Merge pull request #63 from Sage-Bionetworks-Workflows/fix_test_workflow

Fix broken CI workflow.

Author: andrewelamb

.github/workflows/ci.yml .github/workflows/CI.yml.github/workflows/ci.yml renamed to .github/workflows/CI.yml

@@ -2,7 +2,7 @@
 # MODIFY IT ACCORDING TO YOUR NEEDS!
 # Reference: https://docs.github.com/en/actions
 
-name: test
+name: CI
 
 on:
   push:
@@ -30,9 +30,9 @@ jobs:
       wheel-path: ${{ steps.distribution-paths.outputs.wheel }}
       tarball-path: ${{ steps.distribution-paths.outputs.tarball }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with: { fetch-depth: 0 } # deep clone for setuptools-scm
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with: { python-version: "3.11" }
       - name: Run static analysis and format checkers
         run: pipx run pre-commit run --all-files --show-diff-on-failure
@@ -49,39 +49,45 @@ jobs:
         # `tests`, `pypi-publish`, and `docker-publish` will use the same
         # pre-built distributions, so we make sure to release the exact
         # same package that was tested
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-distribution-files
           path: dist/
           retention-days: 1
-      - name: Keepalive Workflow
-        uses: gautamkrishnar/keepalive-workflow@1.1.0
-        with:
-          time_elapsed: 44
-          gh_token: ${{ secrets.GITHUB_TOKEN }}
+      # TODO: Fix or remove: https://sagebionetworks.jira.com/browse/ORCA-347
+      #- name: Keepalive Workflow
+      #  uses: gautamkrishnar/keepalive-workflow@1.1.0
+      #  with:
+      #    time_elapsed: 44
+      #    gh_token: ${{ secrets.GITHUB_TOKEN }}
 
   test:
     needs: prepare
     strategy:
       matrix:
         python:
-          - "3.9" # oldest Python that is supported
-          - "3.11" # newest Python that is stable
+        # TODO: Sunset 3.10: https://sagebionetworks.jira.com/browse/ORCA-352
+        # TODO: Allow more recent Python versions: https://sagebionetworks.jira.com/browse/ORCA-346
+          - "3.10"
+          - "3.11"
+          #- "3.12"
+          #- "3.13"
+          #- "3.14"
         platform:
           - ubuntu-latest
           - macos-latest
-        # TODO: Debug the Windows issues
-        # - windows-latest
+          # TODO: Fix or remove Windows testing:  https://sagebionetworks.jira.com/browse/ORCA-348
+          #- windows-latest
     env:
       OS: ${{ matrix.platform }}
       PYTHON: ${{ matrix.python }}
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with: { name: python-distribution-files, path: dist/ }
       - name: Install tox-gh plugin
         run: python -m pip install tox-gh>=1.2
@@ -109,10 +115,10 @@ jobs:
     if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with: { python-version: "3.11" }
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with: { name: python-distribution-files, path: dist/ }
       - name: Publish Python Package to PyPI
         env:
@@ -122,12 +128,13 @@ jobs:
         run: pipx run --spec 'tox!=3.0' tox -e publish
 
   docker-publish:
+    permissions: write-all
     needs: [prepare, test]
     if: ${{ github.event_name == 'push' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/download-artifact@v3
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
         with: { name: python-distribution-files, path: dist/ }
       - uses: docker/setup-qemu-action@v2
       - uses: docker/setup-buildx-action@v2

.pre-commit-config.yaml

@@ -18,17 +18,17 @@ repos:
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
 - repo: https://github.com/PyCQA/autoflake
-  rev: v2.0.0
+  rev: v2.3.1
   hooks:
   - id: autoflake
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 6.0.1
   hooks:
   - id: isort
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 25.1.0
   hooks:
   - id: black
     language_version: python3
@@ -40,23 +40,24 @@ repos:
 #     additional_dependencies: [black]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.3.0
   hooks:
   - id: flake8
     additional_dependencies: [flake8-bugbear, flake8-pyproject]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
+  # TODO: update mypy: https://sagebionetworks.jira.com/browse/ORCA-350
   rev: 'v0.991'
   hooks:
   - id: mypy
 
 - repo: https://github.com/kynan/nbstripout
-  rev: '0.6.1'
+  rev: 0.8.1
   hooks:
   - id: nbstripout
 
 - repo: https://github.com/econchick/interrogate
-  rev: 1.5.0
+  rev: 1.7.0
   hooks:
   - id: interrogate
     args: [--verbose, --fail-under=0]

Pipfile

@@ -8,6 +8,3 @@ dcqc = {editable = true, path = ".", extras = ["all"]}
 
 [dev-packages]
 dcqc = {editable = true, path = ".", extras = ["testing", "dev"]}
-
-[requires]
-python_version = "3.11"