gentoo auto-resync : 08:04:2023 - 23:33:13

4 files changed, 32 insertions, 1 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index e1df1b8a6ad9..fbf7c03b0357 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 931d51cf12e1..4a490595f41b 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,4 +1,5 @@
+AUX pysam-0.21.0-cython-3.patch 946 BLAKE2B 6b74b084d4f0308a77266c748209a91aa23fc0f51635b45bb2e47efc7d1e2f4a67993305d0f12c74964add24ec49ebb8b56bff720aec065a76257bda5a677cdb SHA512 763bee599547059dfff39f7ae087402dfca67acabc048012663d6cd792c605d6dc07210f777d22e9373c086cd9cd468e7ae3060a501962157ba5f6971c8033a1
 DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7
-EBUILD pysam-0.21.0.ebuild 1591 BLAKE2B 2b0673c61cb83eaeba7b05ad325d0f61de530b1c8de0a2e2cb0e7399f8b1ba0d7489160086d7264056c675b4e8785fcb79cdd0a9f9506bc4e57a36ea65121b25 SHA512 47d3101651a21e6d59fba0641d76ac34dfe608b267ba726fddbdab2aaa25dd5be6bf51bc707fc4c19b6e9e0222fa0419368b5d4b70a168cfec4c0666429ce114
+EBUILD pysam-0.21.0.ebuild 1744 BLAKE2B d6211a396810673da6392e4377a412bc6886c5eb9d5ad45ae85b278ae9d2202c4a706186b64ae3b1ae88fc0b32c532dad494bf69757b3c66dbf96e7001b48d2a SHA512 41be02962a1af5463dcc4ca98ec2af0e6986ec8d8a8101b813954754865c95d75f5f8a0ae20d3c76465475aa94e30fade45734931221eea01ab05cb7746acfce
 EBUILD pysam-9999.ebuild 1709 BLAKE2B b7297d21abf0e581c5c2d8a72a7e6805cb5f96f6e878cc979fc0f5a34e57bdd25a2f50abaa9ee10040559e66ee42d3a24696a7093103658175b27858acaac95c SHA512 7e7a782243897a89a3539b3eb79ccd0790c6b0afcf79453526c30371f867faaf8eca6454e64d3bea250ff13753ff400fe5ff3352c080c85285cafa2346e3564a
 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7
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'