test_changed_notebook.yml

# 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=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/changed-files@v38.1.0
      with:
        files: "books/**"
        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: ubuntu-22.04
    
    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
      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"
        sed -i 's/timeout:.*/timeout: 200/' _config.yml
        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/actions-gh-pages@v3.7.3
      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/actions-gh-pages@v3.7.3
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: ./books/_build/html
        keep_files: true
        cname: www.neurodesk.org