[med-svn] [Git][med-team/python-biopython][master] 3 commits: add mkdssp4.patch

[Étienne Mollier]

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


Commits:
9e6f8193 by Étienne Mollier at 2020-12-05T23:32:08+01:00
add mkdssp4.patch

- - - - -
0a733cc5 by Étienne Mollier at 2020-12-05T23:32:33+01:00
routine-update: Standards-Version: 4.5.1

- - - - -
a8ec62f6 by Étienne Mollier at 2020-12-05T23:48:51+01:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/mkdssp4.path
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biopython (1.78+dfsg-4) unstable; urgency=medium
+
+  * Add mkdssp4.patch. (Closes: #976542)
+  * Standards-Version: 4.5.1 (routine-update)
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Sat, 05 Dec 2020 23:32:40 +0100
+
 python-biopython (1.78+dfsg-3) unstable; urgency=medium
 
   * Bumped ncbi-blast+ version requirement to 2.10.1-3


=====================================
debian/control
=====================================
@@ -45,7 +45,7 @@ Build-Depends: debhelper-compat (= 13),
                samtools <!nocheck>,
                t-coffee <!nocheck>,
                wise <!nocheck>
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-biopython
 Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git
 Homepage: http://biopython.org


=====================================
debian/patches/mkdssp4.path
=====================================
@@ -0,0 +1,27 @@
+Description: port PDB DSSP module to use dssp version 4
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Bug: https://github.com/biopython/biopython/issues/3433
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=976542
+Last-Update: 2020-12-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Bio/PDB/DSSP.py
++++ python-biopython/Bio/PDB/DSSP.py
+@@ -229,7 +229,7 @@
+     # (Debian distribution of DSSP includes a symlink for 'dssp' argument)
+     try:
+         p = subprocess.Popen(
+-            [DSSP, in_file],
++            [DSSP, "--output-format=dssp", in_file],
+             universal_newlines=True,
+             stdout=subprocess.PIPE,
+             stderr=subprocess.PIPE,
+@@ -238,7 +238,7 @@
+         if DSSP == "mkdssp":
+             raise
+         p = subprocess.Popen(
+-            ["mkdssp", in_file],
++            ["mkdssp", "--output-format=dssp", in_file],
+             universal_newlines=True,
+             stdout=subprocess.PIPE,
+             stderr=subprocess.PIPE,


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ fix-use-of-unversioned-python.patch
 stabilize-phyml-test.patch
 spelling-error-in-binaries.patch
 reproduciblebuild.patch
+mkdssp4.path



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e
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