Configurable spatial connectivity feature - #307
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anyaevostinar merged 125 commits intoJul 10, 2026
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…rmatting in SpatialStructure.h. Add example spatial structure files.
…atial structure setup code into smaller helper functions for each spatial structure mode.
…incorporating spatial structure into SymWorld
…on to sgp world, more spacing consistency fixes
…m backend. Move corresponding setup code into helper functions.
…ake cure updates config a size_t instead of int
…wo examples in tests
…unctions for unit testing, continue updating tests to work with spatial structure changes
…e spatial structure updates
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| TEST_CASE("SetupSymbionts with tag matching on", "[default]"){ | ||
| // NOTE: This test is a little bit frustrating to maintain if we change calls to |
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| config.PGG(1); | ||
| config.MUTATION_SIZE(0.05); | ||
| config.UPDATES(2000); | ||
| // @AML: These world size parameters weren't taking effect in the original test |
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Awesome, thanks! We can remove this comment now
| cfg.MUTATION_SIZE(0); | ||
| } | ||
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| // Wrapper for Symbumlation world classes intended to expose protected |
anyaevostinar
requested changes
Jul 8, 2026
anyaevostinar
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anyaevostinar
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Whew, some things to change and some questions
…ni/SymbulationEmp into spatial-struct-lalejini
… accomodate change
Removed commented-out debug output for new host position.
anyaevostinar
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Jul 10, 2026
anyaevostinar
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anyaevostinar
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Yey, looks good, thank you!!!!
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The main feature added by this pull request is the ability to load any graph structure (either in a matrix format or in a csv, one row per edge) to define the population's structure (i.e, which individuals neighbor each other). This feature is implemented in default mode, so it should work for all currently implemented downstream modes.
Adding arbitrary spatial structure configuration required a few fundamental tweaks to basic setup, such as requiring that spatial structure be configured before initializing the population. This motivated shifting SetupHosts and SetupSymbionts to protected functions that should be called only from the World's Setup function.
Other less major changes:
) {, etc.). Mainly in files that were already being touched by this pull request.source/test/test_utils.h. E.g., a world wrapper for exposing public functions to tests.source/utils.hActive TODOS before merging:
Questions / notes to reviewer(s)