visualization-ci.yml

name: Run tutorials (visualization)

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

env:
  debug: 'true'

jobs:
  visualization:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
        python-version: ["3.10"]

    steps:
      - uses: actions/checkout@v4

      - name: File tree
        run: tree

      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          auto-activate-base: true
          auto-update-conda: true
          channels: conda-forge
          channel-priority: strict
          activate-environment: pipeline_env
          environment-file: pipeline_env.yaml

      - name: Install Panpipes
        shell: bash -el {0}
        run: |
          pip install -e .
          conda list

      - name: Conda info
        shell: bash -el {0}
        run: conda info

      - name: Conda list
        shell: pwsh
        run: conda list

      # Note: all three files are renamed during the download to trim the "subsample_" prefix
      - name: Preparing the data
        run: |
          mkdir -p teaseq/vis/data && cd teaseq/vis/data
          curl -L -o teaseq_clustered.h5mu https://figshare.com/ndownloader/files/43246446

      - name: Preparing the data
        run: |
          mkdir -p teaseq/vis && cd  teaseq/vis
          curl -o paired_scatters.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/69bf8febdd6c95141c3e20de10f533c4/paired_scatters.csv
          curl -o custom_markers.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/cd6f66ea922d4bd2b896050780f0d8dd/custom_markers.csv
          curl -o paired_scatters_markers.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/68a767929ecdc47cf945f855f58e046a/paired_scatters_markers.csv

      # Note: we run the following to test that the commands works
      # However, the following task will replacing the file anyway
      - name: Preparing the configuration file
        shell: bash -el {0}
        run: |
          cd teaseq/vis/data
          panpipes vis config

      - name: Edit the submission file
        run: |
          cd teaseq/vis
          curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/visualization/pipeline.yml

      - name: File tree
        run: tree teaseq

      - name: Review pipeline tasks
        shell: bash -el {0}
        run: |
          cd teaseq/vis
          panpipes vis show full --local

      - name: Run pipeline tasks
        shell: bash -el {0}
        run: |
          cd teaseq/vis
          panpipes vis make full --local  

      - name: File tree
        if: always()
        run: tree teaseq