Remove tau sobolevs from plasma #2874

andrewfullard · 2024-11-11T20:29:49Z

📝 Description

Type: 🚀 feature

This PR creates an alternative plasma without the tau Sobolevs, beta Sobolevs or macro atom properties. It modifies the plasma factory, formal integral and opacity state to handle this while still passing tests.

🚦 Testing

How did you test these changes?

Testing pipeline
Other method (describe)
My changes can't be tested (explain why)

☑️ Checklist

I requested two reviewers for this pull request
I updated the documentation according to my changes
I built the documentation by applying the build_docs label

Note: If you are not allowed to perform any of these actions, ping (@) a contributor.

tardis-bot · 2024-11-11T20:31:39Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (43cc7b9).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

175	F405  	[ ] `AdiabaticCoolingRate` may be undefined, or defined from star imports
11	G004  	[ ] Logging statement uses f-string
8	W293  	[*] Blank line contains whitespace
5	RET505	[ ] Unnecessary `else` after `return` statement
4	E999  	[ ] SyntaxError: Expected an expression
4	F401  	[*] `numpy` imported but unused
3	INP001	[ ] File `tardis/opacities/tests/test_opacity_solver.py` is part of an implicit namespace package. Add an `__init__.py`.
3	RET506	[ ] Unnecessary `else` after `raise` statement
3	I001  	[*] Import block is un-sorted or un-formatted
2	E722  	[ ] Do not use bare `except`
2	F403  	[ ] `from tardis.plasma.properties import *` used; unable to detect undefined names
1	ANN204	[ ] Missing return type annotation for special method `__getitem__`
1	E701  	[ ] Multiple statements on one line (colon)
1	W291  	[*] Trailing whitespace
1	W292  	[*] No newline at end of file
1	D202  	[*] No blank lines allowed after function docstring (found 1)
1	D406  	[*] Section name should end with a newline ("Returns")
1	D407  	[*] Missing dashed underline after section ("Returns")
1	D411  	[*] Missing blank line before section ("Parameters")
1	UP008 	[*] Use `super()` instead of `super(__class__, self)`
1	TRY300	[ ] Consider moving this statement to an `else` block

Complete output(might be large):

.github/workflows/post-release.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/post-release.yml:124:37: W291 [*] Trailing whitespace
.github/workflows/pre-release.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/release.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/release.yml:16:7: E701 Multiple statements on one line (colon)
.github/workflows/release.yml:48:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:51:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:58:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:61:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:64:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:69:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:73:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:89:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:97:23: W292 [*] No newline at end of file
.mailmap:1:38: E999 SyntaxError: Expected an expression
tardis/opacities/macro_atom/base.py:120:5: D411 [*] Missing blank line before section ("Parameters")
tardis/opacities/macro_atom/base.py:226:5: E722 Do not use bare `except`
tardis/opacities/macro_atom/base.py:245:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/opacities/macro_atom/base.py:347:9: E722 Do not use bare `except`
tardis/opacities/opacity_state.py:210:9: ANN204 Missing return type annotation for special method `__getitem__`
tardis/opacities/opacity_state.py:216:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/opacities/opacity_state.py:216:9: D406 [*] Section name should end with a newline ("Returns")
tardis/opacities/opacity_state.py:251:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/tests/test_opacity_solver.py:1:1: INP001 File `tardis/opacities/tests/test_opacity_solver.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/opacities/tests/test_opacity_solver.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/tests/test_opacity_solver.py:2:17: F401 [*] `numpy` imported but unused
tardis/opacities/tests/test_opacity_solver.py:7:44: F401 [*] `tardis.opacities.opacity_state.OpacityState` imported but unused
tardis/opacities/tests/test_opacity_solver.py:8:42: F401 [*] `tardis.opacities.tau_sobolev.calculate_sobolev_line_opacity` imported but unused
tardis/opacities/tests/test_opacity_state_numba.py:1:1: INP001 File `tardis/opacities/tests/test_opacity_state_numba.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/opacities/tests/test_opacity_state_numba.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/tests/test_tau_sobolev.py:1:1: INP001 File `tardis/opacities/tests/test_tau_sobolev.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/plasma/assembly/__init__.py:1:41: F401 `tardis.plasma.assembly.base.PlasmaSolverFactory` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/properties/legacy_property_collections.py:10:1: F403 `from tardis.plasma.properties import *` used; unable to detect undefined names
tardis/plasma/properties/legacy_property_collections.py:19:9: F405 `DilutePlanckianRadField` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:20:9: F405 `NumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:21:9: F405 `TimeExplosion` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:22:9: F405 `AtomicData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:23:9: F405 `JBlues` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:24:9: F405 `LinkTRadTElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:25:9: F405 `HeliumTreatment` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:26:9: F405 `ContinuumInteractionSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:27:9: F405 `NLTEIonizationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:28:9: F405 `NLTEExcitationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:33:9: F405 `TRadiative` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:34:9: F405 `DilutionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:35:9: F405 `BetaRadiation` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:36:9: F405 `Levels` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:37:9: F405 `Lines` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:38:9: F405 `PartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:39:9: F405 `GElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:40:9: F405 `IonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:41:9: F405 `LinesLowerLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:42:9: F405 `LinesUpperLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:44:9: F405 `StimulatedEmissionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:45:9: F405 `SelectedAtoms` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:46:9: F405 `ElectronTemperature` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:49:55: F405 `PhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:50:55: F405 `LevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:52:44: F405 `MacroAtomData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:55:6: F405 `PhiSahaNebular` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:55:22: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:55:32: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:55:46: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:58:6: F405 `LevelBoltzmannFactorDiluteLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:60:49: F405 `LevelBoltzmannFactorNoNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:63:9: F405 `LevelBoltzmannFactorNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:64:9: F405 `NLTEData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:65:9: F405 `PreviousElectronDensities` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:66:9: F405 `PreviousBetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:71:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:71:23: F405 `NLTEPopulationSolverRoot` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:74:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:74:23: F405 `NLTEPopulationSolverLU` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:78:9: F405 `HeliumNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:79:9: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:80:9: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:81:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:82:9: F405 `LevelNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:83:9: F405 `IonNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:87:6: F405 `LevelNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:87:26: F405 `IonNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:90:6: F405 `HeliumNumericalNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:94:9: F405 `PhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:95:9: F405 `StimRecombRateFactor` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:96:9: F405 `BfHeatingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:97:9: F405 `StimRecombCoolingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:98:9: F405 `YgData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:103:9: F405 `StimRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:104:9: F405 `PhotoIonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:105:9: F405 `SpontRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:106:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:107:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:108:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:109:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:110:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:111:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:112:9: F405 `CorrPhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:113:9: F405 `SpontRecombCoolingRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:114:9: F405 `RawRecombTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:115:9: F405 `RawPhotoIonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:116:9: F405 `RawRadBoundBoundTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:117:9: F405 `MarkovChainTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:118:9: F405 `NonContinuumTransProbsMask` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:119:9: F405 `YgInterpolator` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:120:9: F405 `CollExcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:121:9: F405 `CollDeexcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:122:9: F405 `RawCollisionTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:123:9: F405 `MarkovChainIndex` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:124:9: F405 `MarkovChainTransProbsCollector` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:126:9: F405 `MonteCarloTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:127:9: F405 `FreeFreeCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:128:9: F405 `FreeBoundCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:130:9: F405 `LevelNumberDensityLTE` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:131:9: F405 `PhotoIonBoltzmannFactor` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:132:9: F405 `FreeBoundEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:133:9: F405 `LevelIdxs2LineIdx` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:134:9: F405 `LevelIdxs2TransitionIdx` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:135:9: F405 `CollIonRateCoeffSeaton` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:136:9: F405 `CollRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:138:9: F405 `ContinuumInteractionHandler` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:142:58: F405 `AdiabaticCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:145:9: F405 `RawTwoPhotonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:146:9: F405 `TwoPhotonData` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:147:9: F405 `TwoPhotonEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/legacy_property_collections.py:148:9: F405 `TwoPhotonFrequencySampler` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:1:1: F403 `from tardis.plasma.properties import *` used; unable to detect undefined names
tardis/plasma/properties/property_collections.py:10:9: F405 `DilutePlanckianRadField` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:11:9: F405 `NumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:12:9: F405 `TimeExplosion` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:13:9: F405 `AtomicData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:14:9: F405 `JBlues` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:15:9: F405 `LinkTRadTElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:16:9: F405 `HeliumTreatment` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:17:9: F405 `ContinuumInteractionSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:18:9: F405 `NLTEIonizationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:19:9: F405 `NLTEExcitationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:24:9: F405 `TRadiative` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:25:9: F405 `DilutionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:26:9: F405 `BetaRadiation` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:27:9: F405 `Levels` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:28:9: F405 `Lines` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:29:9: F405 `PartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:30:9: F405 `GElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:31:9: F405 `IonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:32:9: F405 `LinesLowerLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:33:9: F405 `LinesUpperLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:34:9: F405 `StimulatedEmissionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:35:9: F405 `SelectedAtoms` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:36:9: F405 `ElectronTemperature` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:39:55: F405 `PhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:40:55: F405 `LevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:43:6: F405 `PhiSahaNebular` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:43:22: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:43:32: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:43:46: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:46:6: F405 `LevelBoltzmannFactorDiluteLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:48:49: F405 `LevelBoltzmannFactorNoNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:51:9: F405 `LevelBoltzmannFactorNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:52:9: F405 `NLTEData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:53:9: F405 `PreviousElectronDensities` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:57:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:57:23: F405 `NLTEPopulationSolverRoot` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:60:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:60:23: F405 `NLTEPopulationSolverLU` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:64:9: F405 `HeliumNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:65:9: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:66:9: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:67:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:68:9: F405 `LevelNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:69:9: F405 `IonNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:73:6: F405 `LevelNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:73:26: F405 `IonNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:76:6: F405 `HeliumNumericalNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:80:9: F405 `PhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:81:9: F405 `StimRecombRateFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:82:9: F405 `BfHeatingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:83:9: F405 `StimRecombCoolingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:84:9: F405 `YgData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:89:9: F405 `StimRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:90:9: F405 `PhotoIonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:91:9: F405 `SpontRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:92:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:93:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:94:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:95:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:96:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:97:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:98:9: F405 `CorrPhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:99:9: F405 `SpontRecombCoolingRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:100:9: F405 `YgInterpolator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:101:9: F405 `CollExcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:102:9: F405 `CollDeexcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:103:9: F405 `RawCollisionTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:104:9: F405 `MarkovChainIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:105:9: F405 `FreeFreeCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:106:9: F405 `FreeBoundCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:107:9: F405 `LevelNumberDensityLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:108:9: F405 `PhotoIonBoltzmannFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:109:9: F405 `FreeBoundEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:110:9: F405 `LevelIdxs2LineIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:111:9: F405 `LevelIdxs2TransitionIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:112:9: F405 `CollIonRateCoeffSeaton` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:113:9: F405 `CollRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:114:9: F405 `ContinuumInteractionHandler` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:117:58: F405 `AdiabaticCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:120:9: F405 `RawTwoPhotonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:121:9: F405 `TwoPhotonData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:122:9: F405 `TwoPhotonEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:123:9: F405 `TwoPhotonFrequencySampler` may be undefined, or defined from star imports
tardis/plasma/standard_plasmas.py:316:9: RET506 Unnecessary `else` after `raise` statement
tardis/simulation/base.py:197:13: RET506 Unnecessary `else` after `raise` statement
tardis/simulation/base.py:261:17: G004 Logging statement uses f-string
tardis/simulation/base.py:268:9: RET505 Unnecessary `else` after `return` statement
tardis/simulation/base.py:445:13: G004 Logging statement uses f-string
tardis/simulation/base.py:543:13: G004 Logging statement uses f-string
tardis/simulation/base.py:650:25: G004 Logging statement uses f-string
tardis/simulation/base.py:653:13: G004 Logging statement uses f-string
tardis/simulation/base.py:658:13: G004 Logging statement uses f-string
tardis/simulation/base.py:709:13: TRY300 Consider moving this statement to an `else` block
tardis/simulation/base.py:711:26: G004 Logging statement uses f-string
tardis/spectrum/formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral.py:358:13: RET506 Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral.py:698:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:734:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral_cuda.py:375:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral_cuda.py:420:5: RET505 Unnecessary `else` after `return` statement
tardis/workflows/simple_tardis_workflow.py:230:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:449:17: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:172:13: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:212:17: G004 Logging statement uses f-string
Found 230 errors.
[*] 20 fixable with the `--fix` option (1 hidden fix can be enabled with the `--unsafe-fixes` option).

andrewfullard · 2024-11-11T20:35:04Z

@jvshields the stardis failure is related to removing TauSobolev from the plasma which is of course no longer required.

tardis-bot · 2024-11-11T20:45:42Z

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

tardis/opacities/macro_atom/macroatom_solver.py

tardis/opacities/opacity_solver.py

tardis/opacities/opacity_state.py

tardis/opacities/tau_sobolev.py

tardis/spectrum/formal_integral.py

codecov · 2024-11-12T16:05:56Z

Codecov Report

Attention: Patch coverage is 79.08497% with 32 lines in your changes missing coverage. Please review.

Project coverage is 69.71%. Comparing base (763c11d) to head (43cc7b9).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/opacities/tau_sobolev.py	65.00%	7 Missing ⚠️
tardis/opacities/macro_atom/macroatom_solver.py	50.00%	5 Missing ⚠️
tardis/spectrum/formal_integral.py	78.26%	5 Missing ⚠️
tardis/workflows/simple_tardis_workflow.py	0.00%	4 Missing ⚠️
tardis/plasma/standard_plasmas.py	0.00%	3 Missing ⚠️
tardis/opacities/opacity_solver.py	83.33%	2 Missing ⚠️
tardis/plasma/assembly/base.py	90.47%	2 Missing ⚠️
tardis/spectrum/tests/test_cuda_formal_integral.py	0.00%	2 Missing ⚠️
tardis/plasma/properties/property_collections.py	0.00%	1 Missing ⚠️
tardis/workflows/standard_tardis_workflow.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2874      +/-   ##
==========================================
- Coverage   70.22%   69.71%   -0.51%     
==========================================
  Files         214      216       +2     
  Lines       15981    16030      +49     
==========================================
- Hits        11223    11176      -47     
- Misses       4758     4854      +96

☔ View full report in Codecov by Sentry.
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Flaky Tests Detection - Detect and resolve failed and flaky tests

tardis/opacities/opacity_solver.py

tardis-bot · 2024-11-12T16:40:32Z

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (763c11d) and the latest commit (43cc7b9).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

| Change   | Before [6ee870e0] <master>   | After [43cc7b9e]    |   Ratio | Benchmark (Parameter)                                                                                              |
|----------|------------------------------|---------------------|---------|--------------------------------------------------------------------------------------------------------------------|
| +        | 30.8±0.06μs                  | 43.0±0.02μs         |    1.39 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [6ee870e0] <master>   | After [43cc7b9e]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 2.64±0.01ms                  | 3.43±0ms            | ~1.30   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 7.47±2μs                     | 9.62±2μs            | ~1.29   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 42.1±20μs                    | 52.7±40μs           | ~1.25   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 1.60±0.4μs                   | 1.79±0.2μs          | ~1.12   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 3.82±0.3μs                   | 3.18±0.5μs          | ~0.83   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 841±100ns                    | 631±100ns           | ~0.75   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 35.6±10μs                    | 20.9±5μs            | ~0.59   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 3.94±0.03ms                  | 4.26±0.02ms         | 1.08    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 2.98±0.3μs                   | 3.21±0.5μs          | 1.07    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 2.21±2μs                     | 2.32±2μs            | 1.05    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 1.74±0.02ms                  | 1.79±0.03ms         | 1.03    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 2.61±0.5ms                   | 2.70±0.4ms          | 1.03    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 207±0.2ns                    | 209±0.3ns           | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 1.20±0μs                     | 1.22±0μs            | 1.01    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 2.08±0m                      | 2.07±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 744±0.06ns                   | 745±0.7ns           | 1.00    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 66.0±0.1ms                   | 66.1±0.2ms          | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 6.74±0.9μs                   | 6.71±1μs            | 1.00    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 1.09±0m                      | 1.07±0m             | 0.98    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 571±100ns                    | 551±200ns           | 0.96    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 41.5±0.06s                   | 39.6±0.02s          | 0.95    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 561±100ns                    | 521±200ns           | 0.93    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 56.2±30μs                    | 52.4±50μs           | 0.93    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |

Benchmarks that have got worse:

| Change   | Before [6ee870e0] <master>   | After [43cc7b9e]    |   Ratio | Benchmark (Parameter)                                                                                              |
|----------|------------------------------|---------------------|---------|--------------------------------------------------------------------------------------------------------------------|
| +        | 30.8±0.06μs                  | 43.0±0.02μs         |    1.39 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |

If you want to see the graph of the results, you can check it here

andrewfullard · 2024-11-12T16:46:33Z

Requires regression data tardis-sn/tardis-regression-data#25

tardis/opacities/macro_atom/macroatom_solver.py

tardis/opacities/opacity_state.py

wkerzendorf · 2024-11-25T18:58:59Z

tardis/opacities/tau_sobolev.py

+    """
+
+    @jit(nopython=True, parallel=True)
+    def numba_calculate_beta_sobolev(tau_sobolevs, beta_sobolevs):


any reason why this is not a "global" function?

Because it doesn't seem useful for any other case, it's basically just a small wrapper around the numba so that the DataFrame can be used for initializing the array.

wkerzendorf

one question as shown.

andrewfullard added 7 commits November 11, 2024 13:32

Create legacy plasma graph

2e3f9e9

Set up legacy plasma collections and factory

d69b49b

Legacy macro atom transition probs

31df1f4

Modifications to the formal integral, and simple workflow testbed

12a8f6e

Partial fix for the formal integral

d4affa0

Drop macro atom data from plasma

95eb875

Fixes formal integral tests

cac82a4

andrewfullard requested a review from wkerzendorf November 11, 2024 20:29

andrewfullard added plasma restructure labels Nov 11, 2024

andrewfullard requested a review from jvshields November 11, 2024 20:33

andrewfullard added the build-docs label Nov 11, 2024