Fix Single Cell Processing (#214)

Author: JoshLoecker

.github/workflows/container_build.yml

@@ -11,8 +11,11 @@ env:
 
 jobs:
   build-and-push-image:
+    # IMPORTANT: Only run the publish job when a tag starting with 'v' is pushed
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+
     name: Build and Push Docker Image
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write

.github/workflows/continuous_integration.yml

@@ -16,14 +16,8 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v5
 
-      - name: Create Virtual Environment
-        run: uv venv
-
-      - name: Install Jupyter
-        run: uv pip install jupyter nbconvert
-
       - name: Strip Notebook Output
-        run: uv run jupyter nbconvert --clear-output --inplace "main/COMO.ipynb"
+        run: uv tool run --from nbconvert jupyter-nbconvert --clear-output --inplace "main/COMO.ipynb"
 
       - name: Format Python Imports
         uses: astral-sh/ruff-action@v3
@@ -62,7 +56,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     steps:
       - name: Checkout
         uses: actions/checkout@v4