Cleanup unused includes

include/amici/defines.h

@@ -6,7 +6,6 @@
 #endif
 
 #include <cmath>
-#include <functional>
 
 /* Math constants in case _USE_MATH_DEFINES is not supported */
 #if defined(_USE_MATH_DEFINES)

include/amici/misc.h

@@ -9,7 +9,6 @@
 #include <algorithm>
 #include <ctime>
 #include <functional>
-#include <memory>
 #include <regex>
 #include <vector>
 
@@ -291,7 +290,7 @@ class CpuTimer {
         return d_milliseconds(clock::now() - start_).count();
     }
 
-    static const bool uses_thread_clock = true;
+    static bool const uses_thread_clock = true;
 
   private:
     /** Start time */
@@ -330,7 +329,7 @@ class CpuTimer {
                / CLOCKS_PER_SEC;
     }
 
-    static const bool uses_thread_clock = false;
+    static bool const uses_thread_clock = false;
 
   private:
     /** Start time */

include/amici/model_dae.h

@@ -10,7 +10,6 @@
 #include <sunmatrix/sunmatrix_sparse.h>
 
 #include <numeric>
-#include <utility>
 #include <vector>
 
 namespace amici {

include/amici/model_ode.h

@@ -10,7 +10,6 @@
 #include <sunmatrix/sunmatrix_dense.h>
 #include <sunmatrix/sunmatrix_sparse.h>
 
-#include <utility>
 #include <vector>
 
 namespace amici {

include/amici/serialization.h

@@ -6,10 +6,7 @@
 #include "amici/solver.h"
 #include "amici/solver_cvodes.h"
 
-#include <cassert>
 #include <chrono>
-#include <fstream>
-#include <iostream>
 
 #include <boost/archive/binary_iarchive.hpp>
 #include <boost/archive/binary_oarchive.hpp>
@@ -35,7 +32,7 @@ template <class Archive, typename T>
 void archiveVector(Archive& ar, T** p, int size) {
     if (Archive::is_loading::value) {
         if (*p != nullptr)
-            delete[] * p;
+            delete[] *p;
         ar& size;
         *p = size ? new T[size] : nullptr;
     } else {

include/amici/spline.h

@@ -1,6 +1,5 @@
 #ifndef amici_spline_h
 #define amici_spline_h
-#include <math.h>
 
 namespace amici {
 

include/amici/steadystateproblem.h

@@ -8,7 +8,6 @@
 
 #include <nvector/nvector_serial.h>
 
-#include <functional>
 #include <memory>
 
 namespace amici {

src/amici.cpp

@@ -13,11 +13,6 @@
 #include <cvodes/cvodes.h>           //return codes
 #include <sundials/sundials_types.h> //realtype
 
-#include <cassert>
-#include <cstdarg>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
 #include <map>
 #include <memory>
 #include <type_traits>

src/backwardproblem.cpp

@@ -8,9 +8,6 @@
 #include "amici/solver.h"
 #include "amici/steadystateproblem.h"
 
-#include <cassert>
-#include <cstring>
-
 namespace amici {
 
 BackwardProblem::BackwardProblem(

src/edata.cpp

@@ -5,7 +5,6 @@
 #include "amici/symbolic_functions.h" // getNaN
 
 #include <algorithm>
-#include <cstring>
 #include <random>
 #include <utility>
 

src/exception.cpp

@@ -3,7 +3,6 @@
 
 #include <cstdarg>
 #include <cstdio>
-#include <cstring>
 
 namespace amici {
 

src/forwardproblem.cpp

@@ -9,7 +9,6 @@
 
 #include <algorithm>
 #include <cmath>
-#include <cstring>
 
 namespace amici {
 

src/hdf5.cpp

@@ -16,7 +16,6 @@
 
 #include <hdf5_hl.h>
 
-
 namespace amici {
 namespace hdf5 {
 
@@ -1161,8 +1160,8 @@ void readModelDataFromHDF5(
         model.setSteadyStateComputationMode(
             static_cast<SteadyStateComputationMode>(getIntScalarAttribute(
                 file, datasetPath, "steadyStateComputationMode"
-                ))
-            );
+            ))
+        );
     }
 
     if (attributeExists(file, datasetPath, "steadyStateSensitivityMode")) {

src/model.cpp

@@ -6,7 +6,7 @@
 #include <amici/symbolic_functions.h>
 
 #include <algorithm>
-#include <assert.h>
+#include <cassert>
 #include <cmath>
 #include <cstring>
 #include <numeric>

src/newton_solver.cpp

@@ -8,10 +8,6 @@
 #include <sunlinsol/sunlinsol_dense.h> // dense solver
 #include <sunlinsol/sunlinsol_klu.h>   // sparse solver
 
-#include <cmath>
-#include <cstring>
-#include <ctime>
-
 namespace amici {
 
 NewtonSolver::NewtonSolver(Model const& model)

src/rdata.cpp

@@ -10,7 +10,6 @@
 #include "amici/symbolic_functions.h"
 
 #include <cmath>
-#include <cstring>
 
 namespace amici {
 

src/solver.cpp

@@ -5,8 +5,6 @@
 #include "amici/symbolic_functions.h"
 
 #include <cstdio>
-#include <cstring>
-#include <ctime>
 #include <memory>
 
 namespace amici {

src/splinefunctions.cpp

@@ -2,9 +2,9 @@
 #include "amici/amici.h"
 #include "amici/defines.h"
 #include "amici/exception.h"
-#include "amici/vector.h"
 
 #include <algorithm> // std::min
+#include <cassert>
 #include <cmath>
 #include <vector>
 

src/steadystateproblem.cpp

@@ -8,7 +8,6 @@
 #include "amici/solver.h"
 
 #include <cmath>
-#include <cstring>
 #include <cvodes/cvodes.h>
 #include <memory>
 #include <sundials/sundials_dense.h>

src/sundials_linsol_wrapper.cpp

@@ -2,7 +2,6 @@
 
 #include <amici/exception.h>
 
-#include <new> // bad_alloc
 #include <utility>
 
 namespace amici {

src/symbolic_functions.cpp

@@ -12,7 +12,6 @@
 #include <cfloat>
 #include <cmath>
 #include <cstdarg>
-#include <cstdlib>
 #if _MSC_VER && !__INTEL_COMPILER
 #include <malloc.h>
 #define alloca _alloca

tests/cpp/unittests/testSerialization.cpp

@@ -5,7 +5,7 @@
 #include "testfunctions.h"
 
 #include <cmath>
-
+#include <fstream>
 #include <gtest/gtest.h>
 
 void