Skip to content

Commit

Permalink
ENH: Add notebook run GitHub Actions workflow file
Browse files Browse the repository at this point in the history
Add notebook run GitHub Actions workflow file, and the accompanying
headless setup shell script.

Left behind by the Carpentries Workbench infrastructure automated
transition tool in commits 560b5b4, and 6dab472.
  • Loading branch information
jhlegarreta committed Feb 18, 2024
1 parent bdee382 commit 04941cc
Show file tree
Hide file tree
Showing 2 changed files with 152 additions and 0 deletions.
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

0 comments on commit 04941cc

Please sign in to comment.