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

v2.2.0

Major changes

• SMART is now compatible with recent changes to MeshView in FEniCS. All cases of dolfin.MeshView.create() are now dolfin.create_meshview() and cases of dolfin.assemble() are dolfin.assemble_mixed()
• Axisymmetric feature by @emmetfrancis in #146 - allows user to define an axisymmetric 3D problem over a 2D mesh.
• Add dolfin timers by @finsberg in #151
• Compute curvature on mesh boundary and use in model specifications by @emmetfrancis in #152 - allows user to compute curvature over a mesh and use in reaction terms or initial condition for species.
• Load curvature from file by @finsberg in #154 - allows user to load curvature (computed in GAMer2) and use in reaction terms or initial condition for species.
• Restrict species and/or reactions to subdomains by @emmetfrancis in #164 - restrict initial condition or reaction to an annotated subregion within a compartment.
• Fix formatting of Latex tables by @emmetfrancis in #162
• Spatial parameters @emmetfrancis in #160 - SMART parameters can now be functions of both space and time.

Other changes

• Changes and additions to mesh_tools for smart-comp-sci examples by @emmetfrancis in #145
• Make compatible with python3.8 by @finsberg in #148
• Set loglevel in UFL_LEGACY by @finsberg in #149
• Add function to load mesh and a test by @finsberg in #150
• Remove dataclasses and termplotlib as dependencies by @finsberg in #155
• Load initial conditions from file by @emmetfrancis in #156
• Add petsc logging for snes solve by @finsberg in #166
• Remove duplicate code and slightly tweak assembly logic by @jorgensd in #168

v2.1.7

Spatial Modeling Algorithms for Reactions and Transport (SMART) is a finite-element-based simulation package for model specification and numerical simulation of spatially-varying reaction-transport processes, especially tailored to modeling such systems within biological cells. SMART is based on the FEniCS finite element library, provides a symbolic representation framework for specifying reaction pathways, and supports large and irregular cell geometries in 2D and 3D.

This is the latest release of SMART for publication to the Journal of Open Source Software.

v2.1.6

Spatial Modeling Algorithms for Reactions and Transport (SMART) is a finite-element-based simulation package for model specification and numerical simulation of spatially-varying reaction-transport processes, especially tailored to modeling such systems within biological cells. SMART is based on the FEniCS finite element library, provides a symbolic representation framework for specifying reaction pathways, and supports large and irregular cell geometries in 2D and 3D.

This is the latest release of SMART for publication to the Journal of Open Source Software.

v2.1.5

Spatial Modeling Algorithms for Reactions and Transport (SMART) is a finite-element-based simulation package for model specification and numerical simulation of spatially-varying reaction-transport processes, especially tailored to modeling such systems within biological cells. SMART is based on the FEniCS finite element library, provides a symbolic representation framework for specifying reaction pathways, and supports large and irregular cell geometries in 2D and 3D.

This is the latest release of SMART for publication to the Journal of Open Source Software.

v2.1.4

What's Changed

• Remove print_assembly by @emmetfrancis in #130
• Update README.md by @emmetfrancis in #135
• Change tolerance in assert in example 4 from 0.01 to 0.012 by @finsberg in #137
• Bump version of actions/checkout from 3 to 4 by @finsberg in #136
• Remove high performance claim from JOSS paper by @emmetfrancis in #139
• Make suggested revisions to examples by @emmetfrancis in #138

Full Changelog: v2.1.3...v2.1.4

v2.1.3

What's Changed

• Add "getting started" doc and add some clarifying details to examples by @emmetfrancis in #124
• Add coverage to GitHub summary and upload html report to artifact by @finsberg in #129
• Add 3D version of Example 2 by @emmetfrancis in #125

Full Changelog: v2.1.2...v2.1.3

v.2.1.2

What's Changed

• Add pyvista and jupyterlab to docker image
• Update documentation

Full Changelog: v2.1.1...v2.1.2

v2.1.1

What's Changed

• Minor edits to examples
• Change description of SMART in pyproject.toml

Full Changelog: v2.1.0...v2.1.1