[med-svn] [Git][med-team/python-biopython][master] 10 commits: croak-on-muscle5.patch: dep3 header.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Thu Nov 24 17:43:22 GMT 2022 


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


Commits:
30826fa4 by Étienne Mollier at 2022-11-24T16:06:16+01:00
croak-on-muscle5.patch: dep3 header.

Gbp-Dch: ignore

- - - - -
359afc42 by Étienne Mollier at 2022-11-24T16:06:43+01:00
d/*.lintian-overrides: refresh override.

- - - - -
5d8086aa by Étienne Mollier at 2022-11-24T16:07:30+01:00
debian/python3-biopython.lintian-overrides: override typo.

The spelling error in binary does not seem to match anything
meaningful on the side of the source code.

- - - - -
6fb0938a by Étienne Mollier at 2022-11-24T16:10:47+01:00
d/s/lintian-overrides: indicate location of Restriction.md.

This justifies overriding a case of missing source code on the html
file, which is produced with pandoc.

- - - - -
6310ba79 by Étienne Mollier at 2022-11-24T16:58:01+01:00
d/python3-biopython.lintian-overrides: fix faulty tags.

Gbp-Dch: ignore

- - - - -
c8dc137d by Étienne Mollier at 2022-11-24T18:34:37+01:00
d/NEWS: experimental version number.

Gbp-Dch: ignore

- - - - -
22de9cb9 by Étienne Mollier at 2022-11-24T18:35:01+01:00
d/copyright: bump copyright years.

- - - - -
d15b974d by Étienne Mollier at 2022-11-24T18:35:55+01:00
croak-on-muscle5.patch: use the passed cmd in argument.

Initial patch proposal hardcoded the muscle command in the
constructor, but the user of the biopython library may specify one's
own command, for instance muscle3 if installed concurrently with
muscle 5.

Gbp-Dch: ignore

- - - - -
36fc56e8 by Étienne Mollier at 2022-11-24T18:37:58+01:00
muscle3.patch: add; default to use muscle3 command if available.

This is in preparation of the availability of a dedicated muscle3
package with the explicitly versionned command.

- - - - -
2f16db1e by Étienne Mollier at 2022-11-24T18:42:38+01:00
ready to upload to experimental.

- - - - -


9 changed files:

- debian/NEWS
- debian/changelog
- debian/copyright
- debian/patches/croak-on-muscle5.patch
- + debian/patches/muscle3.patch
- debian/patches/series
- debian/python-biopython-doc.lintian-overrides
- + debian/python3-biopython.lintian-overrides
- + debian/source/lintian-overrides


Changes:

=====================================
debian/NEWS
=====================================
@@ -1,4 +1,4 @@
-python-biopython (1.80+dfsg-1) experimental; urgency=medium
+python-biopython (1.80+dfsg-1~0exp0) experimental; urgency=medium
 
   Starting with biopython 1.79, command wrappers are being deprecated,
   and may be removed past biopython 1.81.  This has the notable


=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-python-biopython (1.80+dfsg-1) UNRELEASED; urgency=medium
+python-biopython (1.80+dfsg-1~0exp0) experimental; urgency=medium
 
   * New upstream version
   * Standards-Version: 4.6.1 (routine-update)
@@ -14,8 +14,19 @@ python-biopython (1.80+dfsg-1) UNRELEASED; urgency=medium
   * d/NEWS: describe incompatibility with muscle 5; also describe possible
     workarounds.
   * d/not-installed: add tree1 and other_trees.
-
- -- Étienne Mollier <emollier at debian.org>  Thu, 24 Nov 2022 00:14:29 +0100
+  * d/*.lintian-overrides: refresh override.
+  * debian/python3-biopython.lintian-overrides: override typo; the reported
+    spelling error does not seem to match anything meaningful on the side of
+    the source code.
+  * d/s/lintian-overrides: indicate location of Restriction.md, source of
+    Restriction.html.
+  * d/copyright: bump copyright years.
+  * muscle3.patch: add; default to use muscle3 command if available.
+    This is in preparation of the availability of a dedicated muscle3
+    package with the explicitly versionned command, since muscle 5 is a very
+    different program but can be installed in parallel.
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 24 Nov 2022 18:39:22 +0100
 
 python-biopython (1.79+dfsg-3) unstable; urgency=medium
 


=====================================
debian/copyright
=====================================
@@ -8,7 +8,7 @@ Source: http://biopython.org/DIST/
 Files-Excluded: Bio/Entrez/DTDs/mathml2-qname-1.mod .gitattributes
 
 Files: *
-Copyright: © 1999-2021 Biopython contributors
+Copyright: © 1999-2022 Biopython contributors
 License: other
  Permission to use, copy, modify, and distribute this software and its
  documentation with or without modifications and for any purpose and
@@ -31,6 +31,7 @@ License: other
 Files: debian/*
 Copyright: © 2009      Charles Plessy <plessy at debian.org>
              2004-2009 Philipp Benner <philipp at debian.org>
+             2020-2022 Étienne Mollier <emollier at debian.org>
 License: GPL-2+
  The Debian packaging information is under the GPL, version 2 or later.
  .


=====================================
debian/patches/croak-on-muscle5.patch
=====================================
@@ -1,3 +1,15 @@
+Description: raise runtime error when trying to use wrapper on muscle 5.
+ The muscle wrapper only supports muscle 3, and the biopython project is aiming
+ to remove wrapper support in an upcoming version.  Port of the wrapping code
+ to support both muscle versions will thus probably never happen.  The affected
+ code section is due to disappear in an upcoming biopython version and it thus
+ not forwarded upstream.
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/biopython/biopython/issues/3902
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009118
+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
 @@ -8,6 +8,7 @@
@@ -12,7 +24,7 @@
              #                           stdout and exit
              _Switch(["-version", "version"], "Write version string to stdout and exit"),
          ]
-+        output = getoutput("muscle -version")
++        output = getoutput(cmd + " -version")
 +        if "muscle 5" in output:
 +            raise RuntimeError("muscle 5 is unsupported in biopython")
 +


=====================================
debian/patches/muscle3.patch
=====================================
@@ -0,0 +1,51 @@
+--- python-biopython.orig/Bio/Align/Applications/_Muscle.py
++++ python-biopython/Bio/Align/Applications/_Muscle.py
+@@ -10,6 +10,12 @@
+ from Bio.Application import _Option, _Switch, AbstractCommandline
+ from subprocess import getoutput
+ 
++# Prefer defaulting to muscle3, as can be installed alongside muscle version 5.
++default_muscle = "muscle3"
++try:
++    _ = getoutput(default_muscle + " --version")
++except FileNotFoundError:
++    default_muscle = "muscle"
+ 
+ class MuscleCommandline(AbstractCommandline):
+     r"""Command line wrapper for the multiple alignment program MUSCLE.
+@@ -43,7 +49,7 @@
+ 
+     """
+ 
+-    def __init__(self, cmd="muscle", **kwargs):
++    def __init__(self, cmd=default_muscle, **kwargs):
+         """Initialize the class."""
+         CLUSTERING_ALGORITHMS = ["upgma", "upgmb", "neighborjoining"]
+         DISTANCE_MEASURES_ITER1 = [
+--- python-biopython.orig/Tests/test_Muscle_tool.py
++++ python-biopython/Tests/test_Muscle_tool.py
+@@ -51,12 +51,18 @@
+ else:
+     from subprocess import getoutput
+ 
+-    output = getoutput("muscle -version")
+-    # Since "not found" may be in another language, try and be sure this is
+-    # really the MUSCLE tool's output
+-    if "not found" not in output and "not recognized" not in output:
+-        if "MUSCLE" in output and "Edgar" in output:
+-            muscle_exe = "muscle"
++    try:
++        output = getoutput("muscle3 -version")
++	# Since "not found" may be in another language, try and be sure this is
++	# really the MUSCLE tool's output
++        if "not found" not in output and "not recognized" not in output:
++            if "MUSCLE" in output and "Edgar" in output:
++                muscle_exe = "muscle3"
++    except FileNotFoundError:
++        output = getoutput("muscle -version")
++        if "not found" not in output and "not recognized" not in output:
++            if "MUSCLE" in output and "Edgar" in output:
++                muscle_exe = "muscle"
+ 
+ if not muscle_exe:
+     raise MissingExternalDependencyError(


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ privacy_breach_ie9.patch
 fix-use-of-unversioned-python.patch
 reproduciblebuild.patch
 croak-on-muscle5.patch
+muscle3.patch


=====================================
debian/python-biopython-doc.lintian-overrides
=====================================
@@ -1,4 +1,4 @@
 # We really need this zero byte file for running the test suite
 # and there was actually done some means to keep it since
 # dh_installdocs ignores the file
-python-biopython-doc: zero-byte-file-in-doc-directory usr/share/doc/python-biopython-doc/Tests/Blast/tab_2226_tblastn_002.txt
+python-biopython-doc: zero-byte-file-in-doc-directory [usr/share/doc/python-biopython-doc/Tests/Blast/tab_2226_tblastn_002.txt]


=====================================
debian/python3-biopython.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# The affected word doesn't show up when scanning the source code.
+python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-310-x86_64-linux-gnu.so]
+python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so]


=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# Missing source is provided as Doc/cookbook/Restriction/Restriction.md
+python-biopython source: source-is-missing [Doc/cookbook/Restriction/Restriction.html]



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/be70b4e77989dc94e56c25a2b92aed72f66cb6d2...2f16db1ee3e44622ae455e528d0dbc150bcbfb2b

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/be70b4e77989dc94e56c25a2b92aed72f66cb6d2...2f16db1ee3e44622ae455e528d0dbc150bcbfb2b
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