dotnet.yml

name: Build and Test

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

env:
  DOTNET_VERSION: 10.0.x

jobs:
  build:
    runs-on: windows-latest
    timeout-minutes: 30
    steps:
    - uses: actions/checkout@v4
    - name: Set up .NET
      uses: actions/setup-dotnet@v4
      with:
        dotnet-version: ${{ env.DOTNET_VERSION }}
    - name: Restore dependencies
      run: cd mzLib && dotnet restore
    # Request the platform explicitly. The solution offers both x64 and Any CPU, and MSBuild silently
    # prefers Any CPU as a solution's default, so an unqualified build would depend on that preference
    # rather than on anything stated here. Any CPU is what the released package is built as.
    - name: Build
      run: cd mzLib && dotnet build --no-restore /p:Platform="Any CPU"
    - name: Build (Test)
      run: cd mzLib && dotnet build --no-restore ./Test/Test.csproj
    # A '.' in a test name is spliced into the fully-qualified name, which Test Explorer / vstest
    # split on '.' -- fragmenting the tree into phantom nodes that cannot be expanded or run.
    # Runs before the suite so a naming regression fails in seconds rather than after the full run.
    - name: Check test name hygiene
      shell: pwsh
      run: ./.github/scripts/Check-TestNameHygiene.ps1 -Project mzLib/Test/Test.csproj -NoBuild
    - name: Add coverlet collector (Test)
      run: cd mzLib && dotnet add Test/Test.csproj package coverlet.collector -v 6.0.2
    - name: Test
      # Exclude live external-service tests (Koina, etc.) from the required run; they run in the
      # separate, non-blocking external-service job below. ExternalService supersedes the old Koina filter.
      run: cd mzLib && dotnet test --no-build --verbosity normal --filter "Category!=ExternalService" --collect:"XPlat Code Coverage" /p:CoverletOutputFormat=cobertura ./Test/Test.csproj
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v4
      env:
        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
        verbose: true
        files: mzLib/Test*/TestResults/*/coverage.cobertura.xml
  # Runs mzLib's live external-service tests (Koina). Intentionally NOT a required status check, so a
  # third-party outage never blocks a PR; the tests self-classify (outage -> Skipped, real break -> Fail).
  # Do NOT add this job to branch-protection required checks.
  external-service-tests:
    runs-on: windows-latest
    timeout-minutes: 20
    steps:
    - uses: actions/checkout@v4
    - name: Set up .NET
      uses: actions/setup-dotnet@v4
      with:
        dotnet-version: ${{ env.DOTNET_VERSION }}
    - name: Restore dependencies
      run: cd mzLib && dotnet restore
    - name: Build (Test)
      run: cd mzLib && dotnet build --no-restore ./Test/Test.csproj
    - name: Test (external services)
      run: cd mzLib && dotnet test --no-build --verbosity normal --filter "Category=ExternalService" ./Test/Test.csproj
  integration:
    runs-on: windows-latest
    timeout-minutes: 45
    steps:
    - uses: actions/checkout@v4
    # This job builds MetaMorpheus as well as mzLib, so it needs whatever SDK MetaMorpheus's
    # global.json asks for. setup-dotnet installs into a user-local dotnet root and the resolver then
    # sees ONLY what this step installed, so the runner's preinstalled SDKs do not count. Both repos
    # are on .NET 10, so one band. Note this job cannot pass while mzLib's target framework is ahead
    # of MetaMorpheus's -- a net10.0-only package is NU1202-incompatible with a net8.0 consumer, which
    # no amount of installed SDKs fixes -- so mzLib retargets only after MetaMorpheus does.
    - name: Set up .NET
      uses: actions/setup-dotnet@v4
      with:
        dotnet-version: ${{ env.DOTNET_VERSION }}
    - name: Restore dependencies
      run: cd mzLib && dotnet restore
    # Any CPU is requested explicitly so this job's output lands in bin/Release, which is where
    # mzLib.nuspec looks. Relying on MSBuild's implicit preference for Any CPU would make the pack step
    # below depend on the ordering of a platform list rather than on an intent stated here.
    - name: Build
      run: cd mzLib && dotnet build --no-restore --configuration Release /p:Platform="Any CPU"
    - name: Change mzLib version, pack, add source
      run: |
        cd mzLib;
        (Get-Content mzLib.nuspec) -replace "\<version\>(.*)\</version\>", "<version>9.9.9</version>" | Set-Content mzLib.nuspec; 
        $mzlibMatch = Select-String -Path mzLib.nuspec -Pattern "(?<=\<version\>)(.*)(?=\</version)";
        $mzlibVersion = $mzlibMatch.Matches[0].Value;
        echo "mzLib version number changed to: $mzlibVersion";
        nuget pack;
        $currentFolder = pwd;
        dotnet nuget add source $currentFolder;
        dotnet nuget list source;
    - name: Clone MetaMorpheus
      uses: actions/checkout@master
      with:
        path: ./MetaMorpheus
        repository: smith-chem-wisc/MetaMorpheus 
        ref: master
    - name: Change MetaMorpheus mzLib version and restore
      run: |
        cd ./MetaMorpheus/MetaMorpheus;
        dotnet remove CMD/CMD.csproj package mzLib;
        dotnet add CMD/CMD.csproj package mzLib -v 9.9.9;
        dotnet remove GUI/GUI.csproj package mzLib;
        dotnet add GUI/GUI.csproj package mzLib -v 9.9.9;
        dotnet remove GuiFunctions/GuiFunctions.csproj package mzLib;
        dotnet add GuiFunctions/GuiFunctions.csproj package mzLib -v 9.9.9;
        dotnet remove EngineLayer/EngineLayer.csproj package mzLib;
        dotnet add EngineLayer/EngineLayer.csproj package mzLib -v 9.9.9;
        dotnet remove Test/Test.csproj package mzLib;
        dotnet add Test/Test.csproj package mzLib -v 9.9.9;
        dotnet remove TaskLayer/TaskLayer.csproj package mzLib;
        dotnet add TaskLayer/TaskLayer.csproj package mzLib -v 9.9.9;
        dotnet restore;
    - name: Build MetaMorpheus
      run: cd ./MetaMorpheus/MetaMorpheus && dotnet build --no-restore
    - name: Test
      # Exclude live external-service tests from the MetaMorpheus integration run: they gate on third-party
      # services (UniProt, etc.), are not relevant to mzLib<->MetaMorpheus compatibility, and MetaMorpheus
      # exercises them in its own non-blocking job. This is what keeps a UniProt outage from reddening
      # every mzLib PR (this integration job clones MetaMorpheus master and runs its suite).
      run: cd ./MetaMorpheus/MetaMorpheus && dotnet test --no-build --verbosity normal --filter "Category!=ExternalService"
    - name: Upload artifact (installer)
      uses: actions/upload-artifact@v4
      with:
        name: MetaMorpheusInstaller
        path: ./MetaMorpheus/MetaMorpheus/MetaMorpheusSetup/bin/Debug/MetaMorpheusInstaller.msi
        compression-level: 0
    - name: Upload artifact (GUI)
      uses: actions/upload-artifact@v4
      with:
        name: MetaMorpheusGUI
        # Globbed rather than pinned to a framework: this is MetaMorpheus's target framework,
        # not mzLib's, so the two repos can move independently.
        path: ./MetaMorpheus/MetaMorpheus/GUI/bin/Debug/net*-windows/