diff options
| author |   David Seifert <soap@gentoo.org> | 2021-10-11 16:55:08 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2021-10-11 16:55:08 +0200 |
| commit | 3b93bba18c14598747eda127476f093040e6b3b6 (patch) | |
| tree | fd479a77018e1125edec1288f0d1815eeb821667 /sci-biology | |
| parent | www-apps/icingaweb2: 2.8.3 / 2.8.4 clean up (diff) | |
| download | gentoo-3b93bba18c14598747eda127476f093040e6b3b6.tar.gz gentoo-3b93bba18c14598747eda127476f093040e6b3b6.tar.bz2 gentoo-3b93bba18c14598747eda127476f093040e6b3b6.zip | |
sci-biology/pysam: drop 0.16.0.1-r1
Closes: https://bugs.gentoo.org/812242
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch | 37 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.16.0.1-r1.ebuild | 60 |
3 files changed, 0 insertions, 98 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 1e305c998da5..91ca2cac79c1 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ -DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28 DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552 diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch deleted file mode 100644 index 9d269878e651..000000000000 --- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch +++ /dev/null @@ -1,37 +0,0 @@ ---- a/tests/pysam_data/Makefile -+++ b/tests/pysam_data/Makefile -@@ -3,7 +3,7 @@ - BAI=$(BAM:%.bam=%.bam.bai) - CRAM=ex1.cram ex2.cram ex3.cram - CRAI=$(CRAM:%.cram=%.cram.crai) --NO_PG:=$(findstring --no-PG,$(shell samtools view)) -+NO_PG:=--no-PG - - # ex2.bam - bam file without index - ---- a/tests/tabix_test.py -+++ b/tests/tabix_test.py -@@ -14,6 +14,7 @@ - import subprocess - import glob - import re -+import pytest - from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \ - load_and_convert, TABIX_DATADIR, get_temp_filename - -@@ -1014,6 +1015,7 @@ - globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,)) - - -+@pytest.mark.skip(reason="requires internet connectivity") - class TestRemoteFileHTTP(unittest.TestCase): - - url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" -@@ -1053,6 +1055,7 @@ - self.assertEqual(list(self.local_file.header), []) - - -+@pytest.mark.skip(reason="requires internet connectivity") - class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP): - - url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz" diff --git a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild deleted file mode 100644 index e27c998bb917..000000000000 --- a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -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 -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.10*:=" -DEPEND="${RDEPEND}" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - <dev-python/setuptools-58[${PYTHON_USEDEP}] - test? ( - =sci-biology/bcftools-1.10* - =sci-biology/samtools-1.10* - )" - -distutils_enable_tests pytest - -DISTUTILS_IN_SOURCE_BUILD=1 - -python_prepare_all() { - # unbundle htslib - export HTSLIB_MODE="external" - export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include - export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) - rm -r htslib || die - - # prevent setup.py from adding RPATHs (except $ORIGIN) - sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ - -i setup.py || die - - eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch - - 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 - local MAKEOPTS=-j1 - distutils-r1_python_compile -} |