Étienne Mollier pushed to branch master at Debian Med / python-ete3
Commits: b8ac6d01 by Étienne Mollier at 2020-11-04T17:51:57+01:00 move python3-numpy to Depends - - - - - 961e7a0f by Étienne Mollier at 2020-11-04T18:58:39+01:00 restore ete3/tools These components are needed for superficial autodep8 autopkgtest to go through; chances are the package does not work without it. - - - - - 0c53f2ed by Étienne Mollier at 2020-11-04T19:08:41+01:00 pmodeltest_executable.patch to address lintian warning - - - - - c0c1d050 by Étienne Mollier at 2020-11-04T19:20:46+01:00 add repository informations to upstream/metadata - - - - - 7e29f172 by Étienne Mollier at 2020-11-04T19:21:18+01:00 Set upstream metadata fields: Bug-Submit. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html - - - - - f25a591c by Étienne Mollier at 2020-11-04T19:22:37+01:00 routine-update: Ready to upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/pmodeltest_executable.patch - debian/patches/series - debian/python3-ete3.pyremove - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +python-ete3 (3.1.2+dfsg-2) unstable; urgency=medium + + * Team upload. + * Moved python3-numpy from Recommends to Depends. (Closes: #972983) + * Restored ete3/tools: + - it allowed autodep8 autopkgtest to succeed, + - pmodeltest_executable.patch wrapped up to address the reintroduced + executable not ELF nor script. + * Added repository information to upstream/metadata. + * Set upstream metadata fields: Bug-Submit. + + -- Étienne Mollier <[email protected]> Wed, 04 Nov 2020 19:21:18 +0100 + python-ete3 (3.1.2+dfsg-1) unstable; urgency=medium [ Andreas Tille ] ===================================== debian/control ===================================== @@ -29,9 +29,9 @@ Architecture: all Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}, + python3-numpy, python3-six Recommends: ${python3:Recommends} - python3-numpy, python3-lxml, python3-qt-binding, python3-pyqt5.qtopengl, ===================================== debian/patches/pmodeltest_executable.patch ===================================== @@ -0,0 +1,25 @@ +Description: make pmodeltest.py a genuine python3 executable + This issue has been caught by lintian, as an executable not ELF nor script. +Author: Étienne Mollier <[email protected]> +Forwarded: not-needed +Last-Update: 2020-11-04 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- python-ete3.orig/ete3/tools/ete_build_lib/apps.py ++++ python-ete3/ete3/tools/ete_build_lib/apps.py +@@ -72,7 +72,7 @@ + 'iqtree' : "%BIN%/iqtree -nt %CORES%", + 'raxml-pthreads' : "%BIN%/raxmlHPC-PTHREADS-SSE3 -T%CORES%", + 'raxml' : "%BIN%/raxmlHPC-SSE3", +- 'pmodeltest' : "python %BIN%/pmodeltest.py --nprocs %CORES% --phyml %BIN%/phyml", ++ 'pmodeltest' : "%BIN%/pmodeltest.py --nprocs %CORES% --phyml %BIN%/phyml", + 'dialigntx' : "%BIN%/dialign-tx %BIN%/dialigntx_conf", + 'fasttree' : "export OMP_NUM_THREADS=%CORES%; %BIN%/FastTree", + 'statal' : "%BIN%/statal", +--- python-ete3.orig/ete3/tools/ete_build_lib/task/pmodeltest.py ++++ python-ete3/ete3/tools/ete_build_lib/task/pmodeltest.py +@@ -1,3 +1,4 @@ ++#! /usr/bin/python3 + from __future__ import absolute_import + import os + import re ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ syntax_fixes.patch +pmodeltest_executable.patch ===================================== debian/python3-ete3.pyremove ===================================== @@ -1,6 +1,5 @@ test.* ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore ete3/test/* -ete3/tools/* ete3/ncbi_taxonomy/SQLite-Levenshtein/* -examples/* \ No newline at end of file +examples/* ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,4 @@ +Bug-Submit: https://github.com/etetoolkit/ete/issues/new Reference: - Author: Jaime Huerta-Cepas and François Serra and Peer Bork Title: > @@ -8,3 +9,6 @@ Reference: URL: https://academic.oup.com/mbe/article/33/6/1635/2579822 eprint: > https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf +Repository: https://github.com/etetoolkit/ete.git +Repository-Browse: https://github.com/etetoolkit/ete +Bug-Database: https://github.com/etetoolkit/ete/issues View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a -- View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/compare/2662092709c77c72bf84b30a0f972a5b1581af7a...f25a591c238f4e9c6fb3cba5de339a3653ec2a5a You're receiving this email because of your account on salsa.debian.org.
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