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build_on_prerelease.yml
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name: (Prerelease) Build Pipy, Dockerhub image and test
on:
release:
types: [prereleased]
jobs:
name: Build documentation
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 -e .[doc]
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: Build the Doc 🔧
run: |
cd docs
make clean
make html
touch _build/html/.nojekyll
- name: Deploy Github Pages 🚀
uses: JamesIves/[email protected]
with:
branch: gh-pages
folder: docs/_build/html/
clean: true
ssh-key: ${{ secrets.DEPLOY_KEY }}
build-n-publish-testpypi:
name: Build and publish Python to Test PyPI
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 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@master
with:
password: ${{ secrets.TEST_PYPI_API_TOKEN }}
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_nomcr
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
run-pretest-ants-t1-marmo:
name: Running all existing pipelines in macapype_CI.zip (ANTS marmo T1)
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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline marmo-marmobrain ANTS_noseg T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-marmo:
name: Running all existing pipelines in macapype_CI.zip (ANTS 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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/
run-pretest-ants-t1-baboon:
name: Running all existing pipelines in macapype_CI.zip (ANTS T1 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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-baboon:
name: Running all existing pipelines in macapype_CI.zip (ANTS 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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/
run-pretest-ants-macaque-t1:
name: Running all existing pipelines in macapype_CI.zip (ANTS macaque T1)
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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline macaque_prime-de ANTS_prep T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-macaque:
name: Running all existing pipelines in macapype_CI.zip (ANTS 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/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline macaque_prime-de ANTS_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 -nprocs 1
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-032140/ses-001/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2