[med-svn] [Git][med-team/q2-feature-table][upstream] New upstream version 2022.8.1+dfsg

Andreas Tille (@tille) gitlab at salsa.debian.org
Mon Dec 12 06:44:43 GMT 2022 


Andreas Tille pushed to branch upstream at Debian Med / q2-feature-table


Commits:
dc2dbb60 by Andreas Tille at 2022-10-07T16:28:49+02:00
New upstream version 2022.8.1+dfsg
- - - - -


14 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/ci.yml
- q2_feature_table/_summarize/_vega_spec.py
- q2_feature_table/_version.py
- q2_feature_table/tests/test_summarize.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/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:
+      - 2022.8-patches
+
+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-feature-table
+        build-target: release
+        additional-tests: py.test --pyargs q2_feature_table
+        library-token: ${{ secrets.LIBRARY_TOKEN }}


=====================================
q2_feature_table/_summarize/_vega_spec.py
=====================================
@@ -15,6 +15,9 @@ def vega_spec(sample_metadata, sample_frequencies):
     sample_metadata = sample_metadata.filter_ids(
         sample_frequencies.index)
     df = sample_metadata.to_dataframe()
+    # Set each column to object so that None remains instead of being converted
+    # back into an appropriate null for the column's dtype
+    df = df.astype(object)
     df = df.where(pd.notnull(df), None)
     # create data in json format for Vega
     for i, row in df.iterrows():


=====================================
q2_feature_table/_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 = "ae4f0a8d29d4a943fae8de7c0ba58019ac609c9c"
-    git_date = "2022-08-23 15:51:36 +0000"
+    git_refnames = " (tag: 2022.8.1, 2022.8-patches)"
+    git_full = "90a5137f0c0050bd09e66265b84df615f20c4240"
+    git_date = "2022-09-06 14:01:49 -0700"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 


=====================================
q2_feature_table/tests/test_summarize.py
=====================================
@@ -300,6 +300,20 @@ class SummarizeTests(TestCase):
                           'SampleType': 'gut'}, 'frequency': 5.0}],
                         spec['data'][0]['values'])
 
+    def test_vega_spec_nandling(self):
+        df = pd.DataFrame({'a': [0.5, float('nan')]})
+        df.index = df.index.map(str)
+        df.index.name = 'id'
+        md = qiime2.Metadata(df)
+        sample_freqs = pd.Series([10, 50])
+        sample_freqs.index = sample_freqs.index.map(str)
+
+        spec = vega_spec(md, sample_freqs)
+        exp = [{'frequency': 10, 'id': '0', 'metadata': {'a': 0.5}},
+               {'frequency': 50, 'id': '1', 'metadata': {'a': None}}]
+
+        self.assertEqual(spec['data'][0]['values'], exp)
+
 
 if __name__ == "__main__":
     main()



View it on GitLab: https://salsa.debian.org/med-team/q2-feature-table/-/commit/dc2dbb601821704c5467ccbc407c010a39c4ff25

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