Packaging and Merging Updates

.github/workflows/label-predicate-changes.yml

@@ -12,21 +12,17 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.9
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
 
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install PyGithub 
+    - name: Set up Python
+      run: uv python install 3.12
 
     - name: Run predicate check
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         ISSUE_NUMBER: ${{ github.event.pull_request.number || github.event.issue.number }}
       run: |
-        python .github/scripts/Bio_QC_check.py
+        uv run --with requests python .github/scripts/Bio_QC_check.py

.github/workflows/pypi.yml

@@ -0,0 +1,35 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  test-pypi:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+      - run: uv build
+      - run: uv publish --trusted-publishing always
+        env:
+          UV_PUBLISH_URL: https://test.pypi.org/legacy/
+  pypi:
+    name: Publish to PyPI
+    needs:
+      - test-pypi
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+      - run: uv build
+      - run: uv publish --trusted-publishing always

.github/workflows/test.yml

@@ -7,9 +7,6 @@ jobs:
   test:
     name: test
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.9]
     steps:
       - name: Checkout the repository
         uses: actions/checkout@v4
@@ -24,15 +21,14 @@ jobs:
           echo "ORION_STORAGE=$PWD/tests/workspace/storage" >> $GITHUB_ENV
           echo "ORION_GRAPHS=$PWD/tests/workspace/graphs" >> $GITHUB_ENV
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python
+        run: uv python install 3.12
 
       - name: Install dependencies
-        run: |
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        run: uv sync --extra robokop --group dev
 
       - name: Run pytest
-        run: |
-          python -m pytest tests/
+        run: uv run pytest tests/

.gitignore

@@ -2,4 +2,8 @@
 **/__pycache__
 *.pycache
 .env
-.idea
+.idea
+.DS_Store
+.pytest_cache/
+dist/
+*.egg-info/

.python-version

@@ -0,0 +1 @@
+3.12