From c182264c11a6e6788b8c596aed21b37ff500ca7d Mon Sep 17 00:00:00 2001
From: "Yu-Hsiang M. Tsai" <yhmtsai@gmail.com>
Date: Mon, 8 Apr 2024 17:49:05 +0200
Subject: [PATCH] fix the doxygen

---
 core/base/types.hpp         | 2 +-
 doc/conf/Doxyfile-dev.in    | 1 +
 doc/examples/CMakeLists.txt | 2 +-
 doc/helpers.cmake           | 2 +-
 doc/scripts/examples.pl     | 6 ++++--
 5 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/core/base/types.hpp b/core/base/types.hpp
index 8c9206c9e16..323dd4a2ce6 100644
--- a/core/base/types.hpp
+++ b/core/base/types.hpp
@@ -99,7 +99,7 @@ constexpr std::enable_if_t<(num_groups > current_shift + 1), int> shift(
  * F is one-to-one function if $0 <= x_i < 2^{b_i}$ for all i.
  * For any encoded result R, we can use the following to get the decoded series.
  * for i = k to 0;
- *   $x_i = R % b_i$;
+ *   $x_i = R \% b_i$;
  *   $R = R / bi$;
  * endfor;
  * For any R in the range $[0, 2^{B_0})$, we have X such that $F(X) = R$.
diff --git a/doc/conf/Doxyfile-dev.in b/doc/conf/Doxyfile-dev.in
index 173fe36ada5..8f6a6117dd0 100644
--- a/doc/conf/Doxyfile-dev.in
+++ b/doc/conf/Doxyfile-dev.in
@@ -9,3 +9,4 @@ SOURCE_BROWSER         = YES
 CALL_GRAPH             = YES
 CALLER_GRAPH           = YES
 EXCLUDE_SYMBOLS        = std::*
+EXTRA_PACKAGES         = mathtools amsfonts amsmath amssymb
diff --git a/doc/examples/CMakeLists.txt b/doc/examples/CMakeLists.txt
index 9363ea5e1dd..66010ba6d91 100644
--- a/doc/examples/CMakeLists.txt
+++ b/doc/examples/CMakeLists.txt
@@ -2,7 +2,7 @@
 FILE(GLOB _ginkgo_examples
     ${PROJECT_SOURCE_DIR}/examples/*
     )
-LIST(REMOVE_ITEM _ginkgo_examples "${PROJECT_SOURCE_DIR}/examples/CMakeLists.txt" "${PROJECT_SOURCE_DIR}/examples/build-setup.sh")
+LIST(REMOVE_ITEM _ginkgo_examples "${PROJECT_SOURCE_DIR}/examples/CMakeLists.txt" "${PROJECT_SOURCE_DIR}/examples/build-setup.sh" "${PROJECT_SOURCE_DIR}/examples/compare-output.py")
 
 ADD_CUSTOM_TARGET(examples)
 
diff --git a/doc/helpers.cmake b/doc/helpers.cmake
index c0b4c7b23a7..afc0f107b21 100644
--- a/doc/helpers.cmake
+++ b/doc/helpers.cmake
@@ -87,7 +87,7 @@ function(ginkgo_doc_gen name in pdf mainpage-in)
         FILE(GLOB _ginkgo_examples
             ${DIR_BASE}/examples/*
             )
-        LIST(REMOVE_ITEM _ginkgo_examples "${DIR_BASE}/examples/CMakeLists.txt" "${DIR_BASE}/examples/build-setup.sh")
+        LIST(REMOVE_ITEM _ginkgo_examples "${DIR_BASE}/examples/CMakeLists.txt" "${DIR_BASE}/examples/build-setup.sh" "${DIR_BASE}/examples/compare-output.py")
         FOREACH(_ex ${_ginkgo_examples})
             GET_FILENAME_COMPONENT(_ex "${_ex}" NAME)
             LIST(APPEND doxygen_depend
diff --git a/doc/scripts/examples.pl b/doc/scripts/examples.pl
index 4194d8ae7a7..3b7dfb0ea31 100644
--- a/doc/scripts/examples.pl
+++ b/doc/scripts/examples.pl
@@ -36,6 +36,7 @@
     "preconditioners" => ',height=.25,width=.25,fillcolor="crimson"',
     "mixed-precision" => ',height=.25,width=.25,fillcolor="aquamarine"',
     "distributed"     => ',height=.25,width=.25,fillcolor="plum"',
+    "batched-functionality"     => ',height=.25,width=.25,fillcolor="darkviolet"',
     "unfinished"     => ',height=.25,width=.25,style="dashed"',
     );
 
@@ -198,6 +199,7 @@
     "preconditioners" => 'Preconditioners',
     "mixed-precision" => 'Mixed Precision',
     "distributed"     => 'Distributed techniques',
+    "batched-functionality" => 'Batch Functionality',
     "unfinished"     => 'Unfinished codes',
     );
 
@@ -215,12 +217,12 @@
 }
 # now add connections to make sure they appear nicely next to each other
 # in the legend
-print "  basic -- techniques -- logging -- stopping_criteria -- preconditioners -- mixed_precision -- distributed -- unfinished;\n";
+print "  basic -- techniques -- logging -- stopping_criteria -- preconditioners -- mixed_precision -- distributed -- batched_functionality -- unfinished;\n";
 
 # we need to tell 'dot' that all of these are at the same
 # rank to ensure they appear next to (as opposed to atop)
 # each other
-print "  {rank=same; basic, techniques, logging, stopping_criteria, preconditioners, mixed_precision, distributed, unfinished}";
+print "  {rank=same; basic, techniques, logging, stopping_criteria, preconditioners, mixed_precision, distributed, batched_functionality, unfinished}";
 
 # end the graph
 print "}\n";