SMART branch for mechanochemical model of nucleus

This branch includes recent updates to support advection within the SMART framework. It is particularly tailored for use with mechanochemical models in the smart-mechanotransduction repository for the paper "A predictive mechanochemical modeling framework for deformation and remodeling of the nuclear lamina".

v2.3.1.alpha.1

Fixes to multicell meshing function, temporary solver fix for returning nan.

v2.3.0.alpha

Updates to multicellular meshing function and introduction of advective transport and associated tests.

v2.3.0.beta.1

Introduce new meshing function create_multicell to generate a multicellular mesh with two different types of cells embedded in a larger cube, including both extracellular and intracellular environments. New example 7 demonstrates its use.

Full Changelog: v2.3.0.beta...v2.3.0.beta.1

v2.3.0.beta

Introduce new meshing function create_multicell to generate a multicellular mesh with two different types of cells embedded in a larger cube, including both extracellular and intracellular environments. New example 7 demonstrates its use.

Full Changelog: v2.3.0-alpha.1...v2.3.0.beta

v2.3.0-alpha.1

Bump version number from alpha version, minor edits to example 5 with SOCE.

v2.3.0-alpha

Testing new mesh features and SOCE-relevant example. This involves defining parameters that can be assigned custom values in different regions of the mesh, as illustrated in example5_withSOCE.ipynb.

Full Changelog: v2.2.3...v2.3.0-alpha

v2.2.3

What's Changed

• Add upper bound on numpy since v2.0 breaks petsc4py by @finsberg in #173
• Fix type for sym_expr in parameter (allow Any for now) by @emmetfrancis in #174
• Update implicit curve function and fix diffusion units check by @emmetfrancis in #178
• Load spatial parameters from XDMF by @emmetfrancis in #176

Full Changelog: v2.2.2...v2.2.3

v2.2.2

What's Changed

• Bump version of base image and change pyvista backend by @finsberg in #172
• Update README with system requirements by @emmetfrancis in #171

Full Changelog: v2.2.1...v2.2.2

v2.2.1

New release for SMART scientific computing manuscript. See 2.2.0 for updates from version 2.1