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Merge pull request #257 from jhlegarreta/LimitNumpyVersion #373

Merge pull request #257 from jhlegarreta/LimitNumpyVersion

Merge pull request #257 from jhlegarreta/LimitNumpyVersion #373

Workflow file for this run

name: Build, test
on:
push:
branches: ['main']
pull_request:
# Allow a subsequently queued workflow run to interrupt previous runs
concurrency:
group: '${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
cancel-in-progress: true
jobs:
build:
if: "!contains(github.event.head_commit.message, '[skip ci]')"
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.9', '3.10', '3.11']
env:
ANTSPATH: /opt/ants
FSLPATH: /opt/fsl
FSLDIR: /opt/fsl
FSLOUTPUTTYPE: NIFTI_GZ
FSLVERSION: 6.0.6.5
steps:
- name: Cache Ubuntu dependencies
uses: actions/cache@v4
with:
path: |
/var/lib/apt
!/var/lib/apt/lists/partial
!/var/lib/apt/lists/lock
key: apt-cache-v1
restore-keys: |
apt-cache-v1
- name: Install Ubuntu dependencies
run: |
sudo apt-get update
sudo apt-get install -y --no-install-recommends \
bc \
bzip2 \
ca-certificates \
curl \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6
sudo apt-get clean
- name: Cache ANTs install
uses: actions/cache@v4
with:
path: /opt/ants
key: ants-v1
restore-keys: |
ants-v1
- name: Install ANTs
run: |
if [[ ! -d "${ANTSPATH}" ]]; then
sudo mkdir -p $ANTSPATH
curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | sudo tar -xzC $ANTSPATH --strip-components 1
fi
- name: Cache FSL install
uses: actions/cache@v4
with:
path: $FSLPATH
key: fsl-v2
restore-keys: |
fsl-v2
# Run with multiple Python versions
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install FSL
run: |
if [[ ! -d "${FSLPATH}" ]]; then
sudo mkdir -p $FSLPATH
curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -o /tmp/fslinstaller.py -s
python /tmp/fslinstaller.py -d ${FSLPATH} -V ${FSLVERSION} -o
sudo rm -rf ${FSLPATH}/data/atlases
rm /tmp/fslinstaller.py
fi
- name: Checkout GitHub repository
uses: actions/checkout@v4
- name: Install dependencies for headless display
run: |
${{ github.workspace }}/.github/scripts/setup_headless.sh
- name: Install Python requirements
if: steps.cache.outputs.cache-hit != 'true'
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install pytest nbval
- name: Download data
run: |
pushd `pwd`
cd ${{ github.workspace }}/data
osf -p cmq8a fetch ds000221_subject/ds000221_sub-010006.zip
unzip ds000221_sub-010006.zip
rm ds000221_sub-010006.zip
popd
- name: Run pytest on Jupyter notebooks
run: |
export PYTHONPATH=$PYTHONPATH:`realpath ${{ github.workspace }}`
export PATH=$FSLPATH/bin:$ANTSPATH:$PATH
pytest --nbval-lax -v code/introduction.ipynb
pytest --nbval-lax -v code/preprocessing.ipynb
pytest --nbval-lax -v code/diffusion_tensor_imaging.ipynb
pytest --nbval-lax -v code/constrained_spherical_deconvolution.ipynb
pytest --nbval-lax -v code/deterministic_tractography.ipynb
pytest --nbval-lax -v code/probabilistic_tractography.ipynb