ingestion-ci.yml

name: Ingestion CI

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

env:
  debug: 'true'

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4
      
      - 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 # consider moving to etc/pipeline_env.yaml

      - 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: Run tests
      #  shell: bash -el {0}
      #  run: |
      #    python -m pytest tests/

      - name: Preparing the data
        run: |
          mkdir -p teaseq/ingest/data.dir
          curl -o teaseq/ingest/data.dir/subsample_adt.h5ad https://figshare.com/ndownloader/files/41671551
          curl -o teaseq/ingest/data.dir/subsample_atac.h5ad https://figshare.com/ndownloader/files/41671554
          curl -o teaseq/ingest/data.dir/subsample_rna.h5ad https://figshare.com/ndownloader/files/41671557
      
      - name: Preparing the configuration file
        shell: bash -el {0}
        run: panpipes ingest config