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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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