[med-svn] [Git][med-team/q2-quality-filter][master] 7 commits: New upstream version 2024.5.0
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Jun 25 12:00:36 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / q2-quality-filter
Commits:
70a17323 by Michael R. Crusoe at 2024-06-25T12:47:20+02:00
New upstream version 2024.5.0
- - - - -
099ad494 by Michael R. Crusoe at 2024-06-25T12:47:20+02:00
routine-update: New upstream version
- - - - -
ef27e040 by Michael R. Crusoe at 2024-06-25T12:47:21+02:00
Update upstream source from tag 'upstream/2024.5.0'
Update to upstream version '2024.5.0'
with Debian dir 90e7ac8425341f53345d6749dc78bc7b979ae105
- - - - -
ea30891b by Michael R. Crusoe at 2024-06-25T12:47:38+02:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
74ae1020 by Michael R. Crusoe at 2024-06-25T12:55:28+02:00
d/patches/configparser.patch: copy from qiime
- - - - -
51853e13 by Michael R. Crusoe at 2024-06-25T12:55:28+02:00
Only build for Python 3.11 until upstream catches up with Python 3.12.
- - - - -
28de38b5 by Michael R. Crusoe at 2024-06-25T12:55:29+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/configparser.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
- q2_quality_filter/_version.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+q2-quality-filter (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> Tue, 25 Jun 2024 12:47:38 +0200
+
q2-quality-filter (2024.2.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,12 +7,12 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
python3-pytest,
- qiime (>= 2024.2),
- q2templates (>= 2024.2),
- q2-types (>= 2024.2)
+ qiime (>= 2024.5),
+ q2templates (>= 2024.5),
+ q2-types (>= 2024.5)
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-quality-filter
Vcs-Git: https://salsa.debian.org/med-team/q2-quality-filter.git
@@ -25,9 +25,9 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-pandas,
- qiime (>= 2024.2),
- q2templates (>= 2024.2),
- q2-types (>= 2024.2)
+ qiime (>= 2024.5),
+ q2templates (>= 2024.5),
+ q2-types (>= 2024.5)
Description: QIIME2 plugin for PHRED-based filtering and trimming
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
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 +1,2 @@
+configparser.patch
skip-test-needing-internet.patch
=====================================
debian/rules
=====================================
@@ -3,6 +3,8 @@
# 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}
# Delete .egg-info and other files that were generated along with .egg-info
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,7 +18,9 @@ if [ ! -e /usr/bin/py.test-3 ] ; 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_quality_filter/_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 = "c01e837a13ccf3ac868294af986d741a83cb6e56"
- git_date = "2024-02-16 21:57:57 +0000"
+ git_refnames = " (tag: 2024.5.0, Release-2024.5)"
+ git_full = "7b433f68b4c0667f9cd20bebaf764ecb7dcd173d"
+ git_date = "2024-05-29 04:17:52 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab: https://salsa.debian.org/med-team/q2-quality-filter/-/compare/77603d9c2e9a0f452c612b2f69ba247b4419867e...28de38b5397c280d1bfdaee9b869de987bd3f77f
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View it on GitLab: https://salsa.debian.org/med-team/q2-quality-filter/-/compare/77603d9c2e9a0f452c612b2f69ba247b4419867e...28de38b5397c280d1bfdaee9b869de987bd3f77f
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