Merge branch 'main' into repro_rate_data

Author: anyaevostinar

source/sgp_mode/DevNotes.md

@@ -1,6 +1,7 @@
 (delete once Anya is done with joint refactoring)
 
 ## Further refactoring list:
+* Remove location from CPUState and have it rely on Organism location instead of maintaining separately and generally trace through to make sure it is tracked cleanly
 * Add SGP mode to API reference doc
 * Move ProcessSymOutputBuffer into SGPSymbiont to parallel host
 * Move SymDoMutation into SGPSymbiont to parallel host
@@ -95,4 +96,4 @@ These are function flows that are complicated to follow:
 [ ] Port Multi infection code from Elias fork
 [ ] Finish implementation of temporally changing environment
 [ ] Make sure spatial structure is working?
-[ ] Go back through for other refactoring todos
+[ ] Go back through for other refactoring todos

source/sgp_mode/SGPConfigSetup.h

@@ -16,9 +16,9 @@ EMP_EXTEND_CONFIG(SymConfigSGP, SymConfigBase,
   GROUP(SGP, "Complex Genomes Settings"),
   VALUE(CYCLES_PER_UPDATE, size_t, 16, "Number of CPU cycles that organisms run every update"),
   VALUE(FIND_NEIGHBOR_HOST_ATTEMPTS, size_t, 5, "How many times to attempt finding a neighboring host for symbiont to horizontally transmit into"),
-  VALUE(DONATION_STEAL_INST, bool, true, "1 if you want donate and steal instructions in the instruction set, 0 if not"),
-  VALUE(SYM_DONATE_PROP, double, 0.2, "Proportion of points for sym to donate to host on donate"),
-  VALUE(SYM_STEAL_PROP, double, 0.2, "Proportion of points for sym to steal from host on steal"),
+  VALUE(DONATION_STEAL_INST, bool, false, "1 if you want donate and steal instructions in the instruction set, 0 if not"),
+  VALUE(SYM_DONATE_PROP, double, 0.0, "Proportion of points for sym to donate to host on donate"),
+  VALUE(SYM_STEAL_PROP, double, 0.0, "Proportion of points for sym to steal from host on steal"),
   VALUE(HOST_MIN_CYCLES_BEFORE_REPRO, size_t, 0, "Number of CPU cycles organisms must wait between reproductions"),
   VALUE(SYM_MIN_CYCLES_BEFORE_REPRO, size_t, 0, "Number of CPU cycles organisms must wait between reproductions"),
 

source/test/sgp_mode_test/unit_tests/Instructions.test.cc

@@ -489,6 +489,7 @@ TEST_CASE("Test host-symbiont interactive instructions", "[sgp]") {
   sgpmode::SymConfigSGP config;
   config.CYCLES_PER_UPDATE(0);
   config.HOST_REPRO_RES(1);
+  config.DONATION_STEAL_INST(true);
   config.SEED(61);
   config.TASK_ENV_CFG_PATH("source/test/sgp_mode_test/hardware-test-env.json");
   config.FILE_PATH("Instructions_test_output");