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

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

6 files changed, 5 insertions, 50 deletions

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-0.8.2.ebuild b/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[${PYTHON_USEDEP}]"
-
 # TODO: fix docs building
 # ModuleNotFoundError: No module named 'pybedtools.cbedtools'
 # even if pybedtools is installed
diff --git a/profiles/updates/2Q-2024 b/profiles/updates/2Q-2024
index bf7fb5174..ad60545f3 100644
--- a/profiles/updates/2Q-2024
+++ b/profiles/updates/2Q-2024
@@ -1 +1,2 @@
 move sci-biology/pyfaidx dev-python/pyfaidx
+move sci-biology/pybedtools dev-python/pybedtools
diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest
deleted file mode 100644
index a952ac4b8..000000000
--- a/sci-biology/pybedtools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe
-DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18
diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
deleted file mode 100644
index bc02bda6f..000000000
--- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Use BED and GFF files from python using BEDtools"
-HOMEPAGE="https://daler.github.io/pybedtools"
-SRC_URI="https://github.com/daler/pybedtools/archive/v${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
-}