[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

["David Seifert" <soap@gentoo.org>]

commit:     3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 15:44:18 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 15:44:18 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3fa05869

sci-biology/pysam: drop 0.19.1

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 -
 sci-biology/pysam/pysam-0.19.1.ebuild | 66 -----------------------------------
 2 files changed, 67 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index fc762c874c2d..fc19ef776276 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479
 DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49

diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild
deleted file mode 100644
index 1164fd6bc091..000000000000
--- a/sci-biology/pysam/pysam-0.19.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.15.1*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.15.1*
-		=sci-biology/samtools-1.15.1*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-)
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	# prevent setup.py from adding RPATHs (except $ORIGIN)
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	esetup.py build_ext --inplace -j1
-	distutils-r1_python_compile -j1
-}