Ionization calculations #3070

andrewfullard · 2025-05-06T14:25:52Z

📝 Description

Type: | 🚀 feature

This PR adds photoionization and recombination rates calculations and population solvers to replace the current NLTE implementation in the near future. The classes are designed to work as standalone modules where possible.

It relies on the merge of #2896 and related Carsus PRs

Also relies on tardis-sn/tardis-regression-data#50 for test data

🚦 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.

- Currently produces weird results

review-notebook-app · 2025-05-06T14:25:58Z

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tardis-bot · 2025-05-06T14:27:44Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (6fb6334).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

Details

110303	       	[ ] syntax-error
 129	W293   	[ ] blank-line-with-whitespace
 118	E701   	[ ] multiple-statements-on-one-line-colon
 102	F405   	[ ] undefined-local-with-import-star-usage
  96	W291   	[ ] trailing-whitespace
  49	COM818 	[ ] trailing-comma-on-bare-tuple
  34	E902   	[ ] io-error
  34	F401   	[ ] unused-import
  26	I001   	[*] unsorted-imports
  16	W292   	[ ] missing-newline-at-end-of-file
  15	E702   	[ ] multiple-statements-on-one-line-semicolon
  15	F821   	[ ] undefined-name
  13	G004   	[ ] logging-f-string
   6	E402   	[ ] module-import-not-at-top-of-file
   6	UP031  	[ ] printf-string-formatting
   5	D204   	[*] incorrect-blank-line-after-class
   5	UP015  	[*] redundant-open-modes
   4	W191   	[ ] tab-indentation
   4	F811   	[ ] redefined-while-unused
   3	E703   	[ ] useless-semicolon
   3	PLW0127	[ ] self-assigning-variable
   3	RET505 	[*] superfluous-else-return
   2	F403   	[ ] undefined-local-with-import-star
   2	PLW0128	[ ] redeclared-assigned-name
   2	RET506 	[*] superfluous-else-raise
   1	E712   	[ ] true-false-comparison
   1	E722   	[ ] bare-except
   1	F541   	[*] f-string-missing-placeholders
   1	INP001 	[ ] implicit-namespace-package
   1	NPY201 	[ ] numpy2-deprecation
   1	PGH004 	[ ] blanket-noqa
   1	PLC0414	[ ] useless-import-alias
   1	RUF015 	[ ] unnecessary-iterable-allocation-for-first-element
   1	RUF021 	[*] parenthesize-chained-operators
   1	TRY300 	[ ] try-consider-else
   1	UP008  	[ ] super-call-with-parameters
   1	UP009  	[*] utf8-encoding-declaration
   1	UP030  	[ ] format-literals
   1	UP032  	[*] f-string
   1	UP034  	[*] extraneous-parentheses
Found 111010 errors.
[*] 84 fixable with the `--fix` option (38 hidden fixes can be enabled with the `--unsafe-fixes` option).

Complete output(might be large):

Details

docs/conf.py:1:1: UP009 [*] UTF-8 encoding declaration is unnecessary
docs/conf.py:27:1: I001 [*] Import block is un-sorted or un-formatted
docs/conf.py:30:8: F401 [*] `tardis` imported but unused
docs/conf.py:37:43: PGH004 Use specific rule codes when using `noqa`
docs/conf.py:47:27: UP015 [*] Unnecessary mode argument
docs/conf.py:68:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:69:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:70:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:71:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:72:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:142:1: W293 Blank line contains whitespace
docs/conf.py:177:1: W293 Blank line contains whitespace
docs/conf.py:194:13: UP030 Use implicit references for positional format fields
docs/conf.py:194:13: UP032 [*] Use f-string instead of `format` call
docs/conf.py:221:1: E402 Module level import not at top of file
docs/conf.py:293:4: E712 Avoid equality comparisons to `True`; use `toml_config_tool_dict["tardis"]['edit_on_github']:` for truth checks
docs/conf.py:315:1: E402 Module level import not at top of file
docs/conf.py:367:1: E402 Module level import not at top of file
docs/conf.py:382:37: UP015 [*] Unnecessary modes, use `w`
docs/conf.py:397:41: UP015 [*] Unnecessary modes, use `w`
docs/conf.py:412:37: UP015 [*] Unnecessary modes, use `w`
docs/physics/pyplot/lte_ionization_balance.py:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/pyplot/lte_ionization_balance.py:1:21: F401 [*] `pathlib.Path` imported but unused
docs/physics/pyplot/lte_ionization_balance.py:22:31: F821 Undefined name `atom_fname`
docs/physics/pyplot/lte_ionization_balance.py:73:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/lte_ionization_balance.py:74:15: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/pyplot/nebular_ionization_balance.py:33:18: F821 Undefined name `plasma`
docs/physics/pyplot/nebular_ionization_balance.py:71:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:72:15: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:117:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:118:15: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/plot_mu_in_out_packet.py:1:1: F403 `from pylab import *` used; unable to detect undefined names
docs/physics/pyplot/plot_mu_in_out_packet.py:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/pyplot/plot_mu_in_out_packet.py:5:1: PLW0127 Self-assignment of variable `x`
docs/physics/pyplot/plot_mu_in_out_packet.py:5:4: PLW0127 Self-assignment of variable `y`
docs/physics/pyplot/plot_mu_in_out_packet.py:5:8: PLW0128 Redeclared variable `x` in assignment
docs/physics/pyplot/plot_mu_in_out_packet.py:5:11: PLW0128 Redeclared variable `y` in assignment
docs/physics/pyplot/plot_mu_in_out_packet.py:5:15: F405 `mgrid` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:10:1: F405 `xlabel` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:11:1: F405 `ylabel` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:12:1: F405 `imshow` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:12:8: F405 `np` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:13:1: F405 `colorbar` may be undefined, or defined from star imports
docs/physics/pyplot/plot_mu_in_out_packet.py:14:1: F405 `show` may be undefined, or defined from star imports
tardis/base.py:106:13: PLW0127 Self-assignment of variable `atom_data`
tardis/io/logger/logger.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/io/logger/logger.py:8:23: F401 [*] `functools.lru_cache` imported but unused
tardis/io/logger/logger.py:23:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:38:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:43:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:79:5: D204 [*] 1 blank line required after class docstring
tardis/io/logger/logger.py:80:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:116:5: D204 [*] 1 blank line required after class docstring
tardis/io/logger/logger.py:117:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:119:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:148:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:170:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:175:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:186:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:193:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:208:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:212:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:241:1: W293 [*] Blank line contains whitespace
tardis/io/logger/logger.py:253:5: D204 [*] 1 blank line required after class docstring
tardis/io/logger/logger.py:254:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:256:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:275:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:284:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:299:21: G004 Logging statement uses f-string
tardis/io/logger/logger.py:361:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:373:1: W293 [*] Blank line contains whitespace
tardis/io/logger/logger.py:380:1: W293 [*] Blank line contains whitespace
tardis/io/logger/logger.py:386:1: W293 [*] Blank line contains whitespace
tardis/io/logger/logger.py:391:5: D204 [*] 1 blank line required after class docstring
tardis/io/logger/logger.py:392:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:403:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:408:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:418:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:421:1: W293 Blank line contains whitespace
tardis/io/logger/logger.py:432:1: W293 Blank line contains whitespace
tardis/io/logger/logger_widget.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/__init__.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/plasma/equilibrium/rates/__init__.py:2:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonCMFGENSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:3:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonRegemorterSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:6:5: F401 `tardis.plasma.equilibrium.rates.collisional_ionization_rates.CollisionalIonizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:9:5: F401 `tardis.plasma.equilibrium.rates.collisional_ionization_strengths.CollisionalIonizationSeaton` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:12:5: F401 `tardis.plasma.equilibrium.rates.collisional_rates.ThermalCollisionalRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:15:5: F401 `tardis.plasma.equilibrium.rates.photoionization_rates.AnalyticPhotoionizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:16:5: F401 `tardis.plasma.equilibrium.rates.photoionization_rates.EstimatedPhotoionizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:19:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.AnalyticPhotoionizationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:20:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.EstimatedPhotoionizationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:21:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.SpontaneousRecombinationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:22:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.AnalyticCorrectedPhotoionizationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:25:5: F401 `tardis.plasma.equilibrium.rates.radiative_rates.RadiativeRatesSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/tests/test_ion_populations.py:5:8: F401 [*] `pytest` imported but unused
tardis/plasma/properties/hydrogen_continuum.py:131:13: F821 Undefined name `elemental_number_density`
tardis/plasma/properties/hydrogen_continuum.py:136:13: F821 Undefined name `partition_function`
tardis/plasma/properties/hydrogen_continuum.py:137:13: F821 Undefined name `boltzmann_factor`
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:37:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:38:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:39:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:40:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:41:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:42:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:45:55: F405 `PhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:46:55: F405 `LevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:49:6: F405 `PhiSahaNebular` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:49:22: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:49:32: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:49:46: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:52:6: F405 `LevelBoltzmannFactorDiluteLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:54:49: F405 `LevelBoltzmannFactorNoNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:57:9: F405 `LevelBoltzmannFactorNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:58:9: F405 `NLTEData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:59:9: F405 `PreviousElectronDensities` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:60:9: F405 `PreviousBetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:64:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:64:23: F405 `NLTEPopulationSolverRoot` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:67:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:67:23: F405 `NLTEPopulationSolverLU` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:71:9: F405 `HeliumNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:72:9: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:73:9: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:74:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:75:9: F405 `LevelNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:76:9: F405 `IonNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:80:6: F405 `LevelNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:80:26: F405 `IonNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:83:6: F405 `HeliumNumericalNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:87:9: F405 `PhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:88:9: F405 `StimRecombRateFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:89:9: F405 `BfHeatingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:90:9: F405 `StimRecombCoolingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:91:9: F405 `YgData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:96:9: F405 `StimRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:97:9: F405 `PhotoIonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:98:9: F405 `SpontRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:99:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:100:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:101:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:102:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:103:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:104:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:105:9: F405 `CorrPhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:106:9: F405 `SpontRecombCoolingRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:107:9: F405 `YgInterpolator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:108:9: F405 `CollExcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:109:9: F405 `CollDeexcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:110:9: F405 `RawCollisionTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:111:9: F405 `MarkovChainIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:112:9: F405 `FreeFreeCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:113:9: F405 `FreeBoundCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:114:9: F405 `LevelNumberDensityLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:115:9: F405 `PhotoIonBoltzmannFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:116:9: F405 `FreeBoundEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:117:9: F405 `LevelIdxs2LineIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:118:9: F405 `LevelIdxs2TransitionIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:119:9: F405 `CollIonRateCoeffSeaton` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:120:9: F405 `CollRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:121:9: F405 `ContinuumInteractionHandler` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:124:58: F405 `AdiabaticCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:127:9: F405 `RawTwoPhotonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:128:9: F405 `TwoPhotonData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:129:9: F405 `TwoPhotonEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:130:9: F405 `TwoPhotonFrequencySampler` may be undefined, or defined from star imports
tardis/plasma/standard_plasmas.py:323:9: RET506 [*] Unnecessary `else` after `raise` statement
tardis/simulation/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/simulation/base.py:245:17: G004 Logging statement uses f-string
tardis/simulation/base.py:418:13: G004 Logging statement uses f-string
tardis/simulation/base.py:519:13: G004 Logging statement uses f-string
tardis/simulation/base.py:605:13: G004 Logging statement uses f-string
tardis/simulation/base.py:610:13: G004 Logging statement uses f-string
tardis/simulation/base.py:661:13: TRY300 Consider moving this statement to an `else` block
tardis/simulation/base.py:663:26: G004 Logging statement uses f-string
tardis/transport/montecarlo/estimators/continuum_radfield_properties.py:3:17: F401 [*] `numpy` imported but unused
tardis/transport/montecarlo/estimators/continuum_radfield_properties.py:5:30: F401 [*] `astropy.units` imported but unused
tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py:1:1: INP001 File `tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py:35:55: F821 Undefined name `u`
tardis/util/base.py:184:20: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/util/base.py:335:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/util/base.py:509:5: E722 Do not use bare `except`
tardis/util/base.py:617:5: RET505 [*] Unnecessary `elif` after `return` statement
tardis/util/environment.py:1:1: E902 No such file or directory (os error 2)
tardis/util/panel_init.py:1:1: E902 No such file or directory (os error 2)
tardis/visualization/__init__.py:3:57: F401 `tardis.visualization.tools.convergence_plot.ConvergencePlots` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:4:49: F401 `tardis.visualization.tools.liv_plot.LIVPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:5:53: F401 `tardis.visualization.tools.rpacket_plot.RPacketPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:6:50: F401 `tardis.visualization.tools.sdec_plot.SDECPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:7:59: F401 `tardis.visualization.widgets.custom_abundance.CustomAbundanceWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:8:51: F401 `tardis.visualization.widgets.grotrian.GrotrianWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:9:52: F401 `tardis.visualization.widgets.line_info.LineInfoWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:11:5: F401 `tardis.visualization.widgets.shell_info.shell_info_from_hdf` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:12:5: F401 `tardis.visualization.widgets.shell_info.shell_info_from_simulation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/tools/tests/test_convergence_plot.py:3:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/tools/tests/test_convergence_plot.py:14:25: F811 [*] Redefinition of unused `defaultdict` from line 3
tardis/visualization/tools/tests/test_convergence_plot.py:15:32: F811 [*] Redefinition of unused `go` from line 6
tardis/visualization/tools/tests/test_convergence_plot.py:16:30: F811 [*] Redefinition of unused `u` from line 8
tardis/visualization/widgets/custom_abundance.py:737:16: RUF021 [*] Parenthesize `a and b` expressions when chaining `and` and `or` together, to make the precedence clear
tardis/visualization/widgets/custom_abundance.py:1127:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/visualization/widgets/custom_abundance.py:1418:9: RET506 [*] Unnecessary `else` after `raise` statement
tardis/visualization/widgets/custom_abundance.py:1721:9: F811 Redefinition of unused `input_d_time_0_eventhandler` from line 1710
tardis/visualization/widgets/custom_abundance.py:1751:13: F821 Undefined name `display`
tardis/visualization/widgets/custom_abundance.py:1753:13: F821 Undefined name `display`
tardis/visualization/widgets/custom_abundance.py:1755:13: F821 Undefined name `display`
tardis/visualization/widgets/line_info.py:3:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/widgets/line_info.py:450:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:454:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:458:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:462:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:467:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:476:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:531:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/line_info.py:715:1: W293 [*] Blank line contains whitespace
tardis/visualization/widgets/tests/test_custom_abundance.py:224:37: RUF015 Prefer `next(iter(unique_v))` over single element slice
tardis/visualization/widgets/tests/test_line_info.py:9:1: E402 Module level import not at top of file
tardis/visualization/widgets/tests/test_shell_info.py:6:1: E402 Module level import not at top of file
tardis/workflows/simple_tardis_workflow.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/workflows/simple_tardis_workflow.py:249:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:470:17: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:170:13: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:210:17: G004 Logging statement uses f-string
tardis/workflows/workflow_logging.py:69:13: G004 Logging statement uses f-string
tardis/workflows/workflow_logging.py:107:21: G004 Logging statement uses f-string
Found 248 errors.
[*] 47 fixable with the `--fix` option (36 hidden fixes can be enabled with the `--unsafe-fixes` option).

Uses mock data and needs a regression data test

Also output electron fractions and remove unneeded assert

tardis/plasma/equilibrium/ion_populations.py

tardis/plasma/assembly/base.py

tardis/plasma/equilibrium/tests/test_coll_ionization_rates.py

tardis/plasma/equilibrium/tests/test_ion_populations.py

jvshields · 2025-08-12T18:09:41Z

tardis/plasma/properties/hydrogen_continuum.py

+            number_density,
+            electron_densities,
+            block_ids,
+            1e-20,  # ION_ZERO_THRESHOLD from ion_population.py


Just checking to make sure this is still supposed to be here and wasn't a testing thing. Feel free to resolve if this is intentional.

Oh woops this is the whole template class we looked at yesterday. Is this supposed to be part of this PR?

It doesn't hurt to be here since it doesn't do anything, but I can cut it.

This reverts commit 4cef991.

jvshields · 2025-08-14T20:10:39Z

Will need new regression data to check against with the appropriate keys.

andrewfullard · 2025-08-14T22:08:37Z

Will need new regression data to check against with the appropriate keys.

Should be done in tardis-sn/tardis-regression-data#56

Rodot-

I'm happy with it

codecov · 2025-08-18T17:44:13Z

Codecov Report

❌ Patch coverage is 77.56233% with 81 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.89%. Comparing base (3ff94ab) to head (6fb6334).
⚠️ Report is 12 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/plasma/properties/hydrogen_continuum.py	0.00%	67 Missing ⚠️
.../plasma/equilibrium/rates/photoionization_rates.py	62.50%	6 Missing ⚠️
tardis/plasma/equilibrium/ion_populations.py	92.30%	3 Missing ⚠️
tardis/plasma/standard_plasmas.py	0.00%	3 Missing ⚠️
...estimators/tests/test_continuum_property_solver.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3070      +/-   ##
==========================================
- Coverage   74.38%   73.89%   -0.50%     
==========================================
  Files         249      259      +10     
  Lines       17425    17852     +427     
==========================================
+ Hits        12961    13191     +230     
- Misses       4464     4661     +197

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andrewfullard added 15 commits January 22, 2025 14:56

Implementation of the rates matrix and level pop solvers into plasma

348d7f1

Demonstration notebook

1f8d852

Vague ideas

1829a04

Functional ion population solver

bdfe800

- Currently produces weird results

Add corrected coefficient solver

0cecf6e

Merge branch 'master' into photoion-rates-implementation

9c61d53

Correct multiplication to compute strengths

1972152

Simplify and fix various parts of the rate construction

9b691f2

Update rate matrix construction

e7da551

Add recombination rates to matrix

b9bd98e

Handle charge conservation and matrix solving

1da22ba

Add collisional rates to the matrix

6251a6c

Correct recombination rate calculation

2f26e34

Iterative ion population solver

4dba751

Formatting

69f3b48

andrewfullard added the plasma label May 6, 2025

andrewfullard added 7 commits May 6, 2025 13:32

Collisional rate index fix, ion solver iteration value

85dc58e

Add demo notebook

49e6edf

Basic collisional ionization strength tests

581371f

Uses mock data and needs a regression data test

Improve estimator-based rate calculation

408eb53

Very basic tests for collisional ionization rate class

94a039a

Hydrogen continuum property

b2bc887

Also output electron fractions and remove unneeded assert

Output electron densities from the continuum solver

d43cb05

Rodot- reviewed May 20, 2025

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tardis/plasma/equilibrium/ion_populations.py Outdated Show resolved Hide resolved

andrewfullard added 4 commits June 2, 2025 10:20

Merge branch 'master' into photoion-rates-implementation

bda79ae

Some basic (failing) tests

ab29b5c

Hydrogen plasma additions

39fb72c

Remove unnecessary lambda

bdb62cf

andrewfullard added 3 commits August 12, 2025 10:58

Address Jack's comments

1b2c51a

Merge branch 'master' into photoion-rates-implementation

fe2577a

Cleanup, renames, comments with equations

7e792f1

andrewfullard requested a review from Rodot- August 12, 2025 15:25

jvshields reviewed Aug 12, 2025

View reviewed changes

tardis/plasma/assembly/base.py Outdated Show resolved Hide resolved

Fix excess unit conversion

a2ccdac

jvshields reviewed Aug 12, 2025

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tardis/plasma/equilibrium/tests/test_coll_ionization_rates.py Outdated Show resolved Hide resolved

jvshields reviewed Aug 12, 2025

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jvshields reviewed Aug 12, 2025

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andrewfullard added 2 commits August 12, 2025 15:10

Use fancy new sync dataframe

4cef991

Revert "Use fancy new sync dataframe"

8934011

This reverts commit 4cef991.

andrewfullard requested a review from jvshields August 13, 2025 17:08

andrewfullard added 2 commits August 13, 2025 13:39

Lock in docs notebooks

fc3cdf5

Use the real fancy new sync dataframe

677fc58

jvshields previously approved these changes Aug 14, 2025

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Rodot- previously approved these changes Aug 15, 2025

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andrewfullard added the git-lfs-pull Allow git lfs pull in PRs label Aug 18, 2025

github-actions bot removed the git-lfs-pull Allow git lfs pull in PRs label Aug 18, 2025

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github-actions bot removed the git-lfs-pull Allow git lfs pull in PRs label Aug 18, 2025

Run tests

4d8a4ad

atharva-2001 added the git-lfs-pull Allow git lfs pull in PRs label Aug 18, 2025

github-actions bot removed the git-lfs-pull Allow git lfs pull in PRs label Aug 18, 2025

Fix test failure in old NLTE solver

6fb6334

andrewfullard dismissed stale reviews from Rodot- and jvshields via 6fb6334 August 18, 2025 17:25

andrewfullard merged commit a732a37 into tardis-sn:master Aug 18, 2025
17 of 20 checks passed

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Ionization calculations #3070

Ionization calculations #3070

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