combine_output.yml

name: combine output
# combine output from all simulations (combinations of forcing) into single files 
# so the combined footprint can be viewed
 
on:
  workflow_call:
    inputs:
      MODEL_TYPE:
        description: 'what kind of model are we running e.g. oil - a user defined input in run_ops.yml'
        required: true
        type: string
      BRANCH_REF:
        description: 'what branch are we on - defined dynamically in run_ops.yml'
        required: true
        type: string
      CONFIG_NAME:
        description: 'configuration name - defined dynamically in run_ops.yml'
        required: true
        type: string
      RUN_DATE:
        description: 'time of T0 of the croco workflow in format YYYYMMDD_HH - defined dynamically in run_ops.yml'
        required: true
        type: string
      RUNNER_NAME:
        description: 'specify the runner name to determine what server we are running on'
        required: true
        type: string
      EXTENTS:
        description: 'spatial extent of the gridded output and plot, in format lon0,lon1,lat0,lat1. If None, then this is dynamically determined from the geographic extent of the particles'
        required: true
        type: string
      DX_M:
        description: 'grid size (m) used to grid particle output. If None, If None, then a 50 x 50 regular grid is generated'
        required: true
        type: string

env:
  # path to the directory containing multiple run directories, as seen inside the local server 
  DIR_WITH_DIRS: /home/somisana/ops/${{ inputs.BRANCH_REF }}/${{ inputs.RUN_DATE }}/opendrift_${{ inputs.MODEL_TYPE }}/${{ inputs.CONFIG_NAME }}

jobs:
  combine_trajectories:
    runs-on: ${{ inputs.RUNNER_NAME }}
    steps:
      - name: combine trajectories files
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              combine_trajectories  \
                --dir_with_dirs /mnt/tmp

  combine_particle_density:
    needs: [combine_trajectories]
    runs-on: ${{ inputs.RUNNER_NAME }}
    steps:
      # I'm specifically not using the combine_gridded function here, as this creates the average over all runs
      # This is more relevant for say oil thickness, but for particle density I think it is better to create
      # The particle density again directly from the combined trajectories file (you can't do this for oil
      # as you'll end up with unrealistic oil thicknesses as you keep adding runs...)
      #- name: combine gridded particle density files
      #  run: |
      #    docker run \
      #      --rm \
      #      --user root \
      #      -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
      #      ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
      #        combine_gridded  \
      #          --dir_with_dirs /mnt/tmp \
      #          --fname_gridded gridded_particle_density.nc \
      #          --var_name particle_density
      - name: combined gridded particle density from combined particles
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              grid_particles  \
                --config_dir /mnt/tmp/combined \
                --fname trajectories.nc \
                --fname_gridded gridded_particle_density.nc \
                --grid_type density \
                --extents ${{ inputs.EXTENTS }} \
                --dx_m ${{ inputs.DX_M }}

      - name: animate the combined gridded particle density
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_particle_density.nc \
                --extents ${{ inputs.EXTENTS }} \
                --gif_out gridded_particle_density.gif

      - name: plot maximum combined gridded particle density
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded_stats  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_particle_density.nc \
                --var_str maximum \
                --cbar_label 'max. particle density (%)' \
                --extents ${{ inputs.EXTENTS }} \
                --jpg_out gridded_particle_density_max.jpg
      
      - name: plot minimum time to arrival
        # this doesn't relate to particle density, but just sneaking it into this job
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded_stats  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_particle_density.nc \
                --var_str minimum_time \
                --ticks 0,0.5,1,1.5,2,3,5,7 \
                --cbar_label 'minimum time (days)' \
                --extents ${{ inputs.EXTENTS }} \
                --jpg_out gridded_min_time.jpg

  combine_surface_oil:
    needs: [combine_trajectories]
    runs-on: ${{ inputs.RUNNER_NAME }}
    if: ${{ inputs.MODEL_TYPE == 'oil' }}
    steps:
      - name: combined surface oil thickness from particles (average over all runs)
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              combine_gridded  \
                --dir_with_dirs /mnt/tmp \
                --fname_gridded gridded_surface_oil.nc \
                --var_name surface_thickness

      - name: animate the combined surface oil thickness
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_surface_oil.nc \
                --extents ${{ inputs.EXTENTS }} \
                --var_str surface_thickness \
                --ticks 0,0.01,0.1,1,10 \
                --cbar_label 'surface oil thickness ($\mu$m)' \
                --cmap Greys \
                --gif_out gridded_surface_oil.gif

      - name: plot maximum surface oil thickness
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded_stats  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_surface_oil.nc \
                --extents ${{ inputs.EXTENTS }} \
                --var_str maximum \
                --ticks 0,0.01,0.1,1,10 \
                --cbar_label 'max. surface oil thickness ($\mu$m)' \
                --cmap Greys \
                --jpg_out gridded_surface_oil_max.jpg

  combine_stranded_oil:
    needs: [combine_trajectories]
    runs-on: ${{ inputs.RUNNER_NAME }}
    if: ${{ inputs.MODEL_TYPE == 'oil' }}
    steps:
      - name: combined gridded stranded oil concentration (average over all runs)
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              combine_gridded  \
                --dir_with_dirs /mnt/tmp \
                --fname_gridded gridded_stranded_oil.nc \
                --var_name stranded_oil

      - name: plot maximum stranded oil concentration
        run: |
          docker run \
            --rm \
            --user root \
            -v ${{ env.DIR_WITH_DIRS }}:/mnt/tmp \
            ghcr.io/saeon/somisana-opendrift_${{ inputs.BRANCH_REF }}:latest \
              animate  \
                --type gridded_stats  \
                --config_dir /mnt/tmp/combined \
                --fname_gridded gridded_stranded_oil.nc \
                --extents ${{ inputs.EXTENTS }} \
                --var_str maximum \
                --ticks 0,10,20,50,100,200,500,1000 \
                --cbar_label 'max. stranded oil (g m$^{-2}$)' \
                --cmap plasma \
                --jpg_out gridded_stranded_oil_max.jpg
  
  # copy data over to where it will be archived
  archive:
    needs: [combine_particle_density,combine_surface_oil,combine_stranded_oil]
    if: always()  # Ensure this job runs, even if the oil jobs are skipped
    runs-on: ${{ inputs.RUNNER_NAME }}
    env:
      ARCHIVE_DIR: /mnt/saeon-somisana/data/opendrift/${{ inputs.RUN_DATE }}/${{ inputs.CONFIG_NAME }}/combined
    steps:
      - name: copy files to the archive directory if needed
        run: |
          # start by changing ownership of all files to the somisana user
          sudo chown -R somisana:somisana ${{ env.DIR_WITH_DIRS }}/combined
          # only copy if we're on the main branch
          # we need to use sudo since the archive directory is owned by root
          # we have set up the somisana user to be able to do this without the need for a password
          if [ ${{ inputs.BRANCH_REF }} = "main" ]; then
            if [ ! -d ${{ env.ARCHIVE_DIR }} ]; then
              sudo mkdir -p ${{ env.ARCHIVE_DIR }}
              sudo chmod -R 775 ${{ env.ARCHIVE_DIR }}
            fi
            sudo cp -f ${{ env.DIR_WITH_DIRS }}/combined/*.nc ${{ env.ARCHIVE_DIR }}
            sudo cp -f ${{ env.DIR_WITH_DIRS }}/combined/*.gif ${{ env.ARCHIVE_DIR }}
            sudo cp -f ${{ env.DIR_WITH_DIRS }}/combined/*.jpg ${{ env.ARCHIVE_DIR }}
          fi