This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pysam.
commit 1f2ef8ccf7a318492501947734ec04c4a1ebaf7c
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Tue Oct 6 00:41:18 2015 -0700
Backport upstream commit 6efb22b to permit building with Cython 0.23.x
Closes: 800794
---
debian/patches/cython23.patch | 39 +++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 40 insertions(+)
diff --git a/debian/patches/cython23.patch b/debian/patches/cython23.patch
new file mode 100644
index 0000000..27afe0f
--- /dev/null
+++ b/debian/patches/cython23.patch
@@ -0,0 +1,39 @@
+From 6efb22b1a3ee4bc57a691f163b456b417da56db3 Mon Sep 17 00:00:00 2001
+From: Andreas Heger <andreas.he...@gmail.com>
+Date: Thu, 3 Sep 2015 21:25:28 +0100
+Subject: [PATCH] change ctypedef enum to typedef enum for cython 0.23
+Bug: https://github.com/pysam-developers/pysam/issues/164
+---
+ pysam/chtslib.pxd | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/pysam/chtslib.pxd b/pysam/chtslib.pxd
+index 2f8c941..299e84a 100644
+--- a/pysam/chtslib.pxd
++++ b/pysam/chtslib.pxd
+@@ -363,7 +363,7 @@ cdef extern from "htslib/hts.h" nogil:
+ hFILE *hfile
+ void *voidp
+
+- ctypedef enum htsFormatCategory:
++ cdef enum htsFormatCategory:
+ unknown_category
+ sequence_data # Sequence data -- SAM, BAM, CRAM, etc
+ variant_data # Variant calling data -- VCF, BCF, etc
+@@ -371,14 +371,14 @@ cdef extern from "htslib/hts.h" nogil:
+ region_list # Coordinate intervals or regions -- BED, etc
+ category_maximum
+
+- ctypedef enum htsExactFormat:
++ cdef enum htsExactFormat:
+ unknown_format
+ binary_format
+ text_format
+ sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
+ format_maximum
+
+- ctypedef enum htsCompression:
++ cdef enum htsCompression:
+ no_compression, gzip, bgzf, custom
+ compression_maximum
+
diff --git a/debian/patches/series b/debian/patches/series
index 55ab446..01d5a2d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ ignore-htslib-dir.patch
improve-python3-compatibility.patch
sam_mpileup.patch
strip_online_tests.patch
+cython23.patch
--
Alioth's /usr/local/bin/git-commit-notice on
/srv/git.debian.org/git/debian-med/python-pysam.git
_______________________________________________
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
