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LibSEDML

Some time ago I developed libSedML a C# library that fully supports SED-ML for SBML as well as CellML models for creation of the description just as for the execution of Simulation Experiments. However, frequently the question to a C++ based library comes up. This project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models.

Dependencies

This library requires libSBML to be present, as its XML parsing layer will be used. for that either expat, xerces-c or libXML2 needs to be available. Additionally libSEDML makes use of libnuml. All dependencies are available as git submodule.

Building Python wheels

Since all dependencies are included as submodules, be sure to checkout the project with submodules:

git clone --recurse-submodules https://github.com/fbergmann/libSEDML

Then a build is as easy as:

cd libSEDML
python src/bindings/python/setup.py build

or install, if you prefer. It requires cmake and swig installed.

Building

This library uses CMake to build the library, so from an initial checkout all you would need todo is to run:

mkdir build  
cd build
cmake -DLIBSBML_LIBRARY=< path to libsbml lib> -DLIBSBML_INCLUDE_DIR=< path to includes > ... -DEXTRA_LIBS= < comma separated list of xml libraries> 
make  
make install

Should libSBML be installed in a default location it will be found automatically. Note that you do need to list the xml libraries that libSBML was linked against. In most cases libSBML is compiled against libXML and have compression enabled, so your EXTRA_LIBS would be:

EXTRA_LIBS=xml2;bz2;z;iconv

note the semicolon denoting the listing of several libraries. Of course you could also enter the full path to each individual file, just to give an example, on windows I use:

EXTRA_LIBS=D:/dependencies/lib/expat.lib

for linking against expat and indicating, that libSBML was compiled without compression.

Documentation

API documentation is something to be added and pull requests are happily accepted to improve them. For now a basic doxygen file is provided and documentation can be generated after checkout like so:

PROJECT_NUMBER=2.0.32 doxygen -x libSEDML.doxyfile > Doxyfile && doxygen

This expands the version number in the doxygen file, creates a temporary Doxyfile and runs doxygen with it. After that the generated documentation is available in the ./doc/html folder.

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Copyright (c) 2013-2023, Frank T. Bergmann
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.