crnsimul is an application that simulates Chemical Reaction Networks.

If you have installed the program, you can just execute them using ./examples/multiply.crn, and they will run. If not, you need to specify the interpreter you are using explicitly, so ./bin/crnsimul -P examples/multiply.crn.

See the examples directory for example reaction networks.

Also, see the manual.

The project uses cmake. To compile a project using cmake, the following commands should be used:

cmake .
make

Besides that, there currently is also one submodule. Run

git submodule update --init --recursive

to download it Afterwards, you should be able to find the executable in the ./bin folder

The dependencies can be found in the dockerfile. For Arch Linux, they can be installed by running

sudo pacman -S clang flex bison boost gnuplot gtest 

Language servers require a compile_commands.json file to be present to enable better autocompletion support. To generate it when running cmake, modify your cmake command to be

cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=1

For convenience, you can add alias cmake="cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=1" to your .bashrc.

Github has a CI step implemented that requires that all code is compliant with the .clang-format file in the root of the project directory. You can use the format.sh file to format the code automatically, or use a tool that implements clang-format on save for instance. For vim I can recommend neoformat.