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

[Andreas Tille (@tille)]

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


Commits:
629f6d43 by Andreas Tille at 2024-02-18T15:01:10+01:00
New upstream version 2024.2.0
- - - - -


5 changed files:

- .github/workflows/ci-dev.yaml
- README.md
- 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
 
-![](https://github.com/qiime2/q2-fragment-insertion/workflows/ci/badge.svg)
+![](https://github.com/qiime2/q2-fragment-insertion/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_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/-/commit/629f6d4360395820e5df9ff444fdd905fb85ca0d

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/commit/629f6d4360395820e5df9ff444fdd905fb85ca0d
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