some clang-tidy fixes

include/core/boundary_conditions/nonuniform_dirichlet.h

@@ -25,12 +25,16 @@ class nonuniformDirichlet : public dealii::Function<dim, double>
    */
   nonuniformDirichlet(const uint &_index, const uint &_boundary_id);
 
+  // NOLINTBEGIN(readability-avoid-const-params-in-decls)
+
   /**
    * \brief Scalar value.
    */
   double
   value(const dealii::Point<dim> &p, const unsigned int component = 0) const override;
 
+  // NOLINTEND(readability-avoid-const-params-in-decls)
+
   /**
    * \brief Vector value.
    */

include/core/timer.h

@@ -1,11 +1,8 @@
 #ifndef timer_h
 #define timer_h
 
-#include <deal.II/base/mpi.h>
 #include <deal.II/base/timer.h>
 
-#include <core/conditional_ostreams.h>
-
 /**
  * \brief Timer class for PRISMS-PF
  */

include/core/triangulation_handler.h

@@ -1,6 +1,7 @@
 #ifndef triangulation_handler_h
 #define triangulation_handler_h
 
+#include <deal.II/distributed/tria.h>
 #include <deal.II/grid/grid_generator.h>
 #include <deal.II/grid/grid_out.h>
 #include <deal.II/grid/grid_tools.h>
@@ -20,9 +21,9 @@ class triangulationHandler
 {
 public:
   using Triangulation =
-    typename std::conditional<dim == 1,
-                              dealii::Triangulation<dim>,
-                              dealii::parallel::distributed::Triangulation<dim>>::type;
+    std::conditional_t<dim == 1,
+                       dealii::Triangulation<dim>,
+                       dealii::parallel::distributed::Triangulation<dim>>;
 
   /**
    * \brief Constructor.
@@ -162,7 +163,7 @@ triangulationHandler<dim>::mark_boundaries() const
            ++face_number)
         {
           // Direction for quad and hex cells
-          uint direction = std::floor(face_number / 2);
+          uint direction = static_cast<uint>(std::floor(face_number / 2));
 
           // Mark the boundary id for x=0, y=0, z=0
           if (std::fabs(cell->face(face_number)->center()(direction) - 0) < tolerance)

include/core/user_inputs/output_parameters.h

@@ -112,7 +112,7 @@ outputParameters::compute_output_list(
       for (uint iteration = 2; iteration <= temporal_discretization.total_increments;
            iteration++)
         {
-          const uint decade    = std::ceil(std::log10(iteration));
+          const auto decade    = static_cast<uint>(std::ceil(std::log10(iteration)));
           const auto step_size = static_cast<uint>(std::pow(10, decade) / n_outputs);
           if (iteration % step_size == 0)
             {

src/core/conditional_ostreams.cc

@@ -5,6 +5,8 @@
 std::ofstream conditionalOStreams::summary_log_file("summary.log",
                                                     std::ios::out | std::ios::trunc);
 
+// NOLINTEND
+
 dealii::ConditionalOStream &
 conditionalOStreams::pout_summary()
 {
@@ -50,5 +52,3 @@ conditionalOStreams::~conditionalOStreams()
       summary_log_file.close();
     }
 }
-
-// NOLINTEND

src/core/timer.cc

@@ -1,4 +1,6 @@
+#include <core/conditional_ostreams.h>
 #include <core/timer.h>
+#include <mpi.h>
 
 dealii::TimerOutput &
 timer::serial_timer()

src/core/variable_attributes.cc

@@ -1,3 +1,5 @@
+#include <deal.II/matrix_free/evaluation_flags.h>
+
 #include <boost/range/algorithm/find.hpp>
 
 #include <core/conditional_ostreams.h>
@@ -46,7 +48,7 @@ variableAttributes::parse_dependencies(AttributesList &other_var_attributes)
   const std::map<std::string, std::pair<dependencyType, EvalFlags>> relevant_flag = []()
   {
     // Modifiers for the dependency types
-    std::vector<std::pair<std::string, dependencyType>> dependency_types = {
+    const std::vector<std::pair<std::string, dependencyType>> dependency_types = {
       {"",        dependencyType::NORMAL},
       {"_change", dependencyType::CHANGE},
       {"_old_1",  dependencyType::OLD_1 },
@@ -56,7 +58,7 @@ variableAttributes::parse_dependencies(AttributesList &other_var_attributes)
     };
 
     // Dependency evaluation types & their corresponding evaluation flag
-    std::vector<std::pair<std::string, EvalFlags>> eval_flags = {
+    const std::vector<std::pair<std::string, EvalFlags>> eval_flags = {
       {"value",              dealii::EvaluationFlags::values   },
       {"gradient",           dealii::EvaluationFlags::gradients},
       {"hessian",            dealii::EvaluationFlags::hessians },
@@ -83,7 +85,7 @@ variableAttributes::parse_dependencies(AttributesList &other_var_attributes)
   {
     // Delimiters for the dependency types. Note that there are
     // various overloads for the delimiters.
-    std::vector<std::pair<std::string, std::pair<std::string, std::string>>>
+    const std::vector<std::pair<std::string, std::pair<std::string, std::string>>>
       dependency_types_delimiters = {
         {"",        {"", ""}        },
         {"_change", {"change(", ")"}},
@@ -94,7 +96,7 @@ variableAttributes::parse_dependencies(AttributesList &other_var_attributes)
     };
 
     // Dependency evaluation types & their corresponding delimiter.
-    std::vector<std::pair<std::string, std::pair<std::string, std::string>>>
+    const std::vector<std::pair<std::string, std::pair<std::string, std::string>>>
       base_delimiters = {
         {"value",              {"", ""}          },
         {"gradient",           {"grad(", ")"}    },
@@ -141,12 +143,12 @@ variableAttributes::parse_dependencies(AttributesList &other_var_attributes)
             // Populate the dependencies
             if (dependencies.find(possible_dependency) != dependencies.end())
               {
-                dependencyType dep_type = relevant_flag.at(variation).first;
-                EvalFlags      flags    = relevant_flag.at(variation).second;
+                const dependencyType dep_type = relevant_flag.at(variation).first;
+                const EvalFlags      flags    = relevant_flag.at(variation).second;
 
                 validate_dependency(variation, dep_type, other_index, context);
 
-                std::pair<uint, dependencyType> key = {other_index, dep_type};
+                const std::pair<uint, dependencyType> key = {other_index, dep_type};
 
                 if (eval_flag_set.find(key) != eval_flag_set.end())
                   {
@@ -349,6 +351,8 @@ variableAttributes::find_circular_dependencies(const AttributesList &other_var_a
   recursive_DFS(other_var_attributes, visited, current_stack, field_index);
 }
 
+// NOLINTBEGIN(misc-no-recursion)
+
 void
 variableAttributes::recursive_DFS(const AttributesList &other_var_attributes,
                                   std::set<uint>       &visited,
@@ -378,3 +382,5 @@ variableAttributes::recursive_DFS(const AttributesList &other_var_attributes,
   // Remove the node from the current recursion stack
   current_stack.erase(vertex);
 }
+
+// NOLINTEND(misc-no-recursion)