Feature/multi file #101
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| 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.dylib" | |
| elif [[ "${{ runner.os }}" == "Linux" ]]; then | |
| RID="linux-x64" | |
| LIB_FILE="ThermoNativeReader.so" | |
| else | |
| RID="win-x64" | |
| LIB_FILE="ThermoNativeReader.dll" | |
| 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 -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 -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 |