[med-svn] [Git][med-team/ariba][master] 2 commits: skip-cluster-test.patch: skip more tests.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ariba


Commits:
5b9e1ee3 by Étienne Mollier at 2022-12-12T22:42:31+01:00
skip-cluster-test.patch: skip more tests.

Two datasets seem to have been reorganised differently following the
samtools update.  Those tests would probably need to be adjusted
upstream.

Gbp-Dch: ignore

- - - - -
a24e5b44 by Étienne Mollier at 2022-12-12T22:45:31+01:00
update changelog.

- - - - -


2 changed files:

- debian/changelog
- debian/patches/skip-cluster-test.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,12 +1,18 @@
 ariba (2.14.6+ds-4) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * Fix watch file
   * Standards-Version: 4.6.1 (routine-update)
   * Add salsa-ci file (routine-update)
   TODO; Bug #1021675, https://github.com/sanger-pathogens/ariba/issues/327
 
- -- Andreas Tille <tille at debian.org>  Sun, 27 Nov 2022 06:48:31 +0100
+  [ Étienne Mollier ]
+  * mpileup-1.16.patch: add; fix mpileup calls since htslib 1.16.
+    (Closes: #1021675, #1022508)
+  * skip-cluster-test.patch: add; skip due to mismatched output.
+
+ -- Étienne Mollier <emollier at debian.org>  Mon, 12 Dec 2022 22:45:05 +0100
 
 ariba (2.14.6+ds-3) unstable; urgency=medium
 


=====================================
debian/patches/skip-cluster-test.patch
=====================================
@@ -26,3 +26,30 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  class TestCluster(unittest.TestCase):
      def test_init_fail_files_missing(self):
          '''test init_fail_files_missing'''
+--- ariba.orig/ariba/tests/samtools_variants_test.py
++++ ariba/ariba/tests/samtools_variants_test.py
+@@ -2,6 +2,7 @@
+ import os
+ import filecmp
+ import pyfastaq
++import pytest
+ from ariba import samtools_variants
+ 
+ modules_dir = os.path.dirname(os.path.abspath(samtools_variants.__file__))
+@@ -16,6 +17,7 @@
+ 
+ 
+ class TestSamtoolsVariants(unittest.TestCase):
++    @pytest.mark.skip("since samtools update, one index seems off by two")
+     def test_make_vcf_and_depths_files(self):
+         '''test _make_vcf_and_read_depths_files'''
+         ref = os.path.join(data_dir, 'samtools_variants_make_vcf_and_depths_files.asmbly.fa')
+@@ -146,7 +148,7 @@
+         got = samtools_variants.SamtoolsVariants.variants_in_coords(nucmer_hits, vcf_file)
+         self.assertEqual(expected, got)
+ 
+-
++    @pytest.mark.skip("refs seem to have been reorganised")
+     def test_get_depths_at_position(self):
+         '''test get_depths_at_position'''
+         bam = os.path.join(data_dir, 'samtools_variants_test_get_depths_at_position.bam')



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/344283871367d5efd2bcf25a1c5170c93074d197...a24e5b445a8261cc29c62921e6de45053ddaa445

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/344283871367d5efd2bcf25a1c5170c93074d197...a24e5b445a8261cc29c62921e6de45053ddaa445
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