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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

OSPSuite.SimModel is the ODE-based calculation engine for PK/PD models built with PK-Sim or MoBi (Open Systems Pharmacology). It consists of a C++ native simulation kernel wrapped by a .NET managed layer via P/Invoke, packaged as a unified multi-platform NuGet package.

Build Commands

Windows (primary development platform)

# 1. Restore native NuGet packages (required before first C++ build)
nuget restore packages.config -PackagesDirectory packages

# 2. Build the C++ native library (use VS Developer Command Prompt or ensure msbuild is on PATH)
msbuild src/OSPSuite.SimModelNative/OSPSuite.SimModelNative.vcxproj /p:Configuration=Release /p:Platform=x64 "/p:SolutionDir=$(pwd)/"

# 3. Build the .NET managed layer and tests
dotnet build OSPSuite.SimModel.sln --configuration Release

The C++ vcxproj projects require MSBuild (not dotnet build). The .NET projects can be built with dotnet build. CI creates a .NetOnly.sln (with C++ projects removed) for the managed build step.

Linux / macOS

./buildNix.sh Linux    # or MacOS

This runs CMake + make for the native library, then dotnet build and dotnet test for the managed layer.

Running Tests

# .NET tests (NUnit, BDD-style)
dotnet test tests/OSPSuite.SimModel.Tests/OSPSuite.SimModel.Tests.csproj --configuration Release

# C++ unit tests (Google Test) — requires SimModelNative to be built first
msbuild tests/OSPSuite.SimModelNative.Tests/OSPSuite.SimModelNative.Tests.vcxproj /p:Configuration=Release /p:Platform=x64 "/p:SolutionDir=$(pwd)/"
Build/Release/x64/OSPSuite.SimModelNative.Tests.exe

Architecture

Native C++ Layer (src/OSPSuite.SimModelNative/)

Headers in include/SimModel/, sources in src/. Namespace: SimModelNative.

Core classes:

  • Simulation — orchestrates loading XML, managing entities, running the ODE solver, collecting results
  • DESolver — wraps CVODES (Adams/BDF methods, sensitivity analysis, band linear solver)
  • Formula hierarchy — Formula base with ~20 subtypes (ExplicitFormula, TableFormula, IfFormula, etc.) loaded from XML FormulaList
  • Species (ODE state variables), Parameter, Observer (computed outputs), Switch (events)
  • PInvokeSimulation.h / PInvokeQuantity.h — flat extern "C" API exported for .NET interop

Platform abstraction:

  • OSPSuite.SysTool — dynamic library loading, file system helpers
  • OSPSuite.XMLWrapper — MSXML6 on Windows, libxml2 on Linux/macOS
  • SIM_EXPORT macro: __declspec(dllexport) on Windows, empty elsewhere

.NET Managed Layer (src/OSPSuite.SimModel/)

Target: net10.0. All P/Invoke uses CallingConvention.Cdecl.

  • Simulation.cs — main public API. Lifecycle: LoadFromXMLFile/LoadFromXMLString → set variable parameters/species → FinalizeSimulation → RunSimulation → read results
  • NativeLibraryPreload.cs — [ModuleInitializer] that preloads transitive native dependencies (FuncParserNative, SimModelSolver_CVODES) via NativeLibrary.Load
  • SimModelImportDefinitions.cs — DLL name constant for [DllImport]

Key Dependencies

  • OSPSuite.SimModelSolver_CVODES — SUNDIALS CVODES ODE solver (native + managed wrapper)
  • OSPSuite.FuncParser — mathematical formula parser (native + managed wrapper)
  • OSPSuite.Utility — shared .NET utilities

Git submodules (clone with --recursive):

  • src/OSPSuite.SimModelSolverBase — abstract solver interface (ISolverCaller)
  • schema/ — XSD schema for SimModel XML format

Build Output Layout

Native binaries go to Build/<Configuration>/x64/ on Windows, or runtimes/<rid>/native/ for NuGet packaging. The unified nupkg includes native binaries for win-x64, linux-x64, and osx-arm64.

Test Conventions

  • .NET tests use OSPSuite.BDDHelper with ContextSpecification<T> pattern. Test classes inherit from concern_for_Simulation and follow the Because/should_* naming convention. XML test fixtures live in tests/TestData/.
  • C++ unit tests (tests/OSPSuite.SimModelNative.Tests/) use Google Test with two distinct build modes:
    • MSBuild (Windows): The .vcxproj lists every SimModelNative .cpp as a ClCompile item, compiling the sources directly rather than linking against the DLL. This gives tests access to non-exported internal classes. Uses NuGet package Microsoft.googletest.v140.windesktop.msvcstl.static.rt-dyn.
    • CMake (Linux/macOS): CMakeLists.txt does not recompile SimModelNative sources; instead it links against the pre-built libOSPSuite.SimModelNative.${EXT} shared library whose location is supplied by buildNix.sh via the SIMMODEL_NATIVE_DIR variable. GoogleTest is fetched at configure time via FetchContent.

Version Management

Version is defined in src/OSPSuite.SimModelNative/version.h with placeholder values (0.0.0.0). CI replaces these with the actual version (currently 5.0.0.<build_number>).

Important Notes

  • macOS Intel (x86_64) support was dropped; only arm64 is supported
  • The ProduceReferenceAssembly is disabled in the .NET csproj to avoid a race condition in mixed C++/C# parallel builds (see comment in csproj)
  • Native NuGet packages (from packages.config) are separate from .NET NuGet packages and must be restored with nuget restore, not dotnet restore