Review changes - #317

Merged

briandrawert merged 121 commits into

Aug 15, 2022

Commits on Jul 26, 2022

Fixed defaults for Domain.add_point. closes #299.
BryanRumsey
committed
4fb7f1e

Commits on Jul 27, 2022

Added a class for cominatory geometry.
BryanRumsey
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0007cae
Added numpy.bool_ to geometry.inside return type check.
BryanRumsey
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1052431
Added the new geometry to the import sturcture.
BryanRumsey
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de83919
Updated cylinder demo to use new geometry for middle type.
BryanRumsey
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a2bc83f
Added a lattice error class.
BryanRumsey
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e5668f7
Added the lattice module.
BryanRumsey
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19aa6ab
Added a base class for lattices.
BryanRumsey
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abcd36e
Added missing kwargs arg to apply.
BryanRumsey
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0f4a5fe
Added the cartesian lattice.
BryanRumsey
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c7e9b0d
Added checks to apply function to ensure proper args are passed. Added spherical lattice.
BryanRumsey
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6c45d5f
Bug fixes.
BryanRumsey
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628eb00
Added the cartesian and spherical lattices to the import structure.
BryanRumsey
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9187fc7

Commits on Jul 29, 2022

Added 2D support to the cartesian lattice.
BryanRumsey
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40383de
Added validation checks to combinatory geometry.
BryanRumsey
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78086d8
Merge branch 'geometry-combinations' of https://github.com/StochSS/SpatialPy into lattice
BryanRumsey
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bd1fa75
Added cylindrical lattice.
BryanRumsey
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165f82c
Added the cylindrical lattice to the import structure.
BryanRumsey
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81a1014
Bug fixes.
BryanRumsey
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3db8f5e
Merge branch 'geometry-combinations' of https://github.com/StochSS/SpatialPy into lattice
BryanRumsey
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0ffc721
Fixed the get bounding box function.
BryanRumsey
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6cf9c8a
Added function to update the domain limits after all particles have been added.
BryanRumsey
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19668bc
Updated the get bounding box function.
BryanRumsey
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afa0ba2
Added the XMLMesh lattice.
BryanRumsey
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b20e2a2
Added the XMLMesh to the import stucture.
BryanRumsey
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762fc7e
More bug fixes.
BryanRumsey
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bb5b312
Merge branch 'geometry-combinations' of https://github.com/StochSS/SpatialPy into lattice
BryanRumsey
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6ed15d8
Added the mesh IO lattice.
BryanRumsey
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8053a63
Added the mesh IO lattice to the import structure.
BryanRumsey
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1fc7323

Commits on Jul 31, 2022

Added stochss lattice class.
BryanRumsey
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a49596d
Added the stochss lattice class to the import structure.
BryanRumsey
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5654ef2

Commits on Aug 1, 2022

Yet more bug fixes.
BryanRumsey
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82c0f73

Commits on Aug 2, 2022

Bug fixes.
BryanRumsey
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99a0c5a
Added the error class for the transformation module.
BryanRumsey
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dea3c8b
Added the transformation module.
BryanRumsey
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36a719c

Commits on Aug 3, 2022

Fixed indentation error.
BryanRumsey
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c9ca676
Added the base transformation class to the import structure.
BryanRumsey
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c5c7b46
Added the rotation transformation class.
BryanRumsey
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c3ba787
Added the rotation transformation class to the import structure.
BryanRumsey
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fb89aca
Moved the apply and inside functions to the base class. Added the translation transformation.
BryanRumsey
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7399a30
Final updates to translation transformation.
BryanRumsey
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61e7c4e
Added translation transformation to the import structure.
BryanRumsey
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cc4487f

Commits on Aug 4, 2022

Fixed issue with tests.
BryanRumsey
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a6afbc1

Commits on Aug 5, 2022

Added actions to domain.
BryanRumsey
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8c65a18
Started a validate action function. Added function for applying fill actions.
BryanRumsey
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de1d346
Added and update flag to find boundary points function.
BryanRumsey
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d2097e2
Extended the action validator to cover remove actions. Added function to apply remove actions.
BryanRumsey
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ab00d76
Added a function to apply multiple actions.
BryanRumsey
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f07bd20
Added actions to the domain constructor and added returns for particles counts in fill actions.
BryanRumsey
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4844451
Bug fixes.
BryanRumsey
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0c21be8
Fixed circular imports.
BryanRumsey
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a802794
Removed unused import.
BryanRumsey
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a6dd4d8
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into transformations
BryanRumsey
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3c5e303
Merge branch 'transformations' of https://github.com/StochSS/SpatialPy into actions-and-apply-funcs
BryanRumsey
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4732e95
Cleanup and restructure.
BryanRumsey
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1ba7580
Added a function to preview a domains actions.
BryanRumsey
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2f8e647

Commits on Aug 7, 2022

Commits on Aug 8, 2022

Refactored create 2D domain to use actions.
BryanRumsey
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fad79fe
Refactored create 3D domain to use actions.
BryanRumsey
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1cdccd5
Refactored create 3D domain to use actions.
BryanRumsey
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73c945a
Refactored import meshio object function to use actions.
BryanRumsey
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5819b69
Refactored read msh file function to use actions.
BryanRumsey
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1666011
Refactored read stochss domain function to use actions.
BryanRumsey
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b4fe762
Refactored read XML mesh function to use actions.
BryanRumsey
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1ed9eb6
Fixed test_solver model.
BryanRumsey
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f76b709
Updated the example in README.
BryanRumsey
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301f04c
Added support for meshio objects to the meshio lattice.
BryanRumsey
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c6fb9a7
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into transformations
BryanRumsey
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39eb3b7
Merge branch 'transformations' of https://github.com/StochSS/SpatialPy into actions-and-apply-funcs
BryanRumsey
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bb8cc7f
Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/SpatialPy into examples-with-actions
BryanRumsey
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68e58ba
Updated doc strings.
BryanRumsey
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e1342a6
Updated the 3D cylinder demo examples.
BryanRumsey
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57313f2
Updated diffusion validation test.
BryanRumsey
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228e2c1
Updated the G-Protien_1D example.
BryanRumsey
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4012d3e
Updated the cdc42 example.
BryanRumsey
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669cd55
Updated coral reef example.
BryanRumsey
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b235122
Updated the start here example.
BryanRumsey
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b09cfdc
Updated the compile time comparison test.
BryanRumsey
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af09cc2
Updated hes1 example.
BryanRumsey
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b08e84e
Updated the polarisome 1D and gravity examples.
BryanRumsey
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c46a216
Updated the polarisome 1D and gravity examples.
BryanRumsey
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b6698e0
Updated the weir example.
BryanRumsey
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ebe6a37
Bug fixes.
BryanRumsey
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95d2c66
Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/SpatialPy into examples-with-actions
BryanRumsey
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3e527f1

Commits on Aug 9, 2022

Commits on Aug 11, 2022

Commits on Aug 12, 2022

Commits on Aug 15, 2022

Fixed issue with get bounding box.
BryanRumsey
committed
4651f16