chore: troubleshooting CI #36
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| name: Python Package CI | |
| on: [push] | |
| jobs: | |
| ci: | |
| needs: [ostest, full-ci] | |
| name: CI | |
| runs-on: 'ubuntu-latest' | |
| steps: | |
| - name: Done | |
| run: exit 0 | |
| full-ci: | |
| runs-on: 'ubuntu-latest' | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| 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 }} | |
| - 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 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 | |
| - 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 | |
| - name: Test table io from commandline | |
| run: | | |
| . .venv/bin/activate | |
| 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 | |
| ostest: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| 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 | |
| - name: Install uv and create venv | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install uv | |
| uv venv | |
| - name: Install project | |
| run: | | |
| . .venv/bin/activate # Use 'call .venv\Scripts\activate' on Windows | |
| uv pip install -e .[dev] | |
| pip list | |
| - name: Test with pytest | |
| run: | | |
| . .venv/bin/activate # Use 'call .venv\Scripts\activate' on Windows | |
| 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 | |
| - 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 |