INSTALL.md

Since version 0.3, tyssue depends on CGAL for collision detection, and thus a c++ compiler toolchain. It is thus advised to use conda for a simple installation procedure.

Installing tyssue with conda

If you have a conda environment ready:

conda install -c conda-forge tyssue

This will install tyssue and all its dependencies, with the pre-compiled binary parts.

Install tyssue using pip

This install a cross-platform, pure python version of tyssue. Some advanced features are not available, namely:

• Collision detection
• Periodic boundary sheet generation

python -m pip install --user --upgrade tyssue

Installing from source

Those are the instructions to install the package from source on a debian-like linux distribution. If you allready have a basic scientific python stack, use it, don't install anaconda.

Install a C++ compiler

With an Debian like system, this is achieved by:

sudo apt install build-essential cmake g++

Download and install tyssue from source

If you want to do that, I assume you allready know how to manage dependencies on your platform. The simplest way to manage dependencies is to use conda to manage the dependencies (you can use mamba as a faster alternative to conda).

Start by cloning tyssue recursively to also grab pybind11:

git clone --recursive https://github.com/damcb/tyssue.git
cd tyssue

Then create a virtual environement:

conda env create -f environment.yml

Then install python:

python setup.py install

If all went well, you have successfully installed tyssue.

Install testing utilities

pip install pytest pytest-cov nbval

A Makefile provides some utility function. Try :

make tests  # Run tests with nose
make coverage  # Run tests with coverage
make flake8  # Check PEP8 on the code
make nbtest # Tests all  the demo notebooks - requires nbval

Building the documentation

The documentation uses nbsphinx to convert the jupyter notebooks in doc/notebooks to html with sphinx.

pip install sphinx nbsphinx sphinx-autobuild
cd tyssue/doc
make html