Andreas Tille pushed to branch upstream at Debian Med / q2-phylogeny
Commits: a0fbb4fa by Andreas Tille at 2023-01-14T16:39:12+01:00 New upstream version 2022.11.1 - - - - - 5 changed files: - + .github/workflows/add-to-project-ci.yml - + 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/[email protected] + with: + project-url: https://github.com/orgs/qiime2/projects/36 + github-token: ${{ secrets.ADD_TO_PROJECT_PAT }} + labeled: skip-triage + label-operator: NOT ===================================== 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/-/commit/a0fbb4fa42c476c2f2b1085dcb6a147951d18a86 -- View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/commit/a0fbb4fa42c476c2f2b1085dcb6a147951d18a86 You're receiving this email because of your account on salsa.debian.org.
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