Building from source

Here, we explain how to build SBMLNetwork from source for different environments:

the native C/C++ library (with optional Python bindings), and
the JavaScript/WebAssembly module for use in browsers.

Building C/C++ library (with optional Python bindings) from source

This section describes how to build the SBMLNetwork native library (C/C++) and, optionally, the associated Python bindings.

Prerequisites

CMake ≥ 3.16 plus a C++17‑capable compiler
libSBML (static) binaries matching your platform – easiest is to download the archive from the libroadrunner-deps release
Python 3.9–3.12 (optional – required only if building the bindings)

Build steps

Download or build the libSBML static binary files (preferably from libroadrunner-deps release) and unpack them to a directory of your choice, e.g., /path/to/libsbml-static. This directory should contain the include and lib subdirectories with the headers and static libraries, respectively.

Clone the SBMLNetwork repository from GitHub:

git clone https://github.com/adelhpour/SBMLNetwork.git

Change into the repository:
```
cd SBMLNetwork
```
Create and enter the build directory:
```
mkdir build
cd build
```

Configure the build:

cmake -DCMAKE_INSTALL_PREFIX=/path/to/install \
      -DCMAKE_BUILD_TYPE=Release \
      -DDEPENDENCIES_INSTALL_PREFIX=/path/to/libsbml-static \
      -DWITH_PYTHON=ON \
      -DPYTHON_INSTALL_WITH_SETUP=ON ..

Compile and install:
```
cmake --build build --target install
```

CMake options

WITH_PYTHON: Build and install the sbmlnetwork and libsbmlnetwork Python packages alongside the native library.
DEPENDENCIES_INSTALL_PREFIX: Path to the folder containing the unpacked static libSBML libraries and headers.
CMAKE_OSX_ARCHITECTURES (macOS only): Override to build arm64 or x86_64‑only binaries instead of a universal build.

For a complete, automated example of this build process across macOS, Linux, and Windows, see the GitHub Actions workflow:

📄 build.yml on GitHub

Building JavaScript/WebAssembly module from source

This section describes how to build the SBMLNetwork JavaScript/WebAssembly module for use in browsers or JavaScript environments like Node.js.

We use Emscripten to compile the C++ core of SBMLNetwork into a .wasm module and generate a corresponding JavaScript interface (.js) that can be loaded in web applications.

Requirements

Before starting, make sure you have:

Emscripten SDK ≥ 3.1.20 – install from https://emscripten.org
CMake ≥ 3.16
GNU Make (or Ninja)
A Linux or macOS build environment (Windows builds are not currently supported)

You will also need to build Expat and libSBML with Emscripten first, before compiling SBMLNetwork.

Build steps

Install and activate Emscripten

git clone https://github.com/emscripten-core/emsdk.git
cd emsdk
./emsdk install 3.1.20
./emsdk activate 3.1.20
source ./emsdk_env.sh

Build Expat with Emscripten

wget https://github.com/libexpat/libexpat/releases/download/R_2_2_10/expat-2.2.10.tar.bz2
tar -xf expat-2.2.10.tar.bz2 && cd expat-2.2.10
mkdir build && cd build
emcmake cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/../../install/expat
emmake make && emmake make install

Build libSBML with layout and render enabled

wget https://github.com/sbmlteam/libsbml/archive/refs/tags/v5.20.0.zip
unzip v5.20.0.zip && cd libsbml-5.20.0
mkdir build && cd build
emcmake cmake .. \
   -DCMAKE_INSTALL_PREFIX=$PWD/../../../install/sbml \
   -DCMAKE_BUILD_TYPE=Release \
   -DWITH_CPP_NAMESPACE=ON \
   -DWITH_EXPAT=ON \
   -DWITH_LIBXML=OFF \
   -DLIBSBML_SKIP_SHARED_LIBRARY=ON \
   -DENABLE_LAYOUT=ON \
   -DENABLE_RENDER=ON \
   -DWITH_STABLE_PACKAGES=ON \
   -DWITH_SWIG=OFF \
   -DEXPAT_INCLUDE_DIR=$PWD/../../../install/expat/include \
   -DEXPAT_LIBRARY=$PWD/../../../install/expat/lib/libexpat.a
emmake make && emmake make install

Build SBMLNetwork

wget https://github.com/sys-bio/SBMLNetwork/archive/refs/tags/v0.4.5.zip
unzip v0.4.5.zip && cd SBMLNetwork-0.4.5
mkdir build && cd build
emcmake cmake .. \
   -DCMAKE_INSTALL_PREFIX=$PWD/../../../install/sbmlnetwork \
   -DCMAKE_BUILD_TYPE=Release \
   -DEXPAT_INSTALL_PREFIX=$PWD/../../../install/expat \
   -DLIBEXPAT_LIBRARY=$PWD/../../../install/expat/lib/libexpat.a \
   -DLIBSBML_INSTALL_PREFIX=$PWD/../../../install/sbml \
   -DLIBSBML_LIBRARY=$PWD/../../../install/sbml/lib/libsbml-static.a \
   -DWITH_PYTHON=OFF
emmake make && emmake make install

Generate the final JavaScript and WASM files

em++ -Iinstall/sbmlnetwork/include \
     -Iinstall/sbml/include \
     -Iinstall/expat/include \
     install/sbmlnetwork/lib/libsbmlnetwork.a \
     install/sbml/lib/libsbml-static.a \
     install/expat/lib/libexpat.a \
     -o libsbmlnetwork.js \
     -s WASM=1 \
     -s LINKABLE=1 \
     -s EXPORT_ALL=1 \
     -s MODULARIZE=1 \
     -s EXPORT_ES6=1 \
     -s EXPORTED_RUNTIME_METHODS='["ccall", "cwrap", "allocateUTF8", "UTF8ToString"]'

This will generate two output files: * libsbmlnetwork.js – the JavaScript wrapper * libsbmlnetwork.wasm – the compiled WebAssembly module

Usage

Once built, the resulting files (libsbmlnetwork.js and libsbmlnetwork.wasm) can be used. See the Installation page for instructions on how to import and use the WebAssembly module in your application.

For a complete, working version of this WebAssembly build pipeline using Emscripten, see the GitHub Actions workflow:

📄 build-libsbmlnetworkjs.yml on GitHub