Fix Doxygen Ref issues

.readthedocs.yaml

@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: ubuntu-24.04
+  os: ubuntu-26.04
   tools:
     python: "3.12"
   apt_packages:

GridKit/Model/PowerElectronics/CircuitComponent.hpp

@@ -445,8 +445,8 @@ namespace GridKit
      *
      * Most components do not need state and residual storages. The most notable exception
      * is currently the system, so a separate flag is provided for the system.
-     * Systems still can't directly access `y_`, `yp_`, and `f_`, so they need
-     * their corresponding `y_int_`, `yp_int_`, and `f_int_` set, since there isn't
+     * Systems still can't directly access \ref y_, \ref yp_, and \ref f_, so they need
+     * their corresponding \ref y_int_, \ref yp_int_, and \ref f_int_ set, since there isn't
      * another system above them to set it.
      *
      * @todo This is a weird exception specifically for systems - and in a hierarchical setting
@@ -478,7 +478,7 @@ namespace GridKit
     /**
      * @brief A set of variable indices which correspond to the external variables. Variables indices not in this set are internal.
      *
-     * @invariant Must have a size of n_extern_. Each element must be in the range [0, `size_` - 1]. Not currently verified anywhere.
+     * @invariant Must have a size of \ref n_extern_. Each element must be in the range [0, \ref size_ - 1]. Not currently verified anywhere.
      */
     std::set<IdxT>          extern_indices_;
     /**
@@ -490,7 +490,7 @@ namespace GridKit
     std::unique_ptr<IdxT[]> connection_nodes_;
 
   protected:
-    /// The number of variables in this component. Should be equal to `n_extern_` plus `n_intern_`. \see size()
+    /// The number of variables in this component. Should be equal to \ref n_extern_ plus \ref n_intern_. \see size()
     IdxT size_{0};
     /// The number of nonzero elements in this component's Jacobian. \see nnz()
     IdxT nnz_{0};
@@ -514,23 +514,23 @@ namespace GridKit
 
     /**
      * An array of (input) pointers to state values for external variables.
-     * \note The size of this array is equal to `size_`, allowing you to index it with the index
+     * \note The size of this array is equal to \ref size_, allowing you to index it with the index
      * of the variable in question (i.e. consisten with \ref extern_indices_). Therefore, accessing
      * and dereferencing the pointer in an internal variable index is undefined behavior.
      * \see setExternalConnectionNodes()
      */
     std::unique_ptr<const ScalarT*[]> y_ext_;
     /**
      * An array of (input) pointers to derivative values for external variables.
-     * \note The size of this array is equal to `size_`, allowing you to index it with the index
+     * \note The size of this array is equal to \ref size_, allowing you to index it with the index
      * of the variable in question (i.e. consisten with \ref extern_indices_). Therefore, accessing
      * and dereferencing the pointer in an internal variable index is undefined behavior.
      * \see setExternalConnectionNodes()
      */
     std::unique_ptr<const ScalarT*[]> yp_ext_;
     /**
      * An array of (output) pointers to residuals for external variables.
-     * \note The size of this array is equal to `size_`, allowing you to index it with the index
+     * \note The size of this array is equal to \ref size_, allowing you to index it with the index
      * of the variable in question (i.e. consisten with \ref extern_indices_). Therefore, accessing
      * and dereferencing the pointer in an internal variable index is undefined behavior.
      * \see setExternalConnectionNodes()

GridKit/Model/PowerElectronics/SystemModelPowerElectronics.hpp

@@ -17,28 +17,27 @@ namespace GridKit
   template <class ScalarT, typename IdxT>
   class PowerElectronicsModel : public CircuitComponent<ScalarT, IdxT>
   {
-    using Base           = CircuitComponent<ScalarT, IdxT>;
-    using RealT          = Base::RealT;
-    using CsrMatrixT     = Base::CsrMatrixT;
+    using RealT          = typename CircuitComponent<ScalarT, IdxT>::RealT;
+    using CsrMatrixT     = typename CircuitComponent<ScalarT, IdxT>::CsrMatrixT;
     using component_type = CircuitComponent<ScalarT, IdxT>;
     using node_type      = PowerElectronics::NodeBase<ScalarT, IdxT>;
 
-    using Base::abs_tol_;
-    using Base::allocated_;
-    using Base::allocateVectors;
-    using Base::alpha_;
-    using Base::f_ext_;
-    using Base::f_int_;
-    using Base::n_extern_;
-    using Base::n_intern_;
-    using Base::nnz_;
-    using Base::size_;
-    using Base::tag_;
-    using Base::time_;
-    using Base::y_ext_;
-    using Base::y_int_;
-    using Base::yp_ext_;
-    using Base::yp_int_;
+    using CircuitComponent<ScalarT, IdxT>::abs_tol_;
+    using CircuitComponent<ScalarT, IdxT>::allocated_;
+    using CircuitComponent<ScalarT, IdxT>::allocateVectors;
+    using CircuitComponent<ScalarT, IdxT>::alpha_;
+    using CircuitComponent<ScalarT, IdxT>::f_ext_;
+    using CircuitComponent<ScalarT, IdxT>::f_int_;
+    using CircuitComponent<ScalarT, IdxT>::n_extern_;
+    using CircuitComponent<ScalarT, IdxT>::n_intern_;
+    using CircuitComponent<ScalarT, IdxT>::nnz_;
+    using CircuitComponent<ScalarT, IdxT>::size_;
+    using CircuitComponent<ScalarT, IdxT>::tag_;
+    using CircuitComponent<ScalarT, IdxT>::time_;
+    using CircuitComponent<ScalarT, IdxT>::y_ext_;
+    using CircuitComponent<ScalarT, IdxT>::y_int_;
+    using CircuitComponent<ScalarT, IdxT>::yp_ext_;
+    using CircuitComponent<ScalarT, IdxT>::yp_int_;
 
   public:
     /**
@@ -290,7 +289,7 @@ namespace GridKit
         component->initialize();
       }
 
-      return Base::initialize();
+      return CircuitComponent<ScalarT, IdxT>::initialize();
     }
 
     int tagDifferentiable() final

docs/CMakeLists.txt

@@ -5,12 +5,14 @@ if(${DOXYGEN_FOUND})
   set(DOXYGEN_GENERATE_TREEVIEW YES)
   set(DOXYGEN_TEMPLATE_RELATIONS YES)
   set(DOXYGEN_BUILTIN_STL_SUPPORT YES)
+  set(DOXYGEN_EXTRACT_ALL YES)
   set(DOXYGEN_EXTRACT_PRIVATE YES)
   set(DOXYGEN_SOURCE_BROWSER YES)
   set(DOXYGEN_INTERACTIVE_SVG YES)
   set(DOXYGEN_DISTRIBUTE_GROUP_DOC YES)
   set(DOXYGEN_USE_MATHJAX YES)
   set(DOXYGEN_CITE_BIB_FILES ${CMAKE_SOURCE_DIR}/docs/citations.bib)
+  set(DOXYGEN_QUIET YES)
 
   doxygen_add_docs(GridKitDocs ${CMAKE_SOURCE_DIR}/GridKit ${CMAKE_SOURCE_DIR}/README.md)
 endif()

docs/Doxyfile

@@ -24,5 +24,6 @@ XML_OUTPUT = xml
 XML_PROGRAMLISTING = NO
 
 EXTRACT_ALL = YES
+EXTRACT_PRIVATE = YES
 WARN_AS_ERROR = FAIL_ON_WARNINGS
 QUIET = YES