[med-svn] [Git][med-team/q2-deblur][upstream] New upstream version 2023.9.0
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 30 19:31:10 GMT 2024
Andreas Tille pushed to branch upstream at Debian Med / q2-deblur
Commits:
1a9f3e16 by Andreas Tille at 2024-01-30T20:25:33+01:00
New upstream version 2023.9.0
- - - - -
20 changed files:
- + .github/workflows/add-to-project-ci.yml
- + .github/workflows/ci-dev.yaml
- − .github/workflows/ci.yml
- + .github/workflows/join-release.yaml
- + .github/workflows/tag-release.yaml
- LICENSE
- ci/recipe/meta.yaml
- + ci/recipe/run_test.sh
- q2_deblur/__init__.py
- q2_deblur/_denoise.py
- + q2_deblur/_examples.py
- q2_deblur/_format.py
- q2_deblur/_transformer.py
- q2_deblur/_type.py
- q2_deblur/_version.py
- q2_deblur/_viz_stats.py
- q2_deblur/plugin_setup.py
- q2_deblur/tests/__init__.py
- q2_deblur/tests/test_denoise.py
- setup.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
=====================================
.github/workflows/ci-dev.yaml
=====================================
@@ -0,0 +1,12 @@
+# Example of workflow trigger for calling workflow (the client).
+name: ci-dev
+on:
+ pull_request:
+ branches: ["dev"]
+ push:
+ branches: ["dev"]
+jobs:
+ ci:
+ uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml at dev
+ with:
+ distro: core
\ No newline at end of file
=====================================
.github/workflows/ci.yml deleted
=====================================
@@ -1,55 +0,0 @@
-# This file is automatically generated by busywork.qiime2.org and
-# template-repos - any manual edits made to this file will be erased when
-# busywork performs maintenance updates.
-
-name: ci
-
-on:
- pull_request:
- push:
- branches:
- - master
-
-jobs:
- lint:
- runs-on: ubuntu-latest
- steps:
- - name: checkout source
- uses: actions/checkout at v2
-
- - name: set up python 3.8
- uses: actions/setup-python at v1
- with:
- python-version: 3.8
-
- - name: install dependencies
- run: python -m pip install --upgrade pip
-
- - name: lint
- run: |
- pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- q2lint
- pip install -q flake8
- flake8
-
- build-and-test:
- needs: lint
- strategy:
- matrix:
- os: [ubuntu-latest, macos-latest]
- runs-on: ${{ matrix.os }}
- steps:
- - name: checkout source
- uses: actions/checkout at v2
- with:
- fetch-depth: 0
-
- - name: set up git repo for versioneer
- run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-
- - uses: qiime2/action-library-packaging at alpha1
- with:
- package-name: q2-deblur
- build-target: dev
- additional-tests: py.test --pyargs q2_deblur
- library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.github/workflows/join-release.yaml
=====================================
@@ -0,0 +1,6 @@
+name: join-release
+on:
+ workflow_dispatch: {}
+jobs:
+ release:
+ uses: qiime2/distributions/.github/workflows/lib-join-release.yaml at dev
\ No newline at end of file
=====================================
.github/workflows/tag-release.yaml
=====================================
@@ -0,0 +1,7 @@
+name: tag-release
+on:
+ push:
+ branches: ["Release-*"]
+jobs:
+ tag:
+ uses: qiime2/distributions/.github/workflows/lib-tag-release.yaml at dev
\ No newline at end of file
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2021, QIIME 2 development team.
+Copyright (c) 2016-2023, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
ci/recipe/meta.yaml
=====================================
@@ -18,12 +18,11 @@ requirements:
run:
- python {{ python }}
- - pandas
+ - pandas {{ pandas }}
- numpy
- deblur >=1.0.4
- # deblur doesn't currently work with click 8, so pinning here.
- - click >=7,<8
- - vsearch <=2.7.0
+ - click >=8.1
+ - vsearch <2.23.0
- qiime2 {{ qiime2_epoch }}.*
- q2templates {{ qiime2_epoch }}.*
- q2-types {{ qiime2_epoch }}.*
@@ -33,12 +32,20 @@ test:
- qiime2 >={{ qiime2 }}
- q2templates >={{ q2templates }}
- q2-types >={{ q2_types }}
- - pytest
+ - nose
imports:
- q2_deblur
- qiime2.plugins.deblur
+ commands:
+ - py.test --pyargs q2_deblur
+
+ # uncomment and remove run_test.sh when 1.1.2 lands (which should include:
+ # https://github.com/biocore/deblur/pull/216)
+ # commands:
+ # - pytest --pyargs deblur
+
about:
home: https://qiime2.org
license: BSD-3-Clause
=====================================
ci/recipe/run_test.sh
=====================================
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+git clone https://github.com/biocore/deblur deblur-upstream
+nosetests --with-doctest deblur-upstream
+rm -rf deblur-upstream
+
+py.test --pyargs q2_deblur
=====================================
q2_deblur/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/_examples.py
=====================================
@@ -0,0 +1,51 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, 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.
+# ----------------------------------------------------------------------------
+
+
+demuxed_seqs_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/demux-filtered.qza')
+denoise_stats_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/deblur-stats.qza')
+
+
+def denoise_16S_example(use):
+ demuxed = use.init_artifact_from_url('demux-filtered', demuxed_seqs_url)
+
+ rep_seqs, table, stats = use.action(
+ use.UsageAction('deblur', 'denoise_16S'),
+ use.UsageInputs(
+ demultiplexed_seqs=demuxed,
+ trim_length=120,
+ sample_stats=True,
+ ),
+ use.UsageOutputNames(
+ representative_sequences='representative_sequences',
+ table='table',
+ stats='denoising_stats'
+ )
+ )
+
+ rep_seqs.assert_output_type('FeatureData[Sequence]')
+ table.assert_output_type('FeatureTable[Frequency]')
+ stats.assert_output_type('DeblurStats')
+
+
+def visualize_stats_example(use):
+ stats = use.init_artifact_from_url('deblur-stats', denoise_stats_url)
+
+ viz, = use.action(
+ use.UsageAction('deblur', 'visualize_stats'),
+ use.UsageInputs(
+ deblur_stats=stats
+ ),
+ use.UsageOutputNames(
+ visualization='deblur-stats-viz'
+ )
+ )
+
+ viz.assert_output_type('Visualization')
=====================================
q2_deblur/_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/_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: 2021.11.0)"
- git_full = "d66965f39a467842629ce28fc7c7e175cd703cfc"
- git_date = "2021-11-22 23:11:49 +0000"
+ git_refnames = " (tag: 2023.9.0, Release-2023.9)"
+ git_full = "8511539162447c597092f7b89e4cea128d87ebbd"
+ git_date = "2023-10-03 21:52:44 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_deblur/_viz_stats.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -13,6 +13,7 @@ from q2_types.sample_data import SampleData
from q2_types.per_sample_sequences import (SequencesWithQuality,
PairedEndSequencesWithQuality,
JoinedSequencesWithQuality)
+import q2_deblur._examples as ex
import q2_deblur
@@ -110,7 +111,10 @@ plugin.methods.register_function(
'platform. The reference is only used to assess whether each '
'sequence is likely to be 16S by a local alignment using '
'SortMeRNA with a permissive e-value; the reference is not '
- 'used to characterize the sequences.')
+ 'used to characterize the sequences.'),
+ examples={
+ 'denoise_16S': ex.denoise_16S_example
+ },
)
@@ -153,7 +157,10 @@ plugin.visualizers.register_function(
},
parameter_descriptions={},
name='Visualize Deblur stats per sample.',
- description='Display Deblur statistics per sample'
+ description='Display Deblur statistics per sample',
+ examples={
+ 'visualize_stats': ex.visualize_stats_example,
+ },
)
importlib.import_module('q2_deblur._transformer')
=====================================
q2_deblur/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_deblur/tests/test_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -222,5 +222,12 @@ class TestDenoiseOther(TestPluginBase):
denoise_other(self.demux_seqs, self.ref, 100, min_reads=-1)
+class TestUsageExamples(TestPluginBase):
+ package = 'q2_deblur.tests'
+
+ def test_examples(self):
+ self.execute_examples()
+
+
if __name__ == '__main__':
unittest.main()
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-deblur/-/commit/1a9f3e1699601922b97d440b3f72308dd5564d7d
--
View it on GitLab: https://salsa.debian.org/med-team/q2-deblur/-/commit/1a9f3e1699601922b97d440b3f72308dd5564d7d
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