Read, write, validate and pool SDRF-Proteomics experimental-design fi… #3407
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| 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/ | |