Stress escapees refactor by Gabe-Rose · Pull Request #328 · anyaevostinar/SymbulationEmp

Gabe-Rose · 2026-08-06T18:02:57Z

Overview:

Stress References removed from SGPWorld* and into SGPW_InteractionMechanismSetup.cc

after_reproduction_sig used to trigger processing of escapees
emp::vector symbiont_stress_escapees and StressEscapee moved to SGPW_InteractionMechanismSettup.cc
Now uses SymDoBirth

SymDoBirth modified to take offspring, parent, and world position

default mode changed to maintain override
Relevant functors/lower level functions changed to align with SymDoBirth

SetupHorizontalTransmissionCompatibilityMode() changed to set one functor

stress-specific functor removed
now takes pointers to the (prospective) host and (offspring) symbiont

Other:

Various useless comments removed
Variables named "baby" renamed to "offspring" where convenient

Next steps:

change all .Delete() calls to SendToGraveyard()
move all sym_offspring SendToGraveyard() calls to SymDoBirth
^^^ same with HostDoBirth()?
Why are we doing the compatibility check with the sym_parent, not the sym_offspring?

…check_functions

anyaevostinar · 2026-08-06T18:43:32Z

-  // TODO - add any signals?
-  const size_t parent_pop_idx = parent_pos.GetPopID();
-  emp::Ptr<Organism> parent = this->GetOrgPtr(parent_pop_idx)->GetSymbionts()[parent_pos.GetIndex() - 1];
  emp_assert(!parent->IsHost());


I'm confused where "parent" is being defined now

your right! that is pretty confusing. I wonder why that passed compile

changed to sym_parent_ptr

anyaevostinar · 2026-08-06T18:47:38Z

  std::function<std::optional<emp::WorldPosition>(
-    size_t,                 /* Parent's host location id in world (pops[0][id])*/
-    emp::Ptr<sgp_sym_t>     /* Pointer to symbiont parent (producing the sym offspring) */
+    emp::Ptr<sgp_sym_t> sym_offspring_ptr,


I don't think that you can include parameter names, hence the previous syntanx

Also, why are we now passing the offspring as well as the parent? We should only need whatever symbiont is being used to check for compatibility

Removed parameter names. Good question with the offspring; They are not used currently and could easily be removed. we are checking the task profile of the parent with the prospective host, but that doesent quite sit right with me. We are determining the "fate" of the offspring based on the parent, not the symbiont itself. In other words fun_horizontal_transmission_compatibility_check determines the compatibility of the parent and prospective host, but that value is used to determine the compatabilty of the sym and prospective host.

See SGPWorld.test.cc comment as well

Let's focus on just refactoring to capture existing functionality and not changing functionality in this PR, since otherwise too many things are changing and it is likely that a bug gets introduced.

The parent is injecting its offspring into a new host and the offspring hasn't done anything yet, so it can't do its own infecting. The fate of offspring is very often dependent on the parent's behavior ;)

anyaevostinar · 2026-08-06T18:57:11Z


    emp::Ptr<sgp_host_t> host = emp::NewPtr<sgp_host_t>(&random, &world, &config);
    emp::Ptr<sgp_sym_t> symbiont = emp::NewPtr<sgp_sym_t>(&random, &world, &config);
+    symbiont->GetHardware().GetCPUState().MarkTaskPerformed(8);


Why was this necessary to add?

I moved it out of the WHEN block below. Initially in my refactor I had:

void SGPWorld::SetupFindHostForHorizontalTransmission() { ... const bool compatible = fun_horizontal_transmission_compatibility_check( *prospective_host_ptr, *sym_offspring_ptr ); ... }

Now:

void SGPWorld::SetupFindHostForHorizontalTransmission() { ... const bool compatible = fun_horizontal_transmission_compatibility_check( *prospective_host_ptr, *sym_parent_ptr //This Line Changed ); ... }

As mentioned earlier in your comment in SGPWorld.h, initially I thought it would make sense to compare the offspring to the host. Plus, I saw this in Reproduce():

offspring_cpu_state.SetParentTasksPerformed( hardware.GetCPUState().GetTasksPerformed() ); offspring_cpu_state.SetParentFirstTaskPerformed( hardware.GetCPUState().GetFirstTaskPerformed() );

By putting MarkTaskPerformed() before Reproduce() in the test, I thought it would properly get copied to the offspring, and then the offspring would be able to pass the compatibility check. When I was wrong, I forgot to move this line back and remove the reproduction.

anyaevostinar · 2026-08-10T13:16:18Z

      symbiont->GetHardware().GetCPUState().MarkTaskPerformed(8);
      WHEN("Task matching is not required for horizontal transmission") {
-        auto pos_found = world.FindHostForHorizontalTrans(source_id, symbiont);
+        auto pos_found = world.FindHostForHorizontalTrans(offspring, symbiont, symbiont->GetLocation());


Pretty sure it should be just "symbiont" being passed since offspring has no useful information

anyaevostinar · 2026-08-10T13:25:48Z

    world.AddOrgAt(host, 0);
-    size_t source_id = symbiont->GetLocation().GetPopID();
+    emp::Ptr<Organism> offspring_org = symbiont->Reproduce();
+    emp::Ptr<sgp_sym_t> offspring = static_cast<sgp_sym_t*>(offspring_org.Raw());


You'll be able to remove these lines once you make the change to not pass offspring, so please don't forget to do so

anyaevostinar

Some things to change back. Make sure to be careful not to change functionality other than the specific thing that is the target. Also, it's good to clean up small things, but try to resist moving small lines around when they really don't change much since it adds to the complication of reviews and merge conflicts

codecov · 2026-08-12T20:31:07Z

Codecov Report

❌ Patch coverage is 93.78238% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.09%. Comparing base (80c2445) to head (0e4e09b).

Files with missing lines	Patch %	Lines
source/sgp_mode/SGPW_InteractionMechanismSetup.cc	75.00%	7 Missing ⚠️
source/sgp_mode/SGPW_TaskProfileSetup.cc	75.00%	3 Missing ⚠️
source/default_mode/SymWorld.h	87.50%	1 Missing ⚠️
source/sgp_mode/SGPWorldSetup.cc	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #328      +/-   ##
==========================================
- Coverage   77.09%   77.09%   -0.01%     
==========================================
  Files         108      108              
  Lines       23155    23131      -24     
  Branches     1615     1613       -2     
==========================================
- Hits        17852    17832      -20     
+ Misses       5232     5229       -3     
+ Partials       71       70       -1

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Gabe-Rose added 11 commits July 28, 2026 13:30

something

eda7289

moved to SymDoBirth() and streamlined horizontal_trans_compatibility_…

8f690e7

…check_functions

something

011755c

Merge branch 'main' into Stress_Escapees_Refactor

fd87c52

working horizontal transmission

22d184a

comment

4f9f3cb

tests passing

f843ca4

something

d8d5f26

fixed seg fault

21128c5

Merge branch 'main' into Stress_Escapees_Refactor

2600950

removed comment

ce46fdf

anyaevostinar reviewed Aug 6, 2026

View reviewed changes

Comment thread source/sgp_mode/SGPWorld.h Outdated

anyaevostinar reviewed Aug 6, 2026

View reviewed changes

Comment thread source/test/sgp_mode_test/unit_tests/SGPWorld.test.cc Outdated

anyaevostinar reviewed Aug 10, 2026

View reviewed changes

anyaevostinar requested changes Aug 10, 2026

View reviewed changes

Gabe-Rose added 4 commits August 10, 2026 15:20

pgg test confusion

bccf85f

added comments for funky test

e44989b

added devnote for other debug tests

2f20a26

Placed symbionts directly in graveyard for stress

7edb3b2

added explanitory comments and information in DevNotes

0e4e09b

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Gabe-Rose commented Aug 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Overview:

Stress References removed from SGPWorld* and into SGPW_InteractionMechanismSetup.cc

SymDoBirth modified to take offspring, parent, and world position

SetupHorizontalTransmissionCompatibilityMode() changed to set one functor

Other:

Next steps:

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codecov Bot commented Aug 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Gabe-Rose commented Aug 6, 2026 •

edited

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codecov Bot commented Aug 12, 2026 •

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