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diffusion_thomas_algorithm.cc refactorized tidy
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‎clang_output.txt‎

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src/diffusion_thomas_algorithm.cc: 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/tmp5joylp3d.yaml src/diffusion_thomas_algorithm.cc
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102368 warnings generated.
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Suppressed 102373 warnings (102211 in non-user code, 162 NOLINT).
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Use -header-filter=.* to display errors from all non-system headers. Use -system-headers to display errors from system headers as well.
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/github/workspace/src/diffusion_thomas_algorithm.cc:22:1: warning: #includes are not sorted properly [llvm-include-order]
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22 | #include <string>
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| ^ ~~~~~~~~
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| "cart_cell.h"
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23 | #include <utility>
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| ~~~~~~~~~
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| "hyperparams.h"
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24 | #include <vector>
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| ~~~~~~~~
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| "tumor_cell.h"
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25 | #include "cart_cell.h"
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| ~~~~~~~~~~~~~
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| <string>
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26 | #include "hyperparams.h"
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| ~~~~~~~~~~~~~~~
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| <utility>
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27 | #include "tumor_cell.h"
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| ~~~~~~~~~~~~~~
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| <vector>
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/github/workspace/src/diffusion_thomas_algorithm.cc:32:51: warning: no header providing "bdm::real_t" is directly included [misc-include-cleaner]
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26 | #include "hyperparams.h"
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27 | #include "tumor_cell.h"
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28 |
28-
29 | namespace bdm {
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30 |
30-
31 | DiffusionThomasAlgorithm::DiffusionThomasAlgorithm(
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32 | int substance_id, std::string substance_name, real_t dc, real_t mu,
32-
| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:33:5: warning: 2 adjacent parameters of 'DiffusionThomasAlgorithm' of convertible types are easily swapped by mistake [bugprone-easily-swappable-parameters]
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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| ^~~~~~~~~~~~~~~~~~~~~~~~~
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/github/workspace/src/diffusion_thomas_algorithm.cc:33:9: note: the first parameter in the range is 'resolution'
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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| ^~~~~~~~~~
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/github/workspace/src/diffusion_thomas_algorithm.cc:33:28: note: the last parameter in the range is 'dt'
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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| ^~
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/github/workspace/src/diffusion_thomas_algorithm.cc:33:5: note:
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:33:21: note: 'int' and 'real_t' may be implicitly converted: 'int' -> 'real_t' (as 'double'), 'real_t' (as 'double') -> 'int'
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:34:7: warning: no header providing "bdm::DiffusionGrid" is directly included [misc-include-cleaner]
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26 | #include "hyperparams.h"
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27 | #include "tumor_cell.h"
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28 |
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29 | namespace bdm {
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30 |
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31 | DiffusionThomasAlgorithm::DiffusionThomasAlgorithm(
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32 | int substance_id, std::string substance_name, real_t dc, real_t mu,
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33 | int resolution, real_t dt, bool dirichlet_border) // time step
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34 | : DiffusionGrid(substance_id, std::move(substance_name), dc, mu,
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:38:3: warning: 'resolution_' should be initialized in a member initializer of the constructor [cppcoreguidelines-prefer-member-initializer]
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35 | resolution) {
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| , resolution_(GetResolution())
@@ -304,60 +246,6 @@ Use -header-filter=.* to display errors from all non-system headers. Use -system
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/github/workspace/src/diffusion_thomas_algorithm.cc:161:39: warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
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161 | ChangeConcentrationBy(idx, amount - GetAllConcentrations()[idx],
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:162:25: warning: no header providing "bdm::InteractionMode" is directly included [misc-include-cleaner]
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162 | InteractionMode::kAdditive, false);
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:189:32: warning: function 'DiffuseChemical' has cognitive complexity of 31 (threshold 25) [readability-function-cognitive-complexity]
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189 | void DiffusionThomasAlgorithm::DiffuseChemical(real_t dt) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:192:3: note: +1, including nesting penalty of 0, nesting level increased to 1
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192 | if (dirichlet_border_) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:198:3: note: +1, including nesting penalty of 0, nesting level increased to 1
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198 | for (unsigned int k = 0; k < resolution_; k++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:199:5: note: +2, including nesting penalty of 1, nesting level increased to 2
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199 | for (unsigned int j = 0; j < resolution_; j++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:204:7: note: +3, including nesting penalty of 2, nesting level increased to 3
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204 | for (unsigned int i = 1; i < resolution_; i++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:212:7: note: +3, including nesting penalty of 2, nesting level increased to 3
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212 | for (int i = resolution_ - 2; i >= 0; i--) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:222:3: note: +1, including nesting penalty of 0, nesting level increased to 1
329-
222 | if (dirichlet_border_) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:228:3: note: +1, including nesting penalty of 0, nesting level increased to 1
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228 | for (unsigned int k = 0; k < resolution_; k++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:229:5: note: +2, including nesting penalty of 1, nesting level increased to 2
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229 | for (unsigned int i = 0; i < resolution_; i++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:234:7: note: +3, including nesting penalty of 2, nesting level increased to 3
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234 | for (unsigned int j = 1; j < resolution_; j++) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:242:7: note: +3, including nesting penalty of 2, nesting level increased to 3
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242 | for (int j = resolution_ - 2; j >= 0; j--) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:252:3: note: +1, including nesting penalty of 0, nesting level increased to 1
344-
252 | if (dirichlet_border_) {
345-
| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:258:3: note: +1, including nesting penalty of 0, nesting level increased to 1
347-
258 | for (unsigned int j = 0; j < resolution_; j++) {
348-
| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:259:5: note: +2, including nesting penalty of 1, nesting level increased to 2
350-
259 | for (unsigned int i = 0; i < resolution_; i++) {
351-
| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:263:7: note: +3, including nesting penalty of 2, nesting level increased to 3
353-
263 | for (unsigned int k = 1; k < resolution_; k++) {
354-
| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:271:7: note: +3, including nesting penalty of 2, nesting level increased to 3
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271 | for (int k = resolution_ - 2; k >= 0; k--) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:280:3: note: +1, including nesting penalty of 0, nesting level increased to 1
359-
280 | if (dirichlet_border_) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:189:55: warning: parameter 'dt' is unused [misc-unused-parameters]
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189 | void DiffusionThomasAlgorithm::DiffuseChemical(real_t dt) {
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| ^~
@@ -479,9 +367,6 @@ Use -header-filter=.* to display errors from all non-system headers. Use -system
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/github/workspace/src/diffusion_thomas_algorithm.cc:298:27: warning: lambda capture 'current_time' is not used [clang-diagnostic-unused-lambda-capture]
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298 | rm->ForEachAgent([this, current_time](bdm::Agent* agent) {
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| ~~^~~~~~~~~~~~
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/github/workspace/src/diffusion_thomas_algorithm.cc:298:46: warning: no header providing "bdm::Agent" is directly included [misc-include-cleaner]
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26 | rm->ForEachAgent([this, current_time](bdm::Agent* agent) {
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| ^
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/github/workspace/src/diffusion_thomas_algorithm.cc:302:7: warning: variable 'conc' of type 'real_t' (aka 'double') can be declared 'const' [misc-const-correctness]
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302 | real_t conc = this->GetValue(pos);
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| ^

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