commit: f49f5a33efadbaadc1fee304b1ca83917ad13700
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 30 15:30:01 2025 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Nov 30 15:30:01 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f49f5a33
sci-biology/pysam: drop 0.23.0
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/pysam/Manifest | 1 -
sci-biology/pysam/pysam-0.23.0.ebuild | 68 -----------------------------------
2 files changed, 69 deletions(-)
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 379197bb8a4a..48717af7c11f 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.23.0.gh.tar.gz 4076476 BLAKE2B
74f5fd99aff357c59aa4cd13214fbb87577d213461feff2afd59679c6b442ccee1fe23a7b7d6ddc723f57f4e00516fb7b67207e8f8619b707d1f909c62663006
SHA512
7c7b3806dbf316f7d9283dbabcd86e55d5dd18a01a127af5f26279e2266fb9b6e44546de0d22c82de963eca19c9e9b3ed1cc00c465acc2ddd810824902c87add
DIST pysam-0.23.3.gh.tar.gz 4077706 BLAKE2B
52ea1866188374b6d832113f49de88b9b4fe1f777f0c81184aadfa5acd1f0e3048996e31a384061f0d1f9a289574c12e3e0a1c28a960e1e2f3f7af0c4e2b8d9a
SHA512
e259a64ed722b72309827695585f429a6e59641223f5432c9cd7e673fd04fcbd5963618e9145315373e557edce532bf1a312db185bcc4235ff699357e453e07b
diff --git a/sci-biology/pysam/pysam-0.23.0.ebuild
b/sci-biology/pysam/pysam-0.23.0.ebuild
deleted file mode 100644
index cac7c9b72ffc..000000000000
--- a/sci-biology/pysam/pysam-0.23.0.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..13} )
-
-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 ->
${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.21*:="
-DEPEND="${RDEPEND}"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- test? (
- =sci-biology/bcftools-1.21*
- =sci-biology/samtools-1.21*
- )"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
- # only work with bundled htslib
- 'tests/tabix_test.py::TestRemoteFileHTTP'
- 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-
- 'tests/AlignedSegment_test.py::TestBaseModifications'
-)
-
-python_prepare_all() {
-
- # unbundle htslib
- export HTSLIB_MODE="external"
- export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
- export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
- rm -r htslib || die
-
- if use test; then
- einfo "Building test data"
- emake -C tests/pysam_data
- emake -C tests/cbcf_data
- fi
-
- # breaks with parallel build
- # need to avoid dropping .so plugins into
- # build-lib, which breaks tests
- DISTUTILS_ARGS=(
- build_ext
- --inplace
- -j1
- )
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- rm -rf pysam || die
- epytest
-}
