Some minor corrections #526
Workflow file for this run
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| name: Checking unit-tests, PEP8 and standard pipeline congruency | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Set up Python 3.10.5 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.10.5 | |
| - name: Install dependencies | |
| run: | | |
| pip install codecov pytest pytest-cov | |
| pip install -e . | |
| pip install flake8 | |
| sudo apt-get install build-essential graphviz libgraphviz-dev | |
| pip install --upgrade pygraphviz graphviz | |
| - name: Test with pytest | |
| run: | |
| py.test --cov macapype --ignore=examples/ --ignore=run_examples/ | |
| - name: Flake8 | |
| run: | |
| flake8 --count macapype | |
| - name: Download dataset | |
| run: | | |
| wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| - name: Running all test pipelines (macaque) | |
| run: | | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -dt T1 T2 | |
| - name: Running all test pipelines (macaque deriv) | |
| run: | | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -deriv -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -deriv -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -deriv -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -deriv -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -dt T1 T2 | |
| - name: Running all test pipelines (macaque deriv pad) | |
| run: | | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -pad -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft ANTS_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -pad -dt T1 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de -out /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results -soft SPM_native_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| - name: Running some test pipelines (baboon / marmo) | |
| run: | | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien -out /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results -soft ANTS_test -species baboon -indiv /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/indiv_params_segment_baboon.json -sub Fidji -ses 01 -deriv -pad -dt T1 T2 | |
| python workflows/segment_pnh.py -data /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain -out /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results -soft ANTS_test -species marmo -indiv /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/indiv_params_segment_marmo.json -sub Percy -ses 01 -deriv -pad -dt T1 T2 |