integration_test.yml

name: Integration Tests

on:
  push:
    branches: 'main'
  pull_request:
    branches: 'main'
  workflow_dispatch:

jobs:
  build:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout repo
        uses: actions/checkout@v1
      
      - name: Set up Python 3.6
        uses: actions/setup-python@v2
        with:
          python-version: '3.6'

      - name: Install dependencies
        run: pip install wheel setuptools
    
      - name: Build package
        run: python setup.py bdist_wheel
    
      - name: Upload Python wheel
        uses: actions/upload-artifact@v3
        with:
          name: "Python wheel"
          path: ./dist/*
          if-no-files-found: error

  integration-tests:
    needs: build
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [macos-latest]
        python: ["3.10"]
    steps:
      - name: Checkout repo
        uses: actions/checkout@v1
      
      - name: Set up Python ${{ matrix.python }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python }}
      
      - name: Install dependencies
        run: pip install wheel setuptools
    
      - name: Download artifact
        uses: actions/download-artifact@v3
        with:
          name: "Python wheel"

      - name: Install wheel
        run: pip install --find-links=. vsi2tif-*
        shell: bash
      
      - name: Install vips
        run: |
          brew install --cask zulu@8
          brew install vips
      
      - name: Install bftools
        run: |
          wget http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip
          unzip bftools.zip
      
      - name: Download test data
        run: |
          wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-1.zip
          wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-2.zip
          unzip OS-1.zip
          unzip OS-2.zip
          mkdir WSI/
          mv OS-* WSI/
      
      - name: Test single conversion
        run: vsi2tif -i ./WSI/OS-2.vsi -o ./OS-2.tif -b bftools/bfconvert -v 0
        shell: bash

      - name: Test batch conversion
        run: vsi2tif -i ./WSI -o ./converted/ -b bftools/bfconvert -v 0
        shell: bash