[med-svn] [Git][med-team/seqmagick][master] 2 commits: replace-ungap.patch: new: fix test failure.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / seqmagick


Commits:
32fca29a by Étienne Mollier at 2024-03-17T17:57:34+01:00
replace-ungap.patch: new: fix test failure.

Closes: #1066772

- - - - -
fb741eab by Étienne Mollier at 2024-03-17T17:58:44+01:00
ready to upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/replace-ungap.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+seqmagick (0.8.6-2) unstable; urgency=medium
+
+  * replace-ungap.patch: new: fix test failure. (Closes: #1066772)
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 17 Mar 2024 17:58:18 +0100
+
 seqmagick (0.8.6-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/patches/replace-ungap.patch
=====================================
@@ -0,0 +1,18 @@
+Description: fix test failure due to call to deprecated ungap.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1066772
+Forwarded: https://github.com/fhcrc/seqmagick/pull/101
+Last-Update: 2024-03-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- seqmagick.orig/seqmagick/subcommands/backtrans_align.py
++++ seqmagick/seqmagick/subcommands/backtrans_align.py
+@@ -102,7 +102,7 @@
+                 prot_seq.id, nucl_seq.id)
+ 
+         # Ungap nucleotides
+-        codons = batch(str(nucl_seq.seq.ungap('-')), 3)
++        codons = batch(str(nucl_seq.seq.replace('-', '')), 3)
+         codons = [''.join(i) for i in codons]
+         codon_iter = iter(codons)
+ 


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 biopython_1.71_dual_coding_support.patch
 pytest.patch
+replace-ungap.patch



View it on GitLab: https://salsa.debian.org/med-team/seqmagick/-/compare/da7847924ed44a681a30f9c969f5ba17ca512615...fb741eaba39c7a9189632307fb2c71006da659f6

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqmagick/-/compare/da7847924ed44a681a30f9c969f5ba17ca512615...fb741eaba39c7a9189632307fb2c71006da659f6
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