[med-svn] [Git][med-team/q2-quality-filter][master] 6 commits: Bump versioned Depends

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Jan 17 11:18:33 GMT 2023



Andreas Tille pushed to branch master at Debian Med / q2-quality-filter


Commits:
cfd0d8ee by Andreas Tille at 2023-01-17T11:39:58+01:00
Bump versioned Depends

- - - - -
9f0e6c90 by Andreas Tille at 2023-01-17T11:40:11+01:00
New upstream version 2022.11.1
- - - - -
2092c391 by Andreas Tille at 2023-01-17T11:40:11+01:00
routine-update: New upstream version

- - - - -
e223cfd5 by Andreas Tille at 2023-01-17T11:40:12+01:00
Update upstream source from tag 'upstream/2022.11.1'

Update to upstream version '2022.11.1'
with Debian dir 256c7fd47919a8408cd161b4a8671d6e47088c35
- - - - -
1925ab39 by Andreas Tille at 2023-01-17T11:40:12+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
e855b658 by Andreas Tille at 2023-01-17T11:49:51+01:00
Upload to experimental

- - - - -


18 changed files:

- + .github/CONTRIBUTING.md
- + .github/ISSUE_TEMPLATE/1-user-need-help.md
- + .github/ISSUE_TEMPLATE/2-dev-need-help.md
- + .github/ISSUE_TEMPLATE/3-found-bug.md
- + .github/ISSUE_TEMPLATE/4-make-better.md
- + .github/ISSUE_TEMPLATE/5-make-new.md
- + .github/ISSUE_TEMPLATE/6-where-to-go.md
- + .github/SUPPORT.md
- + .github/pull_request_template.md
- + .github/rubric.png
- + .github/workflows/add-to-project-ci.yml
- + .github/workflows/ci.yml
- debian/changelog
- debian/control
- + q2_quality_filter/_examples.py
- q2_quality_filter/_version.py
- q2_quality_filter/plugin_setup.py
- q2_quality_filter/test/test_filter.py


Changes:

=====================================
.github/CONTRIBUTING.md
=====================================
@@ -0,0 +1,23 @@
+# Contributing to this project
+
+Thanks for thinking of us :heart: :tada: - we would love a helping hand!
+
+## I just have a question
+
+> Note: Please don't file an issue to ask a question. You'll get faster results
+> by using the resources below.
+
+### QIIME 2 Users
+
+Check out the [User Docs](https://docs.qiime2.org) - there are many tutorials,
+walkthroughs, and guides available. If you still need help, please visit us at
+the [QIIME 2 Forum](https://forum.qiime2.org/c/user-support).
+
+### QIIME 2 Developers
+
+Check out the [Developer Docs](https://dev.qiime2.org) - there are many
+tutorials, walkthroughs, and guides available. If you still need help, please
+visit us at the [QIIME 2 Forum](https://forum.qiime2.org/c/dev-discussion).
+
+This document is based heavily on the following:
+https://github.com/atom/atom/blob/master/CONTRIBUTING.md


=====================================
.github/ISSUE_TEMPLATE/1-user-need-help.md
=====================================
@@ -0,0 +1,14 @@
+---
+name: I am a user and I need help with QIIME 2...
+about: I am using QIIME 2 and have a question or am experiencing a problem
+
+---
+
+Have you had a chance to check out the docs?
+https://docs.qiime2.org
+There are many tutorials, walkthroughs, and guides available.
+
+If you still need help, please visit:
+https://forum.qiime2.org/c/user-support
+
+Help requests filed here will not be answered.


=====================================
.github/ISSUE_TEMPLATE/2-dev-need-help.md
=====================================
@@ -0,0 +1,12 @@
+---
+name: I am a developer and I need help with QIIME 2...
+about: I am developing a QIIME 2 plugin or interface and have a question or a problem
+
+---
+
+Have you had a chance to check out the developer docs?
+https://dev.qiime2.org
+There are many tutorials, walkthroughs, and guides available.
+
+If you still need help, please visit:
+https://forum.qiime2.org/c/dev-discussion


=====================================
.github/ISSUE_TEMPLATE/3-found-bug.md
=====================================
@@ -0,0 +1,36 @@
+---
+name: I am a developer and I found a bug...
+about: I am a developer and I found a bug that I can describe
+
+---
+
+**Bug Description**
+A clear and concise description of what the bug is.
+
+**Steps to reproduce the behavior**
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Computation Environment**
+- OS: [e.g. macOS High Sierra]
+- QIIME 2 Release [e.g. 2018.6]
+
+**Questions**
+1. An enumerated list with any questions about the problem here.
+2. If not applicable, please delete this section.
+
+**Comments**
+1. An enumerated list with any other context or comments about the problem here.
+2. If not applicable, please delete this section.
+
+**References**
+1. An enumerated list of links to relevant references, including forum posts, stack overflow, etc.
+2. If not applicable, please delete this section.


=====================================
.github/ISSUE_TEMPLATE/4-make-better.md
=====================================
@@ -0,0 +1,26 @@
+---
+name: I am a developer and I have an idea for an improvement...
+about: I am a developer and I have an idea for an improvement to existing functionality
+
+---
+
+**Improvement Description**
+A clear and concise description of what the improvement is.
+
+**Current Behavior**
+Please provide a brief description of the current behavior.
+
+**Proposed Behavior**
+Please provide a brief description of the proposed behavior.
+
+**Questions**
+1. An enumerated list of questions related to the proposal.
+2. If not applicable, please delete this section.
+
+**Comments**
+1. An enumerated list of comments related to the proposal that don't fit anywhere else.
+2. If not applicable, please delete this section.
+
+**References**
+1. An enumerated list of links to relevant references, including forum posts, stack overflow, etc.
+2. If not applicable, please delete this section.


=====================================
.github/ISSUE_TEMPLATE/5-make-new.md
=====================================
@@ -0,0 +1,26 @@
+---
+name: I am a developer and I have an idea for a new feature...
+about: I am a developer and I have an idea for new functionality
+
+---
+
+**Addition Description**
+A clear and concise description of what the addition is.
+
+**Current Behavior**
+Please provide a brief description of the current behavior, if applicable.
+
+**Proposed Behavior**
+Please provide a brief description of the proposed behavior.
+
+**Questions**
+1. An enumerated list of questions related to the proposal.
+2. If not applicable, please delete this section.
+
+**Comments**
+1. An enumerated list of comments related to the proposal that don't fit anywhere else.
+2. If not applicable, please delete this section.
+
+**References**
+1. An enumerated list of links to relevant references, including forum posts, stack overflow, etc.
+2. If not applicable, please delete this section.


=====================================
.github/ISSUE_TEMPLATE/6-where-to-go.md
=====================================
@@ -0,0 +1,147 @@
+---
+name: I don't know where to file my issue...
+about: I am a developer and I don't know which repo to file this in
+
+---
+
+The repos within the QIIME 2 GitHub Organization are listed below, with a brief description about the repo.
+
+Sorted alphabetically by repo name.
+
+- The CI automation engine that builds and distributes QIIME 2
+  https://github.com/qiime2/busywork/issues
+
+- A Concourse resource for working with conda
+  https://github.com/qiime2/conda-channel-resource/issues
+
+- Web app for vanity URLs for QIIME 2 data assets
+  https://github.com/qiime2/data.qiime2.org/issues
+
+- The Developer Documentation
+  https://github.com/qiime2/dev-docs/issues
+
+- A discourse plugin for handling queued/unqueued topics
+  https://github.com/qiime2/discourse-unhandled-tagger/issues
+
+- The User Documentation
+  https://github.com/qiime2/docs/issues
+
+- Rendered QIIME 2 environment files for conda
+  https://github.com/qiime2/environment-files/issues
+
+- Google Sheets Add-On for validating tabular data
+  https://github.com/qiime2/Keemei/issues
+
+- A docker image for linux-based busywork workers
+  https://github.com/qiime2/linux-worker-docker/issues
+
+- Official project logos
+  https://github.com/qiime2/logos/issues
+
+- The q2-alignment plugin
+  https://github.com/qiime2/q2-alignment/issues
+
+- The q2-composition plugin
+  https://github.com/qiime2/q2-composition/issues
+
+- The q2-cutadapt plugin
+  https://github.com/qiime2/q2-cutadapt/issues
+
+- The q2-dada2 plugin
+  https://github.com/qiime2/q2-dada2/issues
+
+- The q2-deblur plugin
+  https://github.com/qiime2/q2-deblur/issues
+
+- The q2-demux plugin
+  https://github.com/qiime2/q2-demux/issues
+
+- The q2-diversity plugin
+  https://github.com/qiime2/q2-diversity/issues
+
+- The q2-diversity-lib plugin
+  https://github.com/qiime2/q2-diversity-lib/issues
+
+- The q2-emperor plugin
+  https://github.com/qiime2/q2-emperor/issues
+
+- The q2-feature-classifier plugin
+  https://github.com/qiime2/q2-feature-classifier/issues
+
+- The q2-feature-table plugin
+  https://github.com/qiime2/q2-feature-table/issues
+
+- The q2-fragment-insertion plugin
+  https://github.com/qiime2/q2-fragment-insertion/issues
+
+- The q2-gneiss plugin
+  https://github.com/qiime2/q2-gneiss/issues
+
+- The q2-longitudinal plugin
+  https://github.com/qiime2/q2-longitudinal/issues
+
+- The q2-metadata plugin
+  https://github.com/qiime2/q2-metadata/issues
+
+- The q2-phylogeny plugin
+  https://github.com/qiime2/q2-phylogeny/issues
+
+- The q2-quality-control plugin
+  https://github.com/qiime2/q2-quality-control/issues
+
+- The q2-quality-filter plugin
+  https://github.com/qiime2/q2-quality-filter/issues
+
+- The q2-sample-classifier plugin
+  https://github.com/qiime2/q2-sample-classifier/issues
+
+- The q2-shogun plugin
+  https://github.com/qiime2/q2-shogun/issues
+
+- The q2-taxa plugin
+  https://github.com/qiime2/q2-taxa/issues
+
+- The q2-types plugin
+  https://github.com/qiime2/q2-types/issues
+
+- The q2-vsearch plugin
+  https://github.com/qiime2/q2-vsearch/issues
+
+- The CLI interface
+  https://github.com/qiime2/q2cli/issues
+
+- The prototype CWL interface
+  https://github.com/qiime2/q2cwl/issues
+
+- The prototype Galaxy interface
+  https://github.com/qiime2/q2galaxy/issues
+
+- An internal tool for ensuring header text and copyrights are present
+  https://github.com/qiime2/q2lint/issues
+
+- The prototype GUI interface
+  https://github.com/qiime2/q2studio/issues
+
+- A base template for use in official QIIME 2 plugins
+  https://github.com/qiime2/q2templates/issues
+
+- The read-only web interface at view.qiime2.org
+  https://github.com/qiime2/q2view/issues
+
+- The QIIME 2 homepage at qiime2.org
+  https://github.com/qiime2/qiime2.github.io/issues
+
+- The QIIME 2 framework
+  https://github.com/qiime2/qiime2/issues
+
+- Centralized templates for repo assets
+  https://github.com/qiime2/template-repo/issues
+
+- Scripts for building QIIME 2 VMs
+  https://github.com/qiime2/vm-playbooks/issues
+
+- Scripts for building QIIME 2 workshop clusters
+  https://github.com/qiime2/workshop-playbooks/issues
+
+- The web app that runs workshops.qiime2.org
+  https://github.com/qiime2/workshops.qiime2.org/issues


=====================================
.github/SUPPORT.md
=====================================
@@ -0,0 +1,112 @@
+# QIIME 2 Users
+
+Check out the [User Docs](https://docs.qiime2.org) - there are many tutorials,
+walkthroughs, and guides available. If you still need help, please visit us at
+the [QIIME 2 Forum](https://forum.qiime2.org/c/user-support).
+
+# QIIME 2 Developers
+
+Check out the [Developer Docs](https://dev.qiime2.org) - there are many
+tutorials, walkthroughs, and guides available. If you still need help, please
+visit us at the [QIIME 2 Forum](https://forum.qiime2.org/c/dev-discussion).
+
+# General Bug/Issue Triage Discussion
+
+![rubric](./rubric.png?raw=true)
+
+# Projects/Repositories in the QIIME 2 GitHub Organization
+
+Sorted alphabetically by repo name.
+
+- [busywork](https://github.com/qiime2/busywork/issues)
+  | The CI automation engine that builds and distributes QIIME 2
+- [conda-channel-resource](https://github.com/qiime2/conda-channel-resource/issues)
+  | A Concourse resource for working with conda
+- [data.qiime2.org](https://github.com/qiime2/data.qiime2.org/issues)
+  | Web app for vanity URLs for QIIME 2 data assets
+- [dev-docs](https://github.com/qiime2/dev-docs/issues)
+  | The Developer Documentation
+- [discourse-unhandled-tagger](https://github.com/qiime2/discourse-unhandled-tagger/issues)
+  | A discourse plugin for handling queued/unqueued topics
+- [docs](https://github.com/qiime2/docs/issues)
+  | The User Documentation
+- [environment-files](https://github.com/qiime2/environment-files/issues)
+  | Rendered QIIME 2 environment files for conda
+- [Keemei](https://github.com/qiime2/Keemei/issues)
+  | Google Sheets Add-On for validating tabular data
+- [linux-worker-docker](https://github.com/qiime2/linux-worker-docker/issues)
+  | A docker image for linux-based busywork workers
+- [logos](https://github.com/qiime2/logos/issues)
+  | Official project logos
+- [q2-alignment](https://github.com/qiime2/q2-alignment/issues)
+  | The q2-alignment plugin
+- [q2-composition](https://github.com/qiime2/q2-composition/issues)
+  | The q2-composition plugin
+- [q2-cutadapt](https://github.com/qiime2/q2-cutadapt/issues)
+  | The q2-cutadapt plugin
+- [q2-dada2](https://github.com/qiime2/q2-dada2/issues)
+  | The q2-dada2 plugin
+- [q2-deblur](https://github.com/qiime2/q2-deblur/issues)
+  | The q2-deblur plugin
+- [q2-demux](https://github.com/qiime2/q2-demux/issues)
+  | The q2-demux plugin
+- [q2-diversity](https://github.com/qiime2/q2-diversity/issues)
+  | The q2-diversity plugin
+- [q2-diversity-lib](https://github.com/qiime2/q2-diversity-lib/issues)
+  | The q2-diversity-lib plugin
+- [q2-emperor](https://github.com/qiime2/q2-emperor/issues)
+  | The q2-emperor plugin
+- [q2-feature-classifier](https://github.com/qiime2/q2-feature-classifier/issues)
+  | The q2-feature-classifier plugin
+- [q2-feature-table](https://github.com/qiime2/q2-feature-table/issues)
+  | The q2-feature-table plugin
+- [q2-fragment-insertion](https://github.com/qiime2/q2-fragment-insertion/issues)
+  | The q2-fragment-insertion plugin
+- [q2-gneiss](https://github.com/qiime2/q2-gneiss/issues)
+  | The q2-gneiss plugin
+- [q2-longitudinal](https://github.com/qiime2/q2-longitudinal/issues)
+  | The q2-longitudinal plugin
+- [q2-metadata](https://github.com/qiime2/q2-metadata/issues)
+  | The q2-metadata plugin
+- [q2-phylogeny](https://github.com/qiime2/q2-phylogeny/issues)
+  | The q2-phylogeny plugin
+- [q2-quality-control](https://github.com/qiime2/q2-quality-control/issues)
+  | The q2-quality-control plugin
+- [q2-quality-filter](https://github.com/qiime2/q2-quality-filter/issues)
+  | The q2-quality-filter plugin
+- [q2-sample-classifier](https://github.com/qiime2/q2-sample-classifier/issues)
+  | The q2-sample-classifier plugin
+- [q2-shogun](https://github.com/qiime2/q2-shogun/issues)
+  | The q2-shogun plugin
+- [q2-taxa](https://github.com/qiime2/q2-taxa/issues)
+  | The q2-taxa plugin
+- [q2-types](https://github.com/qiime2/q2-types/issues)
+  | The q2-types plugin
+- [q2-vsearch](https://github.com/qiime2/q2-vsearch/issues)
+  | The q2-vsearch plugin
+- [q2cli](https://github.com/qiime2/q2cli/issues)
+  | The CLI interface
+- [q2cwl](https://github.com/qiime2/q2cwl/issues)
+  | The prototype CWL interface
+- [q2galaxy](https://github.com/qiime2/q2galaxy/issues)
+  | The prototype Galaxy interface
+- [q2lint](https://github.com/qiime2/q2lint/issues)
+  | An internal tool for ensuring header text and copyrights are present
+- [q2studio](https://github.com/qiime2/q2studio/issues)
+  | The prototype GUI interface
+- [q2templates](https://github.com/qiime2/q2templates/issues)
+  | A base template for use in official QIIME 2 plugins
+- [q2view](https://github.com/qiime2/q2view/issues)
+  | The read-only web interface at view.qiime2.org
+- [qiime2.github.io](https://github.com/qiime2/qiime2.github.io/issues)
+  | The QIIME 2 homepage at qiime2.org
+- [qiime2](https://github.com/qiime2/qiime2/issues)
+  | The QIIME 2 framework
+- [template-repo](https://github.com/qiime2/template-repo/issues)
+  | Centralized templates for repo assets
+- [vm-playbooks](https://github.com/qiime2/vm-playbooks/issues)
+  | Scripts for building QIIME 2 VMs
+- [workshop-playbooks](https://github.com/qiime2/workshop-playbooks/issues)
+  | Scripts for building QIIME 2 workshop clusters
+- [workshops.qiime2.org](https://github.com/qiime2/workshops.qiime2.org/issues)
+  | The web app that runs workshops.qiime2.org


=====================================
.github/pull_request_template.md
=====================================
@@ -0,0 +1,11 @@
+Brief summary of the Pull Request, including any issues it may fix using the GitHub closing syntax:
+
+https://help.github.com/articles/closing-issues-using-keywords/
+
+Also, include any co-authors or contributors using the GitHub coauthor tag:
+
+https://help.github.com/articles/creating-a-commit-with-multiple-authors/
+
+---
+
+Include any questions for reviewers, screenshots, sample outputs, etc.


=====================================
.github/rubric.png
=====================================
Binary files /dev/null and b/.github/rubric.png differ


=====================================
.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.yml
=====================================
@@ -0,0 +1,55 @@
+# 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-quality-filter
+        build-target: dev
+        additional-tests: py.test --pyargs q2_quality_filter
+        library-token: ${{ secrets.LIBRARY_TOKEN }}


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-quality-filter (2022.11.1-1) experimental; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Bump versioned Depends
+  * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 17 Jan 2023 11:40:29 +0100
+
 q2-quality-filter (2022.8.0-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -9,10 +9,10 @@ Build-Depends: debhelper-compat (= 13),
                python3,
                python3-setuptools,
                python3-pytest,
-               qiime (>= 2022.8.1),
-               q2templates (>= 2022.8.0),
-               q2-types (>= 2022.8.0)
-Standards-Version: 4.6.1
+               qiime (>= 2022.11.1),
+               q2templates (>= 2022.11.1),
+               q2-types (>= 2022.11.1)
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/q2-quality-filter
 Vcs-Git: https://salsa.debian.org/med-team/q2-quality-filter.git
 Homepage: https://qiime2.org/
@@ -24,9 +24,9 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends},
          python3-pandas,
-         qiime (>= 2022.8.1),
-         q2templates (>= 2022.8.0),
-         q2-types (>= 2022.8.0)
+         qiime (>= 2022.11.1),
+         q2templates (>= 2022.11.1),
+         q2-types (>= 2022.11.1)
 Description: QIIME2 plugin for PHRED-based filtering and trimming
  QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
  package with a focus on data and analysis transparency. QIIME 2 enables


=====================================
q2_quality_filter/_examples.py
=====================================
@@ -0,0 +1,27 @@
+# ----------------------------------------------------------------------------
+# 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.
+# ----------------------------------------------------------------------------
+demuxed_seqs_url = ('https://data.qiime2.org/usage-examples/moving-pictures/'
+                    'demux.qza')
+
+
+def q_score_example(use):
+    demuxed = use.init_artifact_from_url('demuxed_seqs', demuxed_seqs_url)
+
+    filtered_seqs, stats = use.action(
+        use.UsageAction('quality_filter', 'q_score'),
+        use.UsageInputs(
+            demux=demuxed
+        ),
+        use.UsageOutputNames(
+            filtered_sequences='dumux-filtered',
+            filter_stats='demux_filter_stats'
+        )
+    )
+
+    filtered_seqs.assert_output_type('SampleData[SequencesWithQuality]')
+    stats.assert_output_type('QualityFilterStats')


=====================================
q2_quality_filter/_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 = "6404123c6eccb46707f06109d8181992119d326b"
-    git_date = "2022-08-23 17:49:37 +0000"
+    git_refnames = " (HEAD -> master, tag: 2022.11.1)"
+    git_full = "c5c78e402a3b50168a360c1dd1b3ee9ddf2b435c"
+    git_date = "2022-12-21 21:39:48 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 


=====================================
q2_quality_filter/plugin_setup.py
=====================================
@@ -18,6 +18,7 @@ import q2_quality_filter
 from q2_quality_filter._type import QualityFilterStats
 from q2_quality_filter._format import (QualityFilterStatsFmt,
                                        QualityFilterStatsDirFmt)
+import q2_quality_filter._examples as ex
 
 citations = qiime2.plugin.Citations.load(
     'citations.bib', package='q2_quality_filter')
@@ -95,7 +96,10 @@ plugin.methods.register_function(
     output_descriptions=_q_score_output_descriptions,
     name='Quality filter based on sequence quality scores.',
     description=('This method filters sequence based on quality scores and '
-                 'the presence of ambiguous base calls.')
+                 'the presence of ambiguous base calls.'),
+    examples={
+        'q_score': ex.q_score_example,
+    },
 )
 
 importlib.import_module('q2_quality_filter._transformer')


=====================================
q2_quality_filter/test/test_filter.py
=====================================
@@ -351,5 +351,12 @@ class TransformerTests(TestPluginBase):
         self.assertEqual(obs.id_header, 'sample-id')
 
 
+class TestUsageExamples(TestPluginBase):
+    package = 'q2_quality_filter.test'
+
+    def test_examples(self):
+        self.execute_examples()
+
+
 if __name__ == '__main__':
     unittest.main()



View it on GitLab: https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d9d3b2745bce44b9ef3e2cd05f9d335c6ef3d834...e855b65817d235602c2cacadbffae7363d8c735a

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d9d3b2745bce44b9ef3e2cd05f9d335c6ef3d834...e855b65817d235602c2cacadbffae7363d8c735a
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