" +RESTRICT="test" # No usable test phases + +DEPEND="sys-fs/fuse:0" +RDEPEND="${DEPEND}" diff --git a/dev-python/fusepy/metadata.xml b/dev-python/fusepy/metadata.xml new file mode 100644 index 000000000..53cf5c2f9 --- /dev/null +++ b/dev-python/fusepy/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <upstream> + <remote-id type="pypi">fusepy</remote-id> + <remote-id type="github">fusepy/fusepy</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/hist/Manifest b/dev-python/hist/Manifest new file mode 100644 index 000000000..f9d572709 --- /dev/null +++ b/dev-python/hist/Manifest @@ -0,0 +1,2 @@ +DIST hist-2.7.2.tar.gz 991866 BLAKE2B 6785114e1a5b3e38b9917c5d8b660e6d03dbe56d7a3238c971686ffc03ec1e9c6361ea6ed73ed61b10a4074b13d4ad785b676a61a856069ba23789985949787e SHA512 92a320a80509eaeaa496c2713b349e3b1442c46a7aeda04e362fdd692aea3f43f06e5bdb35293ca70f9b24536c24494fa1c806e9f9e8573559c13abeee22c4ce +DIST hist-2.7.3.tar.gz 992241 BLAKE2B 865e4a7d65633c42d114139390040872d630527292f2941eb70732c1456d5f2571026d2a131f0bc09015a5922d6f6557342f4fb00ec91eeb83bb8b2bc25f28fd SHA512 85c7231f2cbc7bd8d7066f664a8fe9cd54092f79a242c353bdf3fad47ae7040f52b836238a92f006cdf30d2a3ae1e3a0c6bc1d8afaf2004f2056f6da5398d2b2 diff --git a/dev-python/hist/hist-2.7.2.ebuild b/dev-python/hist/hist-2.7.2.ebuild new file mode 100644 index 000000000..082844a5f --- /dev/null +++ b/dev-python/hist/hist-2.7.2.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Histogramming for analysis powered by boost-histogram " +HOMEPAGE="https://github.com/scikit-hep/hist" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/boost-histogram-1.3.1[${PYTHON_USEDEP}] + >=dev-python/histoprint-2.2.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.14.5[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +RESTRICT="test" +# needs mplhep and dask_histogram ... +#distutils_enable_tests pytest diff --git a/dev-python/hist/hist-2.7.3.ebuild b/dev-python/hist/hist-2.7.3.ebuild new file mode 100644 index 000000000..082844a5f --- /dev/null +++ b/dev-python/hist/hist-2.7.3.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Histogramming for analysis powered by boost-histogram " +HOMEPAGE="https://github.com/scikit-hep/hist" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/boost-histogram-1.3.1[${PYTHON_USEDEP}] + >=dev-python/histoprint-2.2.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.14.5[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +RESTRICT="test" +# needs mplhep and dask_histogram ... +#distutils_enable_tests pytest diff --git a/dev-python/hist/metadata.xml b/dev-python/hist/metadata.xml new file mode 100644 index 000000000..566083fe3 --- /dev/null +++ b/dev-python/hist/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Hist is an analyst-friendly front-end for boost-histogram, designed for Python 3.7+ (3.6 users get version 2.4) + </longdescription> + <upstream> + <remote-id type="pypi">hist</remote-id> + <remote-id type="github">scikit-hep/hist</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/histoprint/Manifest b/dev-python/histoprint/Manifest new file mode 100644 index 000000000..2914a2419 --- /dev/null +++ b/dev-python/histoprint/Manifest @@ -0,0 +1 @@ +DIST histoprint-2.4.0.tar.gz 359154 BLAKE2B f10abcff02875f1a27b31256c5daf00500e0177986052f3fc9b013a0be0f63daf58f9d9b7bf2b6b5510758e080a118c6ad07801b055019e7e226ee631da57154 SHA512 bbf7c90acb66c298588304a15c7ae3ec0536fb01a468b4aa7b944115e242a0ef3e2ef21c181e8476845f5d7611a944f43de0c9cf80faeab2ddbb8422432e2fa6 diff --git a/dev-python/histoprint/histoprint-2.4.0.ebuild b/dev-python/histoprint/histoprint-2.4.0.ebuild new file mode 100644 index 000000000..b6395b898 --- /dev/null +++ b/dev-python/histoprint/histoprint-2.4.0.ebuild @@ -0,0 +1,20 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Pretty print histograms to the console" +HOMEPAGE="https://github.com/scikit-hep/histoprint" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/click-7.0.0[${PYTHON_USEDEP}] + >=dev-python/uhi-0.2.1[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/histoprint/metadata.xml b/dev-python/histoprint/metadata.xml new file mode 100644 index 000000000..78373f05f --- /dev/null +++ b/dev-python/histoprint/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Histoprint uses a mix of terminal color codes and Unicode trickery (i.e. combining characters) to plot overlaying histograms. Some terminals are not able to display Unicode combining characters correctly. Histoprint can still be used in those terminals, but the character set needs to be constrained to the non-combining ones (see below). + </longdescription> + <upstream> + <remote-id type="pypi">histoprint</remote-id> + <remote-id type="github">scikit-hep/histoprint</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/linesep/Manifest b/dev-python/linesep/Manifest new file mode 100644 index 000000000..99369e648 --- /dev/null +++ b/dev-python/linesep/Manifest @@ -0,0 +1 @@ +DIST linesep-0.5.0.tar.gz 23979 BLAKE2B 78413c41b5002c8d4edf28c97eb8867416710ed5164d872bce845debfd4d17ac6aa03d7f4a36ef3e22160f517913e1f57c2d99a1ef4963941001892211f0386f SHA512 fe91aea8f4f36e722edc025fbfc452488bcef9a8dfef85b36a446f33a5a0c079102538a0f141ec7474325d5948214082790c53a928d1b7453d7d1e56622714fb diff --git a/dev-python/linesep/files/linesep-0.5.0-nocov.patch b/dev-python/linesep/files/linesep-0.5.0-nocov.patch new file mode 100644 index 000000000..a27bbd4b8 --- /dev/null +++ b/dev-python/linesep/files/linesep-0.5.0-nocov.patch @@ -0,0 +1,12 @@ +diff --git a/tox.ini b/tox.ini +index 4d45597..cdd9e18 100644 +--- a/tox.ini ++++ b/tox.ini +@@ -31,7 +31,6 @@ commands = + mypy src test + + [pytest] +-addopts = --cov=linesep --no-cov-on-fail + asyncio_mode = strict + doctest_optionflags = IGNORE_EXCEPTION_DETAIL + filterwarnings = error diff --git a/dev-python/linesep/linesep-0.5.0.ebuild b/dev-python/linesep/linesep-0.5.0.ebuild new file mode 100644 index 000000000..148ff0883 --- /dev/null +++ b/dev-python/linesep/linesep-0.5.0.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) +inherit distutils-r1 pypi + +DESCRIPTION="Handling lines with arbitrary separators" +HOMEPAGE="https://github.com/jwodder/linesep" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +BDEPEND=" + test? ( + dev-python/pytest-subtests[${PYTHON_USEDEP}] + ) +" + +PATCHES=( "${FILESDIR}/${P}-nocov.patch" ) + +distutils_enable_tests pytest diff --git a/dev-python/linesep/metadata.xml b/dev-python/linesep/metadata.xml new file mode 100644 index 000000000..017856905 --- /dev/null +++ b/dev-python/linesep/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">jwodder/linesep</remote-id> + <remote-id type="pypi">linesep</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/methodtools/Manifest b/dev-python/methodtools/Manifest new file mode 100644 index 000000000..f11018f95 --- /dev/null +++ b/dev-python/methodtools/Manifest @@ -0,0 +1 @@ +DIST methodtools-0.4.7.gh.tar.gz 6789 BLAKE2B 83da6aae76dc8fe7035e21a03396398c3c72ab7e94bf5850da233dbc95da0c549f2f64a24e3ace4cc093243e846f418e97a6427f66a8ad9ba910bafd11217d61 SHA512 78fbdd3232673159bbef0ea53d8bc1502d70335751e6e91106a02ff9ddea99d44a69037506516492b3e864137b80819b1679809b287049270e623b4ebe667554 diff --git a/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch new file mode 100644 index 000000000..e2ff8a4c1 --- /dev/null +++ b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch @@ -0,0 +1,9 @@ +--- a/setup.cfg 2023-02-05 08:15:17.000000000 -0500 ++++ b/setup.cfg 2024-05-06 11:19:57.822360100 -0400 +@@ -35,6 +35,5 @@ + [aliases] + test=pytest + [tool:pytest] +-addopts=--verbose --cov-config .coveragerc --cov methodtools + python_files = tests/test*.py + norecursedirs=.git py ci diff --git a/dev-python/methodtools/metadata.xml b/dev-python/methodtools/metadata.xml new file mode 100644 index 000000000..e85efd512 --- /dev/null +++ b/dev-python/methodtools/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">youknowone/methodtools</remote-id> + <remote-id type="pypi">methodtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/methodtools/methodtools-0.4.7.ebuild b/dev-python/methodtools/methodtools-0.4.7.ebuild new file mode 100644 index 000000000..79e7739c5 --- /dev/null +++ b/dev-python/methodtools/methodtools-0.4.7.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) +inherit distutils-r1 + +DESCRIPTION="Expand functools features to methods, classmethods, staticmethods" +HOMEPAGE="https://github.com/youknowone/methodtools" +# Not using PyPI archive because it misses test files: +# https://github.com/youknowone/methodtools/issues/24 +SRC_URI="https://github.com/youknowone/methodtools/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/wirerope[${PYTHON_USEDEP}]" + +PATCHES=( "${FILESDIR}/${P}-nocov.patch" ) + +distutils_enable_tests pytest diff --git a/dev-python/prov/Manifest b/dev-python/prov/Manifest new file mode 100644 index 000000000..afbcb1608 --- /dev/null +++ b/dev-python/prov/Manifest @@ -0,0 +1 @@ +DIST prov-2.0.0.tar.gz 131878 BLAKE2B 65f14ad3a7dc6e10d03b0d778be02d3a3a7e4cae7b8aedf54117446eefe51546fb30e9ca602b2d5780fab8abde4ed1d56ed7385815db64a7879623a481b050be SHA512 6d05c88855f23d5dc22b0eccce0af935c0ad3d227b7a257ff205ad8566ed9607f614c13427ac8dd922e79bd477ca125b9d3f9492f5f65ae55ab8e8f3b9b97307 diff --git a/dev-python/prov/metadata.xml b/dev-python/prov/metadata.xml new file mode 100644 index 000000000..d1559163d --- /dev/null +++ b/dev-python/prov/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <!-- maintainer-needed --> + <longdescription lang="en"> + A library for W3C Provenance Data Model supporting PROV-O + (RDF), PROV-XML, PROV-JSON import/export Interface to + Graphviz’s Dot language. + </longdescription> + <upstream> + <remote-id type="pypi">prov</remote-id> + <remote-id type="github">trungdong/prov</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/prov/prov-2.0.0.ebuild b/dev-python/prov/prov-2.0.0.ebuild new file mode 100644 index 000000000..a87b15c6f --- /dev/null +++ b/dev-python/prov/prov-2.0.0.ebuild @@ -0,0 +1,43 @@ +# 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_{9..12} ) +inherit distutils-r1 pypi + +DESCRIPTION="W3C provenance data dodel library" +HOMEPAGE="https://pypi.org/project/prov/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + >=dev-python/networkx-1.10[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest + +# Reported upstream: +# https://github.com/trungdong/prov/issues/156 +EPYTEST_DESELECT=( + src/prov/tests/test_model.py::TestAttributesBase + src/prov/tests/test_rdf.py::TestStatementsBase + src/prov/tests/test_rdf.py::TestAttributesBase2 + src/prov/tests/test_rdf.py::TestQualifiedNamesBase + src/prov/tests/test_rdf.py::TestAttributesBase + src/prov/tests/test_model.py::TestStatementsBase + src/prov/tests/test_model.py::TestExamplesBase::test_all_examples + src/prov/tests/test_model.py::TestQualifiedNamesBase + src/prov/tests/test_rdf.py::RoundTripRDFTests::test_namespace_inheritance + src/prov/tests/test_rdf.py::RoundTripRDFTests::test_default_namespace_inheritance + src/prov/tests/test_rdf.py::TestRDFSerializer::test_json_to_ttl_match + src/prov/tests/test_rdf.py::TestJSONExamplesBase::test_all_examples + src/prov/tests/test_rdf.py::TestExamplesBase::test_all_examples +) diff --git a/dev-python/wirerope/Manifest b/dev-python/wirerope/Manifest new file mode 100644 index 000000000..ae2ee16cb --- /dev/null +++ b/dev-python/wirerope/Manifest @@ -0,0 +1 @@ +DIST wirerope-0.4.7.gh.tar.gz 12220 BLAKE2B 1ed861b71cfbfb4c0d18a2c09f6cf96f545d9a88617e7618053c4e5459317532e12195a02e3f3d99a0cc91bf0601c39404b80e4e631a86b24a5926718b4cb287 SHA512 cfa7222503a9c03f9afe6cab9acc45d7115795169325692c5c519913406f8abc4d78d84769d24ff123ca47333f7ea8dde3a8a7961d34d0e20aebc02e0a420aaf diff --git a/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch new file mode 100644 index 000000000..64d47d0b7 --- /dev/null +++ b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch @@ -0,0 +1,10 @@ +--- a/setup.cfg 2023-02-05 08:00:42.000000000 -0500 ++++ b/setup.cfg 2024-05-06 11:01:02.896234948 -0400 +@@ -33,7 +33,6 @@ + sphinx + + [tool:pytest] +-addopts=--verbose --cov-config .coveragerc --cov wirerope + python_files = tests/test_*.py + norecursedirs=.git py ci + [flake8] diff --git a/dev-python/wirerope/metadata.xml b/dev-python/wirerope/metadata.xml new file mode 100644 index 000000000..6e39bae5d --- /dev/null +++ b/dev-python/wirerope/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">youknowone/wirerope</remote-id> + <remote-id type="pypi">wirerope</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/wirerope/wirerope-0.4.7.ebuild b/dev-python/wirerope/wirerope-0.4.7.ebuild new file mode 100644 index 000000000..74e7f40bd --- /dev/null +++ b/dev-python/wirerope/wirerope-0.4.7.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) +inherit distutils-r1 + +DESCRIPTION="A wrapper interface for python callables" +HOMEPAGE="https://github.com/youknowone/wirerope" +# Not using PyPI archive because it misses test files: +# https://github.com/youknowone/wirerope/issues/20 +SRC_URI="https://github.com/youknowone/wirerope/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/six[${PYTHON_USEDEP}] +" + +PATCHES=( "${FILESDIR}/${P}-nocov.patch" ) + +distutils_enable_tests pytest diff --git a/dev-vcs/datalad-fuse/Manifest b/dev-vcs/datalad-fuse/Manifest new file mode 100644 index 000000000..cebf299ec --- /dev/null +++ b/dev-vcs/datalad-fuse/Manifest @@ -0,0 +1 @@ +DIST datalad-fuse-0.5.1.gh.tar.gz 66846 BLAKE2B 7b6311060bc8434ff48006775199c8bcac30a37feb55a516dd5df754a2c81f062bcd6717f977365d4db08f97e587fc105e7721ff54e08ae90db159b2fb1c81c3 SHA512 9e479008325b6673bb0714dcfc86776361a6764f2218ed70ca229a76ac04e352c76b7c41e1aba13939ccfec186f2ad00b0c1a15eefc42f9b81af4041fcb4fe32 diff --git a/dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild new file mode 100644 index 000000000..e043b122f --- /dev/null +++ b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild @@ -0,0 +1,32 @@ +# 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="Keep code, data, containers under control with git and git-annex" +HOMEPAGE="https://github.com/datalad/datalad" +SRC_URI="https://github.com/datalad/datalad-fuse/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/aiohttp-retry[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + dev-python/methodtools[${PYTHON_USEDEP}] + dev-python/linesep[${PYTHON_USEDEP}] + dev-python/fusepy[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + sys-fs/fuse +" + +distutils_enable_tests pytest + +PATCHES=( + "${FILESDIR}/${P}-git_config.patch" +) diff --git a/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch new file mode 100644 index 000000000..f62fc412e --- /dev/null +++ b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch @@ -0,0 +1,15 @@ +Upstreamed and perhaps removable for future releases: +https://github.com/datalad/datalad-fuse/pull/113 +diff --git a/datalad_fuse/tests/test_fsspec_head.py b/datalad_fuse/tests/test_fsspec_head.py +index 75a6efc..1ffc60f 100644 +--- a/datalad_fuse/tests/test_fsspec_head.py ++++ b/datalad_fuse/tests/test_fsspec_head.py +@@ -131,6 +131,8 @@ def test_git_repo(tmp_path): + TEXT = (Path(__file__).with_name("data") / "text.txt").read_bytes() + (tmp_path / "text.txt").write_bytes(TEXT) + subprocess.run(["git", "add", "text.txt"], cwd=tmp_path, check=True) ++ subprocess.run(["git", "config", "user.email", "place@holder.org"], cwd=tmp_path, check=True) ++ subprocess.run(["git", "config", "user.name", "Place Holder"], cwd=tmp_path, check=True) + subprocess.run(["git", "commit", "-m", "Add a file"], cwd=tmp_path, check=True) + ds = Dataset(tmp_path) + assert_in_results( diff --git a/dev-vcs/datalad-fuse/metadata.xml b/dev-vcs/datalad-fuse/metadata.xml new file mode 100644 index 000000000..97f1a33f3 --- /dev/null +++ b/dev-vcs/datalad-fuse/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">datalad/datalad-fuse</remote-id> + <remote-id type="pypi">datalad-fuse</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest index 7875ed2b6..6d9dda572 100644 --- a/dev-vcs/datalad/Manifest +++ b/dev-vcs/datalad/Manifest @@ -1 +1,2 @@ DIST datalad-0.19.6.tar.gz 1420979 BLAKE2B 49d8e19449652f284f89f99e6696c6d1abf7ddcc58a8eb00004c657be38ce2532ed9c11855dca4a0a8f82c55fbf1633f53ff2bdea063fd18ad946145d27a3404 SHA512 db7cd807a8106727f0b6f587be8c0ce3abcf0dc7cf72b4757e6b44650adca05482e6b0a6c1719050fba37660dcd5de2a6f27df044a8db180ac6855ee7ff8cbda +DIST datalad-1.0.2.tar.gz 1420919 BLAKE2B 0a5209b11cb2eaa710a423be72ad500a6b0041d7248d22be469d5e2ad7699fad30600f34f52d32c59bf069c3c5698f020fa0b7a07ce7b63e1154b548e63a6e73 SHA512 8c1bc7742687699ac21b5495b3dd6ef495da172e7c1d4e48206fd957943b18cf7c21887f4bae623b5352c34fa5e1192789b1d2a8c23883e3617e47946b8789cf diff --git a/dev-vcs/datalad/datalad-1.0.2.ebuild b/dev-vcs/datalad/datalad-1.0.2.ebuild new file mode 100644 index 000000000..de5b6cd6a --- /dev/null +++ b/dev-vcs/datalad/datalad-1.0.2.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="Keep code, data, containers under control with git and git-annex" +HOMEPAGE="https://github.com/datalad/datalad" +#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test +downloaders +metadata +publish misc" +RESTRICT="!test? ( test )" + +RDEPEND=" + >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] + app-arch/p7zip + app-arch/patool[${PYTHON_USEDEP}] + dev-python/annexremote[${PYTHON_USEDEP}] + dev-python/distro[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/iso8601[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/platformdirs[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/wraps[${PYTHON_USEDEP}] + dev-vcs/git-annex + downloaders? ( + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/msgpack[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + ) + metadata? ( + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/whoosh[${PYTHON_USEDEP}] + ) + misc? ( + dev-python/argcomplete[${PYTHON_USEDEP}] + dev-python/pyperclip[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + ) + publish? ( + dev-vcs/python-gitlab[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + test? ( + ${RDEPEND} + dev-python/beautifulsoup4[${PYTHON_USEDEP}] + dev-python/httpretty[${PYTHON_USEDEP}] + dev-python/mypy[${PYTHON_USEDEP}] + dev-python/vcrpy[${PYTHON_USEDEP}] + ) +" +# Also wants test dep: +# dev-python/types-requests +# dev-python/types-python-dateutil + +distutils_enable_tests pytest + +EPYTEST_DESELECT=( + tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time + tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time_with_func + tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_hello +) + +python_test() { + local -x DATALAD_TESTS_NONETWORK=1 + # see test groups in "tox.ini" + epytest -k "not turtle and not slow and not usecase" +} diff --git a/profiles/package.mask b/profiles/package.mask index efc64be51..48068ccf9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -35,10 +35,4 @@ sci-biology/multiqc # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24) -# Dependencies dev-python/prov removed -sci-libs/nipype # reverse deps -sci-biology/samri -sci-biology/samri_bidsdata -sci-biology/samri_bindata -dev-python/heudiconv diff --git a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild index 09f89265f..c7d2bd0c3 100644 --- a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild +++ b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild @@ -9,8 +9,8 @@ inherit cmake fortran-2 DESCRIPTION="Fortran library to compute positions of celestial bodies" HOMEPAGE="http://libthesky.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz - mirror://sourceforge/${PN}/libthesky-data-20160409.tar.bz2 +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz + https://downloads.sourceforge.net/${PN}/libthesky-data-20160409.tar.bz2 " LICENSE="GPL-3" diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild index 49f2b6d9f..096349f5a 100644 --- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild +++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild @@ -16,7 +16,7 @@ KEYWORDS="~amd64" RDEPEND=" >=sci-biology/bioperl-1.4 >=sci-biology/velvet-0.7.5.1 - dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh + dev-lang/perl[perl_features_ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh src_install(){ dobin VelvetOptimiser.pl diff --git a/sci-biology/afni-datasets/Manifest b/sci-biology/afni-datasets/Manifest new file mode 100644 index 000000000..99d2de1a8 --- /dev/null +++ b/sci-biology/afni-datasets/Manifest @@ -0,0 +1 @@ +DIST afni-datasets-20240503.tar.gz 57863597 BLAKE2B 07508c1d7b7d162a8116887ead440e3dd728ec53c19eb5b6c6662dfcc7c51ed13b1e9fdce2289410c1225010329b6ab3f9917d45f48a906571ba9c83747470f4 SHA512 5636ab403335c0ed8b34c00d89b38344654cda783fd928af632dd72f7cb51803b35caa60bc0561b8a1684870670d2977f3471ef6083676db33f172b41adb47f5 diff --git a/sci-biology/afni-datasets/afni-datasets-20240503.ebuild b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild new file mode 100644 index 000000000..4d554a633 --- /dev/null +++ b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_P="afni_atlases_dist_2024_0503" + +DESCRIPTION="Datasets for using and testing sci-biology/afni" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI="https://afni.nimh.nih.gov/pub/dist/atlases/${MY_P}.tgz -> ${P}.tar.gz" + +S="${WORKDIR}/${MY_P}" +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_install() { + insinto /usr/share/${PN} + doins -r * +} diff --git a/sci-biology/afni-datasets/metadata.xml b/sci-biology/afni-datasets/metadata.xml new file mode 100644 index 000000000..cb6710311 --- /dev/null +++ b/sci-biology/afni-datasets/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>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index d1e783ff1..ef61a42fb 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,4 +1,3 @@ -DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8 DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild deleted file mode 100644 index 557fbd579..000000000 --- a/sci-biology/afni/afni-24.0.04-r1.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..12} ) - -DISTUTILS_USE_PEP517=setuptools -inherit cmake distutils-r1 toolchain-funcs - -GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" -NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" -GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" - -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" -SRC_URI=" - https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz - https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz - https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz - " - -SLOT="0" -LICENSE="GPL-3+" -KEYWORDS="~amd64 ~x86" -IUSE="test whirlgif" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-libs/glib:2 - dev-libs/libf2c - dev-libs/expat - dev-build/ninja - media-libs/freeglut - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sci-libs/gts - sys-devel/llvm:* - sys-libs/libomp - virtual/jpeg-compat:62 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXmu - x11-libs/libXpm - x11-libs/libXt - x11-libs/motif[-static-libs] - " -DEPEND=" - ${RDEPEND} - app-shells/tcsh - " - -S="${WORKDIR}/afni-AFNI_${PV}" - -src_prepare() { - tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die - tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die - cmake_src_prepare - default - } - -src_configure() { - if use !whirlgif; then - eapply "${FILESDIR}/${P}-whirlgif.patch" - fi - export CFLAGS="-pthread ${CFLAGS}" - export GIT_REPO_VERSION=3.0.1.1 - local mycmakeargs=( - -DLIBDIR=/usr/$(get_libdir) - -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) - -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) - -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) - -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) - -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) - -DCOMP_COREBINARIES=ON - -DUSE_SYSTEM_NIFTI=OFF - -DUSE_SYSTEM_GIFTI=OFF - -DUSE_SYSTEM_XMHTML=OFF - -DUSE_SYSTEM_GTS=ON - -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" - -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" - -DCOMP_GUI=ON - -DCOMP_PLUGINS=ON - -DUSE_OMP=ON - -DCOMP_PYTHON=OFF - -DUSE_SYSTEM_F2C=ON - ) - tc-export CC - cmake_src_configure -} - -src_compile() { - cmake_src_compile - pushd src/python_scripts - distutils-r1_src_compile - popd -} - -src_install() { - cmake_src_install - pushd src/python_scripts - distutils-r1_src_install - popd - cd "${D}" - rm usr/bin/mpeg_encode -} diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r3.ebuild index 20293877f..12d6c8f87 100644 --- a/sci-biology/afni/afni-24.0.08-r1.ebuild +++ b/sci-biology/afni/afni-24.0.08-r3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) DISTUTILS_USE_PEP517=setuptools inherit cmake distutils-r1 toolchain-funcs @@ -12,30 +12,33 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" SRC_URI=" https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz " -SLOT="0" +S="${WORKDIR}/afni-AFNI_${PV}" + LICENSE="GPL-3+" +SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test whirlgif" RESTRICT="!test? ( test )" RDEPEND=" + dev-build/ninja + dev-libs/expat dev-libs/glib:2 dev-libs/libf2c - dev-libs/expat - dev-build/ninja media-libs/freeglut media-libs/glu media-libs/netpbm media-libs/qhull media-video/mpeg-tools + sci-biology/afni-datasets sci-libs/gsl sci-libs/gts sys-devel/llvm:* @@ -57,8 +60,6 @@ DEPEND=" #Update jpeg-compat to virtual/jpeg:0 # look for xmhtlm -S="${WORKDIR}/afni-AFNI_${PV}" - #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die src_prepare() { tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die @@ -71,8 +72,9 @@ src_configure() { if use !whirlgif; then eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake export CFLAGS="-pthread ${CFLAGS}" - export GIT_REPO_VERSION=3.0.1.1 local mycmakeargs=( -DLIBDIR=/usr/$(get_libdir) -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) @@ -111,4 +113,13 @@ src_install() { popd cd "${D}" rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo } diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni new file mode 100644 index 000000000..dbf463f47 --- /dev/null +++ b/sci-biology/afni/files/97afni @@ -0,0 +1 @@ +export AFNI_ATLAS_PATH=/usr/share/afni-datasets diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 49bf65452..56c76a408 100644 --- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -7,7 +7,7 @@ inherit toolchain-funcs DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage" HOMEPAGE="https://codonw.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz +SRC_URI="https://downloads.sourceforge.net/${PN}/CodonWSourceCode_${PV//./_}.tar.gz https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" LICENSE="GPL-2" diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild index 5d89c0822..42fc0b62d 100644 --- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild +++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild @@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs DESCRIPTION="Micro Read Fast Alignment Search Tool" HOMEPAGE="http://mrfast.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index 3064c0ba5..92c788f28 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -27,7 +27,7 @@ BDEPEND=" RDEPEND=" >=dev-python/joblib-0.12[${PYTHON_USEDEP}] >=dev-python/numpy-1.16[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.21[${PYTHON_USEDEP}] >=dev-python/scipy-1.2[${PYTHON_USEDEP}] >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}] >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}] diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index 425e79444..4dbe5101e 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -25,7 +25,7 @@ RDEPEND=" >=dev-python/requests-2[${PYTHON_USEDEP}] >=dev-python/scipy-1.5[${PYTHON_USEDEP}] >=sci-libs/nibabel-3[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.22[${PYTHON_USEDEP}] " PATCHES=( "${FILESDIR}/${P}-tests.patch" ) diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild index bae672851..bc15bb8f4 100644 --- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild +++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild @@ -5,7 +5,7 @@ EAPI=7 DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR" HOMEPAGE="http://perlprimer.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2" LICENSE="GPL-2" SLOT="0" diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild index c1000fea9..467fa623c 100644 --- a/sci-libs/gdcm/gdcm-3.0.14.ebuild +++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild @@ -9,8 +9,8 @@ inherit cmake python-single-r1 DESCRIPTION="Cross-platform DICOM implementation" HOMEPAGE="http://gdcm.sourceforge.net/" -SRC_URI="mirror://sourceforge/gdcm/${P}.tar.bz2 - test? ( mirror://sourceforge/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release +SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2 + test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release LICENSE="BSD" SLOT="0" diff --git a/sci-libs/libsufr/libsufr-0.7.7.ebuild b/sci-libs/libsufr/libsufr-0.7.7.ebuild index 3515005bc..cd49de6b5 100644 --- a/sci-libs/libsufr/libsufr-0.7.7.ebuild +++ b/sci-libs/libsufr/libsufr-0.7.7.ebuild @@ -9,7 +9,7 @@ inherit cmake fortran-2 DESCRIPTION="LIBrary of Some Useful Fortran Routines" HOMEPAGE="http://libsufr.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" diff --git a/sci-libs/lwpr/lwpr-1.2.5.ebuild b/sci-libs/lwpr/lwpr-1.2.5.ebuild index 3415656a9..2f040a86e 100644 --- a/sci-libs/lwpr/lwpr-1.2.5.ebuild +++ b/sci-libs/lwpr/lwpr-1.2.5.ebuild @@ -9,7 +9,7 @@ inherit docs DESCRIPTION="The Locally Weighted Projection Regression Library" HOMEPAGE="https://web.inf.ed.ac.uk/slmc" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="LGPL-2.1" SLOT="0" diff --git a/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild index de2fa76c1..123404533 100644 --- a/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild +++ b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild @@ -9,7 +9,7 @@ inherit cmake fortran-2 DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs" HOMEPAGE="http://pg2plplot.sourceforge.net" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild index c6ab40229..7c5137bca 100644 --- a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild +++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild @@ -9,7 +9,7 @@ MY_P=${PN}${PV//.} DESCRIPTION="Java interface to WordNet dictionary data" HOMEPAGE="https://sourceforge.net/projects/jwordnet/" -SRC_URI="mirror://sourceforge/jwordnet/${MY_P//_rc/-rc}.zip" +SRC_URI="https://downloads.sourceforge.net/jwordnet/${MY_P//_rc/-rc}.zip" LICENSE="BSD" SLOT="0" diff --git a/sci-physics/jaxodraw-bin/Manifest b/sci-physics/jaxodraw-bin/Manifest new file mode 100644 index 000000000..a449139fe --- /dev/null +++ b/sci-physics/jaxodraw-bin/Manifest @@ -0,0 +1,3 @@ +DIST axodraw4j_2008_11_19.tar.gz 20930 BLAKE2B f2478df46f47c931bba71b1f43717d2d01a1a8282acc54582ed1ba5596dec8f03600e01f93a61ef4949f95a274a00b8ec62d2dffb283353de244950c4763531e SHA512 81bfcbd1b121104e0058654ac5520d0f570f9a915e9f6dfb8c52c11e9cf92f1e01c800182c2dc34e503a6eceafdff462b4f57dfa5bb5db979101a106c10d88c8 +DIST jaxodraw-2.1-0-bin.tar.gz 1241010 BLAKE2B 6dd5bbc09ed5b497c9c39a235a2f15c3b9cf2135f121af7d866a11a3458856c87a613e702f6dc71523506870fd94063992af42d1fc8ddd26c1be9ab83bf363b0 SHA512 4dbccabe22e8849af71e386b464201c2616d0f6475b905feb9fffc2687420b2b72af5c751d05aa1374a2806693ab2d6e256c3029bb0167f9ba6ea699b253669a +DIST jaxodraw-2.1-0-src.tar.gz 3777234 BLAKE2B df659a27762e7a05b461b520b9076a7eef1b5006a9ef3338fb0d5ec173a8cc6b0abf2f2de3d90a6c998439b19dad5dc9965a82622afc4e85227f175a9355183b SHA512 a829249823ec6b23248000a70ed5ccdc70d10f7212614e64162ba8bef53e6b59db042ff1f5205f07b1d521899f6505562311955fc95d8f374e81eec1135391aa diff --git a/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild new file mode 100644 index 000000000..e23381514 --- /dev/null +++ b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild @@ -0,0 +1,54 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +JAVA_PKG_IUSE="doc source" + +inherit desktop java-pkg-2 latex-package + +MY_PN="jaxodraw" +MY_PV=$(ver_rs 2 '-') +MY_P=${MY_PN}-${MY_PV} + +DESCRIPTION="Java program for drawing Feynman diagrams" +HOMEPAGE=" + https://jaxodraw.sourceforge.io/index.html + http://jaxodraw.sourceforge.net/ +" +SRC_URI=" + https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-bin.tar.gz + https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-src.tar.gz + latex? ( https://downloads.sourceforge.net/${MY_PN}/axodraw4j_2008_11_19.tar.gz ) +" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+latex" + +DEPEND=" + >=virtual/jdk-1.8 + latex? ( dev-texlive/texlive-pstricks:0 ) +" + +RDEPEND=">=virtual/jre-1.8" + +src_install() { + java-pkg_newjar ${MY_P}.jar + + newicon src/site/resources/images/favicon.ico jaxodraw.ico + make_desktop_entry jaxodraw JaxoDraw jaxodraw.ico + + use source && java-pkg_dosrc src/main/java/net + + dodoc src/doc/BUGS src/doc/CHANGELOG src/doc/README src/doc/TODO + use doc && java-pkg_dojavadoc build/javadoc + + java-pkg_dolauncher "${MY_P}" + + if use latex; then + cd "${WORKDIR}" || die "Failed to cd ${WORKDIR}" + latex-package_src_doinstall + fi +} diff --git a/sci-physics/jaxodraw-bin/metadata.xml b/sci-physics/jaxodraw-bin/metadata.xml new file mode 100644 index 000000000..7a665fa37 --- /dev/null +++ b/sci-physics/jaxodraw-bin/metadata.xml @@ -0,0 +1,15 @@ +<?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> + <upstream> + <remote-id type="sourceforge">jaxodraw</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/madgraph5/Manifest b/sci-physics/madgraph5/Manifest new file mode 100644 index 000000000..2a2eb6ab2 --- /dev/null +++ b/sci-physics/madgraph5/Manifest @@ -0,0 +1 @@ +DIST MadGraph5-3.5.3.tar.gz 30234007 BLAKE2B 092462f8a5653b11abff554b733f64e06ce35fc9559400208e9db1412d3b8357dcb3bd3653b99fd48ca9727f195099591d177f33e607a2fff3d339dee9aafb3b SHA512 b9d75a4c37e30a11a7e041b7c657a221a2ef27a5c3fafd09ec37ec5b2cfe953e0baa28dea73061ee155324f992b780259b8ddd6930b37a56894ffcf235ee960a diff --git a/sci-physics/madgraph5/files/cuttools.patch b/sci-physics/madgraph5/files/cuttools.patch new file mode 100644 index 000000000..0d6249af8 --- /dev/null +++ b/sci-physics/madgraph5/files/cuttools.patch @@ -0,0 +1,44 @@ +diff -Naru MG5_aMC_v2_9_6.orig/vendor/CutTools/makefile MG5_aMC_v2_9_6/vendor/CutTools/makefile +--- MG5_aMC_v2_9_6.orig/vendor/CutTools/makefile 2022-04-13 11:13:28.277248753 +0200 ++++ MG5_aMC_v2_9_6/vendor/CutTools/makefile 2022-04-13 11:13:43.702292725 +0200 +@@ -42,15 +42,15 @@ + endif + + cpmp: +- cp -p ./src/cts/cts_mpr.in ./src/cts/cts_mpr.h +- cp -p ./src/cts/cts_mpc.in ./src/cts/cts_mpc.h +- cp -p ./src/cts/cts_mprec.in ./src/cts/cts_mprec.h +- cp -p ./src/cts/cts_mpinit.in ./src/cts/cts_mpinit.h ++ cp ./src/cts/cts_mpr.in ./src/cts/cts_mpr.h ++ cp ./src/cts/cts_mpc.in ./src/cts/cts_mpc.h ++ cp ./src/cts/cts_mprec.in ./src/cts/cts_mprec.h ++ cp ./src/cts/cts_mpinit.in ./src/cts/cts_mpinit.h + cpqp: +- cp -p ./src/cts/cts_qpr.in ./src/cts/cts_mpr.h +- cp -p ./src/cts/cts_qpc.in ./src/cts/cts_mpc.h +- cp -p ./src/cts/cts_qprec.in ./src/cts/cts_mprec.h +- cp -p ./src/cts/cts_qpinit.in ./src/cts/cts_mpinit.h ++ cp ./src/cts/cts_qpr.in ./src/cts/cts_mpr.h ++ cp ./src/cts/cts_qpc.in ./src/cts/cts_mpc.h ++ cp ./src/cts/cts_qprec.in ./src/cts/cts_mprec.h ++ cp ./src/cts/cts_qpinit.in ./src/cts/cts_mpinit.h + + clean$(BLD): default + rm -fr $(BLD)/*.f +@@ -68,11 +68,11 @@ + + $(BLD)/version.h: + -mkdir -p $(BLD) +- cp -p ./src/avh/* $(BLD)/ +- cp -p ./src/cts/* $(BLD)/ +- cp -p ./src/mpfun90/* $(BLD)/ +- cp -p ./src/qcdloop/* $(BLD)/ +- cp -p ./src/makefile $(BLD)/ ++ cp ./src/avh/* $(BLD)/ ++ cp ./src/cts/* $(BLD)/ ++ cp ./src/mpfun90/* $(BLD)/ ++ cp ./src/qcdloop/* $(BLD)/ ++ cp ./src/makefile $(BLD)/ + + tar: + tar -czvf $(CTS_TAR) * diff --git a/sci-physics/madgraph5/madgraph5-3.5.3.ebuild b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild new file mode 100644 index 000000000..3ced7918c --- /dev/null +++ b/sci-physics/madgraph5/madgraph5-3.5.3.ebuild @@ -0,0 +1,93 @@ +# Copyright 2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# does not escape strings properly, so no python3_12 for now +PYTHON_COMPAT=( python3_11 ) +inherit fortran-2 python-single-r1 + +MY_PNN="MadGraph5" +MY_PV=$(ver_rs 1-3 '_') +MY_PN="MG5_aMC_v" +MY_PF=${MY_PN}${MY_PV} + +DESCRIPTION="MadGraph5_aMC@NLO" +HOMEPAGE="https://launchpad.net/mg5amcnlo" +SRC_URI="https://launchpad.net/mg5amcnlo/$(ver_cut 1).0/$(ver_cut 1-2).x/+download/${MY_PN}${PV}.tar.gz -> ${MY_PNN}-${PV}.tar.gz" +S="${WORKDIR}/${MY_PF}" + +LICENSE="UoI-NCSA" +SLOT="3" +KEYWORDS="~amd64" +# TODO add pineapple, herwig, syscalc, pjfrym, pineappl +IUSE="+hepmc2 +lhapdf +fastjet pythia collier thepeg" # td madanalysis5 ninja samurai golem95 +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + sys-libs/zlib + sys-devel/gcc:*[fortran] + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + ') + lhapdf? ( sci-physics/lhapdf[${PYTHON_SINGLE_USEDEP}] ) + fastjet? ( sci-physics/fastjet[${PYTHON_SINGLE_USEDEP}] ) + pythia? ( sci-physics/pythia:8=[examples] ) + hepmc2? ( sci-physics/hepmc:2 ) + collier? ( sci-physics/collier[static-libs] ) + thepeg? ( + sci-physics/thepeg[hepmc3(-),fastjet?,lhapdf?] + ) +" +# madanalysis5? ( sci-physics/madanalysis5 ) +# td? ( sci-physics/topdrawer ) +# ninja? ( sci-physics/ninja[static-libs] ) +# samurai? ( sci-physics/samurai ) +# golem95? ( sci-physics/golem95 ) +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}"/cuttools.patch ) + +src_unpack() { + # Perserve permissions + tar xvzf "${DISTDIR}/${MY_PNN}-${PV}.tar.gz" -C "${WORKDIR}" || die +} + +src_configure() { + cat <<-EOF >> input/mg5_configuration.txt || die + $(usex lhapdf "lhapdf_py3 = ${EPREFIX}/usr/bin/lhapdf-config" "") + $(usex fastjet "fastjet = ${EPREFIX}/usr/bin/fastjet-config" "") + $(usex pythia "pythia8_path = ${EPREFIX}/usr" "") + $(usex hepmc2 "hepmc_path = ${EPREFIX}/usr" "") + $(usex collier "collier = ${EPREFIX}/usr/$(get_libdir)" "") + $(usex thepeg "thepeg_path = ${EPREFIX}/usr/$(get_libdir)" "") + auto_update = 0 + EOF + + #use ninja && echo "ninja = ${EPREFIX}/usr/$(get_libdir)" >> input/mg5_configuration.txt + #use samurai && echo "samurai = ${EPREFIX}/usr/$(get_libdir)" >> input/mg5_configuration.txt + #use golem95 && echo "golem = ${EPREFIX}/usr/$(get_libdir)" >> input/mg5_configuration.txt + #use td && echo "td_path = ${EPREFIX}/usr/bin/td" >> input/mg5_configuration.txt + #use madanalysis5 && echo "madanalysis5_path = ${EPREFIX}/opt/MadAnalysis5/" >> input/mg5_configuration.txt +} + +src_compile() { + # MadGraph needs to generate `Template/LO/Source/make_opts` which is done + # automatically at startup. This needs to be done during setup (or with root access) + echo "exit" > tmpfile || die + bin/mg5_aMC ./tmpfile || die + rm tmpfile || die +} + +src_install() { + # symlink entrypoint + dosym ../../opt/${MY_PF}/bin/mg5_aMC /usr/bin/mg5_aMC3 + dosym ../opt/${MY_PF} /opt/"${MY_PNN}" + mv "${WORKDIR}/${MY_PF}" "${ED}/opt/" || die + + # allow all users to modify mg directory + # as it changes it self + #fperms -R a=u /opt/${MY_PF} + #fperms a=u /opt/${MY_PF} +} diff --git a/sci-physics/madgraph5/metadata.xml b/sci-physics/madgraph5/metadata.xml new file mode 100644 index 000000000..8fc26f579 --- /dev/null +++ b/sci-physics/madgraph5/metadata.xml @@ -0,0 +1,32 @@ +<?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> + <longdescription lang="en"> + MadGraph5_aMC@NLO is a framework that aims at providing all the elements necessary for SM and BSM phenomenology, such as the computations of cross sections, the generation of hard events and their matching with event generators, and the use of a variety of tools relevant to event manipulation and analysis. Processes can be simulated to LO accuracy for any user-defined Lagrangian, an the NLO accuracy in the case of models that support this kind of calculations -- prominent among these are QCD and EW corrections to SM processes. Matrix elements at the tree- and one-loop-level can also be obtained. + </longdescription> + <use> + <flag name="lhapdf">USE system LHAPDF</flag> + <flag name="fastjet">USE system FASTJET</flag> + <flag name="pythia">USE system PYTHIA</flag> + <flag name="hepmc2">USE system hepmc version 2</flag> + <flag name="thepeg">USE system thepeg</flag> + <flag name="collier">USE system collier</flag> +<!-- + <flag name="ninja">USE system ninja</flag> + <flag name="samurai">USE system samurai</flag> + <flag name="pineappl">USE system pineappl</flag> + <flag name="herwig">USE system herwig</flag> + <flag name="madanalysis5">USE system madanalysis5</flag> + <flag name="golem95">USE system golem95</flag> + <flag name="td">USE system topdrawer</flag> + <flag name="rivet">USE system rivet</flag> +--> + </use> + <upstream> + <remote-id type="launchpad">mg5amcnlo</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/pyhf/Manifest b/sci-physics/pyhf/Manifest index 756bfb423..3155872d4 100644 --- a/sci-physics/pyhf/Manifest +++ b/sci-physics/pyhf/Manifest @@ -1 +1,2 @@ DIST pyhf-0.7.3.tar.gz 113423 BLAKE2B 216ef186c539481e2819e3f3a198203f085aa99652ab335b1153309a780857c5ad53bc848bb1b12615cfa9b8ee97a67553cef5a0f899bbcf178bfea1b2ca11c5 SHA512 904491f9c161f0231d1e109cfa3a12b31a31b1aa7477752e1eafd1e6c4cec75551e53ce1f6d447bed8f295371dc20b032888a5175af0f2eb808e03c0a8993930 +DIST pyhf-0.7.5.tar.gz 113812 BLAKE2B 747dc59de4e80d883145dd6b5643507c6faca2c1cb53b2aaea93cfcf31ed474ed3807f9f5a79d45f49a330f9c6260d5373e8134be814b07e1a1ae161844ad960 SHA512 83a5e02d7278e3e835ecf49d5b01fd6614923bf5e80d58ec2a96da89a67ad80bcdad4be90b598d314caf83a293c3bb69c3e995c292c0b62ef109662c061d91e8 diff --git a/sci-physics/pyhf/pyhf-0.7.5.ebuild b/sci-physics/pyhf/pyhf-0.7.5.ebuild new file mode 100644 index 000000000..22a36af7f --- /dev/null +++ b/sci-physics/pyhf/pyhf-0.7.5.ebuild @@ -0,0 +1,37 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 pypi + +DESCRIPTION="pure-python fitting/limit-setting/interval estimation HistFactory-style" +HOMEPAGE=" + https://github.com/scikit-hep/pyhf + https://doi.org/10.5281/zenodo.1169739 + https://zenodo.org/record/8256635 + https://doi.org/10.21105/joss.02823 + https://inspirehep.net/literature/2598491 + https://arxiv.org/abs/2211.15838 + https://doi.org/10.22323/1.414.0245 +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +# test needs missing scrapbook papermill pydocstyle ... +RESTRICT="test" + +RDEPEND=" + >=dev-python/click-8.0.0[${PYTHON_USEDEP}] + >=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}] + >=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}] + >=dev-python/pyyaml-5.1[${PYTHON_USEDEP}] + >=dev-python/scipy-1.5.2[${PYTHON_USEDEP}] + >=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sci-physics/qgraf/Manifest b/sci-physics/qgraf/Manifest index 32519be3c..c633a5b46 100644 --- a/sci-physics/qgraf/Manifest +++ b/sci-physics/qgraf/Manifest @@ -1,3 +1,4 @@ DIST qgraf-3.4.2.tgz 358979 BLAKE2B 06c5cf82faab531d6d17387d62e80b2e395ad0ffd80a69dc49608588f4acdf23d226877db047d3906963b5f64d85329665fed0e10359ddbb649122fb328b78f8 SHA512 e86f94480eaf7cd0b4d79b60ec1420c21f0285133f2184d1c0a1d05ec0d9abc3e483d100d43c38fafc06bf8cecea413c0304adcb64d900522e877b1a24e7b61b DIST qgraf-3.5.2.tgz 426930 BLAKE2B 0bd50cbefee9a91cdfe9a15a53fb018c1b15088b211a03dde63f08410bbac4acd7586ef4cece17debd5197d3d5b7a8c889aeec27d7f3f137df7ef95f1687a709 SHA512 1e1fbafc80c60a663537a5ca555f405ec1517beccf09e2f68fcd9c84963b4b20d3a66e77980c4c4ff68f82950dc41f4492dc0272fdf5e3c105861fcf4c0e8c80 DIST qgraf-3.6.7.tgz 460592 BLAKE2B d4275d7e5b9138eab3a2848b1e75883a4d52b61bdddd2ecbefe674559a56d9315bb03bd86c5a607f01d708c634f35b180f4cfde99242e65a40bf3f81ce6fa9e3 SHA512 c721eb82975a6077da77a82f7875d0e0346e21932d0312109d1bab68391a0210fc3f7ff79327d515668dedee0c5fce4e01d7433177232c43a4e39d8204f01405 +DIST qgraf-4.0.1.tgz 420190 BLAKE2B 3f13757da764c6b9653e1c3463557223d5e87cc7f376967300c094c8d96942ab807500a0a2d570a66600cb926681bbda5ed6c69c44dbffbba1f481d2eb7f8459 SHA512 e5f3b586b29413c71434ac144dc2355959f4e736aa5ad55fa17f888d4ddc7cc1bf2ff92cc544e538471c13aea95ddd1d9248f71622f84d4daa173abbbbb0dc8a diff --git a/sci-physics/qgraf/qgraf-4.0.1.ebuild b/sci-physics/qgraf/qgraf-4.0.1.ebuild new file mode 100644 index 000000000..942ef732a --- /dev/null +++ b/sci-physics/qgraf/qgraf-4.0.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models" +HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html" +SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz" +S="${WORKDIR}" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples" +RESTRICT="bindist mirror" + +src_compile() { + $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" +} + +src_install() { + dobin ${PN} + + use doc && dodoc *.pdf + if use examples; then + docinto examples + dodoc phi3 qed qcd *.sty *.dat + docompress -x /usr/share/doc/${PF}/examples + fi +} |