[med-svn] [Git][med-team/q2-alignment][upstream] New upstream version 2024.2.0

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / q2-alignment


Commits:
58ecf3af by Andreas Tille at 2024-02-18T12:45:14+01:00
New upstream version 2024.2.0
- - - - -


6 changed files:

- .github/workflows/ci-dev.yaml
- README.md
- 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
 
-![](https://github.com/qiime2/q2-alignment/workflows/ci/badge.svg)
+![](https://github.com/qiime2/q2-alignment/workflows/ci-dev/badge.svg)
 
 This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
\ No newline at end of file


=====================================
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/-/commit/58ecf3af8d243a0d7e52ccb1bbcd34cba0a3bf51

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View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/commit/58ecf3af8d243a0d7e52ccb1bbcd34cba0a3bf51
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