diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1fe522059..1080c55fc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 project(QuEST
-  VERSION 4.0.0
+  VERSION 4.1.0
   DESCRIPTION "Quantum Exact Simulation Toolkit"
   LANGUAGES CXX C
 )
diff --git a/quest/include/debug.h b/quest/include/debug.h
index 3168e023b..48ef22527 100644
--- a/quest/include/debug.h
+++ b/quest/include/debug.h
@@ -131,8 +131,8 @@ void setNumReportedNewlines(int numNewlines);
 
 
 /** 
- * @notdoced
- * @nottested
+ * @notyetdoced
+ * @notyettested
  * @myexample
  * ```
    PauliStr str = getInlinePauliStr("XYZ", {0,10,20});
@@ -146,8 +146,8 @@ void setReportedPauliChars(const char* paulis);
 
 
 /** 
- * @notdoced
- * @nottested
+ * @notyetdoced
+ * @notyettested
  * @myexample
  * ```
    PauliStr str = getInlinePauliStr("XYZ", {0,10,20});
diff --git a/quest/include/version.h b/quest/include/version.h
index 1f788004e..bd3e99a50 100644
--- a/quest/include/version.h
+++ b/quest/include/version.h
@@ -11,8 +11,8 @@
 
 // TODO: automate this from git somehow
 #define QUEST_VERSION_MAJOR 4
-#define QUEST_VERSION_MINOR 0
+#define QUEST_VERSION_MINOR 1
 #define QUEST_VERSION_PATCH 0
-#define QUEST_VERSION_STRING "4.0.0"
+#define QUEST_VERSION_STRING "4.1.0"
 
 #endif // VERSION_H
\ No newline at end of file
diff --git a/utils/docs/Doxyfile b/utils/docs/Doxyfile
index a01ce3d85..4eb40b524 100644
--- a/utils/docs/Doxyfile
+++ b/utils/docs/Doxyfile
@@ -51,7 +51,7 @@ PROJECT_NAME           = "The Quantum Exact Simulation Toolkit"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "v4.0.0"
+PROJECT_NUMBER         = "v4.1.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -373,8 +373,9 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 #
 # Note see also the list of default file extension mappings.
 
-# all source code (even headers) is C++, but example.c code is C
-EXTENSION_MAPPING      = h=C++ hpp=C++ cpp=C++ cu=C++ cuh=C++ c=C
+# all source code (even headers) is C++, but example.c code is C.
+# in=C is necessary to parse quest.h.in (a CMake configured header)
+EXTENSION_MAPPING      = h=C++ hpp=C++ cpp=C++ cu=C++ cuh=C++ c=C in=C
 
 # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
@@ -1088,7 +1089,7 @@ INPUT_FILE_ENCODING    =
 # be provided as Doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
 # *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
 
-FILE_PATTERNS          = *.c *.cpp *.cu *.cuh *.h *.hpp *.md *.sh
+FILE_PATTERNS          = *.c *.cpp *.cu *.cuh *.h *.h.in *.hpp *.md *.sh
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.