commit: b29c8f32c0c043d2fcb82195fb58d00fcd771449
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:11:01 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:11:01 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b29c8f32
sci-biology/pysam: add 9999
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/pysam/pysam-9999.ebuild | 72 +++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/sci-biology/pysam/pysam-9999.ebuild
b/sci-biology/pysam/pysam-9999.ebuild
new file mode 100644
index 000000000000..a162ddf2158b
--- /dev/null
+++ b/sci-biology/pysam/pysam-9999.ebuild
@@ -0,0 +1,72 @@
+# 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
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git";
+else
+
SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz ->
${P}.gh.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping
format"
+HOMEPAGE="
+ https://github.com/pysam-developers/pysam
+ https://pypi.org/project/pysam/";
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND=">=sci-libs/htslib-1.17"
+DEPEND="${RDEPEND}
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+ test? (
+ >=sci-biology/bcftools-1.17
+ >=sci-biology/samtools-1.17
+ )"
+
+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
+}
