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@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 -- View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/commit/58ecf3af8d243a0d7e52ccb1bbcd34cba0a3bf51 You're receiving this email because of your account on salsa.debian.org.
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