Merge branch 'master' into regress_out

.azure-pipelines.yml

@@ -4,25 +4,29 @@ trigger:
 variables:
   python.version: '3.9'
   PIP_CACHE_DIR: $(Pipeline.Workspace)/.pip
+  PYTEST_ADDOPTS: '-v --color=yes --nunit-xml=nunit/test-results.xml'
   ANNDATA_DEV: no
   RUN_COVERAGE: no
   TEST_EXTRA: 'test-full'
+  PRERELEASE_DEPENDENCIES: no
 
 jobs:
 - job: PyTest
   pool:
-    vmImage: 'ubuntu-18.04'
+    vmImage: 'ubuntu-22.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python38:
+        python.version: '3.8'
       Python39: {}
       minimal_tests:
         TEST_EXTRA: 'test-min'
       anndata_dev:
         python.version: '3.9'
         ANNDATA_DEV: yes
         RUN_COVERAGE: yes
+        PRERELEASE_DEPENDENCIES: yes
+
   steps:
   - task: UsePythonVersion@0
     inputs:
@@ -45,9 +49,17 @@ jobs:
 
   - script: |
       python -m pip install --upgrade pip
-      pip install pytest-cov wheel
+      pip install wheel coverage
       pip install .[dev,$(TEST_EXTRA)]
     displayName: 'Install dependencies'
+    condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'no')
+
+  - script: |
+      python -m pip install --pre --upgrade pip
+      pip install --pre wheel coverage
+      pip install --pre .[dev,$(TEST_EXTRA)]
+    displayName: 'Install dependencies release candidates'
+    condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'yes')
 
   - script: |
       pip install -v "anndata[dev,test] @ git+https://github.com/scverse/anndata"
@@ -58,21 +70,21 @@ jobs:
       pip list
     displayName: 'Display installed versions'
 
-  - script: |
-      pytest --color=yes --ignore=scanpy/tests/_images --nunit-xml="nunit/test-results.xml"
+  - script: pytest
     displayName: 'PyTest'
     condition: eq(variables['RUN_COVERAGE'], 'no')
 
   - script: |
-      pytest --color=yes --ignore=scanpy/tests/_images --nunit-xml="nunit/test-results.xml" --cov=scanpy --cov-report=xml
+      coverage run -m pytest
+      coverage xml
     displayName: 'PyTest (coverage)'
     condition: eq(variables['RUN_COVERAGE'], 'yes')
 
   - task: PublishCodeCoverageResults@1
     inputs:
       codeCoverageTool: Cobertura
       summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-      reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
+      failIfCoverageEmpty: true
     condition: eq(variables['RUN_COVERAGE'], 'yes')
 
   - task: PublishTestResults@2
@@ -88,7 +100,7 @@ jobs:
 
 - job: CheckBuild
   pool:
-    vmImage: 'ubuntu-18.04'
+    vmImage: 'ubuntu-22.04'
   steps:
 
   - task: UsePythonVersion@0

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,60 @@
+name: Bug report
+description: Scanpy 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 scanpy.
+      required: true
+    - label: (optional) I have confirmed this bug exists on the master branch of scanpy.
+      required: false
+- type: markdown
+  attributes:
+    value: |
+      **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug.
+- type: textarea
+  id: description
+  attributes:
+    label: What happened?
+    description: Describe what you tried to do, and what happened instead.
+  validations:
+    required: true
+- type: textarea
+  id: code
+  attributes:
+    label: Minimal code sample
+    description: (that we can copy&paste without having any data)
+    render: python
+  validations:
+    required: true
+- type: textarea
+  id: traceback
+  attributes:
+    label: Error output
+    description: Produced by the code above. Leave empty if the issue is unexpected behavior instead of an error.
+    render: pytb
+  validations:
+    required: false
+- type: textarea
+  id: versions
+  attributes:
+    label: Versions
+    description: Paste the output of `import scanpy; scanpy.logging.print_versions()` between the lines of backticks (\`\`\`)
+    value: |
+      <details>
+
+      ```
+
+      ```
+
+      </details>
+  validations:
+    required: true

.github/ISSUE_TEMPLATE/enhancement-request.yml

@@ -0,0 +1,23 @@
+name: Enhancement request
+description: Anything you’d like to see in scanpy?
+#title: ...
+labels: ['Enhancement ✨']
+#assignees: []
+body:
+- type: dropdown
+  id: kind
+  attributes:
+    label: What kind of feature would you like to request?
+    options:
+    - 'Additional function parameters / changed functionality / changed defaults?'
+    - 'New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?'
+    - 'New plotting function: A kind of plot you would like to seein `sc.pl`?'
+    - 'Other?'
+  validations:
+    required: true
+- type: textarea
+  id: description
+  attributes:
+    label: Please describe your wishes
+  validations:
+    required: true

.github/workflows/check-pr.yml

@@ -0,0 +1,31 @@
+name: Pull Request Validation
+
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+    types:
+      # milestone changes
+      - milestoned
+      - demilestoned
+      # label changes for “no milestone”
+      - labeled
+      - unlabeled
+      # initial check
+      - opened
+      - edited
+      - reopened
+      # code change (e.g. this workflow)
+      - synchronize
+
+env:
+  LABELS: ${{ join( github.event.pull_request.labels.*.name, '|' ) }}
+
+jobs:
+  check-milestone:
+    name: Check Milestone
+    runs-on: ubuntu-latest
+    steps:
+      - if: github.event.pull_request.milestone == null && contains( env.LABELS, 'no milestone' ) == false
+        run: exit 1

.gitignore

@@ -7,17 +7,24 @@
 /docs/_build/
 /docs/generated/
 /docs/data/
+/docs/api/generated
+/docs/external/generated
+/docs/jupyter_execute
 
 # tests
+/*coverage*
+/nunit/
 /.cache/
 /.pytest_cache/
 /scanpy/tests/test*.h5ad
 /scanpy/tests/figures/
 /scanpy/tests/notebooks/figures/
 
 # Environment management
+/hatch.toml
 /Pipfile
 /Pipfile.lock
+/requirements*.lock
 
 # always-ignore extensions
 *~
@@ -29,6 +36,7 @@ __pycache__/
 /scanpy.egg-info/
 /*-env/
 /env-*/
+/environment.yml
 
 # OS stuff
 .DS_Store
@@ -39,6 +47,3 @@ Thumbs.db
 # IDEs and editors
 /.idea/
 /.vscode/
-
-# Test artifacts
-**/test-results.xml

.pre-commit-config.yaml

@@ -1,17 +1,13 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.7.0
     hooks:
     -   id: black
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.280
     hooks:
-    -   id: flake8
--   repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v2.0.1
-    hooks:
-    -   id: autopep8
-        args: ["-i"]
+    -   id: ruff
+        args: ["--fix"]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -25,6 +21,8 @@ repos:
     -   id: check-yaml
     -   id: check-merge-conflict
     -   id: detect-private-key
+    -   id: no-commit-to-branch
+        args: ["--branch=master", "--branch=main"]
 
 ci:
     autofix_prs: false