filtering-ci.yml

name: Run tutorials (preprocessing)

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

env:
  debug: 'true'

jobs:
  preprocessing:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
        python-version: ["3.11"]

    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 -e .
          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

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

      - name: Preparing the data (artifact)
        uses: actions/download-artifact@v3
        with:
          name: teaseq_unfilt.h5mu
          path: teaseq/preprocessing/teaseq_unfilt.h5mu

      # 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/preprocessing
          panpipes preprocessing config

      - name: Edit the submission file
        run: |
          cd teaseq/preprocessing
          curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/efb55f083a8aeb1bc12f18ac61f6637b/pipeline.yml

      # - name: Replace template contents in configuration file
      #   run: |
      #     cd teaseq/preprocessing
      #     sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml

      - name: File tree
        if: env.debug == 'true'
        run: tree teaseq

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

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

      - name: File tree
        if: env.debug == 'true'
        run: tree teaseq