macos_test.yaml

name: Macos Tests

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

env:
  JSON_FPATH: outputs.json
  MACRO_FPATH: macro.ijm

jobs:
  integration-tests:
    strategy:
      fail-fast: false
      matrix:
        include:
          - name: ubuntu
            os: ubuntu-latest
            url_file_name: fiji-linux64.zip
            fiji_executable: ImageJ-linux64
          - name: macos-arm64
            os: macos-14
            url_file_name: fiji-macosx.zip
            fiji_executable: Contents/MacOS/ImageJ-macosx
          - name: macos-x86_64
            os: macos-13
            url_file_name: fiji-macosx.zip
            fiji_executable: Contents/MacOS/ImageJ-macosx
    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout code
        uses: actions/checkout@v4
      - name: Install Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.13'

      - name: Set up JDK 8
        uses: actions/setup-java@v4
        with:
          java-version: '8'
          distribution: 'zulu'

      - name: Set up Fiji
        shell: bash
        run: |
          mkdir -p fiji
          curl -L -o fiji.zip https://downloads.imagej.net/fiji/latest/${{ matrix.url_file_name }}
          unzip fiji.zip -d fiji

      - name: Build Plugin
        run: mvn clean package

      - name: Get plugin name and version
        shell: bash
        run: |
          MVN_VERSION=$(mvn -q \
            -Dexec.executable=echo \
            -Dexec.args='${project.version}' \
            --non-recursive \
            exec:exec)
          MVN_NAME=$(mvn -q \
            -Dexec.executable=echo \
            -Dexec.args='${project.name}' \
            --non-recursive \
            exec:exec)
          echo "version=${MVN_VERSION}" >> $GITHUB_OUTPUT
          echo "name=${MVN_NAME}" >> $GITHUB_OUTPUT
        id: mvn_info

      - name: Copy Plugin to Fiji
        shell: bash
        run: cp target/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/

      - name: Copy Plugin to Fiji
        shell: bash
        run: cp dl-modelrunner-0.5.11-SNAPSHOT.jar fiji/Fiji.app/plugins/

      - name: Download dependencies
        shell: bash
        run: |
          #curl -L --output-dir fiji/Fiji.app/jars/ -O "https://maven.scijava.org/content/groups/public/io/bioimage/dl-modelrunner/0.5.11-SNAPSHOT/dl-modelrunner-0.5.11-20241123.134210-7.jar"
          curl -L --output-dir fiji/Fiji.app/jars/ -O "https://repo1.maven.org/maven2/net/java/dev/jna/jna-platform/5.13.0/jna-platform-5.13.0.jar"
          curl -L --output-dir fiji/Fiji.app/jars/ -O "https://maven.scijava.org/content/groups/public/net/imglib2/imglib2/7.1.4/imglib2-7.1.4.jar"

      - name: Set up engine using Jython script and Fiji headless
        shell: bash
        run: |
          fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console scripts/download_engines.py -engines_path fiji/Fiji.app/engines

      - name: Unzip model to models folder
        shell: bash
        run: |
          unzip test_samples/brightfield_nuclei_.zip -d fiji/Fiji.app/models

      - name: check model is there
        shell: bash
        run: |
          ls fiji/Fiji.app/models/brightfield_nuclei

      - name: rm file
        shell: bash
        run: |
          rm fiji/Fiji.app/jars/imglib2-6.1.0.jar
          #rm /Users/runner/work/deepimagej-plugin/deepimagej-plugin/fiji/Fiji.app/jars/imglib2-6.1.0.jar
          #rm /home/runner/work/deepimagej-plugin/deepimagej-plugin/fiji/Fiji.app/jars/imglib2-6.1.0.jar

      - name: Create a New Directory
        run: mkdir -p outputs

      - name: Create a New Directory 2
        run: mkdir -p outputs_npy

      - name: CHEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEECK
        shell: bash
        run: |
          #ls fiji/Fiji.app/engines/pytorch-2.0.0-2.0.0-macosx-x86_64-cpu
          #ls fiji/Fiji.app/engines/pytorch-1.13.1-1.13.1-macosx-x86_64-cpu

      - name: Run macros
        shell: bash
        run: |
          fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console -macro test_samples/test.ijm

      - name: Convert to npy
        shell: bash
        run: |
          ls .github
          fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/to_numpy.py

      - name: Run final python
        shell: bash
        run: |
          python -m pip install numpy
          python .github/check_numpy_vals.py