main.yml

name: smart heating workflow

on:
  schedule:
    # * is a special character in YAML so you have to quote this string
    - cron:  '30 0,12 * * *'
    
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: cdo
          python-version: 3.9
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: true
      - name: Install packages
        run: |
          conda install cdo=1.9.10 s3fs=2021.8.1 pip=21.2.4 pandas=1.3.3 bokeh=2.3.3
          conda list
      # Runs a set of commands using the runners shell
      - name: Fetch Hirlam FMI grib data, select area and convert to netCDF
        run: |
          python get_hirlam_FMI.py
          cdo -f nc -t ecmwf copy -sellonlatbox,10,11,59,60 numerical-hirlam74-forecast-Temperature.grb2 numerical-hirlam74-forecast-Temperature.netcdf
      - name: Start Galaxy workflow with planemo
        run: |
          python -m venv planemo
          . planemo/bin/activate
          pip install galaxy-tool-util==21.9.2 planemo==0.74.11
          GALAXY_TAG=$(cat numerical-hirlam74-forecast-Temperature.txt)
          planemo run af528de055395eae smart_heating.yml --galaxy_url https://usegalaxy.eu/ --galaxy_user_key ${{ secrets.GALAXY_API_KEY }} --history_name "smart heating" --tags "smart_heating,$GALAXY_TAG"
      - name: Fetch and plot results from Galaxy history
        run: |
          pip install bioblend==0.18.0 click
          python get_dataset_from_history.py --galaxy-server https://usegalaxy.eu/ --galaxy-user-key ${{ secrets.GALAXY_API_KEY }} --tags "smart_heating,$GALAXY_TAG" --dataset-name "Filter Tabular on data 5"
          python plotting_temperature.py --in-file Filter_Tabular_on_data_5 --out-file plotting_temperature.html
      - name: Commit changes to branch
        run: |
          git config --global user.name 'Anne Fouilloux'
          git config --global user.email 'annefou@users.noreply.github.com'
          git commit -am "Automated plotting $GALAXY_TAG"
          git push