chore: troubleshooting CI

.github/workflows/CI.yml

@@ -2,6 +2,9 @@ name: Python Package CI
 
 on: [push]
 
+env:
+  UV_SYSTEM_PYTHON: 1
+
 jobs:
   ci:
     needs: [ostest, full-ci]
@@ -19,90 +22,29 @@ jobs:
         python-version: ["3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
 
-      - name: Install uv and create venv
-        run: |
-          python -m pip install --upgrade pip
-          pip install uv
-          uv venv
-      - name: Debug - Check venv
-        run: |
-          echo "Python version:"
-          python --version
-          echo "Pip version:"
-          pip --version
-          echo "Virtual env path:"
-          echo $VIRTUAL_ENV
-          echo "Python path:"
-          which python
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
 
       - name: Install project
         run: |
-          . .venv/bin/activate
-          uv pip install -vv -e .[dev]
-          echo "Installed packages:"
-          pip list
-
-      - name: Debug - Check installation
-        run: |
-          . .venv/bin/activate
-          echo "Current directory:"
-          pwd
-          echo "Directory contents:"
-          ls -R
-          echo "Pip show geomux:"
-          pip show -f geomux
-          echo "Python path:"
-          python -c "import sys; print(sys.path)"
-          echo "Try importing geomux:"
-          python -c "import geomux; print(geomux.__file__)"
-
-      - name: Debug - Print Python path and package contents
-        run: |
-          . .venv/bin/activate
-          python -c "import sys; print(sys.path)"
-          python -c "import geomux; print(dir(geomux)); print(geomux.__file__)"
-
-      - name: Debug - Check package structure
-        run: |
-          . .venv/bin/activate
-          pip show -f geomux
-
-      - name: Debug - Print __main__.py contents
-        run: |
-          echo "Contents of __main__.py:"
-          cat geomux/__main__.py
+          uv sync --all-extras --dev
 
       - name: Test with pytest
         run: |
-          . .venv/bin/activate
-          pytest -v
-
-      - name: Debug - Check Python path for CLI
-        run: |
-          . .venv/bin/activate
-          python -c "import sys; import geomux; print(sys.path); print(geomux.__file__)"
-          which geomux
-
-      - name: Debug - Run module directly
-        run: |
-          . .venv/bin/activate
-          python -m geomux -i example/example.tsv.gz -o results_table.tab
+          uv run pytest -v
 
       - name: Test table io from commandline
         run: |
-          . .venv/bin/activate
-          geomux -i example/example.tsv.gz -o results_table.tab
+          uv run geomux -i example/example.tsv.gz -o results_table.tab
 
       - name: Test adat io from commandline
         run: |
-          . .venv/bin/activate
-          geomux -i example/example.h5ad -o results_table.tab
+          uv run geomux -i example/example.h5ad -o results_table.tab
 
   ostest:
     runs-on: ${{ matrix.os }}
@@ -112,35 +54,26 @@ jobs:
         os: ["windows-latest", "macos-latest"]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.11
+    - uses: actions/checkout@v4
 
-    - name: Install uv and create venv
-      run: |
-        python -m pip install --upgrade pip
-        pip install uv
-        uv venv
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
+    - name: Set up Python 3.11
+      run: uv python install 3.11
 
     - name: Install project
       run: |
-        . .venv/bin/activate  # Use 'call .venv\Scripts\activate' on Windows
-        uv pip install -e .[dev]
-        pip list
+        uv sync --all-extras --dev
 
     - name: Test with pytest
       run: |
-        . .venv/bin/activate  # Use 'call .venv\Scripts\activate' on Windows
-        pytest -v
+        uv run pytest -v
 
     - name: Test table io from commandline
       run: |
-        . .venv/bin/activate  # Use 'call .venv\Scripts\activate' on Windows
-        geomux -i example/example.tsv.gz -o results_table.tab
+        uv run geomux -i example/example.tsv.gz -o results_table.tab
 
     - name: Test adat io from commandline
       run: |
-        . .venv/bin/activate  # Use 'call .venv\Scripts\activate' on Windows
-        geomux -i example/example.h5ad -o results_table.tabg
+        uv run geomux -i example/example.h5ad -o results_table.tab