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

[David Seifert]

commit:     52fc6e9547d84e09c0e13658617c46ceab10d3a1
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 13:16:01 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 13:16:01 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52fc6e95

sci-biology/HTSeq: sync live ebuild

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

 sci-biology/HTSeq/HTSeq-9999.ebuild | 49 +++++++++++++++++++++++++++++++------
 1 file changed, 42 insertions(+), 7 deletions(-)

diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild 
b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 548684fd531b..678968788ff7 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python3_{7..9} )
+DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{8..10} )
 
-inherit distutils-r1
+inherit distutils-r1 flag-o-matic
 
 DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
 HOMEPAGE="https://htseq.readthedocs.io/";
@@ -14,7 +15,7 @@ if [[ ${PV} == *9999 ]]; then
        inherit git-r3
        EGIT_REPO_URI="https://github.com/htseq/htseq.git";
 else
-       SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> 
${P}.tar.gz"
+       SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> 
${P}.gh.tar.gz"
 
        S="${WORKDIR}"/htseq-release_${PV}
        KEYWORDS="~amd64"
@@ -22,12 +23,46 @@ fi
 
 LICENSE="GPL-3+"
 SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
        dev-python/numpy[${PYTHON_USEDEP}]
-       dev-python/matplotlib[${PYTHON_USEDEP}]
        sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+       test? (
+               dev-python/matplotlib[${PYTHON_USEDEP}]
+               dev-python/pandas[${PYTHON_USEDEP}]
+               dev-python/scipy[${PYTHON_USEDEP}]
+       )"
 BDEPEND="
        >=dev-lang/swig-3.0.8
        dev-python/cython[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+src_configure() {
+       # mask broken asserts in src/step_vector.h:72
+       append-cppflags -DNDEBUG
+
+       distutils-r1_src_configure
+}
+
+python_test() {
+       distutils_install_for_testing
+
+       # Due to the build directories creating a competing
+       # hierarchy, we move to the test/ dir to avoid implicitly
+       # injecting the root HTSeq/ dir into the PYTHONPATH,
+       # which leads the python module lookup astray:
+       #   ${PWD}
+       #   ├── build
+       #   │   ├── lib
+       #   │   │   └── HTSeq
+       #   │   [...]
+       #   ├── HTSeq
+       #   └── test
+       cd test/ || die
+       ln -s ../example_data || die
+       epytest
+}