Merge branch 'mabe-systematics' into sum-distance-sys

devosoft · Feb 29, 2024 · f11a154 · f11a154
2 parents 1b323cf + ab563bf
commit f11a154
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Showing 6 changed files with 57 additions and 57 deletions.
diff --git a/include/emp/Evolve/Systematics.hpp b/include/emp/Evolve/Systematics.hpp
@@ -1,11 +1,11 @@
+/*
+ *  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
+*/
 /**
- *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
- *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
- *  @date 2017-2023
- *
- *  @file Systematics.hpp
- *  @brief Track genotypes, species, clades, or lineages of organisms in a world.
- *
+ *  @file
+ *  @brief TODO.
  *  @todo We should provide an option to back up systematics data to a file so that it doesn't all
  *        need to be kept in memory, especially if we're only doing post-analysis.
  *  @todo This inheritance system makes adding new systematics-related data tracking kind of a pain.

diff --git a/include/emp/base/_optional_throw.hpp b/include/emp/base/_optional_throw.hpp
@@ -1,15 +1,15 @@
+/*
+ *  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
+*/
 /**
- *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
- *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
- *  @date 2023.
- *
- *  @file _optional_throw.hpp
- *  @brief Variant of asserts that throws exception
- *  @note This is useful for writing code that gets wrapped in Python via pybind11
+ *  @file
+ *  @brief TODO.
  */
 
-#ifndef EMP_BASE__OPTIONAL_THROW_TRIGGER_HPP_INCLUDE
-#define EMP_BASE__OPTIONAL_THROW_TRIGGER_HPP_INCLUDE
+#ifndef EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE
+#define EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE
 
 #include <sstream>
 #include <string>
@@ -19,42 +19,42 @@
 namespace emp {
 
     /// Base case for assert_print...
-    inline void assert_print(std::stringstream &) { ; }
+    inline void assert_print_opt(std::stringstream &) { ; }
 
     /// Print out information about the next variable and recurse...
     template <typename T, typename... EXTRA>
-    void assert_print(std::stringstream & ss, std::string name, T && val, EXTRA &&... 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(ss, std::forward<EXTRA>(extra)...);
+        assert_print_opt(ss, std::forward<EXTRA>(extra)...);
     }
 
     template <typename T, typename... EXTRA>
-    void assert_print_second(std::stringstream & ss, std::string name, T && val, EXTRA &&... extra) {
-        assert_print(ss, std::forward<EXTRA>(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(std::stringstream & ss, std::string name, T && val) {;}
+    void assert_print_second_opt(std::stringstream & ss, std::string name, T && val) {;}
 
     template <typename T, typename... EXTRA>
-    void assert_print_first(std::stringstream & ss, std::string name, T && val, EXTRA &&... 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(ss, std::forward<EXTRA>(extra)...);
+        assert_print_second_opt(ss, std::forward<EXTRA>(extra)...);
     }
 
-    void assert_print_first(std::stringstream & ss, int placeholder) {;}
+    void assert_print_first_opt(std::stringstream & ss, int placeholder) {;}
 
     template <typename... EXTRA>
-    void assert_throw(std::string filename, size_t line, std::string expr, std::string message, EXTRA &&... 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(ss, std::forward<EXTRA>(extra)...);
+        assert_print_first_opt(ss, std::forward<EXTRA>(extra)...);
         throw(std::runtime_error(ss.str()));
     }
 }
 
-#endif // #ifndef EMP_BASE__OPTIONAL_THROW_TRIGGER_HPP_INCLUDE
+#endif // #ifndef EMP_BASE__OPTIONAL_THROW_HPP_INCLUDE
diff --git a/include/emp/base/always_assert.hpp b/include/emp/base/always_assert.hpp
@@ -59,7 +59,7 @@
 
   #define emp_always_assert_impl(TEST) emp_always_assert_msvc_impl(TEST)
 
-#elif defined(IN_PYTHON)
+#elif defined(EMP_OPTIONAL_THROW_ON)
 
   #define emp_always_assert_impl(...)                                     \
     do {                                                                  \

diff --git a/include/emp/base/optional_throw.hpp b/include/emp/base/optional_throw.hpp
@@ -1,11 +1,11 @@
+/*
+ *  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
+*/
 /**
- *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
- *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
- *  @date 2023.
- *
- *  @file optional_throw.hpp
- *  @brief Like emp_assert, but throws an exception if in Python
- *  @note Status: RELEASE
+ *  @file
+ *  @brief TODO.
  *
  */
 
@@ -20,14 +20,14 @@
 #endif
 
 
-#if defined( IN_PYTHON )
+#if defined( EMP_OPTIONAL_THROW_ON )
 
   // #if defined (_MSC_VER )
 
   #define emp_optional_throw(TEST, MESSAGE)                                     \
     do {                                                                  \
       if (!(TEST)) {                                                      \
-        emp::assert_throw(__FILE__, __LINE__, #TEST, MESSAGE, 0);                \
+        emp::assert_throw_opt(__FILE__, __LINE__, #TEST, MESSAGE, 0);                \
       }                                                                   \
     } while(0)
 

diff --git a/tests/Evolve/Systematics.cpp b/tests/Evolve/Systematics.cpp
@@ -1,14 +1,14 @@
+/*
+ *  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
+*/
 /**
- *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
- *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
- *  @date 2021
- *
- *  @file Systematics.cpp
- */
-
+ *  @file
+ *  @brief TODO.
 #include <filesystem>
 #include <iostream>
-#include <sstream>
+ */
 
 #include "third-party/Catch/single_include/catch2/catch.hpp"
 
@@ -920,7 +920,7 @@ TEST_CASE("Run world", "[evo]") {
   for (size_t i = 0; i < 100; i++) {
       EliteSelect(world, 1, 1);
   }
-    
+
   for (size_t i = 0; i < world.GetSize(); i++) {
     record_fit_sig.Trigger(i, world.CalcFitnessID(i));
     record_phen_sig.Trigger(i, phen_fun(world.GetOrg(i)));

diff --git a/tests/base/optional_throw.cpp b/tests/base/optional_throw.cpp
@@ -1,13 +1,13 @@
+/*
+ *  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
+*/
 /**
- *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
- *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
- *  @date 2023
- *
- *  @file optional_throw.cpp
- */
-
+ *  @file
+ *  @brief TODO.
 #include <iostream>
-#include <sstream>
+ */
 
 #include "third-party/Catch/single_include/catch2/catch.hpp"
 
@@ -19,11 +19,11 @@ TEST_CASE("Optional throw" "[asserts]") {
   emp_optional_throw(false);
   REQUIRE(emp::assert_last_fail);
 
-  #define IN_PYTHON 1
+  #define EMP_OPTIONAL_THROW_ON 1
   try {
     emp_optional_throw(false);
   }
   catch (std::runtime_error & error) {
     REQUIRE(std::string(error.what()) == "Internal Error (in always_assert.cpp line 37): false,\nfalse: [0]\n");
   }
-}
+}