Update ct pipe #74
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Checking unit-tests, PEP8 and standard pipeline congruency | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@main | |
| - name: Set up Python 3.10.5 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.10.5 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install build-essential graphviz libgraphviz-dev | |
| pip install --upgrade pygraphviz graphviz | |
| # pip install --no-deps --index-url https://test.pypi.org/simple/ --pre macapype | |
| pip install -e .[test] | |
| python -c "import skullTo3d; print(skullTo3d.__version__)" | |
| cd .. | |
| git clone https://github.com/macatools/macapype.git | |
| cd macapype | |
| pip install -e . | |
| python -c "import macapype; print(macapype.__version__)" | |
| cd ../skullTo3d | |
| pwd | |
| - name: Test with pytest | |
| run: | |
| py.test --cov skullTo3d | |
| - name: Flake8 | |
| run: | |
| flake8 --count skullTo3d | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/swYxNZ3P6LjfqN4 --output skullTo3d_CI.zip | |
| unzip -o skullTo3d_CI.zip -d skullTo3d_CI | |
| - name: Running all test pipelines (ANTS SPM) | |
| run: | | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft SPM_native_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft SPM_native_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft SPM_native_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra | |
| - name: Running all test pipelines (ANTS SPM deriv pad) | |
| run: | | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft SPM_native_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft SPM_native_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad | |
| python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft SPM_native_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |