~ 35.63% faster filtering

.azure-pipelines.yml

@@ -15,16 +15,16 @@ jobs:
     vmImage: 'ubuntu-22.04'
   strategy:
     matrix:
-      Python3.9:
-        python.version: '3.9'
+      Python3.10:
+        python.version: '3.10'
       Python3.12: {}
       minimal_dependencies:
         TEST_EXTRA: 'test-min'
       anndata_dev:
         DEPENDENCIES_VERSION: "pre-release"
         TEST_TYPE: "coverage"
       minimum_versions:
-        python.version: '3.9'
+        python.version: '3.10'
         DEPENDENCIES_VERSION: "minimum-version"
         TEST_TYPE: "coverage"
 
@@ -103,6 +103,12 @@ jobs:
       testResultsFormat: NUnit
       testRunTitle: 'Publish test results for $(Agent.JobName)'
 
+  - task: PublishBuildArtifacts@1
+    inputs:
+      pathToPublish: '.pytest_cache/d/debug'
+      artifactName: debug-data
+    condition: eq(variables['TEST_TYPE'], 'coverage')
+
   - script: bash <(curl -s https://codecov.io/bash)
     displayName: 'Upload to codecov.io'
     condition: eq(variables['TEST_TYPE'], 'coverage')

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -1,8 +1,8 @@
 name: Bug report
 description: Scanpy doesn’t do what it should? Please help us fix it!
 #title: ...
+type: Bug
 labels:
-- Bug 🐛
 - Triage 🩺
 #assignees: []
 body:

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
-blank_issues_enabled: true
+blank_issues_enabled: false
 contact_links:
   - name: Scanpy Community Forum
     url: https://discourse.scverse.org/

.github/ISSUE_TEMPLATE/enhancement-request.yml

@@ -1,8 +1,8 @@
 name: Enhancement request
 description: Anything you’d like to see in scanpy?
 #title: ...
+type: Enhancement
 labels:
-- Enhancement ✨
 - Triage 🩺
 #assignees: []
 body:
@@ -14,6 +14,7 @@ body:
     - '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`?'
+    - 'Improved documentation or error message?'
     - 'Other?'
   validations:
     required: true

.github/workflows/benchmark.yml

@@ -48,8 +48,7 @@ jobs:
           key: benchmark-state-${{ hashFiles('benchmarks/**') }}
 
       - name: Install dependencies
-        # TODO: revert once this PR is merged: https://github.com/airspeed-velocity/asv/pull/1397
-        run: pip install 'asv @ git+https://github.com/ivirshup/asv@fix-conda-usage'
+        run: pip install 'asv>=0.6.4'
 
       - name: Configure ASV
         working-directory: ${{ env.ASV_DIR }}

.github/workflows/check-pr.yml

@@ -49,13 +49,13 @@ jobs:
         with:
           fetch-depth: 0
           filter: blob:none
-      - name: Find out if relevant release notes are modified
-        uses: dorny/paths-filter@v2
+      - name: Find out if a relevant release fragment is added
+        uses: dorny/paths-filter@v3
         id: changes
         with:
           filters: | # this is intentionally a string
-            relnotes: 'docs/release-notes/${{ github.event.pull_request.milestone.title }}.md'
-      - name: Check if relevant release notes are modified
+            relnotes: 'docs/release-notes/${{ github.event.pull_request.number }}.*.md'
+      - name: Check if a relevant release fragment is added
         uses: flying-sheep/check@v1
         with:
           success: ${{ steps.changes.outputs.relnotes }}

.gitignore

@@ -18,7 +18,6 @@
 /tests/**/*failed-diff.png
 
 # Environment management
-/hatch.toml
 /Pipfile
 /Pipfile.lock
 /requirements*.lock
@@ -29,6 +28,7 @@
 # Python build files
 __pycache__/
 /src/scanpy/_version.py
+/ci/scanpy-min-deps.txt
 /dist/
 /*-env/
 /env-*/
@@ -42,7 +42,6 @@ Thumbs.db
 
 # IDEs and editors
 /.idea/
-/.vscode/
 
 # asv benchmark files
 /benchmarks/.asv

.pre-commit-config.yaml

@@ -1,16 +1,13 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.9
+    rev: v0.9.1
     hooks:
     -   id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--fix"]
     -   id: ruff-format
-        types_or: [python, pyi, jupyter]
     # The following can be removed once PLR0917 is out of preview
     -   name: ruff preview rules
         id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--preview", "--select=PLR0917"]
 -   repo: https://github.com/flying-sheep/bibfmt
     rev: v4.3.0
@@ -19,8 +16,17 @@ repos:
         args:
         - --sort-by-bibkey
         - --drop=abstract
+-   repo: https://github.com/biomejs/pre-commit
+    rev: v0.6.1
+    hooks:
+    -   id: biome-format
+        additional_dependencies: ["@biomejs/[email protected]"]
+-   repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+    -   id: taplo-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
         exclude: tests/_data
@@ -34,6 +40,3 @@ repos:
     -   id: detect-private-key
     -   id: no-commit-to-branch
         args: ["--branch=main"]
-
-ci:
-    autofix_prs: false

.readthedocs.yml

@@ -2,9 +2,16 @@ version: 2
 submodules:
   include: all
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: '3.12'
+  jobs:
+    post_checkout:
+      # unshallow so version can be derived from tag
+      - git fetch --unshallow || true
+    pre_build:
+      # run towncrier to preview the next version’s release notes
+      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
 sphinx:
   fail_on_warning: true # do not change or you will be fired
   configuration: docs/conf.py
@@ -14,4 +21,5 @@ python:
     path: .
     extra_requirements:
     - doc
+    - dev  # for towncrier
     - leiden

.taplo.toml

@@ -0,0 +1,5 @@
+[formatting]
+array_auto_collapse = false
+column_width = 120
+compact_arrays = false
+indent_string = '    '

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": { "PYTEST_ADDOPTS": "--color=yes" },
+            "presentation": { "hidden": true },
+        },
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+    "[python][toml][json][jsonc]": {
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit",
+            "source.fixAll": "explicit",
+        },
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+    },
+    "[toml]": {
+        "editor.defaultFormatter": "tamasfe.even-better-toml",
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+    "python.testing.pytestEnabled": true,
+    "python.terminal.activateEnvironment": true,
+}

benchmarks/README.md

@@ -8,3 +8,14 @@ Benchmarks are run using the [benchmark bot][].
 [asv]: https://asv.readthedocs.io/
 [`benchmark.yml`]: ../.github/workflows/benchmark.yml
 [benchmark bot]: https://github.com/apps/scverse-benchmark
+
+## Data processing in benchmarks
+
+Each dataset is processed so it has
+
+- `.layers['counts']` (containing data in C/row-major format) and `.layers['counts-off-axis']` (containing data in FORTRAN/column-major format)
+- `.X` and `.layers['off-axis']` with log-transformed data (formats like above)
+- a `.var['mt']` boolean column indicating mitochondrial genes
+
+The benchmarks are set up so the `layer` parameter indicates the layer that will be moved into `.X` before the benchmark.
+That way, we don’t need to add `layer=layer` everywhere.

benchmarks/asv.conf.json

@@ -54,7 +54,7 @@
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
-    // "pythons": ["3.9", "3.12"],
+    // "pythons": ["3.10", "3.12"],
 
     // The list of conda channel names to be searched for benchmark
     // dependency packages in the specified order
@@ -78,13 +78,14 @@
         "natsort": [""],
         "pandas": [""],
         "memory_profiler": [""],
-        "zarr": [""],
+        "zarr": ["2.18.4"],
         "pytest": [""],
         "scanpy": [""],
         "python-igraph": [""],
         // "psutil": [""]
         "pooch": [""],
         "scikit-image": [""],
+        // "scikit-misc": [""],
     },
 
     // Combinations of libraries/python versions can be excluded/included