[med-svn] [Git][med-team/q2-phylogeny][master] 6 commits: Bump versioned Depends
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Jan 14 16:08:24 GMT 2023
Andreas Tille pushed to branch master at Debian Med / q2-phylogeny
Commits:
8ab4f579 by Andreas Tille at 2023-01-14T16:38:53+01:00
Bump versioned Depends
- - - - -
a0fbb4fa by Andreas Tille at 2023-01-14T16:39:12+01:00
New upstream version 2022.11.1
- - - - -
fb81b397 by Andreas Tille at 2023-01-14T16:39:12+01:00
routine-update: New upstream version
- - - - -
5f14909a by Andreas Tille at 2023-01-14T16:39:15+01:00
Update upstream source from tag 'upstream/2022.11.1'
Update to upstream version '2022.11.1'
with Debian dir 7809d479452a016e8a3671d15d17ea36ab138e4b
- - - - -
e3f31e83 by Andreas Tille at 2023-01-14T16:39:22+01:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
0f3a56fc by Andreas Tille at 2023-01-14T17:08:07+01:00
Upload to experimental
- - - - -
7 changed files:
- + .github/workflows/add-to-project-ci.yml
- debian/changelog
- debian/control
- + q2_phylogeny/_examples.py
- q2_phylogeny/_version.py
- q2_phylogeny/plugin_setup.py
- + q2_phylogeny/tests/test_examples.py
Changes:
=====================================
.github/workflows/add-to-project-ci.yml
=====================================
@@ -0,0 +1,21 @@
+name: Add new issues and PRs to triage project board
+
+on:
+ issues:
+ types:
+ - opened
+ pull_request_target:
+ types:
+ - opened
+
+jobs:
+ add-to-project:
+ name: Add issue to project
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/add-to-project at v0.3.0
+ with:
+ project-url: https://github.com/orgs/qiime2/projects/36
+ github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}
+ labeled: skip-triage
+ label-operator: NOT
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+q2-phylogeny (2022.11.1-1) experimental; urgency=medium
+
+ * New upstream version
+ * Bump versioned Depends
+
+ -- Andreas Tille <tille at debian.org> Sat, 14 Jan 2023 16:39:48 +0100
+
q2-phylogeny (2022.8.0-3) unstable; urgency=high
* Team Upload.
=====================================
debian/control
=====================================
@@ -26,8 +26,8 @@ Depends: ${shlibs:Depends},
iqtree,
mafft,
raxml,
- q2-types (>= 2022.8.0),
- q2-alignment (>= 2022.8.0)
+ q2-types (>= 2022.11.1),
+ q2-alignment (>= 2022.11.1)
Description: QIIME 2 plugin for phylogeny
QIIME 2 plugin for phylogenetic reconstruction, and operations on
phylogenetic trees.
=====================================
q2_phylogeny/_examples.py
=====================================
@@ -0,0 +1,31 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+
+rep_seqs_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/rep-seqs-dada2.qza')
+
+
+def phylogeny_align_to_tree_mafft_fasttree(use):
+ rep_seqs = use.init_artifact_from_url('rep_seqs', rep_seqs_url)
+
+ alignment, masked_alignment, tree, rooted_tree = use.action(
+ use.UsageAction('phylogeny', 'align_to_tree_mafft_fasttree'),
+ use.UsageInputs(sequences=rep_seqs),
+ use.UsageOutputNames(
+ alignment='aligned-rep-seqs',
+ masked_alignment='masked-aligned-rep-seqs',
+ tree='unrooted-tree',
+ rooted_tree='rooted-tree',
+ )
+ )
+
+ alignment.assert_output_type('FeatureData[AlignedSequence]')
+ masked_alignment.assert_output_type('FeatureData[AlignedSequence]')
+ tree.assert_output_type('Phylogeny[Unrooted]')
+ rooted_tree.assert_output_type('Phylogeny[Rooted]')
=====================================
q2_phylogeny/_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: 2022.8.0)"
- git_full = "2474e0992e445460e758284a0c66116592b5f464"
- git_date = "2022-08-23 17:49:14 +0000"
+ git_refnames = " (HEAD -> master, tag: 2022.11.1)"
+ git_full = "85dc5265c9b5f9bb45da0ba95b2b053d5211aa90"
+ git_date = "2022-12-21 22:07:16 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_phylogeny/plugin_setup.py
=====================================
@@ -16,6 +16,7 @@ from q2_types.feature_table import (FeatureTable, Frequency,
from q2_types.distance_matrix import DistanceMatrix
import q2_phylogeny
+import q2_phylogeny._examples as ex
_RAXML_MODEL_OPT = ['GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI']
_RAXML_VERSION_OPT = ['Standard', 'SSE3', 'AVX2']
@@ -554,7 +555,11 @@ plugin.pipelines.register_function(
'masked MAFFT alignment from q2-alignment methods, and both '
'the rooted and unrooted phylogenies from q2-phylogeny '
'methods.'
- )
+ ),
+ examples={
+ 'align_to_tree_mafft_fasttree':
+ ex.phylogeny_align_to_tree_mafft_fasttree,
+ }
)
plugin.pipelines.register_function(
=====================================
q2_phylogeny/tests/test_examples.py
=====================================
@@ -0,0 +1,16 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from qiime2.plugin.testing import TestPluginBase
+
+
+class TestUsageExample(TestPluginBase):
+ package = 'q2_phylogeny.tests'
+
+ def test_usage_examples(self):
+ self.execute_examples()
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/623945a3755b589fc687b3f759a7e6874ec726a0...0f3a56fcf5e54f211356e73a641457e106f27352
--
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/623945a3755b589fc687b3f759a7e6874ec726a0...0f3a56fcf5e54f211356e73a641457e106f27352
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