update and add tutorials for SpaTrack #379
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| name: CPU PyTest in Conda Dev/Work Branch Image | |
| on: | |
| push: | |
| branches: | |
| - 'dev' | |
| - 'work' | |
| paths-ignore: | |
| - '.github/workflows/**' | |
| - 'docs/**' | |
| jobs: | |
| build-linux-and-start-pytest: | |
| runs-on: cpu | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # - name: Add conda to system path | |
| # run: | | |
| # # $CONDA_PREFIX is an environment variable pointing to the root of the miniconda directory | |
| # echo $CONDA_PREFIX/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| echo "use conda in $(which conda)" | |
| conda env update --file tests/workflows_conf/environment_linux_py38.yml --name test_image -q | |
| - name: Activate conda enviroment | |
| run: | | |
| echo "use conda in $(which conda)" | |
| conda init --all | |
| source ~/.bashrc | |
| conda activate test_image | |
| echo "use pip in $(which pip)" | |
| echo "use python in $(which python)" | |
| - name: Install Stereopy dependencies | |
| run: | | |
| echo "use conda in $(which conda)" | |
| conda init --all | |
| source ~/.bashrc | |
| conda activate test_image | |
| echo "use pip in $(which pip)" | |
| echo "use python in $(which python)" | |
| pip install -r requirements.txt -q | |
| # TODO temporarily not install `tests/extra_requirements.txt` | |
| pip install -r tests/extra_requirements.txt -q | |
| pip install -r tests/image_requirements.txt -q | |
| pip install pathlib -q | |
| python setup.py develop | |
| - name: Show Env Info | |
| run: | | |
| echo "use conda in $(which conda)" | |
| conda init --all | |
| source ~/.bashrc | |
| conda activate test_image | |
| echo "use pip in $(which pip)" | |
| echo "use python in $(which python)" | |
| conda info | |
| env | |
| pip list | |
| - name: Test with pytest | |
| run: | | |
| echo "use conda in $(which conda)" | |
| conda init --all | |
| source ~/.bashrc | |
| conda activate test_image | |
| echo "use python in $(which python)" | |
| python -m pytest -m "cell_cut_env" --durations=0 |