[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

["David Seifert" <soap@gentoo.org>]

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 <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'