spatial_ingestion_merscope-ci.yml

name: Run tutorials (spatial ingest merscope)

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

env:
  debug: 'true'

jobs:
  spatial_ingest_merscope:
    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
        if: env.debug == 'true'
        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 .[spatial]
          conda list

      - name: Conda info
        if: env.debug == 'true'
        shell: bash -el {0}
        run: conda info

      - name: Conda list
        if: env.debug == 'true'
        shell: pwsh
        run: conda list


      - name: Preparing the data
        run: |
          mkdir spatial spatial/ingestion_merscope spatial/ingestion_merscope/data
          cd spatial/ingestion_merscope/data 
          curl -L -o cell_by_gene.csv https://figshare.com/ndownloader/files/50899455
          curl -L -o cell_metadata.csv https://figshare.com/ndownloader/files/50899452
          curl -L -o cellpose_micron_space.parquet https://figshare.com/ndownloader/files/50899458
          # curl -L -o detected_transcripts.csv https://figshare.com/ndownloader/files/50899476
          mkdir images
          cd images 
          curl -L -o micron_to_mosaic_pixel_transform.csv https://figshare.com/ndownloader/files/50899449
        

      # Note: we run the following to test that the commands works
      - name: Preparing the configuration file
        shell: bash -el {0}
        run: |
          cd spatial/ingestion_merscope
          panpipes qc_spatial config

      - name: Preparing the submission file
        run: |
          cd spatial/ingestion_merscope
          curl -o sample_file_qc_merscope.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_merscope_data/sample_file_qc_merscope.txt

      - name: Preparing the yaml file
        run: |
          cd spatial/ingestion_merscope
          curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_merscope_data/pipeline.yml

      - name: File tree
        if: env.debug == 'true'
        run: tree spatial/ingestion_merscope

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

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

      - name: File tree
        if: env.debug == 'true'
        run: tree spatial/ingestion_merscope