pymecht 1.0.1

This is PYthon-based repository is for MECHanics of Tissue mechanics. The focus is on flexibility of adding new constitutive models and varying their parameters.

pyMechT

pyMechT is a Python package for simulating the mechanical response of soft biological tissues. The focus is on flexibility of defining models (referred to as MatModels). The ethos of pyMechT is to create simplified virtual experimental setups. That is, a sample is created of which there are the following options:

• Uniaxial extension;
• Biaxial extension; and
• Inflation-extension.

The MatModel is applied to the sample, such that the parameters encompass both the material parameters and those which define the corresponding sample setup (an example being the dimensions of the specimen). Finally, the samples can be simulated in either displacement-controlled or force-controlled loading to allow the use of Bayesian inference methods.

Required dependencies are:

• matplotlib
• numpy
• pandas
• pyDOE
• scipy
• torch
• sympy
• tqdm

Installation

Step 1 (optional): Create a virtual environment

To create an environment in Anaconda, execute:

conda create -n pymecht

To activate this virtual environment, execute:

conda activate pymecht

This is an option, but recommended step. There are other options for create and managing environments (such as venv or virtualenv)

Step 2: Install via pip

User

pyMechT can be installed directly from PyPI via pip by using:

pip install pymecht

Developer

To install as a devloper, it is recommended to fork from the repo and clone this fork locally.

Step 2.1 Fork from ankushaggarwal/pymecht

To fork a branch, head to the Github repository and click the fork button in the top right-hand corner.

Step 2.2 Clone the forked repo

To clone this repo locally, use the

git clone <repo-address>

where <repo-address> can be replaced by either the https or ssh addresses of the forked repo.

Step 2.3 Install developer version of pyMechT

To install a developer version of pyMechT, navigate to the locally cloned repo and execute:

python setup.py develop

An editable version of pyMechT is now installed. All local changes to the cloned source code files will be reflected when pyMechT is imported.

Step 3: Check installation

Ensure that pyMechT has been installed by executing:

pip list

The package and version should be visible in the resulting list.

Documentation

Find the full documentation at https://pymecht.readthedocs.io/en/latest/.

Contributing to pyMechT

To contribute to the pyMechT framework, install pyMechT using the developer options. All changes should be made to your forked repo. If there is a new feature or bug fix, raise a pull request. In the case that an additional feature is added, a corresponding example and test should be written in the respective python scripts.