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-rw-r--r--dev-python/aiohttp-retry/Manifest1
-rw-r--r--dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild31
-rw-r--r--dev-python/aiohttp-retry/metadata.xml16
-rw-r--r--dev-python/argparse-dataclass/Manifest1
-rw-r--r--dev-python/argparse-dataclass/argparse-dataclass-2.0.0.ebuild19
-rw-r--r--dev-python/argparse-dataclass/metadata.xml16
-rw-r--r--dev-python/conda-inject/Manifest1
-rw-r--r--dev-python/conda-inject/conda-inject-1.3.1.ebuild21
-rw-r--r--dev-python/conda-inject/metadata.xml16
-rw-r--r--dev-python/connection_pool/connection_pool-0.0.3.ebuild2
-rw-r--r--dev-python/datrie/datrie-0.8.2-r1.ebuild2
-rw-r--r--dev-python/fusepy/Manifest1
-rw-r--r--dev-python/fusepy/fusepy-3.0.1.ebuild20
-rw-r--r--dev-python/fusepy/metadata.xml16
-rw-r--r--dev-python/google-cloud-storage/Manifest2
-rw-r--r--dev-python/google-cloud-storage/google-cloud-storage-2.17.0.ebuild (renamed from dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild)5
-rw-r--r--dev-python/hist/Manifest2
-rw-r--r--dev-python/hist/hist-2.7.2.ebuild26
-rw-r--r--dev-python/hist/hist-2.7.3.ebuild26
-rw-r--r--dev-python/hist/metadata.xml19
-rw-r--r--dev-python/histoprint/Manifest1
-rw-r--r--dev-python/histoprint/histoprint-2.4.0.ebuild20
-rw-r--r--dev-python/histoprint/metadata.xml19
-rw-r--r--dev-python/immutables/Manifest1
-rw-r--r--dev-python/immutables/immutables-0.20.ebuild21
-rw-r--r--dev-python/immutables/metadata.xml16
-rw-r--r--dev-python/linesep/Manifest1
-rw-r--r--dev-python/linesep/files/linesep-0.5.0-nocov.patch12
-rw-r--r--dev-python/linesep/linesep-0.5.0.ebuild25
-rw-r--r--dev-python/linesep/metadata.xml16
-rw-r--r--dev-python/meshpy/meshpy-2020.1.ebuild2
-rw-r--r--dev-python/methodtools/Manifest1
-rw-r--r--dev-python/methodtools/files/methodtools-0.4.7-nocov.patch9
-rw-r--r--dev-python/methodtools/metadata.xml16
-rw-r--r--dev-python/methodtools/methodtools-0.4.7.ebuild24
-rw-r--r--dev-python/prov/Manifest1
-rw-r--r--dev-python/prov/metadata.xml14
-rw-r--r--dev-python/prov/prov-2.0.0.ebuild43
-rw-r--r--dev-python/reproject/reproject-0.8.ebuild2
-rw-r--r--dev-python/reretry/reretry-0.11.8.ebuild2
-rw-r--r--dev-python/smart-open/smart-open-6.3.0.ebuild11
-rw-r--r--dev-python/snakemake-interface-common/Manifest1
-rw-r--r--dev-python/snakemake-interface-common/metadata.xml16
-rw-r--r--dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild22
-rw-r--r--dev-python/snakemake-interface-executor-plugins/Manifest1
-rw-r--r--dev-python/snakemake-interface-executor-plugins/metadata.xml16
-rw-r--r--dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.1.1.ebuild23
-rw-r--r--dev-python/snakemake-interface-report-plugins/Manifest1
-rw-r--r--dev-python/snakemake-interface-report-plugins/metadata.xml16
-rw-r--r--dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.0.0.ebuild21
-rw-r--r--dev-python/snakemake-interface-storage-plugins/Manifest1
-rw-r--r--dev-python/snakemake-interface-storage-plugins/metadata.xml16
-rw-r--r--dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.2.ebuild24
-rw-r--r--dev-python/snakemake/Manifest1
-rw-r--r--dev-python/snakemake/snakemake-7.32.4.ebuild4
-rw-r--r--dev-python/snakemake/snakemake-8.14.0.ebuild74
-rw-r--r--dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild2
-rw-r--r--dev-python/stopit/stopit-1.1.2.ebuild2
-rw-r--r--dev-python/throttler/throttler-1.2.2.ebuild2
-rw-r--r--dev-python/vector/Manifest1
-rw-r--r--dev-python/vector/vector-1.4.1.ebuild34
-rw-r--r--dev-python/wirerope/Manifest1
-rw-r--r--dev-python/wirerope/files/wirerope-0.4.7-nocov.patch10
-rw-r--r--dev-python/wirerope/metadata.xml16
-rw-r--r--dev-python/wirerope/wirerope-0.4.7.ebuild26
-rw-r--r--dev-vcs/datalad-fuse/Manifest1
-rw-r--r--dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild32
-rw-r--r--dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch15
-rw-r--r--dev-vcs/datalad-fuse/metadata.xml16
-rw-r--r--dev-vcs/datalad/Manifest1
-rw-r--r--dev-vcs/datalad/datalad-1.0.2.ebuild79
-rw-r--r--profiles/package.mask3
-rw-r--r--sci-astronomy/libthesky/libthesky-0.4.2.ebuild4
-rw-r--r--sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild2
-rw-r--r--sci-biology/afni-datasets/Manifest1
-rw-r--r--sci-biology/afni-datasets/afni-datasets-20240503.ebuild20
-rw-r--r--sci-biology/afni-datasets/metadata.xml12
-rw-r--r--sci-biology/afni/Manifest4
-rw-r--r--sci-biology/afni/afni-24.0.08-r3.ebuild (renamed from sci-biology/afni/afni-24.0.08-r1.ebuild)29
-rw-r--r--sci-biology/afni/afni-24.1.15.ebuild (renamed from sci-biology/afni/afni-24.0.04-r1.ebuild)35
-rw-r--r--sci-biology/afni/afni-24.1.16.ebuild127
-rw-r--r--sci-biology/afni/files/97afni1
-rw-r--r--sci-biology/afni/files/afni-24.1.16-niftiio.patch27
-rw-r--r--sci-biology/codonw/codonw-1.4.4-r2.ebuild2
-rw-r--r--sci-biology/imagej/Manifest4
-rw-r--r--sci-biology/imagej/imagej-1.54i-r1.ebuild (renamed from sci-biology/imagej/imagej-1.54h-r1.ebuild)9
-rw-r--r--sci-biology/imagej/imagej-9999.ebuild9
-rw-r--r--sci-biology/mrfast/mrfast-2.6.0.1.ebuild2
-rw-r--r--sci-biology/multiqc/Manifest2
-rw-r--r--sci-biology/multiqc/multiqc-1.19.ebuild40
-rw-r--r--sci-biology/multiqc/multiqc-1.22.2.ebuild42
-rw-r--r--sci-biology/nilearn/nilearn-0.8.1.ebuild2
-rw-r--r--sci-biology/nilearn/nilearn-0.9.1.ebuild2
-rw-r--r--sci-biology/perlprimer/perlprimer-1.1.21.ebuild2
-rw-r--r--sci-libs/gdcm/gdcm-3.0.14.ebuild4
-rw-r--r--sci-libs/libsufr/libsufr-0.7.7.ebuild2
-rw-r--r--sci-libs/lwpr/lwpr-1.2.5.ebuild2
-rw-r--r--sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild2
-rw-r--r--sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild2
-rw-r--r--sci-mathematics/pulp/Manifest1
-rw-r--r--sci-mathematics/pulp/pulp-2.7.0.ebuild2
-rw-r--r--sci-mathematics/pulp/pulp-2.8.0.ebuild21
-rw-r--r--sci-misc/jwnl/jwnl-1.4_rc2.ebuild2
-rw-r--r--sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild (renamed from sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild)12
-rw-r--r--sci-physics/jaxodraw-bin/Manifest3
-rw-r--r--sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild54
-rw-r--r--sci-physics/jaxodraw-bin/metadata.xml15
-rw-r--r--sci-physics/madgraph5/Manifest1
-rw-r--r--sci-physics/madgraph5/files/cuttools.patch44
-rw-r--r--sci-physics/madgraph5/madgraph5-3.5.3.ebuild93
-rw-r--r--sci-physics/madgraph5/metadata.xml32
-rw-r--r--sci-physics/oneloop/metadata.xml3
-rw-r--r--sci-physics/oneloop/oneloop-2020.07.31.ebuild5
-rw-r--r--sci-physics/particle/Manifest1
-rw-r--r--sci-physics/particle/particle-0.24.0.ebuild44
-rw-r--r--sci-physics/pyhf/Manifest1
-rw-r--r--sci-physics/pyhf/pyhf-0.7.5.ebuild37
-rw-r--r--sci-physics/qgraf/Manifest1
-rw-r--r--sci-physics/qgraf/qgraf-4.0.1.ebuild32
119 files changed, 1658 insertions, 114 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/argparse-dataclass/Manifest b/dev-python/argparse-dataclass/Manifest
new file mode 100644
index 000000000..f06efe6a9
--- /dev/null
+++ b/dev-python/argparse-dataclass/Manifest
@@ -0,0 +1 @@
+DIST argparse_dataclass-2.0.0.tar.gz 6395 BLAKE2B 85dd27449281cde82a4afc1740bc4ba51c2d9259f910fe2146d866c7d8a83d59a6198236acb1b65e9ee7e6b7cca896b713e13d03f309e6583287afa2eef17c06 SHA512 88d706ae49dcc65947cb2eb0a0456c2ed8839fa7a3283e9f5b62da69ed9dd7cd66d45e57e7c3cff4e1104b9aee7a762f751d939cea8f0945301ec91598dbdc35
diff --git a/dev-python/argparse-dataclass/argparse-dataclass-2.0.0.ebuild b/dev-python/argparse-dataclass/argparse-dataclass-2.0.0.ebuild
new file mode 100644
index 000000000..af05cd319
--- /dev/null
+++ b/dev-python/argparse-dataclass/argparse-dataclass-2.0.0.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2018 Gentoo Foundation
+# 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="Declarative CLIs with argparse and dataclasses"
+HOMEPAGE="https://pypi.org/project/argparse-dataclass/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/argparse-dataclass/metadata.xml b/dev-python/argparse-dataclass/metadata.xml
new file mode 100644
index 000000000..803ccead7
--- /dev/null
+++ b/dev-python/argparse-dataclass/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mivade/argparse_dataclass</remote-id>
+ <remote-id type="pypi">argparse-dataclass</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/conda-inject/Manifest b/dev-python/conda-inject/Manifest
new file mode 100644
index 000000000..e011d3573
--- /dev/null
+++ b/dev-python/conda-inject/Manifest
@@ -0,0 +1 @@
+DIST conda_inject-1.3.1.tar.gz 3580 BLAKE2B 84761ceddc0d01802502c09fea814eef86140ff28d7018900ce6b4b7666f0fbc8172ee4e25700e0ccfbe278dd228dc009ece2478d7e298f958333cc0d05fbd6e SHA512 6de6d190c1207cd36c1c03c24716158f6990c64d9764fcf79acf1a94682f38ecef4e02de7206ffd5f1c586ca73d375d46002edd9160a46f97e4eb3f5ff0ef6a1
diff --git a/dev-python/conda-inject/conda-inject-1.3.1.ebuild b/dev-python/conda-inject/conda-inject-1.3.1.ebuild
new file mode 100644
index 000000000..f30c70bae
--- /dev/null
+++ b/dev-python/conda-inject/conda-inject-1.3.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Helper functions for injecting a conda environment into the current python environment"
+HOMEPAGE="https://pypi.org/project/conda-inject/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/conda-inject/metadata.xml b/dev-python/conda-inject/metadata.xml
new file mode 100644
index 000000000..5637d6506
--- /dev/null
+++ b/dev-python/conda-inject/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">koesterlab/conda-inject</remote-id>
+ <remote-id type="pypi">conda-inject</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/connection_pool/connection_pool-0.0.3.ebuild b/dev-python/connection_pool/connection_pool-0.0.3.ebuild
index 96d3c1f62..17a9c439e 100644
--- a/dev-python/connection_pool/connection_pool-0.0.3.ebuild
+++ b/dev-python/connection_pool/connection_pool-0.0.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 pypi
diff --git a/dev-python/datrie/datrie-0.8.2-r1.ebuild b/dev-python/datrie/datrie-0.8.2-r1.ebuild
index e8f9f9336..3bbd197d7 100644
--- a/dev-python/datrie/datrie-0.8.2-r1.ebuild
+++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
# Fails to compile with pep517
#DISTUTILS_USE_PEP517=setuptools
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/google-cloud-storage/Manifest b/dev-python/google-cloud-storage/Manifest
index 6bd5af5b0..3e88f92ee 100644
--- a/dev-python/google-cloud-storage/Manifest
+++ b/dev-python/google-cloud-storage/Manifest
@@ -1 +1 @@
-DIST google-cloud-storage-2.7.0.tar.gz 5490914 BLAKE2B 582fcf9a84bedcff41de2b26558ccae96474cbbe91c86bbe6bf53ff6a2fe38d7eb8dbe396fccd36ad252f171ed7eda45974ca9e7867e3ee9542c85570a951aef SHA512 89c4208781735bb0e8b0978202877af324154d5233d7abafd1b2b14b4bb381c18572cfdc791e42577ad929f3c4ded0857d9bd9f4eb52a93ed74e8884d797b365
+DIST google-cloud-storage-2.17.0.tar.gz 5526712 BLAKE2B 8ba53a31eb838aca31ee6891c3ad5b465732967f7393b6fe597f4dedd653ee7cd28af392d25fe9d279387b722621160f3ddd8e49c5f5c9917fc27296e4e8879e SHA512 82ba6b13eb79dd2fdebc8b1dd16876c26b07d8e0da38e9dcb9c43f34eba903fc2e29187c718d5f06cb556abed9537c19ac8d90069b546573343067230c5390a1
diff --git a/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild b/dev-python/google-cloud-storage/google-cloud-storage-2.17.0.ebuild
index 403f75dee..bd641a215 100644
--- a/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild
+++ b/dev-python/google-cloud-storage/google-cloud-storage-2.17.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1
@@ -22,4 +22,5 @@ RDEPEND="
dev-python/requests[${PYTHON_USEDEP}]
"
-distutils_enable_tests pytest
+RESTRICT="test" # ImportError: cannot import name '_helpers' from 'google.cloud'
+#distutils_enable_tests pytest
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/immutables/Manifest b/dev-python/immutables/Manifest
new file mode 100644
index 000000000..dfee7ecc9
--- /dev/null
+++ b/dev-python/immutables/Manifest
@@ -0,0 +1 @@
+DIST immutables-0.20.tar.gz 88933 BLAKE2B 07ae33ea62e85ea8c9b26a7e634f018b6e614ecd493faa74cdbdb20864b6af78b30fbadd1c21d9b9e3e971086893dcc7053ba88f8c78d7dbb588d54b8a9d0175 SHA512 1b74236517964573fd26072b6bf1b8a93456822b2b6ccc5f544f8a49b91f2e0bd110ef2ac23358ba14deceaaee8dde6f24e5589e9078dce961a7b9d4fcd2d3bd
diff --git a/dev-python/immutables/immutables-0.20.ebuild b/dev-python/immutables/immutables-0.20.ebuild
new file mode 100644
index 000000000..8cd5bf37b
--- /dev/null
+++ b/dev-python/immutables/immutables-0.20.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2024 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_EXT=1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="A high-performance immutable mapping type for Python"
+HOMEPAGE="https://pypi.org/project/immutables/"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="test? ( dev-python/mypy[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
diff --git a/dev-python/immutables/metadata.xml b/dev-python/immutables/metadata.xml
new file mode 100644
index 000000000..1bec01ba5
--- /dev/null
+++ b/dev-python/immutables/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">MagicStack/immutables</remote-id>
+ <remote-id type="pypi">immutables</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}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/linesep/metadata.xml b/dev-python/linesep/metadata.xml
new file mode 100644
index 000000000..017856905
--- /dev/null
+++ b/dev-python/linesep/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">jwodder/linesep</remote-id>
+ <remote-id type="pypi">linesep</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/meshpy/meshpy-2020.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild
index 78ee45fbc..1c730f5df 100644
--- a/dev-python/meshpy/meshpy-2020.1.ebuild
+++ b/dev-python/meshpy/meshpy-2020.1.ebuild
@@ -33,7 +33,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
-distutils_enable_tests --install pytest
+distutils_enable_tests pytest
python_prepare_all() {
sed 's:delay=10:delay=1:g' -i aksetup_helper.py || die
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/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild
index cf57e7d73..93efdd361 100644
--- a/dev-python/reproject/reproject-0.8.ebuild
+++ b/dev-python/reproject/reproject-0.8.ebuild
@@ -33,4 +33,4 @@ RDEPEND="
# requires self to be installed
# distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib
-distutils_enable_tests --install pytest
+distutils_enable_tests pytest
diff --git a/dev-python/reretry/reretry-0.11.8.ebuild b/dev-python/reretry/reretry-0.11.8.ebuild
index 64da7215b..9aa7f3979 100644
--- a/dev-python/reretry/reretry-0.11.8.ebuild
+++ b/dev-python/reretry/reretry-0.11.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/smart-open/smart-open-6.3.0.ebuild b/dev-python/smart-open/smart-open-6.3.0.ebuild
index b585f1d4b..f61752492 100644
--- a/dev-python/smart-open/smart-open-6.3.0.ebuild
+++ b/dev-python/smart-open/smart-open-6.3.0.ebuild
@@ -1,16 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Utils for streaming large files (S3, HDFS, gzip, bz2...) "
-HOMEPAGE="https://github.com/RaRe-Technologies/smart_open"
-SRC_URI="https://github.com/RaRe-Technologies/smart_open/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+HOMEPAGE="https://github.com/piskvorky/smart_open"
+SRC_URI="https://github.com/piskvorky/smart_open/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
S="${WORKDIR}/${PN//-/_}-${PV}"
LICENSE="MIT"
@@ -26,10 +26,11 @@ RDEPEND="
BDEPEND="
test? (
- dev-python/moto[${PYTHON_USEDEP}]
+ <dev-python/moto-5[${PYTHON_USEDEP}]
dev-python/responses[${PYTHON_USEDEP}]
dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
)
"
+RESTRICT="test" # 329 tests, 1 error: missing azure-storage-blob, azure-common[no ebuild], azure-core
distutils_enable_tests pytest
diff --git a/dev-python/snakemake-interface-common/Manifest b/dev-python/snakemake-interface-common/Manifest
new file mode 100644
index 000000000..f83a8f47e
--- /dev/null
+++ b/dev-python/snakemake-interface-common/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_common-1.17.2.tar.gz 9928 BLAKE2B 91be90640adb5f19fb97185ef84954cececd9e26e9c64f59b4ff014eca257575c5d5501ea7a8d74d9de2bb3280e88be500d1a2df2ec3296f2ecd30acbda27c87 SHA512 08d1688f70863825e76832250ee9da0be3a8baae9e67eb9bafaab30d862fe33fb9508eb4571f39322579699a4cd98d8878854ad9a94615e3b73255d18fe38c14
diff --git a/dev-python/snakemake-interface-common/metadata.xml b/dev-python/snakemake-interface-common/metadata.xml
new file mode 100644
index 000000000..b70ef47c9
--- /dev/null
+++ b/dev-python/snakemake-interface-common/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">snakemake/snakemake-interface-common</remote-id>
+ <remote-id type="pypi">snakemake-interface-common</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild
new file mode 100644
index 000000000..943af2cfc
--- /dev/null
+++ b/dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Common functions and classes for Snakemake and its plugins"
+HOMEPAGE="https://pypi.org/project/snakemake-interface-common/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/argparse-dataclass[${PYTHON_USEDEP}]
+ dev-python/ConfigArgParse[${PYTHON_USEDEP}]"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/snakemake-interface-executor-plugins/Manifest b/dev-python/snakemake-interface-executor-plugins/Manifest
new file mode 100644
index 000000000..8b038d413
--- /dev/null
+++ b/dev-python/snakemake-interface-executor-plugins/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_executor_plugins-9.1.1.tar.gz 16342 BLAKE2B d478afe4fdbb91c0e7a1447de002b93a5583089b9ed2164c9086f536d7b8b6c9f3e52687fc0b299830a86639c1dca0e682f01b17349a58deac5efa884ddc381a SHA512 bcb589ab251fbab69cdddb5eb23257b18164c42c7b3e5014e43aeec278c5453d9713e7c1791ecb15899a8593a5cb302cfc56b8e35539a6474ad1c6d79d892592
diff --git a/dev-python/snakemake-interface-executor-plugins/metadata.xml b/dev-python/snakemake-interface-executor-plugins/metadata.xml
new file mode 100644
index 000000000..a58905c97
--- /dev/null
+++ b/dev-python/snakemake-interface-executor-plugins/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">snakemake/snakemake-interface-executor-plugins</remote-id>
+ <remote-id type="pypi">snakemake-interface-executor-plugins</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.1.1.ebuild b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.1.1.ebuild
new file mode 100644
index 000000000..41008ef8b
--- /dev/null
+++ b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.1.1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2024 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{11..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Stable interface for interactions between Snakemake and its executor plugins"
+HOMEPAGE="https://pypi.org/project/snakemake-interface-executor-plugins/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/argparse-dataclass[${PYTHON_USEDEP}]
+ dev-python/snakemake-interface-common[${PYTHON_USEDEP}]
+ dev-python/throttler[${PYTHON_USEDEP}]"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/snakemake-interface-report-plugins/Manifest b/dev-python/snakemake-interface-report-plugins/Manifest
new file mode 100644
index 000000000..4f890f9e6
--- /dev/null
+++ b/dev-python/snakemake-interface-report-plugins/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_report_plugins-1.0.0.tar.gz 4239 BLAKE2B efda3664614d123b0cd0f3d246d324ef7a4e67b2a069a5b1dde929921cf7e2251f67d6fcc1806864488dcc9c9b586681908e5a11b13f78206342ff0383efdbdc SHA512 2f5ac7e0ccd02c10aebcbe0eebfdb617cb32f66204e91316e3bc2b0053c3606207baa5de5bdda570f5559db366c637adf614f9ac23c7a33fb06d64560bd780aa
diff --git a/dev-python/snakemake-interface-report-plugins/metadata.xml b/dev-python/snakemake-interface-report-plugins/metadata.xml
new file mode 100644
index 000000000..6e4b04ba4
--- /dev/null
+++ b/dev-python/snakemake-interface-report-plugins/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">snakemake/snakemake-interface-report-plugins</remote-id>
+ <remote-id type="pypi">snakemake-interface-report-plugins</remote-id>
+ </upstream>
+</pkgmetadata>
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-1.0.0.ebuild
new file mode 100644
index 000000000..25f8d53c7
--- /dev/null
+++ b/dev-python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.0.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2024 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{11..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="The interface for Snakemake report plugins"
+HOMEPAGE="https://pypi.org/project/snakemake-interface-report-plugins/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/snakemake-interface-common[${PYTHON_USEDEP}]"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/snakemake-interface-storage-plugins/Manifest b/dev-python/snakemake-interface-storage-plugins/Manifest
new file mode 100644
index 000000000..543284907
--- /dev/null
+++ b/dev-python/snakemake-interface-storage-plugins/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_storage_plugins-3.2.2.tar.gz 11949 BLAKE2B 56e33546c1a9a0eeb92560ff2eb3950b2b91edaa5c527b4b504082bd2ed3f0fbd1b8e8cd24d1391375e99c2b2041aa47a30ac62dd009ec1188cffee65fa606cb SHA512 0151f297ae5f597016e02937021af2583982d5df0cb0c353274618799f68a4a99a30a19f631f1a8c4dabf74833f39c47a4405f7c0e9be8b3397ae350ae23e62d
diff --git a/dev-python/snakemake-interface-storage-plugins/metadata.xml b/dev-python/snakemake-interface-storage-plugins/metadata.xml
new file mode 100644
index 000000000..8b49faffd
--- /dev/null
+++ b/dev-python/snakemake-interface-storage-plugins/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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">snakemake/snakemake-interface-storage-plugins</remote-id>
+ <remote-id type="pypi">snakemake-interface-storage-plugins</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.2.ebuild b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.2.ebuild
new file mode 100644
index 000000000..39c8b08a2
--- /dev/null
+++ b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.2.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2024 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{11..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Stable interface for interactions between Snakemake and its storage plugins"
+HOMEPAGE="https://pypi.org/project/snakemake-interface-storage-plugins/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/snakemake-interface-common[${PYTHON_USEDEP}]
+ dev-python/wrapt[${PYTHON_USEDEP}]
+ dev-python/reretry[${PYTHON_USEDEP}]
+ dev-python/throttler[${PYTHON_USEDEP}]"
+
+RESTRICT="test" # no tests collected
+#distutils_enable_tests pytest
diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest
index eca03bc0e..3195e9070 100644
--- a/dev-python/snakemake/Manifest
+++ b/dev-python/snakemake/Manifest
@@ -1 +1,2 @@
DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
+DIST snakemake-8.14.0.gh.tar.gz 8662241 BLAKE2B fc36722b00cb3da11e836d5c521fe6600d176fd6fc3bd8a39336bc6a3d34bfcb689727d9990351cde247e377dca1131bda5dd84852a32ddb91fed44aa62c020e SHA512 68a0aabeed435e032d01f4d38d37c4b37ed7f624bf3768a1654daccdbf95ceb06646d7302ca04ea4f20695ec9706e015d146794aa000ec108d18d6ad09f3671b
diff --git a/dev-python/snakemake/snakemake-7.32.4.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild
index 711aac286..8ff44fdb5 100644
--- a/dev-python/snakemake/snakemake-7.32.4.ebuild
+++ b/dev-python/snakemake/snakemake-7.32.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
@@ -54,7 +54,7 @@ RDEPEND="
dev-python/toposort[${PYTHON_USEDEP}]
dev-python/wrapt[${PYTHON_USEDEP}]
dev-python/yte[${PYTHON_USEDEP}]
- sci-mathematics/pulp[${PYTHON_USEDEP}]
+ <sci-mathematics/pulp-2.8[${PYTHON_USEDEP}]
"
distutils_enable_sphinx docs \
diff --git a/dev-python/snakemake/snakemake-8.14.0.ebuild b/dev-python/snakemake/snakemake-8.14.0.ebuild
new file mode 100644
index 000000000..fed1a1bbb
--- /dev/null
+++ b/dev-python/snakemake/snakemake-8.14.0.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make-like task language"
+HOMEPAGE="https://snakemake.readthedocs.io"
+SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# cannot import name '_helpers' from 'google.cloud'
+RESTRICT="test"
+
+BDEPEND="
+ dev-python/tomli[${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[${PYTHON_USEDEP}]
+ dev-python/ConfigArgParse[${PYTHON_USEDEP}]
+ dev-python/connection_pool[${PYTHON_USEDEP}]
+ dev-python/datrie[${PYTHON_USEDEP}]
+ dev-python/docutils[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/humanfriendly[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/nbformat[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/reretry[${PYTHON_USEDEP}]
+ dev-python/smart-open[${PYTHON_USEDEP}]
+ dev-python/snakemake-interface-executor-plugins[${PYTHON_USEDEP}]
+ dev-python/snakemake-interface-common[${PYTHON_USEDEP}]
+ dev-python/snakemake-interface-storage-plugins[${PYTHON_USEDEP}]
+ dev-python/snakemake-interface-report-plugins[${PYTHON_USEDEP}]
+ dev-python/stopit[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ dev-python/throttler[${PYTHON_USEDEP}]
+ dev-python/toposort[${PYTHON_USEDEP}]
+ dev-python/wrapt[${PYTHON_USEDEP}]
+ dev-python/yte[${PYTHON_USEDEP}]
+ dev-python/dpath[${PYTHON_USEDEP}]
+ dev-python/conda-inject[${PYTHON_USEDEP}]
+ sci-mathematics/pulp[${PYTHON_USEDEP}]
+"
+
+# distutils_enable_sphinx docs \
+# dev-python/sphinxcontrib-napoleon \
+# dev-python/sphinx-argparse \
+# dev-python/sphinx-rtd-theme \
+# dev-python/docutils \
+# dev-python/recommonmark \
+# dev-python/myst-parser
+distutils_enable_tests pytest
diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild
index 0a962fd5e..4293a6dd5 100644
--- a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild
+++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1
diff --git a/dev-python/stopit/stopit-1.1.2.ebuild b/dev-python/stopit/stopit-1.1.2.ebuild
index 64d63502a..df9346cfd 100644
--- a/dev-python/stopit/stopit-1.1.2.ebuild
+++ b/dev-python/stopit/stopit-1.1.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 pypi
diff --git a/dev-python/throttler/throttler-1.2.2.ebuild b/dev-python/throttler/throttler-1.2.2.ebuild
index 0d0d62a16..c19480ca7 100644
--- a/dev-python/throttler/throttler-1.2.2.ebuild
+++ b/dev-python/throttler/throttler-1.2.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest
index 541d150c6..a64079e01 100644
--- a/dev-python/vector/Manifest
+++ b/dev-python/vector/Manifest
@@ -1,2 +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
diff --git a/dev-python/vector/vector-1.4.1.ebuild b/dev-python/vector/vector-1.4.1.ebuild
new file mode 100644
index 000000000..a57240b49
--- /dev/null
+++ b/dev-python/vector/vector-1.4.1.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+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[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+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/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[${PYTHON_USEDEP}]
+ )
+"
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
+
+distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+ tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time
+ tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_frozen_time_with_func
+ tests/test_datetimes.py::TestUnitTestMethodDecorator::test_method_decorator_works_on_unittest_kwarg_hello
+)
+
+python_test() {
+ local -x DATALAD_TESTS_NONETWORK=1
+ # see test groups in "tox.ini"
+ epytest -k "not turtle and not slow and not usecase"
+}
diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..1b622a85b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,6 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
+# reverse deps
diff --git a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
index 09f89265f..c7d2bd0c3 100644
--- a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
+++ b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
@@ -9,8 +9,8 @@ inherit cmake fortran-2
DESCRIPTION="Fortran library to compute positions of celestial bodies"
HOMEPAGE="http://libthesky.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${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..cc0d96468 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,4 +1,6 @@
-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 afni-24.1.15.gh.tar.gz 53136605 BLAKE2B aab19b572b3d3f32e4d91414c127a8ef5cfd5cef04cb55836060298340c3d0e6cf0ec2f5f324590ce432e920842358007858a278198b37b47e6eeb8f318855b3 SHA512 ca8e3d26a32feea0118e4219c5915f8541bf5194f0db8e4b51637fb79a08c15d1772bc75499b71a47af5cac831bbd484efb3fce848d499f51ef002f9f52a6e10
+DIST afni-24.1.16.gh.tar.gz 53139168 BLAKE2B dff31b9b6e89cd2c62e2ab8cb1b7d1ed28e7bc3bbeb586ae7218ccc276237b0632d06c65928469560684871b8fd25dc382e5bdffcc4c5181c5b9855565398df8 SHA512 c507bc8d3bbad8b61daef3321e48bd88c2f020c940c61a7c3ff4dafe1d2823dad5c87b96080716ab6c59d5312b7fa33c8289426f3fcc4938d3ef049df54134b3
DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2
DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5
+DIST nifti-f24bec503f1a5d501c0413c1bb8aa3d6e04aebda.tar.gz 451555 BLAKE2B d83e8e265d996bb041fa7c712e4f67f6ab3c4e7e7b9713f5d5a0e045b11c2c5c34a193a0d6f69594d37ff1ac09bb295f9be6b04a7a29711cfad8d27167c15058 SHA512 8a4707edfd11112bdb0c359223bb39c6e1d9281234759ebf65bffe34b52a0530053b2e9368c36a77b788194113db5ac66ddf44204036983fffda3d81699e1d5b
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 "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
}
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.1.15.ebuild
index 557fbd579..12d6c8f87 100644
--- a/sci-biology/afni/afni-24.0.04-r1.ebuild
+++ b/sci-biology/afni/afni-24.1.15.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=setuptools
inherit cmake distutils-r1 toolchain-funcs
@@ -12,30 +12,33 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
SRC_URI="
https://github.com/afni/afni/archive/refs/tags/AFNI_${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:*
@@ -53,9 +56,11 @@ DEPEND="
${RDEPEND}
app-shells/tcsh
"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
-S="${WORKDIR}/afni-AFNI_${PV}"
-
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
src_prepare() {
tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
@@ -65,10 +70,11 @@ src_prepare() {
src_configure() {
if use !whirlgif; then
- eapply "${FILESDIR}/${P}-whirlgif.patch"
+ eapply "${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/$(get_libdir)
@@ -107,4 +113,13 @@ src_install() {
popd
cd "${D}"
rm usr/bin/mpeg_encode
+ doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
}
diff --git a/sci-biology/afni/afni-24.1.16.ebuild b/sci-biology/afni/afni-24.1.16.ebuild
new file mode 100644
index 000000000..0759d30a0
--- /dev/null
+++ b/sci-biology/afni/afni-24.1.16.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="f24bec503f1a5d501c0413c1bb8aa3d6e04aebda"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${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-${GIFTI_HASH}.tar.gz
+ "
+
+S="${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
+ 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:*
+ 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="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+PATCHES=("${FILESDIR}/afni-24.1.16-niftiio.patch")
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ # We need a name without the hash to reference in patches
+ mv "${WORKDIR}/nifti_clib-${NIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github"
+ mv "${WORKDIR}/gifti_clib-${GIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github"
+ cmake_src_prepare
+}
+
+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 ${CFLAGS}"
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(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}/afni-AFNI_24.1.16/nifti_clib_from_github"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+ doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni
new file mode 100644
index 000000000..dbf463f47
--- /dev/null
+++ b/sci-biology/afni/files/97afni
@@ -0,0 +1 @@
+export AFNI_ATLAS_PATH=/usr/share/afni-datasets
diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
new file mode 100644
index 000000000..a4eb35435
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
@@ -0,0 +1,27 @@
+From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001
+From: Yaroslav Halchenko <debian@onerussian.com>
+Date: Mon, 3 Jun 2024 19:28:21 -0400
+Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent
+ propagating linking against it
+
+I am just a messanger from the cmake-wise @leej3 at
+https://github.com/afni/afni/issues/639#issuecomment-2145703256
+
+Supposedly closes #639
+---
+ src/nifti/nifticdf/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt
+index 473be7e3be..01b18a14d8 100644
+--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt
++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt
+@@ -8,7 +8,7 @@ set_target_properties(
+ "${CMAKE_CURRENT_LIST_DIR}/nifticdf.h"
+ )
+ target_compile_options(${NIFTI_CDFLIB_NAME} PRIVATE "-D__COMPILE_UNUSED_FUNCTIONS__")
+-target_link_libraries(${NIFTI_CDFLIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio)
++target_link_libraries(${NIFTI_CDFLIB_NAME} PRIVATE ${NIFTI_PACKAGE_PREFIX}niftiio)
+ get_lib_version_vars("nifticdf_version.h" NIFTICDF_VERSION NIFTICDF_MAJOR_VERSION)
+ if(BUILD_SHARED_LIBS)
+ set_target_properties(${NIFTI_CDFLIB_NAME}
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/imagej/Manifest b/sci-biology/imagej/Manifest
index 4c5068f0a..c8a1eba20 100644
--- a/sci-biology/imagej/Manifest
+++ b/sci-biology/imagej/Manifest
@@ -1,3 +1,3 @@
-DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9
-DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615
+DIST imagej-1.54i.gh.tar.gz 5826446 BLAKE2B 05a21929a29e7c4109a91714d0d4d2763f9fe5d83500d334a717d7050765d50c08119b8a7bb54b9290ccf4f82a75cfb392fdf2ee269ee0b05e0f7447aa7c2d1b SHA512 13a0ec252328f972570ccbd85881b64cff25b03f92eb5f68bb6b1b00d7530ba31cd2ff617c462aa428158027f042ea1d18682f3e0deb4d0728ae56965ed5f8e8
+DIST imagej.png 14480 BLAKE2B a507afad5be462cf7a6e693b7930e40abc10877d137d1adeea7938c2b95fecef1b73eb401dc32670ccee6d83a5ecdfc4b6487ed908820bfaa09bec39400cd576 SHA512 87a2bbc17353488a17adb446f2199fb75292ba3bdf00cb97c0508107ee56c12f282bebd8d6618bf6e12ebbcfca7a12bf24057803aeb570edefa992d975b386f5
diff --git a/sci-biology/imagej/imagej-1.54h-r1.ebuild b/sci-biology/imagej/imagej-1.54i-r1.ebuild
index 0252d6613..f95167bcd 100644
--- a/sci-biology/imagej/imagej-1.54h-r1.ebuild
+++ b/sci-biology/imagej/imagej-1.54i-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
HOMEPAGE="
- https://imagej.nih.gov/ij/
+ https://imagej.net/software/imagej/
https://github.com/imagej
"
SRC_URI="
- https://imagej.nih.gov/ij/images/ImageJ.png
+ https://imagej.net/media/icons/imagej.png
plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
@@ -50,12 +50,11 @@ DEPEND="
"
BDEPEND="
- dev-java/ant-core
app-arch/unzip
"
src_prepare() {
- cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+ cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index 0252d6613..f95167bcd 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154
DESCRIPTION="Image Processing and Analysis in Java"
HOMEPAGE="
- https://imagej.nih.gov/ij/
+ https://imagej.net/software/imagej/
https://github.com/imagej
"
SRC_URI="
- https://imagej.nih.gov/ij/images/ImageJ.png
+ https://imagej.net/media/icons/imagej.png
plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
@@ -50,12 +50,11 @@ DEPEND="
"
BDEPEND="
- dev-java/ant-core
app-arch/unzip
"
src_prepare() {
- cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+ cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die
if [[ ${PV} == 9999 ]]; then
if use plugins ; then
diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
index 5d89c0822..42fc0b62d 100644
--- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
+++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
@@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs
DESCRIPTION="Micro Read Fast Alignment Search Tool"
HOMEPAGE="http://mrfast.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
index 3585038a3..77bfbc723 100644
--- a/sci-biology/multiqc/Manifest
+++ b/sci-biology/multiqc/Manifest
@@ -1 +1 @@
-DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
+DIST multiqc-1.22.2.gh.tar.gz 5611004 BLAKE2B 238af92830fe903b09651701072053a4d09de7ff626894b51d246ac53c02e86955690d3b072961833648574ae07412f03fdafd0f39e629c574eb0346cdd95710 SHA512 cf4a448bd353cbd38e7f585c9c62f68481d3fa919edf0a974d3448782134e14e6f210cedbac0e59235a2813166d07b9a407e17e7eb1904176406cc4326182699
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
deleted file mode 100644
index 187f06c22..000000000
--- a/sci-biology/multiqc/multiqc-1.19.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit pypi distutils-r1
-
-DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
-HOMEPAGE="https://multiqc.info/"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
-
-RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/click[${PYTHON_USEDEP}]
- dev-python/coloredlogs[${PYTHON_USEDEP}]
- dev-python/future[${PYTHON_USEDEP}]
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/lzstring[${PYTHON_USEDEP}]
- dev-python/markdown[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
- dev-python/rich[${PYTHON_USEDEP}]
- dev-python/rich-click[${PYTHON_USEDEP}]
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/spectra[${PYTHON_USEDEP}]
- dev-python/importlib-metadata[$PYTHON_USEDEP]
- dev-python/humanize[$PYTHON_USEDEP]
- dev-python/pyaml-env[$PYTHON_USEDEP]"
-
-# pypi tarball does not include tests
-RESTRICT="test"
-#distutils_enable_tests pytest
diff --git a/sci-biology/multiqc/multiqc-1.22.2.ebuild b/sci-biology/multiqc/multiqc-1.22.2.ebuild
new file mode 100644
index 000000000..bf45065aa
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.22.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2024 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="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 -> ${P}.gh.tar.gz"
+S="${WORKDIR}"/MultiQC-${PV}
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[${PYTHON_USEDEP}]
+ >=dev-python/jinja-3.0.0[${PYTHON_USEDEP}]
+ dev-python/markdown[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ >=dev-python/pillow-10[${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[${PYTHON_USEDEP}] # tested and is optional
+
+RESTRICT="test" # no items collected
+#distutils_enable_tests pytest
diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index 3064c0ba5..92c788f28 100644
--- a/sci-biology/nilearn/nilearn-0.8.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -27,7 +27,7 @@ BDEPEND="
RDEPEND="
>=dev-python/joblib-0.12[${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}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 9b9233020..49ca40b32 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -34,4 +34,4 @@ RDEPEND="
DEPEND="${RDEPEND}"
distutils_enable_sphinx docs_sphinx --no-autodoc
-distutils_enable_tests --install pytest
+distutils_enable_tests pytest
diff --git a/sci-mathematics/pulp/Manifest b/sci-mathematics/pulp/Manifest
index abe10a827..9d87e82b0 100644
--- a/sci-mathematics/pulp/Manifest
+++ b/sci-mathematics/pulp/Manifest
@@ -1 +1,2 @@
DIST pulp-2.7.0.gh.tar.gz 28000854 BLAKE2B d2ec0f2e795ffc93051189e236ddefc92c1e0fbfc825f8bd32b6f8569c1e0ec290acaa418e93768587238ff25c3ae9a4d27457c7e5eb0635fc919ebb80b3de3b SHA512 be89eaeaac81cb79f6533b8764283f1f4ba85570f7626db6fa3e760124a26dcc1ee3ff3b293c67de2ed48083fe611ae0ca93db83da801456a34fe7cff816ba61
+DIST pulp-2.8.0.gh.tar.gz 31434075 BLAKE2B 65d0abc19d7677818dab3417c4ada9e171357c3e568ab23d224417287a6b28d41b0c82771e293d8793f5bc70ea84510538e2c84b1409aabd85517f7d1881a0ed SHA512 28fcec6d5c47778a46e8ea3316884a1f22777de9b692a47c3222c1aedc27106f711d19f6ce7af97b07322f947fc76cafa69e2c6636c7cc6d96ca19e96a766e8d
diff --git a/sci-mathematics/pulp/pulp-2.7.0.ebuild b/sci-mathematics/pulp/pulp-2.7.0.ebuild
index 641a91622..7432b49c1 100644
--- a/sci-mathematics/pulp/pulp-2.7.0.ebuild
+++ b/sci-mathematics/pulp/pulp-2.7.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
diff --git a/sci-mathematics/pulp/pulp-2.8.0.ebuild b/sci-mathematics/pulp/pulp-2.8.0.ebuild
new file mode 100644
index 000000000..9a5cee909
--- /dev/null
+++ b/sci-mathematics/pulp/pulp-2.8.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Create MPS/LP files, call solvers, and present results"
+HOMEPAGE="https://coin-or.github.io/pulp/"
+SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests setup.py
+# ToDo: package theme
+#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme
diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild
index c6ab40229..7c5137bca 100644
--- a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild
+++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild
@@ -9,7 +9,7 @@ MY_P=${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/${MY_P//_rc/-rc}.zip"
LICENSE="BSD"
SLOT="0"
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
index 326fadde3..93220dffb 100644
--- a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
@@ -1,9 +1,8 @@
EAPI=8
CMAKE_MAKEFILE_GENERATOR="emake"
-inherit cmake fortran-2
+inherit cmake fortran-2 flag-o-matic
-MY_P="${P}"
DESCRIPTION="CERN program library for High Energy Physics"
HOMEPAGE="https://cernlib.web.cern.ch/cernlib/"
SRC_URI="
@@ -17,7 +16,8 @@ LICENSE="
"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+free"
+# static-libs as default since otherwise test fail...
+IUSE="+free +static-libs"
RESTRICT="mirror"
RDEPEND="
@@ -60,6 +60,12 @@ src_configure() {
# docs follow rpm like spliting into packages cernlib, cernlib-devel, etc.
# we move them into a folder that agrees with gentoo doc structure.
sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die
+ # with -O2 some tests fail
+ # let upstream decide on optimization (-O0) since code is fragile
+ filter-flags -O1 -O2 -O3 -Os -Oz -Og -Ofast
+ local mycmakeargs=(
+ -DBUILD_SHARED_LIBS=$(usex static-libs OFF ON)
+ )
cmake_src_configure
}
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/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml
index bdee6992b..35b6c2bd9 100644
--- a/sci-physics/oneloop/metadata.xml
+++ b/sci-physics/oneloop/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-physics@gentoo.org</email>
<name>Gentoo Physics Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="bitbucket">hameren/oneloop</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
index 8b98d1e1d..9344d1513 100644
--- a/sci-physics/oneloop/oneloop-2020.07.31.ebuild
+++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
@@ -5,7 +5,7 @@ EAPI=8
# python only needed for create.py to get binaries
PYTHON_COMPAT=( python3_{10..11} )
-inherit toolchain-funcs python-any-r1
+inherit toolchain-funcs python-any-r1 fortran-2
DESCRIPTION="Library of one-loop scalar functions"
HOMEPAGE="https://bitbucket.org/hameren/oneloop"
@@ -16,12 +16,9 @@ LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64"
-DEPEND=""
-RDEPEND="${DEPEND}"
BDEPEND="
${PYTHON_DEPS}
app-arch/unzip
- virtual/fortran
"
PATCHES=(
diff --git a/sci-physics/particle/Manifest b/sci-physics/particle/Manifest
index a91580388..2f92c548b 100644
--- a/sci-physics/particle/Manifest
+++ b/sci-physics/particle/Manifest
@@ -1,2 +1,3 @@
DIST particle-0.23.0.tar.gz 313512 BLAKE2B 33a0dc1cf612af8242b5080d0862f3b1e587254b46fa90f235cd6edba3919594c5077733600dfe88ad0959be889271c301324789abf0511a7fbe588942086877 SHA512 582c42beade0b28f28f3ee9f83f6d8cc75558f8a9aa5fbe3679c7aa68af40bd04f374741211d6f214bb828c24a017a89b541f780739a36d61d85a2fd5e00b530
DIST particle-0.23.1.tar.gz 313729 BLAKE2B fc35163955e065b350dfa0825612a64214baeb1f5be41404af259136e6689e23419891513c059ccdfbe2cbf5891596fccd0b0b7f283031bb3352600b5be43441 SHA512 1b4f4516357fd9725d9d5b0a481467896e93e23a8956b2ce321b9cac1d200a8ee8dd9cc1b22d940b4708f29abe3417988677ac685b78287abe10afafa79fb381
+DIST particle-0.24.0.tar.gz 314302 BLAKE2B bbb2d52a80b4d9aafaf86a3cc1b28106253bf0edfe5a6127c03242a32973feaefeb32562063e5ff0438f5df946a905d03baa36c445093ce185d3be71c10e5135 SHA512 5a73079d9120ab509162189ba5992c615fc00e00d37a6556338130739bbf53fd5db01e973cb1b509ef7ce569021c0462ac77e5fcafe40df31e5cef0a89923a2a
diff --git a/sci-physics/particle/particle-0.24.0.ebuild b/sci-physics/particle/particle-0.24.0.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.24.0.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+ inherit pypi
+ KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+ >=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+ >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+ dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ )
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+ default
+
+ sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+ epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/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
+}