feat: ProForma 2.0 reader/writer and Layer-2 modification converter #3200
Workflow file for this run
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| name: Build and Test | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: windows-latest | |
| timeout-minutes: 15 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up .NET | |
| uses: actions/setup-dotnet@v1 | |
| with: | |
| dotnet-version: 8.0.x | |
| - name: Restore dependencies | |
| run: cd mzLib && dotnet restore | |
| - name: Build | |
| run: cd mzLib && dotnet build --no-restore | |
| - name: Build (Test) | |
| run: cd mzLib && dotnet build --no-restore ./Test/Test.csproj | |
| - 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@v2 | |
| - name: Set up .NET | |
| uses: actions/setup-dotnet@v1 | |
| with: | |
| dotnet-version: 8.0.x | |
| - 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@v2 | |
| - name: Set up .NET | |
| uses: actions/setup-dotnet@v1 | |
| with: | |
| dotnet-version: 8.0.x | |
| - name: Restore dependencies | |
| run: cd mzLib && dotnet restore | |
| - name: Build | |
| run: cd mzLib && dotnet build --no-restore --configuration Release | |
| - 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 | |
| path: ./MetaMorpheus/MetaMorpheus/GUI/bin/Debug/net8.0-windows/ | |