Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: Add notebook run GitHub Actions workflow file #251

Merged
merged 1 commit into from
Feb 18, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 17 additions & 0 deletions .github/scripts/setup_headless.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
#!/bin/bash

echo "DISPLAY=:99.0" >> $GITHUB_ENV

if [ "$RUNNER_OS" == "Linux" ]; then
echo "LIBGL_ALWAYS_SOFTWARE=1" >> $GITHUB_ENV
echo "LIBGL_ALWAYS_INDIRECT=0" >> $GITHUB_ENV
sudo apt-get install -y libgl1-mesa-glx xvfb
Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
sleep 3
elif [ "$RUNNER_OS" == "Windows" ]; then
powershell ./tools/ci/install_opengl.ps1
elif [ "$RUNNER_OS" == "macOS" ]; then
echo 'Install Xquartz package for headless'
brew install --cask xquartz
fi

135 changes: 135 additions & 0 deletions .github/workflows/build-test.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,135 @@
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@v3
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@v3
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@v3
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@v4
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@v3

- 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
Empty file added data/.gitkeep
Empty file.
Loading