render.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.

name: Render Rmd

on:
  push:
    branches: [ "main" ]
  pull_request:

defaults:
  run:
    shell: bash -l {0}

jobs:
  jupyter-build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest] #, macos-latest]

    steps:
      - uses: actions/checkout@v3

      - uses: mamba-org/provision-with-micromamba@main
        with:
          cache-downloads: true
          cache-env: true
          environment-name: qmn
          environment-file: environment.yml

      - name: Execute and export
        run: |
          jupytext --to notebook modules/**/*.py
          jupyter nbconvert --NbConvertApp.recursive_glob=True --output-dir=modules/jupyter --execute --to html modules/**/*.ipynb

      - name: Upload artifacts
        uses: actions/upload-artifact@v3
        with:
          path: modules/jupyter/

  Rmd-build:
    needs: jupyter-build
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest] #, macos-latest]

    steps:
      - uses: actions/checkout@v3

      - name: Set up R
        uses: r-lib/actions/setup-r@v2

      - name: Set up Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2

      - name: Cache Reference
        uses: actions/cache@v3
        with:
          path: modules/module_3/data/reference
          key: constant

      # - uses: mxschmitt/action-tmate@v3

#       - name: Render
#         run: Rscript render.R

      - name: Download jupyter artifacts
        uses: actions/download-artifact@v3
        with:
          path: modules/jupyter/

      - name: Generate index
        if: matrix.os == 'ubuntu-latest' && github.ref == 'refs/heads/main'
        run: Rscript genIndex.R

      - name: Deploy
        if: matrix.os == 'ubuntu-latest' && github.ref == 'refs/heads/main'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: .