aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--dev-python/archspec/Manifest3
-rw-r--r--dev-python/archspec/archspec-0.1.4.ebuild19
-rw-r--r--dev-python/archspec/archspec-0.2.4.ebuild (renamed from dev-python/archspec/archspec-0.2.2.ebuild)10
-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/awkward-cpp/Manifest1
-rw-r--r--dev-python/awkward-cpp/awkward-cpp-35.ebuild26
-rw-r--r--dev-python/awkward/Manifest1
-rw-r--r--dev-python/awkward/awkward-2.6.6.ebuild44
-rw-r--r--dev-python/boost-histogram/Manifest2
-rw-r--r--dev-python/boost-histogram/boost-histogram-1.4.1.ebuild (renamed from dev-python/boost-histogram/boost-histogram-1.4.0.ebuild)1
-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.ebuild6
-rw-r--r--dev-python/dpath/Manifest2
-rw-r--r--dev-python/dpath/dpath-2.2.0.ebuild (renamed from dev-python/dpath/dpath-2.1.6.ebuild)9
-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/Manifest1
-rw-r--r--dev-python/hist/hist-2.7.3.ebuild26
-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/meshpy/meshpy-2020.1.ebuild2
-rw-r--r--dev-python/plac/Manifest2
-rw-r--r--dev-python/plac/plac-1.4.3.ebuild (renamed from dev-python/plac/plac-1.4.2.ebuild)2
-rw-r--r--dev-python/pybedtools/Manifest1
-rw-r--r--dev-python/pybedtools/metadata.xml (renamed from sci-biology/pybedtools/metadata.xml)0
-rw-r--r--dev-python/pybedtools/pybedtools-0.10.0.ebuild (renamed from sci-biology/pybedtools/pybedtools-0.9.0.ebuild)8
-rw-r--r--dev-python/pyfaidx/Manifest1
-rw-r--r--dev-python/pyfaidx/metadata.xml (renamed from sci-biology/pyfaidx/metadata.xml)4
-rw-r--r--dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild25
-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/rich-click/Manifest2
-rw-r--r--dev-python/rich-click/rich-click-1.8.3.ebuild (renamed from dev-python/rich-click/rich-click-1.7.2.ebuild)4
-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-9.2.0.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-3.2.3.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-8.16.0.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/Manifest2
-rw-r--r--dev-python/vector/vector-1.4.1.ebuild (renamed from dev-python/vector/vector-1.4.0.ebuild)0
-rw-r--r--dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild (renamed from dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild)13
-rw-r--r--profiles/package.mask9
-rw-r--r--profiles/updates/2Q-20242
-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/bx-python/Manifest3
-rw-r--r--sci-biology/bx-python/bx-python-0.12.0.ebuild41
-rw-r--r--sci-biology/bx-python/bx-python-0.8.9.ebuild35
-rw-r--r--sci-biology/bx-python/bx-python-0.9.0.ebuild35
-rw-r--r--sci-biology/bx-python/bx-python-9999.ebuild35
-rw-r--r--sci-biology/bx-python/files/no-doctest.patch9
-rw-r--r--sci-biology/bx-python/metadata.xml4
-rw-r--r--sci-biology/gffutils/Manifest2
-rw-r--r--sci-biology/gffutils/gffutils-0.11.1.ebuild42
-rw-r--r--sci-biology/gffutils/gffutils-0.13.ebuild32
-rw-r--r--sci-biology/gffutils/metadata.xml4
-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/multiqc/Manifest2
-rw-r--r--sci-biology/multiqc/multiqc-1.19.ebuild40
-rw-r--r--sci-biology/multiqc/multiqc-1.23.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/pybedtools/Manifest2
-rw-r--r--sci-biology/pybedtools/pybedtools-0.8.2.ebuild43
-rw-r--r--sci-biology/pyfaidx/Manifest2
-rw-r--r--sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild22
-rw-r--r--sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild24
-rw-r--r--sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild2
-rw-r--r--sci-mathematics/Oid/Oid-4.0-r1.ebuild (renamed from sci-mathematics/Oid/Oid-4.0.ebuild)26
-rw-r--r--sci-mathematics/Oid/files/Oid-4.0-bezier.patch11
-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-physics/cuttools/Manifest1
-rw-r--r--sci-physics/cuttools/cuttools-1.8.2.ebuild52
-rw-r--r--sci-physics/cuttools/files/mpnumdummy.f9026
-rw-r--r--sci-physics/cuttools/metadata.xml22
-rw-r--r--sci-physics/evtgen/Manifest1
-rw-r--r--sci-physics/evtgen/evtgen-02.02.01.ebuild39
-rw-r--r--sci-physics/evtgen/metadata.xml23
-rw-r--r--sci-physics/herwig/Manifest1
-rw-r--r--sci-physics/herwig/herwig-7.3.0.ebuild65
-rw-r--r--sci-physics/herwig/metadata.xml26
-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/mcfm/mcfm-10.2.1.ebuild2
-rw-r--r--sci-physics/oneloop/Manifest3
-rw-r--r--sci-physics/oneloop/files/oneloop-3.6_p20200731-config.patch (renamed from sci-physics/oneloop/files/oneloop-2020.07.31-config.patch)0
-rw-r--r--sci-physics/oneloop/metadata.xml16
-rw-r--r--sci-physics/oneloop/oneloop-2020.07.31.ebuild46
-rw-r--r--sci-physics/oneloop/oneloop-3.6.ebuild106
-rw-r--r--sci-physics/oneloop/oneloop-3.6_p20200731.ebuild104
-rw-r--r--sci-physics/openloops/Manifest1
-rw-r--r--sci-physics/openloops/files/openloops-2.1.2-ldflags.patch11
-rw-r--r--sci-physics/openloops/files/openloops-2.1.2-python3.12.patch34
-rw-r--r--sci-physics/openloops/metadata.xml23
-rw-r--r--sci-physics/openloops/openloops-2.1.3.ebuild108
-rw-r--r--sci-physics/photos/Manifest1
-rw-r--r--sci-physics/photos/metadata.xml23
-rw-r--r--sci-physics/photos/photos-3.64.ebuild82
-rw-r--r--sci-physics/qgraf/Manifest1
-rw-r--r--sci-physics/qgraf/qgraf-4.0.1.ebuild32
-rw-r--r--sci-physics/sherpa/Manifest1
-rw-r--r--sci-physics/sherpa/metadata.xml27
-rw-r--r--sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild94
-rw-r--r--sci-physics/sherpa/sherpa-9999.ebuild94
-rw-r--r--sci-physics/tauola/files/tauola-1.1.8-tau-spinner-makefile-install.patch22
-rw-r--r--sci-physics/tauola/metadata.xml13
-rw-r--r--sci-physics/tauola/tauola-1.1.8-r1.ebuild80
144 files changed, 2296 insertions, 464 deletions
diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest
index 8ad1830fc..c3dd31924 100644
--- a/dev-python/archspec/Manifest
+++ b/dev-python/archspec/Manifest
@@ -1,2 +1 @@
-DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286
-DIST archspec-0.2.2.tar.gz 38306 BLAKE2B c8f8011e122d31a603120231b5f4f034316e06412d64e0bb0fe38886508470d264f7a20da5ef79634fa5ba2f3d3b176b08151f9b5d72d64dbc5c90ce9bd6ff42 SHA512 e2310ca041064109358c918abbdfb581a1494d51d4c0f41e6172fdb9defcefd60f1b80ae2187c8143e37569c815fdc29508d52c048fe88c8c198e85997cef34d
+DIST archspec-0.2.4.tar.gz 52834 BLAKE2B cb8b9fce38b44783a361568667d5690e5c5169149ebdd3d4bf0943c056a4c8c9e2cb3a13a0b9b39e07f9b907b8f5ec4d1552a925d2e9bee76acf858d1a3f3ed5 SHA512 40a83854982670cb5cf77aab496198b3c6723a5cc386f05b8a020d9e94834d4109436cade9b9c89abac909c17b912f00aab8df2d6b05251c0afba9cee1932a62
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild
deleted file mode 100644
index 35500e00d..000000000
--- a/dev-python/archspec/archspec-0.1.4.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=poetry
-inherit distutils-r1 pypi
-
-DESCRIPTION="labels for various aspects of a system architecture like CPU, etc."
-HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- >=dev-python/six-1.16.0[${PYTHON_USEDEP}]
- <=dev-python/six-2.0.0[${PYTHON_USEDEP}]
- >=dev-python/click-7.1.2[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/archspec/archspec-0.2.2.ebuild b/dev-python/archspec/archspec-0.2.4.ebuild
index a7287fc72..002a57ba1 100644
--- a/dev-python/archspec/archspec-0.2.2.ebuild
+++ b/dev-python/archspec/archspec-0.2.4.ebuild
@@ -1,6 +1,6 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=poetry
inherit distutils-r1 pypi
@@ -11,3 +11,11 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
+BDEPEND="
+ test? (
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/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/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest
index 8d27c5f19..4c59bb8cb 100644
--- a/dev-python/awkward-cpp/Manifest
+++ b/dev-python/awkward-cpp/Manifest
@@ -1 +1,2 @@
DIST awkward-cpp-28.tar.gz 1422514 BLAKE2B ec87c37a37e3aceb0a35b580122a8c632070dc9fd284e34de66db2611cf1024dbd7ec8a355f52349783258cdaa91e0f966156689c82427f72574230c8b6ae6e1 SHA512 bbe0df527a7863b192c3c85a90c1295d2eb788eb7670a04a001838294dcdd434b49bdc2b4c3f71e34f5f160b4b9cafdea1cf290206fdcb14c0555005797a666d
+DIST awkward-cpp-35.tar.gz 1591781 BLAKE2B 4218f3a9e5e9c267135508a39303d2c44d5ce2f9ee94d7c034fb117b8833e7cea5ee16f8acbba464a3e61c5baf92b7f9e1f16d22a36478da3e44d2b33d837a3c SHA512 31ed7b99ee51407db0b76d9876a425863948a45fe9c3df61090fd679739af4091837436a14f54cad54f05c472b09a9130d1626f745d476a59baed627293000e7
diff --git a/dev-python/awkward-cpp/awkward-cpp-35.ebuild b/dev-python/awkward-cpp/awkward-cpp-35.ebuild
new file mode 100644
index 000000000..57634d120
--- /dev/null
+++ b/dev-python/awkward-cpp/awkward-cpp-35.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+DISTUTILS_USE_PEP517=scikit-build-core
+PYPI_NO_NORMALIZE=1
+
+inherit pypi distutils-r1
+
+DESCRIPTION="awkward-cpp bindings for Python"
+HOMEPAGE="https://github.com/scikit-hep/awkward/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ >=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward/Manifest b/dev-python/awkward/Manifest
index d3422fc99..3f4ebd5df 100644
--- a/dev-python/awkward/Manifest
+++ b/dev-python/awkward/Manifest
@@ -1 +1,2 @@
DIST awkward-2.5.2.tar.gz 5561040 BLAKE2B 4799eeb25fa7433b4889328f9f147b435024c3f507ce66b5cbfcfc5b9c50e63f77131a43b8acd3d9f22d20915eaeb129162e26ffa83fd2071b9a393fbc441e7e SHA512 b6f4f2841e642bfc17aaf40779030d125e9737ef0ded20cc8a898c4b8c15c2932f12c8a0bda3e8c48bb8d13729cf97e181866f15913317bd2dba13b0dad6b929
+DIST awkward-2.6.6.tar.gz 6088969 BLAKE2B a2b1db5fe9daae32272348b7bf92894fd805806bcec66ef57acf51af9bc99f033723c637515530a2867ec4bafa51bce5d90ad2b651ed008790ae8f7bee3e73f7 SHA512 2b7c0f1c1f3bd06f1b9fc06ca7cd482b136986d7b5f1648c45627083df5042668d122db7f93e9dbe606630270e577bc53472b9fdca837b12b390ef5c86e8fe48
diff --git a/dev-python/awkward/awkward-2.6.6.ebuild b/dev-python/awkward/awkward-2.6.6.ebuild
new file mode 100644
index 000000000..bd393bcd2
--- /dev/null
+++ b/dev-python/awkward/awkward-2.6.6.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms."
+HOMEPAGE="https://github.com/scikit-hep/awkward"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+ ~dev-python/awkward-cpp-35[${PYTHON_USEDEP}]
+ dev-python/fsspec[${PYTHON_USEDEP}]
+ $(python_gen_cond_dep '
+ >=dev-python/importlib-metadata-4.13.0[${PYTHON_USEDEP}]
+ ' python3_{10..11})
+ $(python_gen_cond_dep '
+ >=dev-python/typing-extensions-4.1.0[${PYTHON_USEDEP}]
+ ' python3_10)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/hatch-vcs[${PYTHON_USEDEP}]
+ dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}]
+ test? (
+ dev-libs/apache-arrow[zstd]
+ dev-python/pyarrow[${PYTHON_USEDEP}]
+ dev-python/numexpr[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_IGNORE=(
+ tests-cuda/
+ tests-cuda-kernels/
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest
index 1fb711744..78bf6ae03 100644
--- a/dev-python/boost-histogram/Manifest
+++ b/dev-python/boost-histogram/Manifest
@@ -1 +1 @@
-DIST boost_histogram-1.4.0.tar.gz 1329002 BLAKE2B 1636ed04c5df2f6c156468ffc0fed7b82469bb903c316b1b9fd209b7072ebb5b0de9969f4f8b50da69db7ee40009df534959db7734f1161da2c6216bddce858b SHA512 e7f61cc2d013a0664646d9edf1f713eb5f06f000ad2105e90229ef9b01b25a08c8e717a2ac241ed990fa2c082a1bb84af18e17b238640de5679d0ab76ff08af6
+DIST boost_histogram-1.4.1.tar.gz 1337723 BLAKE2B 42087abfd34471f42b06571ab4e701e7fbc071a5b9f3133f6f80831a0fd01ef95f65cae7bdcc6892674a415fd9b48a20bb0ecd5fd294a4880a6f5e3922e60a09 SHA512 fda8085929677a1664030fd29beb01caf37b42413fe941c2760fed17325301c4bf6b8ec5fa3b0e128558a52dee3245ec3a3fc2f4ca145dd09dea0b88fcfa33d4
diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.4.1.ebuild
index 96950ebe5..679109b59 100644
--- a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
+++ b/dev-python/boost-histogram/boost-histogram-1.4.1.ebuild
@@ -2,6 +2,7 @@ EAPI=8
PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
inherit distutils-r1 pypi
DESCRIPTION="Python bindings for the C++14 Boost::Histogram library"
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..94fcd2777 100644
--- a/dev-python/datrie/datrie-0.8.2-r1.ebuild
+++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild
@@ -1,9 +1,9 @@
-# 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} )
# Fails to compile with pep517
#DISTUTILS_USE_PEP517=setuptools
@@ -28,5 +28,7 @@ distutils_enable_tests pytest
python_prepare_all() {
# do not depend on pytest-runner
sed -i "/pytest-runner/d" setup.py || die
+ # https://github.com/pytries/datrie/pull/99
+ sed -i "12s/struct AlphaMap:/ctypedef struct AlphaMap:/" src/cdatrie.pxd || die
distutils-r1_python_prepare_all
}
diff --git a/dev-python/dpath/Manifest b/dev-python/dpath/Manifest
index 81aa6ca1c..1a325c16d 100644
--- a/dev-python/dpath/Manifest
+++ b/dev-python/dpath/Manifest
@@ -1 +1 @@
-DIST dpath-2.1.6.tar.gz 28142 BLAKE2B 78cb4a8eb7278cd0c1818ffba9d77a917d89f3454a047a82d9031028b34ea2969fe98ed7086d26f6697a166b81cd50439b7b3bd545ab7e6cadcd0606c24be61e SHA512 2f2dac39b6e1ad2effd8d61ac4acf6619205423389ecebc54061aa10ec11ce3236ea666b632a7dca349e9b7a6579815c97e01c930eaa1a99d965e37b9825b82c
+DIST dpath-2.2.0.tar.gz 28266 BLAKE2B 7606e588a41b97cc44c592e65634b3c050accbec3c21634653d83aafa500d62bd8f4ce8d4d12db213f5e22554bf467cd9c140cf01b08885a705f5b4c4a481166 SHA512 d7ab814299580fb54bd2436bb437ae6af6ad1c9057ba4dda708d023f1e49658d41f33260b66348c1d03ff598543f5d68fc759d462ed709ec7da534780e37603c
diff --git a/dev-python/dpath/dpath-2.1.6.ebuild b/dev-python/dpath/dpath-2.2.0.ebuild
index 55da56b96..a761ac4ea 100644
--- a/dev-python/dpath/dpath-2.1.6.ebuild
+++ b/dev-python/dpath/dpath-2.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2024 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -15,4 +15,11 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+BDEPEND="
+ test? (
+ dev-python/hypothesis[${PYTHON_USEDEP}]
+ dev-python/nose2[${PYTHON_USEDEP}]
+ )
+"
+
distutils_enable_tests pytest
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
index 722ab9aa8..f9d572709 100644
--- a/dev-python/hist/Manifest
+++ b/dev-python/hist/Manifest
@@ -1 +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-2.7.3.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[${PYTHON_USEDEP}]
+"
+
+RESTRICT="test"
+# needs mplhep and dask_histogram ...
+#distutils_enable_tests pytest
diff --git a/dev-python/immutables/Manifest b/dev-python/immutables/Manifest
new file mode 100644
index 000000000..dfee7ecc9
--- /dev/null
+++ b/dev-python/immutables/Manifest
@@ -0,0 +1 @@
+DIST immutables-0.20.tar.gz 88933 BLAKE2B 07ae33ea62e85ea8c9b26a7e634f018b6e614ecd493faa74cdbdb20864b6af78b30fbadd1c21d9b9e3e971086893dcc7053ba88f8c78d7dbb588d54b8a9d0175 SHA512 1b74236517964573fd26072b6bf1b8a93456822b2b6ccc5f544f8a49b91f2e0bd110ef2ac23358ba14deceaaee8dde6f24e5589e9078dce961a7b9d4fcd2d3bd
diff --git a/dev-python/immutables/immutables-0.20.ebuild b/dev-python/immutables/immutables-0.20.ebuild
new file mode 100644
index 000000000..8cd5bf37b
--- /dev/null
+++ b/dev-python/immutables/immutables-0.20.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2024 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_EXT=1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="A high-performance immutable mapping type for Python"
+HOMEPAGE="https://pypi.org/project/immutables/"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="test? ( dev-python/mypy[${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/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/plac/Manifest b/dev-python/plac/Manifest
index f50e462dc..ec977e410 100644
--- a/dev-python/plac/Manifest
+++ b/dev-python/plac/Manifest
@@ -1 +1 @@
-DIST plac-1.4.2.tar.gz 37595 BLAKE2B 5205e9d8a5a775eb2e23ea7ad30e576417a8ba944cb196ccb7a16b514b6c4902856a7191b1bbf71ab0176910b5d8dc163ab36fe3fb0c5bb5765c02d16ae347b1 SHA512 c8c320cabda42f33071d7675b64befab8344bde746d0befe661a9bb26f658559435d2895dad0a27dc1d7c2dc59f07a359b529880e115d900b4fca8f245186742
+DIST plac-1.4.3.tar.gz 38984 BLAKE2B 39ede8377710b1cd3a53d3d1fd2285c2cdb3b9f79c9c11f3b9888a2dc954433488799a4ee31cdcf9b17d15214cc390c424f13504a862136e093842f3a546e416 SHA512 2222657bc524307e342ff21cfbbf0278ac618f2b9db8788362325ad955e5ca5181cf9770564bdef9bbb6acbb52750771593311c0d32aa85f343f51a7b28d0caa
diff --git a/dev-python/plac/plac-1.4.2.ebuild b/dev-python/plac/plac-1.4.3.ebuild
index 50b269f42..8f2be2238 100644
--- a/dev-python/plac/plac-1.4.2.ebuild
+++ b/dev-python/plac/plac-1.4.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2024 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=8
diff --git a/dev-python/pybedtools/Manifest b/dev-python/pybedtools/Manifest
new file mode 100644
index 000000000..7db62a4c4
--- /dev/null
+++ b/dev-python/pybedtools/Manifest
@@ -0,0 +1 @@
+DIST pybedtools-0.10.0.tar.gz 12497095 BLAKE2B d9fb44bd3afcb8748e0cadbe0c4d55c7325911331d0719b79bd04eff264bd6299d407dee7f511bc05a7e12dd46e92a9c25ce0607b8926e6542e4dd652cc9d23f SHA512 cec04464fcfaa12bb660f223d6f656a30ac5822ea9053455dbc5717d2afbc998db9fd4b7424d8458445450a6ce5aafb65463fa1274b2691b26bfda7fe84bef56
diff --git a/sci-biology/pybedtools/metadata.xml b/dev-python/pybedtools/metadata.xml
index b80afba97..b80afba97 100644
--- a/sci-biology/pybedtools/metadata.xml
+++ b/dev-python/pybedtools/metadata.xml
diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/dev-python/pybedtools/pybedtools-0.10.0.ebuild
index bc02bda6f..ae51c24ce 100644
--- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
+++ b/dev-python/pybedtools/pybedtools-0.10.0.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
-
+DISTUTILS_EXT=1
inherit distutils-r1
DESCRIPTION="Use BED and GFF files from python using BEDtools"
@@ -25,8 +25,6 @@ RDEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
"
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
-
# TODO: fix docs building
# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
# even if pybedtools is installed
diff --git a/dev-python/pyfaidx/Manifest b/dev-python/pyfaidx/Manifest
new file mode 100644
index 000000000..c66bceba8
--- /dev/null
+++ b/dev-python/pyfaidx/Manifest
@@ -0,0 +1 @@
+DIST pyfaidx-0.8.1.1.tar.gz 103060 BLAKE2B 6910b77950a55885d1e0ae9f30172ec5c1d14320fdb2bad264e21d8f2e7f212f725f2608297ac5b6a2ec8d366b1385245694b2a70410deca8be1765db0683835 SHA512 26d130770069aed9bd378e54f338b6c66840114e6cddfdc971b6496fa30ee651181f2225d372499992b63ba8b0c6d0a7ed827a210dc3f78c0c8592bdb73211b3
diff --git a/sci-biology/pyfaidx/metadata.xml b/dev-python/pyfaidx/metadata.xml
index 47cc39d79..b0e39cc41 100644
--- a/sci-biology/pyfaidx/metadata.xml
+++ b/dev-python/pyfaidx/metadata.xml
@@ -5,10 +5,6 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
<upstream>
<remote-id type="pypi">pyfaidx</remote-id>
<remote-id type="github">mdshw5/pyfaidx</remote-id>
diff --git a/dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild b/dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild
new file mode 100644
index 000000000..86465aecd
--- /dev/null
+++ b/dev-python/pyfaidx/pyfaidx-0.8.1.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Efficient pythonic random access to fasta subsequences"
+HOMEPAGE="https://github.com/mdshw5/pyfaidx"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+REPEND="dev-python/importlib_metadata[${PYTHON_USEDEP}]"
+
+EPYTEST_DESELECT=(
+ # needs external file
+ tests/test_Fasta_bgzip.py
+)
+
+distutils_enable_tests pytest
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/rich-click/Manifest b/dev-python/rich-click/Manifest
index ae8d92c2f..4971bebd8 100644
--- a/dev-python/rich-click/Manifest
+++ b/dev-python/rich-click/Manifest
@@ -1 +1 @@
-DIST rich-click-1.7.2.tar.gz 39362 BLAKE2B c4ad70d449ce9ceb3d9bbbccf7c7d3cd43386c35061d60c6395ff7845f606558af36a7c465a3393484008ece244f8e684ca9d71cea14463f04cac21803108543 SHA512 f4046e54874c4f3cc4f77651fdeb1f888d9435ff282f54d320c16c7c42f57c48018c0159230e780684336d29edff6e654454b8940b5b8df5a19139d2219c671b
+DIST rich_click-1.8.3.tar.gz 38209 BLAKE2B c87386d729585a579ce881f83737427a250a0c56cf7eda832be308de121590d7af17f7672a78aa3f3dc8834720b858ee1f9ac65e1ddf031acac16a791f91f0db SHA512 2410b7e4d69fa79e41f2394fecf1f4809e9eceaf2d463c91914bf27603842b8ba9550c6aaa90812dd725ce0a74f61fb69b35b0b1ccd87b5412b7bd727eeed74c
diff --git a/dev-python/rich-click/rich-click-1.7.2.ebuild b/dev-python/rich-click/rich-click-1.8.3.ebuild
index e642303e2..5394cb4e3 100644
--- a/dev-python/rich-click/rich-click-1.7.2.ebuild
+++ b/dev-python/rich-click/rich-click-1.8.3.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
@@ -6,7 +6,6 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..12} )
-PYPI_NO_NORMALIZE=1
inherit pypi distutils-r1
DESCRIPTION="Format click help output nicely with rich"
@@ -17,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~amd64-linux"
RDEPEND="dev-python/click[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[${PYTHON_USEDEP}]
dev-python/rich[${PYTHON_USEDEP}]
dev-python/typing-extensions[${PYTHON_USEDEP}]"
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..fae5302d8
--- /dev/null
+++ b/dev-python/snakemake-interface-executor-plugins/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_executor_plugins-9.2.0.tar.gz 16490 BLAKE2B e239c68edbb14c89322a2bd91bb60beb73a939e523e01bec882ee6762412478bc28d856182cf82d62a7879b65797b299cce34aa69cea6d216b6e3bfb3aa59bca SHA512 d6f6ec6cba2649b801bf2352ac60a66bfdc419e53987c77ce64aa37ed08aebec54d07d0e99b1ef212f122b87b40e7f0cb0a0713a2b756e28228dbb9b27b27fce
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-9.2.0.ebuild b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.2.0.ebuild
new file mode 100644
index 000000000..41008ef8b
--- /dev/null
+++ b/dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.2.0.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..65939aa80
--- /dev/null
+++ b/dev-python/snakemake-interface-storage-plugins/Manifest
@@ -0,0 +1 @@
+DIST snakemake_interface_storage_plugins-3.2.3.tar.gz 11930 BLAKE2B 5f46a52d46c11a2feb9840e5a3eb67374ad4a148ff2366953be0285877d1a33c344fcf9930a8145fccd1987995ddaf177997e393a9f21bbd316102d620b4bc9d SHA512 7692c9cacc5ece8e76dab67be3a8ed1a32930b27ce7edaa3998b23305723e7e01b3c04954b61585d876b5410caf3036efd0cb9569e159abcc5a95d9ab2446494
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-3.2.3.ebuild b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.3.ebuild
new file mode 100644
index 000000000..39c8b08a2
--- /dev/null
+++ b/dev-python/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.3.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..de4027537 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-8.16.0.gh.tar.gz 8665306 BLAKE2B 76d3455ce9a7ccc749adb5a729ab954d7a3fd97dc2432c3a0e9aba1ace1cb08e377244a2a2527c676b9709f9bb8b5af29948c0385657755bbbc8449b136fc26d SHA512 29b6ba6da5dbbd347dee45114b949c976973555c9234f8a150dcd83e4af1638c1773590320bc44284cf20ea445efb377dcf9199921ed2b4d62bad3a60a41af3c
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[${PYTHON_USEDEP}]
"
distutils_enable_sphinx docs \
diff --git a/dev-python/snakemake/snakemake-8.16.0.ebuild b/dev-python/snakemake/snakemake-8.16.0.ebuild
new file mode 100644
index 000000000..f83e8feb9
--- /dev/null
+++ b/dev-python/snakemake/snakemake-8.16.0.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make-like task language"
+HOMEPAGE="https://snakemake.readthedocs.io"
+SRC_URI="https://github.com/${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-0.0.3[${PYTHON_USEDEP}]
+ dev-python/datrie[${PYTHON_USEDEP}]
+ dev-python/docutils[${PYTHON_USEDEP}]
+ dev-python/GitPython[${PYTHON_USEDEP}]
+ dev-python/humanfriendly[${PYTHON_USEDEP}]
+ >=dev-python/jinja-3.0[${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[${PYTHON_USEDEP}]
+ >=dev-python/requests-2.8.1[${PYTHON_USEDEP}]
+ dev-python/reretry[${PYTHON_USEDEP}]
+ >=dev-python/smart-open-4.0[${PYTHON_USEDEP}]
+ >=dev-python/snakemake-interface-common-1.17.0[${PYTHON_USEDEP}]
+ >=dev-python/snakemake-interface-executor-plugins-9.2.0[${PYTHON_USEDEP}]
+ >=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}]
+ >=dev-python/snakemake-interface-report-plugins-1.0.0[${PYTHON_USEDEP}]
+ dev-python/stopit[${PYTHON_USEDEP}]
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ dev-python/throttler[${PYTHON_USEDEP}]
+ >=dev-python/toposort-1.10[${PYTHON_USEDEP}]
+ dev-python/wrapt[${PYTHON_USEDEP}]
+ >=dev-python/yte-1.5.1[${PYTHON_USEDEP}]
+ >=dev-python/dpath-2.1.6[${PYTHON_USEDEP}]
+ >=dev-python/conda-inject-1.3.1[${PYTHON_USEDEP}]
+ >=sci-mathematics/pulp-2.3.1[${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 df652f966..a64079e01 100644
--- a/dev-python/vector/Manifest
+++ b/dev-python/vector/Manifest
@@ -1,3 +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-1.4.0.tar.gz 368490 BLAKE2B 443922bc00bfddd3601a414af1a2ba70bed0caff0dd5516573a557d736b65ebf42f191c6de776a3a28b2399d4cbe3db56f69864051758839a00e2703e6b3b53c SHA512 f8caba973fe7739537c41b5a86b435134bfa1f59b355a2246ae0cff76b6be5ea8ddae90c11326d439e4c31aacbbf21061479fa0d1d9e644292307bf2a77c416e
+DIST vector-1.4.1.tar.gz 374576 BLAKE2B 863984ed98dbe6920380f467931c9b80b3a57934dfcf0de049de77a7d6ec8f9c9335333609ab28b794ed31a2f6a859bd1475b0bb2976fa9c1f4ca1f2aecbfea9 SHA512 5a08c49f6bf09d07768b90d79a9a0b9aa9b1068c6c03be96f960605d2a708cb80f0ff7fc2da807383d1e652bd454c27048702adffa1a55ee3ca9b740c5b0f2f0
diff --git a/dev-python/vector/vector-1.4.0.ebuild b/dev-python/vector/vector-1.4.1.ebuild
index a57240b49..a57240b49 100644
--- a/dev-python/vector/vector-1.4.0.ebuild
+++ b/dev-python/vector/vector-1.4.1.ebuild
diff --git a/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild
index 1359f4e0d..e043b122f 100644
--- a/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
+++ b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1-r1.ebuild
@@ -20,6 +20,7 @@ RDEPEND="
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
"
@@ -29,15 +30,3 @@ distutils_enable_tests pytest
PATCHES=(
"${FILESDIR}/${P}-git_config.patch"
)
-
-python_test() {
- #git init -q || die
- #git config --global user.email "placeholder@gentoo.org" || die
- #git config --global user.name "Place Holder" || die
- #git add . || die
- #git commit -m "init" || die
- ##GIT_AUTHOR_NAME="Place Holder" GIT_AUTHOR_EMAIL="placeholder@gentoo.org" epytest
- ##export GIT_AUTHOR_NAME="Place Holder"
- ##export GIT_AUTHOR_EMAIL="placeholder@gentoo.org"
- epytest
-}
diff --git a/profiles/package.mask b/profiles/package.mask
index 48068ccf9..c184ca27b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,9 +30,6 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
-# Dependencies dev-python/future removed
-sci-biology/multiqc
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
-# reverse deps
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18)
+# Requires java openmpi bindings, no longer packaged.
+sci-biology/BBmap
diff --git a/profiles/updates/2Q-2024 b/profiles/updates/2Q-2024
new file mode 100644
index 000000000..ad60545f3
--- /dev/null
+++ b/profiles/updates/2Q-2024
@@ -0,0 +1,2 @@
+move sci-biology/pyfaidx dev-python/pyfaidx
+move sci-biology/pybedtools dev-python/pybedtools
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/bx-python/Manifest b/sci-biology/bx-python/Manifest
index 90147dff7..69572ef1e 100644
--- a/sci-biology/bx-python/Manifest
+++ b/sci-biology/bx-python/Manifest
@@ -1,2 +1 @@
-DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea
-DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc
+DIST bx-python-0.12.0.gh.tar.gz 1660806 BLAKE2B 0eddb9b9a93520319d275001067a3518015483605cf4d096729ec92e14c0eb35f2ceb34db964216dd3c6687351a7415c46061960b1f66a7564c90efeba3a587b SHA512 821b33841dd2935485669f6c112277d404475b1cd778deb3eaa1194f3b21594335a219d9345e279e7afc3adb1e347e71e60f0029712fc58e95d1e70f9e8fbb55
diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.12.0.ebuild
new file mode 100644
index 000000000..1a00b0395
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.12.0.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# doctests have external deps
+PATCHES=(
+ "${FILESDIR}/no-doctest.patch"
+)
+
+distutils_enable_tests pytest
+
+# https://github.com/bxlab/bx-python/issues/101
+EPYTEST_DESELECT=(
+ lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo
+ lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer
+)
+
+python_test() {
+ cd "${BUILD_DIR}/build" || die
+ ln -s "${S}/pytest.ini" . || die
+ ln -s "${S}/test_data" . || die
+ epytest
+}
diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
deleted file mode 100644
index 6cffba1be..000000000
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-inherit distutils-r1
-
-DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://github.com/bxlab/bx-python"
-SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
-# (and might need some more work beyond that)
-RESTRICT=test
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
-"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-# has file collision with sci-biology/RSeQC
-
-# ToDo: fix doc building:
-# Reason: TemplateNotFound('i')
-#distutils_enable_sphinx doc/source
-
-distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
deleted file mode 100644
index 6cffba1be..000000000
--- a/sci-biology/bx-python/bx-python-0.9.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-inherit distutils-r1
-
-DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://github.com/bxlab/bx-python"
-SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
-# (and might need some more work beyond that)
-RESTRICT=test
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
-"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-# has file collision with sci-biology/RSeQC
-
-# ToDo: fix doc building:
-# Reason: TemplateNotFound('i')
-#distutils_enable_sphinx doc/source
-
-distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
deleted file mode 100644
index b29975b58..000000000
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://github.com/bxlab/bx-python"
-EGIT_REPO_URI="https://github.com/bxlab/bx-python"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
-# (and might need some more work beyond that)
-RESTRICT=test
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
-"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
-"
-
-# has file collision with sci-biology/RSeQC
-
-# ToDo: fix doc building:
-# Reason: TemplateNotFound('i')
-#distutils_enable_sphinx doc/source
-
-distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/files/no-doctest.patch b/sci-biology/bx-python/files/no-doctest.patch
new file mode 100644
index 000000000..d0c2b2e62
--- /dev/null
+++ b/sci-biology/bx-python/files/no-doctest.patch
@@ -0,0 +1,9 @@
+diff --git a/pytest.ini b/pytest.ini
+index e77e08f..4184247 100644
+--- a/pytest.ini
++++ b/pytest.ini
+@@ -1,4 +1,3 @@
+ [pytest]
+-addopts = --doctest-cython --doctest-modules
+ python_files = *_tests.py
+ testpaths = lib script_tests/
diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index f1fc4360e..2ead27d78 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -5,10 +5,6 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
<upstream>
<remote-id type="github">bxlab/bx-python</remote-id>
<remote-id type="pypi">bx-python</remote-id>
diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest
index e8b006cbf..ca30cec83 100644
--- a/sci-biology/gffutils/Manifest
+++ b/sci-biology/gffutils/Manifest
@@ -1 +1 @@
-DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb
+DIST gffutils-0.13.gh.tar.gz 1644910 BLAKE2B c8c4bc5d8a51e2e63d359bed8953730dc2d64ab04a96021fbaa891443f77c259886bcb81bab59eff622f23aeaed77c30bd1635b03761607ec562fa52d92ebea7 SHA512 617f84aeaa4d16b140083012c6b3656d5ea44a9a0619f8516e51379f92e9be85dff42e31c9ac2c3a77d7e3715f43c0106cd534317cc6ff4b6257fce56a1b635f
diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild
deleted file mode 100644
index 8ee8fd4b5..000000000
--- a/sci-biology/gffutils/gffutils-0.11.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://gffutils.readthedocs.io/en/latest/"
-SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Nose tests no longer supported, migration on next release
-#RESTRICT="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/argh[${PYTHON_USEDEP}]
- dev-python/argcomplete[${PYTHON_USEDEP}]
- sci-biology/biopython[${PYTHON_USEDEP}]
- sci-biology/pybedtools[${PYTHON_USEDEP}]
- sci-biology/pyfaidx[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
- if use test; then
- sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- distutils_install_for_testing
- nosetests -v -x --with-doctest -a '!slow' || die
-}
diff --git a/sci-biology/gffutils/gffutils-0.13.ebuild b/sci-biology/gffutils/gffutils-0.13.ebuild
new file mode 100644
index 000000000..fbd90b6d9
--- /dev/null
+++ b/sci-biology/gffutils/gffutils-0.13.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="GFF and GTF file manipulation and interconversion"
+HOMEPAGE="https://gffutils.readthedocs.io/en/latest/"
+SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/argh[${PYTHON_USEDEP}]
+ dev-python/argcomplete[${PYTHON_USEDEP}]
+ dev-python/pyfaidx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+# https://github.com/daler/gffutils/issues/233 + cli not installed yet
+EPYTEST_DESELECT=(
+ gffutils/test/test_biopython_integration.py::test_roundtrip
+ gffutils/test/test_cli.py::test_issue_224
+)
+
+distutils_enable_tests pytest
diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml
index c9fe23ced..dc2c60220 100644
--- a/sci-biology/gffutils/metadata.xml
+++ b/sci-biology/gffutils/metadata.xml
@@ -5,10 +5,6 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
<upstream>
<remote-id type="github">daler/gffutils</remote-id>
</upstream>
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 [[ ${PV} == 9999 ]]; then
if use plugins ; then
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
index 3585038a3..cf36e2eb5 100644
--- a/sci-biology/multiqc/Manifest
+++ b/sci-biology/multiqc/Manifest
@@ -1 +1 @@
-DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
+DIST multiqc-1.23.gh.tar.gz 5639815 BLAKE2B 1cd02d82d5a1856470777cdd5db48fbf2d86a37e713fa32118edb608703c9fbf1d23af6254a0ed15c47f2c073999a58c53a5a67c6df9a6bfc61cb773fc857bae SHA512 f7d910122ec34373dfa2d60dd7436ec66494980daf7e46729fbae90481bcceb1318c5dbafc64725dca2079deb5fe66834371813aa4dda7e9bf676dff5a043995
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
deleted file mode 100644
index 187f06c22..000000000
--- a/sci-biology/multiqc/multiqc-1.19.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit pypi distutils-r1
-
-DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
-HOMEPAGE="https://multiqc.info/"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
-
-RDEPEND="dev-python/matplotlib[${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-1.23.ebuild b/sci-biology/multiqc/multiqc-1.23.ebuild
new file mode 100644
index 000000000..bf45065aa
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.23.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}/${P}-tests.patch" )
diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest
deleted file mode 100644
index a952ac4b8..000000000
--- a/sci-biology/pybedtools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe
-DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18
diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
deleted file mode 100644
index bc02bda6f..000000000
--- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Use BED and GFF files from python using BEDtools"
-HOMEPAGE="https://daler.github.io/pybedtools"
-SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- sci-biology/bedtools
- sci-biology/pysam[${PYTHON_USEDEP}]
- dev-python/six[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
-"
-
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
-
-# TODO: fix docs building
-# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
-# even if pybedtools is installed
-#distutils_enable_sphinx docs/source
-distutils_enable_tests pytest
-
-python_test() {
- # Requires network
- local EPYTEST_DESELECT=(
- test/test_helpers.py::test_chromsizes
- )
- cd "${T}" || die
- epytest --pyargs pybedtools
-}
diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest
deleted file mode 100644
index 0bb3b35f4..000000000
--- a/sci-biology/pyfaidx/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4
-DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c
diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild
deleted file mode 100644
index bec223f6c..000000000
--- a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1
-
-DESCRIPTION="Efficient pythonic random access to fasta subsequences"
-HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx"
-SRC_URI="https://github.com/mdshw5/pyfaidx/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-REPEND="dev-python/six[${PYTHON_USEDEP}]"
-
-#distutils_enable_tests nose
diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild
deleted file mode 100644
index 14f557869..000000000
--- a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="Efficient pythonic random access to fasta subsequences"
-HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-# Test issues reported upstream:
-# https://github.com/mdshw5/pyfaidx/issues/208
-RESTRICT="test"
-
-REPEND="dev-python/six[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 9b9233020..49ca40b32 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -34,4 +34,4 @@ RDEPEND="
DEPEND="${RDEPEND}"
distutils_enable_sphinx docs_sphinx --no-autodoc
-distutils_enable_tests --install pytest
+distutils_enable_tests pytest
diff --git a/sci-mathematics/Oid/Oid-4.0.ebuild b/sci-mathematics/Oid/Oid-4.0-r1.ebuild
index ce967fd46..2c02ef51b 100644
--- a/sci-mathematics/Oid/Oid-4.0.ebuild
+++ b/sci-mathematics/Oid/Oid-4.0-r1.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit java-pkg-2
@@ -9,28 +9,38 @@ MY_PV="${PV//./-}"
MY_P="${PN}${MY_PV}"
DESCRIPTION="An interactive, extensible software system for experimenting with matroids"
-HOMEPAGE="https://sites.google.com/site/wwwmatroids/"
+HOMEPAGE="http://userhome.brooklyn.cuny.edu/skingan/matroids/software.html"
SRC_URI="
- https://sites.google.com/site/wwwmatroids/${MY_P}.tar.gz -> ${P}.tar.gz
- https://sites.google.com/site/wwwmatroids/${PN}UserManual${MY_PV}.pdf
+ http://userhome.brooklyn.cuny.edu/skingan/matroids/${MY_P}.tar.gz -> ${P}.tar.gz
+ http://userhome.brooklyn.cuny.edu/skingan/matroids/${PN}UserManual${MY_PV}.pdf
"
KEYWORDS="~amd64 ~x86"
SLOT="0"
LICENSE="GPL-2"
-DEPEND=">=virtual/jdk-1.4:*"
-RDEPEND=">=virtual/jre-1.4:*"
+DEPEND=">=virtual/jdk-1.7:*"
+RDEPEND=">=virtual/jre-1.7:*"
# The source uses 'enum' as an identifier, therefore:
-JAVA_PKG_WANT_SOURCE="1.4"
+JAVA_PKG_WANT_SOURCE="1.7"
+JAVA_PKG_WANT_TARGET="1.7"
S="${WORKDIR}"
+PATCHES=(
+ "${FILESDIR}/${P}-bezier.patch"
+)
+
src_prepare () {
mkdir classes || die
# change path names
sed -i -e 's:NAME = ":NAME = "/usr/share/Oid/:' MatroidToolkit.java || die
+ # replace all enum, since after 1.4 java it is a keywords
+ sed -i -e 's:enum:enum_as_a_key_is_no_longer_allowed:g' \
+ Oid/PGFactory.java \
+ DisplayGeom.java \
+ VisRank3ModularCuts.java || die
default
}
@@ -45,7 +55,7 @@ src_install () {
java-pkg_dojar Oid.jar
java-pkg_dolauncher
- dodoc "${DISTDIR}"/OidUserManual4-0.pdf
+ dodoc "${DISTDIR}"/${PN}UserManual${MY_PV}.pdf
insinto /usr/share/Oid
doins matroid*.txt
diff --git a/sci-mathematics/Oid/files/Oid-4.0-bezier.patch b/sci-mathematics/Oid/files/Oid-4.0-bezier.patch
new file mode 100644
index 000000000..56dd64a99
--- /dev/null
+++ b/sci-mathematics/Oid/files/Oid-4.0-bezier.patch
@@ -0,0 +1,11 @@
+--- a/DisplayGeom.java 2024-02-16 22:01:22.213390949 +0100
++++ b/DisplayGeom.java 2024-02-16 22:01:26.106781457 +0100
+@@ -7844,7 +7844,7 @@
+ // are c1 and c2. The tangent of the curve at p1 is determined
+ // by the line between p1 and c1. Likewise, the tangent at p2
+ // is determined by a line from p2 to c2. These curves are also
+- // called Bézier curves.
++ // called Bezier curves.
+
+ //permStorage.removeAllElements();
+ //finalStorage.removeAllElements();
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 -> ${P}.gh.tar.gz"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests setup.py
+# ToDo: package theme
+#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme
diff --git a/sci-physics/cuttools/Manifest b/sci-physics/cuttools/Manifest
new file mode 100644
index 000000000..590c6fd51
--- /dev/null
+++ b/sci-physics/cuttools/Manifest
@@ -0,0 +1 @@
+DIST cuttools_v1.8.2.tar.gz 962232 BLAKE2B aaec06cc892577c2e562e8ee07e9863dd42a8bbf878b4e2aee01d2bbf5bb27bb9e4f50ef3c3a66fe00e73cc527e23b0274f9c3df169779c5fb529c9ff5610cb0 SHA512 6f1af82caa2a86669271346fa4a4f1d13b39f1c1ee7562c5fc29f250276d59017722a55256358bd006819a442acd3198901b642039be9f6a78d3cf31fe0ca976
diff --git a/sci-physics/cuttools/cuttools-1.8.2.ebuild b/sci-physics/cuttools/cuttools-1.8.2.ebuild
new file mode 100644
index 000000000..d72b6def0
--- /dev/null
+++ b/sci-physics/cuttools/cuttools-1.8.2.ebuild
@@ -0,0 +1,52 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2 toolchain-funcs
+
+DESCRIPTION="Computing 1-loop amplitudes at the integrand level"
+HOMEPAGE="https://www.ugr.es/~pittau/CutTools/"
+SRC_URI="https://www.ugr.es/~pittau/CutTools/${PN}_v${PV}.tar.gz"
+S="${WORKDIR}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="+dummy"
+DEPEND="
+ sci-physics/qcdloop
+ sci-physics/oneloop[dpkind,qpkind16,-qpkind,-tlevel]
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ default
+ sed -i 's/^ALL =.*$/ALL = $(CTS)/' src/makefile || die
+ if use dummy ; then
+ cp "${FILESDIR}"/mpnumdummy.f90 src/cts/mpnumdummy.f90 || die
+ fi
+ if use dummy ; then
+ sed -i 's/CTS =/CTS = mpnumdummy.o/' src/makefile || die
+ fi
+}
+
+src_compile() {
+ emake -j1 FFLAGS="${FFLAGS} -I${ESYSROOT}/usr/include -fPIC -std=legacy"
+ tc-export AR CXX
+ cd includects || die
+ ${AR} -x libcts.a || die
+ ${CXX} ${CXXFLAGS} -shared *.o -o lib${PN}.so || die
+}
+
+src_install() {
+ cd includects || die
+ dolib.so lib${PN}.so
+ cd .. || die
+ mv includects ${PN} || die
+ rm ${PN}/*.a || die
+ rm ${PN}/*.so || die
+ rm ${PN}/*.o || die
+ doheader -r ${PN}
+}
diff --git a/sci-physics/cuttools/files/mpnumdummy.f90 b/sci-physics/cuttools/files/mpnumdummy.f90
new file mode 100644
index 000000000..be1e0d52b
--- /dev/null
+++ b/sci-physics/cuttools/files/mpnumdummy.f90
@@ -0,0 +1,26 @@
+
+module cts_numdummies
+ implicit none
+ contains
+
+ subroutine dpnumdummy(q,amp)
+ ! dummy numerator in double precision. Always returns zero.
+ implicit none
+ include 'cts_dpc.h'
+ , intent(in), dimension(0:3) :: q
+ include 'cts_dpc.h'
+ , intent(out) :: amp
+ amp = 0
+ end subroutine dpnumdummy
+
+ subroutine mpnumdummy(q,amp)
+ ! dummy numerator in quad precision. Always returns zero.
+ include 'cts_mprec.h'
+ implicit none
+ include 'cts_mpc.h'
+ , intent(in), dimension(0:3) :: q
+ include 'cts_mpc.h'
+ , intent(out) :: amp
+ amp = 0
+ end subroutine mpnumdummy
+end module cts_numdummies
diff --git a/sci-physics/cuttools/metadata.xml b/sci-physics/cuttools/metadata.xml
new file mode 100644
index 000000000..ceddefcf0
--- /dev/null
+++ b/sci-physics/cuttools/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription>
+ A package for evaluation of scalar and tensor one-loop integrals
+ based on the FF package by G.J. van Oldenborgh.
+ It features an easy Fortran, C++, and Mathematica interface
+ to the scalar one-loop functions of FF and in addition provides
+ the 2-, 3-, and 4-point tensor coefficient functions.
+ </longdescription>
+ <use>
+ <flag name="dummy">Add dummy module for OpenLoops</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/evtgen/Manifest b/sci-physics/evtgen/Manifest
new file mode 100644
index 000000000..174d16349
--- /dev/null
+++ b/sci-physics/evtgen/Manifest
@@ -0,0 +1 @@
+DIST evtgen-02.02.01.tar.gz 2941525 BLAKE2B 8672f2d2e7452ba2330180a7e385d020372bdb436d22b12507ee22344f5013b439f68817e70ed50afbc3585beb15f01b0c29ee35dcbbaac8ec1ee0f8d573b3e2 SHA512 652424dae1d3e3d69c19fa946cd00e61ca5117e38eee20a41a98972374d79261fe7267311c06ecab497729f31e5842e340d6739434f09e5088972c95d2ce9c17
diff --git a/sci-physics/evtgen/evtgen-02.02.01.ebuild b/sci-physics/evtgen/evtgen-02.02.01.ebuild
new file mode 100644
index 000000000..32c0ab3a8
--- /dev/null
+++ b/sci-physics/evtgen/evtgen-02.02.01.ebuild
@@ -0,0 +1,39 @@
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake
+
+MY_PN="EvtGen"
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="EvtGen is a Monte Carlo event generator that simulates the decays"
+HOMEPAGE="https://evtgen.hepforge.org/"
+SRC_URI="https://evtgen.hepforge.org/downloads?f=${MY_P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}/R$(ver_rs 1-2 '-')"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+hepmc3 pythia photos tauola"
+
+RDEPEND="
+ !hepmc3? ( sci-physics/hepmc:2= )
+ hepmc3? ( sci-physics/hepmc:3= )
+ pythia? ( >=sci-physics/pythia-8.3.0:= )
+ photos? ( >=sci-physics/photos-3.64:= )
+ tauola? ( >=sci-physics/tauola-1.1.8:= )
+"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local mycmakeargs=(
+ -DEVTGEN_HEPMC3=$(usex hepmc3 ON OFF)
+ -DHEPMC3_ROOT_DIR="${ESYSROOT}/usr"
+ -DEVTGEN_PYTHIA=$(usex pythia ON OFF)
+ $(usex pythia -DPYTHIA8_ROOT_DIR="${ESYSROOT}/usr")
+ -DEVTGEN_PHOTOS=$(usex photos ON OFF)
+ -DEVTGEN_TAUOLA=$(usex tauola ON OFF)
+ )
+ cmake_src_configure
+}
diff --git a/sci-physics/evtgen/metadata.xml b/sci-physics/evtgen/metadata.xml
new file mode 100644
index 000000000..08f4b4aec
--- /dev/null
+++ b/sci-physics/evtgen/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+
+ <longdescription lang="en">
+ EvtGen is a Monte Carlo event generator that simulates the decays of heavy flavour particles, primarily B and D mesons. It contains a range of decay models for intermediate and final states containing scalar, vector and tensor mesons or resonances, as well as leptons, photons and baryons. Decay amplitudes are used to generate each branch of a given full decay tree, taking into account angular and time-dependent correlations which allows for the simulation of CP-violating processes. Originally written by Anders Ryd and David Lange, this package is used by many particle physics experiments worldwide, including ATLAS, BaBar, Belle(-II), BES III, CDF, CLEO(-c), CMS, D0, and LHCb. The maintenance and development of the package is now performed by the particle physics group at the University of Warwick (in particular by John Back, Michal Kreps, and Thomas Latham).
+ </longdescription>
+
+ <use>
+ <flag name="pythia">Build with pythia</flag>
+ <flag name="photos">Build with photos</flag>
+ <flag name="tauola">Build with tauola</flag>
+ <flag name="hepmc3">Build with hepmc version 3 support, else hepmc version2 is used</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/herwig/Manifest b/sci-physics/herwig/Manifest
new file mode 100644
index 000000000..01457a201
--- /dev/null
+++ b/sci-physics/herwig/Manifest
@@ -0,0 +1 @@
+DIST herwig-7.3.0.tar.bz2 4264666 BLAKE2B 33b9bbce0f69f5c73ddc16c19d98323ea60d89fb00dacdbb069440b574721bd44eee6528d78b2e9aaf3bea1d59e5112ca3f4c780032da9807e6d2a676ebacde5 SHA512 29254026c715550d0cd537a33ac37d17ab93279087901e284fea4209091fd3f84244ecbd223e0fe3fd30923c755d630cf066b17bc35288c5f3ab6f4e8d4a5bbe
diff --git a/sci-physics/herwig/herwig-7.3.0.ebuild b/sci-physics/herwig/herwig-7.3.0.ebuild
new file mode 100644
index 000000000..5576f3cf7
--- /dev/null
+++ b/sci-physics/herwig/herwig-7.3.0.ebuild
@@ -0,0 +1,65 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit fortran-2 python-single-r1 autotools
+
+MY_PN="Herwig"
+MY_PF=${MY_PN}-${PV}
+
+DESCRIPTION="Herwig is a multi-purpose particle physics event generator."
+HOMEPAGE="https://herwig.hepforge.org/"
+SRC_URI="https://herwig.hepforge.org/downloads?f=${MY_PF}.tar.bz2 -> ${P}.tar.bz2"
+S="${WORKDIR}/${MY_PF}"
+
+LICENSE="GPL-3+"
+SLOT="7"
+KEYWORDS="~amd64"
+IUSE="+pythia" # madgraph openloops gosam vbfnlo njet
+REQUIRED_USE="
+ ${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+ >=dev-libs/boost-1.62
+ >=sci-libs/gsl-2.6
+ sci-physics/fastjet
+ sci-physics/lhapdf-sets[lhapdf_sets_ct14lo,lhapdf_sets_ct14nlo]
+ >=sci-physics/lhapdf-6.1.6[python(+),${PYTHON_SINGLE_USEDEP}]
+ >=sci-physics/thepeg-2.1.0[lhapdf,fastjet,-hepmc2(-),hepmc3(-),rivet(-)]
+ >=sci-physics/evtgen-02.02.00[pythia]
+ pythia? ( sci-physics/pythia:8= )
+ ${PYTHON_DEPS}
+"
+# madgraph? ( sci-physics/madgraph5 )
+# openloops? ( sci-physics/openloops )
+# gosam? ( sci-physics/gosam )
+# vbfnlo? ( sci-physics/vbfnlo )
+# njet? ( sci-physics/njet )
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+# https://herwig.hepforge.org/tutorials/installation/manual.html
+# Minimal installation for now
+src_configure() {
+ CONFIG_SHELL=${ESYSROOT}/bin/bash \
+ econf \
+ --with-evtgen="${EPREFIX}"/usr \
+ --with-fastjet="${EPREFIX}"/usr \
+ --with-thepeg="${EPREFIX}"/usr \
+ --with-boost="${EPREFIX}"/usr \
+ $(use_with pythia pythia "${EPREFIX}"/usr) \
+ # $(use_with madgraph madgraph "${EPREFIX}"/opt/MadGraph5/ ) \
+ # $(use_with openloops openloops "${EPREFIX}"/opt/OpenLoops2/ ) \
+ # $(use_with gosam gosam "${EPREFIX}"/usr) \
+ # $(use_with vbfnlo vbfnlo "${EPREFIX}"/usr) \
+ # $(use_with njet njet "${EPREFIX}"/usr)
+}
+
+src_install() {
+ default
+}
diff --git a/sci-physics/herwig/metadata.xml b/sci-physics/herwig/metadata.xml
new file mode 100644
index 000000000..804bc3361
--- /dev/null
+++ b/sci-physics/herwig/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+
+ <longdescription lang="en">
+ Herwig provides significantly improved and extended physics capabilities when compared to both its predecessors, HERWIG 6 and Herwig++ 2, while keeping the key model motivations such as coherent parton showers (including angular-ordered and dipole-based evolution), the cluster hadronization model, an eikonal multiple-interaction model, highly flexible BSM capabilities and improved perturbative input using next-to-leading order QCD.
+ </longdescription>
+ <use>
+ <flag name="pythia">Build with pythia support </flag>
+<!--
+ <flag name="openloops">Build with openloops support </flag>
+ <flag name="gosam">Build with gosam support </flag>
+ <flag name="madgraph">Build with madgraph support </flag>
+ <flag name="vbfnlo">Build with vbfnlo support </flag>
+ <flag name="njet">Build with njet support </flag>
+-->
+ </use>
+</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/mcfm/mcfm-10.2.1.ebuild b/sci-physics/mcfm/mcfm-10.2.1.ebuild
index bfc795247..e2b3b0bcb 100644
--- a/sci-physics/mcfm/mcfm-10.2.1.ebuild
+++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild
@@ -25,7 +25,7 @@ DEPEND="
sci-physics/lhapdf
>=sci-libs/qd-2.3.22
>=sci-physics/qcdloop-2.0.5
- >=sci-physics/oneloop-2020.07.31
+ >=sci-physics/oneloop-3.6_p20200731
>=sci-libs/handyg-0.1.5
"
RDEPEND="${DEPEND}"
diff --git a/sci-physics/oneloop/Manifest b/sci-physics/oneloop/Manifest
index f698d0a23..baeb504b0 100644
--- a/sci-physics/oneloop/Manifest
+++ b/sci-physics/oneloop/Manifest
@@ -1 +1,2 @@
-DIST oneloop-2020.07.31.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220
+DIST OneLOop-3.6.tgz 111734 BLAKE2B 61e1638b17ec356c29d40c2af187464d5499b9172c2858fc47486bd527f0f47e90eba4d836697176a1ecbb01b7344d774bc595c722a92abede143b3df90067d9 SHA512 979981ad5ecdf1f71424c7b8a8d12c7d30aa140c62295a4452d3e5c0e260d42b431c12efcc0d7f0ab55ee2f9af08d4ab204ada5860f65343b24552cbdd3f3cd2
+DIST oneloop-3.6_p20200731.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220
diff --git a/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch b/sci-physics/oneloop/files/oneloop-3.6_p20200731-config.patch
index 4af47e066..4af47e066 100644
--- a/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch
+++ b/sci-physics/oneloop/files/oneloop-3.6_p20200731-config.patch
diff --git a/sci-physics/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml
index 35b6c2bd9..40e059101 100644
--- a/sci-physics/oneloop/metadata.xml
+++ b/sci-physics/oneloop/metadata.xml
@@ -9,7 +9,23 @@
<email>sci-physics@gentoo.org</email>
<name>Gentoo Physics Project</name>
</maintainer>
+ <longdescription lang="en">
+ Library of one-loop scalar functions by Andreas van Hameren.
+ Commonly named avh_olo and used by/for cuttools.
+ </longdescription>
<upstream>
<remote-id type="bitbucket">hameren/oneloop</remote-id>
</upstream>
+ <use>
+ <flag name="dpkind">double precision</flag>
+ <flag name="qpkind">quad precision</flag>
+ <flag name="dpkind16">double16 precision</flag>
+ <flag name="qpkind16">quad16 precision</flag>
+ <flag name="ddcpp">double use sci-libs/qd</flag>
+ <flag name="qdcpp">quad use sci-libs/qd</flag>
+ <flag name="arprec"> use sci-libs/arprec</flag>
+ <flag name="mpfun90"> use sci-libs/mpfun90</flag>
+ <flag name="tlevel"> enable tlevel</flag>
+ <flag name="cppintf"> enable cppintf</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
deleted file mode 100644
index 9344d1513..000000000
--- a/sci-physics/oneloop/oneloop-2020.07.31.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-# python only needed for create.py to get binaries
-PYTHON_COMPAT=( python3_{10..11} )
-inherit toolchain-funcs python-any-r1 fortran-2
-
-DESCRIPTION="Library of one-loop scalar functions"
-HOMEPAGE="https://bitbucket.org/hameren/oneloop"
-SRC_URI="https://bitbucket.org/hameren/oneloop/get/3762b8bad6ad.zip -> ${P}.zip"
-S="${WORKDIR}/hameren-oneloop-3762b8bad6ad"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
- ${PYTHON_DEPS}
- app-arch/unzip
-"
-
-PATCHES=(
- "${FILESDIR}"/${P}-config.patch
-)
-
-src_configure() {
- tc-export FC
- sed -i "/FC = /s/gfortran/${FC}/g" Config || die
- sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die
-}
-
-src_compile() {
- tc-export FC
- emake -f make_cuttools
- ${EPYTHON} ./create.py || die "Failed to compile"
- #./create.py dynamic || die
- ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so avh_olo.o || die "Failed to link"
-}
-
-src_install() {
- dolib.a libavh_olo.a
- dolib.so libavh_olo.so
- doheader avh_olo.mod
-}
diff --git a/sci-physics/oneloop/oneloop-3.6.ebuild b/sci-physics/oneloop/oneloop-3.6.ebuild
new file mode 100644
index 000000000..1a7f5d864
--- /dev/null
+++ b/sci-physics/oneloop/oneloop-3.6.ebuild
@@ -0,0 +1,106 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_P=OneLOop-${PV}
+
+# python only needed for create.py to get binaries
+PYTHON_COMPAT=( python3_{10..12} )
+inherit fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Library of one-loop scalar functions"
+HOMEPAGE="
+ https://helac-phegas.web.cern.ch/OneLOop.html
+ https://bitbucket.org/hameren/oneloop
+"
+SRC_URI="http://helac-phegas.web.cern.ch/helac-phegas/tar-files/${MY_P}.tgz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+dpkind +qpkind qpkind16 dpkind16 qdcpp ddcpp mpfun90 arprec tlevel cppintf"
+REQUIRED_USE="
+ ?? ( dpkind dpkind16 ddcpp )
+ ?? ( qpkind qpkind16 qdcpp )
+ ?? ( arprec mpfun90 )
+ || ( dpkind dpkind16 ddcpp qpkind qpkind16 qdcpp )
+"
+
+DEPEND="
+ qpkind? ( sci-libs/qd )
+ qpkind16? ( sci-libs/qd )
+ arprec? ( sci-libs/arprec )
+ mpfun90? ( sci-libs/mpfun90 )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ ${PYTHON_DEPS}
+ app-arch/unzip
+"
+
+src_configure() {
+ tc-export FC
+ # set fortran
+ sed -i "/FC = /s/gfortran/${FC}/g" Config || die
+ sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die
+ # Clear config
+ sed -i "s/^DPKIND.*$//g" Config || die
+ sed -i "s/^QPKIND.*$//g" Config || die
+
+ if use dpkind ; then
+ echo "DPKIND = kind(1d0)" >> Config || die
+ fi
+ if use qpkind ; then
+ echo "QPKIND = kind(1d0)" >> Config || die
+ fi
+ if use dpkind16 ; then
+ echo "DPKIND = 16" >> Config || die
+ fi
+ if use qpkind16 ; then
+ echo "QPKIND = 16" >> Config || die
+ fi
+
+ if use qdcpp ; then
+ echo "QDTYPE = qdcpp" >> Config || die
+ fi
+ if use ddcpp ; then
+ echo "DDTYPE = qdcpp" >> Config || die
+ fi
+
+ if use mpfun90 ; then
+ echo "MPTYPE = mpfun90" >> Config || die
+ fi
+ if use arprec ; then
+ echo "MPTYPE = arprec" >> Config || die
+ fi
+
+ if use tlevel ; then
+ sed -i "s/^.*TLEVEL.*$/TLEVEL = yes/" Config || die
+ else
+ sed -i "s/^.*TLEVEL.*$/TLEVEL = no/" Config || die
+ fi
+ if use cppintf ; then
+ sed -i "s/^.*CPPINTF.*$/CPPINTF = yes/" Config || die
+ else
+ sed -i "s/^.*CPPINTF.*$/CPPINTF = no/" Config || die
+ fi
+}
+
+src_compile() {
+ tc-export FC
+ #emake -f make_cuttools
+ ${EPYTHON} ./create.py source || die "Failed to compile"
+ # create.py does not use soname, so we do it ourself
+ #./create.py dynamic || die
+ ${FC} -O -fPIC -c avh_olo.f90 -o avh_olo.o || die
+ ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so *.o || die
+}
+
+src_install() {
+ #dolib.a libavh_olo.a
+ dolib.so libavh_olo.so
+ doheader *.mod
+ dosym libavh_olo.so /usr/$(get_libdir)/liboneloop.so
+}
diff --git a/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild b/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild
new file mode 100644
index 000000000..e25833759
--- /dev/null
+++ b/sci-physics/oneloop/oneloop-3.6_p20200731.ebuild
@@ -0,0 +1,104 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# python only needed for create.py to get binaries
+PYTHON_COMPAT=( python3_{10..12} )
+inherit fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Library of one-loop scalar functions"
+HOMEPAGE="
+ https://helac-phegas.web.cern.ch/OneLOop.html
+ https://bitbucket.org/hameren/oneloop
+"
+SRC_URI="https://bitbucket.org/hameren/oneloop/get/3762b8bad6ad.zip -> ${P}.zip"
+S="${WORKDIR}/hameren-oneloop-3762b8bad6ad"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+dpkind +qpkind qpkind16 dpkind16 qdcpp ddcpp mpfun90 arprec tlevel cppintf"
+REQUIRED_USE="
+ ?? ( dpkind dpkind16 ddcpp )
+ ?? ( qpkind qpkind16 qdcpp )
+ ?? ( arprec mpfun90 )
+ || ( dpkind dpkind16 ddcpp qpkind qpkind16 qdcpp )
+"
+
+DEPEND="
+ qpkind? ( sci-libs/qd )
+ qpkind16? ( sci-libs/qd )
+ arprec? ( sci-libs/arprec )
+ mpfun90? ( sci-libs/mpfun90 )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ ${PYTHON_DEPS}
+ app-arch/unzip
+"
+
+src_configure() {
+ tc-export FC
+ # set fortran
+ sed -i "/FC = /s/gfortran/${FC}/g" Config || die
+ sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die
+ # Clear config
+ sed -i "s/^DPKIND.*$//g" Config || die
+ sed -i "s/^QPKIND.*$//g" Config || die
+
+ if use dpkind ; then
+ echo "DPKIND = kind(1d0)" >> Config || die
+ fi
+ if use qpkind ; then
+ echo "QPKIND = kind(1d0)" >> Config || die
+ fi
+ if use dpkind16 ; then
+ echo "DPKIND = 16" >> Config || die
+ fi
+ if use qpkind16 ; then
+ echo "QPKIND = 16" >> Config || die
+ fi
+
+ if use qdcpp ; then
+ echo "QDTYPE = qdcpp" >> Config || die
+ fi
+ if use ddcpp ; then
+ echo "DDTYPE = qdcpp" >> Config || die
+ fi
+
+ if use mpfun90 ; then
+ echo "MPTYPE = mpfun90" >> Config || die
+ fi
+ if use arprec ; then
+ echo "MPTYPE = arprec" >> Config || die
+ fi
+
+ if use tlevel ; then
+ sed -i "s/^.*TLEVEL.*$/TLEVEL = yes/" Config || die
+ else
+ sed -i "s/^.*TLEVEL.*$/TLEVEL = no/" Config || die
+ fi
+ if use cppintf ; then
+ sed -i "s/^.*CPPINTF.*$/CPPINTF = yes/" Config || die
+ else
+ sed -i "s/^.*CPPINTF.*$/CPPINTF = no/" Config || die
+ fi
+}
+
+src_compile() {
+ tc-export FC
+ #emake -f make_cuttools
+ ${EPYTHON} ./create.py source || die "Failed to compile"
+ # create.py does not use soname, so we do it ourself
+ #./create.py dynamic || die
+ ${FC} -O -fPIC -c avh_olo.f90 -o avh_olo.o || die
+ ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so *.o || die
+}
+
+src_install() {
+ #dolib.a libavh_olo.a
+ dolib.so libavh_olo.so
+ doheader *.mod
+ dosym libavh_olo.so /usr/$(get_libdir)/liboneloop.so
+}
diff --git a/sci-physics/openloops/Manifest b/sci-physics/openloops/Manifest
new file mode 100644
index 000000000..053e3b83d
--- /dev/null
+++ b/sci-physics/openloops/Manifest
@@ -0,0 +1 @@
+DIST OpenLoops-OpenLoops-2.1.3.tar.bz2 3769562 BLAKE2B ddb664a7310662e2d0891e31870d614c191b0248f1b4c8816d4f33b6709005eea7435fda73c354092a28d55a0b106ec9358fb4e4a7a6ed592d61208ff5334e85 SHA512 a5ae2431506f8e169c42dd1d5fa3db70b4e2d62dfa744041fcd61d8554daba0700d453e9198e50a3e85cb3f196277c0f011fb408fd5913cd6a1c42ed71bb9d51
diff --git a/sci-physics/openloops/files/openloops-2.1.2-ldflags.patch b/sci-physics/openloops/files/openloops-2.1.2-ldflags.patch
new file mode 100644
index 000000000..5f5076581
--- /dev/null
+++ b/sci-physics/openloops/files/openloops-2.1.2-ldflags.patch
@@ -0,0 +1,11 @@
+--- a/pyol/tools/OLBaseConfig.py 2024-05-07 17:59:46.060792049 +0200
++++ b/pyol/tools/OLBaseConfig.py 2024-05-07 18:02:07.269403340 +0200
+@@ -182,7 +182,7 @@
+ parse_option(config, 'f90_flags', interpolate=True, converter=split_list)
+ parse_option(config, 'f_flags', interpolate=True, converter=split_list)
+ parse_option(config, 'common_flags', interpolate=True, converter=split_list)
+- parse_option(config, 'link_flags', interpolate=True, converter=split_list)
++ parse_option(config, 'link_flags', interpolate=True, converter=str.split)
+ parse_option(config, 'debug_flags_1', converter=split_list)
+ parse_option(config, 'debug_flags_4', interpolate=True,
+ converter=split_list)
diff --git a/sci-physics/openloops/files/openloops-2.1.2-python3.12.patch b/sci-physics/openloops/files/openloops-2.1.2-python3.12.patch
new file mode 100644
index 000000000..1e76a1835
--- /dev/null
+++ b/sci-physics/openloops/files/openloops-2.1.2-python3.12.patch
@@ -0,0 +1,34 @@
+--- a/SConstruct 2024-05-07 15:56:26.162295325 +0200
++++ b/SConstruct 2024-05-07 15:56:14.115460655 +0200
+@@ -404,8 +404,9 @@
+ F90FLAGS = config['f90_flags'] + config['generic_optimisation'],
+ LINKFLAGS = config['link_flags'],
+ LIBPATH = [config['generic_lib_dir']],
+- DOLLAR = '\$$',
+- RPATH = [HashableLiteral('\$$ORIGIN')],
++ DOLLAR = '\\$$',
++ RPATH = [HashableLiteral('\\$$ORIGIN')],
++ SHLIBVERSION = release_version,
+ F90 = config['fortran_compiler'],
+ FORTRAN = config['fortran_compiler'],
+ CC = config['cc'])
+@@ -719,7 +719,7 @@
+ processes_seen[processlib] = loops
+ process_list = process_list_nodup
+
+-env.Append(RPATH = [HashableLiteral('\$$ORIGIN/../lib')])
++env.Append(RPATH = [HashableLiteral('\\$$ORIGIN/../lib')])
+
+
+ for (loops, process_api, processlib) in process_list:
+--- a/SConstruct 2024-05-07 15:59:46.808415000 +0200
++++ b/SConstruct 2024-05-07 16:00:46.839244667 +0200
+@@ -796,7 +796,7 @@
+ env = env,
+ shared = config['shared_libraries'],
+ env_mod = [
+- ('^(virtual_\d|tensorsum_|loop_)',
++ ('^(virtual_\\d|tensorsum_|loop_)',
+ {'F90FLAGS': config['f90_flags'] + config['loop_optimisation']}),
+ ('',
+ {'F90FLAGS': config['f90_flags'] + config['born_optimisation']})]
diff --git a/sci-physics/openloops/metadata.xml b/sci-physics/openloops/metadata.xml
new file mode 100644
index 000000000..5bec6ac4c
--- /dev/null
+++ b/sci-physics/openloops/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The OpenLoops 2 program is a fully automated implementation of the Open Loops algorithm combined with on-the-fly reduction methods, which allows for the fast and stable numerical evaluation of tree and one-loop matrix elements for any Standard Model process at NLO QCD and NLO EW.
+ </longdescription>
+ <upstream>
+ <remote-id type="gitlab">openloops/OpenLoops</remote-id>
+ </upstream>
+ <use>
+ <flag name="collier">Build with collier</flag>
+ <flag name="extra">Build libs with extra</flag>
+ <flag name="cuttools">Build with cuttools</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/openloops/openloops-2.1.3.ebuild b/sci-physics/openloops/openloops-2.1.3.ebuild
new file mode 100644
index 000000000..a53eb1f9e
--- /dev/null
+++ b/sci-physics/openloops/openloops-2.1.3.ebuild
@@ -0,0 +1,108 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit fortran-2 python-single-r1 scons-utils toolchain-funcs
+
+MY_PN=OpenLoops
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="Evaluation of tree and one-loop matrix elements for any Standard Model."
+HOMEPAGE="https://openloops.hepforge.org/index.html"
+#SRC_URI="https://openloops.hepforge.org/downloads?f=${MY_P}.tar.gz -> ${MY_P}.tar.gz"
+#S="${WORKDIR}/${MY_P}"
+SRC_URI="https://gitlab.com/openloops/OpenLoops/-/archive/${MY_P}/${MY_PN}-${MY_P}.tar.bz2"
+S="${WORKDIR}/${MY_PN}-${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+collier +cuttools +extra"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ sci-physics/qcdloop
+ sci-physics/oneloop[dpkind,qpkind16,-qpkind,-cppintf]
+ collier? ( sci-physics/collier[-static-libs] )
+ cuttools? ( sci-physics/cuttools[dummy] )
+ ${PYTHON_DEPS}
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.1.2-ldflags.patch"
+)
+
+src_prepare() {
+ default
+ mv openloops.cfg.tmpl openloops.cfg || die
+ sed -i "s|scons -Q|scons -Q -C /opt/${MY_P}/|g" openloops || die
+ if use extra ; then
+ sed -i "s|#compile_extra.*|compile_extra = 1|" openloops.cfg || die
+ fi
+
+ cat <<-EOF >> openloops.cfg || die
+ compile_libraries = rambo trred
+ link_libraries = $(usev collier) $(usev cuttools)
+ ccflags = ${CFLAGS}
+ cxxflags = ${CXXFLAGS}
+ f_flags = ${FFLAGS} -I${ESYSROOT}/usr/include/ -I${ESYSROOT}/usr/include/cuttools -lcollier
+ link_flags = ${LDFLAGS} -I${ESYSROOT}/usr/include/ -I${ESYSROOT}/usr/include/cuttools -lcollier
+ cc = $(tc-getCC)
+ cxx = $(tc-getCXX)
+ fortran_compiler = $(tc-getFC)
+ process_src_dir = ${EPREFIX}/opt/${MY_P}/process_src/
+ process_obj_dir = ${EPREFIX}/opt/${MY_P}/process_obj/
+ process_lib_dir = ${EPREFIX}/opt/${MY_P}/proclib/
+ release = $PV
+ import_env = @all
+ EOF
+
+ # fix rename for py3.12
+ sed -i 's/SafeConfigParser/ConfigParser/g' pyol/tools/OLBaseConfig.py || die
+ # wipe local scons
+ rm -r scons-local || die
+ rm scons || die
+}
+
+src_compile() {
+ escons --cache-disable
+}
+
+src_install() {
+ dosym ../opt/${MY_P} /opt/OpenLoops2
+ dobin openloops
+ cd include || die
+ doheader openloops.h
+ cd ../lib || die
+ # Also install so.version links
+ dolib.so libolcommon.so* libopenloops.so* librambo.so* libtrred.so*
+ cd ../lib_src/olcommon/mod || die
+ doheader *.mod
+ cd ../../openloops/mod || die
+ doheader *.mod
+ cd ../../rambo/mod || die
+ doheader *.mod
+ cd ../../trred/mod || die
+ doheader *.mod
+
+ cd "${S}" || die "Failed to cd into ${S}"
+ insinto /opt/${MY_P}
+ doins openloops.cfg SConstruct
+ doins -r pyol
+
+ # Previous method of allowing everyone everything
+ # maybe better to use a group for that
+ # for now like lhapdf just let root install
+ #fperms -R a=u /opt/${MY_P}
+ #fperms a=u /opt/${MY_P}
+
+}
+
+pkg_postinst() {
+ elog "Install processes with openloops libinstall."
+ elog "They are installed in /opt/${MY_P}/proclib."
+}
diff --git a/sci-physics/photos/Manifest b/sci-physics/photos/Manifest
new file mode 100644
index 000000000..5fcd8e48e
--- /dev/null
+++ b/sci-physics/photos/Manifest
@@ -0,0 +1 @@
+DIST PHOTOS.3.64.tar.gz 1415406 BLAKE2B 503247dbcaa15d801850e8cf4981aaffd7b04c13c6542543fab88d00e08ebd6831b828ddfbd3d26469f2cddcfc21acfbeaae171f3778deaabd5abddcc1d64d0e SHA512 750e213a257479b41ac9b4848787a61035ab5ed2157d3b4e3b4b0a081241f5c76e882f66b401dcfbea363e7154aa2a4ae1ba05ac1e40a35c2e5687d10910085e
diff --git a/sci-physics/photos/metadata.xml b/sci-physics/photos/metadata.xml
new file mode 100644
index 000000000..0a24d3422
--- /dev/null
+++ b/sci-physics/photos/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+
+ <longdescription lang="en">
+ The main application of PHOTOS is the generation of QED radiative corrections in decays of any resonances, simulated by a "host" Monte Carlo generator
+ </longdescription>
+
+ <use>
+ <flag name="pythia">Build with pythia</flag>
+ <flag name="hepmc2">Build with hepmc 2</flag>
+ <flag name="hepmc3">Build with hepmc 3</flag>
+ <flag name="tauola">Build with tauola</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/photos/photos-3.64.ebuild b/sci-physics/photos/photos-3.64.ebuild
new file mode 100644
index 000000000..32c09af64
--- /dev/null
+++ b/sci-physics/photos/photos-3.64.ebuild
@@ -0,0 +1,82 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2 autotools
+
+MY_PN="PHOTOS"
+MY_P=${MY_PN}.${PV}
+
+DESCRIPTION="Monte Carlo for bremsstrahlung in the decay of particles and resonances"
+HOMEPAGE="
+ https://gitlab.cern.ch/photospp/photospp
+ http://photospp.web.cern.ch/photospp/
+"
+SRC_URI="https://photospp.web.cern.ch/resources/${MY_P}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_PN}"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples hepmc2 hepmc3 pythia tauola"
+
+RDEPEND="
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+ pythia? ( sci-physics/pythia:8= )
+ tauola? ( sci-physics/tauola[hepmc2?,hepmc3?,pythia?] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ doc? (
+ app-text/doxygen[dot]
+ app-text/ghostscript-gpl
+ app-text/texlive
+ )
+"
+REQUIRED_USE=" || ( hepmc2 hepmc3 )"
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --without-mc-tester \
+ $(use_with hepmc3 hepmc3 "${EPREFIX}/usr") \
+ $(use_with hepmc2 hepmc "${EPREFIX}/usr") \
+ $(use_with pythia pythia8 "${EPREFIX}/usr") \
+ $(use_with tauola tauola "${EPREFIX}/usr")
+ # weird autoconf + Makefile
+ cat <<-EOF >> make.inc || die
+ LDFLAGS += ${LDFLAGS}
+ CFLAGS += ${CFLAGS}
+ FFLAGS += ${FFLAGS}
+ EOF
+}
+
+src_compile() {
+ emake -j1
+
+ if use doc; then
+ cd "${S}/documentation/doxy_documentation" || die
+ default
+ cd "${S}/documentation/latex_documentation" || die
+ default
+ fi
+}
+
+src_install() {
+ emake DESTDIR="${D}" install
+
+ if use doc; then
+ dodoc documentation/doxy_documentation/html/*
+ dodoc documentation/latex_documentation/*.pdf
+ fi
+
+ if use examples; then
+ dodoc -r examples
+ fi
+}
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
+}
diff --git a/sci-physics/sherpa/Manifest b/sci-physics/sherpa/Manifest
new file mode 100644
index 000000000..6913c06e1
--- /dev/null
+++ b/sci-physics/sherpa/Manifest
@@ -0,0 +1 @@
+DIST sherpa-v3.0.0beta1.tar.bz2 5836616 BLAKE2B 5347b6a83b80b148740c6fbf44c4d8f547a30eb85ba70ae4ad620cb3cca3f9d8255c45502969a83dca98d2825207a192ac3cae11dc3b914afdaaf9d65f2e6932 SHA512 9c34851193227a233c962b19cdff00302608d1695841d97de09d2bd40b84ccbd2a2a9f3c89e68e288bdf522e9b4c7fb8fc52032f199014898ac6bacbf628c8ce
diff --git a/sci-physics/sherpa/metadata.xml b/sci-physics/sherpa/metadata.xml
new file mode 100644
index 000000000..8018d7c68
--- /dev/null
+++ b/sci-physics/sherpa/metadata.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>APN-Pucky@users.noreply.github.com</email>
+ <name>APN-Pucky</name>
+ </maintainer>
+ <longdescription lang="en">
+ Sherpa is a Monte Carlo event generator for the Simulation of High-Energy Reactions of PArticles in lepton-lepton, lepton-photon, photon-photon, lepton-hadron and hadron-hadron collisions. Simulation programs - also dubbed event generators - like Sherpa are indispensable work horses for current particle physics phenomenology and are (at) the interface between theory and experiment.
+ </longdescription>
+ <upstream>
+ <remote-id type="gitlab">sherpa-team/sherpa</remote-id>
+ </upstream>
+ <use>
+ <flag name="hepmc2">Build with HepMC2</flag>
+ <flag name="fastjet">Build with FastJet</flag>
+ <flag name="pythia6">Build with Pythia6</flag>
+ <flag name="pythia8">Build with Pythia8</flag>
+ <flag name="rivet">Build with Rivet</flag>
+ <flag name="root">Build with Root</flag>
+ <flag name="ufo">UFO python interface</flag>
+ <flag name="lhole">lhole support</flag>
+ <flag name="analysis">analysis support</flag>
+ <flag name="openloops">Openloops support</flag>
+ </use>
+
+</pkgmetadata>
diff --git a/sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild b/sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild
new file mode 100644
index 000000000..79f0efccd
--- /dev/null
+++ b/sci-physics/sherpa/sherpa-3.0.0_beta1.ebuild
@@ -0,0 +1,94 @@
+# Copyright 2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+inherit cmake fortran-2 python-single-r1
+
+MY_PN="SHERPA-MC"
+MY_PV=${PV//_/}
+MY_P=${MY_PN}-${MY_PV}
+
+DESCRIPTION="Simulation of High-Energy Reactions of PArticles"
+HOMEPAGE="
+ https://sherpa-team.gitlab.io/
+ https://gitlab.com/sherpa-team/sherpa
+"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://gitlab.com/sherpa-team/sherpa"
+ EGIT_BRANCH="master"
+else
+ #SRC_URI="https://www.hepforge.org/archive/sherpa/${MY_P}.tar.gz"
+ SRC_URI="https://gitlab.com/sherpa-team/${PN}/-/archive/v${MY_PV}/${PN}-v${MY_PV}.tar.bz2"
+ S="${WORKDIR}/${PN}-v${MY_PV}"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+
+IUSE="+fastjet +pythia6 pythia8 rivet ufo hepmc2 root gzip mpi lhole analysis openloops" # blackhat recola gosam hztool madloop pgs mcfm
+REQUIRED_USE="
+ ufo? ( ${PYTHON_REQUIRED_USE} )
+"
+
+DEPEND="
+ sci-physics/lhapdf
+ dev-db/sqlite:3=
+ sci-physics/hepmc:3=
+ dev-libs/libzip
+ rivet? ( sci-physics/rivet )
+ gzip? ( app-arch/gzip )
+ pythia8? ( sci-physics/pythia:8= )
+ hepmc2? ( sci-physics/hepmc:2= )
+ fastjet? ( sci-physics/fastjet )
+ root? ( sci-physics/root )
+ mpi? ( virtual/mpi[cxx,fortran] )
+ ufo? ( ${PYTHON_DEPS} )
+ openloops? ( sci-physics/openloops )
+"
+# blackhat? ( sci-physics/blackhat )
+# gosam? ( sci-physics/gosam )
+# recola? ( sci-physics/recola )
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+ use ufo && python-single-r1_pkg_setup
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DSHERPA_ENABLE_THREADING=ON
+ -DSHERPA_ENABLE_ANALYSIS=$(usex analysis ON OFF)
+ -DSHERPA_ENABLE_GZIP=$(usex gzip ON OFF)
+ -DSHERPA_ENABLE_HEPMC2=$(usex hepmc2 ON OFF)
+ -DSHERPA_ENABLE_HEPMC3=ON
+ -DSHERPA_ENABLE_LHAPDF=ON
+ -DSHERPA_ENABLE_LHOLE=$(usex lhole ON OFF)
+ -DSHERPA_ENABLE_MPI=$(usex mpi ON OFF)
+ $(usex mpi -DCMAKE_C_COMPILER=mpicc)
+ $(usex mpi -DCMAKE_CXX_COMPILER=mpic++)
+ $(usex mpi -DCMAKE_Fortran_COMPILER=mpif90)
+ -DSHERPA_ENABLE_PYTHIA6=$(usex pythia6 ON OFF)
+ -DSHERPA_ENABLE_PYTHIA8=$(usex pythia8 ON OFF)
+ -DSHERPA_ENABLE_RIVET=$(usex rivet ON OFF)
+ -DSHERPA_ENABLE_ROOT=$(usex root ON OFF)
+ -DSHERPA_ENABLE_UFO=$(usex ufo ON OFF)
+ -DSHERPA_ENABLE_OPENLOOPS=$(usex openloops ON OFF)
+ -DOPENLOOPS_PREFIX=$(usex openloops "${ESYSROOT}/opt/OpenLoops2")
+ #-DSHERPA_ENABLE_GOSAM=$(usex gosam ON OFF)
+ #-DSHERPA_ENABLE_BLACKHAT=$(usex blackhat ON OFF)
+ #-DSHERPA_ENABLE_RECOLA=$(usex recola ON OFF)
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ use ufo && python_optimize
+}
diff --git a/sci-physics/sherpa/sherpa-9999.ebuild b/sci-physics/sherpa/sherpa-9999.ebuild
new file mode 100644
index 000000000..79f0efccd
--- /dev/null
+++ b/sci-physics/sherpa/sherpa-9999.ebuild
@@ -0,0 +1,94 @@
+# Copyright 2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+inherit cmake fortran-2 python-single-r1
+
+MY_PN="SHERPA-MC"
+MY_PV=${PV//_/}
+MY_P=${MY_PN}-${MY_PV}
+
+DESCRIPTION="Simulation of High-Energy Reactions of PArticles"
+HOMEPAGE="
+ https://sherpa-team.gitlab.io/
+ https://gitlab.com/sherpa-team/sherpa
+"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://gitlab.com/sherpa-team/sherpa"
+ EGIT_BRANCH="master"
+else
+ #SRC_URI="https://www.hepforge.org/archive/sherpa/${MY_P}.tar.gz"
+ SRC_URI="https://gitlab.com/sherpa-team/${PN}/-/archive/v${MY_PV}/${PN}-v${MY_PV}.tar.bz2"
+ S="${WORKDIR}/${PN}-v${MY_PV}"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+
+IUSE="+fastjet +pythia6 pythia8 rivet ufo hepmc2 root gzip mpi lhole analysis openloops" # blackhat recola gosam hztool madloop pgs mcfm
+REQUIRED_USE="
+ ufo? ( ${PYTHON_REQUIRED_USE} )
+"
+
+DEPEND="
+ sci-physics/lhapdf
+ dev-db/sqlite:3=
+ sci-physics/hepmc:3=
+ dev-libs/libzip
+ rivet? ( sci-physics/rivet )
+ gzip? ( app-arch/gzip )
+ pythia8? ( sci-physics/pythia:8= )
+ hepmc2? ( sci-physics/hepmc:2= )
+ fastjet? ( sci-physics/fastjet )
+ root? ( sci-physics/root )
+ mpi? ( virtual/mpi[cxx,fortran] )
+ ufo? ( ${PYTHON_DEPS} )
+ openloops? ( sci-physics/openloops )
+"
+# blackhat? ( sci-physics/blackhat )
+# gosam? ( sci-physics/gosam )
+# recola? ( sci-physics/recola )
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+ use ufo && python-single-r1_pkg_setup
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DSHERPA_ENABLE_THREADING=ON
+ -DSHERPA_ENABLE_ANALYSIS=$(usex analysis ON OFF)
+ -DSHERPA_ENABLE_GZIP=$(usex gzip ON OFF)
+ -DSHERPA_ENABLE_HEPMC2=$(usex hepmc2 ON OFF)
+ -DSHERPA_ENABLE_HEPMC3=ON
+ -DSHERPA_ENABLE_LHAPDF=ON
+ -DSHERPA_ENABLE_LHOLE=$(usex lhole ON OFF)
+ -DSHERPA_ENABLE_MPI=$(usex mpi ON OFF)
+ $(usex mpi -DCMAKE_C_COMPILER=mpicc)
+ $(usex mpi -DCMAKE_CXX_COMPILER=mpic++)
+ $(usex mpi -DCMAKE_Fortran_COMPILER=mpif90)
+ -DSHERPA_ENABLE_PYTHIA6=$(usex pythia6 ON OFF)
+ -DSHERPA_ENABLE_PYTHIA8=$(usex pythia8 ON OFF)
+ -DSHERPA_ENABLE_RIVET=$(usex rivet ON OFF)
+ -DSHERPA_ENABLE_ROOT=$(usex root ON OFF)
+ -DSHERPA_ENABLE_UFO=$(usex ufo ON OFF)
+ -DSHERPA_ENABLE_OPENLOOPS=$(usex openloops ON OFF)
+ -DOPENLOOPS_PREFIX=$(usex openloops "${ESYSROOT}/opt/OpenLoops2")
+ #-DSHERPA_ENABLE_GOSAM=$(usex gosam ON OFF)
+ #-DSHERPA_ENABLE_BLACKHAT=$(usex blackhat ON OFF)
+ #-DSHERPA_ENABLE_RECOLA=$(usex recola ON OFF)
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ use ufo && python_optimize
+}
diff --git a/sci-physics/tauola/files/tauola-1.1.8-tau-spinner-makefile-install.patch b/sci-physics/tauola/files/tauola-1.1.8-tau-spinner-makefile-install.patch
new file mode 100644
index 000000000..2d93959c5
--- /dev/null
+++ b/sci-physics/tauola/files/tauola-1.1.8-tau-spinner-makefile-install.patch
@@ -0,0 +1,22 @@
+--- a/Makefile 2020-01-28 18:43:43.000000000 +0100
++++ b/Makefile 2024-05-07 21:51:01.306908458 +0200
+@@ -48,7 +48,7 @@
+ mkdir -p $(DESTDIR)/$(PREFIX)/include/Tauola
+ install -m 644 include/Tauola/* $(DESTDIR)/$(PREFIX)/include/Tauola/.
+ mkdir -p $(DESTDIR)/$(LIBDIR)
+- install lib/*so.$(LIB_VER) $(DESTDIR)/$(LIBDIR)/
++ install lib/*so.* $(DESTDIR)/$(LIBDIR)/
+ install lib/*a $(DESTDIR)/$(LIBDIR)/
+ cp -P lib/*so $(DESTDIR)/$(LIBDIR)/
+
+--- a/TauSpinner/Makefile 2024-05-07 21:57:58.542875180 +0200
++++ b/TauSpinner/Makefile 2024-05-07 21:58:42.993509785 +0200
+@@ -52,7 +52,7 @@
+
+ libTauSpinner: $(TAU_SPINNER_OBJECTS)
+ ar cr lib/$(LIB_TAU_SPINNER_A) $(TAU_SPINNER_OBJECTS)
+- $(LD) $(LDFLAGS) $(SOFLAGS) $(TAU_SPINNER_OBJECTS) -o lib/$(LIB_TAU_SPINNER_SO).$(LIB_VER)
++ $(LD) $(LDFLAGS) $(SOFLAGS) $(TAU_SPINNER_OBJECTS) -o lib/$(LIB_TAU_SPINNER_SO).$(LIB_VER) -Wl,-soname,$(LIB_TAU_SPINNER_SO)
+ ln -sf $(LIB_TAU_SPINNER_SO).$(LIB_VER) lib/$(LIB_TAU_SPINNER_SO)
+
+ clean:
diff --git a/sci-physics/tauola/metadata.xml b/sci-physics/tauola/metadata.xml
index b0f8228f8..fcbc9de77 100644
--- a/sci-physics/tauola/metadata.xml
+++ b/sci-physics/tauola/metadata.xml
@@ -2,14 +2,23 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>piatlicki@gmail.com</email>
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
</maintainer>
<maintainer type="project">
<email>sci-physics@gentoo.org</email>
<name>Gentoo Physics Project</name>
</maintainer>
+
+ <longdescription lang="en">
+ TAUOLA is a program that simulates the decays of polarized tau leptons, which are elementary particles that belong to the lepton family. Tau leptons are heavier than electrons and muons, and they can decay into various final states, such as hadrons, leptons, and neutrinos. TAUOLA can generate Monte Carlo events for tau lepton decays, taking into account the polarization, spin correlations, and radiative corrections. TAUOLA can also model anomalous and lepton flavor violating decays, which are beyond the standard model of particle physics.
+ </longdescription>
<use>
- <flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag>
+ <flag name="hepmc"> Compile with <pkg>sci-physics/hepmc</pkg> version 2 interface </flag>
+ <flag name="hepmc2"> Compile with <pkg>sci-physics/hepmc</pkg> version 2 interface </flag>
+ <flag name="hepmc3"> Compile with <pkg>sci-physics/hepmc</pkg> version 3 interface </flag>
+ <flag name="pythia"> Compile with <pkg>sci-physics/pythia</pkg> connection </flag>
+ <flag name="lhapdf"> Compile with <pkg>sci-physics/lhapdf</pkg> connection </flag>
<flag name="tau-spinner">Compile with TauSpinner library</flag>
</use>
</pkgmetadata>
diff --git a/sci-physics/tauola/tauola-1.1.8-r1.ebuild b/sci-physics/tauola/tauola-1.1.8-r1.ebuild
new file mode 100644
index 000000000..0e2b3fc3a
--- /dev/null
+++ b/sci-physics/tauola/tauola-1.1.8-r1.ebuild
@@ -0,0 +1,80 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN="TAUOLA"
+MY_P=${MY_PN}.${PV}
+
+DESCRIPTION="Tau decay Monte Carlo generator"
+HOMEPAGE="http://tauolapp.web.cern.ch/"
+SRC_URI="https://tauolapp.web.cern.ch/resources/${MY_P}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_PN}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+hepmc3 +lhapdf doc examples hepmc2 pythia tau-spinner"
+REQUIRED_USE=" || ( hepmc2 hepmc3 ) tau-spinner? ( lhapdf )"
+
+RDEPEND="
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+ pythia? ( sci-physics/pythia:8= )
+ lhapdf? ( sci-physics/lhapdf )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ doc? (
+ app-text/doxygen[dot]
+ app-text/ghostscript-gpl
+ app-text/texlive
+ )
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.1.8-tau-spinner-makefile-install.patch
+)
+
+src_configure() {
+ econf \
+ $(use_with lhapdf) \
+ $(use_with tau-spinner) \
+ $(use_with pythia pythia8 "${EPREFIX}/usr") \
+ $(use_with hepmc2 hepmc "${EPREFIX}/usr") \
+ $(use_with hepmc3 hepmc3 "${EPREFIX}/usr") \
+ --without-mc-tester
+ # weird autoconf + Makefile
+ cat <<-EOF >> make.inc || die
+ LDFLAGS += ${LDFLAGS}
+ CFLAGS += ${CFLAGS}
+ FFLAGS += ${FFLAGS}
+ EOF
+}
+
+src_compile() {
+ emake -j1
+
+ if use doc; then
+ cd "${S}/documentation/doxy_documentation" || die
+ default
+ cd "${S}/documentation/latex_documentation" || die
+ default
+ fi
+}
+
+src_install() {
+ emake DESTDIR="${D}" install
+
+ if use doc; then
+ dodoc documentation/doxy_documentation/html/*
+ dodoc documentation/latex_documentation/*.pdf
+ fi
+
+ if use examples; then
+ dodoc -r examples
+ docinto tau-spinner && dodoc -r TauSpinner/examples
+ fi
+}