test.yml

name:Test

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main, development ]

jobs:
  test:
    runs-on: ${{ matrix.os }}
    env:
      PYTHONNET_RUNTIME: coreclr
    strategy:
      matrix:
        os: [ubuntu-latest]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Setup .NET
      uses: actions/setup-dotnet@v4
      with:
        dotnet-version: 8.0.x

    - name: Install NativeAOT dependencies (Linux)
      if: runner.os == 'Linux'
      run: |
        sudo apt-get update
        sudo apt-get install -y clang zlib1g-dev libkrb5-dev

    - name: Publish NativeAOT lib
      run: |
        cd native/ThermoNativeReader
        if [[ "${{ runner.os }}" == "macOS" ]]; then
          ARCH=$(uname -m)
          if [[ "$ARCH" == "arm64" ]]; then RID="osx-arm64"; else RID="osx-x64"; fi
          LIB_FILE="ThermoNativeReader"
        elif [[ "${{ runner.os }}" == "Linux" ]]; then
          RID="linux-x64"
          LIB_FILE="ThermoNativeReader"
        else
          RID="win-x64"
          LIB_FILE="ThermoNativeReader.exe"
        fi
        dotnet publish -r $RID -c Release -p:PublishAot=true
        echo "DYLIB_PATH=$(pwd)/bin/Release/net8.0/$RID/publish/$LIB_FILE" >> $GITHUB_ENV

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.12'

    - name: Install Rust
      uses: dtolnay/rust-toolchain@stable

    - name: Install dependencies
      run: |
        python -m venv .venv
        source .venv/bin/activate
        pip install maturin pytest numpy
        pip install fisher-py

    - name: Decompress test data
      run: gunzip -d -k test_data/*.gz
    - name: Download test data
      run: |
        wget -q -P test_data ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD066718/20250411_Ast0_500SPD_EVO685_JVO_EV1107_050ng_HEK-CPR_380-980_2Th_1P5ms_OFF_05_20250413081131.raw
        wget -q -P test_data https://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD066944/20250307_AST0_NEO5_JVO_MV50_DR_100SPD_10ng_HEK_Ref_DDA_2Th_1p5ms_10ms_v2Ref_cycle_03.raw

    - name: Build and test
      run: |
        source .venv/bin/activate
        # Patch fisher-py
        python .github/patch_fisher_py.py
        # Copy native lib for bundling
        cp ${{ env.DYLIB_PATH }} native_fisher_py/python/native_fisher_py/
        
        # Install the package
        pip install ./native_fisher_py
        
        # Parity tests will automatically fall back to ground_truth.json if fisher-py fails
        python -m pytest tests