Fixed some spacing issues.

include/emp/base/notify.hpp

@@ -334,7 +334,7 @@ namespace notify {
   /// Send out a notification of an ERROR.
   template <typename... Ts>
   static bool Error(Ts... args) {
-    bool success = Notify(Type::ERROR, std::forward<Ts>(args)...);    
+    bool success = Notify(Type::ERROR, std::forward<Ts>(args)...);
     if (!success) {
 #ifdef NDEBUG
       Exit(1);

include/emp/bits/Bits.hpp

@@ -9,7 +9,7 @@
  *
  *  The Bits template allows the user to recreate the functionality of std::vector<bool>,
  *  array<bool>, std::bitset, and other such bit-handling classes.
- * 
+ *
  *  This class stores an arbitrary number of bits in a set of "fields" (typically 32 bits or 64
  *  bits per field, depending on which should be faster.)  Individual bits can be extracted,
  *  -or- bitwise logic (including more complex bit magic) can be used on the groups of bits.
@@ -25,13 +25,13 @@
  *    StaticBitValue  : Like BitValue, but max size and fixed memory.
  *    BitArray        : A replacement for std::array<bool> (index 0 is on left)
  *    BitSet          : A replacement for std::bitset (index 0 is on right)
- * 
+ *
  *  In the case of replacements, the aim was for identical functionality, but many additional
  *  features, especially associated with bitwise logic operations.
- * 
+ *
  *  @note Compile with -O3 and -msse4.2 for fast bit counting.
  *
- * 
+ *
  *  @todo Most of the operators don't check to make sure that both Bit groups are the same size.
  *        We should create versions (Intersection() and Union()?) that adjust sizes if needed.
  *  @todo Do small BitVector optimization.  Currently we have number of bits (8 bytes) and a
@@ -76,7 +76,7 @@ namespace emp {
 
   /// @brief A flexible base template to handle BitVector, BitArray, BitSet, & other combinations.
   /// @tparam DATA_T How is this Bits object allowed to change size?
-  /// @tparam ZERO_LEFT Should the index of zero be the left-most bit? (right-most if false) 
+  /// @tparam ZERO_LEFT Should the index of zero be the left-most bit? (right-most if false)
   template <typename DATA_T, bool ZERO_LEFT>
   class Bits {
     using this_t = Bits<DATA_T, ZERO_LEFT>;
@@ -160,7 +160,7 @@ namespace emp {
 
   public:
     /// @brief Default constructor; will build the default number of bits (often 0, but not always)
-    /// @param init_val Initial value of all default bits. 
+    /// @param init_val Initial value of all default bits.
     Bits(bool init_val=0) { if (init_val) SetAll(); else Clear(); }
 
     /// @brief Build a new Bits with specified bit count and initialization (default 0)

include/emp/bits/Bits_Data.hpp

@@ -183,15 +183,15 @@ namespace emp {
       Bits_Data_Mem_Static_Base & operator=(Bits_Data_Mem_Static_Base &&) = default;
 
       // --- Helper functions --
-      
+
       [[nodiscard]] Ptr<field_t> FieldPtr() { return bits.data(); }
       [[nodiscard]] Ptr<const field_t> FieldPtr() const { return bits.data(); }
 
       void RawResize(const size_t new_size, const bool preserve_data=false) {
         const size_t old_num_fields = BASE_T::NumFields();
         BASE_T::SetSize(new_size);
         if (preserve_data && BASE_T::NumEndBits()) {
-          bits[BASE_T::LastField()] &= BASE_T::EndMask();          
+          bits[BASE_T::LastField()] &= BASE_T::EndMask();
           for (size_t id = BASE_T::NumFields(); id < old_num_fields; ++id) bits[id] = 0;
         }
       }
@@ -208,7 +208,7 @@ namespace emp {
       }
 
     };
-    
+
     template <size_t CAPACITY, size_t DEFAULT_SIZE=0>
     using Bits_Data_Mem_Static =
       Bits_Data_Mem_Static_Base< Bits_Data_Size_Var<DEFAULT_SIZE>, CAPACITY >;
@@ -373,7 +373,7 @@ namespace emp {
         base_t::SetSize(new_size);
 
         if (preserve_data) {
-          // Clear any new (or previously unused) fields.            
+          // Clear any new (or previously unused) fields.
           for (size_t i = num_old_fields; i < num_new_fields; ++i) bits[i] = 0;
 
           // Clear out any extra end bits.

include/emp/bits/bitset_utils.hpp

@@ -44,7 +44,7 @@ namespace emp {
   [[nodiscard]] static std::string BitFieldsToString(emp::Ptr<bits_field_t> bits, size_t count) {
     std::stringstream ss;
     for (size_t i = 0; i < count; ++i) {
-      if (i) ss << ' ';            
+      if (i) ss << ' ';
       ss << BitFieldToString(bits[i]);
     }
     return ss.str();

include/emp/compiler/Lexer.hpp

@@ -6,24 +6,24 @@
  *  @file Lexer.hpp
  *  @brief A general-purpose, fast lexer.
  *  @note Status: BETA
- * 
+ *
  *  Build a lexer that can convert input strings or streams into a series of provided tokens.
- * 
+ *
  *  Use AddToken(name, regex) to list out the relevant tokens.
  *   'name' is the unique name for this token.
  *   'regex' is the regular expression that describes this token.
  *  It will return a unique ID associated with this lexeme.
- * 
+ *
  *  IgnoreToken(name, regex) uses the same arguments, but is used for tokens that
  *  should be skipped over.
- * 
+ *
  *  Names and IDs can be recovered later using GetTokenID(name) and GetTokenName(id).
- * 
+ *
  *  Tokens can be retrieved either one at a time with Process(string) or Process(stream),
  *  which will return the next (non-ignored) token, removing it from the input.
- * 
+ *
  *  Alternatively, an entire series of tokens can be processed with Tokenize().
- * 
+ *
  *  Finally, GetLexeme() can be used to retrieve the lexeme from the most recent token found.
  */
 
@@ -349,7 +349,7 @@ namespace emp {
     }
 
     /// Turn a vector of strings into a vector of tokens.
-    TokenStream Tokenize(const emp::vector<std::string> & str_v, 
+    TokenStream Tokenize(const emp::vector<std::string> & str_v,
                          const std::string & name="in_string vector") const
     {
       std::stringstream ss;

include/emp/config/FlagManager.hpp

@@ -6,24 +6,24 @@
  *  @file FlagManager.hpp
  *  @brief This file contains tools for dealing with command-line flags (from argv and argc).
  *  @note Status: ALPHA
- * 
+ *
  *  The FlagManager class will take command line arguments (either in its constructor or with
  *  the AddFlags() function) and process them appropriately.
- * 
+ *
  *  For setup, the user must run AddOption with the function to call.  Functions to call can take
  *  zero, one, or two Strings as arguments OR they can take a vector of Strings and the range of
  *  allowed arguments should be specified.  When Process() is run, the appropriate function will
  *  be called on each and any invalid arguments will trigger an error.
- * 
+ *
  *  Flags are expected to begin with a '-' and non-flags are expected to NOT begin with a '-'.
- * 
+ *
  *  If a single dash is followed by multiple characters, each will be processed independently.
  *  So, "-abc" will be the same as "-a -b -c".
- * 
+ *
  *  Extra command line arguments will be saves as a vector of strings called "extras" and must
  *  be processed manually.  They can be retrieved with GetExtras().
- * 
- * 
+ *
+ *
  *  @todo: Make variable numbers of flag arguments work.
  */
 

include/emp/data/DataMap.hpp

@@ -402,7 +402,7 @@ namespace emp {
 
     /// Return a function that takes in a data map and (efficiently) returns a Datum using the
     /// specified name.
-    static auto MakeDatumAccessor(const emp::DataLayout & layout, const std::string & name) { 
+    static auto MakeDatumAccessor(const emp::DataLayout & layout, const std::string & name) {
       emp_assert(layout.HasName(name), "DatumAccessor not pointing to valid name", name);
       return MakeDatumAccessor(layout, layout.GetID(name));
     }

include/emp/data/README.md

@@ -43,7 +43,7 @@ This directory contains a set of tools for managing more or less genetic data.
 * DataMapParser.hpp - A parser to take an equation based on variables in a DataLayout that
   will produce a lambda.  If a DataMap is passed into the lambda the equation will be
   calculated and the result returned.
-  
+
 * Trait.hpp - ?
 
 
@@ -55,7 +55,7 @@ DataRow - Same interface as DataMap; refers to associated DataFrame.
 
 DataTracker - Handles all of the functionality of DataNode, DataLog, etc., but more dynamic
   using lambdas to deal with values as needed.
-  
+
 
 ## To modify?
 

include/emp/data/SimpleParser.hpp

@@ -12,7 +12,7 @@
  *  Allowed map types include std::map<std::string,T>, std::unordered_map<std::string,T>,
  *  emp::DataMap, and (soon) derivations from emp::AnnotatedType.  For standard maps, T must be
  *  convertable to emp::Datum.
- * 
+ *
  *  Developer TODO:
  *  - Setup operator RegEx to be built dynamically
  *  - Setup LVALUES as a type, and allow assignment

include/emp/datastructs/IndexSet.hpp

@@ -138,7 +138,7 @@ namespace emp {
     size_t GetEnd() const {
       return range_set.size() ? range_set.back().GetEnd() : 0;
     }
-    
+
     size_t GetNumRanges() const { return range_set.size(); }
 
     /// @brief Calculate the total combined size of all ranges.

include/emp/datastructs/QueueCache.hpp

@@ -126,7 +126,7 @@
         if (found != cache_map.end()) {
           Delete(found);
         }
-        
+
         cache_list.emplace_front(key, val);         // Put element into the cache
         cache_map.emplace(key, cache_list.begin()); // Add element pointer to map
         Shrink();                                   // Reduce if we are over capacity

include/emp/datastructs/UnorderedIndexMap.hpp

@@ -79,7 +79,7 @@ namespace emp {
       emp_assert(num_items > 0, "UnorderedIndexMaps should not be initialized with empty weights");
       for (size_t i = 0; i < num_items; i++) weights[i + num_nodes] = in_weights[i];
     }
-    
+
     UnorderedIndexMap(const UnorderedIndexMap &) = default;
     UnorderedIndexMap(UnorderedIndexMap &&) = default;
     ~UnorderedIndexMap() = default;

include/emp/datastructs/ra_map.hpp

@@ -6,7 +6,7 @@
  *  @file ra_map.hpp
  *  @brief This file defines a Random Access Map template.
  *  @note Status: ALPHA
- * 
+ *
  *  A random access map allows for simple traversal by index and a guarantee that a value at a
  *  given index will always be at that index unless any map element is deleted.  This allows
  *  storage of indices for maps with a fixed layout, resulting in easy access.
@@ -131,7 +131,7 @@ namespace emp {
       return true;
     }
 
-    
+
     size_t count(const KEY_T & key) const { return id_map.count(key); } /// Is value included? (0 or 1).
 
     /// Index into the ra_map by key.

include/emp/hardware/VirtualCPU.hpp

@@ -127,7 +127,7 @@ namespace emp{
       size_t write_head;                       ///< Write head, signals where to copy next
                                                ///< instruction
       size_t cooldown_timer = 0;               ///< Do not process inst if value > 0.
-                                               ///< Decrease this value instead 
+                                               ///< Decrease this value instead
       //////// HELPER CONSTRUCTS
       emp::unordered_map<size_t, size_t> nop_id_map;/**< NOP inst id -> Nop index
                                                          (e.g., NopA -> 0, NopB -> 1,
@@ -252,7 +252,7 @@ namespace emp{
       /// Redirect literal ints to PushInst(size_t) overload.
       void PushInst(int idx) { PushInst(static_cast<size_t>(idx)); }
 
-      /// Add a new instruction to the end of the genome, by the instruction's symbol/char 
+      /// Add a new instruction to the end of the genome, by the instruction's symbol/char
       void PushInst(char c) { PushInst( GetInstLib()->GetIndexFromSymbol(c) ); }
 
       /// Add a new instruction to the end of the genome, by name
@@ -353,7 +353,7 @@ namespace emp{
 
 
       //////// HEAD MANIPULATION
-      
+
       void ResetIP() { inst_ptr = 0; }   ///< Move instruction pointer to beginning of the genome.
       void ResetRH() { read_head = 0; }  ///< Move read head to beginning of the genome.
       void ResetWH() { write_head = 0; } ///< Move write head to beginning of the genome.

include/emp/in_progress/SimpleParser.hpp

@@ -6,7 +6,7 @@
  *  @file SimpleParser.hpp
  *  @brief Common praser functionality with custom plugins for variables and functions.
  *  @note Status: ALPHA
- * 
+ *
  *  Developer TODO:
  *  - Make ${ ... } actually work
  *  - Setup operator RegEx to be built dynamically
@@ -234,7 +234,7 @@ namespace emp {
           if (pos->lexeme == ",") ++pos;
         }
         ++pos;
-        
+
         // Now build the function based on its argument count.
         value_fun_t out_fun;
         switch (args.size()) {

include/emp/io/File.hpp

@@ -211,7 +211,7 @@ namespace emp {
         if constexpr ( std::is_same<return_t, String>() ) {
           cur_line = fun(cur_line);
         } else {
-          fun(cur_line);          
+          fun(cur_line);
         }
       }
       return *this;

include/emp/math/Range.hpp

@@ -82,7 +82,7 @@ namespace emp {
       lower = (MaxLimit() - shift > lower) ? (lower + shift) : MaxLimit();
     }
     void Shift(T shift) {
-      if (shift > 0) ShiftUp(shift); 
+      if (shift > 0) ShiftUp(shift);
       else ShiftDown(-shift);
     }
 

include/emp/math/RangeSet.hpp

@@ -41,8 +41,8 @@ namespace emp {
     // }
     size_t _FindRange(T value) const {
       auto it = std::lower_bound(
-        range_set.begin(), 
-        range_set.end(), 
+        range_set.begin(),
+        range_set.end(),
         value,
         [](const range_t & range, T value) { return range.GetUpper() < value; }
       );
@@ -155,7 +155,7 @@ namespace emp {
 
     /// @return Overall end of all ranges (or min value if no ranges exist.)
     [[nodiscard]] T GetEnd() const { return IsEmpty() ? MinLimit() : range_set.back().Upper(); }
-    
+
     [[nodiscard]] size_t GetNumRanges() const { return range_set.size(); }
 
     /// @brief Calculate the total combined size of all ranges.
@@ -284,7 +284,7 @@ namespace emp {
       }
 
       // Otherwise insert as a new range.
-      else _InsertRange(start_id, in);  
+      else _InsertRange(start_id, in);
 
       return *this;
     }
@@ -366,7 +366,7 @@ namespace emp {
         range_set[start_id].SetUpper(rm_range.Lower());
         return *this;
       }
-      
+
       // Deal with beginning of removal - cut it down if needed, and move on to next range.
       if (rm_range.Lower() > start_range.Lower()) {
         start_range.Upper() = rm_range.Lower();
@@ -472,7 +472,7 @@ namespace emp {
       return out;
     }
 
-    /// @brief Check for internal errors in this RangeSet. 
+    /// @brief Check for internal errors in this RangeSet.
     bool OK() const {
       // Check each range individually.
       for (const auto & range : range_set) {

include/emp/text/EmphaticEncoding.hpp

@@ -6,7 +6,7 @@
  *  @file EmphaticEncoding.hpp
  *  @brief Plugs into emp::Text, setting up inputs and output to be Emphatic encoded.
  *  @note Status: ALPHA
- * 
+ *
  */
 
 #ifndef EMP_TEXT_EMPHATICENCODING_HPP_INCLUDE
@@ -64,7 +64,7 @@ namespace emp {
 
   public:
     EmphaticEncoding() { SetupTags(); }
-    ~EmphaticEncoding() = default; 
+    ~EmphaticEncoding() = default;
 
     String GetName() const override { return "emphatic"; }
     emp::Ptr<TextEncoding_Interface> Clone() const override {

include/emp/text/HTMLEncoding.hpp

@@ -6,7 +6,7 @@
  *  @file HTMLEncoding.hpp
  *  @brief Plugs into emp::Text, setting up inputs and output to be HTML encoded.
  *  @note Status: ALPHA
- * 
+ *
  */
 
 #ifndef EMP_TEXT_HTMLENCODING_HPP_INCLUDE