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dev-python/snakemake: add version 8 #1278

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dev-python/snakemake: add version 8 #1278

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507ffad
dev-python/connection_pool: py3.12 compat
mschubert Jun 17, 2024
6e4bd38
dev-python/reretry: py3.12 compat
mschubert Jun 17, 2024
d66d3c9
dev-python/stopit: py3.12 compat
mschubert Jun 17, 2024
ed81b4b
dev-python/throttler: py3.12 compat
mschubert Jun 17, 2024
c006d7c
dev-python/argparse-dataclass: add ebuild
mschubert Jun 17, 2024
cf0f533
dev-python/conda-inject: add ebuild
mschubert Jun 17, 2024
c0f2fef
dev-python/immutables: add ebuild
mschubert Jun 17, 2024
e81131c
dev-python/snakemake-interface-common: add ebuild
mschubert Jun 17, 2024
0c0c664
dev-python/snakemake-executor-plugins: add ebuild
mschubert Jun 17, 2024
b51d8ca
dev-python/snakemake-report-plugins: add ebuild
mschubert Jun 17, 2024
b0fbdd8
dev-python/snakemake-storage-plugins: add ebuild
mschubert Jun 17, 2024
e817f73
dev-python/datrie: py3.12 compat
mschubert Jun 17, 2024
85f5a13
dev-python/google-cloud-storage: version bump 2.17.0
mschubert Jun 17, 2024
4172145
dev-python/smart-open: py3.12 compat; disable tests (broken in py3.11)
mschubert Jun 17, 2024
61cc227
dev-python/snakemake: add version 8
mschubert Jun 17, 2024
77a8601
sci-mathematics/pulp: tests pass with python3.12
mschubert Jun 17, 2024
3f7a03a
dev-python/snakemake: version 7.32.4 is compat with py3.12
mschubert Jun 17, 2024
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1 change: 1 addition & 0 deletions dev-python/argparse-dataclass/Manifest
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DIST argparse_dataclass-2.0.0.tar.gz 6395 BLAKE2B 85dd27449281cde82a4afc1740bc4ba51c2d9259f910fe2146d866c7d8a83d59a6198236acb1b65e9ee7e6b7cca896b713e13d03f309e6583287afa2eef17c06 SHA512 88d706ae49dcc65947cb2eb0a0456c2ed8839fa7a3283e9f5b62da69ed9dd7cd66d45e57e7c3cff4e1104b9aee7a762f751d939cea8f0945301ec91598dbdc35
19 changes: 19 additions & 0 deletions dev-python/argparse-dataclass/argparse-dataclass-2.0.0.ebuild
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# 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
16 changes: 16 additions & 0 deletions dev-python/argparse-dataclass/metadata.xml
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<?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>
1 change: 1 addition & 0 deletions dev-python/conda-inject/Manifest
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DIST conda_inject-1.3.1.tar.gz 3580 BLAKE2B 84761ceddc0d01802502c09fea814eef86140ff28d7018900ce6b4b7666f0fbc8172ee4e25700e0ccfbe278dd228dc009ece2478d7e298f958333cc0d05fbd6e SHA512 6de6d190c1207cd36c1c03c24716158f6990c64d9764fcf79acf1a94682f38ecef4e02de7206ffd5f1c586ca73d375d46002edd9160a46f97e4eb3f5ff0ef6a1
21 changes: 21 additions & 0 deletions dev-python/conda-inject/conda-inject-1.3.1.ebuild
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# 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
16 changes: 16 additions & 0 deletions dev-python/conda-inject/metadata.xml
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<?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>
2 changes: 1 addition & 1 deletion dev-python/connection_pool/connection_pool-0.0.3.ebuild
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EAPI=8

PYTHON_COMPAT=( python3_{10..11} )
PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools

inherit distutils-r1 pypi
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2 changes: 1 addition & 1 deletion dev-python/datrie/datrie-0.8.2-r1.ebuild
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Expand Up @@ -3,7 +3,7 @@

EAPI=8

PYTHON_COMPAT=( python3_{10..11} )
PYTHON_COMPAT=( python3_{10..12} )
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datrie fails to compile with gcc-14

# Fails to compile with pep517
#DISTUTILS_USE_PEP517=setuptools

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2 changes: 1 addition & 1 deletion dev-python/google-cloud-storage/Manifest
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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
5 changes: 3 additions & 2 deletions ...storage/google-cloud-storage-2.7.0.ebuild → ...torage/google-cloud-storage-2.17.0.ebuild
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EAPI=8

PYTHON_COMPAT=( python3_{10..11} )
PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1

Expand All @@ -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
1 change: 1 addition & 0 deletions dev-python/immutables/Manifest
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DIST immutables-0.20.tar.gz 88933 BLAKE2B 07ae33ea62e85ea8c9b26a7e634f018b6e614ecd493faa74cdbdb20864b6af78b30fbadd1c21d9b9e3e971086893dcc7053ba88f8c78d7dbb588d54b8a9d0175 SHA512 1b74236517964573fd26072b6bf1b8a93456822b2b6ccc5f544f8a49b91f2e0bd110ef2ac23358ba14deceaaee8dde6f24e5589e9078dce961a7b9d4fcd2d3bd
20 changes: 20 additions & 0 deletions dev-python/immutables/immutables-0.20.ebuild
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# Copyright 1999-2024 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

EAPI=8

DISTUTILS_USE_PEP517=setuptools
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@Nowa-Ammerlaan Nowa-Ammerlaan Jun 19, 2024 •
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* The directory immutables occludes package installed for python3.12.
* The installed package includes additional files:
*
*     immutables/_map.cpython-312-x86_64-linux-gnu.so
*
* For more information on occluded packages, please see:
* https://projects.gentoo.org/python/guide/test.html#importerrors-for-c-extensions
* Python extension modules (*.so) found installed. Please set:
*   DISTUTILS_EXT=1
*

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
16 changes: 16 additions & 0 deletions dev-python/immutables/metadata.xml
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<?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>
2 changes: 1 addition & 1 deletion dev-python/reretry/reretry-0.11.8.ebuild
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Expand Up @@ -3,7 +3,7 @@

EAPI=8

PYTHON_COMPAT=( python3_{10..11} )
PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools

inherit distutils-r1
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25 changes: 13 additions & 12 deletions dev-python/smart-open/smart-open-6.3.0.ebuild
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@@ -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"
Expand All @@ -24,12 +24,13 @@ RDEPEND="
dev-python/paramiko[${PYTHON_USEDEP}]
"

BDEPEND="
test? (
dev-python/moto[${PYTHON_USEDEP}]
dev-python/responses[${PYTHON_USEDEP}]
dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
)
"
#BDEPEND="
# test? (
# <dev-python/moto-5[${PYTHON_USEDEP}]
# dev-python/responses[${PYTHON_USEDEP}]
# dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
# )
#"

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We don't have to comment out the deps, restricting the test phase is sufficient.

distutils_enable_tests pytest
RESTRICT="test" # 329 tests, 1 error: missing azure-storage-blob, azure-common[no ebuild], azure-core
#distutils_enable_tests pytest
1 change: 1 addition & 0 deletions dev-python/snakemake-interface-common/Manifest
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DIST snakemake_interface_common-1.17.2.tar.gz 9928 BLAKE2B 91be90640adb5f19fb97185ef84954cececd9e26e9c64f59b4ff014eca257575c5d5501ea7a8d74d9de2bb3280e88be500d1a2df2ec3296f2ecd30acbda27c87 SHA512 08d1688f70863825e76832250ee9da0be3a8baae9e67eb9bafaab30d862fe33fb9508eb4571f39322579699a4cd98d8878854ad9a94615e3b73255d18fe38c14
16 changes: 16 additions & 0 deletions dev-python/snakemake-interface-common/metadata.xml
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<?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>
22 changes: 22 additions & 0 deletions dev-python/snakemake-interface-common/snakemake-interface-common-1.17.2.ebuild
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# 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
1 change: 1 addition & 0 deletions dev-python/snakemake-interface-executor-plugins/Manifest
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DIST snakemake_interface_executor_plugins-9.1.1.tar.gz 16342 BLAKE2B d478afe4fdbb91c0e7a1447de002b93a5583089b9ed2164c9086f536d7b8b6c9f3e52687fc0b299830a86639c1dca0e682f01b17349a58deac5efa884ddc381a SHA512 bcb589ab251fbab69cdddb5eb23257b18164c42c7b3e5014e43aeec278c5453d9713e7c1791ecb15899a8593a5cb302cfc56b8e35539a6474ad1c6d79d892592
16 changes: 16 additions & 0 deletions dev-python/snakemake-interface-executor-plugins/metadata.xml
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<?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>
23 changes: 23 additions & 0 deletions ...on/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.1.1.ebuild
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# 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
1 change: 1 addition & 0 deletions dev-python/snakemake-interface-report-plugins/Manifest
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DIST snakemake_interface_report_plugins-1.0.0.tar.gz 4239 BLAKE2B efda3664614d123b0cd0f3d246d324ef7a4e67b2a069a5b1dde929921cf7e2251f67d6fcc1806864488dcc9c9b586681908e5a11b13f78206342ff0383efdbdc SHA512 2f5ac7e0ccd02c10aebcbe0eebfdb617cb32f66204e91316e3bc2b0053c3606207baa5de5bdda570f5559db366c637adf614f9ac23c7a33fb06d64560bd780aa
16 changes: 16 additions & 0 deletions dev-python/snakemake-interface-report-plugins/metadata.xml
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<?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>
21 changes: 21 additions & 0 deletions ...python/snakemake-interface-report-plugins/snakemake-interface-report-plugins-1.0.0.ebuild
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# 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
1 change: 1 addition & 0 deletions dev-python/snakemake-interface-storage-plugins/Manifest
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DIST snakemake_interface_storage_plugins-3.2.2.tar.gz 11949 BLAKE2B 56e33546c1a9a0eeb92560ff2eb3950b2b91edaa5c527b4b504082bd2ed3f0fbd1b8e8cd24d1391375e99c2b2041aa47a30ac62dd009ec1188cffee65fa606cb SHA512 0151f297ae5f597016e02937021af2583982d5df0cb0c353274618799f68a4a99a30a19f631f1a8c4dabf74833f39c47a4405f7c0e9be8b3397ae350ae23e62d
16 changes: 16 additions & 0 deletions dev-python/snakemake-interface-storage-plugins/metadata.xml
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<?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>
24 changes: 24 additions & 0 deletions ...thon/snakemake-interface-storage-plugins/snakemake-interface-storage-plugins-3.2.2.ebuild
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# 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
1 change: 1 addition & 0 deletions dev-python/snakemake/Manifest
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DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
DIST snakemake-8.14.0.gh.tar.gz 8662241 BLAKE2B fc36722b00cb3da11e836d5c521fe6600d176fd6fc3bd8a39336bc6a3d34bfcb689727d9990351cde247e377dca1131bda5dd84852a32ddb91fed44aa62c020e SHA512 68a0aabeed435e032d01f4d38d37c4b37ed7f624bf3768a1654daccdbf95ceb06646d7302ca04ea4f20695ec9706e015d146794aa000ec108d18d6ad09f3671b
4 changes: 2 additions & 2 deletions dev-python/snakemake/snakemake-7.32.4.ebuild
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EAPI=8

PYTHON_COMPAT=( python3_{10..11} )
PYTHON_COMPAT=( python3_{10..12} )
DISTUTILS_USE_PEP517=setuptools

inherit distutils-r1
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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 \
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