Python project for surface confined electrochemistry problems - a work in progress!
Obtain the software by running the following command in an appropriate directory
git clone https://github.com/HOLL95/Surface_confined_inference/ --recurse-submodules
This project depends on many things, most of which are downloaded automatically. However, the C++ ODE solver package CVODE requires user install
To install CVODE please download the software here and follow the installation instructions found here, which tells you to make a buildir
Once you have installed CVODE, please tell CMake the location of the buildir, either by editing in your .bashrc file
export CVODE_PATH="/absolute/path/to/builddir"
and running
source .bashrc
running the command in your terminal
export CVODE_PATH="/absolute/path/to/builddir"
or replacing the appropriate line in the Surface_confined_inference/C_src/CMakeLists.txt file directly.
set (SUNDIALS_DIR /path/to/builddir)
You can check that the former two approaches have worked by noting the output from
echo $CVODE_PATH
We recommend that you use a virtual environment (install instructions). To activate:
python -m venv venv
source venv/bin/activate
In the virtual environment, navigate to the Surface_confined_inference directory, and run
python -m pip install . -r requirements.txt
check that your installation has worked by running
python example_usage.py