run-all-notebooks.yaml

# This notebook will run all Python notebooks
#
# The environment variable NOTEBOOKS should contain all notebooks, so if you
# create a new one or notice a missing notebook, please feel free to add it!

name: run all notebooks

on:
  workflow_dispatch:
  schedule:
      - cron: '40 12 * * 1'

jobs:
  run_all_notebooks:
    runs-on: ubuntu-latest
    env:
        NOTEBOOKS: |
          (
            "examples/core_examples/FileIO_DataStore.ipynb"
            "examples/core_examples/hyperbolic_magnitude_test.ipynb"
            "examples/core_examples/iterator_test.ipynb"
            "examples/core_examples/Run_Pipe.ipynb"
            "examples/core_examples/Pipe_Example.ipynb"
            "examples/creation_examples/posterior-demo.ipynb"
            "examples/creation_examples/degradation-demo.ipynb"
            "examples/creation_examples/example_GridSelection_for_HSC.ipynb"
            "examples/creation_examples/example_SpecSelection_for_zCOSMOS.ipynb"
            "examples/estimation_examples/NZDir.ipynb"
            "examples/estimation_examples/test_sampled_summarizers.ipynb"
            "examples/goldenspike_examples/goldenspike.ipynb"
          )
    steps:
      - name: Checkout repo
        uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.9'

      - name: Install dependencies
        run: |
         python -m pip install --upgrade pip
         pip install wheel numpy # For somoclu
         pip install .
         pip install git+https://github.com/LSSTDESC/rail_bpz@lynn/rail-directory-match
         pip install flake8 pytest pytest-cov mockmpi pytest-timeout
         pip install -r docs/requirements.txt
         pip install -r docs/nbconvert-requirements.txt
         pip install jupyter nbconvert nbformat

      - name: Core notebooks
        shell: bash
        run: |
          allnotebooks=${{ env.NOTEBOOKS }}
          for notebook in ${allnotebooks[*]}; do
            if [[ $notebook == *"core_examples"* ]]; then
              jupyter nbconvert --to html --execute "$notebook"
            fi
          done
          
      - name: Creation notebooks
        shell: bash
        run: |
          allnotebooks=${{ env.NOTEBOOKS }}
          for notebook in ${allnotebooks[*]}; do
            if [[ $notebook == *"creation_examples"* ]]; then
              jupyter nbconvert --to html --execute "$notebook"
            fi
          done
          
      - name: Estimation notebooks
        shell: bash
        run: |
          allnotebooks=${{ env.NOTEBOOKS }}
          for notebook in ${allnotebooks[*]}; do
            if [[ $notebook =~ "estimation_examples" ]]; then
              jupyter nbconvert --to html --execute "$notebook"
            fi
          done
          
      - name: Goldenspike notebooks
        shell: bash
        run: |
          allnotebooks=${{ env.NOTEBOOKS }}
          for notebook in ${allnotebooks[*]}; do
            if [[ $notebook =~ "goldenspike_examples" ]]; then
              jupyter nbconvert --to html --execute "$notebook"
            fi
          done
          
      - name: Other notebooks
        shell: bash
        run: |
          allnotebooks=${{ env.NOTEBOOKS }}
          for notebook in ${allnotebooks[*]}; do
            if [[ ! $notebook =~ "core_examples" &&
                  ! $notebook =~ "creation_examples" &&
                  ! $notebook =~ "estimation_examples" &&
                  ! $notebook =~ "goldenspike_examples" ]]; then
              jupyter nbconvert --to html --execute "$notebook"
            fi
          done