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
-}
