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build_on_prerelease.yml
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name: (Prerelease) Build TestPipy, Dockerhub image and test
on:
release:
types: [prereleased]
jobs:
build-n-publish-testpypi:
name: Build and publish Python to Test PyPI
runs-on: ubuntu-latest
permissions:
id-token: write
environment:
name: testpypi
url: https://test.pypi.org/p/macapype
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 pypa/build
run: >-
python -m
pip install
build
--user
- name: Build a binary wheel and a source tarball
run: >-
python -m
build
--sdist
--wheel
--outdir dist/
- name: Publish distribution to Test PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
repository-url: https://test.pypi.org/legacy/
docker-build:
name: Build Docker image and Push to Docker Hub
needs: build-n-publish-testpypi
runs-on: ubuntu-latest
steps:
- name: Check out the repo
uses: actions/checkout@v2
- name: Log in to Docker Hub
uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
with:
images: macatools/macapype
- name: Build and push Docker image
uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
with:
context: .
file: Dockerfile_testpypi
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
run-pretest-ants-macaque:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep macaque)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_macaque
echo ""
- name: Running test pipeline cerimed_macaque ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_macaque/ -out /data/cerimed_macaque/results -soft ANTS_robustreg_prep -species macaque -sub Stevie -ses 01 -deriv -pad -dt T1 T2 -nprocs 1
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/sub-Stevie/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results
run-pretest-ants-macaque_0p5:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg macaque_0p5)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_macaque
echo ""
- name: Running test pipeline cerimed_macaque ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_macaque/ -out /data/cerimed_macaque/results -soft ANTS_robustreg -species macaque_0p5 -sub Stevie -ses 01 -deriv -pad -dt T1 T2 -nprocs 1
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/sub-Stevie/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results
run-pretest-ants-4animal-macaque_0p5:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_4animal_robustreg macaque_0p5)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_macaque
echo ""
- name: Running test pipeline cerimed_macaque ANTS_4animal_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_macaque/ -out /data/cerimed_macaque/results -soft ANTS_4animal_robustreg -species macaque_0p5 -sub Stevie -ses 01 -deriv -pad -dt T1 T2 -nprocs 1
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants_4animal/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants_4animal/sub-Stevie/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results
run-pretest-ants-marmo:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_marmo
echo ""
- name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/sub-Tresor/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
run-pretest-ants-4animal-marmo:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_4animal_noseg marmo)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_marmo
echo ""
- name: Running test pipeline cerimed_marmo ANTS_4animal_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_4animal_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants_4animal/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants_4animal/sub-Tresor/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
run-pretest-ants-marmoT2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo T2)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_marmo
echo ""
- name: Running test pipeline cerimed_marmo ANTS_noseg T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmoT2 -sub Tresor -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/sub-Tresor/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
run-pretest-ants-baboon:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results -soft ANTS_robustreg_prep -species baboon -sub Prune -ses 3 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/macapype_ants/sub-Prune/ses-3/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results
run-pretest-ants-baboon3:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg_prep -species baboon3 -sub Prune -ses 3 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/sub-Prune/ses-3/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3
run-pretest-ants-baboon2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg_prep -species baboon2 -sub Prune -ses 2 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/sub-Prune/ses-2/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2
run-pretest-ants-baboon1:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg_prep -species baboon1 -sub Prune -ses 1 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/sub-Prune/ses-1/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1
run-pretest-ants-baboon0:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon0)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_robustreg_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0
run-pretest-ants-4animal-baboon3-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_4animal_robustreg baboon3_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_4animal_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_4animal_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants_4animal/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants_4animal/sub-Prune/ses-3/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3
run-pretest-ants-4animal-baboon2-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_4animal_robustreg baboon2_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_4animal_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_4animal_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants_4animal/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants_4animal/sub-Prune/ses-2/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2
run-pretest-ants-4animal-baboon1-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_4animal_robustreg baboon1_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_4animal_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_4animal_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants_4animal/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants_4animal/sub-Prune/ses-2/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1
run-pretest-ants-baboon3-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon3_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/sub-Prune/ses-3/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3
run-pretest-ants-baboon2-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon2_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/sub-Prune/ses-2/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2
run-pretest-ants-baboon1-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon1_0p6)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
pwd
echo ""
ls macapype_CI_v2.1
echo ""
ls macapype_CI_v2.1/cerimed_baboon
echo ""
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/sub-Prune/ses-2/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1