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Scaling Transformations #312

Merged
merged 102 commits into from
Aug 15, 2022
Merged

Scaling Transformations #312

merged 102 commits into from
Aug 15, 2022

Commits on Jul 26, 2022

  1. Fixed defaults for Domain.add_point. closes #299.

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Commits on Jul 27, 2022

  1. Added a class for cominatory geometry.

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  2. Added numpy.bool_ to geometry.inside return type check.

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  3. Added the new geometry to the import sturcture.

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  4. Updated cylinder demo to use new geometry for middle type.

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  5. Added a lattice error class.

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  6. Added the lattice module.

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  7. Added a base class for lattices.

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  8. Added missing kwargs arg to apply.

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  9. Added the cartesian lattice.

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  10. Added checks to apply function to ensure proper args are passed. Adde… 

    …d spherical lattice.
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  11. Bug fixes.

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  12. Added the cartesian and spherical lattices to the import structure.

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Commits on Jul 29, 2022

  1. Added 2D support to the cartesian lattice.

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  2. Added validation checks to combinatory geometry.

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  3. Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp… 

    …atialPy into lattice
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  4. Added cylindrical lattice.

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  5. Added the cylindrical lattice to the import structure.

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  6. Bug fixes.

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  7. Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp… 

    …atialPy into lattice
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  8. Fixed the get bounding box function.

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  9. Added function to update the domain limits after all particles have b… 

    …een added.
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  10. Updated the get bounding box function.

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  11. Added the XMLMesh lattice.

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  12. Added the XMLMesh to the import stucture.

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  13. More bug fixes.

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  14. Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp… 

    …atialPy into lattice
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  15. Added the mesh IO lattice.

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  16. Added the mesh IO lattice to the import structure.

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Commits on Jul 31, 2022

  1. Added stochss lattice class.

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  2. Added the stochss lattice class to the import structure.

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Commits on Aug 1, 2022

  1. Yet more bug fixes.

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Commits on Aug 2, 2022

  1. Bug fixes.

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  2. Added the error class for the transformation module.

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  3. Added the transformation module.

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Commits on Aug 3, 2022

  1. Fixed indentation error.

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  2. Added the base transformation class to the import structure.

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  3. Added the rotation transformation class.

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  4. Added the rotation transformation class to the import structure.

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  5. Moved the apply and inside functions to the base class. Added the tra… 

    …nslation transformation.
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  6. Final updates to translation transformation.

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  7. Added translation transformation to the import structure.

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Commits on Aug 4, 2022

  1. Fixed issue with tests.

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Commits on Aug 5, 2022

  1. Added actions to domain.

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  2. Started a validate action function. Added function for applying fill … 

    …actions.
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  3. Added and update flag to find boundary points function. 

    Extended the action validator to cover set actions.
Added helper function to set particle properties.

Added fuction to apply set actions.
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  4. Extended the action validator to cover remove actions. Added function… 

    … to apply remove actions.
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  5. Added a function to apply multiple actions.

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  6. Added actions to the domain constructor and added returns for particl… 

    …es counts in fill actions.
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  7. Bug fixes.

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  8. Fixed circular imports.

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  9. Removed unused import.

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  10. Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t… 

    …ransformations
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  11. Merge branch 'transformations' of https://github.com/StochSS/SpatialPy … 

    …into actions-and-apply-funcs
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  12. Cleanup and restructure.

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  13. Added a function to preview a domains actions.

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Commits on Aug 7, 2022

  1. Added an add fill action function and refactored the fill with partic… 

    …les function to use the new function.
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  2. Added an add set action function and refactored the set properties fu… 

    …nction to use the new function.
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  3. Added an add remove action function.

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Commits on Aug 8, 2022

  1. Refactored create 2D domain to use actions.

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  2. Refactored create 3D domain to use actions.

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  3. Refactored create 3D domain to use actions.

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  4. Refactored import meshio object function to use actions.

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  5. Refactored read msh file function to use actions.

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  6. Refactored read stochss domain function to use actions.

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  7. Refactored read XML mesh function to use actions.

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  8. Fixed test_solver model.

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  9. Updated the example in README.

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  10. Added support for meshio objects to the meshio lattice.

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  11. Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t… 

    …ransformations
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  12. Merge branch 'transformations' of https://github.com/StochSS/SpatialPy … 

    …into actions-and-apply-funcs
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  13. Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/… 

    …SpatialPy into examples-with-actions
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  14. Updated doc strings.

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  15. Updated the 3D cylinder demo examples.

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  16. Updated diffusion validation test.

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  17. Updated the G-Protien_1D example.

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  18. Updated the cdc42 example.

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  19. Updated coral reef example.

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  20. Updated the start here example.

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  21. Updated the compile time comparison test.

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  22. Updated hes1 example.

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  23. Updated the polarisome 1D and gravity examples.

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  24. Updated the polarisome 1D and gravity examples.

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  25. Updated the weir example.

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  26. Bug fixes.

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  27. Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/… 

    …SpatialPy into examples-with-actions
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Commits on Aug 9, 2022

  1. Added the reflection transformation class.

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  2. Added reflect transformation to import structure.

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  3. Added a class for scaling transformations.

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  4. Added scaling transformations to import structure.

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  5. Fixed issue with center transformation being applied too early.

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Commits on Aug 11, 2022

  1. Fixed type_id error message

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Commits on Aug 12, 2022

  1. Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t… 

    …ransformations
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  2. Merge branch 'transformations' of https://github.com/StochSS/SpatialPy … 

    …into actions-and-apply-funcs
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  3. Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/… 

    …SpatialPy into actions-and-apply-funcs
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  4. Merge branch 'develop' of https://github.com/StochSS/SpatialPy into g… 

    …eometry-combinations
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  5. Merge branch 'geometry-combinations' of https://github.com/StochSS/Sp… 

    …atialPy into lattice
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  6. Merge branch 'lattice' of https://github.com/StochSS/SpatialPy into t… 

    …ransformations
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  7. Merge branch 'transformations' of https://github.com/StochSS/SpatialPy … 

    …into actions-and-apply-funcs
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  8. Merge branch 'actions-and-apply-funcs' of https://github.com/StochSS/… 

    …SpatialPy into examples-with-actions
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  9. Merge branch 'examples-with-actions' of https://github.com/StochSS/Sp… 

    …atialPy into reflect-transform
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  10. Merge branch 'reflect-transform' of https://github.com/StochSS/SpatialPy 

     into scaling-transform
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