commit: e88f627a3bada9db443b5234ac3fa71c6102c63d Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Apr 8 17:53:38 2023 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Apr 8 17:53:38 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e88f627a
sci-biology/pysam: fix build with cython 3 Closes: https://bugs.gentoo.org/898730 Signed-off-by: David Seifert <soap <AT> gentoo.org> .../pysam/files/pysam-0.21.0-cython-3.patch | 24 ++++++++++++++++++++++ sci-biology/pysam/pysam-0.21.0.ebuild | 6 ++++++ 2 files changed, 30 insertions(+) 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 new file mode 100644 index 000000000000..303a4fb0dcdc --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch @@ -0,0 +1,24 @@ +From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 +From: John Marshall <jmarsh...@hey.com> +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 index 588cd1bc4f1b..77292ed29613 100644 --- a/sci-biology/pysam/pysam-0.21.0.ebuild +++ b/sci-biology/pysam/pysam-0.21.0.ebuild @@ -31,6 +31,12 @@ 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'
