[med-svn] [Git][med-team/python-biopython][master] 3 commits: d/control: restore muscle3 instead of muscle (v5).

[Étienne Mollier (@emollier)]

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


Commits:
5c275149 by Étienne Mollier at 2022-12-03T20:17:07+01:00
d/control: restore muscle3 instead of muscle (v5).

- - - - -
0088c489 by Étienne Mollier at 2022-12-04T19:15:16+01:00
port_tutorial_to_muscle3.patch: add; fix doctest failures.

- - - - -
7d9547f4 by Étienne Mollier at 2022-12-04T19:47:57+01:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/port_tutorial_to_muscle3.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,13 @@
-python-biopython (1.80+dfsg-2) UNRELEASED; urgency=medium
+python-biopython (1.80+dfsg-2) unstable; urgency=medium
 
   * d/NEWS: fix typo in news item.
   * d/control: bring back t_coffee tests since upstream version revert.
-  * d/control: update fixme item related to muscle5 since muscle3 is uploaded.
+    Closes: #1022307
+  * d/control: restore muscle3 instead of plain muscle (version 5).
+    Closes: #1009118
+  * port_tutorial_to_muscle3.patch: add; fix doctest failures.
 
- -- Étienne Mollier <emollier at debian.org>  Tue, 29 Nov 2022 20:14:55 +0100
+ -- Étienne Mollier <emollier at debian.org>  Sun, 04 Dec 2022 19:15:42 +0100
 
 python-biopython (1.80+dfsg-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -25,9 +25,7 @@ Build-Depends: debhelper-compat (= 13),
                emboss <!nocheck>,
                fasttree <!nocheck>,
                mafft <!nocheck>,
-# FIXME: restore muscle wrapper checks when muscle3 passes through NEW, or
-# remove entirely when wrapper support is removed upstream:
-#               muscle [i386 amd64 x32] <!nocheck>,
+               muscle3 [i386 amd64 x32] <!nocheck>,
                ncbi-blast+ <!nocheck>,
                phylip <!nocheck>,
                phyml [any-amd64 any-i386] <!nocheck>,
@@ -74,7 +72,7 @@ Suggests: python3-tk,
           emboss,
           fasttree,
           mafft,
-          muscle,
+          muscle3,
           phylip,
           phyml,
           prank,


=====================================
debian/patches/port_tutorial_to_muscle3.patch
=====================================
@@ -0,0 +1,55 @@
+Description: adjust tutorial to document muscle3 usage.
+ In addition to being up to date with the way of doing things for the upcoming
+ Debian version, this fixes the doctest failures.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2022-12-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Doc/Tutorial/chapter_align.tex
++++ python-biopython/Doc/Tutorial/chapter_align.tex
+@@ -1116,7 +1116,7 @@
+ >>> from Bio.Align.Applications import MuscleCommandline
+ >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.txt")
+ >>> print(cline)
+-muscle -in opuntia.fasta -out opuntia.txt
++muscle3 -in opuntia.fasta -out opuntia.txt
+ \end{minted}
+ 
+ Note that MUSCLE uses ``-in'' and ``-out'' but in Biopython we have to use
+@@ -1133,7 +1133,7 @@
+ >>> from Bio.Align.Applications import MuscleCommandline
+ >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clw=True)
+ >>> print(cline)
+-muscle -in opuntia.fasta -out opuntia.aln -clw
++muscle3 -in opuntia.fasta -out opuntia.aln -clw
+ \end{minted}
+ 
+ Or, strict ClustalW output where the original ClustalW header line is
+@@ -1144,7 +1144,7 @@
+ >>> from Bio.Align.Applications import MuscleCommandline
+ >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clwstrict=True)
+ >>> print(cline)
+-muscle -in opuntia.fasta -out opuntia.aln -clwstrict
++muscle3 -in opuntia.fasta -out opuntia.aln -clwstrict
+ \end{minted}
+ 
+ \noindent The \verb|Bio.AlignIO| module should be able to read these alignments
+@@ -1174,7 +1174,7 @@
+ >>> from Bio.Align.Applications import MuscleCommandline
+ >>> muscle_cline = MuscleCommandline(input="opuntia.fasta")
+ >>> print(muscle_cline)
+-muscle -in opuntia.fasta
++muscle3 -in opuntia.fasta
+ \end{minted}
+ 
+ If we run this via the wrapper, we get back the output as a string. In order
+@@ -1254,7 +1254,7 @@
+ >>> from Bio.Align.Applications import MuscleCommandline
+ >>> muscle_cline = MuscleCommandline(clwstrict=True)
+ >>> print(muscle_cline)
+-muscle -clwstrict
++muscle3 -clwstrict
+ \end{minted}
+ 
+ Now for the fiddly bits using the \verb|subprocess| module, stdin and stdout:


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ fix-use-of-unversioned-python.patch
 reproduciblebuild.patch
 croak-on-muscle5.patch
 muscle3.patch
+port_tutorial_to_muscle3.patch



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/fcc111db1e861fa9a20ecdcae2a5e1636ce83563...7d9547f4504743c2f6164e0d0cc9220dbe1fca43

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/fcc111db1e861fa9a20ecdcae2a5e1636ce83563...7d9547f4504743c2f6164e0d0cc9220dbe1fca43
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