try to fix kernel error #134
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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: ${{ steps.select_runner.outputs.runner }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Select runner | |
| id: select_runner | |
| run: | | |
| if [ "${{ github.repository }}" = "NeuroDesk/example-notebooks" ]; then | |
| echo "runner=self-hosted" >> $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@v4 | |
| - 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@v4 | |
| - 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 osfclient osfclient | |
| - 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: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./books/_build/**/**/html | |
| keep_files: true | |
| cname: www.neurodesk.org | |
| build-structure: | |
| needs: [ test-notebooks ] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install jupyter-book ghp-import graphviz ipyniivue | |
| - name: Run all | |
| shell: bash | |
| working-directory: ./books | |
| run: | | |
| export PATH=$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 |