Add GitHub Actions release workflow and CMake pre-built managed artifact support

[Copilot]

Downstream C++ consumers currently need a full .NET 8 SDK at build time solely to run dotnet publish for the managed shim. This PR pre-builds and publishes the managed output directory as GitHub Release artifacts and adds CMake options to consume them, so only the .NET 8 runtime is required at build/runtime.

Release workflow (.github/workflows/release.yml)

• Triggers on v* tags; builds a 3-leg matrix (linux-x64, win-x64, osx-x64)
• macOS leg uses the existing x64/Rosetta workaround (curl-install to ~/.dotnet-x64, --os osx -a x64)
• Each leg downloads Thermo vendor .nupkg files, writes a local NuGet config, runs dotnet publish, and zips the output as openms-thermo-bridge-managed-<platform>-<version>.zip
• A dependent publish-release job collects all three zips and creates the GitHub Release via softprops/action-gh-release@v2
• actions/download-artifact pinned to v4.1.3 (fixes arbitrary file write CVE affecting >= 4.0.0, < 4.1.3)

New CMake options

OPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR (empty PATH, default off)
Point at an unpacked release artifact zip. Skips dotnet publish; validates that ThermoWrapperManaged.dll and ThermoWrapperManaged.runtimeconfig.json are present before proceeding.

cmake -S . -B build \
  -DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR=/path/to/unpacked/zip

OPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED (BOOL, default OFF)
Auto-fetches the correct platform zip from GitHub Releases at configure time, extracts it into ${CMAKE_CURRENT_BINARY_DIR}/prebuilt-managed/, and uses it. Re-configure skips the download if the zip is already cached. Falls back with FATAL_ERROR if download fails and no SDK is available.

cmake -S . -B build \
  -DOPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON

On Apple Silicon both options always resolve to the osx-x64 artifact (Rosetta), consistent with the existing workaround. The add_dependencies / openms_thermo_bridge_copy_runtime_files build graph is unchanged in both paths.

Documentation (README.md)

• New "Option 3: use pre-built managed DLLs" section covering both manual and auto-download workflows
• Requirements updated: .NET 8 SDK not required when using pre-built artifacts

Original prompt

Goal

Pre-build and publish the managed C# output directory as GitHub Release artifacts so downstream C++ users only need CMake and a .NET runtime (not SDK) at build time.

Tasks

1. Add GitHub Actions release workflow (.github/workflows/release.yml)

• Trigger on push to tags matching v*.
• Build a matrix of three platform targets: ubuntu-latest → linux-x64, windows-latest → win-x64, macos-latest → osx-x64 (using the existing arm64/Rosetta workaround so the artifact works on Apple Silicon via --os osx -a x64).
• Each matrix leg:
  • Checks out the repo.
  • Installs .NET 8 SDK (macOS uses the existing x64 workaround: curl-install to ~/.dotnet-x64, set DOTNET_ROOT, DOTNET_ROOT_X64).
  • Runs dotnet publish ThermoWrapperManaged.csproj -c Release --nologo --self-contained false (macOS adds -r osx-x64) to produce the managed directory.
  • Zips the output as openms-thermo-bridge-managed-<platform>-<version>.zip.
• The final step uses softprops/action-gh-release to create a GitHub Release and attach all three zips as assets.
• Grants contents: write permission to the job.

2. Extend CMake with OPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR option

• Add a new CMake cache variable OPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR (empty by default).
• When set:
  • Skip the add_custom_command that runs dotnet publish.
  • Validate that ThermoWrapperManaged.dll and ThermoWrapperManaged.runtimeconfig.json exist in the given directory.
  • Set OPENMS_THERMO_BRIDGE_MANAGED_DIR to the provided path.
  • Emit a status message confirming the pre-built path is being used.
• The existing add_dependencies(openms_thermo_bridge openms_thermo_bridge_managed) and openms_thermo_bridge_copy_runtime_files machinery already uses OPENMS_THERMO_BRIDGE_MANAGED_DIR, so everything downstream works unchanged.

3. Add OPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED for auto-download

• Add a boolean option OPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED (default OFF).
• When ON, CMake (using file(DOWNLOAD ...)) fetches the correct platform zip from the GitHub Releases API URL (parameterised by project version tag).
• Extracts the zip into ${CMAKE_CURRENT_BINARY_DIR}/prebuilt-managed/ using cmake -E tar.
• Sets OPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR to that extracted directory.
• Falls back gracefully with a FATAL_ERROR message if the download fails and neither a local prebuilt nor a dotnet SDK is available.

4. macOS arm64 workaround for the pre-built artifact

• In the release workflow, the macOS leg always uses the x64 workaround (dotnet publish --os osx -a x64), so the published zip is always osx-x64.
• In CMake, when OPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON on Apple Silicon:
  • The platform-detection code selects the osx-x64 artifact URL.
  • CMAKE_OSX_ARCHITECTURES is still forced to x86_64 (existing behaviour).
  • A STATUS message informs the user that the pre-built osx-x64 artifact is being used through Rosetta.
• If OPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR is set manually on Apple Silicon, CMake emits the same Rosetta performance warning it currently does, but does not block the build.

5. Update documentation (README.md)

• Add a new "Option 3: use pre-built managed DLLs" section below the existing two build options:
  • Show how to pass -DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR=/path/to/unpacked/zip for manually downloaded artifacts.
  • Show how to use -DOPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON for automatic download.
• Update the Requirements section: note that dotnet SDK is not required when using pre-built artifacts (only the .NET 8 runtime is needed at runtime).
• Add a note that on Apple Silicon, pre-built artifacts are always osx-x64 and run via Rosetta, consistent with the existing workaround documentation.

The following is the prior conversation context from the user's chat exploration (may be truncated):

User: Analysis: Can the C# Wrapper Be Eliminated?

No — the C# wrapper (ThermoWrapperManaged.cs) cannot be removed.

The Thermo RawFileReader library (ThermoFisher.CommonCore.*) is a managed .NET assembly. It exposes entirely managed types: IRawDataPlus, Scan, ChromatogramTraceSettings, managed strings, LINQ, managed exceptions, etc. There is no native C or C++ API surface — the library exists only in managed code.

The nethost/hostfxr mechanism that the C++ side uses can only call across the managed/native boundary via [UnmanagedCallersOnly] entry points. Those entry points are the methods in ThermoWrapperManaged.cs that:

1. Receive raw IntPtr/int/double arguments from C++,

2. Unmarshal them into managed .NET types,

3. Call the RawFileReader managed API,

4. Marshal results back into native-compatible primitives (blittable arrays via Marshal.Copy, UTF-8 strings into caller-provided buffers, sentinel error values, etc.).

Without this shim, C++ would have no way to turn a managed IRawDat...

This pull request was created from Copilot chat.