[med-svn] [Git][med-team/q2-alignment][master] 5 commits: New upstream version 2024.2.0
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 18 13:40:42 GMT 2024
Andreas Tille pushed to branch master at Debian Med / q2-alignment
Commits:
58ecf3af by Andreas Tille at 2024-02-18T12:45:14+01:00
New upstream version 2024.2.0
- - - - -
fc1a076c by Andreas Tille at 2024-02-18T12:45:14+01:00
routine-update: New upstream version
- - - - -
9802577e by Andreas Tille at 2024-02-18T12:45:14+01:00
Update upstream source from tag 'upstream/2024.2.0'
Update to upstream version '2024.2.0'
with Debian dir 6733bac3af74cdcc696809a0d2cdfb6f84612b5d
- - - - -
89a937d3 by Andreas Tille at 2024-02-18T12:45:41+01:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
b484335c by Andreas Tille at 2024-02-18T14:38:16+01:00
Upload to unstable
- - - - -
8 changed files:
- .github/workflows/ci-dev.yaml
- README.md
- debian/changelog
- debian/control
- q2_alignment/_mafft.py
- q2_alignment/_version.py
- q2_alignment/plugin_setup.py
- q2_alignment/tests/test_mafft.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-alignment
-
+
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 +1,11 @@
+q2-alignment (2024.2.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Regenerate debian/control from debian/control.in (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Feb 2024 12:45:41 +0100
+
q2-alignment (2023.9.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -11,8 +11,8 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-skbio,
python3-pytest-cov,
- qiime (>= 2023.9),
- q2-types (>= 2023.9),
+ qiime (>= 2024.2),
+ q2-types (>= 2024.2),
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 (>= 2023.9),
- q2-types (>= 2023.9)
+ qiime (>= 2024.2),
+ q2-types (>= 2024.2)
Suggests: sina
Description: QIIME 2 plugin for generating and manipulating alignments
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
=====================================
q2_alignment/_mafft.py
=====================================
@@ -79,7 +79,7 @@ def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments):
# mafft's signal for utilizing all cores is -1. We want to our users
# to enter auto for using all cores. This is to prevent any confusion and
# to keep the UX consisent.
- if n_threads == 'auto':
+ if n_threads == 0:
n_threads = -1
# `--inputorder` must be turned on because we need the input and output in
=====================================
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: 2023.9.0, Release-2023.9)"
- git_full = "53e02d286914e927f233ed38757058607b1fce00"
- git_date = "2023-10-03 21:50:02 +0000"
+ git_refnames = " (tag: 2024.2.0, Release-2024.2)"
+ git_full = "8d0288a5cf8784a687e940f188889477252b0c27"
+ git_date = "2024-02-16 21:54:40 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_alignment/plugin_setup.py
=====================================
@@ -7,7 +7,7 @@
# ----------------------------------------------------------------------------
from qiime2.plugin import (
- Plugin, Float, Int, Bool, Range, Citations, Str, Choices)
+ Plugin, Float, Bool, Range, Citations, Threads)
from q2_types.feature_data import FeatureData, Sequence, AlignedSequence
import q2_alignment
@@ -26,7 +26,7 @@ plugin = Plugin(
plugin.methods.register_function(
function=q2_alignment.mafft,
inputs={'sequences': FeatureData[Sequence]},
- parameters={'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
+ parameters={'n_threads': Threads,
'parttree': Bool},
outputs=[('alignment', FeatureData[AlignedSequence])],
input_descriptions={'sequences': 'The sequences to be aligned.'},
@@ -45,7 +45,7 @@ plugin.methods.register_function(
function=q2_alignment.mafft_add,
inputs={'alignment': FeatureData[AlignedSequence],
'sequences': FeatureData[Sequence]},
- parameters={'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
+ parameters={'n_threads': Threads,
'parttree': Bool,
'addfragments': Bool},
outputs=[('expanded_alignment', FeatureData[AlignedSequence])],
=====================================
q2_alignment/tests/test_mafft.py
=====================================
@@ -45,7 +45,7 @@ class MafftTests(TestPluginBase):
input_sequences, exp = self._prepare_sequence_data()
with redirected_stdio(stderr=os.devnull):
- result = mafft(input_sequences, n_threads='auto')
+ result = mafft(input_sequences, n_threads=0)
obs = skbio.io.read(str(result), into=skbio.TabularMSA,
constructor=skbio.DNA)
self.assertEqual(obs, exp)
View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/compare/addbfe6ff9e3d9ece6e6184467c1320ea88d72ea...b484335c49caafb0439d8637af3e80c5a9daedd6
--
View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/compare/addbfe6ff9e3d9ece6e6184467c1320ea88d72ea...b484335c49caafb0439d8637af3e80c5a9daedd6
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