Releases | Open Source Science

SMART - v2.3.1.alpha.1

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

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 10 months ago

SMART - v2.3.0.alpha

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

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 10 months ago

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: https://github.com/RangamaniLabUCSD/smart/compare/v2.3.0.beta...v2.3.0.beta.1

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 11 months ago

SMART - 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: https://github.com/RangamaniLabUCSD/smart/compare/v2.3.0-alpha.1...v2.3.0.beta

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 11 months ago

SMART - v2.3.0-alpha.1

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

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 11 months ago

SMART - 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: https://github.com/RangamaniLabUCSD/smart/compare/v2.2.3...v2.3.0-alpha

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis 12 months ago

SMART - v2.2.3

What's Changed

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

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.2.2...v2.2.3

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis over 1 year ago

SMART - v2.2.2

What's Changed

Bump version of base image and change pyvista backend by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/172
Update README with system requirements by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/171

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.2.1...v2.2.2

Scientific Software - Peer-reviewed - Python
Published by finsberg almost 2 years ago

SMART - v2.2.1

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

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis about 2 years ago

SMART - 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 https://github.com/RangamaniLabUCSD/smart/pull/146 - allows user to define an axisymmetric 3D problem over a 2D mesh.
Add dolfin timers by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/151
Compute curvature on mesh boundary and use in model specifications by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/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 https://github.com/RangamaniLabUCSD/smart/pull/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 https://github.com/RangamaniLabUCSD/smart/pull/164 - restrict initial condition or reaction to an annotated subregion within a compartment.
Fix formatting of Latex tables by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/162
Spatial parameters @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/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 https://github.com/RangamaniLabUCSD/smart/pull/145
Make compatible with python3.8 by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/148
Set loglevel in UFL_LEGACY by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/149
Add function to load mesh and a test by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/150
Remove dataclasses and termplotlib as dependencies by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/155
Load initial conditions from file by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/156
Add petsc logging for snes solve by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/166
Remove duplicate code and slightly tweak assembly logic by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/168

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis about 2 years ago

SMART - 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.

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis over 2 years ago

SMART - 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.

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis over 2 years ago

SMART - 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.

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis over 2 years ago

SMART - v2.1.4

What's Changed

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

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.1.3...v2.1.4

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis over 2 years ago

SMART - v2.1.3

What's Changed

Add "getting started" doc and add some clarifying details to examples by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/124
Add coverage to GitHub summary and upload html report to artifact by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/129
Add 3D version of Example 2 by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/125

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.1.2...v2.1.3

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis almost 3 years ago

SMART - v.2.1.2

What's Changed

Add pyvista and jupyterlab to docker image
Update documentation

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.1.1...v2.1.2

Scientific Software - Peer-reviewed - Python
Published by finsberg almost 3 years ago

SMART - v2.1.1

What's Changed

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

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.1.0...v2.1.1

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis almost 3 years ago

SMART - v2.1.0

What's Changed

Documentation updates

Update installation instructions (Docker or pip installation) by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/95
Add docs explaining the math by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/93
Add API documentation and reorganize README file by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/98

Dependency updates

Add gmsh and meshio as optional dependencies by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/96
Move matplotlib to examples by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/104

New features

Support for running multiple meshes in parallel via MPI by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/90
Added mesh creation functions in mesh_tools - now can create cubes, spheres, ellipsoids, cylinders, or ellipses, by @emmetfrancis

Updated examples

Develop 2D examples and renumber examples from simple to most complex by @emmetfrancis
Visualization of examples using added visualization module by @emmetfrancis and @jorgensd

JOSS paper

Write JOSS paper by @meg-simula in https://github.com/RangamaniLabUCSD/smart/pull/55

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v2.0.1...v2.1.0

Scientific Software - Peer-reviewed - Python
Published by emmetfrancis almost 3 years ago

SMART - v2.0.1

Bump version to 2.0.1

Scientific Software - Peer-reviewed - Python
Published by finsberg about 3 years ago

SMART - v2.0.0

What's Changed

Renaming

Renaming stubs to smart by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/84

Formatting

Apply black formatter (@jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/45)
Add pre-commit hooks (@finsberg in https://github.com/RangamaniLabUCSD/smart/pull/71)

Documentation

Swap out readthedocs with github pages and jupyterbook (@finsberg in https://github.com/RangamaniLabUCSD/smart/pull/54)
Add contributing guidelines by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/72

Packaging and distribution

Move from setup.py to pyproject.toml by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/61
Add workflow for publishing to pypi by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/92

Dependencies

Fix for modern sympy by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/48
Add h5py deps as it is required for two unused post-processing functions by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/49
Fix deprecated pandas DataFrame.append by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/80

Examples

Implementation of example 2 by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/56
Add/update examples 2-4 by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/60

Clean up

Add deprecation notice by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/57
Remove files that should not be in the repository by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/62
make deprecated return error by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/63
Remove deprecations, improve docs. by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/69
Updated time step reduction feature and added another method to set initial conditions by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/77
Remove unused code by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/78
Remove more deprecated functions and methods by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/79
Replace fancy print function with logging by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/82
Move pint related conversions into units file. by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/86
Clean up utils.py by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/87
Various fixes to solver class. by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/88

Tests

Test example1 by @emmetfrancis in https://github.com/RangamaniLabUCSD/smart/pull/47
Add Example 1 to CI by @jorgensd in https://github.com/RangamaniLabUCSD/smart/pull/51
Add first unit tests by @finsberg in https://github.com/RangamaniLabUCSD/smart/pull/58

New Contributors

@jorgensd made their first contribution in https://github.com/RangamaniLabUCSD/smart/pull/45
@emmetfrancis made their first contribution in https://github.com/RangamaniLabUCSD/smart/pull/47
@finsberg made their first contribution in https://github.com/RangamaniLabUCSD/smart/pull/54

Full Changelog: https://github.com/RangamaniLabUCSD/smart/compare/v1.0.0...v2.0.0

Scientific Software - Peer-reviewed - Python
Published by finsberg about 3 years ago

SMART - v1.0.0

Code before refactoring.

What's Changed

Parameter Sweep JSON Generation by @willxu1234 in https://github.com/justinlaughlin/stubs/pull/15
Cleaning up logic for config file parsing. Also adding example f-string. by @ctlee in https://github.com/justinlaughlin/stubs/pull/23
Mass test by @Rabona17 in https://github.com/justinlaughlin/stubs/pull/28
Merging rtd_testing into development by @justinlaughlin in https://github.com/justinlaughlin/stubs/pull/31
volume_surface forms by @justinlaughlin in https://github.com/justinlaughlin/stubs/pull/33
Linear preassemble by @justinlaughlin in https://github.com/justinlaughlin/stubs/pull/42
Snes parallel lgmaps by @justinlaughlin in https://github.com/justinlaughlin/stubs/pull/43

New Contributors

@willxu1234 made their first contribution in https://github.com/justinlaughlin/stubs/pull/15
@ctlee made their first contribution in https://github.com/justinlaughlin/stubs/pull/23
@Rabona17 made their first contribution in https://github.com/justinlaughlin/stubs/pull/28

Full Changelog: https://github.com/justinlaughlin/stubs/commits/v1.0.0

Scientific Software - Peer-reviewed - Python
Published by jorgensd over 3 years ago

Recent Releases of SMART

SMART - v2.3.1.alpha.1

SMART - v2.3.0.alpha

SMART - v2.3.0.beta.1

SMART - v2.3.0.beta

SMART - v2.3.0-alpha.1

SMART - v2.3.0-alpha

SMART - v2.2.3

What's Changed

SMART - v2.2.2

What's Changed

SMART - v2.2.1

SMART - v2.2.0

Major changes

Other changes

SMART - v2.1.7

SMART - v2.1.6

SMART - v2.1.5

SMART - v2.1.4

What's Changed

SMART - v2.1.3

What's Changed

SMART - v.2.1.2

What's Changed

SMART - v2.1.1

What's Changed

SMART - v2.1.0

What's Changed

Documentation updates

Dependency updates

New features

Updated examples

JOSS paper

SMART - v2.0.1

SMART - v2.0.0

What's Changed

Renaming

Formatting

Documentation

Packaging and distribution

Dependencies

Examples

Clean up

Tests

New Contributors

SMART - v1.0.0

What's Changed

New Contributors