[med-svn] [Git][med-team/q2-taxa][master] 7 commits: Bump versioned Depends
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 13 12:07:45 GMT 2023
Andreas Tille pushed to branch master at Debian Med / q2-taxa
Commits:
69b7cbdc by Andreas Tille at 2023-01-13T12:37:40+01:00
Bump versioned Depends
- - - - -
ef87250d by Andreas Tille at 2023-01-13T12:37:55+01:00
New upstream version 2022.11.1+dfsg
- - - - -
4b720e09 by Andreas Tille at 2023-01-13T12:37:55+01:00
routine-update: New upstream version
- - - - -
949a899c by Andreas Tille at 2023-01-13T12:37:56+01:00
Update upstream source from tag 'upstream/2022.11.1+dfsg'
Update to upstream version '2022.11.1+dfsg'
with Debian dir d06b2bb4ff7d6d228e317b69dcc610572a84d6d4
- - - - -
704ddb53 by Andreas Tille at 2023-01-13T12:37:56+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
4292486e by Andreas Tille at 2023-01-13T12:44:48+01:00
Delaying true testing to autopkgtests since QIIME2 module cannot be registered at build time.
- - - - -
3f98bc9a by Andreas Tille at 2023-01-13T13:07:15+01:00
Upload to experimental
- - - - -
19 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
- debian/rules
- + q2_taxa/_examples.py
- q2_taxa/_version.py
- q2_taxa/plugin_setup.py
- q2_taxa/tests/test_methods.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
+
+
+
+# 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-taxa
+ build-target: dev
+ additional-tests: py.test --pyargs q2_taxa
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+q2-taxa (2022.11.1+dfsg-1) experimental; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Bump versioned Depends
+ * Standards-Version: 4.6.2 (routine-update)
+ * Delaying true testing to autopkgtests since QIIME2 module cannot be
+ registered at build time.
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Jan 2023 12:36:31 +0100
+
q2-taxa (2022.8.0+dfsg-1) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -11,9 +11,9 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest-cov,
python3-pandas,
nodejs,
- 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),
webpack (>= 5.0~),
node-terser-webpack-plugin,
node-babel-loader,
@@ -21,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),
node-natural-sort,
node-thenby,
node-d3
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-taxa
Vcs-Git: https://salsa.debian.org/med-team/q2-taxa.git
Homepage: https://qiime2.org/
@@ -33,9 +33,9 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-pandas,
- qiime (>= 2022.8.1),
- q2templates (>= 2022.8.0),
- q2-types (>= 2022.8.0),
+ qiime (>= 2022.11.1),
+ q2templates (>= 2022.11.1),
+ q2-types (>= 2022.11.1),
node-d3-scale-chromatic,
node-natural-sort,
node-thenby
=====================================
debian/rules
=====================================
@@ -15,9 +15,11 @@ override_dh_auto_build:
cd q2_taxa/assets/barplot && \
webpack --bail
+#FIXME: Delaying true testing to autopkgtests since QIIME2 module cannot be registered
+# at build time.
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_taxa"
+ dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_taxa" || true
endif
override_dh_auto_clean:
=====================================
q2_taxa/_examples.py
=====================================
@@ -0,0 +1,56 @@
+# ----------------------------------------------------------------------------
+# 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.
+# ----------------------------------------------------------------------------
+
+import qiime2
+
+table_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/gut-table.qza')
+taxonomy_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/taxonomy.qza')
+
+metadata_url = (f'https://data.qiime2.org/{qiime2.__release__}/tutorials/'
+ 'moving-pictures/sample_metadata.tsv')
+
+
+def collapse_example(use):
+ table = use.init_artifact_from_url('table', table_url)
+ taxonomy = use.init_artifact_from_url('taxonomy', taxonomy_url)
+
+ collapsed, = use.action(
+ use.UsageAction('taxa', 'collapse'),
+ use.UsageInputs(
+ table=table,
+ taxonomy=taxonomy,
+ level=6,
+ ),
+ use.UsageOutputNames(
+ collapsed_table='collapsed_table_l6',
+ )
+ )
+
+ collapsed.assert_output_type('FeatureTable[Frequency]')
+
+
+def barplot_example(use):
+ table = use.init_artifact_from_url('table', table_url)
+ taxonomy = use.init_artifact_from_url('taxonomy', taxonomy_url)
+ md = use.init_metadata_from_url('sample-metadata', metadata_url)
+
+ viz, = use.action(
+ use.UsageAction('taxa', 'barplot'),
+ use.UsageInputs(
+ table=table,
+ taxonomy=taxonomy,
+ metadata=md,
+ ),
+ use.UsageOutputNames(
+ visualization='taxa-bar-plots',
+ )
+ )
+
+ viz.assert_output_type('Visualization')
=====================================
q2_taxa/_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 = "3c0cf866d308203914ae83e66f7fa21ceb3facae"
- git_date = "2022-08-23 15:52:58 +0000"
+ git_refnames = " (HEAD -> master, tag: 2022.11.1)"
+ git_full = "d3288c4e0882df166b7f40205a83d3cc50318609"
+ git_date = "2022-12-21 21:39:27 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_taxa/plugin_setup.py
=====================================
@@ -15,6 +15,7 @@ from q2_types.feature_table import FeatureTable, Frequency
from . import barplot, collapse, filter_table, filter_seqs
+import q2_taxa._examples as ex
plugin = qiime2.plugin.Plugin(
@@ -57,7 +58,10 @@ plugin.methods.register_function(
name='Collapse features by their taxonomy at the specified level',
description='Collapse groups of features that have the same taxonomic '
'assignment through the specified level. The frequencies of '
- 'all features will be summed when they are collapsed.'
+ 'all features will be summed when they are collapsed.',
+ examples={
+ 'collapse': ex.collapse_example,
+ },
)
plugin.methods.register_function(
@@ -191,5 +195,8 @@ plugin.visualizers.register_function(
description='This visualizer produces an interactive barplot visualization'
' of taxonomies. Interactive features include multi-level '
'sorting, plot recoloring, sample relabeling, and SVG '
- 'figure export.'
+ 'figure export.',
+ examples={
+ 'barplot': ex.barplot_example,
+ },
)
=====================================
q2_taxa/tests/test_methods.py
=====================================
@@ -13,6 +13,7 @@ import biom
import pandas as pd
import pandas.testing as pdt
import qiime2
+from qiime2.plugin.testing import TestPluginBase
from q2_taxa import collapse, filter_table, filter_seqs
@@ -873,3 +874,10 @@ class FilterSeqs(unittest.TestCase):
with self.assertRaisesRegex(ValueError, expected_regex='All.*feat2'):
filter_seqs(seqs, taxonomy, include='bb')
+
+
+class TestUsageExamples(TestPluginBase):
+ package = 'q2_taxa.tests'
+
+ def test_examples(self):
+ self.execute_examples()
View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/98cc283aea21860edfb11899e9509b648c592b89...3f98bc9a1e3df4751ae75cb86bbd428ebb9fd750
--
View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/98cc283aea21860edfb11899e9509b648c592b89...3f98bc9a1e3df4751ae75cb86bbd428ebb9fd750
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