Merge branch 'multicell-parasite' into master

CMakeLists.txt

@@ -26,6 +26,7 @@ SET(LIBRARY_OUTPUT_PATH
 
 
 ADD_SUBDIRECTORY(libs/apto)
+
 if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
   ADD_SUBDIRECTORY(libs/backward-cpp)
 endif()

avida-core/source/actions/PopulationActions.cc

@@ -681,23 +681,31 @@ class cActionInjectParasite : public cAction
   cString m_label;
   int m_cell_start;
   int m_cell_end;
+  int m_cell_stride;
+  int m_only_if_parasites_extinct;
 public:
-  cActionInjectParasite(cWorld* world, const cString& args, Feedback&) : cAction(world, args), m_cell_start(0), m_cell_end(-1)
+  cActionInjectParasite(cWorld* world, const cString& args, Feedback&) : cAction(world, args), m_cell_start(0), m_cell_end(-1), m_cell_stride(1), m_only_if_parasites_extinct(0)
   {
     cString largs(args);
     m_filename = largs.PopWord();
     m_label = largs.PopWord();
     if (largs.GetSize()) m_cell_start = largs.PopWord().AsInt();
     if (largs.GetSize()) m_cell_end = largs.PopWord().AsInt();
+    if (largs.GetSize()) m_cell_stride = largs.PopWord().AsInt();
+    if (largs.GetSize()) m_only_if_parasites_extinct = largs.PopWord().AsInt();
 
     if (m_cell_end == -1) m_cell_end = m_cell_start + 1;
   }
 
-  static const cString GetDescription() { return "Arguments: <string filename> <string label> [int cell_start=0] [int cell_end=-1]"; }
+  static const cString GetDescription() { return "Arguments: <string filename> <string label> [int cell_start=0] [int cell_end=-1] [int cell_stride=1] [int only_if_parasites_extinct=0]"; }
 
   void Process(cAvidaContext& ctx)
   {
-    if (m_cell_start < 0 || m_cell_end > m_world->GetPopulation().GetSize() || m_cell_start >= m_cell_end) {
+    if (m_only_if_parasites_extinct && m_world->GetStats().GetNumParasites()) {
+      return;
+    }
+
+    if (m_cell_start < 0 || m_cell_end > m_world->GetPopulation().GetSize() || m_cell_start >= m_cell_end || m_cell_stride <= 0) {
       ctx.Driver().Feedback().Warning("InjectParasite has invalid range!");
     } else {
       GenomePtr genome;
@@ -714,7 +722,7 @@ class cActionInjectParasite : public cAction
       if (!genome) return;
       ConstInstructionSequencePtr seq;
       seq.DynamicCastFrom(genome->Representation());
-      for (int i = m_cell_start; i < m_cell_end; i++) {
+      for (int i = m_cell_start; i < m_cell_end; i+=m_cell_stride) {
         m_world->GetPopulation().InjectParasite(m_label, *seq, i);
       }
       m_world->GetPopulation().SetSyncEvents(true);
@@ -850,8 +858,6 @@ class cActionInjectParasitePair : public cAction
  Parameters:
  filename (string):
  The filename of the genotype to load.
- cell ID (integer) default: 0
- The grid-point into which the organism should be placed.
  merit (double) default: -1
  The initial merit of the organism. If set to -1, this is ignored.
  lineage label (integer) default: 0
@@ -5182,23 +5188,27 @@ class cActionKillWithinRadiusBelowResourceThresholdTestAll : public cAction {
  
  Parameters:
  - The percent of living organisms to kill (default: 0)
+ - The targeted deme to kill (default: -1, targets all demes)
  */
 
 class cActionKillDemePercent : public cAction
 {
 private:
   double m_pctkills;
+  int m_target_demeid;
 public:
-  cActionKillDemePercent(cWorld* world, const cString& args, Feedback&) : cAction(world, args), m_pctkills(0)
+  cActionKillDemePercent(cWorld* world, const cString& args, Feedback&) : cAction(world, args), m_pctkills(0), m_target_demeid(-1)
   {
     cString largs(args);
     if (largs.GetSize()) m_pctkills = largs.PopWord().AsDouble();
+    if (largs.GetSize()) m_target_demeid = largs.PopWord().AsInt();
 
     assert(m_pctkills >= 0);
     assert(m_pctkills <= 1);
+    assert(m_target_demeid >= -1);
   }
 
-  static const cString GetDescription() { return "Arguments: [double pctkills=0.0]"; }
+  static const cString GetDescription() { return "Arguments: [double pctkills=0.0] [int target_demeid=-1]"; }
 
   void Process(cAvidaContext& ctx)
   {
@@ -5208,8 +5218,13 @@ class cActionKillDemePercent : public cAction
     long cells_scanned = 0;
     long orgs_killed = 0;
     long cells_empty = 0;
-
-    for (int d = 0; d < pop.GetNumDemes(); d++) {
+
+    const int start = (m_target_demeid == -1) ? 0 : m_target_demeid;
+    assert(start < pop.GetNumDemes());
+    const int stop = (
+      (m_target_demeid == -1) ? pop.GetNumDemes() : m_target_demeid + 1
+    );
+    for (int d = start; d < stop; d++) {
 
       cDeme &deme = pop.GetDeme(d);
 
@@ -6061,6 +6076,7 @@ void RegisterPopulationActions(cActionLibrary* action_lib)
   action_lib->Register<cActionKillDemePercent>("KillDemePercent");
   action_lib->Register<cActionKillDemesHighestParasiteLoad>("KillDemesHighestParasiteLoad");
   action_lib->Register<cActionReplicateDemesHighestBirthCount>("ReplicateDemesHighestBirthCount");
+  action_lib->Register<cActionSetDemeTreatmentAges>("SetDemeTreatmentAges");
   action_lib->Register<cActionKillMeanBelowThresholdPaintable>("KillMeanBelowThresholdPaintable");
 
   action_lib->Register<cActionDiffuseHGTGenomeFragments>("DiffuseHGTGenomeFragments");

avida-core/source/actions/PrintActions.cc

@@ -64,6 +64,7 @@
 
 #include <cmath>
 #include <cerrno>
+#include <cstdlib>
 #include <map>
 #include <algorithm>
 
@@ -1074,6 +1075,25 @@ class cActionEcho : public cAction
   }
 };
 
+class cActionShell : public cAction
+{
+private:
+  cString m_filename;
+public:
+  cActionShell(cWorld* world, const cString& args, Feedback&) : cAction(world, args) { ; }
+
+  static const cString GetDescription() { return "Arguments: <cString message>"; }
+
+  void Process(cAvidaContext& ctx)
+  {
+    const int res = std::system(m_args);
+    std::stringstream ss;
+    ss << "Command `" << m_args << "` gave result " << res;
+
+    ctx.Driver().Feedback().Notify(ss.str().c_str());
+  }
+};
+
 
 class cActionPrintGenotypeAbundanceHistogram : public cAction
 {
@@ -5662,6 +5682,7 @@ void RegisterPrintActions(cActionLibrary* action_lib)
   action_lib->Register<cActionPrintParasiteDepthHistogram>("PrintParasiteDepthHistogram");
   action_lib->Register<cActionPrintHostDepthHistogram>("PrintHostDepthHistogram");
   action_lib->Register<cActionEcho>("Echo");
+  action_lib->Register<cActionShell>("Shell");
   action_lib->Register<cActionPrintGenotypeAbundanceHistogram>("PrintGenotypeAbundanceHistogram");
   //  action_lib->Register<cActionPrintSpeciesAbundanceHistogram>("PrintSpeciesAbundanceHistogram");
   //  action_lib->Register<cActionPrintLineageTotals>("PrintLineageTotals");

avida-core/source/cpu/cHardwareTransSMT.cc

@@ -20,6 +20,8 @@
  */
 
 #include "cHardwareTransSMT.h"
+#include "avida/core/Feedback.h"
+#include "avida/core/WorldDriver.h"
 #include "avida/systematics/Unit.h"
 
 #include "cAvidaContext.h"
@@ -38,6 +40,8 @@
 
 #include "AvidaTools.h"
 
+#include <algorithm>
+#include <cstdio>
 #include <iomanip>
 
 using namespace std;
@@ -1064,9 +1068,52 @@ void cHardwareTransSMT::Inject_DoMutations(cAvidaContext& ctx, double mut_multip
   // Insert Mutations (per site)
   num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
                                             m_organism->GetInjectInsProb());
-  // If would make creature to big, insert up to MAX_GENOME_LENGTH
-  if( num_mut + injected_code.GetSize() > MAX_GENOME_LENGTH )
-    num_mut = MAX_GENOME_LENGTH - injected_code.GetSize();
+
+  // use strongest restrictions
+  const int min_genome_size = std::max(
+    // don't need to account for unset cfg (i.e., 0) due to max
+    m_world->GetConfig().MIN_GENOME_SIZE.Get(),
+    MIN_GENOME_LENGTH  // hardcoded implementation limit
+  );
+  const int max_genome_size = m_world->GetConfig().MAX_GENOME_SIZE.Get()
+    // MAX_GENOME_LENGTH is hardcoded implementation limit
+    ? std::min(m_world->GetConfig().MAX_GENOME_SIZE.Get(), MAX_GENOME_LENGTH)
+    : MAX_GENOME_LENGTH
+  ;
+
+  // @MAM
+  // (somehow) parasites shrink despite del and implicit muts being disabled
+  // so, enforce min genome size by growing up to min genome size if need be
+  if (min_genome_size && injected_code.GetSize() < min_genome_size) {
+    if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 1) {
+      num_mut = std::max(num_mut, min_genome_size - injected_code.GetSize());
+      // ctx.Driver().Feedback().Warning(
+      printf("warning: "
+        "Grew genome of size %d back to min genome size %d with %d inserts.\n",
+        injected_code.GetSize(), min_genome_size, num_mut
+      );
+    } else if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 2) {
+      printf("warning: "
+        "Sterilized too-small genome of size %d by setting insts to Nop-X.\n",
+        injected_code.GetSize()
+      );
+      for (int site = 0; site < injected_code.GetSize(); ++site) {
+        injected_code[site] = m_inst_set->GetInst("Nop-X");
+      }
+    } else if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 3) {
+      printf("warning: "
+        "Sterilized too-small genome of size %d by setting insts to Nop-A.\n",
+        injected_code.GetSize()
+      );
+      for (int site = 0; site < injected_code.GetSize(); ++site) {
+        injected_code[site] = m_inst_set->GetInst("Nop-A");
+      }
+    }
+  }
+
+  // If would make creature to big, insert up to max_genome_size
+  if( num_mut + injected_code.GetSize() > max_genome_size )
+    num_mut = max_genome_size - injected_code.GetSize();
   // If we have lines to insert...
   if( num_mut > 0 ){
     // Build a list of the sites where mutations occured
@@ -1083,9 +1130,37 @@ void cHardwareTransSMT::Inject_DoMutations(cAvidaContext& ctx, double mut_multip
   // Delete Mutations (per site)
   num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
                                             m_organism->GetInjectDelProb());
-  // If would make creature too small, delete down to MIN_GENOME_LENGTH
-  if (injected_code.GetSize() - num_mut < MIN_GENOME_LENGTH) {
-    num_mut = injected_code.GetSize() - MIN_GENOME_LENGTH;
+
+  if (max_genome_size && injected_code.GetSize() > max_genome_size) {
+    if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 1) {
+      num_mut = std::max(num_mut, injected_code.GetSize() - max_genome_size);
+      // ctx.Driver().Feedback().Warning(
+      printf("warning: "
+        "Shrank genome of size %d back to max genome size %d with %d deletes.\n",
+        injected_code.GetSize(), max_genome_size, num_mut
+      );
+    } else if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 2) {
+      printf("warning: "
+        "Sterilized too-large genome of size %d by setting insts to Nop-X.\n",
+        injected_code.GetSize()
+      );
+      for (int site = 0; site < injected_code.GetSize(); ++site) {
+        injected_code[site] = m_inst_set->GetInst("Nop-X");
+      }
+    } else if (m_world->GetConfig().GENOME_SIZE_RECOVERY.Get() == 3) {
+      printf("warning: "
+        "Sterilized too-large genome of size %d by setting insts to Nop-A.\n",
+        injected_code.GetSize()
+      );
+      for (int site = 0; site < injected_code.GetSize(); ++site) {
+        injected_code[site] = m_inst_set->GetInst("Nop-A");
+      }
+    }
+  }
+
+  // If would make creature too small, delete down to min_genome_size
+  if (injected_code.GetSize() - num_mut < min_genome_size) {
+    num_mut = injected_code.GetSize() - min_genome_size;
   }
 
   // If we have lines to delete...
@@ -1094,8 +1169,6 @@ void cHardwareTransSMT::Inject_DoMutations(cAvidaContext& ctx, double mut_multip
     injected_code.Remove(site);
   }
 
-  int max_genome_size = m_world->GetConfig().MAX_GENOME_SIZE.Get();
-  int min_genome_size = m_world->GetConfig().MIN_GENOME_SIZE.Get();
   cCPUMemory& memory = GetMemory();
 
   // Parent Substitution Mutations (per site)
@@ -1656,6 +1729,15 @@ bool cHardwareTransSMT::Inst_ThreadKill(cAvidaContext&)
 // into the complement template found in a neighboring organism.
 bool cHardwareTransSMT::Inst_Inject(cAvidaContext& ctx)
 {
+  const bool is_nonparasite = !(
+    ThreadGetOwner()->UnitSource().transmission_type == Systematics::HORIZONTAL
+    || ThreadGetOwner()->UnitSource().transmission_type == Systematics::VERTICAL
+  );
+  if (
+    m_world->GetConfig().TRANSSMT_DISABLE_NONPARASITE_INJECT.Get()
+    && is_nonparasite
+  ) return true;  // do nothing, successfully
+
   ReadLabel(MAX_MEMSPACE_LABEL);
 
   if(ThreadGetOwner()->UnitSource().transmission_type == Systematics::HORIZONTAL)

avida-core/source/main/cAvidaConfig.h

@@ -393,6 +393,7 @@ class cAvidaConfig {
   CONFIG_ADD_VAR(MIN_EXE_LINES, double, 0.5, "Code fraction that must be executed before divide");
   CONFIG_ADD_VAR(MIN_GENOME_SIZE, int, 0, "Minimum number of instructions allowed in a genome. 0 = OFF");
   CONFIG_ADD_VAR(MAX_GENOME_SIZE, int, 0, "Maximum number of instructions allowed in a genome. 0 = OFF");
+  CONFIG_ADD_VAR(GENOME_SIZE_RECOVERY, int, 0, "How should genomes that arise outside the too-small or too-large size bounds be corrected? 0: do nothing, 1: use standard indel mutations to put within size bounds, 2: sterilize by replaceing all insts with Nop-X, 3: sterilize by replaceing all insts with Nop-A.");
   CONFIG_ADD_VAR(MIN_CYCLES, int, 0, "Min number of CPU cycles (age) required before reproduction.");
   CONFIG_ADD_VAR(REQUIRE_ALLOCATE, int, 1, "(Original CPU Only) Require allocate before divide?");
   CONFIG_ADD_VAR(REQUIRED_TASK, int, -1, "Task ID required for successful divide");
@@ -439,6 +440,7 @@ class cAvidaConfig {
 
   // -------- Parasite options --------
   CONFIG_ADD_GROUP(PARASITE_GROUP, "Parasite config options");
+  CONFIG_ADD_VAR(LOG_PARASITE_INJECTIONS, bool, 0, "Log parasite replications?");
   CONFIG_ADD_VAR(INJECT_METHOD, int, 0, "What should happen to a parasite when it gives birth?\n0 = Leave the parasite thread state untouched.\n1 = Resets the state of the calling thread (for SMT parasites, this must be 1)");
   CONFIG_ADD_VAR(INFECTION_MECHANISM, int, 1, "0: Infection always succeeds. \n1: Infection succeeds if parasite matches at least one host task.\n2: Infection succeeds if parasite does NOT match at least one task.\n3: Parasite tasks must match host tasks exactly (Matching Alleles).");
   CONFIG_ADD_ALIAS(INJECT_IS_TASK_SPECIFIC);
@@ -461,6 +463,7 @@ class cAvidaConfig {
   CONFIG_ADD_VAR(HOST_USE_GENOTYPE_FILE, int, 0, "Host Genotypes are loaded from a file rather than replicated from parent -- see LoadHostGenotypeList");
 
   CONFIG_ADD_VAR(FULL_VERTICAL_TRANS, double, 0.0, "Determines if offspring of infected host is automatically infected. 0 for no, 1 for yes. If you want to keep parent infected as well, you need to set DIVIDE_METHOD to 2.");
+  CONFIG_ADD_VAR(TRANSSMT_DISABLE_NONPARASITE_INJECT, double, 0.0, "Should inject instruction be a no-op for non-parasites? Prevents host-generated pseudo-parasites. 0 for no, 1 for yes.");
 
 
   // -------- CPU Archetecture

avida-core/source/main/cDeme.cc

@@ -1236,7 +1236,7 @@ int cDeme::GetSlotFlowRate() const
 bool cDeme::IsTreatableAtAge(const int age)
 {  
   if (isTreatable()) {
-    if (treatment_ages.size() == 0) { return false; } // implies treatable every update
+    if (treatment_ages.size() == 0) { return true; } // implies treatable every update
     set<int>::iterator it;
     it = treatment_ages.find(age);
     if(it != treatment_ages.end()) return true;