[med-svn] [Git][med-team/python-pysam][master] 2 commits: htslib-1.20.patch: new: anticipate test failure.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-pysam


Commits:
95a63e2a by Étienne Mollier at 2024-05-29T13:21:22+02:00
htslib-1.20.patch: new: anticipate test failure.

Upcoming upload of htslib 1.20 comes with improvements causing a test
failure in pysam.  This change anticipates the correction without
introduction of regressions with existing releases of htslib.

Thanks: John Marshall

- - - - -
a0548822 by Étienne Mollier at 2024-05-29T13:23:33+02:00
ready to upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/htslib-1.20.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-pysam (0.22.1+ds-2) unstable; urgency=medium
+
+  * htslib-1.20.patch: new: anticipate test failure.
+    Upcoming upload of htslib 1.20 comes with improvements causing a test
+    failure in pysam.  This change anticipates the correction without
+    introduction of regressions with existing releases of htslib.
+    Thanks to John Marshall
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 29 May 2024 13:23:03 +0200
+
 python-pysam (0.22.1+ds-1) unstable; urgency=medium
 
   * New upstream version 0.22.1+ds


=====================================
debian/patches/htslib-1.20.patch
=====================================
@@ -0,0 +1,19 @@
+Description: fix test failure with htslib 1.20.
+ This data file contains invalid data, which is diagnosed by
+ improvements in bam_parse_basemod2() in HTSlib 1.20. Updating these
+ base modification data files to the versions in htslib and hts-specs
+ corrects the problem.
+
+Author: John Marshall
+Origin: upstream, https://github.com/pysam-developers/pysam/issues/1291#issuecomment-2131146211
+Bug: https://github.com/pysam-developers/pysam/issues/1291
+Reviewed-by: Étienne Mollier <emollier at debian.org>
+Last-Update: 2024-05-29
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pysam.orig/tests/pysam_data/MM-chebi.sam
++++ python-pysam/tests/pysam_data/MM-chebi.sam
+@@ -1,2 +1,2 @@
+ @CO	Separate m, h and N modifications
+-*	0	*	0	0	*	*	0	0	AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA	*	Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15;	Ml:B:C,102,128,153,179,204,161,187,212,169
++*	0	*	0	0	*	*	0	0	AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA	*	Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15;	Ml:B:C,102,128,153,179,204,161,187,212


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 skip_test_remote.patch
 clean_less
 skip-test-on-32-bit.patch
+htslib-1.20.patch



View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/97456260302d085ea6f5ae54f2b679dc41a657e7...a0548822fe326d405407d653cdf9ff19a362a28f

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