hyperameters.h tidy

Author: salva24

clang_output.txt

@@ -1,56 +1,4 @@
-Suppressed 102227 warnings (102065 in non-user code, 162 NOLINT).
-Use -header-filter=.* to display errors from all non-system headers. Use -system-headers to display errors from system headers as well.
-src/hyperparams.h: clang-tidy-18 -p=build -line-filter=[{\"name\":\"src/cart_cell.cc\",\"lines\":[[1,321]]},{\"name\":\"src/cart_cell.h\",\"lines\":[[1,250]]},{\"name\":\"src/cart_tumor.cc\",\"lines\":[[1,133]]},{\"name\":\"src/cart_tumor.h\",\"lines\":[[1,36]]},{\"name\":\"src/diffusion_thomas_algorithm.cc\",\"lines\":[[1,319]]},{\"name\":\"src/diffusion_thomas_algorithm.h\",\"lines\":[[1,194]]},{\"name\":\"src/forces_tumor_cart.cc\",\"lines\":[[1,163]]},{\"name\":\"src/forces_tumor_cart.h\",\"lines\":[[1,60]]},{\"name\":\"src/hyperparams.h\",\"lines\":[[1,216]]},{\"name\":\"src/tumor_cell.cc\",\"lines\":[[1,673]]},{\"name\":\"src/tumor_cell.h\",\"lines\":[[1,301]]},{\"name\":\"src/utils_aux.cc\",\"lines\":[[1,176]]},{\"name\":\"src/utils_aux.h\",\"lines\":[[1,96]]}] --enable-check-profile -store-check-profile=clang-tidy-review-profile --config-file=.clang-tidy --export-fixes=/tmp/tmpb2o1s_sd/tmpg5dwfux3.yaml src/hyperparams.h
-/github/workspace/src/hyperparams.h:22:9: warning: header guard does not follow preferred style [llvm-header-guard]
-   22 | #ifndef TUMOR_HYPERPARAMS_H_
-      |         ^~~~~~~~~~~~~~~~~~~~
-      |         GITHUB_WORKSPACE_SRC_HYPERPARAMS_H
-   23 | #define TUMOR_HYPERPARAMS_H_
-      |         ~~~~~~~~~~~~~~~~~~~~
-      |         GITHUB_WORKSPACE_SRC_HYPERPARAMS_H
-/github/workspace/src/hyperparams.h:25:1: warning: #includes are not sorted properly [llvm-include-order]
-   25 | #include <cmath>
-      | ^
-note: this fix will not be applied because it overlaps with another fix
-/github/workspace/src/hyperparams.h:26:1: warning: included header biodynamo.h is not used directly [misc-include-cleaner]
-   26 | #include "biodynamo.h"
-      | ^~~~~~~~~~~~~~~~~~~~~~
-   27 | 
-/github/workspace/src/hyperparams.h:39:11: warning: no header providing "bdm::real_t" is directly included [misc-include-cleaner]
-   27 | 
-   28 | namespace bdm {
-   29 | 
-   30 | /// This file contains hyperparameters used in the simulation. Change: In a
-   31 | /// future version it needs to be changed into a params file with no need to be
-   32 | /// recompiled
-   33 | 
-   34 | ///
-   35 | /// TumorCell Hyperparameters
-   36 | ///
-   37 | 
-   38 | /// Rate of secretion of immunostimulatory factor of tumor cells per minute
-   39 | constexpr real_t kRateSecretionImmunostimulatoryFactor = 10.0;
-      |           ^
-/github/workspace/src/hyperparams.h:128:6: warning: result of integer division used in a floating point context; possible loss of precision [bugprone-integer-division]
-  128 |     (kBoundedSpaceLength / kResolutionGridSubstances) *
-      |      ^
-/github/workspace/src/hyperparams.h:129:6: warning: result of integer division used in a floating point context; possible loss of precision [bugprone-integer-division]
-  129 |     (kBoundedSpaceLength / kResolutionGridSubstances) *
-      |      ^
-/github/workspace/src/hyperparams.h:130:6: warning: result of integer division used in a floating point context; possible loss of precision [bugprone-integer-division]
-  130 |     (kBoundedSpaceLength /
-      |      ^
-/github/workspace/src/hyperparams.h:189:14: warning: invalid case style for global constant 'kLengthBoxMechanics' [readability-identifier-naming]
-  189 | const real_t kLengthBoxMechanics =
-      |              ^~~~~~~~~~~~~~~~~~~
-      |              gKLengthBoxMechanics
-/github/workspace/src/hyperparams.h:194:14: warning: invalid case style for global constant 'kSquaredMaxDistanceNeighborsForce' [readability-identifier-naming]
-  194 | const real_t kSquaredMaxDistanceNeighborsForce = std::pow(
-      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-      |              gKSquaredMaxDistanceNeighborsForce
-/github/workspace/src/hyperparams.h:195:54: warning: no header providing "bdm::Math" is directly included [misc-include-cleaner]
-   27 |     0.1 + std::cbrt(kDefaultVolumeNewTumorCell * 6 / Math::kPi) *
-      |                                                      ^
+                                                  ^
 102078 warnings generated.
 Suppressed 102230 warnings (102068 in non-user code, 162 NOLINT).
 Use -header-filter=.* to display errors from all non-system headers. Use -system-headers to display errors from system headers as well.

src/cart_cell.cc

@@ -159,7 +159,7 @@ Real3 CartCell::CalculateDisplacement(const InteractionForce* force,
   Real3 movement_at_next_step{0, 0, 0};
   // this should be chaged in a future version of BioDynaMo in order to have a
   // cleaner code instead of hardcoding it here
-  squared_radius = kSquaredMaxDistanceNeighborsForce;
+  squared_radius = gKSquaredMaxDistanceNeighborsForce;
 
   // the physics force to move the point mass
 

src/cart_tumor.cc

@@ -56,7 +56,7 @@ int Simulate(int argc, const char** argv) {
   auto* env = dynamic_cast<UniformGridEnvironment*>(
       Simulation::GetActive()->GetEnvironment());
   // Fix the box length for the uniform grid environment
-  env->SetBoxLength(kLengthBoxMechanics);
+  env->SetBoxLength(gKLengthBoxMechanics);
 
   // Define Substances
   auto* rm = Simulation::GetActive()->GetResourceManager();

src/hyperparams.h

@@ -23,7 +23,8 @@
 #define TUMOR_HYPERPARAMS_H_
 
 #include <cmath>
-#include "biodynamo.h"
+#include "core/real_t.h"
+#include "core/util/math.h"
 
 namespace bdm {
 
@@ -125,10 +126,9 @@ constexpr real_t kReductionConsumptionDeadCells = 0.1;
 constexpr int kResolutionGridSubstances = 50;  // 50 // voxels per axis
 /// Volume of a single voxel in μm³ (do not modify this line)
 constexpr real_t kVoxelVolume =
-    (kBoundedSpaceLength / kResolutionGridSubstances) *
-    (kBoundedSpaceLength / kResolutionGridSubstances) *
-    (kBoundedSpaceLength /
-     kResolutionGridSubstances);  // Do not modify this line
+    (static_cast<real_t>(kBoundedSpaceLength) / kResolutionGridSubstances) *
+    (static_cast<real_t>(kBoundedSpaceLength) / kResolutionGridSubstances) *
+    (static_cast<real_t>(kBoundedSpaceLength) / kResolutionGridSubstances);  // Do not modify this line
 /// Diffusion coefficient of oxygen in μm²/min
 constexpr real_t kDiffusionCoefficientOxygen =
     100000;  // 100000 micrometers^2/minute
@@ -186,12 +186,12 @@ constexpr real_t kDnew = 1.5 * kDtMechanics;
 constexpr real_t kDold = -0.5 * kDtMechanics;
 
 /// Do not change this line
-const real_t kLengthBoxMechanics =
+const real_t gKLengthBoxMechanics =
     22;  // Length of the box for mechanics in micrometers
 
 /// Max Distance for considering two cells as neighbours for force calculations
 /// in μm Do not change this line
-const real_t kSquaredMaxDistanceNeighborsForce = std::pow(
+const real_t gKSquaredMaxDistanceNeighborsForce = std::pow(
     0.1 + std::cbrt(kDefaultVolumeNewTumorCell * 6 / Math::kPi) *
               kMaxRelativeAdhesionDistance,
     2);  // (twice biggest cell radius (in case to cells tha maximum size

src/tumor_cell.cc

@@ -277,7 +277,7 @@ Real3 TumorCell::CalculateDisplacement(const InteractionForce* force,
   Real3 movement_at_next_step{0, 0, 0};
   // this should be chaged in a future version of BioDynaMo in order to have a
   // cleaner code instead of hardcoding it here
-  squared_radius = kSquaredMaxDistanceNeighborsForce;
+  squared_radius = gKSquaredMaxDistanceNeighborsForce;
 
   Real3 translation_velocity_on_point_mass{0, 0, 0};