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