main.yml

# Analysis workflow code

name: Analysis CI # ===========================================================

on: # controls when the workflow will run

  push: # trigger workflow on push events, but only for the master branch
    branches: [ master ]
    paths-ignore:
      - "README.md" # don't rebuild on documentation changes

  pull_request: # triggers workflow on pull request events (master branch only)
    branches: [ master ] # ensure changes are "mergeable"

  workflow_dispatch: # permits manual triggers from the Actions tab

jobs: # =======================================================================

  # ---------------------------------------------------------------------------
  fit: # fit Bayesian models and apply Horvitz–Thompson estimators
  # ---------------------------------------------------------------------------

    strategy:
      matrix:
        rfiles: [example-1/complete, example-1/null, example-1/ht,
                 example-2/hrs_wyppt_mm, example-2/wyppt_mm, example-2/ht,
                 example-3/canopy-gaps-2021, example-3/canopy-gaps-naive-2021,
                 example-3/ht]
    runs-on: ubuntu-latest

    steps:

      # Checkout the repo so the workflow can access it
      - name: Checkout this repo's action(s)
        uses: actions/checkout@v2

      # Pull the needed, protected data from the NPS Data Store
      # At the moment this is VERY inefficient because it's repeated for each job
      - name: Get protected data from the Data Store
        run: |
          ./get-inputs.sh
          ls -R

      # Run analyses and compile results
      - name: Fit models and compile results
        id: compile
        uses: ./.github/actions/call-r
        with:
          rfile: ${{ matrix.rfiles }}/calling-script.R

      # # Replace slashes with dashes in rfile path (for valid artifact names)
      # - name: Run find-and-replace to remove slashes
      #   uses: mad9000/actions-find-and-replace-string@1
      #   id: findandreplace
      #   with:
      #     source: ${{ matrix.rfiles }}
      #     find: '/'
      #     replace: '-'

      # Each artifact behaves as a file share. Uploading to the same artifact
      # multiple times in the same workflow can overwrite and append already
      # uploaded files.
      - name: Upload artifacts
        uses: actions/upload-artifact@v2
        with:
          name: artifact-${{ github.sha }} # ${{ steps.findandreplace.outputs.value }}-artifact
          path: output # ${{ github.workspace }}
          retention-days: 1

  # ---------------------------------------------------------------------------
  design: # study area map and missingness concept figs
  # ---------------------------------------------------------------------------

    # strategy:
    #   matrix:
    #     rfiles: [map.R, panel-design/cartoon.R]
    runs-on: ubuntu-latest

    steps:

      # Checkout the repo so the workflow can access it
      - name: Checkout this repo's action(s)
        uses: actions/checkout@v2

      # Download and unpack NPS boundaries
      - name: Download geospatial data
        run: |
          wget -P assets https://irma.nps.gov/DataStore/DownloadFile/662130
          unzip assets/662130 -d assets/nps_boundary
          rm assets/662130

      # Use leaflet to create study area map
      - name: Create map
        uses: ./.github/actions/call-r
        with:
          rfile: map.R

      # Create concept figure for revisit design
      - name: Revisit schedule
        uses: ./.github/actions/call-r
        with:
          rfile: panel-design/cartoon.R

      # Push changes made to the repo during a workflow run
      - name: Commit context figs
        uses: EndBug/add-and-commit@v7
        with:
          default_author: github_actions
          branch: master
          add: "assets/*.jpg"
          message: Automatic update of map

  # ---------------------------------------------------------------------------
  visualize: # use outputs from previous job to develop manuscript figures
  # ---------------------------------------------------------------------------

    needs: fit
    strategy:
      matrix:
        plotters: [example-1, example-2, example-3]
    runs-on: ubuntu-latest

    steps:

      # Checkout the repo so the workflow can access it
      - name: Checkout this repo's action(s)
        uses: actions/checkout@v2
        with:
          lfs: true

      # Cache LFS assets
      - name: generate lfs file list
        run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
      - name: restore lfs cache
        uses: actions/cache@v2
        id: lfs-cache
        with:
          path: .git/lfs
          key: ${{ runner.os }}-lfs-${{ hashFiles('.lfs-assets-id') }}-v1
      - name: pull lfs files
        run: git lfs pull

      # Download artifacts
      - name: Download file share
        uses: actions/download-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: output
      - name: Display structure of downloaded files
        run: ls -R

      # Use the cached results
      - name: Use cached results
        # id: publish
        uses: ./.github/actions/call-r
        with:
          rfile: ${{ matrix.plotters }}/plotting.R

      # # Delete temporary file store
      # - uses: geekyeggo/delete-artifact@v1
      #   with:
      #     name: artifact-${{ github.sha }}
      #     # failOnError: false

      # Upload results
      - name: Upload Artifact
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.plotters }}-results # was: ${{ steps.findandreplace.outputs.value }}-artifact
          path: assets/${{ matrix.plotters }}
          retention-days: 1

      # Push changes made to the repo during a workflow run
      - name: Commit changes
        uses: EndBug/add-and-commit@v7
        with:
          default_author: github_actions
          branch: master
          add: "assets/${{ matrix.plotters }}/example-*-fig*.jpg" # --force
          message: Automatic update of all tracked analysis assets
          # push: origin assets --force

      # # Use the output from the `publish` step
      # - name: Get task completion time
      #   run: echo "The time was ${{ steps.publish.outputs.time }}"

  # ---------------------------------------------------------------------------
  cleanup: # misc housekeeping
  # ---------------------------------------------------------------------------

    needs: [fit, visualize]
    runs-on: ubuntu-latest

    steps:

      # Delete temporary file store
      - uses: geekyeggo/delete-artifact@v1
        with:
          name: artifact-${{ github.sha }}
          # failOnError: false