Merge branch 'main' into feature/gpu_ci

.azure-pipelines.yml

@@ -1,92 +1,109 @@
 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"

.editorconfig

@@ -6,8 +6,8 @@ end_of_line = lf
 insert_final_newline = true
 trim_trailing_whitespace = true
 max_line_length = 88
-
-[*.py]
 indent_size = 4
 indent_style = space
 
+[*.{yml,yaml}]
+indent_size = 2

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,61 @@
+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

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+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.

.github/ISSUE_TEMPLATE/enhancement-request.yml

@@ -0,0 +1,13 @@
+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

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,3 @@
+- [ ] Closes #
+- [ ] Tests added
+- [ ] Release note added (or unnecessary)