commit: a300fad43f75217ec5ca16d5262e578e0af853a9 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Fri May 24 09:54:01 2024 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Fri May 24 09:54:01 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a300fad4
sci-biology/pysam: drop 0.21.0 Closes: https://bugs.gentoo.org/923243 Closes: https://bugs.gentoo.org/927872 Closes: https://bugs.gentoo.org/929754 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/pysam/Manifest | 1 - .../pysam/files/pysam-0.21.0-cython-3.patch | 24 -------- sci-biology/pysam/pysam-0.21.0.ebuild | 72 ---------------------- 3 files changed, 97 deletions(-) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index fae7b9793388..2859d25293fc 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ -DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350 diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch deleted file mode 100644 index 303a4fb0dcdc..000000000000 --- a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch +++ /dev/null @@ -1,24 +0,0 @@ -From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 -From: John Marshall <[email protected]> -Date: Sat, 8 Apr 2023 11:00:46 +1200 -Subject: [PATCH] Remove incorrect type annotation - -The annotation already in pysam/libcbcf.pyi is correct. -Fixes #1179 as reopened on April 6th. ---- - pysam/libcbcf.pyx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx -index 8c088af2..8ecfe5f3 100644 ---- a/pysam/libcbcf.pyx -+++ b/pysam/libcbcf.pyx -@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object): - return bcf_format_get_alleles(self) - - @alleles.setter -- def alleles(self, value: tuple): -+ def alleles(self, value): - # Sets the genotype, supply a tuple of alleles to set. - # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord - # The genotype is reset when an empty tuple, None or (None,) is supplied diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild deleted file mode 100644 index 77292ed29613..000000000000 --- a/sci-biology/pysam/pysam-0.21.0.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# 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 - -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 -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.17*:=" -DEPEND="${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 - -PATCHES=( - # backport - # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 - "${FILESDIR}"/${P}-cython-3.patch -) - -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 -}
