[med-svn] [Git][med-team/q2-alignment][master] 8 commits: d/{copyright, source/options}: ignore egg-info, don't exclude it
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jun 26 11:12:06 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / q2-alignment
Commits:
7b124239 by Michael R. Crusoe at 2024-06-26T11:38:03+02:00
d/{copyright,source/options}: ignore egg-info, don't exclude it
- - - - -
1e43d540 by Michael R. Crusoe at 2024-06-26T11:38:30+02:00
d/patches/configparser.patch: copy from qiime
- - - - -
8bde7347 by Michael R. Crusoe at 2024-06-26T11:39:24+02:00
New upstream version 2024.5.0
- - - - -
46da2ec9 by Michael R. Crusoe at 2024-06-26T11:39:24+02:00
routine-update: New upstream version
- - - - -
0f765361 by Michael R. Crusoe at 2024-06-26T11:39:25+02:00
Update upstream source from tag 'upstream/2024.5.0'
Update to upstream version '2024.5.0'
with Debian dir 3623413a3162f1cb9871d42ad1f358ef4d433ae4
- - - - -
192a499e by Michael R. Crusoe at 2024-06-26T11:39:43+02:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
ec39d53f by Michael R. Crusoe at 2024-06-26T11:58:44+02:00
Only build for Python 3.11 until upstream catches up with Python 3.12.
- - - - -
1aeb5a7c by Michael R. Crusoe at 2024-06-26T12:09:59+02:00
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/control.in
- debian/copyright
- + debian/patches/configparser.patch
- debian/patches/series
- debian/rules
- + debian/source/options
- debian/tests/control
- debian/tests/run-unit-test
- q2_alignment/_version.py
Changes:
=====================================
ci/recipe/meta.yaml
=====================================
@@ -21,7 +21,7 @@ requirements:
- scikit-bio {{ scikit_bio }}
- qiime2 {{ qiime2_epoch }}.*
- q2-types {{ qiime2_epoch }}.*
- - mafft >=7.394
+ - mafft {{ mafft }}
test:
requires:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+q2-alignment (2024.5.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * d/{copyright,source/options}: ignore egg-info, don't exclude it
+ * d/patches/configparser.patch: copy from qiime
+ * Regenerate debian/control from debian/control.in (routine-update)
+ * 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 12:03:17 +0200
+
q2-alignment (2024.2.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,12 +7,12 @@ Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
Steffen Moeller <moeller at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
python3-skbio,
python3-pytest-cov,
- qiime (>= 2024.2),
- q2-types (>= 2024.2),
+ qiime (>= 2024.5),
+ q2-types (>= 2024.5),
mafft
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-alignment
@@ -28,8 +28,8 @@ Depends: ${shlibs:Depends},
python3-setuptools,
python3-skbio,
mafft,
- qiime (>= 2024.2),
- q2-types (>= 2024.2)
+ qiime (>= 2024.5),
+ q2-types (>= 2024.5)
Suggests: sina
Description: QIIME 2 plugin for generating and manipulating alignments
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
=====================================
debian/control.in
=====================================
@@ -6,7 +6,7 @@ Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
Steffen Moeller <moeller at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
python3-skbio,
python3-pytest-cov,
=====================================
debian/copyright
=====================================
@@ -1,7 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: QIIME 2
Source: https://github.com/qiime2/q2-alignment/releases
-Files-Excluded: q2_alignment.egg-info
Files: *
Copyright: 2016-2018 QIIME 2 development team
=====================================
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
py.test-3.patch
=====================================
debian/rules
=====================================
@@ -6,6 +6,8 @@ export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
VERSION_UPSTREAM=$(shell echo $(DEB_VERSION_UPSTREAM) | sed -e 's/\(20[0-9][0-9]\.[0-9]\+\)\..*/\1/')
+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/source/options
=====================================
@@ -0,0 +1 @@
+extend-diff-ignore="^[^/]+.(egg-info|dist-info)/"
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov
+Depends: @, python3-pytest-cov, python3-all
Restrictions: allow-stderr, skip-not-installable
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,4 +18,4 @@ if [ ! -f /usr/lib/python3/dist-packages/pytest_cov/__init__.py ] ; then
fi
# Run build-time tests
-py.test-3 --cov=${pkg}
+python3.11 -m pytest --cov=${pkg}
=====================================
q2_alignment/_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 = "8d0288a5cf8784a687e940f188889477252b0c27"
- git_date = "2024-02-16 21:54:40 +0000"
+ git_refnames = " (tag: 2024.5.0, Release-2024.5)"
+ git_full = "ab65ff4b18275fd81ef63b6e3d2baa7c9c55e4a2"
+ git_date = "2024-05-29 04:11:38 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/compare/b484335c49caafb0439d8637af3e80c5a9daedd6...1aeb5a7cae9d31f2c89df3a96afaf58212a52412
--
This project does not include diff previews in email notifications.
View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/compare/b484335c49caafb0439d8637af3e80c5a9daedd6...1aeb5a7cae9d31f2c89df3a96afaf58212a52412
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240626/c8c08b0f/attachment-0001.htm>
More information about the debian-med-commit
mailing list