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trigger: | ||
- master | ||
- main | ||
|
||
variables: | ||
PIP_CACHE_DIR: $(Pipeline.Workspace)/.pip | ||
RUN_COVERAGE: no | ||
PYTEST_ADDOPTS: --color=yes --junitxml=junit/test-results.xml | ||
PRERELEASE_DEPENDENCIES: no | ||
|
||
jobs: | ||
- job: PyTest | ||
pool: | ||
vmImage: 'ubuntu-22.04' | ||
strategy: | ||
matrix: | ||
Python310: | ||
python.version: '3.10' | ||
RUN_COVERAGE: yes | ||
Python38: | ||
python.version: '3.8' | ||
steps: | ||
- task: UsePythonVersion@0 | ||
inputs: | ||
versionSpec: '$(python.version)' | ||
displayName: 'Use Python $(python.version)' | ||
|
||
- task: Cache@2 | ||
inputs: | ||
key: '"python $(python.version)" | "$(Agent.OS)" | pyproject.toml' | ||
restoreKeys: | | ||
python | "$(Agent.OS)" | ||
python | ||
path: $(PIP_CACHE_DIR) | ||
displayName: Cache pip packages | ||
|
||
- script: | | ||
python -m pip install --upgrade pip | ||
pip install pytest-cov wheel | ||
pip install .[dev,test] | ||
displayName: 'Install dependencies' | ||
- script: | | ||
pip list | ||
displayName: 'Display installed versions' | ||
- script: | | ||
pytest --color=yes --junitxml=junit/test-results.xml | ||
displayName: 'PyTest' | ||
condition: eq(variables['RUN_COVERAGE'], 'no') | ||
- script: | | ||
pytest --color=yes --junitxml=junit/test-results.xml --cov --cov-report=xml --cov-context=test | ||
displayName: 'PyTest (coverage)' | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
- task: PublishCodeCoverageResults@1 | ||
inputs: | ||
codeCoverageTool: Cobertura | ||
summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml' | ||
reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov' | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
|
||
- task: PublishTestResults@2 | ||
condition: succeededOrFailed() | ||
inputs: | ||
testResultsFiles: 'junit/test-*.xml' | ||
testRunTitle: 'Publish test results for Python $(python.version)' | ||
|
||
- script: bash <(curl -s https://codecov.io/bash) | ||
displayName: 'Upload to codecov.io' | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
|
||
- job: CheckBuild | ||
pool: | ||
vmImage: 'ubuntu-22.04' | ||
steps: | ||
|
||
- task: UsePythonVersion@0 | ||
inputs: | ||
versionSpec: '3.10' | ||
displayName: 'Use Python 3.10' | ||
|
||
- script: | | ||
python -m pip install --upgrade pip | ||
pip install build twine | ||
displayName: 'Install build tools and requirements' | ||
- script: pip list | ||
displayName: 'Display installed versions' | ||
|
||
- script: | | ||
python -m build --sdist --wheel . | ||
twine check dist/* | ||
displayName: 'Build & Twine check' | ||
- job: PyTest | ||
pool: | ||
vmImage: "ubuntu-22.04" | ||
strategy: | ||
matrix: | ||
Python310: | ||
python.version: "3.10" | ||
RUN_COVERAGE: yes | ||
Python38: | ||
python.version: "3.8" | ||
PreRelease: | ||
python.version: "3.10" | ||
PRERELEASE_DEPENDENCIES: yes | ||
steps: | ||
- task: UsePythonVersion@0 | ||
inputs: | ||
versionSpec: "$(python.version)" | ||
displayName: "Use Python $(python.version)" | ||
|
||
- task: Cache@2 | ||
inputs: | ||
key: '"python $(python.version)" | "$(Agent.OS)" | pyproject.toml' | ||
restoreKeys: | | ||
python | "$(Agent.OS)" | ||
python | ||
path: $(PIP_CACHE_DIR) | ||
displayName: Cache pip packages | ||
|
||
- script: | | ||
python -m pip install --upgrade pip | ||
pip install pytest-cov wheel | ||
pip install .[dev,test] | ||
displayName: "Install dependencies" | ||
condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'no') | ||
- script: | | ||
python -m pip install --pre --upgrade pip | ||
pip install --pre pytest-cov wheel | ||
pip install --pre .[dev,test] | ||
displayName: "Install dependencies release candidates" | ||
condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'yes') | ||
- script: | | ||
pip list | ||
displayName: "Display installed versions" | ||
- script: | | ||
pytest | ||
displayName: "PyTest" | ||
condition: eq(variables['RUN_COVERAGE'], 'no') | ||
- script: | | ||
pytest --cov --cov-report=xml --cov-context=test | ||
displayName: "PyTest (coverage)" | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
- task: PublishCodeCoverageResults@1 | ||
inputs: | ||
codeCoverageTool: Cobertura | ||
summaryFileLocation: "$(System.DefaultWorkingDirectory)/**/coverage.xml" | ||
reportDirectory: "$(System.DefaultWorkingDirectory)/**/htmlcov" | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
|
||
- task: PublishTestResults@2 | ||
condition: succeededOrFailed() | ||
inputs: | ||
testResultsFiles: "junit/test-*.xml" | ||
testRunTitle: "Publish test results for Python $(python.version)" | ||
|
||
- script: bash <(curl -s https://codecov.io/bash) | ||
displayName: "Upload to codecov.io" | ||
condition: eq(variables['RUN_COVERAGE'], 'yes') | ||
|
||
- job: CheckBuild | ||
pool: | ||
vmImage: "ubuntu-22.04" | ||
steps: | ||
- task: UsePythonVersion@0 | ||
inputs: | ||
versionSpec: "3.10" | ||
displayName: "Use Python 3.10" | ||
|
||
- script: | | ||
python -m pip install --upgrade pip | ||
pip install build twine | ||
displayName: "Install build tools and requirements" | ||
- script: pip list | ||
displayName: "Display installed versions" | ||
|
||
- script: | | ||
python -m build --sdist --wheel . | ||
twine check dist/* | ||
displayName: "Build & Twine check" | ||
- script: | | ||
pip install dist/*.whl | ||
python -c 'import anndata; print(anndata.__version__)' | ||
displayName: "Check runtime version" |
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Original file line number | Diff line number | Diff line change |
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name: Bug report | ||
description: anndata doesn’t do what it should? Please help us fix it! | ||
#title: ... | ||
labels: ["Bug 🐛"] | ||
#assignees: [] | ||
body: | ||
- type: checkboxes | ||
id: terms | ||
attributes: | ||
label: Please make sure these conditions are met | ||
# description: ... | ||
options: | ||
- label: I have checked that this issue has not already been reported. | ||
required: true | ||
- label: I have confirmed this bug exists on the latest version of anndata. | ||
required: true | ||
- label: (optional) I have confirmed this bug exists on the master branch of anndata. | ||
required: false | ||
- type: markdown | ||
attributes: | ||
value: | | ||
**Note**: Please read [this guide][] detailing how to provide the necessary information for us to reproduce your bug. | ||
[this guide]: https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports | ||
- type: textarea | ||
id: Report | ||
attributes: | ||
label: Report | ||
description: | | ||
Describe the bug you encountered, and what you were trying to do. Please use [github markdown][] features for readability. | ||
[github markdown]: https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax | ||
value: | | ||
Code: | ||
```python | ||
``` | ||
Traceback: | ||
```pytb | ||
``` | ||
validations: | ||
required: true | ||
- type: textarea | ||
id: versions | ||
attributes: | ||
label: Versions | ||
description: | | ||
Which version of anndata and other related software you used. | ||
Please install `session-info`, run the following command, then paste the results into the text box below. | ||
```python | ||
>>> import anndata, session_info; session_info.show(html=False, dependencies=True) | ||
``` | ||
render: python | ||
validations: | ||
required: true |
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blank_issues_enabled: false | ||
contact_links: | ||
- name: Scverse Community Forum | ||
url: https://discourse.scverse.org/ | ||
about: If you have questions about “How to do X”, please ask them here. |
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name: Enhancement request | ||
description: Anything you’d like to see in anndata? | ||
#title: ... | ||
labels: [enhancement] | ||
#assignees: [] | ||
body: | ||
- type: textarea | ||
id: description | ||
attributes: | ||
label: | | ||
Please describe your wishes and possible alternatives to achieve the desired result. | ||
validations: | ||
required: true |
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---|---|---|
@@ -0,0 +1,3 @@ | ||
- [ ] Closes # | ||
- [ ] Tests added | ||
- [ ] Release note added (or unnecessary) |
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