PhysicellPython

This project has two primary goals: cmake compilation of PhysiCell and a resulting Python API for building physicell projects.

Build/Installation Process

Windows

64-bit gcc/OpenMP

Before installing the software, I reccomend following the tutorial on how to set up a 64-bit gcc/OpenMP environment on Windows.

CMake

Once you've completed that you will need to install cmake. There are several precompliled binaries available here.

Using CMake for Install

CMake is the build system for this project. You will likely need to configure your build according to the specifics of your system. Basic CMake usage for this project is as follows:

>mkdir build
>cmake path_to_your_source_directory -DCMAKE_INSTALL_PREFIX=your_path_to_a_directory_for_install -DCMAKE_BUILD_TYPE=Release
>cmake --build .
>cmake --install .

Running the Executable

Once you have completed installation you can go to your_path_to_a_directory_for_install. From here you have a folder for each sample project.

Heterogeneity

In the heterogeneity folder you will have the executable (heterogeneity.exe), config folder,output folder, and associated .dll files. Settings and default initial conditions can be adjusted in the config folders. You can run the executable in the target directory by:

>heterogeneity.exe

Linux

CMake is the build system for this project. You will likely need to configure your build according to the specifics of your system. Basic CMake usage for this project is as follows:

$cd YOUR_Physicell-Cmake_Directory
$mkdir build
cd build
$cmake path_to_source_code_directory -DCMAKE_INSTALL_PREFIX=your_path_to_a_directory_for_install
$make install

Running the Executable

Once you have completed installation you can go to your_path_to_a_directory_for_install. From here you have a folder for each sample project.

Heterogeneity

In the heterogeneity folder you will have the executable (heterogeneity), config folder, and output folder. Settings and default initial conditions can be adjusted in the config folders. You can run the executable in the target directory by:

$.heterogeneity

After running your output files will be in the output directory.

Mac

CMake

CMake is the build system for this project. There are several precompliled binaries available here.You will likely need to configure your build according to the specifics of your system. Basic CMake usage for this project is as follows:

~/git/PhysicellPython$ mkdir build
~/git/PhysicellPython$ cd build
~/git/PhysicellPython/build$ mkdir installed

this installation provides custom compilers and paths

cmake  -DCMAKE_CXX_COMPILER=g++-11 -DCMAKE_C_COMPILER=gcc-11 \
-DCMAKE_INSTALL_PREFIX:PATH=installed  \
-DPYTHON_EXECUTABLE:FILEPATH=/Users/USERNAME/opt/anaconda3/bin/python \
-DPYTHON_INCLUDE_DIR:PATH=/Users/USERNAME/opt/anaconda3/include/python3.8 \
-DPYTHON_LIBRARY:FILEPATH=/Users/USERNAME/opt/anaconda3/lib/libpython3.8.dylib ..

After setting the cmake configuration you can make and install the project.

make -j2
make install   # this will put everything in ./installed (specified above)