[med-svn] [Git][med-team/python-biopython][master] 2 commits: muscle3.patch: ensure muscle3 is default even if unavailable.

[Étienne Mollier (@emollier)]

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


Commits:
74d38831 by Étienne Mollier at 2022-12-23T20:17:46+01:00
muscle3.patch: ensure muscle3 is default even if unavailable.

This fixes the test_doctest failure which occurs because of a
mismatch between "muscle" and "muscle3" when none of them is
available.

- - - - -
c478d0ff by Étienne Mollier at 2022-12-23T20:19:39+01:00
ready to upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/patches/muscle3.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-biopython (1.80+dfsg-3) unstable; urgency=medium
+
+  * muscle3.patch: ensure muscle3 is default even if unavailable.
+    This fixes the test_doctest failure which occurs because of a
+    mismatch between "muscle" and "muscle3" when none of them is
+    available.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 23 Dec 2022 20:19:21 +0100
+
 python-biopython (1.80+dfsg-2) unstable; urgency=medium
 
   * d/NEWS: fix typo in news item.


=====================================
debian/patches/muscle3.patch
=====================================
@@ -13,7 +13,7 @@ Last-Update: 2022-11-24
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- python-biopython.orig/Bio/Align/Applications/_Muscle.py
 +++ python-biopython/Bio/Align/Applications/_Muscle.py
-@@ -10,6 +10,11 @@
+@@ -10,6 +10,14 @@
  from Bio.Application import _Option, _Switch, AbstractCommandline
  from subprocess import getoutput
  
@@ -21,11 +21,14 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 +default_muscle = "muscle3"
 +output = getoutput(default_muscle + " --version")
 +if "not found" in output or "not recognized" in output:
-+    default_muscle = "muscle"
++    # The below should ascertain plain muscle is muscle 3 indeed.
++    output = getoutput("muscle --version")
++    if "MUSCLE" in output and "Edgar" in output:
++        default_muscle = "muscle"
  
  class MuscleCommandline(AbstractCommandline):
      r"""Command line wrapper for the multiple alignment program MUSCLE.
-@@ -43,7 +48,7 @@
+@@ -43,7 +51,7 @@
  
      """
  



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/7d9547f4504743c2f6164e0d0cc9220dbe1fca43...c478d0ff7cea16ff72f6cd3def7a85c8c3a3ff5c

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/7d9547f4504743c2f6164e0d0cc9220dbe1fca43...c478d0ff7cea16ff72f6cd3def7a85c8c3a3ff5c
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