[med-svn] [Git][med-team/python-pysam][master] 2 commits: Upload to experimental

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / python-pysam


Commits:
8e8d4312 by Nilesh Patra at 2021-10-15T02:28:13+05:30
Upload to experimental

- - - - -
db2f9625 by Nilesh Patra at 2021-10-15T02:54:23+05:30
Attempt skipping failing test on 32-bit

- - - - -


3 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/skip-test-on-32-bit.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-python-pysam (0.17.0+ds-1) UNRELEASED; urgency=medium
+python-pysam (0.17.0+ds-1) experimental; urgency=medium
 
   * Team Upload.
   [ Andreas Tille ]


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ skip_test_remote.patch
 # samtools_v1.10
 #bcftools_v1.10_full
 clean_less
+skip-test-on-32-bit.patch


=====================================
debian/patches/skip-test-on-32-bit.patch
=====================================
@@ -0,0 +1,29 @@
+--- a/tests/samtools_test.py
++++ b/tests/samtools_test.py
+@@ -20,6 +20,7 @@
+     check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \
+     make_data_files, BAM_DATADIR
+ 
++import platform
+ 
+ IS_PYTHON3 = sys.version_info[0] >= 3
+ 
+@@ -92,7 +93,7 @@
+         "flagstat ex1.bam > %(out)s_ex1.flagstat",
+         # Fails python 3.3 on linux, passes on OsX and when
+         # run locally
+-        "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
++        #"calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
+         # use -s option, otherwise the following error in samtools 1.2:
+         # Samtools-htslib-API: bam_get_library() not yet implemented
+         # causes downstream problems
+@@ -118,6 +119,9 @@
+         # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg",
+     ]
+ 
++    if platform.architecture()[0] == '64bit':
++        statements.append("calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam")
++
+     map_command = {
+     }
+ 



View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/150b2da809637a893c13e019b1896389bd871891...db2f96255e25fb72306e62741cee567f29c52ed8

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/150b2da809637a893c13e019b1896389bd871891...db2f96255e25fb72306e62741cee567f29c52ed8
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