Disable bugprone-easily-swappable-parameters

Author: vgvassilev

.clang-tidy

@@ -12,6 +12,7 @@ Checks: >
   performance-*,
   portability-*,
   readability-*,
+  -bugprone-easily-swappable-parameters,
   -modernize-use-trailing-return-type,
   -readability-identifier-length
 

src/cart_cell.cc

@@ -67,9 +67,8 @@ real_t CartCell::GetTargetTotalVolume() const {
 // volume (and proportions) smoothly toward a desired target volume over time
 // whe the cell is apoptotic. The relaxations rate controls the speed of
 // convergence
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 void CartCell::ChangeVolumeExponentialRelaxationEquation(
-    real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus,  // NOLINT
+    real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus,
     real_t relaxation_rate_fluid) {
   // Exponential relaxation towards the target volume
   const real_t current_total_volume = GetVolume();
@@ -189,7 +188,6 @@ Real3 CartCell::CalculateDisplacement(const InteractionForce* force,
 
 // Compute new oxygen or immunostimulatory factor concentration after
 // consumption/ secretion
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 real_t CartCell::ConsumeSecreteSubstance(int substance_id,
                                          real_t old_concentration) {
   real_t res = NAN;  // NOLINT
@@ -307,4 +305,4 @@ void StateControlCart::Run(Agent* agent) {
   }
 }
 
-}  // namespace bdm
+}  // namespace bdm

src/cart_cell.h

@@ -151,8 +151,7 @@ class CartCell : public Cell {
   /// @param relaxation_rate_fluid Relaxation rate for fluid volume changes
   void ChangeVolumeExponentialRelaxationEquation(
       real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus,
-      real_t
-          relaxation_rate_fluid);  // NOLINT(bugprone-easily-swappable-parameters)
+      real_t relaxation_rate_fluid);
 
   /// Calculate displacement of the cell
   ///

src/cart_tumor.cc

@@ -117,7 +117,6 @@ int Simulate(int argc, const char** argv) {
       kImmunostimulatoryFactor, BoundaryConditionType::kNeumann, nullptr);
 
   // Initialize oxygen voxels
-  // NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
   ModelInitializer::InitializeSubstance(kOxygen, [](real_t /*x*/, real_t /*y*/,
                                                     real_t /*z*/) {
     return kInitialOxygenLevel;  // Set all voxels to kInitialOxygenLevel mmHg
@@ -152,4 +151,4 @@ int Simulate(int argc, const char** argv) {
 
 }  // namespace bdm
 
-int main(int argc, const char** argv) { return bdm::Simulate(argc, argv); }
+int main(int argc, const char** argv) { return bdm::Simulate(argc, argv); }

src/diffusion_thomas_algorithm.cc

@@ -36,13 +36,11 @@
 
 namespace bdm {
 
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
-DiffusionThomasAlgorithm::DiffusionThomasAlgorithm(
-    int substance_id,              // NOLINT
-    std::string substance_name,    // NOLINT
-    real_t dc, real_t mu,          // NOLINT
-    real_t resolution, real_t dt,  // NOLINT
-    bool dirichlet_border)         // NOLINT
+DiffusionThomasAlgorithm::DiffusionThomasAlgorithm(int substance_id,
+                                                   std::string substance_name,
+                                                   real_t dc, real_t mu,
+                                                   real_t resolution, real_t dt,
+                                                   bool dirichlet_border)
     : DiffusionGrid(substance_id, std::move(substance_name), dc, mu,
                     static_cast<int>(
                         resolution)),  // Added cast for consistency with parent
@@ -267,7 +265,6 @@ void DiffusionThomasAlgorithm::SolveDirectionThomas(unsigned int direction) {
   }
 }
 
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 void DiffusionThomasAlgorithm::ForwardElimination(
     unsigned int direction, unsigned int outer, unsigned int middle,
     const std::vector<real_t>& thomas_denom, unsigned int jump) {
@@ -288,7 +285,6 @@ void DiffusionThomasAlgorithm::ForwardElimination(
   }
 }
 
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 void DiffusionThomasAlgorithm::BackSubstitution(
     unsigned int direction, unsigned int outer, unsigned int middle,
     const std::vector<real_t>& thomas_c, unsigned int jump) {
@@ -306,7 +302,6 @@ void DiffusionThomasAlgorithm::BackSubstitution(
   }
 }
 
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 size_t DiffusionThomasAlgorithm::GetLoopIndex(unsigned int direction,
                                               unsigned int outer,
                                               unsigned int middle,
@@ -351,4 +346,4 @@ void DiffusionThomasAlgorithm::ComputeConsumptionsSecretions() {
   });
 }
 
-}  // namespace bdm
+}  // namespace bdm

src/tumor_cell.cc

@@ -192,9 +192,8 @@ real_t TumorCell::GetTargetTotalVolume() const {
 // differential equation using a discrete update step. It is used to grow or
 // shrink the volume (and proportions) smoothly toward a desired target volume
 // over time. The relaxations rate controls the speed of convergence
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 void TumorCell::ChangeVolumeExponentialRelaxationEquation(
-    real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus,  // NOLINT
+    real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus,
     real_t relaxation_rate_fluid) {
   // Exponential relaxation towards the target volume
   const real_t current_total_volume = GetVolume();
@@ -337,7 +336,6 @@ Real3 TumorCell::CalculateDisplacement(const InteractionForce* force,
 
 // Compute new oxygen or immunostimulatory factor concentration after
 // consumption/ secretion
-// NOLINTNEXTLINE(bugprone-easily-swappable-parameters)
 real_t TumorCell::ConsumeSecreteSubstance(int substance_id,
                                           real_t old_concentration) {
   // constant1_oxygen_ = 0;  // Debug
@@ -653,4 +651,4 @@ bool StateControlGrowProliferate::ShouldEnterNecrosis(real_t oxygen_level,
   return enter_necrosis;  // Return whether the cell entered necrosis
 }
 
-}  // namespace bdm
+}  // namespace bdm