Add iso surface #413
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 3.7 | |
uses: actions/setup-python@v1 | |
with: | |
python-version: 3.7 | |
- 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 | |
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 | |
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_T1_test -species macaque -sub 032140 -ses 001 -deriv | |
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_test -species macaque -sub 032140 -ses 001 -deriv | |
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_T1_test -species macaque -sub 032140 -ses 001 -deriv | |
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 | |
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_T1_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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_T1_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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_template_test -species macaque -sub 032140 -ses 001 -deriv | |
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_template_T1_test -species macaque -sub 032140 -ses 001 -deriv | |
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 | |
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_T1_test -species macaque -sub 032140 -ses 001 -deriv | |
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_template_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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_template_T1_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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 | |
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_T1_test -species macaque -indiv /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/indiv_params_segment_macaque.json -sub 032140 -ses 001 -deriv | |
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 | |
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 |