From 7ac47c2c2941a85030fba8c3dd427336a1cd80f9 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Thu, 4 Jan 2024 11:15:12 +0100
Subject: [PATCH] Update Doxygen to 1.10 (#2253)

Update Doxygen to 1.10 and fix some documentation issues that popped up with the new version.
---
 include/amici/misc.h               | 8 ++++++++
 include/amici/solver.h             | 7 ++++---
 scripts/downloadAndBuildDoxygen.sh | 2 +-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/include/amici/misc.h b/include/amici/misc.h
index 81543b399d..6dc3294240 100644
--- a/include/amici/misc.h
+++ b/include/amici/misc.h
@@ -290,6 +290,10 @@ class CpuTimer {
         return d_milliseconds(clock::now() - start_).count();
     }
 
+    /**
+     * @brief Whether the timer uses a thread clock (i.e. provides proper,
+     * thread-specific CPU time).
+     */
     static bool const uses_thread_clock = true;
 
   private:
@@ -329,6 +333,10 @@ class CpuTimer {
                / CLOCKS_PER_SEC;
     }
 
+    /**
+     * @brief Whether the timer uses a thread clock (i.e. provides proper,
+     * thread-specific CPU time).
+     */
     static bool const uses_thread_clock = false;
 
   private:
diff --git a/include/amici/solver.h b/include/amici/solver.h
index 120a963ba4..4a1c95b96a 100644
--- a/include/amici/solver.h
+++ b/include/amici/solver.h
@@ -48,7 +48,8 @@ class Solver {
   public:
     /** Type of what is passed to Sundials solvers as user_data */
     using user_data_type = std::pair<Model*, Solver const*>;
-
+    /** Type of the function to free a raw sundials solver pointer */
+    using free_solver_ptr = std::function<void(void*)>;
     /**
      * @brief Default constructor
      */
@@ -1608,10 +1609,10 @@ class Solver {
     void applySensitivityTolerances() const;
 
     /** pointer to solver memory block */
-    mutable std::unique_ptr<void, std::function<void(void*)>> solver_memory_;
+    mutable std::unique_ptr<void, free_solver_ptr> solver_memory_;
 
     /** pointer to solver memory block */
-    mutable std::vector<std::unique_ptr<void, std::function<void(void*)>>>
+    mutable std::vector<std::unique_ptr<void,free_solver_ptr>>
         solver_memory_B_;
 
     /** Sundials user_data */
diff --git a/scripts/downloadAndBuildDoxygen.sh b/scripts/downloadAndBuildDoxygen.sh
index 19d86be5a1..4efa9ab483 100755
--- a/scripts/downloadAndBuildDoxygen.sh
+++ b/scripts/downloadAndBuildDoxygen.sh
@@ -9,7 +9,7 @@ DOXYGEN_DIR="${AMICI_PATH}"/ThirdParty/doxygen
 cd "${AMICI_PATH}"/ThirdParty
 if [[ ! -d ${DOXYGEN_DIR} ]]; then
   git clone --single-branch \
-            --branch Release_1_9_7 \
+            --branch Release_1_10_0 \
             --depth 1 \
             -c advice.detachedHead=false \
             https://github.com/doxygen/doxygen.git "${DOXYGEN_DIR}"