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| author |   David Seifert <soap@gentoo.org> | 2023-04-08 19:53:38 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2023-04-08 19:53:38 +0200 |
| commit | e88f627a3bada9db443b5234ac3fa71c6102c63d (patch) | |
| tree | ad409ce779160c98cd748a77d1ec799a03e1ba89 /sci-biology | |
| parent | net-print/hplip-plugin: Stabilize 3.22.10 amd64, #899282 (diff) | |
| download | gentoo-e88f627a3bada9db443b5234ac3fa71c6102c63d.tar.gz gentoo-e88f627a3bada9db443b5234ac3fa71c6102c63d.tar.bz2 gentoo-e88f627a3bada9db443b5234ac3fa71c6102c63d.zip | |
sci-biology/pysam: fix build with cython 3
Closes: https://bugs.gentoo.org/898730
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/files/pysam-0.21.0-cython-3.patch | 24 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.21.0.ebuild | 6 |
2 files changed, 30 insertions, 0 deletions
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 <jmarshall@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' |