From 99532c070fa0b2fb530a0e555c8a7d92a90ddb6c Mon Sep 17 00:00:00 2001
From: Emily Dolson <EmilyLDolson@gmail.com>
Date: Sat, 6 Mar 2021 23:11:20 -0500
Subject: [PATCH] Additional doc fixes

---
 Doxyfile                                | 11 ++++++-----
 Makefile                                |  5 ++---
 README.md                               |  2 +-
 include/emp/datastructs/BloomFilter.hpp |  1 +
 include/emp/debug/mem_track.hpp         |  2 +-
 include/emp/math/distances.hpp          |  2 +-
 include/emp/meta/TypePack.hpp           |  2 +-
 include/emp/meta/ValPack.hpp            |  2 +-
 include/emp/meta/meta.hpp               |  6 +++---
 include/emp/web/RawImage.hpp            |  2 +-
 include/emp/web/d3/visualizations.hpp   |  2 +-
 11 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/Doxyfile b/Doxyfile
index 2843dc2eca..8fc9188076 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -821,10 +821,10 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS        = */demos/* 
-EXCLUDE_PATTERNS       += */examples/* 
-EXCLUDE_PATTERNS       += */tests/config/* 
-EXCLUDE_PATTERNS       += */third-party/* 
+EXCLUDE_PATTERNS        = */demos/*
+EXCLUDE_PATTERNS       += */examples/*
+EXCLUDE_PATTERNS       += */tests/config/*
+EXCLUDE_PATTERNS       += */third-party/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -835,7 +835,8 @@ EXCLUDE_PATTERNS       += */third-party/*
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
 
-EXCLUDE_SYMBOLS        = EMP_* EM_* internal emp::internal
+EXCLUDE_SYMBOLS        = EMP_*
+EXCLUDE_SYMBOLS        += EM_*
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include
diff --git a/Makefile b/Makefile
index 96e61580ae..be3efaa5fd 100644
--- a/Makefile
+++ b/Makefile
@@ -53,9 +53,8 @@ install-coverage-dependencies:
 	cd third-party && make install-coverage-dependencies
 
 clean:
-	rm -rf doc/_build/*
-	rm -rf doc/api
-	rm -rf doc/doxyoutput
+	cd docs && make clean
 	cd tests && make clean
+
 clean-dep:
 	cd third-party && make clean
diff --git a/README.md b/README.md
index 5a3a48a7cd..b1a52869d4 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ Tools in Empirical include:
 * A signal-action system that allows for efficient customization of tools, and flexible
   software that can easily facilitate plug-in functionality.
 
-See [https://empirical.readthedocs.io/en/latest](https://empirical.readthedocs.io/en/latest) for more detailed documentation
+See <https://empirical.readthedocs.io/en/latest> for more detailed documentation
 on the available source files.
 
 # Directory Structure
diff --git a/include/emp/datastructs/BloomFilter.hpp b/include/emp/datastructs/BloomFilter.hpp
index 048117aacc..1f1f9565b2 100644
--- a/include/emp/datastructs/BloomFilter.hpp
+++ b/include/emp/datastructs/BloomFilter.hpp
@@ -4,6 +4,7 @@
  * 
  * @copyright Arash Partow, 2000 (modified slightly by Emily Dolson)
  * @brief A Bloom filter implementation
+ * @file  BloomFilter.hpp
 */ 
 
 /*
diff --git a/include/emp/debug/mem_track.hpp b/include/emp/debug/mem_track.hpp
index e4bab924ea..3b968430e5 100644
--- a/include/emp/debug/mem_track.hpp
+++ b/include/emp/debug/mem_track.hpp
@@ -111,7 +111,7 @@ namespace emp {
     }
 
   }
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 }
 #endif
diff --git a/include/emp/math/distances.hpp b/include/emp/math/distances.hpp
index 726459d465..23ac6217e1 100644
--- a/include/emp/math/distances.hpp
+++ b/include/emp/math/distances.hpp
@@ -50,7 +50,7 @@ namespace emp {
       return sqrt(dist);
   }
 
-  #endif
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 }
 
diff --git a/include/emp/meta/TypePack.hpp b/include/emp/meta/TypePack.hpp
index 1f5efdeaaf..91828c8d9d 100644
--- a/include/emp/meta/TypePack.hpp
+++ b/include/emp/meta/TypePack.hpp
@@ -197,7 +197,7 @@ namespace emp {
       using result_t = emp::TypePack<emp::TypePack<>>;
     };
   }
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   template <typename T, int N>
   using TypePackFill = typename internal::tp_pad<TypePack<>,T,N>::type;
diff --git a/include/emp/meta/ValPack.hpp b/include/emp/meta/ValPack.hpp
index b17a53b042..3e10561fc9 100644
--- a/include/emp/meta/ValPack.hpp
+++ b/include/emp/meta/ValPack.hpp
@@ -110,7 +110,7 @@ namespace emp {
     };
     template <> struct vp_sort<ValPack<>> { using result = ValPack<>; };
   } // End internal namespace
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   /// Generate a ValPack with a specified range of values.
   template <auto START, auto END, auto STEP=1>
diff --git a/include/emp/meta/meta.hpp b/include/emp/meta/meta.hpp
index 9a6c5f3f55..e657a071cb 100644
--- a/include/emp/meta/meta.hpp
+++ b/include/emp/meta/meta.hpp
@@ -45,7 +45,7 @@ namespace emp {
 
   template <size_t ID, typename... Ts>
   using pack_id = typename internal::pack_id_impl<ID,Ts...>::type;
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   // Trim off the last type from a pack.
   template <typename... Ts> using last_type = pack_id<sizeof...(Ts)-1,Ts...>;
@@ -131,7 +131,7 @@ namespace emp {
     template <template <typename...> class FILTER, typename T>
     constexpr bool tt_exist_impl(...) { return false; }
   }
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   template <template <typename...> class TEST, typename T>
   constexpr bool test_type_exist() { return internal::tt_exist_impl<TEST, T>(true); }
@@ -252,7 +252,7 @@ namespace emp {
       using type = T<U...>;
     };
   }
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   template<typename T, typename... U>
   using AdaptTemplate = typename internal::AdaptTemplateHelper<T, U...>::type;
diff --git a/include/emp/web/RawImage.hpp b/include/emp/web/RawImage.hpp
index 72efdcf43e..6ae88b874a 100644
--- a/include/emp/web/RawImage.hpp
+++ b/include/emp/web/RawImage.hpp
@@ -120,7 +120,7 @@ namespace emp {
     };
 
   } // End internal namespace
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
   /// Fundamental information about a single image.
   class RawImage {
diff --git a/include/emp/web/d3/visualizations.hpp b/include/emp/web/d3/visualizations.hpp
index aafc8ca8db..c2cb2c62d2 100644
--- a/include/emp/web/d3/visualizations.hpp
+++ b/include/emp/web/d3/visualizations.hpp
@@ -807,7 +807,7 @@ class TreeVisualization : public D3Visualization {
   std::function<std::string(NODE, int)> color_fun_link = [](NODE d, int i){
     return "black";
   };
-  #endif DOXYGEN_SHOULD_SKIP_THIS
+  #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 public:
   D3::TreeLayout<NODE> tree;