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check_on_PR.yml
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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 (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