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4fb7f1e
Fixed defaults for Domain.add_point. closes #299.
BryanRumsey Jul 26, 2022
0007cae
Added a class for cominatory geometry.
BryanRumsey Jul 27, 2022
1052431
Added numpy.bool_ to geometry.inside return type check.
BryanRumsey Jul 27, 2022
de83919
Added the new geometry to the import sturcture.
BryanRumsey Jul 27, 2022
a2bc83f
Updated cylinder demo to use new geometry for middle type.
BryanRumsey Jul 27, 2022
e5668f7
Added a lattice error class.
BryanRumsey Jul 27, 2022
19aa6ab
Added the lattice module.
BryanRumsey Jul 27, 2022
abcd36e
Added a base class for lattices.
BryanRumsey Jul 27, 2022
0f4a5fe
Added missing kwargs arg to apply.
BryanRumsey Jul 27, 2022
c7e9b0d
Added the cartesian lattice.
BryanRumsey Jul 27, 2022
6c45d5f
Added checks to apply function to ensure proper args are passed. Add…
BryanRumsey Jul 27, 2022
628eb00
Bug fixes.
BryanRumsey Jul 27, 2022
9187fc7
Added the cartesian and spherical lattices to the import structure.
BryanRumsey Jul 27, 2022
40383de
Added 2D support to the cartesian lattice.
BryanRumsey Jul 29, 2022
78086d8
Added validation checks to combinatory geometry.
BryanRumsey Jul 29, 2022
bd1fa75
Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp…
BryanRumsey Jul 29, 2022
165f82c
Added cylindrical lattice.
BryanRumsey Jul 29, 2022
81a1014
Added the cylindrical lattice to the import structure.
BryanRumsey Jul 29, 2022
3db8f5e
Bug fixes.
BryanRumsey Jul 29, 2022
0ffc721
Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp…
BryanRumsey Jul 29, 2022
6cf9c8a
Fixed the get bounding box function.
BryanRumsey Jul 29, 2022
19668bc
Added function to update the domain limits after all particles have b…
BryanRumsey Jul 29, 2022
afa0ba2
Updated the get bounding box function.
BryanRumsey Jul 29, 2022
b20e2a2
Added the XMLMesh lattice.
BryanRumsey Jul 29, 2022
762fc7e
Added the XMLMesh to the import stucture.
BryanRumsey Jul 29, 2022
bb5b312
More bug fixes.
BryanRumsey Jul 29, 2022
6ed15d8
Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp…
BryanRumsey Jul 29, 2022
8053a63
Added the mesh IO lattice.
BryanRumsey Jul 29, 2022
1fc7323
Added the mesh IO lattice to the import structure.
BryanRumsey Jul 29, 2022
a49596d
Added stochss lattice class.
BryanRumsey Jul 31, 2022
5654ef2
Added the stochss lattice class to the import structure.
BryanRumsey Jul 31, 2022
82c0f73
Yet more bug fixes.
BryanRumsey Aug 1, 2022
99a0c5a
Bug fixes.
BryanRumsey Aug 2, 2022
dea3c8b
Added the error class for the transformation module.
BryanRumsey Aug 2, 2022
36a719c
Added the transformation module.
BryanRumsey Aug 2, 2022
c9ca676
Fixed indentation error.
BryanRumsey Aug 3, 2022
c5c7b46
Added the base transformation class to the import structure.
BryanRumsey Aug 3, 2022
c3ba787
Added the rotation transformation class.
BryanRumsey Aug 3, 2022
fb89aca
Added the rotation transformation class to the import structure.
BryanRumsey Aug 3, 2022
7399a30
Moved the apply and inside functions to the base class. Added the tr…
BryanRumsey Aug 3, 2022
61e7c4e
Final updates to translation transformation.
BryanRumsey Aug 3, 2022
cc4487f
Added translation transformation to the import structure.
BryanRumsey Aug 3, 2022
a6afbc1
Fixed issue with tests.
BryanRumsey Aug 4, 2022
8c65a18
Added actions to domain.
BryanRumsey Aug 5, 2022
de1d346
Started a validate action function. Added function for applying fill …
BryanRumsey Aug 5, 2022
d2097e2
Added and update flag to find boundary points function.
BryanRumsey Aug 5, 2022
ab00d76
Extended the action validator to cover remove actions. Added function…
BryanRumsey Aug 5, 2022
f07bd20
Added a function to apply multiple actions.
BryanRumsey Aug 5, 2022
4844451
Added actions to the domain constructor and added returns for particl…
BryanRumsey Aug 5, 2022
0c21be8
Bug fixes.
BryanRumsey Aug 5, 2022
a802794
Fixed circular imports.
BryanRumsey Aug 5, 2022
a6dd4d8
Removed unused import.
BryanRumsey Aug 5, 2022
3c5e303
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t…
BryanRumsey Aug 5, 2022
4732e95
Merge branch 'transformations' of https://github.com/StochSS/SpatialP…
BryanRumsey Aug 5, 2022
1ba7580
Cleanup and restructure.
BryanRumsey Aug 5, 2022
2f8e647
Added a function to preview a domains actions.
BryanRumsey Aug 5, 2022
4b01a61
Added an add fill action function and refactored the fill with partic…
BryanRumsey Aug 7, 2022
5fc1dc5
Added an add set action function and refactored the set properties fu…
BryanRumsey Aug 7, 2022
db5e600
Added an add remove action function.
BryanRumsey Aug 7, 2022
fad79fe
Refactored create 2D domain to use actions.
BryanRumsey Aug 8, 2022
1cdccd5
Refactored create 3D domain to use actions.
BryanRumsey Aug 8, 2022
73c945a
Refactored create 3D domain to use actions.
BryanRumsey Aug 8, 2022
5819b69
Refactored import meshio object function to use actions.
BryanRumsey Aug 8, 2022
1666011
Refactored read msh file function to use actions.
BryanRumsey Aug 8, 2022
b4fe762
Refactored read stochss domain function to use actions.
BryanRumsey Aug 8, 2022
1ed9eb6
Refactored read XML mesh function to use actions.
BryanRumsey Aug 8, 2022
f76b709
Fixed test_solver model.
BryanRumsey Aug 8, 2022
c6fb9a7
Added support for meshio objects to the meshio lattice.
BryanRumsey Aug 8, 2022
39eb3b7
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t…
BryanRumsey Aug 8, 2022
bb8cc7f
Merge branch 'transformations' of https://github.com/StochSS/SpatialP…
BryanRumsey Aug 8, 2022
e1342a6
Updated doc strings.
BryanRumsey Aug 8, 2022
95d2c66
Bug fixes.
BryanRumsey Aug 8, 2022
e9e3cda
Fixed issue with center transformation being applied too early.
BryanRumsey Aug 9, 2022
7e39491
Fixed type_id error message
BryanRumsey Aug 11, 2022
feff10e
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t…
BryanRumsey Aug 12, 2022
c0b4b01
Merge branch 'transformations' of https://github.com/StochSS/SpatialP…
BryanRumsey Aug 12, 2022
7c7da80
Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/…
BryanRumsey Aug 12, 2022
d8b0a30
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into g…
BryanRumsey Aug 12, 2022
1f34493
Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp…
BryanRumsey Aug 12, 2022
55c304a
Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t…
BryanRumsey Aug 12, 2022
7ed76df
Merge branch 'transformations' of https://github.com/StochSS/SpatialP…
BryanRumsey Aug 12, 2022
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14,657 changes: 43 additions & 14,614 deletions examples/3D_Cylinder_Demo.ipynb

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14 changes: 14 additions & 0 deletions spatialpy/core/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
from .datafunction import DataFunction
from .domain import Domain
from .geometry import (
CombinatoryGeometry,
Geometry,
GeometryAll,
GeometryExterior,
Expand All @@ -37,13 +38,26 @@
UniformInitialCondition,
ScatterInitialCondition
)
from .lattice import (
CartesianLattice,
SphericalLattice,
CylindricalLattice,
XMLMeshLattice,
MeshIOLattice,
StochSSLattice
)
from .model import Model, export_StochSS
from .parameter import Parameter
from .reaction import Reaction
from .result import Result
from .spatialpyerror import *
from .species import Species
from .timespan import TimeSpan
from .transformation import (
Transformation,
TranslationTransformation,
RotationTransformation
)
from .visualization import Visualization
from .vtkreader import *

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