Add type-checking

.github/workflows/mypy.yml

@@ -0,0 +1,27 @@
+name: mypy
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Extract max Python version from classifiers
+        run: |
+          classifiers=$(yq .project.classifiers pyproject.toml -oy  | grep --only-matching --perl-regexp '(?<=Python :: )(\d\.\d+)')
+          max_version=$(echo "$classifiers" | sort -V | tail -1)
+          echo "max_python_version=$max_version" >> $GITHUB_ENV
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.max_python_version }}
+      - name: Install mypy
+        run: |
+          pip install 'mypy @ git+https://github.com/python/mypy.git'
+      - name: Run mypy
+        run: |
+          mypy --show-traceback src

.pre-commit-config.yaml

@@ -1,5 +1,6 @@
 ci:
   autoupdate_commit_msg: "ci: pre-commit autoupdate"
+  skip: [mypy]  # too big
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
@@ -39,3 +40,25 @@ repos:
       - id: codespell
         additional_dependencies:
           - tomli
+# See https://github.com/scverse/anndata/pull/2174
+# Running `pre-commit run -a` gives the following error:
+# tests/conftest.py: error: Duplicate module named "conftest" (also at "./tests/lazy/conftest.py")
+# tests/conftest.py: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-file-paths-to-modules for more info
+# This seems to be the same failure we get on the prec-commit.ci
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.2
+    hooks:
+      - id: mypy
+        args: [--config-file=pyproject.toml, --tb, .]
+        pass_filenames: false
+        additional_dependencies:
+          - array-api-compat
+          - h5py
+          - legacy-api-wrap
+          - natsort
+          - numpy
+          - packaging
+          - pandas
+          - scipy
+          - types-docutils
+          - zarr

ci/scripts/min-deps.py

@@ -63,7 +63,7 @@ def extract_min_deps(
     dependencies = deque(dependencies)  # We'll be mutating this
     project_name = pyproject["project"]["name"]
 
-    deps = {}
+    deps: dict[str, Requirement] = {}
     while len(dependencies) > 0:
         req = dependencies.pop()
 

pyproject.toml

@@ -265,3 +265,46 @@ fragment.perf.name = "Performance"
 fragment.chore.name = "Miscellaneous changes"
 fragment.revert.name = "Revert"
 fragment.breaking.name = "Breaking changes"   # add `!` to commit type (e.g. “feature!:”)
+
+[tool.mypy]
+exclude = [
+    '^src/testing/anndata/__init__\.py$',
+    '^src/testing/anndata/_doctest\.py$',
+]
+explicit_package_bases = true
+ignore_missing_imports = true
+mypy_path = [ '$MYPY_CONFIG_FILE_DIR/src' ]
+
+[[tool.mypy.overrides]]
+module = [ "anndata/*" ]
+
+disable_error_code = [
+    "import-untyped",
+    "no-redef",
+    "attr-defined",
+    "union-attr",
+    "index",
+    "assignment",
+    "arg-type",
+    "return-value",
+    "type-arg",
+    "type-var",
+    "return",
+    "call-arg",
+    "misc",
+    "override",
+    "valid-type",
+    "has-type",
+    "name-defined",
+    "var-annotated",
+    "call-overload",
+    "operator",
+    "list-item",
+]
+
+[[tool.mypy.overrides]]
+module = [ "testing/*" ]
+
+disable_error_code = [
+    "attr-defined",
+]