PD-2 Support Python 3.9 to 3.13 (#281)

Author: paulineribeyre

.github/workflows/docs.yaml

@@ -22,10 +22,10 @@ jobs:
         repository: ${{github.event.pull_request.head.repo.full_name}}
         # Passing a PAT from the PlanXCybrog bot account here, since otherwise commits pushed by this action won't be able to trigger other actions, see https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#commits-made-by-this-action-do-not-trigger-new-workflow-runs
         token: ${{ secrets.PLANXCYBORG_PAT }}
-    - name: Set up Python 3.9
+    - name: Set up Python 3.13
       uses: actions/setup-python@v1
       with:
-        python-version: 3.9
+        python-version: 3.13
     - uses: actions/cache@preview
       with:
         path: ~/.cache/pypoetry/virtualenvs
@@ -48,7 +48,7 @@ jobs:
     - name: Build docs
       run: |
         sphinx-build --version
-        export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.9/site-packages"
+        export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.13/site-packages"
         cd docs
         poetry run make html
         cd ..

.github/workflows/pypi.yaml

@@ -8,7 +8,7 @@ jobs:
     name: PyPI Poetry Publish
     uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master
     with:
-        PYTHON_VERSION: '3.9'
+        PYTHON_VERSION: '3.13'
         # This will attempt push to test PyPI first and only push to prod if it works
         DO_TEST_PUBLISH_FIRST: true
     secrets:

.gitignore

@@ -108,18 +108,9 @@ tests/resources/keys/*.pem
 schema.json
 
 # pytest outputs
+tests/outputs
 *.sq3
-merged-output-test-manifest.*
 gen3/tools/indexing/tmp/
-indexing-output-manifest.csv
-object-manifest.csv
-output_manifest.csv
 
 .dccache
 .idea
-# pytest output
-/input.csv
-/test_combined_discovery_metadata.tsv
-/test_combined_discovery_metadata_exact_match.tsv
-/tmp_output_file.csv
-/tmp_output_file_info.csv

.readthedocs.yml

@@ -608,42 +608,42 @@
         "filename": "tests/test_manifests.py",
         "hashed_secret": "7c35c215b326b9463b669b657c1ff9873ff53d9a",
         "is_verified": false,
-        "line_number": 641
+        "line_number": 642
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "f9e664db75c7f23a299b0b055c10e08d47073e93",
         "is_verified": false,
-        "line_number": 675
+        "line_number": 677
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "14bafb268df75cc8f8d8f87f61468d249de936ba",
         "is_verified": false,
-        "line_number": 803
+        "line_number": 809
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "bce350451d95a06da0423916d228575c633008ef",
         "is_verified": false,
-        "line_number": 811
+        "line_number": 817
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "0d515eaf06062d52e8c80abb4d3b713a65396d30",
         "is_verified": false,
-        "line_number": 893
+        "line_number": 900
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "b4cff7c2af45cdfe66195ec574a7b8832f8621ea",
         "is_verified": false,
-        "line_number": 898
+        "line_number": 905
       }
     ],
     "tests/test_submission.py": [
@@ -656,5 +656,5 @@
       }
     ]
   },
-  "generated_at": "2024-12-05T20:51:45Z"
+  "generated_at": "2025-11-07T21:07:45Z"
 }