From 45eacba59a5cb5bfd342b49cd30677887efac7f0 Mon Sep 17 00:00:00 2001 From: Michael Schubert Date: Fri, 19 Jul 2024 08:51:36 +0000 Subject: [PATCH] dev-python/bedtools: move from sci-biology, version bump 0.10.0 Signed-off-by: Michael Schubert Closes: https://github.com/gentoo/sci/pull/1285 Signed-off-by: Andrew Ammerlaan --- dev-python/pybedtools/Manifest | 1 + .../pybedtools/metadata.xml | 0 .../pybedtools/pybedtools-0.10.0.ebuild | 8 ++-- profiles/updates/2Q-2024 | 1 + sci-biology/pybedtools/Manifest | 2 - .../pybedtools/pybedtools-0.9.0.ebuild | 43 ------------------- 6 files changed, 5 insertions(+), 50 deletions(-) create mode 100644 dev-python/pybedtools/Manifest rename {sci-biology => dev-python}/pybedtools/metadata.xml (100%) rename sci-biology/pybedtools/pybedtools-0.8.2.ebuild => dev-python/pybedtools/pybedtools-0.10.0.ebuild (88%) delete mode 100644 sci-biology/pybedtools/Manifest delete mode 100644 sci-biology/pybedtools/pybedtools-0.9.0.ebuild diff --git a/dev-python/pybedtools/Manifest b/dev-python/pybedtools/Manifest new file mode 100644 index 00000000000..7db62a4c423 --- /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 similarity index 100% rename from sci-biology/pybedtools/metadata.xml rename to dev-python/pybedtools/metadata.xml diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/dev-python/pybedtools/pybedtools-0.10.0.ebuild similarity index 88% rename from sci-biology/pybedtools/pybedtools-0.8.2.ebuild rename to dev-python/pybedtools/pybedtools-0.10.0.ebuild index bc02bda6f27..ae51c24ce68 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.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/profiles/updates/2Q-2024 b/profiles/updates/2Q-2024 index bf7fb517460..ad60545f3ec 100644 --- a/profiles/updates/2Q-2024 +++ b/profiles/updates/2Q-2024 @@ -1 +1,2 @@ move sci-biology/pyfaidx dev-python/pyfaidx +move sci-biology/pybedtools dev-python/pybedtools diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest deleted file mode 100644 index a952ac4b842..00000000000 --- 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-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild deleted file mode 100644 index bc02bda6f27..00000000000 --- a/sci-biology/pybedtools/pybedtools-0.9.0.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 -}