Fix uv install in CI: replace --system with uv sync + uv run

The --system flag conflicts with active virtual environments on GitHub
Actions runners. Switch to uv sync (which manages its own .venv) and
prefix commands with uv run so they execute in that environment.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: jdebacker

.github/workflows/build_and_test.yml

@@ -36,9 +36,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install package and dependencies
-        run: uv pip install -e ".[dev]" --system
+        run: uv sync --extra dev
       - name: Test
-        run: python -m pytest -m "not local and not benchmark" --cov=./ --cov-report=xml
+        run: uv run python -m pytest -m "not local and not benchmark" --cov=./ --cov-report=xml
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest' && contains(github.repository, 'PSLmodels/OG-Core')
         uses: codecov/codecov-action@v4

.github/workflows/deploy_docs.yml

@@ -27,12 +27,12 @@ jobs:
           python-version: "3.13"
 
       - name: Install package and dependencies
-        run: uv pip install -e ".[dev,docs]" --system
+        run: uv sync --extra dev --extra docs
 
       - name: Build # Build Jupyter Book
         run: |
-          python -m ipykernel install --user --name=ogcore-dev
-          make build-docs
+          uv run python -m ipykernel install --user --name=ogcore-dev
+          uv run make build-docs
 
       - name: Deploy
         uses: JamesIves/github-pages-deploy-action@v4

.github/workflows/docs_check.yml

@@ -25,9 +25,9 @@ jobs:
           python-version: "3.13"
 
       - name: Install package and dependencies
-        run: uv pip install -e ".[dev,docs]" --system
+        run: uv sync --extra dev --extra docs
 
       - name: Build # Build Jupyter Book
         run: |
-          python -m ipykernel install --user --name=ogcore-dev
-          make build-docs
+          uv run python -m ipykernel install --user --name=ogcore-dev
+          uv run make build-docs