update GHA action and pre-commit versions (chanzuckerberg#829)

* update action/checkout to v4

* update pre-commit versions and fix new lint detected

.github/workflows/docsite-build-deploy.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/py-build.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -45,7 +45,7 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/py-formatting.yml

@@ -12,7 +12,7 @@ jobs:
     name: pre-commit checks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: "3.10"

.github/workflows/py-unittests.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ${{matrix.os}}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -50,7 +50,7 @@ jobs:
     runs-on: ${{matrix.os}}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -75,7 +75,7 @@ jobs:
       - unit_tests_python_api
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/download-artifact@v3

.github/workflows/r-check.yml

@@ -15,7 +15,7 @@ jobs:
         tiledbsoma_version: [tiledbsoma_release, tiledbsoma_latest]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
         with:
           extra-repositories: https://tiledb-inc.r-universe.dev

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: (^doc/)|(.*/venv/)
 default_stages: [commit]
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.10.1
     hooks:
       - id: black-jupyter
         name: black-notebooks
@@ -18,7 +18,7 @@ repos:
         args: ["--config", "./tools/pyproject.toml"]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.275
+    rev: v0.1.3
     hooks:
       - id: ruff
         name: ruff-cellxgene-census
@@ -30,7 +30,7 @@ repos:
         args: [ "--config=./tools/pyproject.toml", "--fix" ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.0
+    rev: v1.6.1
     hooks:
       - id: mypy
         name: mypy-cellxgene-census
@@ -74,6 +74,6 @@ repos:
         files: ^api/python/notebooks
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.35.0
+    rev: v0.37.0
     hooks:
     - id: markdownlint

api/python/cellxgene_census/tests/test_directory.py

@@ -88,8 +88,8 @@ def test_get_census_version_directory(directory_mock: Any) -> None:
 
     assert isinstance(directory, dict)
     assert len(directory) > 0
-    assert all((type(k) == str for k in directory.keys()))
-    assert all((type(v) == dict for v in directory.values()))
+    assert all(isinstance(k, str) for k in directory.keys())
+    assert all(isinstance(v, dict) for v in directory.values())
 
     assert "_dangling" not in directory