Configurable spatial connectivity feature - #307

Merged

anyaevostinar merged 125 commits into

anyaevostinar:mainfrom

amlalejini:spatial-struct-lalejini

Jul 10, 2026

Commits on Jun 11, 2026

Fixed the mean pesky Bug and things should be working :)
Owen Hillary
committed
0a6f0c3
Spacial Struct for Testing Purposes
Owen Hillary
committed
d58c7ae

Commits on Jun 16, 2026

Renae SpatialStructures.h => SpatialStructure.h
amlalejini
committed
5e44007
Add bidirectional connect and disconnect functions, tweak comments/formatting in SpatialStructure.h. Add example spatial structure files.
amlalejini
committed
dff9228

Commits on Jun 17, 2026

Commits on Jun 18, 2026

Commits on Jun 19, 2026

Commits on Jun 20, 2026

Commits on Jun 22, 2026

Switch to AddOrgAt function for sgp mode setup hosts function
amlalejini
committed
8354e68

Commits on Jun 23, 2026

Shift SetupHosts, SetupSymbionts to protected in pggmode, use AddOrgAt instead of inject in population setup
amlalejini
committed
7e96bc5
Shift SetupHosts and SetupSymbionts to protected, use AddOrgAt instead of inject in pop setup functions
amlalejini
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b4a1d78
Combine sgp and default utils.h, move into source/ with base classes
amlalejini
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6d05526
Expose SetupHosts and SetupSymbionts in test world wrapper utility
amlalejini
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7e08479
Found and Updated test
Owen Hillary
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f526128
Tests compiling again after shifting SetupHosts and SetupSymbionts to be protected functions
amlalejini
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21829d6
Updated test that used old 'Grid' config Var
Owen Hillary
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795c3de

Commits on Jun 24, 2026

Commits on Jun 26, 2026

Add GetSymbiont accessors to host for convenience
amlalejini
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8f9220f
STARTING_TAGS_ONE_PROB renamed to HOST_STARTING_TAGS_ONE_PROB
amlalejini
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7b5b67f
Continue updating tests
amlalejini
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172c3e5
Continue updating tests
amlalejini
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b4a1c32
InjectHost no longer grows world capacity, update tests accordingly
amlalejini
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d3d388d
Move resize to protected, add additional const getters
amlalejini
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5ff05e7
Update tests to accomodate changes to Inject functions, AddOrgAt, and Resize
amlalejini
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edee9f8
Update instructions unit tests
amlalejini
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69a3d08
Update sgp health mode tests
amlalejini
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2cbe01f
Update nutrient functional tests
amlalejini
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367a3c6

Commits on Jun 27, 2026

Update program builder functional test
amlalejini
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6f4092c
Update sense task test
amlalejini
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ad380de
Update sgp symbiont task test
amlalejini
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b75b960
Update sgp host sgp symbiont test
amlalejini
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f538915
Update SGPSymbiont_Reproduce tests
amlalejini
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fa8a160

Commits on Jun 29, 2026

Update SGPWorld functional tests
amlalejini
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7108a3f
Update SGPWorld data functional tests
amlalejini
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3c0c5cc
Update stress mode functional tests
amlalejini
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ef2c21b
Update temp changing environments functional tests
amlalejini
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3fdde17
Deleted commented out redundant config
amlalejini
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10a715a
Add testing utils for zeroing out mutation rate
amlalejini
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f3ebe21
Update program builder unit tests
amlalejini
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24faf29
Update cure hosts unit test
amlalejini
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8202340
Update sgp world data unit test
amlalejini
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db727a4
Update sgp world setup unit tests
amlalejini
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3b8d7ea
Update sgp world unit tests
amlalejini
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6c77b90
Update sgp host unit tests
amlalejini
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7d5b15c
Update sgp symbiont unit test
amlalejini
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4e0f198
Update sgp host tasks functional tests
amlalejini
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ca24857
Update sgp host reproduce functional test
amlalejini
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0427ab4
Update sgp hardware tasks functional tests
amlalejini
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5216a78

Commits on Jun 30, 2026

Update cmdline parameters on run symbulation CI action
amlalejini
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51a92f6
Update spatial structure vt integration test, formatting edits for consistency, change world width and height defaults to 100x100 as they were prior to name change
amlalejini
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bf1e94b
Adjust whitespace for consistency
amlalejini
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261eed6
Update lysongeny plr integration test
amlalejini
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eef19dc
Adjust whitespace for consistency
amlalejini
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a6a751d
Updates to dirty transmission integration test
amlalejini
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cd22128
Update multi-infection integration test
amlalejini
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e6ede9c
Adjust path to utilities tests
amlalejini
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87f2e87
Remove unused type aliases
amlalejini
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f8caf86
Merged Owen's unit tests
amlalejini
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5f41010
Consolidate Owen's spatial structure tests into existing spatial structure test file. Sill need to update tests to run
amlalejini
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11a97ee
Merge main, resolve conflicts
amlalejini
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0882dec
Update whitespace for consistency
amlalejini
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00a4905

Commits on Jul 2, 2026

Implement tests for SpatialStructure class
amlalejini
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35e5942
Move prior spatial structure tests into new file to distinguish from SpatialStructure class unit tests
amlalejini
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43b5552
Tag spatial structure class unit tests with default-mode
amlalejini
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398e71e
Implement tests for custom population structure for SymWorld
amlalejini
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ad4778a
Add spatial structure config files for tests
amlalejini
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ea40c86
Remove old commented out test
amlalejini
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2b162a0
Implement sgpmode version of population structure tests, fix bug in SGPHost SetLocation function
amlalejini
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033ec92
Add population structure test files to test main
amlalejini
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ac2815d
Add asserts to run experiment functions to check spatial structure setup
amlalejini
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4cbc4b8
Add tag length to run config snapshot
amlalejini
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296be61
Merge main, resolve conflicts
amlalejini
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c12bf5b
Resolve missed conflict in program builder test
amlalejini
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623edb0
Fixup previous merge conflict resolution in stress mode test
amlalejini
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83ec073
Fix tags and test names in sgp mode population structure test
amlalejini
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6e50f9e
Update tests to accomodate setup spatial structure assert
amlalejini
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0b8bbfe
Update tests to accomodate spatial structure setup assert
amlalejini
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fd27b67

Commits on Jul 8, 2026

Merge branch 'main' into spatial-struct-lalejini
anyaevostinar
authored
604aea2

Commits on Jul 9, 2026

Add doc strings requested in pull request review
amlalejini
committed
afb6682
Merge branch 'spatial-struct-lalejini' of https://github.com/amlalejini/SymbulationEmp into spatial-struct-lalejini
amlalejini
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ad0f1a8
Switch if statement / exception throw to emp assert for SetIntVal function
amlalejini
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bd6180a
Fix comment typo in Symbiont.h
amlalejini
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64b8b03
Fix docstring formatting in spatial structure class
amlalejini
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8b55823
Implement SGPWorld SetMutationZero function
amlalejini
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a0a653b
Addressed pull request comments in SymWorld.h
amlalejini
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5a54258
Remove commented out print statement
amlalejini
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36ed5ca
Remove comment addressed in PR dicussion
amlalejini
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5ea1bef
Remove inaccurate comment from tag matching test
amlalejini
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6f8fea9
Remove comment as discussed in PR
amlalejini
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e6b09ff
Fix typo in comment
amlalejini
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ad7fa5b
Add docstrings to utils functions
amlalejini
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cb0478b
Get rid of warning about control reaching end of non-void function without a return
amlalejini
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8877aba
Remove duplicate function definition
amlalejini
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a03d668
Remove throw test for switch to emp_assert
amlalejini
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05d8970
Fix asserts in SetIntVal functions
amlalejini
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86c88db
Update tests to accomodate switch to emp_assert in SetIntVal functions
amlalejini
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33835f6
Move grid 2d utility functions to spatial_utils.h, update SymWorld to accomodate change
amlalejini
committed
d450238

Commits on Jul 10, 2026

Remove debug output for new host position
anyaevostinar
authored
15d2e38