remove compute_timestamps #866
Conversation
WalkthroughWalkthroughThe recent changes primarily focus on simplifying the diagnostics handling in the codebase by removing the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Diagnostics
participant FluidDiagnostics
participant ElectromagDiagnostics
User->>Diagnostics: Request diagnostics
Diagnostics->>FluidDiagnostics: Instantiate with quantity, write_timestamps
Diagnostics->>ElectromagDiagnostics: Instantiate with quantity, write_timestamps
FluidDiagnostics->>Diagnostics: Return diagnostics data
ElectromagDiagnostics->>Diagnostics: Return diagnostics data
Diagnostics->>User: Deliver diagnostics results
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (3)
tests/functional/td/td1d.py (1)
104-106: Verify the removal ofcompute_timestampsfromFluidDiagnostics.The
compute_timestampsparameter is still present in multiple parts of the codebase, includingpyphare/pyphare/pharein/diagnostics.py, where theFluidDiagnosticsclass is defined. This indicates that the parameter has not been fully removed.
pyphare/pyphare/pharein/diagnostics.py: Contains multiple references tocompute_timestamps.Please ensure that all references to
compute_timestampsare removed from the codebase to avoid potential issues.Analysis chain
Verify the removal of
compute_timestampsfromFluidDiagnostics.Ensure that the removal of the
compute_timestampsparameter does not affect the functionality ofFluidDiagnostics.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `FluidDiagnostics`. # Test: Search for the function definition of `FluidDiagnostics` and check for the `compute_timestamps` parameter. rg --type python 'def FluidDiagnostics' -A 5Length of output: 77
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `FluidDiagnostics`. # Test: Search for the function definition of `FluidDiagnostics` and check for the `compute_timestamps` parameter. rg 'def FluidDiagnostics' -A 10 # Test: Search for any references to `compute_timestamps` in the codebase. rg 'compute_timestamps'Length of output: 878
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `FluidDiagnostics`. # Test: Search for the class definition of `FluidDiagnostics` and check for the `compute_timestamps` parameter. rg 'class FluidDiagnostics' -A 10 # Test: Search for any references to `FluidDiagnostics` in non-Python files to determine its type. rg 'FluidDiagnostics'Length of output: 6658
tests/simulator/test_advance.py (2)
153-153: Issue with the removal ofcompute_timestampsparameterThe
compute_timestampsparameter is still used within theElectromagDiagnosticsclass. Removing it from the instantiation may lead to functional issues.
pyphare/pyphare/pharein/diagnostics.py: Thecompute_timestampsparameter is assigned the value ofwrite_timestampsand is used multiple times within the class.Analysis chain
Ensure correctness of the
ElectromagDiagnosticsinstantiation.The
compute_timestampsparameter is removed. Ensure that this change does not affect the functionality.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the instantiation of `ElectromagDiagnostics` without `compute_timestamps`. # Test: Search for the `ElectromagDiagnostics` class definition to ensure `compute_timestamps` is not required. rg --type python -A 5 'class ElectromagDiagnostics'Length of output: 84
Script:
#!/bin/bash # Description: Verify the instantiation of `ElectromagDiagnostics` without `compute_timestamps`. # Test: Search for the `ElectromagDiagnostics` class definition to ensure `compute_timestamps` is not required. rg -A 5 'class ElectromagDiagnostics'Length of output: 458
Script:
#!/bin/bash # Description: Verify if `compute_timestamps` is used within the `ElectromagDiagnostics` class. # Test: Search for the usage of `compute_timestamps` within the `ElectromagDiagnostics` class. rg 'compute_timestamps' pyphare/pyphare/pharein/diagnostics.pyLength of output: 354
167-167: Ensure correctness of theParticleDiagnosticsinstantiation.The
compute_timestampsparameter is still used within thediagnostics.pyfile. Its removal from the instantiation ofParticleDiagnosticscould affect functionality. Please review the usage ofcompute_timestampsto ensure that this change does not cause any issues.
pyphare/pyphare/pharein/diagnostics.pyAnalysis chain
Ensure correctness of the
ParticleDiagnosticsinstantiation.The
compute_timestampsparameter is removed. Ensure that this change does not affect the functionality.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the instantiation of `ParticleDiagnostics` without `compute_timestamps`. # Test: Search for the `ParticleDiagnostics` class definition to ensure `compute_timestamps` is not required. rg --type python -A 5 'class ParticleDiagnostics'Length of output: 82
Script:
#!/bin/bash # Description: Verify the instantiation of `ParticleDiagnostics` without `compute_timestamps`. # Test: Search for the `ParticleDiagnostics` class definition to ensure `compute_timestamps` is not required. ast-grep --lang python --pattern $'class ParticleDiagnostics($_, $_):\n def __init__($_):\n $$$'Length of output: 105
Script:
#!/bin/bash # Description: Verify the instantiation of `ParticleDiagnostics` without `compute_timestamps`. # Test: Search for the `ParticleDiagnostics` class definition to ensure `compute_timestamps` is not required. rg 'class ParticleDiagnostics'Length of output: 111
Script:
#!/bin/bash # Description: Verify the instantiation of `ParticleDiagnostics` without `compute_timestamps`. # Test: Search for the `__init__` method of the `ParticleDiagnostics` class to ensure `compute_timestamps` is not required. rg -A 10 'class ParticleDiagnostics' pyphare/pyphare/pharein/diagnostics.pyLength of output: 453
Script:
#!/bin/bash # Description: Verify the instantiation of `ParticleDiagnostics` without `compute_timestamps`. # Test: Search for the usage of `compute_timestamps` within the `ParticleDiagnostics` class and its parent class `Diagnostics`. rg 'compute_timestamps' pyphare/pyphare/pharein/diagnostics.pyLength of output: 354
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (19)
- pyphare/pyphare/pharein/diagnostics.py (2 hunks)
- pyphare/pyphare_tests/test_pharesee/test_hierarchy.py (1 hunks)
- src/phare/phare_init.py (1 hunks)
- src/phare/phare_init_small.py (1 hunks)
- tests/diagnostic/init.py (3 hunks)
- tests/functional/alfven_wave/alfven_wave1d.py (1 hunks)
- tests/functional/conservation/conserv.py (1 hunks)
- tests/functional/dispersion/dispersion.py (2 hunks)
- tests/functional/ionIonBeam/ion_ion_beam1d.py (1 hunks)
- tests/functional/shock/shock.py (1 hunks)
- tests/functional/td/td1d.py (1 hunks)
- tests/functional/tdtagged/td1dtagged.py (1 hunks)
- tests/functional/translation/translat1d.py (2 hunks)
- tests/simulator/refinement/test_2d_10_core.py (1 hunks)
- tests/simulator/refinement/test_2d_2_core.py (1 hunks)
- tests/simulator/test_advance.py (2 hunks)
- tests/simulator/test_diagnostic_timestamps.py (2 hunks)
- tests/simulator/test_initialization.py (2 hunks)
- tools/bench/real/bench_harris.py (1 hunks)
Files skipped from review due to trivial changes (3)
- tests/functional/translation/translat1d.py
- tests/simulator/refinement/test_2d_10_core.py
- tests/simulator/refinement/test_2d_2_core.py
Additional context used
Ruff
tools/bench/real/bench_harris.py
36-36: Ambiguous variable name:
l(E741)
Additional comments not posted (29)
tests/diagnostic/__init__.py (2)
23-23: Removal ofcompute_timestampsparameter fromInfoDiagnosticsThe
compute_timestampsparameter has been removed from theph.InfoDiagnosticscall. Ensure that this change does not affect the functionality of the diagnostics.
28-28: Removal ofcompute_timestampsparameter from commented-outMetaDiagnosticsThe
compute_timestampsparameter has been removed from the commented-outph.MetaDiagnosticscall. This change is consistent with the removal in other diagnostic calls.src/phare/phare_init.py (2)
101-101: Removal ofcompute_timestampsparameter fromElectromagDiagnosticsThe
compute_timestampsparameter has been removed from theph.ElectromagDiagnosticsinstantiation. Ensure that this change does not affect the functionality of the diagnostics.
105-105: Removal ofcompute_timestampsparameter fromFluidDiagnosticsThe
compute_timestampsparameter has been removed from theph.FluidDiagnosticsinstantiation. Ensure that this change does not affect the functionality of the diagnostics.src/phare/phare_init_small.py (2)
104-104: Removal ofcompute_timestampsparameter fromElectromagDiagnosticsThe
compute_timestampsparameter has been removed from theph.ElectromagDiagnosticsinstantiation. Ensure that this change does not affect the functionality of the diagnostics.
108-108: Removal ofcompute_timestampsparameter fromFluidDiagnosticsThe
compute_timestampsparameter has been removed from theph.FluidDiagnosticsinstantiation. Ensure that this change does not affect the functionality of the diagnostics.tests/functional/td/td1d.py (1)
101-102: Verify the removal ofcompute_timestampsfromElectromagDiagnostics.Ensure that the removal of the
compute_timestampsparameter does not affect the functionality ofElectromagDiagnostics.Verification successful
Verify the removal of
compute_timestampsfromElectromagDiagnostics.The
compute_timestampsparameter is not found in the class definition or invocations ofElectromagDiagnostics. The functionality appears to rely on thewrite_timestampsparameter instead. The removal ofcompute_timestampsdoes not affect the functionality ofElectromagDiagnostics.
pyphare/pyphare/pharein/diagnostics.py: Class definition and__init__method ofElectromagDiagnostics.- Multiple test files and source files invoking
ElectromagDiagnosticswithwrite_timestamps.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `ElectromagDiagnostics`. # Test: Search for the function definition of `ElectromagDiagnostics` and check for the `compute_timestamps` parameter. rg --type python 'def ElectromagDiagnostics' -A 5Length of output: 82
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `ElectromagDiagnostics`. # Test: Search for the function definition of `ElectromagDiagnostics` and check for the `compute_timestamps` parameter. rg --type py 'def ElectromagDiagnostics' -A 5Length of output: 47
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `ElectromagDiagnostics`. # Test 1: Search for the class definition of `ElectromagDiagnostics`. rg --type py 'class ElectromagDiagnostics' -A 10 # Test 2: Search for any method definitions within the `ElectromagDiagnostics` class. rg --type py 'def ' -A 5 | rg 'ElectromagDiagnostics' # Test 3: Search for invocations of `ElectromagDiagnostics` to check for parameters used. rg --type py 'ElectromagDiagnostics(' -A 2Length of output: 1594
Script:
#!/bin/bash # Description: Verify the removal of `compute_timestamps` from `ElectromagDiagnostics`. # Test: Search for invocations of `ElectromagDiagnostics` to check for parameters used. rg --type py 'ElectromagDiagnostics\(' -A 2Length of output: 6725
tools/bench/real/bench_harris.py (2)
81-84: Enhance readability with formatting improvements.The formatting improvements in the
configfunction enhance readability and maintainability.
122-123: Verify the removal of redundant parameters fromElectromagDiagnostics.Ensure that the removal of redundant parameters does not affect the functionality of
ElectromagDiagnostics.tests/functional/dispersion/dispersion.py (3)
89-90: Verify the removal ofcompute_timestampsfromElectromagDiagnostics.Ensure that the removal of the
compute_timestampsparameter does not affect the functionality ofElectromagDiagnostics.
171-172: Verify the removal ofcompute_timestampsfromElectromagDiagnostics.Ensure that the removal of the
compute_timestampsparameter does not affect the functionality ofElectromagDiagnostics.
174-175: Verify the removal ofcompute_timestampsfromFluidDiagnostics.Ensure that the removal of the
compute_timestampsparameter does not affect the functionality ofFluidDiagnostics.tests/functional/shock/shock.py (2)
108-108: LGTM! But verify the usage ofElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
LGTM! But verify the usage of
ElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'ElectromagDiagnostics'Length of output: 76
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type py -A 5 $'ElectromagDiagnostics'Length of output: 16962
111-111: LGTM! But verify the usage ofFluidDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
The usage of
FluidDiagnosticsis verified and correct.All instances of
FluidDiagnosticsin the codebase use the updated parametersquantityandwrite_timestamps. The removal of thecompute_timestampsparameter does not affect the functionality.
src/phare/phare_init.pysrc/phare/phare_init_small.pytests/simulator/test_initialization.pytests/simulator/test_advance.pytests/simulator/test_run.pytests/simulator/refinement/test_2d_2_core.pytests/simulator/refinement/test_2d_10_core.pytests/diagnostic/__init__.pytests/functional/harris/harris_2d_lb.pytests/functional/td/td1d.pytests/functional/shock/shock.pytests/functional/tdtagged/td1dtagged.pytests/functional/dispersion/dispersion.pytests/functional/alfven_wave/alfven_wave1d.pytests/functional/translation/translat1d.pypyphare/pyphare_tests/test_pharesee/test_hierarchy.pypyphare/pyphare/pharein/diagnostics.pypyphare/pyphare/pharein/examples/job.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `FluidDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `FluidDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'FluidDiagnostics'Length of output: 71
Script:
#!/bin/bash # Description: Verify the usage of `FluidDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `FluidDiagnostics`. Expect: Only occurrences with the updated parameters. rg --glob '*.py' -A 5 'FluidDiagnostics'Length of output: 14848
tests/functional/alfven_wave/alfven_wave1d.py (2)
97-97: LGTM! But verify the usage ofFluidDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
LGTM! The
compute_timestampsparameter has been removed, and the remaining parameters are correctly passed. The functionality remains intact.
tests/functional/alfven_wave/alfven_wave1d.py: Line 97Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `FluidDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `FluidDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'FluidDiagnostics'Length of output: 71
Script:
#!/bin/bash # Description: Verify the usage of `FluidDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `FluidDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type py -A 5 $'FluidDiagnostics'Length of output: 14844
94-94: LGTM! But verify the usage ofElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
LGTM! The usage of
ElectromagDiagnosticshas been verified.The
compute_timestampsparameter has been removed consistently across the codebase. The remaining parametersquantityandwrite_timestampsare correctly passed, ensuring the functionality remains intact.
- Instances found in:
tests/simulator/test_initialization.pytests/diagnostic/__init__.pytests/functional/translation/translat1d.pytests/functional/conservation/conserv.pytests/functional/tdtagged/td1dtagged.pytests/functional/td/td1d.pytests/functional/shock/shock.pytests/functional/ionIonBeam/ion_ion_beam1d.pytests/functional/harris/harris_2d.pytests/functional/harris/harris_2d_lb.pytests/functional/dispersion/dispersion.pytests/functional/alfven_wave/alfven_wave1d.pytests/simulator/test_run.pytests/simulator/test_advance.pytests/simulator/test_diagnostic_timestamps.pytests/simulator/refinement/test_2d_2_core.pytests/simulator/refinement/test_2d_10_core.pytools/bench/real/bench_harris.pysrc/phare/phare_init_small.pysrc/phare/phare_init.pypyphare/pyphare_tests/test_pharesee/test_hierarchy.pypyphare/pyphare/pharein/examples/job.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'ElectromagDiagnostics'Length of output: 76
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type py -A 5 'ElectromagDiagnostics'Length of output: 16962
tests/simulator/test_diagnostic_timestamps.py (2)
Line range hint
61-61:
LGTM! But verify the usage ofElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
LGTM! The removal of the
compute_timestampsparameter from theElectromagDiagnosticsinstantiation is correctly handled across the codebase.
- The remaining parameters (
quantityandwrite_timestamps) are correctly passed in all instances.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'ElectromagDiagnostics'Length of output: 76
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg 'ElectromagDiagnostics' --glob '*.py' -A 5Length of output: 16966
Line range hint
101-101:
LGTM! But verify the usage ofElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.Verification successful
LGTM! But verify the usage of
ElectromagDiagnostics.The
compute_timestampsparameter has been removed. Ensure that the remaining parameters are correctly passed and the functionality remains intact.
- The removal of the
compute_timestampsparameter has been consistently applied across the codebase.- The remaining parameters (
quantity,write_timestamps,flush_every) are correctly passed in the instantiations.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type python -A 5 $'ElectromagDiagnostics'Length of output: 76
Script:
#!/bin/bash # Description: Verify the usage of `ElectromagDiagnostics` to ensure correct parameters are passed. # Test: Search for the instantiation of `ElectromagDiagnostics`. Expect: Only occurrences with the updated parameters. rg --type py -A 5 $'ElectromagDiagnostics'Length of output: 16962
tests/functional/tdtagged/td1dtagged.py (2)
119-119: Simplified diagnostic function call forElectromagDiagnostics.The removal of the
compute_timestampsparameter simplifies the function call. Ensure that the removal does not affect the intended functionality.
121-121: Simplified diagnostic function call forFluidDiagnostics.The removal of the
compute_timestampsparameter simplifies the function call. Ensure that the removal does not affect the intended functionality.tests/functional/ionIonBeam/ion_ion_beam1d.py (2)
99-99: Simplified diagnostic function call forElectromagDiagnostics.The removal of the
compute_timestampsparameter simplifies the function call. Ensure that the removal does not affect the intended functionality.
103-103: Simplified diagnostic function call forParticleDiagnostics.The removal of the
compute_timestampsparameter simplifies the function call. Ensure that the removal does not affect the intended functionality.tests/functional/conservation/conserv.py (1)
86-86: Simplified diagnostic function call forElectromagDiagnostics.The removal of the
compute_timestampsparameter simplifies the function call. Ensure that the removal does not affect the intended functionality.pyphare/pyphare_tests/test_pharesee/test_hierarchy.py (1)
148-148: Simplified instantiation ofFluidDiagnostics.The
compute_timestampsparameter has been removed from the instantiation ofFluidDiagnostics. Ensure that this change aligns with the updated class definition and that the diagnostics are correctly handled without this parameter.pyphare/pyphare/pharein/diagnostics.py (1)
119-123: Simplified timestamp handling inDiagnosticsconstructor.The
compute_timestampsparameter has been removed and is now assigned the same value aswrite_timestamps. This change simplifies the logic but ensure that future enhancements allow for different timestamp computations based on the type of diagnostics.tests/simulator/test_initialization.py (2)
170-170: Simplified instantiation ofElectromagDiagnostics.The
compute_timestampsparameter has been removed from the instantiation ofElectromagDiagnostics. Ensure that this change aligns with the updated class definition and that the diagnostics are correctly handled without this parameter.
175-175: Simplified instantiation ofFluidDiagnostics.The
compute_timestampsparameter has been removed from the instantiation ofFluidDiagnostics. Ensure that this change aligns with the updated class definition and that the diagnostics are correctly handled without this parameter.tests/simulator/test_advance.py (2)
156-156: Ensure correctness of theFluidDiagnosticsinstantiation.The
compute_timestampsparameter is removed. Ensure that this change does not affect the functionality.Verification successful
The
compute_timestampsparameter is not required for theFluidDiagnosticsinstantiation.
- The
FluidDiagnosticsclass constructor does not include acompute_timestampsparameter, and the instantiation logic is based on thequantityprovided inkwargs.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the instantiation of `FluidDiagnostics` without `compute_timestamps`. # Test: Search for the `FluidDiagnostics` class definition to ensure `compute_timestamps` is not required. rg --type python -A 5 'class FluidDiagnostics'Length of output: 79
Script:
#!/bin/bash # Description: Verify the instantiation of `FluidDiagnostics` without `compute_timestamps`. # Corrected Test: Search for the `FluidDiagnostics` class definition and inspect its constructor. rg 'class FluidDiagnostics' -A 20Length of output: 3076
Line range hint
162-162:
Ensure correctness of theFluidDiagnosticsinstantiation for population.The
compute_timestampsparameter is removed. Ensure that this change does not affect the functionality.
from #773
Summary by CodeRabbit
New Features
compute_timestampsparameter from various diagnostic classes, enhancing overall clarity and performance.Bug Fixes
Documentation
Style