Petra itk debias optional #77
Workflow file for this run
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| 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 | |