Introduce pre-commit to GitHub workflows.

This adds a pre-commit step to the GitHub workflow. It replaces the
separate Black and Ruff runs, but does not fully replace MyPy.

.github/workflows/python-somacore.yaml

@@ -15,19 +15,30 @@ jobs:
       PYTHON_VERSION: "3.7"
     steps:
       - uses: actions/checkout@v3
+
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           cache: pip
           cache-dependency-path: python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
-      - uses: psf/black@stable
+
       - name: Install static analysis packages
         run: |
           pip install -r python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
+
+      - name: Restore pre-commit cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
       - name: Run mypy
         run: mypy ./python-spec/src
-      - name: Run ruff
-        run: ruff .
+        # We maintain this full mypy step since running mypy in pre-commit is
+        # somewhat limited (cf. comments in .pre-commit-config.yaml).
+
+      - name: Pre-commit check
+        run: pre-commit run -a -v
 
   run-tests:
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
   # Then others in alphabetical order:
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.243
+    rev: v0.0.265
     hooks:
       - id: ruff
 

python-spec/requirements-py3.7-lint.txt

@@ -1,27 +1,35 @@
 anndata==0.8.0
 attrs==23.1.0
 black==23.3.0
+cfgv==3.3.1
 click==8.1.3
+distlib==0.3.6
+filelock==3.12.0
 h5py==3.8.0
+identify==2.5.24
 importlib-metadata==6.6.0
 isort==5.11.5
 llvmlite==0.39.1
 mypy==1.2.0
 mypy-extensions==1.0.0
 natsort==8.3.1
+nodeenv==1.7.0
 numba==0.56.4
 numpy==1.21.6
 packaging==23.1
 pandas==1.3.5
 pathspec==0.11.1
 platformdirs==3.5.0
+pre-commit==2.21.0
 pyarrow==12.0.0
 python-dateutil==2.8.2
 pytz==2023.3
+PyYAML==6.0
 ruff==0.0.265
 scipy==1.7.3
 six==1.16.0
 tomli==2.0.1
 typed-ast==1.5.4
 typing_extensions==4.5.0
+virtualenv==20.23.0
 zipp==3.15.0

python-spec/update-requirements-txt

@@ -26,7 +26,7 @@ CONDIR="$TEMPDIR/py-$LINTVER-lint"
 conda create -y -p "$CONDIR" "python=$LINTVER"
 (
   conda activate "$CONDIR"
-  pip install .[dev] mypy
+  pip install .[dev] mypy pre-commit
   mypy --install-types --non-interactive ./python-spec/src
   pip freeze --exclude somacore >"./python-spec/requirements-py$LINTVER-lint.txt"
 )