[med-svn] [Git][med-team/q2-phylogeny][master] 7 commits: New upstream version 2024.5.0
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jun 26 12:27:24 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / q2-phylogeny
Commits:
9f8c17ef by Michael R. Crusoe at 2024-06-26T11:14:56+02:00
New upstream version 2024.5.0
- - - - -
71db5232 by Michael R. Crusoe at 2024-06-26T11:14:56+02:00
routine-update: New upstream version
- - - - -
2d32b976 by Michael R. Crusoe at 2024-06-26T11:14:57+02:00
Update upstream source from tag 'upstream/2024.5.0'
Update to upstream version '2024.5.0'
with Debian dir 7b1a381736281ff15d711fbd83410735fc1e625d
- - - - -
50c192ca by Michael R. Crusoe at 2024-06-26T11:15:53+02:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
0d77c6bb by Michael R. Crusoe at 2024-06-26T11:34:24+02:00
d/patches/configparser.patch: copy from qiime
- - - - -
fea5390e by Michael R. Crusoe at 2024-06-26T12:53:25+02:00
Only build for Python 3.11 until upstream catches up with Python 3.12.
- - - - -
60c22a7a by Michael R. Crusoe at 2024-06-26T13:24:29+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/control.in
- + debian/patches/configparser.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
- q2_phylogeny/_version.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+q2-phylogeny (2024.5.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Regenerate debian/control from debian/control.in (routine-update)
+ * d/patches/configparser.patch: copy from qiime
+ * Only build for Python 3.11 until upstream catches up with Python
+ 3.12.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 26 Jun 2024 13:22:45 +0200
+
q2-phylogeny (2024.2.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
iqtree
Standards-Version: 4.6.2
@@ -28,8 +28,8 @@ Depends: ${shlibs:Depends},
iqtree,
mafft,
raxml,
- q2-types (>= 2024.2),
- q2-alignment (>= 2024.2)
+ q2-types (>= 2024.5),
+ q2-alignment (>= 2024.5)
Description: QIIME 2 plugin for phylogeny
QIIME 2 plugin for phylogenetic reconstruction, and operations on
phylogenetic trees.
=====================================
debian/control.in
=====================================
@@ -6,7 +6,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
iqtree
Standards-Version: 4.6.2
=====================================
debian/patches/configparser.patch
=====================================
@@ -0,0 +1,27 @@
+From: Athos Ribeiro <athos.ribeiro at canonical.com>
+Date: Mon, 3 Jun 2024 11:31:54 -0300
+Subject: Use ConfigParser instead of SafeConfigParser
+
+The configparser's SafeConfigParser has been renamed to ConfigParser in
+Python 3.2 [1]. It was finally removed in Python 3.12 [2].
+
+[1] https://docs.python.org/dev/whatsnew/3.2.html#configparser
+[2] https://docs.python.org/3/whatsnew/3.12.html#configparser
+
+Last-Update: 2024-06-03
+Forwarded: not-needed, see https://github.com/qiime2/q2-sample-classifier/pull/229
+
+--- q2-types.orig/versioneer.py
++++ q2-types/versioneer.py
+@@ -340,9 +340,9 @@
+ # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+ # the top of versioneer.py for instructions on writing your setup.cfg .
+ setup_cfg = os.path.join(root, "setup.cfg")
+- parser = configparser.SafeConfigParser()
++ parser = configparser.ConfigParser()
+ with open(setup_cfg, "r") as f:
+- parser.readfp(f)
++ parser.read_file(f)
+ VCS = parser.get("versioneer", "VCS") # mandatory
+
+ def get(parser, name):
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+configparser.patch
iqtree2.patch
fix-tests-and-binary-names-and-options.patch
skip-test-needing-internet.patch
=====================================
debian/rules
=====================================
@@ -3,6 +3,7 @@
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
+export PYBUILD_DISABLE=python3.12
# For testing, we need .egg-info so the entry points are available.
export PYBUILD_BEFORE_TEST=python{version} setup.py develop --install-dir {build_dir}
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,7 +18,9 @@ if [ ! -f /usr/lib/python3/dist-packages/pytest_cov/__init__.py ] ; then
fi
# Run build-time tests
-for py in $(py3versions -s 2> /dev/null)
-do
- ${py} -m pytest -v --cov=${pkg}
-done
+# for py in $(py3versions -s 2> /dev/null)
+# do
+# ${py} -m pytest -v --cov=${pkg}
+# done
+
+python3.11 -m pytest -v --cov=${pkg}
=====================================
q2_phylogeny/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 2024.2.0, Release-2024.2)"
- git_full = "f0ffa35ea1132d9eb7a26bb23510521a020ec463"
- git_date = "2024-02-16 21:58:36 +0000"
+ git_refnames = " (tag: 2024.5.0, Release-2024.5)"
+ git_full = "c4bce028d895892382c4575bbb7d84236d109410"
+ git_date = "2024-05-29 04:17:17 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/8e0e5957a63f5a2853e25bc7c432499ad6574b03...60c22a7a1e5aae03ae5d56c6012f53738bf87b3f
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