CI version bumps, deps factor (#225)

* bump GHA `checkout`, `setup-python` versions

* remove dupes from `requirements-py3.8-lint.txt`

* rm unnecessary lint deps

.github/workflows/python-somacore.yaml

@@ -20,11 +20,11 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           cache: pip
-          cache-dependency-path: python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
+          cache-dependency-path: "python-spec/requirements-py${{ env.PYTHON_VERSION }}*.txt"
 
       - name: Install static analysis packages
-        run: |
-          pip install -r python-spec/requirements-py${{ env.PYTHON_VERSION }}-lint.txt
+        working-directory: python-spec
+        run: pip install -r requirements-py${PYTHON_VERSION}.txt -r requirements-py${PYTHON_VERSION}-lint.txt
 
       - name: Restore pre-commit cache
         uses: actions/cache@v3
@@ -47,12 +47,12 @@ jobs:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # setuptools-scm needs a deep clone so it can look through history
           # to find a relevant tag.
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -78,8 +78,8 @@ jobs:
       && startsWith(github.event.release.tag_name, 'python-')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           cache: pip
           cache-dependency-path: python-spec/requirements-py3.10.txt

python-spec/requirements-py3.8-lint.txt

@@ -1,38 +1,3 @@
-anndata==0.9.2
-attrs==23.2.0
-black==24.4.2
-cfgv==3.4.0
-click==8.1.7
-distlib==0.3.8
-filelock==3.15.1
-h5py==3.11.0
-identify==2.5.36
-importlib_metadata==7.1.0
-isort==5.13.2
-llvmlite==0.41.1
-mypy==1.10.0
-mypy-extensions==1.0.0
-natsort==8.4.0
-nodeenv==1.9.1
-numba==0.58.1
-numpy==1.24.4
-packaging==24.1
-pandas==2.0.3
-pandas-stubs==2.0.3.230814
-pathspec==0.12.1
-platformdirs==4.2.2
+mypy==1.11.2
+pandas-stubs==2.0.3.230814  # last version that supports Python 3.8
 pre-commit==3.5.0
-pyarrow==16.1.0
-pyarrow-hotfix==0.6
-python-dateutil==2.9.0.post0
-pytz==2024.1
-PyYAML==6.0.1
-ruff==0.4.9
-scipy==1.10.1
-six==1.16.0
-tomli==2.0.1
-types-pytz==2024.1.0.20240417
-typing_extensions==4.12.2
-tzdata==2024.1
-virtualenv==20.26.2
-zipp==3.19.2