[med-svn] [Git][med-team/q2-fragment-insertion][master] 6 commits: Autopkgtest for all supported Python3 versions
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 18 14:03:35 GMT 2024
Andreas Tille pushed to branch master at Debian Med / q2-fragment-insertion
Commits:
7c1a1e8b by Andreas Tille at 2024-02-18T15:00:56+01:00
Autopkgtest for all supported Python3 versions
- - - - -
7ece59b8 by Andreas Tille at 2024-02-18T15:01:09+01:00
routine-update: New upstream version
- - - - -
629f6d43 by Andreas Tille at 2024-02-18T15:01:10+01:00
New upstream version 2024.2.0
- - - - -
b5ba2fc4 by Andreas Tille at 2024-02-18T15:01:10+01:00
Update upstream source from tag 'upstream/2024.2.0'
Update to upstream version '2024.2.0'
with Debian dir d608289a9bc7757fd5042b7e69bc51d4534f98ef
- - - - -
42f282a5 by Andreas Tille at 2024-02-18T15:01:28+01:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
9050cd3d by Andreas Tille at 2024-02-18T15:02:58+01:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- .github/workflows/ci-dev.yaml
- README.md
- debian/changelog
- debian/control
- debian/tests/control
- debian/tests/run-unit-test
- q2_fragment_insertion/_insertion.py
- q2_fragment_insertion/_version.py
- q2_fragment_insertion/plugin_setup.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-fragment-insertion
-
+
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-fragment-insertion (2024.2.0-1) 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 15:01:28 +0100
+
q2-fragment-insertion (2023.9.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3,
python3-setuptools,
- qiime (>= 2023.9),
+ qiime (>= 2024.2),
python3-pytest <!nocheck>,
python3-pytest-cov <!nocheck>,
python3-biom-format <!nocheck>,
@@ -27,8 +27,8 @@ Depends: ${shlibs:Depends},
${python3:Depends},
python3-biom-format,
python3-skbio,
- qiime (>= 2023.9),
- q2-types (>= 2023.9)
+ qiime (>= 2024.2),
+ q2-types (>= 2024.2)
Recommends: sepp,
python3-ijson,
default-jdk
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,4 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov
+Depends: @, python3-pytest-cov, python3-all
# sepp (>= 4.3.10+dfsg-4)
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,4 +18,7 @@ if [ ! -f /usr/lib/python3/dist-packages/pytest_cov/__init__.py ] ; then
fi
# Run build-time tests
-py.test-3 --cov=${pkg}
+for py in $(py3versions -s 2> /dev/null)
+do
+ ${py} -m pytest -v --cov=${pkg}
+done
=====================================
q2_fragment_insertion/_insertion.py
=====================================
@@ -19,6 +19,7 @@ from q2_types.feature_data import (DNASequencesDirectoryFormat,
DNAFASTAFormat,
DNAIterator)
from q2_types.tree import NewickFormat
+from qiime2.plugin import get_available_cores
from q2_fragment_insertion._format import PlacementsFormat, SeppReferenceDirFmt
@@ -61,6 +62,9 @@ def sepp(representative_sequences: DNASequencesDirectoryFormat,
debug: bool = False,
) -> (NewickFormat, PlacementsFormat):
+ if threads == 0:
+ threads = get_available_cores()
+
placements = 'q2-fragment-insertion_placement.json'
tree = 'q2-fragment-insertion_placement.tog.relabelled.tre'
=====================================
q2_fragment_insertion/_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: 2023.9.0, Release-2023.9)"
- git_full = "998a8dde8ea556003f002eae8c5e6527e132cb81"
- git_date = "2023-10-03 21:58:49 +0000"
+ git_refnames = " (tag: 2024.2.0, Release-2024.2)"
+ git_full = "ac538814710d0feabe680d6411d9cbf7217180a9"
+ git_date = "2024-02-16 21:58:03 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_fragment_insertion/plugin_setup.py
=====================================
@@ -39,7 +39,7 @@ plugin.methods.register_function(
'reference_database': SeppReferenceDatabase,
},
parameters={
- 'threads': qiime2.plugin.Int,
+ 'threads': qiime2.plugin.Threads,
'alignment_subset_size': qiime2.plugin.Int,
'placement_subset_size': qiime2.plugin.Int,
'debug': qiime2.plugin.Bool,
@@ -55,7 +55,8 @@ plugin.methods.register_function(
'representative sequences into.',
},
parameter_descriptions={
- 'threads': 'The number of threads to use.',
+ 'threads': 'The number of threads to use. Pass 0 to use one per '
+ 'available core.',
'alignment_subset_size': 'Each placement subset is further broken '
'into subsets of at most these many '
'sequences and a separate HMM is trained on '
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/b27b52cd479dc2db705e05bcc9036dcddcc92870...9050cd3d129fdba9db1e75981d7517fc797ed4e5
--
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/b27b52cd479dc2db705e05bcc9036dcddcc92870...9050cd3d129fdba9db1e75981d7517fc797ed4e5
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