[med-svn] [Git][med-team/python-pysam][master] 5 commits: remove todo item.

[Étienne Mollier (@emollier)]

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


Commits:
e32ed350 by Étienne Mollier at 2023-06-23T19:15:31+02:00
remove todo item.

- - - - -
035acef7 by Étienne Mollier at 2023-06-23T19:15:31+02:00
d/copyright: bump copyright year.

- - - - -
bf07c583 by Étienne Mollier at 2023-06-23T19:54:39+02:00
d/rules: delete extra license files.

- - - - -
b607816d by Étienne Mollier at 2023-06-23T20:10:32+02:00
typos.patch: add; fix typos caught by lintian.

- - - - -
4f1a6155 by Étienne Mollier at 2023-06-23T20:11:12+02:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- debian/patches/series
- + debian/patches/typos.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,4 @@
-python-pysam (0.21.0+ds-1) UNRELEASED; urgency=medium
-
- TODO: upgrade samtools (and the whole htslib ecosystem) to version 1.17,
- otherwise pysam build fails with:
- samtools/cram_size.c.pysam.c:61:19: error: ‘CRAM_COMP_RAW’ undeclared here (not in a function)
+python-pysam (0.21.0+ds-1) unstable; urgency=medium
 
   * New upstream version
   * Patches triage:
@@ -11,8 +7,11 @@ python-pysam (0.21.0+ds-1) UNRELEASED; urgency=medium
     - skip_test_remote.patch: forwarding not-needed
     - skip-test-on-32-bit.patch: provide dep3 header
     - clean_less patch: forwarding not-needed
+  * d/copyright: bump copyright year.
+  * d/rules: delete extra license files.
+  * typos.patch: add; fix typos caught by lintian.
 
- -- Étienne Mollier <emollier at debian.org>  Sun, 11 Jun 2023 14:57:16 +0200
+ -- Étienne Mollier <emollier at debian.org>  Fri, 23 Jun 2023 20:10:54 +0200
 
 python-pysam (0.20.0+ds-3) unstable; urgency=medium
 


=====================================
debian/copyright
=====================================
@@ -12,7 +12,7 @@ Copyright: 2009-2018 Andreas Heger,
                       Tildon Grant Belgrad,
                       Martin Goodson,
                       Kevin Jacobs <jacobs at bionformed.com>
-            2008-2010 Genome Research Ltd.
+           2008-2023 Genome Research Ltd.
 License: MIT
 
 Files: bcftools/*


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


=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,50 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/pysam-developers/pysam/pull/1198
+Last-Update: 2023-06-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pysam.orig/samtools/bam_ampliconclip.c
++++ python-pysam/samtools/bam_ampliconclip.c
+@@ -1014,7 +1014,7 @@
+ 
+     if (param.tol < 0) {
+         fprintf(stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+-                        " reseting tolerance to default of 5.\n", param.tol);
++                        " resetting tolerance to default of 5.\n", param.tol);
+         param.tol = 5;
+     }
+ 
+--- python-pysam.orig/samtools/bam_ampliconclip.c.pysam.c
++++ python-pysam/samtools/bam_ampliconclip.c.pysam.c
+@@ -1016,7 +1016,7 @@
+ 
+     if (param.tol < 0) {
+         fprintf(samtools_stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+-                        " reseting tolerance to default of 5.\n", param.tol);
++                        " resetting tolerance to default of 5.\n", param.tol);
+         param.tol = 5;
+     }
+ 
+--- python-pysam.orig/samtools/bamshuf.c
++++ python-pysam/samtools/bamshuf.c
+@@ -537,7 +537,7 @@
+             "      -l INT   Compression level [%d]\n" // DEF_CLEVEL
+             "      -n INT   Number of temporary files [%d]\n" // n_files
+             "      -T PREFIX\n"
+-            "               Write tempory files to PREFIX.nnnn.bam\n"
++            "               Write temporary files to PREFIX.nnnn.bam\n"
+             "      --no-PG  do not add a PG line\n",
+             reads_store, DEF_CLEVEL, n_files);
+ 
+--- python-pysam.orig/samtools/bamshuf.c.pysam.c
++++ python-pysam/samtools/bamshuf.c.pysam.c
+@@ -539,7 +539,7 @@
+             "      -l INT   Compression level [%d]\n" // DEF_CLEVEL
+             "      -n INT   Number of temporary files [%d]\n" // n_files
+             "      -T PREFIX\n"
+-            "               Write tempory files to PREFIX.nnnn.bam\n"
++            "               Write temporary files to PREFIX.nnnn.bam\n"
+             "      --no-PG  do not add a PG line\n",
+             reads_store, DEF_CLEVEL, n_files);
+ 


=====================================
debian/rules
=====================================
@@ -24,6 +24,7 @@ clean: clean-tests
 override_dh_install: clean-tests
 	dh_install -Xtest.gtf.gz
 	find debian -name log.txt -delete
+	find debian -name LICENSE -delete
 
 ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
 override_dh_auto_test: pysam_data.all cbcf_data.all



View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/b855d1e8f9b42b7d242b268dd1581cf3ba390b7e...4f1a61551e5ca1476a082075003cda438a4fcef7

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