commit: f1a1cfe44dd61cde8a3f99e1f0b05b8e2cce7e7e
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 22 20:04:04 2025 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 20:06:33 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f1a1cfe4
sci-biology/pysam: Remove old
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-biology/pysam/Manifest | 1 -
sci-biology/pysam/pysam-0.22.1.ebuild | 68 -----------------------------------
2 files changed, 69 deletions(-)
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 74b074fbd507..787349b265e0 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B
6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480
SHA512
fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350
DIST pysam-0.23.0.gh.tar.gz 4076476 BLAKE2B
74f5fd99aff357c59aa4cd13214fbb87577d213461feff2afd59679c6b442ccee1fe23a7b7d6ddc723f57f4e00516fb7b67207e8f8619b707d1f909c62663006
SHA512
7c7b3806dbf316f7d9283dbabcd86e55d5dd18a01a127af5f26279e2266fb9b6e44546de0d22c82de963eca19c9e9b3ed1cc00c465acc2ddd810824902c87add
diff --git a/sci-biology/pysam/pysam-0.22.1.ebuild
b/sci-biology/pysam/pysam-0.22.1.ebuild
deleted file mode 100644
index 9070476873e1..000000000000
--- a/sci-biology/pysam/pysam-0.22.1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-
-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 ->
${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.20*:="
-DEPEND="${RDEPEND}
- dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- test? (
- =sci-biology/bcftools-1.20*
- =sci-biology/samtools-1.20*
- )"
-
-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'
-
- 'tests/AlignedSegment_test.py::TestBaseModifications'
-)
-
-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
-}
