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test_changed_notebook.yml
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# This workflows executes new or modified example notebooks.
name: test_changed_notebooks
defaults:
run:
shell: bash # To override PowerShell on Windows
on:
# Trigger the workflow on push or PR to any branch
push:
paths:
- '**/*.ipynb'
pull_request:
paths:
- '**/*.ipynb'
# don't trigger for draft PRs
types: [ opened, synchronize, reopened, ready_for_review ]
# Trigger the workflow on manual dispatch
workflow_dispatch:
jobs:
select-runner:
runs-on: ubuntu-22.04
outputs:
runner: ${{ steps.select_runner.outputs.runner }}
steps:
- uses: actions/checkout@v3
- name: Select runner
id: select_runner
run: |
if [ "${{ github.repository }}" = "NeuroDesk/example-notebooks" ]; then
echo "runner=self-hosted" >> $GITHUB_OUTPUT
# echo "runner=cirun-oracle--${{ github.run_id }}" >> $GITHUB_OUTPUT
else
echo "runner=ubuntu-22.04" >> $GITHUB_OUTPUT
fi
get-notebooks:
runs-on: ubuntu-22.04
outputs:
notebook_list: ${{ steps.list_changed_notebooks.outputs.notebook_list }}
steps:
- uses: actions/checkout@v3
- name: Find all notebooks with changes
id: find_changed_notebooks
uses: tj-actions/[email protected]
with:
path: "./books"
files: "**/*.ipynb"
dir_names_exclude_current_dir: "true"
- name: Filter down to changed notebooks
id: list_changed_notebooks
run: |
echo ${{ steps.find_changed_notebooks.outputs.all_changed_and_modified_files }}
changed_notebooks=$(echo "${{ steps.find_changed_notebooks.outputs.all_changed_and_modified_files }}")
notebook_list='['
for NOTEBOOK in $(echo "${changed_notebooks}"); do
notebook_list+="\"${NOTEBOOK}\","
done
notebook_list=$(sed '$s/,$//' <<< $notebook_list)
notebook_list+=']'
echo "notebook_list=${notebook_list}"
echo "notebook_list=${notebook_list}" >> $GITHUB_OUTPUT
test-notebooks:
needs: [ select-runner, get-notebooks ]
if: ${{ needs.get-notebooks.outputs.notebook_list != '[]' }}
runs-on: ${{ needs.select-runner.outputs.runner }}
timeout-minutes: 1400
strategy:
fail-fast: false
matrix:
notebooks: ${{ fromJson(needs.get-notebooks.outputs.notebook_list) }}
steps:
- uses: actions/checkout@v3
- name: Test singularity and cvmfs before pushing to neurocommand
run:
/bin/bash .github/workflows/setup_cvmfs.sh
- name: Install dependencies
shell: bash
run: |
python -m pip install --upgrade pip
python -m pip install jupyter-book ghp-import graphviz ipyniivue
- name: Run ${{ matrix.notebooks }}
shell: bash
timeout-minutes: 1400
working-directory: ./books
run: |
echo ${{ github.workspace }}
echo $GITHUB_WORKSPACE
export PATH=$HOME/.local/bin:$PATH
echo "PATH=$PATH"
export LD_PRELOAD=
echo "LD_PRELOAD=$LD_PRELOAD"
export APPTAINER_BINDPATH=${{ github.workspace }},/cvmfs
echo "APPTAINER_BINDPATH=$APPTAINER_BINDPATH"
export LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod
export MPLCONFIGDIR=${{ github.workspace }}/matplotlib-mpldir
export MODULEPATH=$(find /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/ -maxdepth 1 -mindepth 1 -type d -exec realpath {} \; | tr '\n' ':')
echo "MODULEPATH=$MODULEPATH"
echo "NOTEBOOK=$(basename -s .ipynb ${{ matrix.notebooks }})" >> $GITHUB_ENV
echo "DIRNAME=$(dirname ${{ matrix.notebooks }})" >> $GITHUB_ENV
jb build ${{ matrix.notebooks }}
- name: Restructure
shell: bash
run: |
tree ./books/_build/**/**/html
mkdir -p ./books/_build/**/**/html/$DIRNAME
cp -R ./books/_build/**/**/html/_static ./books/_build/**/**/html/$DIRNAME
if [ -d ./books/_build/**/**/html/_images ]; then
cp -R ./books/_build/**/**/html/_images ./books/_build/**/**/html/$DIRNAME
fi
cp ./books/_build/**/**/html/$NOTEBOOK.html ./books/_build/**/**/html/$DIRNAME
- name: Push to GitHub Pages
uses: peaceiris/[email protected]
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./books/_build/**/**/html
keep_files: true
cname: www.neurodesk.org
build-structure:
needs: [ test-notebooks ]
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- name: Install dependencies
shell: bash
run: |
python -m pip install --upgrade pip
python -m pip install jupyter-book ghp-import graphviz ipyniivue
- name: Run all
shell: bash
working-directory: ./books
run: |
export PATH=$HOME/.local/bin:$PATH
sed -i 's/execute_notebooks: .*/execute_notebooks: off/' _config.yml
cat _config.yml
jb build .
- name: Push to GitHub Pages
uses: peaceiris/[email protected]
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./books/_build/html
keep_files: true
cname: www.neurodesk.org