[med-svn] [Git][med-team/q2-demux][master] 6 commits: Autopkgtest for all supported Python3 versions
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 18 13:56:38 GMT 2024
Andreas Tille pushed to branch master at Debian Med / q2-demux
Commits:
5aa20ea6 by Andreas Tille at 2024-02-18T14:48:22+01:00
Autopkgtest for all supported Python3 versions
- - - - -
2e4aaca5 by Andreas Tille at 2024-02-18T14:48:37+01:00
New upstream version 2024.2.0+dfsg
- - - - -
2850d856 by Andreas Tille at 2024-02-18T14:48:37+01:00
routine-update: New upstream version
- - - - -
5d27ac75 by Andreas Tille at 2024-02-18T14:48:38+01:00
Update upstream source from tag 'upstream/2024.2.0+dfsg'
Update to upstream version '2024.2.0+dfsg'
with Debian dir 08a1eb00c91cbde6bac853e76173d5aa0e1f31be
- - - - -
f119c742 by Andreas Tille at 2024-02-18T14:48:57+01:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
a2774af6 by Andreas Tille at 2024-02-18T14:51:36+01:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- .github/workflows/ci-dev.yaml
- README.md
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/tests/control
- debian/tests/run-unit-test
- q2_demux/_version.py
- q2_demux/tests/test_demux.py
Changes:
=====================================
.github/workflows/ci-dev.yaml
=====================================
@@ -9,4 +9,4 @@ jobs:
ci:
uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml at dev
with:
- distro: core
\ No newline at end of file
+ distro: amplicon
=====================================
README.md
=====================================
@@ -1,5 +1,5 @@
# q2-demux
-
+
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
\ No newline at end of file
=====================================
ci/recipe/meta.yaml
=====================================
@@ -49,7 +49,7 @@ test:
- qiime2.plugins.demux
commands:
- - py.test --pyargs q2_demux
+ - py.test --pyargs q2_demux
about:
home: https://qiime2.org
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-demux (2024.2.0+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Autopkgtest for all supported Python3 versions
+ * Regenerate debian/control from debian/control.in (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Feb 2024 14:48:57 +0100
+
q2-demux (2023.9.1+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -19,9 +19,9 @@ Build-Depends: debhelper-compat (= 13),
python3-skbio,
python3-psutil,
python3-seaborn,
- qiime (>= 2023.9),
- q2-types (>= 2023.9.0-2~),
- q2templates (>= 2023.9)
+ qiime (>= 2024.2),
+ q2-types (>= 2024.2),
+ q2templates (>= 2024.2)
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-demux
Vcs-Git: https://salsa.debian.org/med-team/q2-demux.git
@@ -41,9 +41,9 @@ Depends: ${shlibs:Depends},
python3-yaml,
python3-psutil,
python3-ipywidgets,
- qiime (>= 2023.9),
- q2-types (>= 2023.9),
- q2templates (>= 2023.9),
+ qiime (>= 2024.2),
+ q2-types (>= 2024.2),
+ q2templates (>= 2024.2),
node-d3
Description: QIIME 2 plugin for demultiplexing of sequence reads
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov
+Depends: @, python3-pytest-cov, python3-all
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,4 +18,7 @@ if [ ! -f /usr/lib/python3/dist-packages/pytest_cov/__init__.py ] ; then
fi
# Run build-time tests
-py.test-3 --cov=${pkg}
+for py in $(py3versions -s 2> /dev/null)
+do
+ ${py} -m pytest -v --cov=${pkg}
+done
=====================================
q2_demux/_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: 2023.9.1, Release-2023.9)"
- git_full = "09097f551d09f026b295962441e90b80c0e5ce81"
- git_date = "2023-10-24 18:43:25 +0000"
+ git_refnames = " (tag: 2024.2.0, Release-2024.2)"
+ git_full = "9e6af01fb0eff039b221f95ee596238f96a3b134"
+ git_date = "2024-02-16 21:56:22 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_demux/tests/test_demux.py
=====================================
@@ -19,7 +19,7 @@ import skbio
import qiime2
import numpy.testing as npt
-from qiime2.plugin.testing import TestPluginBase
+from qiime2.plugin.testing import TestPluginBase, assert_no_nans_in_tables
from q2_demux._demux import (BarcodeSequenceFastqIterator,
BarcodePairedSequenceFastqIterator)
from q2_demux import (emp_single, emp_paired, partition_samples_single,
@@ -1269,6 +1269,7 @@ class SummarizeTests(TestPluginBase):
self.assertTrue(os.path.exists(qual_forward_fp))
self.assertTrue(os.path.getsize(qual_forward_fp) > 0)
with open(index_fp, 'r') as fh:
+ assert_no_nans_in_tables(fh)
html = fh.read()
self.assertIn('<th>Minimum</th>\n <td>1</td>', html)
self.assertIn('<th>Maximum</th>\n <td>3</td>', html)
@@ -1305,6 +1306,7 @@ class SummarizeTests(TestPluginBase):
png_fp = os.path.join(output_dir, 'demultiplex-summary.png')
self.assertFalse(os.path.exists(png_fp))
with open(index_fp, 'r') as fh:
+ assert_no_nans_in_tables(fh)
html = fh.read()
self.assertIn('<th>Minimum</th>\n <td>1</td>', html)
self.assertIn('<th>Maximum</th>\n <td>1</td>', html)
View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/compare/a0d93246c282276847b3ec9fbcd9c341cb8b33b8...a2774af6e535396d77a88101822002c4c7fc568a
--
View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/compare/a0d93246c282276847b3ec9fbcd9c341cb8b33b8...a2774af6e535396d77a88101822002c4c7fc568a
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