Enable CI/clang-tidy #3
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…ture paper including forces and diffusion modules
Co-authored-by: Vassil Vassilev <[email protected]>
Co-authored-by: Vassil Vassilev <[email protected]>
* all work I have done untill the midterm: tumor replicated from the nature paper including forces and diffusion modules * car-t oxygen consumption * Update README.md Co-authored-by: Vassil Vassilev <[email protected]> * Update src/cart_cell.cc Co-authored-by: Vassil Vassilev <[email protected]> * still in progress CAR-T displacement * cleaned comments to follow Doxygen-style * changed comments to follow doxygen-style * Remove draft_code_my_own_analysis/ from tracking and add to .gitignore * remove draft_code_my_own_analysis * add to gitignore draft_code_my_own_analysis * fixing comments * [ci] Add basic github actions infrastructure * Update CMakeLists.txt Co-authored-by: Vassil Vassilev <[email protected]> * Update README.md Co-authored-by: Vassil Vassilev <[email protected]> * Update README.md Co-authored-by: Vassil Vassilev <[email protected]> * Update src/cart_cell.cc use *Simulation::GetActive()->GetResourceManager() just once Co-authored-by: Vassil Vassilev <[email protected]> * Update src/cart_cell.cc Co-authored-by: Vassil Vassilev <[email protected]> * Update src/forces_tumor_cart.cc Co-authored-by: Vassil Vassilev <[email protected]> * changed some things to imporve code quality * cart_cell comments fixed * changed all comments to /// in the .h and changed some of them * changed the project name + new readme part Results * minor change spelling * 30-days simulation --------- Co-authored-by: Vassil Vassilev <[email protected]>
This reverts commit 858ba08.
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| const std::vector<Real3> positions = | ||
| CreateSphereOfTumorCells(kInitialRadiusTumor); | ||
| for (const auto& pos : positions) { | ||
| auto* tumor_cell = new TumorCell(pos); |
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warning: initializing non-owner 'TumorCell *' with a newly created 'gsl::owner<>' [cppcoreguidelines-owning-memory]
auto* tumor_cell = new TumorCell(pos);
^| #include "core/diffusion/diffusion_grid.h" | ||
| #include "core/real_t.h" | ||
| #include "core/util/root.h" | ||
|
|
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warning: included header root.h is not used directly [misc-include-cleaner]
| DiffusionThomasAlgorithm::DiffusionThomasAlgorithm(int substance_id, | ||
| std::string substance_name, | ||
| real_t dc, real_t mu, | ||
| int resolution, real_t dt, |
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warning: 2 adjacent parameters of 'DiffusionThomasAlgorithm' of convertible types are easily swapped by mistake [bugprone-easily-swappable-parameters]
int resolution, real_t dt,
^Additional context
src/diffusion_thomas_algorithm.cc:42: the first parameter in the range is 'resolution'
int resolution, real_t dt,
^src/diffusion_thomas_algorithm.cc:42: the last parameter in the range is 'dt'
int resolution, real_t dt,
^src/diffusion_thomas_algorithm.cc:42:
int resolution, real_t dt,
^src/diffusion_thomas_algorithm.cc:42: 'int' and 'real_t' may be implicitly converted: 'int' -> 'real_t' (as 'double'), 'real_t' (as 'double') -> 'int'
int resolution, real_t dt,
^|
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||
| // Apply Dirichlet boundary conditions to the grid | ||
| void DiffusionThomasAlgorithm::ApplyDirichletBoundaryConditions() { | ||
| const real_t origin = GetDimensionsPtr() |
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warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
const real_t origin = GetDimensionsPtr()
^| ChangeConcentrationBy( | ||
| idx, | ||
| amount - | ||
| all_concentrations |
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warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
all_concentrations
^|
|
||
| void DiffusionThomasAlgorithm::SolveDirectionThomas(unsigned int direction) { | ||
| const auto& thomas_denom = (direction == 0) ? thomas_denom_x_ | ||
| : (direction == 1) ? thomas_denom_y_ |
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warning: conditional operator is used as sub-expression of parent conditional operator, refrain from using nested conditional operators [readability-avoid-nested-conditional-operator]
: (direction == 1) ? thomas_denom_y_
^Additional context
src/diffusion_thomas_algorithm.cc:225: parent conditional operator here
const auto& thomas_denom = (direction == 0) ? thomas_denom_x_
^| : (direction == 1) ? thomas_denom_y_ | ||
| : thomas_denom_z_; | ||
| const auto& thomas_c = (direction == 0) ? thomas_c_x_ | ||
| : (direction == 1) ? thomas_c_y_ |
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warning: conditional operator is used as sub-expression of parent conditional operator, refrain from using nested conditional operators [readability-avoid-nested-conditional-operator]
: (direction == 1) ? thomas_c_y_
^Additional context
src/diffusion_thomas_algorithm.cc:228: parent conditional operator here
const auto& thomas_c = (direction == 0) ? thomas_c_x_
^| : thomas_c_z_; | ||
| const unsigned int jump = | ||
| (direction == 0) ? static_cast<unsigned int>(jump_i_) | ||
| : (direction == 1) ? static_cast<unsigned int>(jump_j_) |
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warning: conditional operator is used as sub-expression of parent conditional operator, refrain from using nested conditional operators [readability-avoid-nested-conditional-operator]
: (direction == 1) ? static_cast<unsigned int>(jump_j_)
^Additional context
src/diffusion_thomas_algorithm.cc:232: parent conditional operator here
(direction == 0) ? static_cast<unsigned int>(jump_i_)
^| GetAllConcentrations(); // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic) | ||
| SetConcentration( | ||
| ind, | ||
| all_concentrations[ind] / |
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warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
all_concentrations[ind] /
^| ind = GetLoopIndex(direction, outer, middle, inner); | ||
| SetConcentration( | ||
| ind, | ||
| (all_concentrations |
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warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
(all_concentrations
^
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