Merge pull request #451 from devosoft/mabe-systematics

include/emp/Evolve/NK.hpp

@@ -157,6 +157,21 @@ namespace emp {
       return GetFitness(n, cur_val);
     }
 
+   /// Get the fitness of a whole bitstring (pass by value so can be modified.)
+    emp::vector<double> GetFitnesses(emp::BitVector genome) const {
+      // Use a double-length genome to easily handle wrap-around.
+      genome.Resize(N*2);
+      genome |= (genome << N);
+      emp::vector<double> fits;
+
+      size_t mask = emp::MaskLow<size_t>(K+1);
+      for (size_t i = 0; i < N; i++) {
+        const size_t cur_val = (genome >> i).GetUInt(0) & mask;
+        const double cur_fit = GetFitness(i, cur_val);
+        fits.push_back(cur_fit);
+      }
+      return fits;
+    }
 
     void SetState(size_t n, size_t state, double in_fit) { landscape[n][state] = in_fit; }
 

include/emp/Evolve/World.hpp

@@ -943,6 +943,7 @@ namespace emp {
 
   };
 
+  #ifndef DOXYGEN_SHOULD_SKIP_THIS
   // =============================================================
   // ===                                                       ===
   // ===  Out-of-class member function definitions from above  ===
@@ -972,7 +973,7 @@ namespace emp {
 
     // Track the new systematics info
     for (Ptr<SystematicsBase<ORG> > s : systematics) {
-      s->AddOrg(*new_org, pos, (int) update);
+      s->AddOrg(*new_org, pos);
     }
 
     SetupOrg(*new_org, pos, *random_ptr);
@@ -996,7 +997,7 @@ namespace emp {
     }
 
     for (Ptr<SystematicsBase<ORG> > s : systematics) {
-      s->RemoveOrgAfterRepro(pos, update);          // Notify systematics about organism removal
+      s->RemoveOrgAfterRepro(pos);                   // Notify systematics about organism removal
     }
 
   }
@@ -1489,6 +1490,13 @@ namespace emp {
       pop.resize(0);
       std::swap(pops[0], pops[1]);            // Move next pop into place.
 
+      // Tell systematics manager to swap next population and population
+      // Needs to happen here so that you can refer to systematics in
+      // OnPlacement functions
+      for (Ptr<SystematicsBase<ORG>> s : systematics) {
+        s->Update();
+      }
+
       // Update the active population.
       num_orgs = 0;
       for (size_t i = 0; i < pop.size(); i++) {
@@ -1498,12 +1506,7 @@ namespace emp {
       }
     }
 
-    // 3. Handle systematics and any data files that need to be printed this update.
-
-    // Tell systematics manager to swap next population and population
-    for (Ptr<SystematicsBase<ORG>> s : systematics) {
-      s->Update();
-    }
+    // 3. Handle any data files that need to be printed this update.
 
     for (auto file : files) file->Update(update);
 
@@ -1734,6 +1737,7 @@ namespace emp {
       os << std::endl;
     }
   }
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 }
 
 #endif // #ifndef EMP_EVOLVE_WORLD_HPP_INCLUDE

include/emp/base/_assert_macros.hpp

@@ -18,6 +18,7 @@
 #define emp_assert_STRINGIFY_IMPL(...) #__VA_ARGS__
 #define emp_assert_TO_PAIR(X) emp_assert_STRINGIFY(X) , X
 #define emp_assert_GET_ARG_1(a, ...) a
+#define emp_assert_GET_ARG_2(a,b, ...) b
 #define emp_assert_GET_ARG_21(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t, u, ...) u
 #define emp_assert_MERGE(A, B) A ## B
 #define emp_assert_ASSEMBLE(BASE, ARG_COUNT, ...) emp_assert_MERGE(BASE, ARG_COUNT) (__VA_ARGS__)

include/emp/base/_optional_throw.hpp

@@ -0,0 +1,60 @@
+/*
+ *  This file is part of Empirical, https://github.com/devosoft/Empirical
+ *  Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
+ *  date: 2024
+*/
+/**
+ *  @file
+ *  @brief Implementation of emp_optional_throw.
+ */
+
+#ifndef EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE
+#define EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE
+
+#include <sstream>
+#include <string>
+
+#include "_is_streamable.hpp"
+
+namespace emp {
+
+  /// Base case for assert_print...
+  inline void assert_print_opt(std::stringstream &) { ; }
+
+  /// Print out information about the next variable and recurse...
+  template <typename T, typename... EXTRA>
+  void assert_print_opt(std::stringstream & ss, std::string name, T && val, EXTRA &&... extra) {
+    if constexpr ( emp::is_streamable<std::stringstream, T>::value ) {
+      ss << name << ": [" << val << "]" << std::endl;
+    } else ss << name << ": (non-streamable type)" << std::endl;
+    assert_print_opt(ss, std::forward<EXTRA>(extra)...);
+  }
+
+  template <typename T, typename... EXTRA>
+  void assert_print_second_opt(std::stringstream & ss, std::string name, T && val, EXTRA &&... extra) {
+    assert_print_opt(ss, std::forward<EXTRA>(extra)...);
+  }
+
+  template <typename T>
+  void assert_print_second_opt(std::stringstream & ss, std::string name, T && val) {;}
+
+  template <typename T, typename... EXTRA>
+  void assert_print_first_opt(std::stringstream & ss, std::string name, T && val, EXTRA &&... extra) {
+    if constexpr ( emp::is_streamable<std::stringstream, T>::value ) {
+      ss << name << ": [" << val << "]" << std::endl;
+    } else ss << name << ": (non-streamable type)" << std::endl;
+    assert_print_second_opt(ss, std::forward<EXTRA>(extra)...);
+  }
+
+  void assert_print_first_opt(std::stringstream & ss, int placeholder) {;}
+
+  template <typename... EXTRA>
+  void assert_throw_opt(std::string filename, size_t line, std::string expr, std::string message, EXTRA &&... extra) {
+    std::stringstream ss;
+    ss << "Internal Error (in " << filename << " line " << line << "): " << expr << ".\n\n Message: " << message << "\n\n";
+    assert_print_first_opt(ss, std::forward<EXTRA>(extra)...);
+    throw(std::runtime_error(ss.str()));
+  }
+}
+
+#endif // #ifndef EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE

include/emp/base/always_assert.hpp

@@ -34,6 +34,7 @@
 
 #include "_assert_macros.hpp"
 #include "_assert_trigger.hpp"
+#include "_optional_throw.hpp"
 
 #if defined( __EMSCRIPTEN__ )
 
@@ -58,6 +59,19 @@
 
   #define emp_always_assert_impl(TEST) emp_always_assert_msvc_impl(TEST)
 
+#elif defined(EMP_OPTIONAL_THROW_ON)
+
+  #define emp_always_assert_impl(...)                                     \
+    do {                                                                  \
+      if (!(emp_assert_GET_ARG_1(__VA_ARGS__, ~))) {                      \
+        emp::assert_throw(                                             \
+        __FILE__, __LINE__,                                               \
+        emp_assert_STRINGIFY( emp_assert_GET_ARG_1(__VA_ARGS__, ~),  ),   \
+        emp_assert_TO_PAIRS(__VA_ARGS__));                                       \
+      }                                                                   \
+    } while(0)
+
+
 #else
 
   #define emp_always_assert_impl(...)                                     \

include/emp/base/optional_throw.hpp

@@ -0,0 +1,70 @@
+/*
+ *  This file is part of Empirical, https://github.com/devosoft/Empirical
+ *  Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
+ *  date: 2024
+*/
+/**
+ *  @file
+ *  @brief A version of emp_assert that throws a runtime error if compiled with -DEMP_OPTIONAL_THROW_ON.
+ *
+ *  This is useful if you want the option to throw a runtime error outside of debug mode. A common use
+ *  case is wrapping C++ code in Python, since segfaults kill the entire Python interpreter.
+ */
+
+#ifndef EMP_BASE_OPTIONAL_THROW_HPP_INCLUDE
+#define EMP_BASE_OPTIONAL_THROW_HPP_INCLUDE
+
+#include "assert.hpp"
+
+/// NDEBUG should trigger its EMP equivalent.
+#ifdef NDEBUG
+#define EMP_NDEBUG
+#endif
+
+
+#if defined( EMP_OPTIONAL_THROW_ON )
+
+  // #if defined (_MSC_VER )
+
+  #define emp_optional_throw(TEST, MESSAGE)                                     \
+    do {                                                                  \
+      if (!(TEST)) {                                                      \
+        emp::assert_throw_opt(__FILE__, __LINE__, #TEST, MESSAGE, 0);                \
+      }                                                                   \
+    } while(0)
+
+  /* #define emp_optional_throw_impl(TEST, MESSAGE) emp_optional_throw_mscv_impl(TEST, MESSAGE)
+
+  / #else
+
+  / #define emp_optional_throw_impl(...)                                     \
+  /   do {                                                                  \
+  /     if (!(emp_assert_GET_ARG_1(__VA_ARGS__, ~))) {                      \
+  /       emp::assert_throw(                                             \
+  /       __FILE__, __LINE__,                                               \
+  /       emp_assert_STRINGIFY( emp_assert_GET_ARG_1(__VA_ARGS__, ~),  ),   \
+  /       emp_assert_STRINGIFY( emp_assert_GET_ARG_2(__VA_ARGS__, ~),  ),   \
+  /       emp_assert_TO_PAIRS(__VA_ARGS__));                                       \
+  /     }                                                                   \
+  /   } while(0)
+
+  /   #endif
+
+    / #define emp_optional_throw(...) emp_optional_throw_impl(__VA_ARGS__)
+  */
+#elif defined( EMP_NDEBUG )
+
+  #define emp_optional_throw(...)
+
+#else
+  /// Require a specified condition to be true. If it is false, immediately
+  /// halt execution. Print also extra information on any variables or
+  /// expressions provided as variadic args. Note: If NDEBUG is defined,
+  /// emp_assert() will not do anything. Due to macro parsing limitations, extra
+  /// information will not be printed when compiling with MSVC.
+  #define emp_optional_throw(...) emp_assert(__VA_ARGS__)
+
+#endif
+
+
+#endif // #ifndef EMP_BASE_OPTIONAL_THROW_HPP_INCLUDE

include/emp/data/DataManager.hpp

@@ -54,6 +54,10 @@ namespace emp {
       return Has(node_map, name);
     }
 
+    bool HasNoNode(const std::string & name) {
+      return !Has(node_map, name);
+    }
+
     /// Creates and adds a new DataNode
     /// @param name the name of the DataNode
     node_t & New(const std::string & name) {

include/emp/datastructs/map_utils.hpp

@@ -41,6 +41,19 @@ namespace emp {
     return in_map.find(key) != in_map.end();
   }
 
+  /// Take a map where the value is an integer and a key.
+  /// Increment value associated with that key if its present
+  /// or if its not add it and set it to 1
+  template <class MAP_T, class KEY_T>
+  inline void IncrementCounter( MAP_T & in_map, const KEY_T & key ) {
+    static_assert( std::is_same< typename MAP_T::key_type, int >::value);
+    if (emp::Has(in_map, key)) {
+      in_map[key]++;
+    } else {
+      in_map[key] = 1;
+    }
+  }
+
   // Check to see if any of the elements in a map satisfy a function.
   template <typename KEY_T, typename ELEMENT_T, typename FUN_T>
   bool AnyOf(const std::map<KEY_T, ELEMENT_T> & c, FUN_T fun) {

include/emp/math/info_theory.hpp

@@ -57,7 +57,7 @@ namespace emp {
     double entropy = 0.0;
     for (auto & o : objs) {
       double p = ((double) fun(o)) / total;
-      entropy -= p * Log2(p);
+      entropy -= p * log2(p);
     }
     return entropy;
   }