[med-svn] [Git][med-team/gubbins][master] 7 commits: d/t/run-example: update the dataset selection.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jan 31 20:29:19 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / gubbins
Commits:
4694aa8d by Étienne Mollier at 2026-01-31T20:01:59+01:00
d/t/run-example: update the dataset selection.
- - - - -
96635635 by Étienne Mollier at 2026-01-31T20:04:10+01:00
d/watch: convert to v5 Github template.
Note that sanger-pathogens redirects to nickjcroucher.
- - - - -
f06643bc by Étienne Mollier at 2026-01-31T20:06:24+01:00
d/control: drop redundant Priority: optional.
- - - - -
95613dae by Étienne Mollier at 2026-01-31T20:06:51+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
0b8f1d4f by Étienne Mollier at 2026-01-31T21:25:18+01:00
remove-pkg-resources.patch: new: ditto.
This patch removes pkg_resouces imports and replaces them by importlib
where needed.
- - - - -
68ddd74c by Étienne Mollier at 2026-01-31T21:26:09+01:00
d/control: drop dependency on python3-pkg-resources.
Closes: #1125845
- - - - -
a9c6dfa8 by Étienne Mollier at 2026-01-31T21:29:01+01:00
d/changelog: ready for upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/remove-pkg-resources.patch
- debian/patches/series
- debian/tests/run-example
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,24 @@
-gubbins (3.4.3-1) UNRELEASED; urgency=medium
+gubbins (3.4.3-1) unstable; urgency=medium
- * Team Upload
+ [ Alexandre Detiste ]
+ * New upstream version 3.4.3
* d/rules: rewrite with shorter syntax, drop old distutils comment
* Update homepage
* Drop "Rules-Requires-Root: no"
- * New upstream version 3.4.3
* Refresh patches, drop Numpy 2 patch, applied upstream
- -- Alexandre Detiste <tchet at debian.org> Sat, 27 Sep 2025 14:38:43 +0200
+ [ Étienne Mollier ]
+ * d/t/run-example: update the dataset selection.
+ * d/watch: convert to v5 Github template.
+ Note that sanger-pathogens redirects to nickjcroucher.
+ * d/control: drop redundant Priority: optional.
+ * d/control: declare compliance to standards version 4.7.3.
+ * remove-pkg-resources.patch: new: ditto.
+ This patch removes pkg_resouces imports and replaces them by importlib
+ where needed.
+ * d/control: drop dependency on python3-pkg-resources. (Closes: #1125845)
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 31 Jan 2026 21:28:16 +0100
gubbins (3.4-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
autoconf-archive,
@@ -22,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),
python3-scipy <!nocheck>,
python3-multiprocess <!nocheck>,
python3-wheel <!nocheck>
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/gubbins
Vcs-Git: https://salsa.debian.org/med-team/gubbins.git
Homepage: https://nickjcroucher.github.io/gubbins/
@@ -33,7 +32,6 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3,
- python3-pkg-resources,
raxml
# FIXME: python3-numba is disabled until version 0.59 makes it back to testing.
# Delete also remove-numba-temporarily.patch when the time comes to bring back
=====================================
debian/patches/remove-pkg-resources.patch
=====================================
@@ -0,0 +1,43 @@
+Description: get rid of pkg_resources invocations.
+ Version informations are notably obtained via the now recommended
+ importlib.metadata.version function.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1125845
+Forwarded: no
+Last-Update: 2026-01-31
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- gubbins.orig/python/gubbins/__init__.py
++++ gubbins/python/gubbins/__init__.py
+@@ -9,7 +9,7 @@
+
+ import sys
+ import os
+-import pkg_resources
++import importlib.metadata
+
+ ###############################################################################
+ ## Populate the 'gubbins' namespace
+@@ -53,11 +53,7 @@
+
+ def version():
+ os.environ["PATH"] = os.environ["PATH"] + ":/usr/lib/gubbins/"
+- program_version = ""
+- try:
+- program_version = str(pkg_resources.get_distribution(__project__).version)
+- except pkg_resources.RequirementParseError:
+- pass
++ program_version = importlib.metadata.version("gubbins")
+ return "%s" % program_version
+
+ __version__ = version()
+--- gubbins.orig/python/gubbins/tests/test_dependencies.py
++++ gubbins/python/gubbins/tests/test_dependencies.py
+@@ -10,7 +10,6 @@
+ import sys
+ import glob
+ import argparse
+-import pkg_resources
+ import shutil
+ from gubbins import common, run_gubbins
+
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ iqtree2.patch
autoupdate_configure.ac.patch
python3-shebang.patch
remove-numba-temporarily.patch
+remove-pkg-resources.patch
=====================================
debian/tests/run-example
=====================================
@@ -1,19 +1,30 @@
#!/bin/sh
# autopkgtest check: Run test data through Gubbins
# Author: Sascha Steinbiss <satta at debian.org>
+# Reviewed-By: Étienne Mollier <emollier at debian.org>
set -e
-
-TESTDIR=$(pwd)/tests/data
-WORKDIR=$(mktemp -d)
+# This is expected to run in autopkgtest context.
+CURDIR="$(pwd)"
+WORKDIR="$(mktemp -d)"
HOME="$WORKDIR"
export HOME
trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
-cd $WORKDIR
+cd "$WORKDIR"
-cp $TESTDIR/*aln .
+# Note several pathological datasets will trigger gubbins to return
+# error without being symptomatic of an actual crash.
+cp "$CURDIR/python/gubbins/tests/data/bootstrapping_test.aln" .
+cp "$CURDIR/python/gubbins/tests/data/masking_multiple.aln" .
+cp "$CURDIR/python/gubbins/tests/data/mislabelled.multiple_recombinations.aln" .
+cp "$CURDIR/tests/data/no_recombinations.aln" .
+cp "$CURDIR/tests/data/one_recombination.aln" .
+cp "$CURDIR/tests/data/recombination_at_root/recombination_at_root.aln" .
+cp "$CURDIR/tests/data/small_phylip_file.aln" .
-for f in alignment_file_multiple_lines_per_sequence.aln alignment_file_one_line_per_sequence.aln alignment_file_with_n.aln multiple_recombinations.aln no_recombinations.aln one_recombination.aln; do
- echo "##### $f #####"
- cp $TESTDIR/$f .
- run_gubbins $f
+for f in *.aln
+do
+ echo "##### $f #####"
+ # See Github issue #442 for the iqtree tree builder.
+ # [1]: https://github.com/nickjcroucher/gubbins/issues/442
+ run_gubbins --tree-builder iqtree $f
done
=====================================
debian/watch
=====================================
@@ -1,4 +1,5 @@
-version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/sanger-pathogens/gubbins/tags \
- (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
+Version: 5
+
+Template: Github
+Owner: nickjcroucher
+Project: gubbins
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/b7ca657d109f746ccdf33304705c6a5f1f3dd765...a9c6dfa85d6f7086428d7650fe77ea8808ba696d
--
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/b7ca657d109f746ccdf33304705c6a5f1f3dd765...a9c6dfa85d6f7086428d7650fe77ea8808ba696d
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