[med-svn] [Git][med-team/python-ete3][master] 6 commits: move python3-numpy to Depends

[Étienne Mollier]

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 <etienne.mollier at mailoo.org>  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 <etienne.mollier at mailoo.org>
+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
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