Lb stats #94
Lb stats #94
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WalkthroughWalkthroughThe recent updates to the Changes
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| void ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute( | ||
| level_t& level, PHARE::solver::IPhysicalModel<amr_types>& model) | ||
| { | ||
| bool static constexpr c_ordering = false; |
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Code scanning / CodeQL
Unused local variable Note
| auto& E = hybridModel.state.electromag.E; | ||
| // magSharedNodesRefiners_.fill(B, levelNumber, initDataTime); | ||
| magGhostsRefiners_.fill(B, levelNumber, initDataTime); | ||
| // elecSharedNodesRefiners_.fill(E, levelNumber, initDataTime); |
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Code scanning / CodeQL
Commented-out code Note
| { | ||
| auto& B = hybridModel.state.electromag.B; | ||
| auto& E = hybridModel.state.electromag.E; | ||
| // magSharedNodesRefiners_.fill(B, levelNumber, initDataTime); |
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Commented-out code Note
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Actionable comments posted: 41
Outside diff range and nitpick comments (15)
tools/config/config.py (1)
Line range hint
150-150: The local variablempi_typeis assigned but never used within the scope ofconfig_mpi_version. This could be an oversight or dead code.- mpi_type = deduce_mpi_type_from(version) + # mpi_type = deduce_mpi_type_from(version) # Uncomment if used laterpyphare/pyphare/simulator/simulator.py (1)
Line range hint
108-108: Avoid using bare except statements.Using bare except statements can catch unexpected exceptions and make debugging difficult. Specify the exception types to improve error handling.
- except: + except Exception as e:Also applies to: 131-131
pyphare/pyphare/pharein/maxwellian_fluid_model.py (2)
Line range hint
4-4: Remove unused import.The import
yee_element_is_primalis unused in this file and should be removed to clean up the code.- from pyphare.core.gridlayout import GridLayout, yee_element_is_primal + from pyphare.core.gridlayout import GridLayout
Line range hint
75-127: Add parameter documentation fordensity_cut_off.The parameter
density_cut_offis added to theadd_populationmethod but is not documented in the method's docstring. Update the docstring to include this parameter.- anisotropy : Pperp/Ppara of the species, float (default = 1) + anisotropy : Pperp/Ppara of the species, float (default = 1) + density_cut_off : The cutoff density below which particles are ignored, float (default = 1e-16)tests/simulator/__init__.py (2)
Line range hint
77-77: Replace lambda expression with a named function for better readability.- _ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i]) + def compute_value(i): + return 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])Tools
Ruff
4-4: Multiple imports on one line (E401)
Line range hint
178-178: Undefined name 'Box' used.Please ensure that
Boxis defined or imported in this file.Also applies to: 184-184, 191-191
Tools
Ruff
4-4: Multiple imports on one line (E401)
pyphare/pyphare/pharesee/particles.py (1)
Line range hint
88-88: Remove unnecessary f-string.- print(f"particles.py:Particles::eq failed with:", ex) + print("particles.py:Particles::eq failed with:", ex)src/core/data/ndarray/ndarray_vector.hpp (1)
216-220: Consider adding documentation for themake_array_viewfunctions.The
make_array_viewfunctions are crucial for creating views over data arrays, but they lack documentation. Adding comments explaining the parameters, the function's purpose, and any side effects would improve code maintainability and readability.Also applies to: 222-226
pyphare/pyphare/pharein/__init__.py (1)
Line range hint
32-46: Remove unused imports or justify their presence.- from .uniform_model import UniformModel - from .maxwellian_fluid_model import MaxwellianFluidModel - from .electron_model import ElectronModel - from .diagnostics import ( - FluidDiagnostics, - ElectromagDiagnostics, - ParticleDiagnostics, - MetaDiagnostics, - InfoDiagnostics, - ) - from .simulation import ( - Simulation, - serialize as serialize_sim, - deserialize as deserialize_sim, - )Several modules are imported but not used within this file. If these are not needed, consider removing them to clean up the codebase. If they are used indirectly (e.g., by being re-exported or dynamically accessed), consider adding them to an
__all__list to clarify their purpose.Tools
Ruff
47-47: Module level import not at top of file (E402)
src/simulator/simulator.hpp (1)
Line range hint
392-401: Ensure that the logging scope is correctly set and used within theadvancemethod.Consider refactoring to avoid duplicate logging scope entries.
- PHARE_LOG_SCOPE(1, "Simulator::advance"); - PHARE_LOG_SCOPE(1, "Simulator::advance"); + PHARE_LOG_SCOPE(1, "Simulator::advance - full");src/amr/multiphysics_integrator.hpp (2)
33-33: Consider organizing related imports together for better readability.Grouping related headers can improve the readability and maintainability of the code. For instance, all
load_balancingrelated headers could be grouped together.Also applies to: 36-37
603-607: Properly document the purpose and usage ofsetLoadBalancerManager.Adding documentation for public methods is a best practice that enhances code maintainability and readability. Consider adding a brief comment explaining what this method does, its parameters, and when it should be called.
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (2)
166-166: Clarify the purpose of the conditional logic inregisterLevel.Consider adding a detailed comment explaining why the schedules are not created if
levelNumberisrootLevelNumber. This will help future maintainers understand the decision-making process behind this conditional logic.
341-341: Improve logging detail.Consider enhancing the log message in
fillIonGhostParticlesto include more context about the operation being performed, such as the level number and the specific ions being processed. This can aid in debugging and understanding the flow of data.pyphare/pyphare/pharesee/hierarchy.py (1)
Line range hint
668-668: Comparison toNoneshould becond is None.- if select is not None: + if select is not None:This change ensures that the comparison to
Noneis done usingisinstead of==, which is the recommended practice in Python for comparing singletons.
Review details
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Files selected for processing (47)
- pyphare/pyphare/core/phare_utilities.py (2 hunks)
- pyphare/pyphare/pharein/init.py (5 hunks)
- pyphare/pyphare/pharein/load_balancer.py (1 hunks)
- pyphare/pyphare/pharein/maxwellian_fluid_model.py (2 hunks)
- pyphare/pyphare/pharein/simulation.py (7 hunks)
- pyphare/pyphare/pharesee/hierarchy.py (6 hunks)
- pyphare/pyphare/pharesee/particles.py (1 hunks)
- pyphare/pyphare/simulator/simulator.py (8 hunks)
- pyphare/pyphare_tests/test_pharesee/test_geometry_3d.py (1 hunks)
- requirements.txt (1 hunks)
- res/cmake/def.cmake (4 hunks)
- res/cmake/dep/samrai.cmake (1 hunks)
- src/amr/CMakeLists.txt (2 hunks)
- src/amr/data/particles/particles_data.hpp (1 hunks)
- src/amr/level_initializer/hybrid_level_initializer.hpp (2 hunks)
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_homogeneous.hpp (1 hunks)
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_nppc.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_details.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_estimator.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_estimator_hybrid.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_hybrid_strategy.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_hybrid_strategy_factory.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_manager.hpp (1 hunks)
- src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (11 hunks)
- src/amr/multiphysics_integrator.hpp (13 hunks)
- src/amr/wrappers/integrator.hpp (4 hunks)
- src/core/data/ions/particle_initializers/maxwellian_particle_initializer.hpp (6 hunks)
- src/core/data/ions/particle_initializers/particle_initializer_factory.hpp (2 hunks)
- src/core/data/ndarray/ndarray_vector.hpp (1 hunks)
- src/core/data/particles/particle_array.hpp (1 hunks)
- src/core/utilities/box/box.hpp (1 hunks)
- src/hdf5/detail/h5/h5_file.hpp (2 hunks)
- src/initializer/data_provider.hpp (1 hunks)
- src/initializer/dictator.cpp (1 hunks)
- src/simulator/simulator.hpp (6 hunks)
- tests/core/data/ions/test_ions.cpp (1 hunks)
- tests/diagnostic/init.py (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
- tests/functional/harris/harris_2d_lb.py (1 hunks)
- tests/simulator/CMakeLists.txt (1 hunks)
- tests/simulator/init.py (2 hunks)
- tests/simulator/test_load_balancing.py (1 hunks)
- tests/simulator/test_tagging.py.off (1 hunks)
- tools/config/config.py (1 hunks)
- tools/python3/init.py (2 hunks)
- tools/python3/caliper.py (1 hunks)
Files skipped from review due to trivial changes (6)
- requirements.txt
- res/cmake/dep/samrai.cmake
- src/amr/data/particles/particles_data.hpp
- src/amr/load_balancing/load_balancer_details.hpp
- tests/core/data/ions/test_ions.cpp
- tests/simulator/test_tagging.py.off
Additional context used
Path-based instructions (19)
src/amr/load_balancing/load_balancer_hybrid_strategy.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/load_balancer_estimator.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/load_balancer_hybrid_strategy_factory.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/load_balancer_estimator_hybrid.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/initializer/data_provider.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_homogeneous.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/load_balancer_manager.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/core/data/ions/particle_initializers/particle_initializer_factory.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_nppc.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/core/utilities/box/box.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/core/data/ions/particle_initializers/maxwellian_particle_initializer.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/level_initializer/hybrid_level_initializer.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/hdf5/detail/h5/h5_file.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/core/data/particles/particle_array.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/wrappers/integrator.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/core/data/ndarray/ndarray_vector.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/simulator/simulator.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/multiphysics_integrator.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Learnings (2)
pyphare/pyphare/pharein/load_balancer.py (1)
User: PhilipDeegan PR: PhilipDeegan/PHARE#87 File: pyphare/pyphare/pharein/__init__.py:177-177 Timestamp: 2024-01-16T16:42:31.598Z Learning: The user has clarified that the validation for the `loadbalancing` parameter is handled within the `simulation.py` file through the `check_loadbalancing` function, which checks for supported types.pyphare/pyphare/pharein/__init__.py (1)
User: PhilipDeegan PR: PhilipDeegan/PHARE#87 File: pyphare/pyphare/pharein/__init__.py:177-177 Timestamp: 2024-01-16T16:42:31.598Z Learning: The user has clarified that the validation for the `loadbalancing` parameter is handled within the `simulation.py` file through the `check_loadbalancing` function, which checks for supported types.
Ruff
pyphare/pyphare_tests/test_pharesee/test_geometry_3d.py
1-1: Undefined name
test_geometry_3d(F821)tests/diagnostic/__init__.py
16-16: Multiple imports on one line (E401)
16-16:
numpyimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)pyphare/pyphare/pharein/load_balancer.py
36-36: f-string without any placeholders (F541)
53-53: f-string without any placeholders (F541)
56-56: f-string without any placeholders (F541)
tools/python3/__init__.py
72-72: Module level import not at top of file (E402)
pyphare/pyphare/core/phare_utilities.py
159-159: Multiple imports on one line (E401)
181-181: Multiple imports on one line (E401)
tests/functional/harris/harris_2d.py
60-60: Ambiguous variable name:
l(E741)
153-153: Undefined name
Run(F821)
156-156: Undefined name
plot_file_for_qty(F821)
162-162: Undefined name
plot_file_for_qty(F821)
166-166: Undefined name
plot_file_for_qty(F821)
171-171: Undefined name
plot_file_for_qty(F821)
176-176: Undefined name
plot_file_for_qty(F821)tools/python3/caliper.py
6-6:
tools.python3.runimported but unused (F401)
20-20:
subprocessimported but unused (F401)tests/functional/harris/harris_2d_lb.py
74-74: Ambiguous variable name:
l(E741)tools/config/config.py
150-150: Local variable
mpi_typeis assigned to but never used (F841)pyphare/pyphare/simulator/simulator.py
108-108: Do not use bare
except(E722)
131-131: Do not use bare
except(E722)
143-143:
pyphare.cpp.cpp_libimported but unused (F401)
162-162: Comparison to
Noneshould becond is not None(E711)tests/simulator/test_load_balancing.py
73-73: Ambiguous variable name:
l(E741)
218-218: Local variable
diag_diris assigned to but never used (F841)pyphare/pyphare/pharein/maxwellian_fluid_model.py
4-4:
pyphare.core.gridlayout.yee_element_is_primalimported but unused (F401)tests/simulator/__init__.py
4-4: Multiple imports on one line (E401)
77-77: Do not assign a
lambdaexpression, use adef(E731)
178-178: Undefined name
Box(F821)
184-184: Undefined name
Box(F821)
191-191: Undefined name
Box(F821)
217-217: Local variable
rankis assigned to but never used (F841)
218-218: Local variable
envis assigned to but never used (F841)pyphare/pyphare/pharesee/particles.py
88-88: f-string without any placeholders (F541)
pyphare/pyphare/pharein/__init__.py
32-32: Module level import not at top of file (E402)
32-32:
.uniform_model.UniformModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
33-33: Module level import not at top of file (E402)
33-33:
.maxwellian_fluid_model.MaxwellianFluidModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
34-34: Module level import not at top of file (E402)
34-34:
.electron_model.ElectronModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
35-41: Module level import not at top of file (E402)
36-36:
.diagnostics.FluidDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
37-37:
.diagnostics.ElectromagDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
38-38:
.diagnostics.ParticleDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
39-39:
.diagnostics.MetaDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
40-40:
.diagnostics.InfoDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
42-46: Module level import not at top of file (E402)
43-43:
.simulation.Simulationimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
47-47: Module level import not at top of file (E402)
pyphare/pyphare/pharein/simulation.py
335-335: Comparison to
Noneshould becond is not None(E711)
355-355: Ambiguous variable name:
l(E741)
561-561: f-string without any placeholders (F541)
569-569: f-string without any placeholders (F541)
588-588:
psutilimported but unused; consider usingimportlib.util.find_specto test for availability (F401)
589-589: Local variable
eis assigned to but never used (F841)
691-691: Comparison to
Noneshould becond is not None(E711)
954-954: Multiple imports on one line (E401)
960-960: Multiple imports on one line (E401)
pyphare/pyphare/pharesee/hierarchy.py
668-668: Comparison to
Noneshould becond is None(E711)
Additional comments not posted (36)
tests/functional/harris/CMakeLists.txt (1)
16-19: Correct implementation of conditional MPI testing.The addition of the
else()block for non-MPI testing is a logical extension and correctly implemented. Ensure that thephare_python3_execfunction is properly defined and works as expected in the non-MPI context.src/amr/load_balancing/load_balancer_hybrid_strategy.hpp (1)
14-25: Well-designed abstract base class for load balancing strategies.The
LoadBalancerHybridStrategyclass is well-designed as an abstract base class with a pure virtual functioncompute, which is a common and recommended practice in C++ for defining interfaces.src/amr/load_balancing/load_balancer_estimator.hpp (1)
17-34: Properly structured base class for load balancing estimation.The
LoadBalancerEstimatorclass is correctly structured with a constructor for initialization, a virtual destructor for safe polymorphic use, and a pure virtual functionestimatefor derived classes to implement specific behaviors.src/amr/load_balancing/load_balancer_estimator_hybrid.hpp (1)
17-37: Well-implemented decorator pattern in load balancing estimation.The
LoadBalancerEstimatorHybridclass effectively uses the decorator pattern to enhance the functionality ofLoadBalancerEstimatorby delegating computation to a strategy object. Ensure that the strategy creation in the constructor handles potential errors or null returns gracefully.tests/simulator/CMakeLists.txt (1)
27-27: LGTM! Ensure the new MPI test for load balancing runs as expected.tests/diagnostic/__init__.py (2)
23-27: Ensure the newInfoDiagnosticsclass is integrated correctly in the diagnostic pipeline.
23-23: Remove unnecessary f-string as there are no placeholders.- raise RuntimeError(f"LoadBalancer cannot work with both 'every' and 'auto'") + raise RuntimeError("LoadBalancer cannot work with both 'every' and 'auto'")Likely invalid or redundant comment.
src/initializer/data_provider.hpp (1)
51-53: LGTM! The newPHAREDicttype is defined correctly and includes all necessary types.src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_homogeneous.hpp (1)
45-66: Ensure thecomputemethod integrates correctly with the load balancing system and performs as expected.tools/python3/__init__.py (1)
14-17: Ensure proper error handling for subprocess calls.The use of
subprocess.runwithcheck=Trueand proper exception handling forCalledProcessErroris a good practice as it ensures that any subprocess errors are caught and handled appropriately.src/amr/load_balancing/load_balancer_manager.hpp (2)
23-32: Review initialization of class members in constructor.The constructor of
LoadBalancerManageris well-organized, initializing class members in the initializer list. This is efficient as it directly constructs members with their final values rather than default-constructing them first and then assigning to them.
69-74: Ensure correct handling of levels inaddLoadBalancerEstimator.The method correctly handles the range of levels from
iLevel_mintoiLevel_max. Using a loop to assign theLoadBalancerEstimatorto each level is appropriate and clear.src/amr/CMakeLists.txt (2)
68-74: Ensure new files are correctly integrated into the build system.The addition of new header files for load balancing strategies in the
CMakeLists.txtis correctly done. This ensures that these files are recognized by the build system and included in the compilation process.
87-87: Verify the correct setting ofMPI_LIBRARY_PATH.Ensure that
MPI_LIBRARY_PATHis correctly set to link against the MPI libraries. This is crucial for ensuring that the project links correctly against the required MPI libraries.src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_nppc.hpp (1)
53-53: Skip commenting on unused local variablec_ordering.The previous comment regarding the unused local variable
c_orderingis still valid and does not need to be repeated.pyphare/pyphare/core/phare_utilities.py (1)
181-196: Ensure proper handling of file operations and system resource queries.The function
write_system_state_statscorrectly handles file operations and queries system resources usingpsutil. The use ofjson.dumpto write data to a file is appropriate and follows good practices for data handling.Tools
Ruff
181-181: Multiple imports on one line (E401)
tests/functional/harris/harris_2d.py (2)
29-30: The calculation oftimestampsusingfinal_time / 3may not include the final time due to floating-point precision issues. Consider usingnp.linspacefor more precise control over the range and endpoint inclusion.
[REFACTOR_SUGGESTion]- timestamps = np.arange(0, final_time + time_step, final_time / 3) + timestamps = np.linspace(0, final_time, num=4, endpoint=True)
36-36: Thefinal_timeparameter is directly passed to theSimulationconstructor. Ensure that this aligns with the simulation's expected behavior and thatfinal_timeis appropriately validated elsewhere in the code.Verification successful
The
final_timeparameter is validated within thecheck_timefunction inpyphare/pyphare/pharein/simulation.py. This function ensures thatfinal_timeis used correctly in conjunction withtime_stepandtime_step_nbr, raising aValueErrorif the parameters are not specified correctly.
pyphare/pyphare/pharein/simulation.py,check_timefunction:
- Validates
final_timein combination withtime_stepandtime_step_nbr.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `final_time` is validated before being used in the simulation. # Test: Search for validation logic. Expect: Validation logic for `final_time`. rg --type python $'final_time' --context 5Length of output: 72
Script:
#!/bin/bash # Description: Verify that `final_time` is validated before being used in the simulation. # Test: Search for validation logic. Expect: Validation logic for `final_time`. rg --type py 'final_time' --context 5Length of output: 50535
Script:
#!/bin/bash # Description: Verify that `final_time` is validated in the `Simulation` class. # Test: Search for the `Simulation` class definition and its initialization logic. ast-grep --lang python --pattern $'class Simulation { $$$ def __init__($$$): $$$ }' --context 10Length of output: 583
Script:
#!/bin/bash # Description: Verify that `final_time` is validated in the `Simulation` class. # Test: Search for the `Simulation` class definition and its initialization logic. ast-grep --lang python --pattern 'class Simulation: def __init__($$$): $$$'Length of output: 83
Script:
#!/bin/bash # Description: Locate the file containing the `Simulation` class and search for its `__init__` method. # Step 1: Locate the file containing the `Simulation` class. fd -e py 'Simulation' | xargs rg 'class Simulation' # Step 2: Search for the `__init__` method within the located file(s). fd -e py 'Simulation' | xargs -I {} rg 'def __init__' {}Length of output: 176
Script:
#!/bin/bash # Description: Display the contents of the `pyphare/pyphare/pharein/simulation.py` file, focusing on the `__init__` method. # Step 1: Display the `Simulation` class definition and its `__init__` method. rg --context 10 'class Simulation' pyphare/pyphare/pharein/simulation.py rg --context 10 'def __init__' pyphare/pyphare/pharein/simulation.pyLength of output: 1654
Script:
#!/bin/bash # Description: Search for the `checker` decorator and any validation logic related to `final_time`. # Step 1: Locate the `checker` decorator definition. rg --context 10 'def checker' pyphare/pyphare/pharein/simulation.py # Step 2: Search for validation logic related to `final_time`. rg --context 10 'final_time' pyphare/pyphare/pharein/simulation.pyLength of output: 4786
tools/python3/caliper.py (1)
79-79: The query string is overwritten without being used in its initial form. This could be an error or unnecessary code. Verify if the initial assignment is required.Verification successful
The initial query assignment is commented out and not used in the code.
- tools/python3/caliper.py: Commented out lines with the initial query assignment.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if the initial query assignment is used elsewhere in the code. # Test: Search for the initial query usage. Expect: No usage found. rg --type python $'select function,%s group by %s format json-split'Length of output: 100
Script:
#!/bin/bash # Description: Check if the initial query assignment is used elsewhere in the code. # Test: Search for the initial query usage. Expect: No usage found. rg --type py $'select function,%s group by %s format json-split'Length of output: 345
src/core/utilities/box/box.hpp (1)
161-162: The use ofautoin the iterator's dereference operators is clear and appropriate here, providing flexibility with the type ofindex_.src/amr/level_initializer/hybrid_level_initializer.hpp (1)
55-55: Ensure proper error handling for dynamic_cast.Dynamic casting can fail and return nullptr if the cast is not valid. It's crucial to verify that
hybMessengeris not a nullptr after this cast to prevent potential dereferencing of a null pointer.src/hdf5/detail/h5/h5_file.hpp (1)
72-72: Ensure method consistency.The method
file()correctly provides access to theh5file_member. This is consistent with the encapsulation practices in C++.pyphare/pyphare/pharein/__init__.py (1)
229-247: Ensure proper initialization and handling of theLoadBalancerinstance.The initialization of
LoadBalancerwithactive=Falseand_register=Falseis crucial for its behavior. Verify that these flags are handled correctly throughout the class to ensure that the load balancing functionality can be safely toggled on and off.Verification successful
The
LoadBalancerclass inpyphare/pyphare/pharein/load_balancer.pycorrectly initializes and handles theactiveand_registerflags. Theactiveflag is initialized with a default value ofTrue, and the_registerflag is also initialized with a default value ofTrue. Additionally, there is a conditional check for_registerwithin the class.
pyphare/pyphare/pharein/load_balancer.py
active: bool = field(default_factory=lambda: True)_register: bool = field(default_factory=lambda: True)if self._register:Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the LoadBalancer class handles the 'active' and '_register' flags correctly. # Test: Search for the LoadBalancer class definition and its handling of the 'active' and '_register' flags. rg --type python $'class LoadBalancer'Length of output: 70
Script:
#!/bin/bash # Description: Verify that the LoadBalancer class handles the 'active' and '_register' flags correctly. # Test: Search for the LoadBalancer class definition and its handling of the 'active' and '_register' flags. rg 'class LoadBalancer'Length of output: 558
Script:
#!/bin/bash # Description: Verify that the LoadBalancer class handles the 'active' and '_register' flags correctly. # Test: Search for the handling of the 'active' and '_register' flags within the LoadBalancer class definition. rg 'active' pyphare/pyphare/pharein/load_balancer.py rg '_register' pyphare/pyphare/pharein/load_balancer.pyLength of output: 346
src/simulator/simulator.hpp (3)
16-18: Ensure that the newly included headers are necessary and correctly placed.Verification successful
The newly included headers are necessary and correctly placed as their entities are used in the file.
amr::LoadBalancerDetailsis used.amr::LoadBalancerManageris used.amr::LoadBalancerEstimatorHybridis used.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the newly included headers are used in the file. # Test: Search for usage of entities from the headers. Expect: At least one usage per header. rg --type cpp 'LoadBalancerDetails|LoadBalancerManager|LoadBalancerEstimatorHybrid' src/simulator/simulator.hppLength of output: 462
266-293: Review the initialization and usage of load balancing classes. Ensure that theLoadBalancerDetailsandLoadBalancerManagerare correctly configured and used.Verification successful
The initialization and usage of
LoadBalancerDetailsandLoadBalancerManagerappear to be correctly configured and used in the codebase. The parameters passed during their initialization and the methods called on these objects are appropriate and consistent with their definitions.
LoadBalancerDetailsis initialized usingamr::LoadBalancerDetails::FROM(dict["simulation"]["AMR"]["loadbalancing"]).LoadBalancerManageris initialized withstd::make_unique<amr::LoadBalancerManager<dim>>(dict)and used withmultiphysInteg_->setLoadBalancerManager(std::move(lbm_)).Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the correct configuration and usage of load balancing classes. # Test: Search for the configuration of `LoadBalancerDetails` and `LoadBalancerManager`. Expect: Correct parameters and methods calls. rg --type cpp 'LoadBalancerDetails|LoadBalancerManager' src/simulator/simulator.hppLength of output: 341
Script:
#!/bin/bash # Description: Verify the correct configuration and usage of load balancing classes. # Search for the definition and methods of `LoadBalancerDetails`. ast-grep --lang cpp --pattern 'class LoadBalancerDetails { $$$ }' # Search for the definition and methods of `LoadBalancerManager`. ast-grep --lang cpp --pattern 'class LoadBalancerManager { $$$ }'Length of output: 825
Script:
#!/bin/bash # Description: Verify the correct configuration and usage of load balancing classes. # Refined search for the definition and methods of `LoadBalancerDetails`. ast-grep --lang cpp --pattern 'class LoadBalancerDetails { $$$ }' # Refined search for the definition and methods of `LoadBalancerManager`. ast-grep --lang cpp --pattern 'class LoadBalancerManager { $$$ }' # Search for the initialization and method calls related to `LoadBalancerDetails` and `LoadBalancerManager` in the entire codebase. rg --type cpp 'LoadBalancerDetails|LoadBalancerManager'Length of output: 2881
297-299: Ensure that theIntegratorconstructor is correctly receiving all necessary parameters.pyphare/pyphare/pharein/simulation.py (2)
Line range hint
127-151: Ensure that thecheck_timefunction correctly calculatestime_step_nbr,time_step, andfinal_timebased on the provided arguments.This modification correctly handles different scenarios for time calculation based on the provided keyword arguments.
Line range hint
631-706: Review thewrapperfunction to ensure that it correctly processes simulation parameters and handles errors appropriately.The function effectively validates and sets up simulation parameters, handling various configurations and defaults.
src/amr/multiphysics_integrator.hpp (2)
107-107: Ensureload_balancer_manager_is properly initialized in all constructors.Verification successful
The constructor for
MultiPhysicsIntegratorinsrc/amr/multiphysics_integrator.hppdoes initializeload_balancer_manager_tonullptr.
load_balancer_manager_is properly initialized in the constructor found.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `load_balancer_manager_` is initialized in all constructors. # Test: Search for all constructors in the file and check initialization of `load_balancer_manager_`. rg --type cpp 'MultiPhysicsIntegrator\(' multiphysics_integrator.hppLength of output: 138
Script:
#!/bin/bash # Locate the `multiphysics_integrator.hpp` file fd multiphysics_integrator.hpp # If the file is found, search for all constructors of the `MultiPhysicsIntegrator` class in the file if [ -f "$(fd multiphysics_integrator.hpp)" ]; then rg --type cpp 'MultiPhysicsIntegrator\(' "$(fd multiphysics_integrator.hpp)" else echo "multiphysics_integrator.hpp file not found" fiLength of output: 338
Script:
#!/bin/bash # Extract the constructor definition from the file rg --type cpp --context 10 'MultiPhysicsIntegrator\(' src/amr/multiphysics_integrator.hppLength of output: 1165
369-369: Verify thatload_balancer_manager_is properly initialized before use.Verification successful
The
setLoadBalancerManagermethod is called insrc/simulator/simulator.hppbefore any method calls onload_balancer_manager_. This ensures thatload_balancer_manager_is properly initialized before use.
setLoadBalancerManageris called before theIntegratoris created and before any other operations that might useload_balancer_manager_.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `load_balancer_manager_` is initialized before use in `estimate`. # Test: Search for all uses of `load_balancer_manager_` and ensure it's initialized. rg --type cpp 'load_balancer_manager_' multiphysics_integrator.hppLength of output: 134
Script:
#!/bin/bash # Locate the file `multiphysics_integrator.hpp` in the repository file_path=$(fd multiphysics_integrator.hpp) # If the file is found, search for the initialization of `load_balancer_manager_` if [[ -n "$file_path" ]]; then echo "File found at: $file_path" rg --type cpp 'load_balancer_manager_' "$file_path" else echo "File not found" fiLength of output: 851
Script:
#!/bin/bash # Extract the relevant code blocks to verify the order of initialization and method calls for `load_balancer_manager_` file_path="src/amr/multiphysics_integrator.hpp" # Extract the class definition and constructor to check initialization rg --type cpp -A 20 'class' "$file_path" rg --type cpp -A 20 'multiphysics_integrator' "$file_path"Length of output: 1267
Script:
#!/bin/bash # Search for the assignment of `load_balancer_manager_` and verify the order of operations file_path="src/amr/multiphysics_integrator.hpp" # Search for the assignment of `load_balancer_manager_` rg --type cpp 'load_balancer_manager_ = std::move' "$file_path" -A 10 -B 10Length of output: 830
Script:
#!/bin/bash # Search for calls to `setLoadBalancerManager` and ensure they occur before any method calls on `load_balancer_manager_` file_path="src/amr/multiphysics_integrator.hpp" # Search for calls to `setLoadBalancerManager` rg --type cpp 'setLoadBalancerManager' "$file_path" -A 10 -B 10Length of output: 680
Script:
#!/bin/bash # Search the entire codebase for calls to `setLoadBalancerManager` rg --type cpp 'setLoadBalancerManager'Length of output: 258
Script:
#!/bin/bash # Extract the relevant code from `src/simulator/simulator.hpp` to verify the order of operations rg --type cpp 'setLoadBalancerManager' src/simulator/simulator.hpp -A 20 -B 20Length of output: 1933
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (1)
222-224: Remove commented-out code.As previously noted by the GitHub Advanced Security bot, commented-out code should be removed unless there is a specific reason to keep it for documentation or future use.
pyphare/pyphare/pharesee/hierarchy.py (5)
13-13: Added import fordataclassfrom thedataclassesmodule.This is a standard import necessary for using dataclasses in Python, which are used later in the file.
91-92: Added equality method forFieldDataclass.This method correctly compares
field_nameand the contents ofdatasetarrays. Ensure thatdatasetcomparison is intended to be element-wise.
229-230: Added equality method forParticleDataclass.This method ensures that two
ParticleDatainstances are considered equal if they have the samenameanddataset. This is a straightforward and effective way to compare these data structures.
258-259: Added__getitem__method to thePatchclass.This method allows for direct indexing into
patch_datasusing keys, which is a useful feature for accessing data more conveniently.
1809-1861: AddedEqualityReportdataclass andhierarchy_comparefunction.The
EqualityReportdataclass is well-defined and used effectively in thehierarchy_comparefunction to provide detailed comparison results between twoPatchHierarchyinstances. This function thoroughly checks for mismatches in class types, dimensions, timesteps, levels, and data keys, ensuring a comprehensive comparison.
| @@ -44,6 +44,7 @@ | |||
| serialize as serialize_sim, | |||
| deserialize as deserialize_sim, | |||
| ) | |||
| from .load_balancer import LoadBalancer | |||
There was a problem hiding this comment.
Address the module level import issue.
- from .load_balancer import LoadBalancer
+ # from .load_balancer import LoadBalancerThe import of LoadBalancer is flagged as not being at the top of the file. Consider moving all imports to the top to comply with PEP 8 standards, unless there's a specific reason they are delayed (e.g., to prevent circular dependencies).
Committable suggestion was skipped due to low confidence.
Tools
Ruff
47-47: Module level import not at top of file (E402)
| @@ -319,17 +323,25 @@ namespace solver | |||
| model.allocate(*patch, initDataTime); | |||
| solver.allocate(model, *patch, initDataTime); | |||
| messenger.allocate(*patch, initDataTime); | |||
| load_balancer_manager_->allocate(*patch, initDataTime); | |||
There was a problem hiding this comment.
Ensure that load_balancer_manager_ is not null before calling allocate.
if (load_balancer_manager_) {
load_balancer_manager_->allocate(*patch, initDataTime);
}This modification ensures that the program does not crash if load_balancer_manager_ is null.
| @@ -195,11 +197,15 @@ namespace amr | |||
| { | |||
| auto& hybridModel = dynamic_cast<HybridModel&>(model); | |||
| auto level = hierarchy->getPatchLevel(levelNumber); | |||
|
|
|||
| bool isRegriddingL0 = levelNumber == 0 and oldLevel; | |||
There was a problem hiding this comment.
Handle potential null pointer dereference.
- bool isRegriddingL0 = levelNumber == 0 and oldLevel;
+ bool isRegriddingL0 = levelNumber == 0 && oldLevel != nullptr;Ensure that oldLevel is checked for nullity before usage to prevent runtime errors.
| @@ -349,7 +365,7 @@ | |||
| void fillIonPopMomentGhosts(IonsT& ions, SAMRAI::hier::PatchLevel& level, | |||
| double const afterPushTime) override | |||
| { | |||
| PHARE_LOG_SCOPE(3, "HybridHybridMessengerStrategy::fillIonMomentGhosts"); | |||
| PHARE_LOG_SCOPE(1, "HybridHybridMessengerStrategy::fillIonMomentGhosts"); | |||
There was a problem hiding this comment.
Validate alpha values rigorously.
if (level.getLevelNumber() > 0 && (alpha < 0.0 || alpha > 1.0))Ensure that alpha is within the expected range (0 to 1) to prevent logical errors in time interpolation calculations. This validation is crucial for maintaining the integrity of the simulation data.
| @@ -81,7 +82,7 @@ | |||
| using DefaultCoarsenOp = BaseCoarsenOp<DefaultFieldCoarsener<dimension>>; | |||
|
|
|||
| public: | |||
| static const std::string stratName; | |||
| static const inline std::string stratName = "HybridModel-HybridModel"; | |||
There was a problem hiding this comment.
Consider using constexpr for stratName if it does not need to be modified.
- static const inline std::string stratName = "HybridModel-HybridModel";
+ static constexpr auto stratName = "HybridModel-HybridModel";This change ensures that stratName is evaluated at compile time, potentially improving performance and reducing memory usage.
| def print_rank0(*args, **kwargs): | ||
| from pyphare.cpp import cpp_lib | ||
|
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||
| if cpp_lib().mpi_rank() == 0: | ||
| print(*args, **kwargs) | ||
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|
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| def plot_timestep_time(timestep_times): | ||
| from pyphare.cpp import cpp_lib | ||
|
|
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| if cpp_lib().mpi_rank() == 0: | ||
| import matplotlib.pyplot as plt | ||
|
|
||
| fig, ax = plt.subplots() | ||
| ax.plot(timestep_times) | ||
| plt.ylabel("timestep time") | ||
| plt.xlabel("timestep") | ||
| fig.savefig("timestep_times.png") | ||
|
|
||
| cpp_lib().mpi_barrier() | ||
|
|
There was a problem hiding this comment.
Tip
Codebase Verification
The functions print_rank0 and plot_timestep_time involve MPI operations but do not have specific error handling for potential MPI errors. Consider adding error handling mechanisms to ensure robustness against MPI failures.
print_rank0functionplot_timestep_timefunction
Analysis chain
Ensure proper error handling in MPI-related functions.
The functions print_rank0 and plot_timestep_time involve MPI operations but do not handle potential MPI errors. It's important to ensure that these functions are robust against MPI failures.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify error handling in MPI-related functions in `simulator.py`.
# Test: Search for MPI error handling. Expect: Proper error handling mechanisms.
rg --type py $'cpp_lib().mpi_rank()' pyphare/pyphare/simulator/simulator.py
Length of output: 76
Script:
#!/bin/bash
# Description: Verify error handling in MPI-related functions in `simulator.py`.
# Test: Search for try-except blocks that might handle MPI errors.
rg --type py 'try:' pyphare/pyphare/simulator/simulator.py
Length of output: 97
Script:
#!/bin/bash
# Description: Extract lines containing try-except blocks and their surrounding context in `simulator.py`.
# Test: Display lines with try-except blocks and 5 lines before and after each occurrence.
rg --type py --context 5 'try:' pyphare/pyphare/simulator/simulator.py
Length of output: 1136
| return | ||
|
|
||
| with self.assertRaises(RuntimeError): | ||
| diag_dir = self.run_sim( |
There was a problem hiding this comment.
Remove unused local variable.
The local variable diag_dir is assigned but never used, which can lead to confusion and clutter in the code.
- diag_dir = self.run_sim(
+ self.run_sim(Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| diag_dir = self.run_sim( | |
| self.run_sim( |
Tools
Ruff
218-218: Local variable
diag_diris assigned to but never used (F841)
| rho[np.where(np.isclose(y, 10, atol=0.1))] = 0 | ||
| return rho | ||
|
|
||
| def S(y, y0, l): |
There was a problem hiding this comment.
Avoid ambiguous variable names.
The variable name l is ambiguous and can be confused with the number 1. Use a more descriptive name.
- def S(y, y0, l):
+ def S(y, y0, length):Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def S(y, y0, l): | |
| def S(y, y0, length): |
Tools
Ruff
73-73: Ambiguous variable name:
l(E741)
| @@ -45,6 +45,7 @@ PYBIND11_MODULE(dictator, m) | |||
| m.def("add_size_t", add<std::size_t>, "add_size_t"); | |||
| m.def("add_optional_size_t", add<std::optional<std::size_t>>, "add_optional_size_t"); | |||
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| m.def("add_bool", add<bool>, "add"); | |||
There was a problem hiding this comment.
Consider improving the documentation strings for each binding to reflect the specific type being added.
- m.def("add_bool", add<bool>, "add");
+ m.def("add_bool", add<bool>, "add boolean value");Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| m.def("add_bool", add<bool>, "add"); | |
| m.def("add_bool", add<bool>, "add boolean value"); |
|
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| def write_system_state_stats(file_path): | ||
| import json, psutil, pathlib, datetime |
There was a problem hiding this comment.
Separate imports onto individual lines.
- import json, psutil, pathlib, datetime
+ import json
+ import psutil
+ import pathlib
+ import datetimeFor better readability and to comply with PEP 8 standards, place each import on a separate line.
Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| import json, psutil, pathlib, datetime | |
| import json | |
| import psutil | |
| import pathlib | |
| import datetime |
Tools
Ruff
181-181: Multiple imports on one line (E401)
There was a problem hiding this comment.
Actionable comments posted: 0
Outside diff range and nitpick comments (1)
tests/functional/harris/harris_2d.py (1)
Line range hint
66-66: Consider renaming the variableltolengthor another descriptive name to avoid confusion with the number1.- def S(y, y0, l): + def S(y, y0, length):
Review details
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Review profile: CHILL
Files selected for processing (3)
- res/cmake/dep/phlop.cmake (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
Files skipped from review due to trivial changes (1)
- res/cmake/dep/phlop.cmake
Files skipped from review as they are similar to previous changes (1)
- tests/functional/harris/CMakeLists.txt
Additional context used
Ruff
tests/functional/harris/harris_2d.py
66-66: Ambiguous variable name:
l(E741)
Additional comments not posted (4)
tests/functional/harris/harris_2d.py (4)
45-45: Consider making thecellstuple configurable or validating it against expected simulation parameters to ensure it meets the necessary conditions for the simulation's spatial resolution.
163-164: Functionplot_file_for_qtycorrectly generates file paths for plots.
168-196: The functionplotis now correctly using defined names for plotting, addressing previous issues.
198-212: Functionmaincorrectly handles simulation execution and potential errors, ensuring robust operation.
There was a problem hiding this comment.
Actionable comments posted: 0
Outside diff range and nitpick comments (9)
tests/functional/shock/shock.py (2)
25-26: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.
Line range hint
49-49: Consider renaming the variableltolengthto avoid ambiguity with the number1.tests/functional/alfven_wave/alfven_wave1d.py (1)
27-28: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.tests/functional/translation/translat1d.py (2)
23-24: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.
Line range hint
131-131: Consider renaming the variableltolengthto avoid ambiguity with the number1.tests/functional/harris/harris_2d.py (2)
40-41: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.
Line range hint
66-66: Consider renaming the variableltolengthto avoid ambiguity with the number1.tests/functional/ionIonBeam/ion_ion_beam1d.py (1)
26-27: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.tests/functional/conservation/conserv.py (1)
25-26: Consider removing or uncommenting thesmallest_patch_sizeandlargest_patch_sizeif they are not intended for future use.
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Review profile: CHILL
Files selected for processing (15)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/alfven_wave/alfven_wave1d.py (1 hunks)
- tests/functional/conservation/CMakeLists.txt (1 hunks)
- tests/functional/conservation/conserv.py (1 hunks)
- tests/functional/dispersion/dispersion.py (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
- tests/functional/ionIonBeam/CMakeLists.txt (1 hunks)
- tests/functional/ionIonBeam/ion_ion_beam1d.py (1 hunks)
- tests/functional/shock/CMakeLists.txt (1 hunks)
- tests/functional/shock/shock.py (1 hunks)
- tests/functional/td/td1d.py (1 hunks)
- tests/functional/tdtagged/CMakeLists.txt (1 hunks)
- tests/functional/translation/CMakeLists.txt (1 hunks)
- tests/functional/translation/translat1d.py (1 hunks)
Files skipped from review due to trivial changes (2)
- tests/functional/tdtagged/CMakeLists.txt
- tests/functional/translation/CMakeLists.txt
Files skipped from review as they are similar to previous changes (1)
- tests/functional/harris/CMakeLists.txt
Additional context used
Ruff
tests/functional/td/td1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
41-41: Ambiguous variable name:
l(E741)tests/functional/dispersion/dispersion.py
7-7:
matplotlib.pyplotimported but unused (F401)tests/functional/shock/shock.py
49-49: Ambiguous variable name:
l(E741)tests/functional/translation/translat1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
131-131: Ambiguous variable name:
l(E741)tests/functional/harris/harris_2d.py
66-66: Ambiguous variable name:
l(E741)tests/functional/ionIonBeam/ion_ion_beam1d.py
8-8:
tests.diagnostic.all_timestampsimported but unused (F401)
15-15:
pyphare.pharesee.plottingimported but unused (F401)
16-16:
pathlib.Pathimported but unused (F401)tests/functional/conservation/conserv.py
8-8:
osimported but unused (F401)
Additional comments not posted (10)
tests/functional/shock/CMakeLists.txt (2)
10-10: Condition correctly checks for necessary components for the test.
13-13: Execution command correctly configured for MPI environment.tests/functional/conservation/CMakeLists.txt (2)
10-10: Condition correctly checks for necessary components for the test.
13-13: Execution command correctly configured for MPI environment.tests/functional/alfven_wave/CMakeLists.txt (2)
10-10: Condition correctly checks for necessary components for the test.
13-13: Execution command correctly configured for MPI environment.tests/functional/ionIonBeam/CMakeLists.txt (2)
10-10: Condition correctly checks for necessary components for the test.
13-13: Execution command correctly configured for MPI environment.tests/functional/td/td1d.py (1)
21-22: Changes in simulation configuration appear to be for testing different scenarios.tests/functional/dispersion/dispersion.py (1)
20-21: Changes in simulation configuration appear to be for testing different scenarios.
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Actionable comments posted: 0
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Files selected for processing (7)
- src/core/CMakeLists.txt (1 hunks)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/conservation/CMakeLists.txt (1 hunks)
- tests/functional/dispersion/CMakeLists.txt (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/ionIonBeam/CMakeLists.txt (1 hunks)
- tests/functional/shock/CMakeLists.txt (1 hunks)
Files skipped from review as they are similar to previous changes (5)
- tests/functional/alfven_wave/CMakeLists.txt
- tests/functional/conservation/CMakeLists.txt
- tests/functional/harris/CMakeLists.txt
- tests/functional/ionIonBeam/CMakeLists.txt
- tests/functional/shock/CMakeLists.txt
Additional comments not posted (2)
tests/functional/dispersion/CMakeLists.txt (1)
10-12: Ensurephare_python3_execis correctly defined and used.Verification successful
Verify the correctness of the
phare_python3_execfunction definition inres/cmake/def.cmake.
Re-verify the definition of
phare_python3_execinres/cmake/def.cmakewith increased context lines.
Re-verify the definition of
phare_python3_execinres/cmake/def.cmakeby extracting a larger portion of the file.
The
phare_python3_execfunction is correctly defined inres/cmake/def.cmakeand matches the expected usage intests/functional/dispersion/CMakeLists.txt.
- The function
phare_python3_execis defined to execute a Python file identified by the target in a specified directory, with or without MPI based on thetestMPIcondition.- The usage in
tests/functional/dispersion/CMakeLists.txtis consistent with this definition.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the definition and usage of `phare_python3_exec`. # Test: Search for the definition of `phare_python3_exec`. Expect: Definition should exist and match expected usage. rg --type cmake $'phare_python3_exec'Length of output: 2095
Script:
#!/bin/bash # Description: Verify the definition of `phare_python3_exec` in `res/cmake/def.cmake`. # Test: Extract the definition of `phare_python3_exec` function. rg --type cmake --context 10 $'function(phare_python3_exec level target file directory)' res/cmake/def.cmakeLength of output: 109
Script:
#!/bin/bash # Description: Verify the definition of `phare_python3_exec` in `res/cmake/def.cmake`. # Test: Extract the definition of `phare_python3_exec` function with increased context lines. rg --type cmake --context 20 $'function(phare_python3_exec level target file directory)' res/cmake/def.cmakeLength of output: 109
Script:
#!/bin/bash # Description: Verify the definition of `phare_python3_exec` in `res/cmake/def.cmake`. # Test: Extract a larger portion of the file containing the `phare_python3_exec` function definition. rg --type cmake --context 50 'phare_python3_exec' res/cmake/def.cmakeLength of output: 7422
src/core/CMakeLists.txt (1)
73-73: Verify the condition for skippingmpicxxin the compile command.Verification successful
The condition for skipping
mpicxxin the compile command is controlled by thephare_configuratoroption. The search results show thatphare_configuratoris defined and used in multiple CMake files, includingsrc/core/CMakeLists.txt.
tools/config/CMakeLists.txt: Defines thephare_configuratorproject.src/core/CMakeLists.txt: Contains the conditionif (NOT phare_configurator).res/cmake/options.cmake: Defines thephare_configuratoroption.res/cmake/def.cmake: Uses thephare_configuratorcondition.The condition appears to be correctly used in the project. Therefore, the review comment regarding the condition for skipping
mpicxxin the compile command is verified.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the condition for skipping `mpicxx`. # Test: Search for the usage of `phare_configurator`. Expect: Condition should be correctly used in the project. rg --type cmake $'phare_configurator'Length of output: 371
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Actionable comments posted: 10
Outside diff range and nitpick comments (17)
tests/diagnostic/__init__.py (1)
Line range hint
16-16: Refactor imports to follow best practices.- import pyphare.pharein as ph, numpy as np + import pyphare.pharein as ph + import numpy as npAlso, ensure that
numpyis used if it's being imported, or remove it if it's not necessary.tests/functional/td/td1d.py (2)
Line range hint
7-7: Remove unused import to clean up the code.- import matplotlib.pyplot as plt
Line range hint
41-41: Clarify ambiguous variable name.- def S(x, x0, l): + def S(x, x0, length):Replace
lwithlengthto improve readability and avoid confusion with the number1.tests/functional/dispersion/dispersion.py (1)
Line range hint
7-7: Remove unused import to clean up the code.- import matplotlib.pyplot as plttests/functional/shock/shock.py (1)
Line range hint
49-49: Rename the variablelto a more descriptive name to avoid confusion with the number1.- def S(x, x0, l): + def S(x, x0, length):tests/functional/translation/translat1d.py (2)
Line range hint
7-7: Remove unused import to clean up the code.- import matplotlib.pyplot as plt
Line range hint
131-131: Rename the variablelto a more descriptive name to avoid confusion with the number1.- def S(x, x0, l): + def S(x, x0, length):tests/functional/harris/harris_2d.py (1)
Line range hint
66-66: The variable namelis ambiguous and could be confused with the number1. Consider renaming it for clarity.- def S(y, y0, l): + def S(y, y0, length):tests/functional/ionIonBeam/ion_ion_beam1d.py (3)
Line range hint
8-8: Remove unused importtests.diagnostic.all_timestampsto clean up the code.- from tests.diagnostic import all_timestamps
Line range hint
15-15: Remove unused importpyphare.pharesee.plottingto clean up the code.- from pyphare.pharesee import plotting
Line range hint
16-16: Remove unused importpathlib.Pathto clean up the code.- from pathlib import Pathtests/functional/conservation/conserv.py (1)
Line range hint
8-8: Remove unused importosto clean up the code.- import ospyphare/pyphare/pharein/simulation.py (4)
Line range hint
127-150: Refactor the handling ofstart_timeincheck_timefunction.- start_time = kwargs.get("restart_options", {}).get("restart_time", 0) + start_time = kwargs.get("restart_options", {}).get("restart_time", None) + if start_time is None: + start_time = 0This change ensures that
start_timeis explicitly checked forNonebefore defaulting to0, aligning with best practices for clarity and error handling.
631-631: Ensure the new keywordsystem_state_write_every_tis documented.It would be beneficial to add a comment or documentation string explaining the purpose and usage of the new keyword
system_state_write_every_tto aid future maintainers and users of the code.
854-854: Initialization ofload_balancershould be documented.Consider adding a comment here to explain why
load_balanceris initialized toNone. This could help in understanding the flow and usage of load balancing within the simulation.
Line range hint
954-954: Correct the style of imports to adhere to best practices.- import dill, codecs + import dill + import codecsSplitting the imports into separate lines enhances readability and adheres to Python's PEP 8 style guide.
Also applies to: 960-960
pyphare/pyphare/pharesee/hierarchy.py (1)
Line range hint
668-668: Comparison toNoneshould becond is None.- if select is not None: + if select is not None:This change ensures that the comparison to
Noneis done using the recommended Pythonic way, which is more readable and can prevent subtle bugs.
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (57)
- pyphare/pyphare/core/phare_utilities.py (2 hunks)
- pyphare/pyphare/pharein/init.py (5 hunks)
- pyphare/pyphare/pharein/load_balancer.py (1 hunks)
- pyphare/pyphare/pharein/maxwellian_fluid_model.py (2 hunks)
- pyphare/pyphare/pharein/simulation.py (7 hunks)
- pyphare/pyphare/pharesee/hierarchy.py (6 hunks)
- pyphare/pyphare/pharesee/particles.py (1 hunks)
- pyphare/pyphare/simulator/simulator.py (8 hunks)
- pyphare/pyphare_tests/test_pharesee/test_geometry_3d.py (1 hunks)
- requirements.txt (1 hunks)
- res/cmake/def.cmake (4 hunks)
- res/cmake/dep/phlop.cmake (1 hunks)
- res/cmake/dep/samrai.cmake (1 hunks)
- src/amr/CMakeLists.txt (2 hunks)
- src/amr/data/particles/particles_data.hpp (1 hunks)
- src/amr/level_initializer/hybrid_level_initializer.hpp (2 hunks)
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_homogeneous.hpp (1 hunks)
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_nppc.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_details.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_estimator.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_estimator_hybrid.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_hybrid_strategy.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_hybrid_strategy_factory.hpp (1 hunks)
- src/amr/load_balancing/load_balancer_manager.hpp (1 hunks)
- src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (11 hunks)
- src/amr/multiphysics_integrator.hpp (13 hunks)
- src/amr/wrappers/integrator.hpp (4 hunks)
- src/core/CMakeLists.txt (1 hunks)
- src/core/data/ions/particle_initializers/maxwellian_particle_initializer.hpp (6 hunks)
- src/core/data/ions/particle_initializers/particle_initializer_factory.hpp (2 hunks)
- src/core/data/ndarray/ndarray_vector.hpp (1 hunks)
- src/core/data/particles/particle_array.hpp (1 hunks)
- src/core/utilities/box/box.hpp (1 hunks)
- src/hdf5/detail/h5/h5_file.hpp (2 hunks)
- src/initializer/data_provider.hpp (1 hunks)
- src/initializer/dictator.cpp (1 hunks)
- src/simulator/simulator.hpp (6 hunks)
- tests/core/data/ions/test_ions.cpp (1 hunks)
- tests/diagnostic/init.py (1 hunks)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/alfven_wave/alfven_wave1d.py (1 hunks)
- tests/functional/conservation/CMakeLists.txt (1 hunks)
- tests/functional/conservation/conserv.py (1 hunks)
- tests/functional/dispersion/CMakeLists.txt (1 hunks)
- tests/functional/dispersion/dispersion.py (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
- tests/functional/harris/harris_2d_lb.py (1 hunks)
- tests/functional/ionIonBeam/CMakeLists.txt (1 hunks)
- tests/functional/ionIonBeam/ion_ion_beam1d.py (1 hunks)
- tests/functional/shock/CMakeLists.txt (1 hunks)
- tests/functional/shock/shock.py (1 hunks)
- tests/functional/td/td1d.py (1 hunks)
- tests/functional/tdtagged/CMakeLists.txt (1 hunks)
- tests/functional/translation/CMakeLists.txt (1 hunks)
- tests/functional/translation/translat1d.py (1 hunks)
- tests/simulator/CMakeLists.txt (1 hunks)
Files not processed due to max files limit (10)
- tests/simulator/init.py
- tests/simulator/refinement/CMakeLists.txt
- tests/simulator/refinement/test_2d_10_core.py
- tests/simulator/refinement/test_2d_2_core.py
- tests/simulator/test_diagnostic_timestamps.py
- tests/simulator/test_load_balancing.py
- tests/simulator/test_tagging.py.off
- tools/config/config.py
- tools/python3/init.py
- tools/python3/caliper.py
Files skipped from review due to trivial changes (1)
- src/core/CMakeLists.txt
Files skipped from review as they are similar to previous changes (37)
- requirements.txt
- res/cmake/def.cmake
- res/cmake/dep/phlop.cmake
- res/cmake/dep/samrai.cmake
- src/amr/CMakeLists.txt
- src/amr/data/particles/particles_data.hpp
- src/amr/level_initializer/hybrid_level_initializer.hpp
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_homogeneous.hpp
- src/amr/load_balancing/concrete_load_balancer_hybrid_strategy_nppc.hpp
- src/amr/load_balancing/load_balancer_details.hpp
- src/amr/load_balancing/load_balancer_estimator.hpp
- src/amr/load_balancing/load_balancer_estimator_hybrid.hpp
- src/amr/load_balancing/load_balancer_hybrid_strategy.hpp
- src/amr/load_balancing/load_balancer_hybrid_strategy_factory.hpp
- src/amr/load_balancing/load_balancer_manager.hpp
- src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp
- src/amr/multiphysics_integrator.hpp
- src/core/data/ions/particle_initializers/maxwellian_particle_initializer.hpp
- src/core/data/ions/particle_initializers/particle_initializer_factory.hpp
- src/core/data/ndarray/ndarray_vector.hpp
- src/core/data/particles/particle_array.hpp
- src/core/utilities/box/box.hpp
- src/hdf5/detail/h5/h5_file.hpp
- src/initializer/data_provider.hpp
- src/initializer/dictator.cpp
- src/simulator/simulator.hpp
- tests/core/data/ions/test_ions.cpp
- tests/functional/alfven_wave/CMakeLists.txt
- tests/functional/alfven_wave/alfven_wave1d.py
- tests/functional/conservation/CMakeLists.txt
- tests/functional/dispersion/CMakeLists.txt
- tests/functional/harris/CMakeLists.txt
- tests/functional/ionIonBeam/CMakeLists.txt
- tests/functional/shock/CMakeLists.txt
- tests/functional/tdtagged/CMakeLists.txt
- tests/functional/translation/CMakeLists.txt
- tests/simulator/CMakeLists.txt
Additional context used
Path-based instructions (1)
src/amr/wrappers/integrator.hpp (1)
Pattern
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Learnings (2)
pyphare/pyphare/pharein/load_balancer.py (1)
User: PhilipDeegan PR: PhilipDeegan/PHARE#87 File: pyphare/pyphare/pharein/__init__.py:177-177 Timestamp: 2024-01-16T16:42:31.598Z Learning: The user has clarified that the validation for the `loadbalancing` parameter is handled within the `simulation.py` file through the `check_loadbalancing` function, which checks for supported types.pyphare/pyphare/pharein/__init__.py (1)
User: PhilipDeegan PR: PhilipDeegan/PHARE#87 File: pyphare/pyphare/pharein/__init__.py:177-177 Timestamp: 2024-01-16T16:42:31.598Z Learning: The user has clarified that the validation for the `loadbalancing` parameter is handled within the `simulation.py` file through the `check_loadbalancing` function, which checks for supported types.
Ruff
pyphare/pyphare_tests/test_pharesee/test_geometry_3d.py
1-1: Undefined name
test_geometry_3d(F821)tests/diagnostic/__init__.py
16-16: Multiple imports on one line (E401)
16-16:
numpyimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)pyphare/pyphare/pharein/load_balancer.py
36-36: f-string without any placeholders (F541)
53-53: f-string without any placeholders (F541)
56-56: f-string without any placeholders (F541)
tests/functional/td/td1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
41-41: Ambiguous variable name:
l(E741)tests/functional/dispersion/dispersion.py
7-7:
matplotlib.pyplotimported but unused (F401)pyphare/pyphare/core/phare_utilities.py
159-159: Multiple imports on one line (E401)
181-181: Multiple imports on one line (E401)
tests/functional/shock/shock.py
49-49: Ambiguous variable name:
l(E741)tests/functional/translation/translat1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
131-131: Ambiguous variable name:
l(E741)tests/functional/harris/harris_2d.py
66-66: Ambiguous variable name:
l(E741)tests/functional/harris/harris_2d_lb.py
74-74: Ambiguous variable name:
l(E741)tests/functional/ionIonBeam/ion_ion_beam1d.py
8-8:
tests.diagnostic.all_timestampsimported but unused (F401)
15-15:
pyphare.pharesee.plottingimported but unused (F401)
16-16:
pathlib.Pathimported but unused (F401)tests/functional/conservation/conserv.py
8-8:
osimported but unused (F401)pyphare/pyphare/simulator/simulator.py
108-108: Do not use bare
except(E722)
131-131: Do not use bare
except(E722)
143-143:
pyphare.cpp.cpp_libimported but unused (F401)
162-162: Comparison to
Noneshould becond is not None(E711)pyphare/pyphare/pharein/maxwellian_fluid_model.py
4-4:
pyphare.core.gridlayout.yee_element_is_primalimported but unused (F401)pyphare/pyphare/pharesee/particles.py
88-88: f-string without any placeholders (F541)
pyphare/pyphare/pharein/__init__.py
32-32: Module level import not at top of file (E402)
32-32:
.uniform_model.UniformModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
33-33: Module level import not at top of file (E402)
33-33:
.maxwellian_fluid_model.MaxwellianFluidModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
34-34: Module level import not at top of file (E402)
34-34:
.electron_model.ElectronModelimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
35-41: Module level import not at top of file (E402)
36-36:
.diagnostics.FluidDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
37-37:
.diagnostics.ElectromagDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
38-38:
.diagnostics.ParticleDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
39-39:
.diagnostics.MetaDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
40-40:
.diagnostics.InfoDiagnosticsimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
42-46: Module level import not at top of file (E402)
43-43:
.simulation.Simulationimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
47-47: Module level import not at top of file (E402)
pyphare/pyphare/pharein/simulation.py
335-335: Comparison to
Noneshould becond is not None(E711)
355-355: Ambiguous variable name:
l(E741)
561-561: f-string without any placeholders (F541)
569-569: f-string without any placeholders (F541)
588-588:
psutilimported but unused; consider usingimportlib.util.find_specto test for availability (F401)
589-589: Local variable
eis assigned to but never used (F841)
691-691: Comparison to
Noneshould becond is not None(E711)
954-954: Multiple imports on one line (E401)
960-960: Multiple imports on one line (E401)
pyphare/pyphare/pharesee/hierarchy.py
668-668: Comparison to
Noneshould becond is None(E711)
Additional comments not posted (16)
pyphare/pyphare_tests/test_pharesee/test_geometry_3d.py (1)
1-1: Skip: The previous comment about the undefined nametest_geometry_3dstill applies.Tools
Ruff
1-1: Undefined name
test_geometry_3d(F821)tests/functional/dispersion/dispersion.py (1)
20-20: The simulation setup infromNoiseandprescribedModesfunctions appears correctly implemented.Also applies to: 21-21
pyphare/pyphare/core/phare_utilities.py (1)
181-181: This comment is still valid and should be addressed:
coderabbitai[bot]: Separate imports onto individual lines.- import json, psutil, pathlib, datetime + import json + import psutil + import pathlib + import datetimeFor better readability and to comply with PEP 8 standards, place each import on a separate line.
Tools
Ruff
181-181: Multiple imports on one line (E401)
tests/functional/harris/harris_2d_lb.py (1)
74-74: The variable namelis ambiguous and could be confused with the number1. Consider renaming it for clarity.Tools
Ruff
74-74: Ambiguous variable name:
l(E741)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
Line range hint
75-127: Addition ofdensity_cut_offparameter approved.The addition of the
density_cut_offparameter to theadd_populationfunction is a sensible enhancement for handling low-density scenarios.src/amr/wrappers/integrator.hpp (5)
36-41: Refactor to improve readability of conditional logic.
166-167: Clarify the necessity of setting SAMRAI MPI.
94-99: Ensure that the rebalance check logic is correctly implemented.Verification successful
The
cadence_rebalance_checkmethod is used as part of the_rebalance_checkfunction, which is called within the_should_rebalance_nowmethod. The logic incadence_rebalance_checkappears to be correctly implemented, as it checks for rebalancing conditions based ontime_step_idxandlb_info_.
- The method checks if
time_step_idxis 0 andlb_info_.on_initis true.- It also checks if
lb_info_.everyis greater than 0,time_step_idxis greater than 0, andtime_step_idxis a multiple oflb_info_.every.These conditions seem appropriate for determining when to perform a rebalance.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the rebalance check logic in `cadence_rebalance_check` method is correctly implemented. # Test: Search for the method usage. Expect: Correct handling of rebalance checks. rg --type cpp $'bool cadence_rebalance_check()'Length of output: 115
Script:
#!/bin/bash # Description: Search for the usage of the `cadence_rebalance_check` method in the codebase. # Test: Find all occurrences of `cadence_rebalance_check` to understand its usage context. rg 'cadence_rebalance_check' --type cppLength of output: 237
Script:
#!/bin/bash # Description: Extract the relevant code around the `std::bind` call to understand how `cadence_rebalance_check` is used. # Test: Print lines around the `std::bind` call to understand the context. rg 'std::bind(&Integrator::cadence_rebalance_check' -A 5 -B 5 --type cppLength of output: 181
Script:
#!/bin/bash # Description: Extract the relevant code around the `std::bind` call to understand how `cadence_rebalance_check` is used. # Test: Print lines around the `std::bind` call to understand the context. rg 'std::bind\(&Integrator::cadence_rebalance_check' -A 5 -B 5 --type cppLength of output: 1055
Script:
#!/bin/bash # Description: Search for the usage of `_rebalance_check` within the `Integrator` class to understand its role. # Test: Find all occurrences of `_rebalance_check` to understand its usage context. rg '_rebalance_check' --type cppLength of output: 574
Script:
#!/bin/bash # Description: Extract the relevant code around the `_rebalance_check` call to understand its usage. # Test: Print lines around the `_rebalance_check` call to understand the context. rg '_rebalance_check\(\)' -A 5 -B 5 --type cppLength of output: 1682
47-53: Ensure that the methodadvancecorrectly handles the rebalancing logic.Verification successful
The
_should_rebalance_nowmethod is implemented as follows:template<std::size_t _dimension> bool Integrator<_dimension>::_should_rebalance_now() { if (is_tagging_refinement and lb_info_.active) return _rebalance_check(); return false; }The
advanceHierarchymethod is used in theadvancemethod of theIntegratorclass:double advance(double dt) { bool rebalance_coarsest_now = _should_rebalance_now(); auto new_time = timeRefIntegrator_->advanceHierarchy(dt, rebalance_coarsest_now); ++time_step_idx; return new_time; }The
_should_rebalance_nowmethod checks if rebalancing is needed based on the conditionsis_tagging_refinementandlb_info_.active. If both conditions are met, it calls_rebalance_check()to determine if rebalancing should occur. The result is then used as a parameter in theadvanceHierarchymethod.Based on the gathered information, the rebalancing logic in the
advancemethod appears to be correctly implemented.
_should_rebalance_nowmethod correctly checks conditions for rebalancing.- The result of
_should_rebalance_nowis used inadvanceHierarchy.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the rebalancing logic in `advance` method is correctly implemented. # Test: Search for the method usage. Expect: Correct handling of rebalancing. rg --type cpp $'bool rebalance_coarsest_now = _should_rebalance_now();'Length of output: 72
Script:
#!/bin/bash # Description: Verify the implementation of `_should_rebalance_now` method. # Search for the `_should_rebalance_now` method definition. ast-grep --lang cpp --pattern $'bool _should_rebalance_now() { $$$ }' # Search for the `advanceHierarchy` method definition. ast-grep --lang cpp --pattern $'$_ timeRefIntegrator_->advanceHierarchy($_, $_) { $$$ }'Length of output: 160
Script:
#!/bin/bash # Description: Verify the implementation of `_should_rebalance_now` method and `advanceHierarchy` method. # Search for the `_should_rebalance_now` method definition. rg --type cpp --pcre2 'bool\s+_should_rebalance_now\s*\(\s*\)\s*\{' # Search for the `advanceHierarchy` method definition. rg --type cpp --pcre2 'advanceHierarchy\s*\(\s*double\s+\w+\s*,\s*bool\s+\w+\s*\)\s*\{'Length of output: 159
Script:
#!/bin/bash # Description: Verify the implementation of `_should_rebalance_now` method and `advanceHierarchy` method. # Search for the `_should_rebalance_now` method definition. fd -e cpp -e h -e hpp -e cxx -e cc -e c | xargs rg 'bool\s+_should_rebalance_now\s*\(\s*\)\s*\{' # Search for the `advanceHierarchy` method definition. fd -e cpp -e h -e hpp -e cxx -e cc -e c | xargs rg 'advanceHierarchy\s*\(\s*double\s+\w+\s*,\s*bool\s+\w+\s*\)\s*\{'Length of output: 217
Script:
#!/bin/bash # Description: Verify the implementation of `_should_rebalance_now` method and `advanceHierarchy` method. # Search for the `_should_rebalance_now` method definition. fd -e cpp -e h -e hpp -e cxx -e cc -e c | xargs rg '_should_rebalance_now' # Search for the `advanceHierarchy` method definition. fd -e cpp -e h -e hpp -e cxx -e cc -e c | xargs rg 'advanceHierarchy'Length of output: 707
Script:
#!/bin/bash # Description: Retrieve the full implementation of `_should_rebalance_now` and `advanceHierarchy` methods. # Get the full implementation of `_should_rebalance_now` method. rg --context 10 'bool Integrator<_dimension>::_should_rebalance_now()' src/amr/wrappers/integrator.hpp # Get the full implementation of `advanceHierarchy` method. rg --context 10 'advanceHierarchy' src/amr/wrappers/integrator.hpp tests/amr/messengers/test_messengers.cppLength of output: 3763
101-127: Review the logic for automatic rebalancing to ensure it adheres to the specified tolerance and backoff settings.pyphare/pyphare/pharein/__init__.py (1)
47-47: Address the module level import issue.- from .load_balancer import LoadBalancer + # from .load_balancer import LoadBalancerThe import of
LoadBalanceris flagged as not being at the top of the file. Consider moving all imports to the top to comply with PEP 8 standards, unless there's a specific reason they are delayed (e.g., to prevent circular dependencies).Tools
Ruff
47-47: Module level import not at top of file (E402)
pyphare/pyphare/pharesee/hierarchy.py (5)
13-13: Added import fordataclassfrom thedataclassesmodule.This is a standard Python import necessary for using dataclasses, which are used later in the file.
91-93: Added equality method__eq__forFieldData.This method correctly compares
field_nameand the contents ofdatasetarrays. It ensures that twoFieldDatainstances are considered equal if they have the same field name and identical data.
229-231: Added equality method__eq__forParticleData.This method ensures that two
ParticleDatainstances are considered equal if they have the same name and identical datasets. This is crucial for operations that require comparison of particle data across different simulations or time steps.
258-260: Added method__getitem__to thePatchclass.This method allows for direct indexing into
patch_datasusing keys, which simplifies access to data within a patch. It enhances the usability of thePatchclass by allowing it to behave more like a dictionary.
1809-1861: AddedEqualityReportdataclass andhierarchy_comparefunction.The
EqualityReportdataclass is well-defined and provides a structured way to report equality checks. Thehierarchy_comparefunction is comprehensive and checks various aspects ofPatchHierarchyobjects to ensure they are equivalent. This is useful for validating the consistency of hierarchies across different parts of the application or in different states of computation.
| auto computeNonUniformWorkLoadForLevel0() const | ||
| { | ||
| auto const& L0 = *timeRefIntegrator_->getPatchHierarchy()->getPatchLevel(0); | ||
| double load = 0.0; | ||
| for (SAMRAI::hier::PatchLevel::iterator ip(L0.begin()); ip != L0.end(); ++ip) | ||
| { | ||
| std::shared_ptr<SAMRAI::hier::Patch> const& patch = *ip; | ||
| load += SAMRAI::mesh::BalanceUtilities::computeNonUniformWorkload( | ||
| patch, loadBalancerPatchId_, patch->getBox()); | ||
| } | ||
| return load; | ||
| } |
There was a problem hiding this comment.
Optimize the computation of non-uniform workload.
- auto const& L0 = *timeRefIntegrator_->getPatchHierarchy()->getPatchLevel(0);
- double load = 0.0;
- for (SAMRAI::hier::PatchLevel::iterator ip(L0.begin()); ip != L0.end(); ++ip)
- {
- std::shared_ptr<SAMRAI::hier::Patch> const& patch = *ip;
- load += SAMRAI::mesh::BalanceUtilities::computeNonUniformWorkload(
- patch, loadBalancerPatchId_, patch->getBox());
- }
- return load;
+ return std::accumulate(L0.begin(), L0.end(), 0.0, [this](double load, auto& patch) {
+ return load + SAMRAI::mesh::BalanceUtilities::computeNonUniformWorkload(
+ patch, loadBalancerPatchId_, patch->getBox());
+ });Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| auto computeNonUniformWorkLoadForLevel0() const | |
| { | |
| auto const& L0 = *timeRefIntegrator_->getPatchHierarchy()->getPatchLevel(0); | |
| double load = 0.0; | |
| for (SAMRAI::hier::PatchLevel::iterator ip(L0.begin()); ip != L0.end(); ++ip) | |
| { | |
| std::shared_ptr<SAMRAI::hier::Patch> const& patch = *ip; | |
| load += SAMRAI::mesh::BalanceUtilities::computeNonUniformWorkload( | |
| patch, loadBalancerPatchId_, patch->getBox()); | |
| } | |
| return load; | |
| } | |
| auto computeNonUniformWorkLoadForLevel0() const | |
| { | |
| auto const& L0 = *timeRefIntegrator_->getPatchHierarchy()->getPatchLevel(0); | |
| return std::accumulate(L0.begin(), L0.end(), 0.0, [this](double load, auto& patch) { | |
| return load + SAMRAI::mesh::BalanceUtilities::computeNonUniformWorkload( | |
| patch, loadBalancerPatchId_, patch->getBox()); | |
| }); | |
| } |
|
|
||
| def __post_init__(self): | ||
| if self.auto and self.every: | ||
| raise RuntimeError(f"LoadBalancer cannot work with both 'every' and 'auto'") |
There was a problem hiding this comment.
Remove unnecessary f-strings as there are no placeholders.
- raise RuntimeError(f"LoadBalancer cannot work with both 'every' and 'auto'")
+ raise RuntimeError("LoadBalancer cannot work with both 'every' and 'auto'")
- raise RuntimeError(f"LoadBalancer cannot be registered as no simulation exists")
+ raise RuntimeError("LoadBalancer cannot be registered as no simulation exists")
- raise RuntimeError(f"LoadBalancer is already registered to simulation")
+ raise RuntimeError("LoadBalancer is already registered to simulation")Also applies to: 53-53, 56-56
Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| raise RuntimeError(f"LoadBalancer cannot work with both 'every' and 'auto'") | |
| raise RuntimeError("LoadBalancer cannot work with both 'every' and 'auto'") |
Tools
Ruff
36-36: f-string without any placeholders (F541)
| def print_rank0(*args, **kwargs): | ||
| from pyphare.cpp import cpp_lib | ||
|
|
||
| if cpp_lib().mpi_rank() == 0: | ||
| print(*args, **kwargs) | ||
|
|
There was a problem hiding this comment.
Add error handling for MPI operations.
Consider adding error handling mechanisms to ensure robustness against MPI failures in the print_rank0 function.
| def write_system_state_stats(self): | ||
| import pyphare.core.phare_utilities as pu | ||
| from pyphare.cpp import cpp_lib | ||
|
|
||
| if self.simulation.system_state_write_every_t == 0: | ||
| return | ||
| diff_time = self.cpp_sim.currentTime() - self.write_system_state_time | ||
| if ( | ||
| pu.fp_equal(diff_time, self.simulation.system_state_write_every_t) | ||
| or diff_time > self.simulation.system_state_write_every_t | ||
| ): | ||
| self.write_system_state_time = self.cpp_sim.currentTime() | ||
| time = "{:.10f}".format(self.cpp_sim.currentTime()) | ||
| pu.write_system_state_stats( | ||
| f".phare/sys/stats/{cpp_lib().mpi_rank()}/{time}" | ||
| ) | ||
|
|
There was a problem hiding this comment.
Add file path validation and exception handling.
The method write_system_state_stats does not include file path validation or exception handling. Consider adding these to ensure robustness and correctness.
| def plot_timestep_time(timestep_times): | ||
| from pyphare.cpp import cpp_lib | ||
|
|
||
| if cpp_lib().mpi_rank() == 0: | ||
| import matplotlib.pyplot as plt | ||
|
|
||
| fig, ax = plt.subplots() | ||
| ax.plot(timestep_times) | ||
| plt.ylabel("timestep time") | ||
| plt.xlabel("timestep") | ||
| fig.savefig("timestep_times.png") | ||
|
|
||
| cpp_lib().mpi_barrier() | ||
|
|
There was a problem hiding this comment.
Add error handling for MPI operations.
Consider adding error handling mechanisms to ensure robustness against MPI failures in the plot_timestep_time function.
| def single_patch_per_level_per_pop_from(hier, only_keep_L0=True): # dragons | ||
| for tidx in hier.times(): | ||
| if only_keep_L0: | ||
| hier.time_hier[tidx] = {0: hier.time_hier[tidx][0]} | ||
|
|
||
| patch_levels = hier.time_hier[tidx] | ||
|
|
||
| for level_idx in patch_levels.keys(): | ||
| patch_level = patch_levels[level_idx] | ||
|
|
||
| patch0 = patch_level.patches[0] | ||
| particles = {} # str:[] | ||
|
|
||
| for key in patch0.patch_datas.keys(): | ||
| if isinstance(patch0[key].dataset, Particles): | ||
| particles[key] = [] | ||
|
|
||
| for patch in patch_level.patches: | ||
| for patch_data_key in patch.patch_datas.keys(): | ||
| particles[key] += [patch[patch_data_key].dataset] | ||
|
|
||
| for key in particles.keys(): | ||
| patch0[key].dataset = aggregate(particles[key]) | ||
|
|
||
| patch_levels[level_idx].patches = [patch0] # just one patch | ||
|
|
||
| return hier |
There was a problem hiding this comment.
Handle empty patches in single_patch_per_level_per_pop_from.
The function single_patch_per_level_per_pop_from does not explicitly handle empty patches. Please add a check to handle empty patches to ensure the function works correctly in all scenarios.
| @@ -1,11 +1,13 @@ | |||
| #!/usr/bin/env python3 | |||
| import os | |||
| import numpy as np | |||
| from pathlib import Path | |||
There was a problem hiding this comment.
Consider removing unused import Path to clean up the code.
- from pathlib import PathCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| from pathlib import Path |
| def check_system_state_writes(**kwargs): | ||
| write_time = kwargs.get("system_state_write_every_t", 0) | ||
| if write_time > 0: | ||
| try: | ||
| import psutil | ||
| except ImportError as e: | ||
| raise ValueError( | ||
| "psutil is not available for writing system usage information" | ||
| ) | ||
| return write_time | ||
|
|
There was a problem hiding this comment.
Handle the import of psutil more gracefully and remove unused variable.
- import psutil
- except ImportError as e:
+ except ImportError:
+ psutil = NoneThis modification ensures that if psutil is not available, the function can still proceed without crashing, and it removes the unused variable e.
Committable suggestion was skipped due to low confidence.
Tools
Ruff
588-588:
psutilimported but unused; consider usingimportlib.util.find_specto test for availability (F401)
589-589: Local variable
eis assigned to but never used (F841)
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Actionable comments posted: 0
Outside diff range and nitpick comments (2)
tests/simulator/test_run.py (1)
Line range hint
60-60: Rename variableltolengthto avoid ambiguity with the number1.- def S(y, y0, l): + def S(y, y0, length):tools/config/config.py (1)
Line range hint
150-150: Remove the unused local variablempi_type.- mpi_type = "unknown"
Review details
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Files selected for processing (12)
- tests/diagnostic/CMakeLists.txt (1 hunks)
- tests/diagnostic/job_1d_1core.py (1 hunks)
- tests/diagnostic/job_1d_2core.py (1 hunks)
- tests/diagnostic/job_2d_1core.py (1 hunks)
- tests/diagnostic/job_2d_2core.py (1 hunks)
- tests/diagnostic/test-diagnostics_1d.cpp (1 hunks)
- tests/diagnostic/test-diagnostics_2d.cpp (1 hunks)
- tests/simulator/refinement/CMakeLists.txt (1 hunks)
- tests/simulator/refinement/test_2d_10_core.py (2 hunks)
- tests/simulator/test_diagnostic_timestamps.py (6 hunks)
- tests/simulator/test_run.py (6 hunks)
- tools/config/config.py (1 hunks)
Files skipped from review due to trivial changes (2)
- tests/diagnostic/job_2d_2core.py
- tests/simulator/refinement/CMakeLists.txt
Additional context used
Ruff
tests/simulator/refinement/test_2d_10_core.py
132-132: Module level import not at top of file (E402)
134-134: Module level import not at top of file (E402)
tests/simulator/test_diagnostic_timestamps.py
6-6: Module level import not at top of file (E402)
7-7: Module level import not at top of file (E402)
9-9: Module level import not at top of file (E402)
10-10: Module level import not at top of file (E402)
11-11: Module level import not at top of file (E402)
12-12: Module level import not at top of file (E402)
13-13: Module level import not at top of file (E402)
14-14: Module level import not at top of file (E402)
15-15: Module level import not at top of file (E402)
16-16: Module level import not at top of file (E402)
17-17: Module level import not at top of file (E402)
tests/simulator/test_run.py
60-60: Ambiguous variable name:
l(E741)tools/config/config.py
150-150: Local variable
mpi_typeis assigned to but never used (F841)
Additional comments not posted (8)
tests/diagnostic/job_1d_1core.py (1)
8-8: Change in output directory is appropriate for organizing diagnostic outputs.tests/diagnostic/job_2d_1core.py (1)
8-8: Change in output directory is consistent with the 2D diagnostic setup.tests/diagnostic/job_1d_2core.py (1)
8-8: Change in output directory is tailored for a 2-core setup, aligning with scaling tests or similar scenarios.tests/diagnostic/test-diagnostics_1d.cpp (1)
6-8: Dynamic configuration of job file and output directory based on the number of cores enhances test flexibility and robustness.tests/diagnostic/test-diagnostics_2d.cpp (1)
6-7: Ensure that the dynamically generatedjob_fileandout_dirare correctly handled in all contexts where they are used.Verification successful
The
job_fileandout_dirvariables are used in multiple test functions withintest-diagnostics_2d.cppandtest-diagnostics_1d.cpp. Specifically, they are used in the following functions intest-diagnostics_2d.cpp:
fluid_test(TypeParam{job_file}, out_dir);particles_test(TypeParam{job_file}, out_dir);electromag_test(TypeParam{job_file}, out_dir);allFromPython_test(TypeParam{job_file}, out_dir);These functions are expected to handle the dynamically generated
job_fileandout_dircorrectly. The same pattern is observed intest-diagnostics_1d.cpp.Based on the results, it appears that the variables are consistently used across the test functions. There are no indications of mishandling or incorrect usage.
tests/diagnostic/test-diagnostics_2d.cpp: fluid_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_2d.cpp: particles_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_2d.cpp: electromag_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_2d.cpp: allFromPython_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_1d.cpp: fluid_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_1d.cpp: particles_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_1d.cpp: electromag_test(TypeParam{job_file}, out_dir);
tests/diagnostic/test-diagnostics_1d.cpp: allFromPython_test(TypeParam{job_file}, out_dir);The review comment is verified, and the dynamically generated
job_fileandout_dirare correctly handled in all contexts where they are used.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `job_file` and `out_dir` are correctly handled. # Test: Search for usages of `job_file` and `out_dir`. Expect: Proper handling in all contexts. rg --type cpp $'job_file|out_dir'Length of output: 1336
tests/diagnostic/CMakeLists.txt (1)
5-8: Ensure that the conditional copying of Python files does not lead to missing dependencies during the build process.tests/simulator/refinement/test_2d_10_core.py (1)
200-200: Ensure that therefinement_boxesdictionary is correctly structured and used within the simulation configuration.Verification successful
The
refinement_boxesdictionary is used extensively throughout the codebase, particularly in various test files and simulation configurations. The structure and usage appear consistent with the intended design.
tests/simulator/refinement/test_2d_10_core.py: Therefinement_boxesdictionary is correctly structured and used within the simulation configuration.No issues were found with the structure or usage of
refinement_boxes.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the structure and usage of `refinement_boxes`. # Test: Search for usages of `refinement_boxes`. Expect: Correct structure and usage. rg --type python $'refinement_boxes'Length of output: 66
Script:
#!/bin/bash # Description: Verify the structure and usage of `refinement_boxes`. # Test: Search for usages of `refinement_boxes`. Expect: Correct structure and usage. rg 'refinement_boxes' --type pyLength of output: 16778
tests/simulator/test_diagnostic_timestamps.py (1)
17-17: Ensure that theSimulatorTestimport is correctly utilized in the test suite.Verification successful
The
SimulatorTestclass is correctly utilized in the test suite, as evidenced by its usage in multiple test files.
tests/simulator/test_diagnostic_timestamps.py:SimulatorTestis imported and used as a base class forDiagnosticsTest.Other files also show similar usage, confirming that the import is appropriate and consistent across the test suite.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `SimulatorTest`. # Test: Search for usages of `SimulatorTest`. Expect: Correct utilization in the test suite. rg --type python $'SimulatorTest'Length of output: 63
Script:
#!/bin/bash # Description: Verify the usage of `SimulatorTest`. # Test: Search for usages of `SimulatorTest`. Expect: Correct utilization in the test suite. rg 'SimulatorTest' --type pyLength of output: 1588
Tools
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17-17: Module level import not at top of file (E402)
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Files selected for processing (7)
- tests/diagnostic/CMakeLists.txt (2 hunks)
- tests/diagnostic/job_1d_1core.py (1 hunks)
- tests/diagnostic/job_1d_2core.py (1 hunks)
- tests/diagnostic/job_2d_1core.py (1 hunks)
- tests/diagnostic/job_2d_2core.py (1 hunks)
- tests/diagnostic/test-diagnostics_1d.cpp (1 hunks)
- tests/diagnostic/test-diagnostics_2d.cpp (1 hunks)
Files skipped from review as they are similar to previous changes (7)
- tests/diagnostic/CMakeLists.txt
- tests/diagnostic/job_1d_1core.py
- tests/diagnostic/job_1d_2core.py
- tests/diagnostic/job_2d_1core.py
- tests/diagnostic/job_2d_2core.py
- tests/diagnostic/test-diagnostics_1d.cpp
- tests/diagnostic/test-diagnostics_2d.cpp
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Files selected for processing (10)
- tests/diagnostic/CMakeLists.txt (2 hunks)
- tests/diagnostic/job_1d_1core.py (1 hunks)
- tests/diagnostic/job_1d_2core.py (1 hunks)
- tests/diagnostic/job_2d_1core.py (1 hunks)
- tests/diagnostic/job_2d_2core.py (1 hunks)
- tests/diagnostic/test-diagnostics_1d.cpp (1 hunks)
- tests/diagnostic/test-diagnostics_2d.cpp (1 hunks)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tools/config/config.py (1 hunks)
Files skipped from review as they are similar to previous changes (9)
- tests/diagnostic/CMakeLists.txt
- tests/diagnostic/job_1d_1core.py
- tests/diagnostic/job_1d_2core.py
- tests/diagnostic/job_2d_1core.py
- tests/diagnostic/job_2d_2core.py
- tests/diagnostic/test-diagnostics_1d.cpp
- tests/diagnostic/test-diagnostics_2d.cpp
- tests/functional/alfven_wave/CMakeLists.txt
- tests/functional/harris/CMakeLists.txt
Additional context used
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tools/config/config.py
150-150: Local variable
mpi_typeis assigned to but never used (F841)
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Outside diff range and nitpick comments (8)
tests/functional/td/td1d.py (1)
Line range hint
41-41: Ambiguous variable name:l.Consider renaming
ltolengthor another descriptive name to improve code readability.tests/functional/dispersion/dispersion.py (1)
Line range hint
7-7: Unused import:matplotlib.pyplot.Consider removing the unused import to clean up the code.
tests/functional/shock/shock.py (1)
Line range hint
49-49: Ambiguous variable name:l.Consider renaming
ltolengthor another descriptive name to improve code readability.tests/functional/translation/translat1d.py (1)
Line range hint
131-131: Ambiguous variable namelused in the functionS. Consider renaming it to something more descriptive to improve code readability.tests/functional/harris/harris_2d.py (1)
Line range hint
67-67: Ambiguous variable namelused in the functionS. Consider renaming it to something more descriptive to improve code readability.tests/simulator/test_run.py (1)
Line range hint
60-60: Consider renaming the variablelto something more descriptive to avoid ambiguity.tests/functional/ionIonBeam/ion_ion_beam1d.py (1)
Line range hint
8-8: Remove unused imports to clean up the code.- from tests.diagnostic import all_timestamps - from pyphare.pharesee.plotting import plotting - from pathlib import PathAlso applies to: 15-15, 16-16
tests/functional/conservation/conserv.py (1)
Line range hint
8-8: Remove the unused import to clean up the code.- import os
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Files selected for processing (31)
- res/cmake/dep/phlop.cmake (1 hunks)
- tests/diagnostic/CMakeLists.txt (2 hunks)
- tests/diagnostic/job_1d_1core.py (1 hunks)
- tests/diagnostic/job_1d_2core.py (1 hunks)
- tests/diagnostic/job_2d_1core.py (1 hunks)
- tests/diagnostic/job_2d_2core.py (1 hunks)
- tests/diagnostic/test-diagnostics_1d.cpp (1 hunks)
- tests/diagnostic/test-diagnostics_2d.cpp (1 hunks)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/alfven_wave/alfven_wave1d.py (1 hunks)
- tests/functional/conservation/CMakeLists.txt (1 hunks)
- tests/functional/conservation/conserv.py (1 hunks)
- tests/functional/dispersion/CMakeLists.txt (1 hunks)
- tests/functional/dispersion/dispersion.py (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
- tests/functional/ionIonBeam/CMakeLists.txt (1 hunks)
- tests/functional/ionIonBeam/ion_ion_beam1d.py (1 hunks)
- tests/functional/shock/CMakeLists.txt (1 hunks)
- tests/functional/shock/shock.py (1 hunks)
- tests/functional/td/td1d.py (1 hunks)
- tests/functional/tdtagged/CMakeLists.txt (1 hunks)
- tests/functional/translation/CMakeLists.txt (1 hunks)
- tests/functional/translation/translat1d.py (1 hunks)
- tests/simulator/CMakeLists.txt (1 hunks)
- tests/simulator/refinement/CMakeLists.txt (1 hunks)
- tests/simulator/refinement/test_2d_10_core.py (2 hunks)
- tests/simulator/test_diagnostic_timestamps.py (6 hunks)
- tests/simulator/test_run.py (6 hunks)
- tools/config/config.py (1 hunks)
- tools/python3/plotting.py (1 hunks)
Files skipped from review due to trivial changes (1)
- tests/functional/shock/CMakeLists.txt
Files skipped from review as they are similar to previous changes (18)
- res/cmake/dep/phlop.cmake
- tests/diagnostic/CMakeLists.txt
- tests/diagnostic/job_1d_1core.py
- tests/diagnostic/job_1d_2core.py
- tests/diagnostic/job_2d_1core.py
- tests/diagnostic/job_2d_2core.py
- tests/diagnostic/test-diagnostics_1d.cpp
- tests/diagnostic/test-diagnostics_2d.cpp
- tests/functional/alfven_wave/CMakeLists.txt
- tests/functional/alfven_wave/alfven_wave1d.py
- tests/functional/conservation/CMakeLists.txt
- tests/functional/dispersion/CMakeLists.txt
- tests/functional/harris/CMakeLists.txt
- tests/functional/ionIonBeam/CMakeLists.txt
- tests/functional/tdtagged/CMakeLists.txt
- tests/functional/translation/CMakeLists.txt
- tests/simulator/CMakeLists.txt
- tests/simulator/refinement/CMakeLists.txt
Additional context used
Ruff
tests/functional/td/td1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
41-41: Ambiguous variable name:
l(E741)tests/functional/dispersion/dispersion.py
7-7:
matplotlib.pyplotimported but unused (F401)tests/functional/shock/shock.py
49-49: Ambiguous variable name:
l(E741)tests/simulator/refinement/test_2d_10_core.py
132-132: Module level import not at top of file (E402)
134-134: Module level import not at top of file (E402)
tests/functional/translation/translat1d.py
7-7:
matplotlib.pyplotimported but unused (F401)
131-131: Ambiguous variable name:
l(E741)tests/functional/harris/harris_2d.py
67-67: Ambiguous variable name:
l(E741)tests/simulator/test_diagnostic_timestamps.py
6-6: Module level import not at top of file (E402)
7-7: Module level import not at top of file (E402)
9-9: Module level import not at top of file (E402)
10-10: Module level import not at top of file (E402)
11-11: Module level import not at top of file (E402)
12-12: Module level import not at top of file (E402)
13-13: Module level import not at top of file (E402)
14-14: Module level import not at top of file (E402)
15-15: Module level import not at top of file (E402)
16-16: Module level import not at top of file (E402)
17-17: Module level import not at top of file (E402)
tests/simulator/test_run.py
60-60: Ambiguous variable name:
l(E741)tests/functional/ionIonBeam/ion_ion_beam1d.py
8-8:
tests.diagnostic.all_timestampsimported but unused (F401)
15-15:
pyphare.pharesee.plottingimported but unused (F401)
16-16:
pathlib.Pathimported but unused (F401)tools/config/config.py
150-150: Local variable
mpi_typeis assigned to but never used (F841)tests/functional/conservation/conserv.py
8-8:
osimported but unused (F401)
Additional comments not posted (5)
tools/python3/plotting.py (1)
18-26: Improved exception handling inplot_run_timer_data.Consider adding more specific logging details for each exception type to aid in debugging.
tests/simulator/refinement/test_2d_10_core.py (1)
200-200: Addedrefinement_boxesto the simulation configuration. Ensure that the specified refinement boxes are appropriate for the simulation's domain and resolution requirements.tests/simulator/test_run.py (2)
186-186: The plotting functionality appears to be correctly implemented.
206-209: The file existence and size check are implemented correctly.tools/config/config.py (1)
247-247: Remove the unused local variablempi_typeas it is assigned but never used.- mpi_type = deduce_mpi_type_from(mpi_results["MPI_Get_library_version"])Likely invalid or redundant comment.
| # smallest_patch_size=20, | ||
| # largest_patch_size=20, |
There was a problem hiding this comment.
Commented-out patch size settings.
Consider removing or explaining these commented-out lines to maintain code clarity.
| # smallest_patch_size=10, | ||
| # largest_patch_size=20, |
There was a problem hiding this comment.
The commented-out parameters for smallest_patch_size, largest_patch_size, and boundary_types are removed. If these are intentional and permanent removals, consider cleaning up by removing these commented lines to avoid confusion.
| # smallest_patch_size=20, | ||
| # largest_patch_size=20, |
There was a problem hiding this comment.
The commented-out parameters for smallest_patch_size and largest_patch_size are removed. If these are intentional and permanent removals, consider cleaning up by removing these commented lines to avoid confusion.
| time_step=time_step, | ||
| # boundary_types="periodic", | ||
| cells=(200, 400), | ||
| dl=(0.2, 0.2), | ||
| cells=(400, 400), |
There was a problem hiding this comment.
The hardcoded cell size (400, 400) might not be flexible for different simulation scenarios. Consider making this configurable.
- cells=(400, 400),
+ cells=configurable_cells, # Ensure `configurable_cells` is defined and validated elsewhereCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cells=(400, 400), | |
| cells=configurable_cells, # Ensure `configurable_cells` is defined and validated elsewhere |
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Actionable comments posted: 11
Outside diff range and nitpick comments (20)
tests/simulator/CMakeLists.txt (1)
27-27: Add a comment explaining why thephare_mpi_python3_execfor load balancing is not applicable in serial mode.tests/functional/td/td1d.py (2)
21-22: Remove or clarify the commented-out patch size settings to enhance code clarity and maintainability.
Line range hint
41-41: Replace ambiguous variable name 'l' with a more descriptive name to improve code readability and avoid potential confusion with the number '1'.- def S(x, x0, l): + def S(x, x0, length):tests/functional/dispersion/dispersion.py (1)
Line range hint
7-7: Remove the unused importmatplotlib.pyplotto clean up the code and adhere to best practices.- import matplotlib.pyplot as plttests/functional/shock/shock.py (3)
Line range hint
39-39: Convert to f-string for consistency and modern Python practices.- "options": {"dir": "shock_{}".format(interp_order), "mode": "overwrite"}, + "options": {"dir": f"shock_{interp_order}", "mode": "overwrite"},
Line range hint
49-49: Consider renaming the variableltolengthto avoid ambiguity with the number1.- def S(x, x0, l): + def S(x, x0, length):
Line range hint
138-138: Convert to f-string for consistency and modern Python practices across multiple lines.- "ffmpeg -r 10 -y -pattern_type glob -i 'shock_{}/shock_By_{}_*.png' -c:v libx264 -crf 0 shock_interp{}.mp4".format( - interp_order, interp_order, interp_order + f"ffmpeg -r 10 -y -pattern_type glob -i 'shock_{interp_order}/shock_By_{interp_order}_*.png' -c:v libx264 -crf 0 shock_interp{interp_order}.mp4"Also applies to: 142-142, 150-152, 156-158, 178-178
tests/simulator/refinement/test_2d_10_core.py (4)
Line range hint
21-21: Avoid using mutable default arguments for function parameters to prevent unexpected behavior.- def config(diag_outputs, model_init={}, refinement_boxes=None): + def config(diag_outputs, model_init=None, refinement_boxes=None): + if model_init is None: + model_init = {}
Line range hint
120-120: Convert to f-string for consistency and modern Python practices.- time = "{:.10f}".format(time) + time = f"{time:.10f}"
Line range hint
142-142: Avoid using mutable default arguments for function parameters to prevent unexpected behavior.- def make_fig(hier, fig_name, ilvl, extra_collections=[]): + def make_fig(hier, fig_name, ilvl, extra_collections=None): + if extra_collections is None: + extra_collections = []
Line range hint
166-166: Rename unused loop control variable to underscore to indicate it's intentionally unused.- for ilvl, lvl in hier.levels().items(): + for _ilvl, lvl in hier.levels().items():tests/functional/alfven_wave/alfven_wave1d.py (1)
Line range hint
188-188: Convert to f-string for consistency and modern Python practices.- ax.set_title(r"$V_\phi = {:6.4f}$".format(vphi.mean())) + ax.set_title(rf"$V_\phi = {vphi.mean():6.4f}$")tests/functional/translation/translat1d.py (2)
Line range hint
7-7: Remove unused import to clean up the code.- import matplotlib.pyplot as plt
Line range hint
131-131: Consider renaming the variableltolengthto avoid ambiguity with the number1.- def S(x, x0, l): + def S(x, x0, length):tests/simulator/test_run.py (2)
Line range hint
214-214: Usesuper()instead ofsuper(RunTest, self)for simplicity and modern Python style.- super(RunTest, self).__init__(*args, **kwargs) + super().__init__(*args, **kwargs)- super(RunTest, self).tearDown() + super().tearDown()Also applies to: 218-218
Line range hint
60-60: Ambiguous variable name:l. Consider renaming it tolengthfor clarity.- def S(y, y0, l): + def S(y, y0, length):tests/functional/ionIonBeam/ion_ion_beam1d.py (1)
26-27: Ensure that the commented outsmallest_patch_sizeandlargest_patch_sizeare intentionally left out or should be removed if not needed.tools/config/config.py (1)
Line range hint
262-262: Rename the unused loop control variablekto_kto indicate it is intentionally unused.- for k, v in GENERATED_CONFIGS.items(): + for _k, v in GENERATED_CONFIGS.items():tests/functional/conservation/conserv.py (2)
Line range hint
34-34: Convert theformatcall to an f-string for improved readability and performance.- "options": {"dir": "vth{}dx{}".format(vth, dl), "mode": "overwrite"}, + "options": {"dir": f"vth{vth}dx{dl}", "mode": "overwrite"},
Line range hint
137-137: Rename the unused loop control variableipto_ipto indicate it is intentionally unused.- for ip, patch in enumerate(lvl.patches): + for _ip, patch in enumerate(lvl.patches):Also applies to: 157-157
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (32)
- res/cmake/dep/phlop.cmake (1 hunks)
- tests/diagnostic/CMakeLists.txt (2 hunks)
- tests/diagnostic/job_1d_1core.py (1 hunks)
- tests/diagnostic/job_1d_2core.py (1 hunks)
- tests/diagnostic/job_2d_1core.py (1 hunks)
- tests/diagnostic/job_2d_2core.py (1 hunks)
- tests/diagnostic/test-diagnostics_1d.cpp (1 hunks)
- tests/diagnostic/test-diagnostics_2d.cpp (1 hunks)
- tests/functional/alfven_wave/CMakeLists.txt (1 hunks)
- tests/functional/alfven_wave/alfven_wave1d.py (1 hunks)
- tests/functional/conservation/CMakeLists.txt (1 hunks)
- tests/functional/conservation/conserv.py (1 hunks)
- tests/functional/dispersion/CMakeLists.txt (1 hunks)
- tests/functional/dispersion/dispersion.py (1 hunks)
- tests/functional/harris/CMakeLists.txt (1 hunks)
- tests/functional/harris/harris_2d.py (4 hunks)
- tests/functional/harris/harris_2d_lb.py (1 hunks)
- tests/functional/ionIonBeam/CMakeLists.txt (1 hunks)
- tests/functional/ionIonBeam/ion_ion_beam1d.py (1 hunks)
- tests/functional/shock/CMakeLists.txt (1 hunks)
- tests/functional/shock/shock.py (1 hunks)
- tests/functional/td/td1d.py (1 hunks)
- tests/functional/tdtagged/CMakeLists.txt (1 hunks)
- tests/functional/translation/CMakeLists.txt (1 hunks)
- tests/functional/translation/translat1d.py (1 hunks)
- tests/simulator/CMakeLists.txt (1 hunks)
- tests/simulator/refinement/CMakeLists.txt (1 hunks)
- tests/simulator/refinement/test_2d_10_core.py (2 hunks)
- tests/simulator/test_diagnostic_timestamps.py (6 hunks)
- tests/simulator/test_run.py (6 hunks)
- tools/config/config.py (1 hunks)
- tools/python3/plotting.py (1 hunks)
Files not summarized due to errors (9)
- tests/diagnostic/job_2d_1core.py: Error: Server error. Please try again later.
- tests/functional/td/td1d.py: Error: Server error. Please try again later.
- tests/functional/shock/CMakeLists.txt: Error: Server error. Please try again later.
- tests/simulator/refinement/test_2d_10_core.py: Error: Server error. Please try again later.
- tests/simulator/CMakeLists.txt: Error: Server error. Please try again later.
- tools/config/config.py: Error: Server error. Please try again later.
- res/cmake/dep/phlop.cmake: Error: Server error. Please try again later.
- tests/diagnostic/CMakeLists.txt: Error: Server error. Please try again later.
- tests/functional/shock/shock.py: Error: Server error. Please try again later.
Files skipped from review as they are similar to previous changes (13)
- tests/diagnostic/job_1d_1core.py
- tests/diagnostic/job_1d_2core.py
- tests/diagnostic/job_2d_2core.py
- tests/diagnostic/test-diagnostics_1d.cpp
- tests/diagnostic/test-diagnostics_2d.cpp
- tests/functional/alfven_wave/CMakeLists.txt
- tests/functional/conservation/CMakeLists.txt
- tests/functional/dispersion/CMakeLists.txt
- tests/functional/harris/CMakeLists.txt
- tests/functional/ionIonBeam/CMakeLists.txt
- tests/functional/tdtagged/CMakeLists.txt
- tests/functional/translation/CMakeLists.txt
- tests/simulator/refinement/CMakeLists.txt
Additional context used
Ruff
tools/python3/plotting.py
18-18:
tools.python3.phlopingimported but unused; consider usingimportlib.util.find_specto test for availability (F401)tests/functional/td/td1d.py
7-7:
matplotlib.pyplotimported but unused (F401)Remove unused import:
matplotlib.pyplot
41-41: Ambiguous variable name:
l(E741)tests/functional/dispersion/dispersion.py
7-7:
matplotlib.pyplotimported but unused (F401)Remove unused import:
matplotlib.pyplottests/functional/shock/shock.py
39-39: Use f-string instead of
formatcall (UP032)Convert to f-string
49-49: Ambiguous variable name:
l(E741)
138-138: Use f-string instead of
formatcall (UP032)Convert to f-string
142-142: Use f-string instead of
formatcall (UP032)Convert to f-string
150-152: Use f-string instead of
formatcall (UP032)Convert to f-string
156-158: Use f-string instead of
formatcall (UP032)Convert to f-string
178-178: Use f-string instead of
formatcall (UP032)Convert to f-string
tests/simulator/refinement/test_2d_10_core.py
21-21: Do not use mutable data structures for argument defaults (B006)
Replace with
None; initialize within function
120-120: Use f-string instead of
formatcall (UP032)Convert to f-string
132-132: Module level import not at top of file (E402)
134-134: Module level import not at top of file (E402)
142-142: Do not use mutable data structures for argument defaults (B006)
Replace with
None; initialize within function
166-166: Loop control variable
ilvlnot used within loop body (B007)Rename unused
ilvlto_ilvltests/functional/alfven_wave/alfven_wave1d.py
188-188: Use f-string instead of
formatcall (UP032)Convert to f-string
tests/functional/translation/translat1d.py
7-7:
matplotlib.pyplotimported but unused (F401)Remove unused import:
matplotlib.pyplot
131-131: Ambiguous variable name:
l(E741)tests/functional/harris/harris_2d.py
67-67: Ambiguous variable name:
l(E741)tests/simulator/test_diagnostic_timestamps.py
6-6: Module level import not at top of file (E402)
7-7: Module level import not at top of file (E402)
9-9: Module level import not at top of file (E402)
10-10: Module level import not at top of file (E402)
11-11: Module level import not at top of file (E402)
12-12: Module level import not at top of file (E402)
13-13: Module level import not at top of file (E402)
14-14: Module level import not at top of file (E402)
15-15: Module level import not at top of file (E402)
16-16: Module level import not at top of file (E402)
17-17: Module level import not at top of file (E402)
87-87: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameters
104-104: Use f-string instead of
formatcall (UP032)Convert to f-string
131-131: Use f-string instead of
formatcall (UP032)Convert to f-string
133-133: Loop control variable
diagnamenot used within loop body (B007)Rename unused
diagnameto_diagname
178-178: Loop control variable
diagnamenot used within loop body (B007)Rename unused
diagnameto_diagnametests/simulator/test_run.py
60-60: Ambiguous variable name:
l(E741)
214-214: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameters
218-218: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameterstests/functional/harris/harris_2d_lb.py
77-77: Ambiguous variable name:
l(E741)
191-191: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameters
195-195: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameterstests/functional/ionIonBeam/ion_ion_beam1d.py
8-8:
tests.diagnostic.all_timestampsimported but unused (F401)Remove unused import:
tests.diagnostic.all_timestamps
15-15:
pyphare.pharesee.plottingimported but unused (F401)Remove unused import:
pyphare.pharesee.plotting
16-16:
pathlib.Pathimported but unused (F401)Remove unused import:
pathlib.Path
209-211: Use f-string instead of
formatcall (UP032)Convert to f-string
247-247: Use f-string instead of
formatcall (UP032)Convert to f-string
tools/config/config.py
150-150: Local variable
mpi_typeis assigned to but never used (F841)Remove assignment to unused variable
mpi_type
262-262: Loop control variable
knot used within loop body (B007)Rename unused
kto_ktests/functional/conservation/conserv.py
8-8:
osimported but unused (F401)Remove unused import:
os
34-34: Use f-string instead of
formatcall (UP032)Convert to f-string
137-137: Loop control variable
ipnot used within loop body (B007)Rename unused
ipto_ip
157-157: Loop control variable
ipnot used within loop body (B007)Rename unused
ipto_ip
Additional comments not posted (11)
tests/functional/shock/CMakeLists.txt (1)
10-13: The condition checks for both HighFive and testMPI, which is appropriate for the required diagnostics. Consider adding a comment to explain why both of these dependencies are necessary for these tests.tests/diagnostic/job_2d_1core.py (1)
8-8: Ensure the output directory exists or is created before running the simulation to avoid runtime errors.res/cmake/dep/phlop.cmake (1)
2-7: Clear instructions are provided for enabling phlop. Consider adding a brief description of what phlop does or why it might be beneficial to enable it, to help future developers make informed decisions.tests/diagnostic/CMakeLists.txt (1)
5-8: The copying of Python files is essential for ensuring that the tests have access to the necessary scripts. Ensure that this step is well-documented in the project's README or developer documentation to clarify its importance.tests/simulator/CMakeLists.txt (1)
30-30: Ensure that the diagnostic timestamps test is adequately covered by unit tests, especially given its importance highlighted by the added specific version.Verification successful
The search results indicate that there are indeed test functions related to
test_diagnostic_timestamps.py, specificallytest_dump_diags_timestampsandtest_hierarchy_timestamp_cadence.
tests/simulator/test_diagnostic_timestamps.py: def test_dump_diags_timestamps(self)tests/simulator/test_diagnostic_timestamps.py: def test_hierarchy_timestamp_cadence(self, refinement_boxes)These functions suggest that the diagnostic timestamps are being tested, addressing the concern about adequate coverage.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify unit test coverage for `test_diagnostic_timestamps.py`. # Test: Search for unit tests covering this file. Expect: At least one test case. rg --type python $'test_diagnostic_timestamps.py' tests/Length of output: 86
Script:
#!/bin/bash # Description: Verify unit test coverage for `test_diagnostic_timestamps.py`. # Test: Search for unit tests covering this file. Expect: At least one test case. rg 'test_diagnostic_timestamps' tests/Length of output: 179
Script:
#!/bin/bash # Description: Search for Python test functions that might indirectly cover `test_diagnostic_timestamps.py`. # Test: Search for test functions in the `tests/` directory. rg -t py 'def test_' tests/Length of output: 7025
tools/python3/plotting.py (1)
17-29: Refactor the exception handling to avoid redundancy and improve clarity. Consider merging the two separateexceptblocks into a single one with enhanced logging that differentiates the exceptions based on their type.
[REFACTOR_Suggestion]- except (ImportError, FileNotFoundError) as e: - if rank == 0: - logger.info( - f"Phlop timings are not active, see: res/cmake/dep/phlop.cmake`: \n{e}" - ) - except Exception as e: - if rank == 0: - logger.error(f"Unknown exception handled during timer plotting: {e}") + except Exception as e: + if rank == 0: + if isinstance(e, (ImportError, FileNotFoundError)): + logger.info(f"Phlop timings are not active, see: res/cmake/dep/phlop.cmake`: \n{e}") + else: + logger.error(f"Unknown exception handled during timer plotting: {e}")Tools
Ruff
18-18:
tools.python3.phlopingimported but unused; consider usingimportlib.util.find_specto test for availability (F401)tests/simulator/refinement/test_2d_10_core.py (1)
25-26: Remove commented-out code for clarity unless there's a specific reason to keep it.tests/functional/translation/translat1d.py (1)
23-24: Remove commented-out code for clarity unless there's a specific reason to keep it.tests/functional/harris/harris_2d.py (2)
46-46: The hardcoded cell size(400, 400)might not be flexible for different simulation scenarios. Consider making this configurable.- cells=(400, 400), + cells=configurable_cells, # Ensure `configurable_cells` is defined and validated elsewhereLikely invalid or redundant comment.
4-4: Consider removing the unused importPathto clean up the code.- from pathlib import PathLikely invalid or redundant comment.
tests/functional/ionIonBeam/ion_ion_beam1d.py (1)
Line range hint
209-211: Replaceformatcalls with f-strings for better readability and performance.
[REFACTOR_SUGGESTion]- "dir": "vth{}dx{}".format(vth, dl) + "dir": f"vth{vth}dx{dl}"- title="t = {:.1f}".format(t) + title=f"t = {t:.1f}"Also applies to: 247-247
| # smallest_patch_size=20, | ||
| # largest_patch_size=20, |
There was a problem hiding this comment.
Consider removing commented-out code to improve code cleanliness.
- # smallest_patch_size=20,
- # largest_patch_size=20,Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # smallest_patch_size=20, | |
| # largest_patch_size=20, |
|
|
||
| def plot_run_timer_data(diag_dir=None, rank=0): | ||
| try: | ||
| import tools.python3.phloping as phloping # check if available |
There was a problem hiding this comment.
Consider using importlib.util.find_spec instead of importing tools.python3.phloping directly to check for its availability, as suggested by static analysis.
- import tools.python3.phloping as phloping # check if available
+ from importlib import util
+ phloping_spec = util.find_spec("tools.python3.phloping")
+ if phloping_spec is None:
+ logger.info("Phlop timings module not available.")
+ else:
+ import tools.python3.phloping as phlopingCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| import tools.python3.phloping as phloping # check if available | |
| from importlib import util | |
| phloping_spec = util.find_spec("tools.python3.phloping") | |
| if phloping_spec is None: | |
| logger.info("Phlop timings module not available.") | |
| else: | |
| import tools.python3.phloping as phloping |
Tools
Ruff
18-18:
tools.python3.phlopingimported but unused; consider usingimportlib.util.find_specto test for availability (F401)
| # smallest_patch_size=50, | ||
| # largest_patch_size=50, |
There was a problem hiding this comment.
Consider removing commented-out code to improve code cleanliness.
- # smallest_patch_size=50,
- # largest_patch_size=50,Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # smallest_patch_size=50, | |
| # largest_patch_size=50, |
| @@ -244,7 +244,7 @@ def write_local_cmake_file(mpi_results): | |||
| if mpi_type == "OMPI": | |||
| # work around for https://github.com/open-mpi/ompi/issues/10761#issuecomment-1236909802 | |||
| file.write( | |||
| """set (PHARE_MPIRUN_POSTFIX "${PHARE_MPIRUN_POSTFIX} -q --bind-to none") | |||
| """set (PHARE_MPIRUN_POSTFIX "${PHARE_MPIRUN_POSTFIX} --bind-to none ") | |||
There was a problem hiding this comment.
Remove the unused local variable mpi_type as it is assigned but never used.
- mpi_type = deduce_mpi_type_from(mpi_results["MPI_Get_library_version"])Committable suggestion was skipped due to low confidence.
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| def plot(diag_dir): | ||
| run = Run(diag_dir) |
There was a problem hiding this comment.
Multiple undefined names such as Run and plot_file_for_qty are used. These need to be defined or imported to avoid runtime errors.
+ from pyphare.pharesee.run import Run
+ def plot_file_for_qty(qty, time):
+ return f"some_directory/{qty}_{time}.png"Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| run = Run(diag_dir) | |
| from pyphare.pharesee.run import Run | |
| def plot_file_for_qty(qty, time): | |
| return f"some_directory/{qty}_{time}.png" | |
| run = Run(diag_dir) |
| @@ -102,6 +103,11 @@ | |||
| def test_dump_diags_timestamps(self): | |||
| print("test_dump_diags dim/interp:{}/{}".format(1, 1)) | |||
There was a problem hiding this comment.
Use f-string instead of format call for better readability and performance.
- print("test_dump_diags dim/interp:{}/{}".format(1, 1))
+ print(f"test_dump_diags dim/interp:{1}/{1}")- return "{:.10f}".format(stamp)
+ return f"{stamp:.10f}"Also applies to: 131-131
Tools
Ruff
104-104: Use f-string instead of
formatcall (UP032)Convert to f-string
| @@ -125,7 +131,7 @@ | |||
| return "{:.10f}".format(stamp) | |||
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| for diagname, diagInfo in ph.global_vars.sim.diagnostics.items(): | |||
There was a problem hiding this comment.
Loop control variable diagname not used within loop body. Consider renaming it to _ if it's intentionally unused.
- for diagname, diagInfo in ph.global_vars.sim.diagnostics.items():
+ for _, diagInfo in ph.global_vars.sim.diagnostics.items():Also applies to: 178-178
Tools
Ruff
133-133: Loop control variable
diagnamenot used within loop body (B007)Rename unused
diagnameto_diagname
| @@ -81,7 +82,7 @@ | |||
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| @ddt | |||
| class DiagnosticsTest(unittest.TestCase): | |||
| class DiagnosticsTest(SimulatorTest): | |||
| def __init__(self, *args, **kwargs): | |||
| super(DiagnosticsTest, self).__init__(*args, **kwargs) | |||
There was a problem hiding this comment.
Use super() instead of super(DiagnosticsTest, self) for simplicity and modern Python style.
- super(DiagnosticsTest, self).__init__(*args, **kwargs)
+ super().__init__(*args, **kwargs)Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| super(DiagnosticsTest, self).__init__(*args, **kwargs) | |
| super().__init__(*args, **kwargs) |
Tools
Ruff
87-87: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameters
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| class HarrisTest(SimulatorTest): | ||
| def __init__(self, *args, **kwargs): | ||
| super(HarrisTest, self).__init__(*args, **kwargs) |
There was a problem hiding this comment.
Use super() instead of super(HarrisTest, self) for simplicity and modern Python style.
- super(HarrisTest, self).__init__(*args, **kwargs)
+ super().__init__(*args, **kwargs)- super(HarrisTest, self).tearDown()
+ super().tearDown()Also applies to: 195-195
Tools
Ruff
191-191: Use
super()instead ofsuper(__class__, self)(UP008)Remove
__super__parameters
| + 1.0 / np.cosh((y - Ly * 0.7) / L) ** 2 | ||
| ) | ||
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| def S(y, y0, l): |
There was a problem hiding this comment.
The variable name l is ambiguous and could be confused with the number 1. Consider renaming it for clarity.
- def S(y, y0, l):
+ def S(y, y0, length):Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def S(y, y0, l): | |
| def S(y, y0, length): |
Tools
Ruff
77-77: Ambiguous variable name:
l(E741)
Summary by CodeRabbit
New Features
LoadBalancerclass for simulations.Bug Fixes
Refactor
${Python_EXECUTABLE}for consistency.Documentation
Chores
psutilpackage torequirements.txtfor system state monitoring.