main.yml

# Model workflow code

name: Model CI # ==============================================================

on: # controls when the workflow will run

  push: # trigger workflow on push events, but only for the main branch
    branches: [ main ]
    paths:
      - "model-api/**"
      - ".github/actions/build-model/**"
      - ".github/workflows/main.yml"
      - "st-kit/**"
      - "!README.md" # don't rebuild on documentation changes

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

  workflow_dispatch: # permits manual triggers from the Actions tab
    # inputs:
    #   debug_enabled:
    #     description: 'Run the build with tmate debugging enabled'
    #     required: false
    #     default: false

  # workflow_run:
  #   workflows: [ "Docker" ]
  #   branches: [ main ]
  #   types: [ completed ]

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

  # ---------------------------------------------------------------------------
  count-vars: # creates template models for count data
  # ---------------------------------------------------------------------------

    strategy:
      matrix:
        likelihood: [ poisson, 
                      negative-binomial-simple, negative-binomial, 
                      gen-pois,
                      zero-inflated-poisson, zero-inflated-negative-binomial ]
        link: [ linear, exponential ]
        gle: [ b0, b0-b1 ]
        include:
          # Includes a new variable demo with a value of true for the matrix leg
          # matching the following likelihood, link, and gle.
          - likelihood: poisson
            link: exponential
            gle: b0-b1
            demo: true
        exclude:
          # excludes parameterizations
          - likelihood: gen-pois
            link: linear
    runs-on: ubuntu-latest
    # if: ${{ github.event.workflow_run.conclusion == 'success' }}

    steps:
      - uses: actions/checkout@v2
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api

      # Build the JAGS model and save it in tmp
      - name: Build model
        uses: ./.github/actions/build-model # composite action to create model
        with:
          data-type: ${{ github.job }}
          likelihood: ${{ matrix.likelihood }}
          link: ${{ matrix.link }}
          gle: ${{ matrix.gle }}
          demo: ${{ matrix.demo }}

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

  # ---------------------------------------------------------------------------
  binomial-vars: # creates template models for successes / trials data
  # ---------------------------------------------------------------------------

    strategy:
      matrix:
        likelihood: [ binomial, beta-binomial ] # zero-inflated-binomial, zero-inflated-beta-binomial
        link: [ inverse-logit ]
        gle: [ b0, b0-b1 ]
        include:
          - likelihood: binomial
            link: inverse-logit
            gle: b0
            demo: true

    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api

      - name: Build model
        uses: ./.github/actions/build-model # composite action to create model
        with:
          data-type: ${{ github.job }}
          likelihood: ${{ matrix.likelihood }}
          link: ${{ matrix.link }}
          gle: ${{ matrix.gle }}
          demo: ${{ matrix.demo }}

      - name: Upload tmp directory as an artifact
        uses: actions/upload-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp
          retention-days: 1

  # ---------------------------------------------------------------------------
  nonnegative-continuous-vars: # template models for non-zero continuous data
  # ---------------------------------------------------------------------------
  
    strategy:
      matrix:
        likelihood: [ lognormal, gamma ] #, beta-binomial
        link: [ linear ] # TODO: is exponential here even an option?
        gle: [ b0, b0-b1 ]
        include:
          - likelihood: gamma
            link: linear
            gle: b0-b1
            demo: true
  
    runs-on: ubuntu-latest
  
    steps:
      - uses: actions/checkout@v2
        # with:
        #   submodules: true  # fetch model and data API submodules
        #   fetch-depth: 0    # fetch all history for .GitInfo and .Lastmod
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api
  
      - name: Build model
        uses: ./.github/actions/build-model # composite action to create model
        with:
          data-type: ${{ github.job }}
          likelihood: ${{ matrix.likelihood }}
          link: ${{ matrix.link }}
          gle: ${{ matrix.gle }}
          demo: ${{ matrix.demo }}
  
      - name: Upload tmp directory as an artifact
        uses: actions/upload-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp
          retention-days: 1

  # ---------------------------------------------------------------------------
  define-jags-model-matrix:
  # ---------------------------------------------------------------------------

    needs: [ count-vars, binomial-vars, nonnegative-continuous-vars ]
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2

      - name: Download file share
        uses: actions/download-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp

      - name: Create JAGS model file list as a JSON array
        id: set-matrix # we need an "id" so we can use it in "outputs" below
        run: |
          echo "::set-output name=matrix::$(find tmp -name "model.jags" | \
          perl -e 'use JSON; @in=grep(s/\n$//, <>); print encode_json(\@in)."\n";')"

      - name: Copy model files into model zoo in assets
        run: |
          find tmp -type f -name '*.jags'
          find tmp -type f -name '*.jags' \
            -exec bash -c '
              ZOO=$(sed "s/tmp/assets\/model-zoo/g" <<< $(dirname $0))
              mkdir -p $(dirname $ZOO) && cp $0 $ZOO-model.jags' {} \;

      # 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: main
          add: "assets/**/*-model.jags" # --force
          message: Automatic update of model files in model zoo

    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}

  # ---------------------------------------------------------------------------
  use-jags-models-to-sim-data: # create dynamic matrix from json, simulate data
  # ---------------------------------------------------------------------------

    needs: [ define-jags-model-matrix ]
    runs-on: ubuntu-latest

    strategy:
      matrix:
        jags-model: ${{ fromJson(needs.define-jags-model-matrix.outputs.matrix) }}
        options: [ --seed=123 ]

    steps:
      - uses: actions/checkout@v2
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api

      - name: Download file share
        uses: actions/download-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp

      - name: Use cached results (simulate data and fit model)
        id: verify
        uses: ./.github/actions/call-r
        with:
          rfile: model-api/demo/sim.R
          args: ${{ matrix.jags-model }}
          opts: ${{ matrix.options }}

      - name: Check status of model verification
        run: echo "The exit status was ${{ steps.verify.outputs.code }}"

      - name: Upload tmp directory as an artifact
        uses: actions/upload-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp
          retention-days: 1

  # ---------------------------------------------------------------------------
  cleanup: # summarize sim fits, and write demo data to assets/_data
  # ---------------------------------------------------------------------------

    needs: [ use-jags-models-to-sim-data ]
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api

      - name: Download file share
        uses: actions/download-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp

      - name: Move datasets flagged for demo to assets/_data
        run: |
          mkdir -p assets/_data
          HINT_FILE=assets/_data/.generating-models.csv
          rm -f $HINT_FILE && touch $HINT_FILE
          echo file, generating_model >> $HINT_FILE
          find tmp -type f -name 'demo' \
            -exec bash -c '
              DD_DIR=$(dirname $0)
              DD_LAB=$(echo $0 | grep -oP "(?<=tmp/).*(?=-vars)")
              DD_CSV=assets/_data/$DD_LAB-data.csv
              echo $DD_CSV, $(basename $DD_DIR) >> assets/_data/.generating-models.csv
              cp $DD_DIR/samples.csv $DD_CSV
              cp $DD_DIR/sample-*.csv assets/_data' {} \;
          ls assets/_data

      # 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: main
          add: "assets/_data/**"
          message: Automatic update of demo data

      - name: Create model config file list as a JSON array
        id: config-file-list # we need an "id" so we can use it in "outputs" below
        run: |
          echo "::set-output name=matrix::$(find assets -name "[a-z]*.yml" | \
          perl -e 'use JSON; @in=grep(s/\n$//, <>); print encode_json(\@in)."\n";')"

    outputs:
      configs: ${{ steps.config-file-list.outputs.matrix }}

  # ---------------------------------------------------------------------------
  test: # use simulated data in the analysis pipeline
  # ---------------------------------------------------------------------------

    needs: [ cleanup ]
    runs-on: ubuntu-latest

    strategy:
      matrix:
        config-file: ${{ fromJson(needs.cleanup.outputs.configs) }}
        # options: [ --n-adapt=1000 --n-update=5000 --n-iter=2500 --n-cores=1 --rm-dqs ]

    steps:
      - uses: actions/checkout@v2
      - name: Pull model API from GitLab
        run: |
          git submodule update --init --remote model-api

      - name: Download file share
        uses: actions/download-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp

      - name: Test model API using data simulated in prior job
        uses: ./.github/actions/call-r
        with:
          rfile: model-api/analysis-pipeline.R
          args: ${{ matrix.config-file }}
          opts: '--n-adapt=2000 --n-update=6000 --n-iter=3000 --n-cores=1 --rm-dqs' # ${{ matrix.options }}

      # # Enable tmate debugging of manually-triggered workflows if the input
      # # option was provided (i.e., debug_enabled=true)
      # - name: Setup tmate session
      #   uses: mxschmitt/action-tmate@v3
      #   # if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}

      - run: sudo mv assets/_output tmp/test-fits
      - name: Upload tmp directory as an artifact
        uses: actions/upload-artifact@v2
        with:
          name: artifact-${{ github.sha }}
          path: tmp
          retention-days: 1