[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/, dev-python/pybedtools/, profiles/updates/

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/, dev-python/pybedtools/, profiles/updates/

[Andrew Ammerlaan]

commit:     45eacba59a5cb5bfd342b49cd30677887efac7f0
Author:     Michael Schubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Fri Jul 19 08:51:36 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jul 19 12:35:08 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=45eacba5

dev-python/bedtools: move from sci-biology, version bump 0.10.0

Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com>
Closes: https://github.com/gentoo/sci/pull/1285
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../pybedtools/metadata.xml                        |  0
 .../pybedtools/pybedtools-0.10.0.ebuild            |  8 ++--
 profiles/updates/2Q-2024                           |  1 +
 sci-biology/pybedtools/pybedtools-0.9.0.ebuild     | 43 ----------------------
 4 files changed, 4 insertions(+), 48 deletions(-)

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 bc02bda6f..ae51c24ce 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 bf7fb5174..ad60545f3 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/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
deleted file mode 100644
index bc02bda6f..000000000
--- 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
-}