Gamma ray spectra dep #2793

Knights-Templars · 2024-08-13T13:55:10Z

This PR refactors the packets sampling, has gamma ray and positron energy deposition, and positronium contribution to the gamma-ray spectra.

Examples, notebooks, and links to useful references.

🚦 Testing

How did you test these changes?

some tests are added

☑️ 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 · 2024-08-13T13:56:22Z

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tardis-bot · 2024-08-13T13:57:02Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (00a34a0).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

95	F405  	[ ] `AdiabaticCoolingRate` may be undefined, or defined from star imports
20	G004  	[ ] Logging statement uses f-string
13	E902  	[ ] No such file or directory (os error 2)
10	F401  	[*] `astropy.units` imported but unused
8	I001  	[*] Import block is un-sorted or un-formatted
7	E999  	[ ] SyntaxError: Expected ',', found ':'
7	D202  	[*] No blank lines allowed after function docstring (found 1)
4	B011  	[*] Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
4	PT015 	[ ] Assertion always fails, replace with `pytest.fail()`
4	RET505	[ ] Unnecessary `elif` after `return` statement
4	UP004 	[*] Class `ConvergencePlots` inherits from `object`
3	RET506	[ ] Unnecessary `else` after `raise` statement
3	F821  	[ ] Undefined name `get_chain_decay_power_per_ejectamass`
2	INP001	[ ] File `tardis/opacities/tests/test_opacity_solver.py` is part of an implicit namespace package. Add an `__init__.py`.
2	E722  	[ ] Do not use bare `except`
2	D406  	[*] Section name should end with a newline ("Returns")
2	D407  	[*] Missing dashed underline after section ("Returns")
2	D411  	[*] Missing blank line before section ("Parameters")
2	UP008 	[*] Use `super()` instead of `super(__class__, self)`
1	ANN204	[ ] Missing return type annotation for special method `__getitem__`
1	S604  	[ ] Function call with truthy `shell` parameter identified, security issue
1	B020  	[ ] Loop control variable `isotope_dict` overrides iterable it iterates
1	ISC003	[ ] Explicitly concatenated string should be implicitly concatenated
1	G001  	[ ] Logging statement uses `str.format`
1	N999  	[ ] Invalid module name: 'GXPacket'
1	W292  	[*] No newline at end of file
1	F403  	[ ] `from tardis.plasma.properties import *` used; unable to detect undefined names
1	F811  	[ ] Redefinition of unused `opacity_state_initialize` from line 13
1	TRY300	[ ] Consider moving this statement to an `else` block

Complete output(might be large):

.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
.mailmap:1:38: E999 SyntaxError: Expected an expression
.mailmap:291:39: W292 [*] No newline at end of file
CHANGELOG.md:4:15: E999 SyntaxError: Expected ',', found ':'
CITATION.cff:3:1: E999 SyntaxError: Invalid annotated assignment target
README.rst:1:1: E999 SyntaxError: Expected a statement
docs/physics/plasma/detailed_balance/collisional_rate_coefficients.hdf:1:1: E902 stream did not contain valid UTF-8
docs/physics/plasma/detailed_balance/comparison.ipynb:cell 31:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/plasma/detailed_balance/test_continuum_template_wkerzen_rate_coeffs.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/physics/plasma/equilibrium/chianti_solver.ipynb:1:1: E902 No such file or directory (os error 2)
docs/physics/plasma/equilibrium/tardis_solver.ipynb:1:1: E902 No such file or directory (os error 2)
docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement
tardis/energy_input/GXPacket.py:1:1: N999 Invalid module name: 'GXPacket'
tardis/energy_input/GXPacket.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/GXPacket.py:41:16: UP004 [*] Class `GXPacket` inherits from `object`
tardis/energy_input/GXPacket.py:75:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/energy_input/GXPacket.py:75:9: D406 [*] Section name should end with a newline ("Returns")
tardis/energy_input/GXPacket.py:202:13: F821 Undefined name `get_chain_decay_power_per_ejectamass`
tardis/energy_input/GXPacket.py:203:17: F821 Undefined name `inventory`
tardis/energy_input/gamma_ray_packet_source.py:1:25: F401 [*] `astropy.units` imported but unused
tardis/energy_input/gamma_ray_packet_source.py:294:53: F821 Undefined name `positronium_continuum`
tardis/energy_input/main_gamma_ray_loop.py:167:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:168:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:212:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:229:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:230:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:284:17: G004 Logging statement uses f-string
tardis/energy_input/tests/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/tests/conftest.py:24:9: S604 Function call with truthy `shell` parameter identified, security issue
tardis/energy_input/tests/test_gamma_ray_channel.py:119:9: B020 Loop control variable `isotope_dict` overrides iterable it iterates
tardis/energy_input/tests/test_gamma_ray_grid.py:12:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:12:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/util.py:409:5: RET505 Unnecessary `elif` after `return` statement
tardis/energy_input/util.py:420:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/util.py:422:5: D411 [*] Missing blank line before section ("Parameters")
tardis/io/atom_data/base.py:198:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:263:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:267:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:704:17: G004 Logging statement uses f-string
tardis/opacities/macro_atom/base.py:120:5: D411 [*] Missing blank line before section ("Parameters")
tardis/opacities/macro_atom/base.py:227:5: E722 Do not use bare `except`
tardis/opacities/macro_atom/base.py:246:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/opacities/macro_atom/base.py:357:9: E722 Do not use bare `except`
tardis/opacities/macro_atom/macroatom_solver.py:8:23: UP004 [*] Class `MacroAtomSolver` inherits from `object`
tardis/opacities/macro_atom/macroatom_solver.py:14:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/macro_atom/macroatom_solver.py:28:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/macro_atom/macroatom_solver.py:90:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/opacity_solver.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/opacity_solver.py:9:21: UP004 [*] Class `OpacitySolver` inherits from `object`
tardis/opacities/opacity_solver.py:17:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/opacity_state.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/opacity_state.py:42:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/opacity_state.py:174:9: ANN204 Missing return type annotation for special method `__getitem__`
tardis/opacities/opacity_state.py:180:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/opacities/opacity_state.py:180:9: D406 [*] Section name should end with a newline ("Returns")
tardis/opacities/opacity_state.py:215:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/tau_sobolev.py:92:14: UP008 Use `super()` instead of `super(__class__, self)`
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: E902 No such file or directory (os error 2)
tardis/plasma/detailed_balance/rates/__init__.py:2:5: F401 `tardis.plasma.detailed_balance.rates.collision_strengths.UpsilonCMFGENSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/detailed_balance/rates/__init__.py:3:5: F401 `tardis.plasma.detailed_balance.rates.collision_strengths.UpsilonRegemorterSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/detailed_balance/rates/__init__.py:6:5: F401 `tardis.plasma.detailed_balance.rates.collisional_rates.ThermalCollisionalRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/detailed_balance/rates/__init__.py:9:5: F401 `tardis.plasma.detailed_balance.rates.radiative_rates.RadiativeRatesSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/electron_energy_distribution/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/electron_energy_distribution/base.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/level_populations.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rate_matrix.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/tests/conftest.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/tests/test_level_populations.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/tests/test_rate_matrix.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/properties/legacy_property_collections.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/properties/property_collections.py:10:1: F403 `from tardis.plasma.properties import *` used; unable to detect undefined names
tardis/plasma/properties/property_collections.py:19:9: F405 `DilutePlanckianRadField` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:20:9: F405 `NumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:21:9: F405 `TimeExplosion` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:22:9: F405 `AtomicData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:23:9: F405 `JBlues` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:24:9: F405 `LinkTRadTElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:25:9: F405 `HeliumTreatment` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:26:9: F405 `ContinuumInteractionSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:27:9: F405 `NLTEIonizationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:28:9: F405 `NLTEExcitationSpecies` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:33:9: F405 `TRadiative` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:34:9: F405 `DilutionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:35:9: F405 `BetaRadiation` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:36:9: F405 `Levels` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:37:9: F405 `Lines` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:38:9: F405 `PartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:39:9: F405 `GElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:40:9: F405 `IonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:41:9: F405 `LinesLowerLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:42:9: F405 `LinesUpperLevelIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:44:9: F405 `StimulatedEmissionFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:45:9: F405 `SelectedAtoms` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:46:9: F405 `ElectronTemperature` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:49:55: F405 `PhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:50:55: F405 `LevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:52:6: F405 `BetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:52:44: F405 `MacroAtomData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:55:6: F405 `PhiSahaNebular` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:55:22: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:55:32: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:55:46: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:58:6: F405 `LevelBoltzmannFactorDiluteLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:60:49: F405 `LevelBoltzmannFactorNoNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:63:9: F405 `LevelBoltzmannFactorNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:64:9: F405 `NLTEData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:65:9: F405 `PreviousElectronDensities` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:66:9: F405 `PreviousBetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:67:9: F405 `BetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:71:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:71:23: F405 `NLTEPopulationSolverRoot` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:74:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:74:23: F405 `NLTEPopulationSolverLU` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:78:9: F405 `HeliumNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:79:9: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:80:9: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:81:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:82:9: F405 `LevelNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:83:9: F405 `IonNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:87:6: F405 `LevelNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:87:26: F405 `IonNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:90:6: F405 `HeliumNumericalNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:94:9: F405 `PhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:95:9: F405 `StimRecombRateFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:96:9: F405 `BfHeatingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:97:9: F405 `StimRecombCoolingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:98:9: F405 `YgData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:103:9: F405 `StimRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:104:9: F405 `PhotoIonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:105:9: F405 `SpontRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:106:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:107:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:108:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:109:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:110:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:111:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:112:9: F405 `CorrPhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:113:9: F405 `SpontRecombCoolingRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:114:9: F405 `RawRecombTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:115:9: F405 `RawPhotoIonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:116:9: F405 `RawRadBoundBoundTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:117:9: F405 `MarkovChainTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:118:9: F405 `NonContinuumTransProbsMask` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:119:9: F405 `YgInterpolator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:120:9: F405 `CollExcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:121:9: F405 `CollDeexcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:122:9: F405 `RawCollisionTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:123:9: F405 `MarkovChainIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:124:9: F405 `MarkovChainTransProbsCollector` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:126:9: F405 `MonteCarloTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:127:9: F405 `FreeFreeCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:128:9: F405 `FreeBoundCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:130:9: F405 `LevelNumberDensityLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:131:9: F405 `PhotoIonBoltzmannFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:132:9: F405 `FreeBoundEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:133:9: F405 `LevelIdxs2LineIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:134:9: F405 `LevelIdxs2TransitionIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:135:9: F405 `CollIonRateCoeffSeaton` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:136:9: F405 `CollRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:138:9: F405 `ContinuumInteractionHandler` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:139:9: F405 `BetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:142:58: F405 `AdiabaticCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:145:9: F405 `RawTwoPhotonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:146:9: F405 `TwoPhotonData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:147:9: F405 `TwoPhotonEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:148:9: 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:449:13: G004 Logging statement uses f-string
tardis/simulation/base.py:547:13: G004 Logging statement uses f-string
tardis/simulation/base.py:654:25: G004 Logging statement uses f-string
tardis/simulation/base.py:657:13: G004 Logging statement uses f-string
tardis/simulation/base.py:662:13: G004 Logging statement uses f-string
tardis/simulation/base.py:713:13: TRY300 Consider moving this statement to an `else` block
tardis/simulation/base.py:715:26: G004 Logging statement uses f-string
tardis/spectrum/formal_integral.py:23:5: F811 Redefinition of unused `opacity_state_initialize` from line 13
tardis/spectrum/formal_integral.py:340:13: RET506 Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral.py:681:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:717:5: RET505 Unnecessary `else` after `return` statement
tardis/visualization/tools/convergence_plot.py:3:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/tools/convergence_plot.py:4:25: F401 [*] `matplotlib.cm` imported but unused
tardis/visualization/tools/convergence_plot.py:5:29: F401 [*] `matplotlib.colors` imported but unused
tardis/visualization/tools/convergence_plot.py:39:24: UP004 [*] Class `ConvergencePlots` inherits from `object`
tardis/visualization/tools/convergence_plot.py:321:13: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/workflows/simple_tardis_workflow.py:218:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:430:17: 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 204 errors.
[*] 32 fixable with the `--fix` option (6 hidden fixes can be enabled with the `--unsafe-fixes` option).

andrewfullard · 2024-08-13T18:49:43Z

tardis/energy_input/gamma_ray_packet_source.py

+        ] = PositroniumSampler().sample_energy(n_samples=
+            np.sum(positronium_formation & annihilation_line & three_photon_decay)
+        )
+        energy_array[positronium_formation & annihilation_line & ~three_photon_decay] = 511.0


This is a cool way to do this!

tardis/energy_input/gamma_ray_packet_source.py

tardis/energy_input/gamma_packet_loop.py

tardis/energy_input/gamma_ray_packet_source.py

tardis/energy_input/main_gamma_ray_loop.py

wkerzendorf · 2024-08-14T19:36:41Z

tardis/energy_input/tests/test_gamma_ray_channel.py

 )

+from tardis.energy_input.gamma_ray_transport import get_taus
+from tardis.energy_input.util import KEV2ERG


this is an astropy units thing

astropy units have been used. Do you want separately in this file?

tardis/energy_input/gamma_ray_packet_source.py

tardis-bot · 2024-08-19T15:35:37Z

*beep* *bop*

Hi, human.

I'm the @tardis-bot and couldn't find your records in my database. I think we don't know each other, or you changed your credentials recently.

Please add your name and email to .mailmap in your current branch and push the changes to this pull request.

In case you need to map an existing alias, follow this example.

codecov · 2024-08-19T15:48:01Z

Codecov Report

Attention: Patch coverage is 42.47104% with 149 lines in your changes missing coverage. Please review.

Project coverage is 70.55%. Comparing base (b95388b) to head (00a34a0).
Report is 5 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/energy_input/main_gamma_ray_loop.py	13.04%	60 Missing ⚠️
tardis/energy_input/gamma_ray_packet_source.py	14.70%	29 Missing ⚠️
tardis/energy_input/util.py	13.63%	19 Missing ⚠️
tardis/energy_input/gamma_ray_channel.py	63.88%	13 Missing ⚠️
tardis/energy_input/gamma_packet_loop.py	0.00%	12 Missing ⚠️
tardis/energy_input/samplers.py	44.44%	10 Missing ⚠️
tardis/energy_input/GXPacket.py	0.00%	5 Missing ⚠️
tardis/energy_input/gamma_ray_grid.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2793      +/-   ##
==========================================
+ Coverage   70.24%   70.55%   +0.30%     
==========================================
  Files         214      221       +7     
  Lines       15981    16261     +280     
==========================================
+ Hits        11226    11473     +247     
- Misses       4755     4788      +33

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

tardis-bot · 2024-08-19T19:01:55Z

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (92df2cf) and the latest commit (9f83760).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

Benchmarks that have improved:

| Change   | Before [b79b61ed] <master>   | After [9f83760a]    | Ratio   | Benchmark (Parameter)                                                                                                                        |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------------------------------|
|          | failed                       | 541±100ns           | n/a     | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                               |
|          | failed                       | 571±200ns           | n/a     | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                         |
|          | failed                       | 602±100ns           | n/a     | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                                       |
|          | failed                       | 3.68±0.02ms         | n/a     | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                            |
|          | failed                       | 2.72±0ms            | n/a     | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                              |
|          | failed                       | 38.9±0.05s          | n/a     | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                                |
|          | failed                       | 1.02±0m             | n/a     | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                               |
|          | failed                       | 2.08±0m             | n/a     | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                          |
|          | failed                       | 207±0.2ns           | n/a     | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                                |
|          | failed                       | 1.18±0μs            | n/a     | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                         |
|          | failed                       | 1.44±0.4μs          | n/a     | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                             |
|          | failed                       | 3.42±2μs            | n/a     | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators                |
|          | failed                       | 43.6±40μs           | n/a     | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                                  |
|          | failed                       | 45.7±30μs           | n/a     | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                                   |
|          | failed                       | 785±3ns             | n/a     | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                                |
|          | failed                       | 1.68±0ms            | n/a     | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                                      |
|          | failed                       | 27.4±9μs            | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list(10, 10)  |
|          | failed                       | 20.8±2μs            | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list(10, 50)  |
|          | failed                       | 26.3±5μs            | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list(100, 10) |
|          | failed                       | 28.7±6μs            | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list(100, 50) |
|          | failed                       | 7.52±0.01μs         | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list(10, 10)                   |
|          | failed                       | 7.74±0μs            | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list(10, 50)                   |
|          | failed                       | 55.7±0.1μs          | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list(100, 10)                  |
|          | failed                       | 50.7±0.02μs         | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list(100, 50)                  |
|          | failed                       | 63.9±0.5ms          | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe(10, 10)                   |
|          | failed                       | 63.3±0.1ms          | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe(10, 50)                   |
|          | failed                       | 62.5±0.04ms         | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe(100, 10)                  |
|          | failed                       | 64.5±0.2ms          | n/a     | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe(100, 50)                  |
|          | failed                       | 2.63±0.3ms          | n/a     | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                                 |
|          | failed                       | 2.94±0.5μs          | n/a     | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                                |
|          | failed                       | 6.16±1μs            | n/a     | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                                    |
|          | failed                       | 7.05±2μs            | n/a     | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                             |
|          | failed                       | 3.29±0.6μs          | n/a     | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                                       |

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

Knights-Templars · 2024-08-30T14:11:42Z

.mailmap

@@ -47,6 +47,7 @@ Atharwa Kharkar <[email protected]> atharwa_24 <[email protected]
 Atul Kumar <[email protected]>

 Anirban Dutta <[email protected]>
+Anirban Dutta <[email protected]>


Change mailmap!

Knights-Templars · 2024-08-30T14:24:38Z

tardis/energy_input/gamma_packet_loop.py

@@ -103,21 +101,23 @@ def gamma_packet_loop(
    escaped_packets = 0
    scattered_packets = 0
    packet_count = len(packets)
+    # Logging does not work with numba


Remove the "print statement".

DeerWhale · 2024-08-30T14:54:07Z

tardis/energy_input/gamma_ray_packet_source.py

-            packet_effective_times,
-        )
+        decay_time_indices = []
+        for i in range(number_of_packets):


If the decay time indices is not needed, perhaps just remove this part of the code?

Yes. True. Added time_index as part of the G_packet. This eliminates the use of the for loop also.

tardis/energy_input/gamma_packet_loop.py

tardis/energy_input/gamma_ray_packet_source.py

tardis/energy_input/main_gamma_ray_loop.py

andrewfullard · 2024-12-03T15:55:14Z

tardis/energy_input/samplers.py

+        n_grid : int, optional
+            Number of grid points for the CDF, by default 1000
+        """
+        self.x_grid = np.linspace(0.01, 0.99, n_grid)


Why doesn't it go from 0 to 1?

Because if you see the pdf there is log(1-x) which is inf at 1. Also in few terms it is (1-x)/x, so the function diverges at 0.

Okay. What effect does this limited grid have? If you're doing 1000 points I would expect 0.001 instead of 0.01 as the min and 0.999 as the max.

Yes. True. We can go as low in the lower end and as high in the higher end. I did not check the differences, but can do that.

tardis/energy_input/samplers.py

jvshields · 2024-12-09T15:27:32Z

tardis/energy_input/gamma_packet_loop.py

@@ -103,21 +101,20 @@ def gamma_packet_loop(
    escaped_packets = 0
    scattered_packets = 0
    packet_count = len(packets)
+    # Logging does not work with numba. Using print instead.
    print("Entering gamma ray loop for " + str(packet_count) + " packets")


I would much prefer using logging, and just doing it right above the function call rather than inside the function.

Yep now this is moving from being in-development, we should formalize some of these logs (which has already been done in some of the other major functions)

andrewfullard · 2024-12-09T15:30:04Z

tardis/energy_input/GXPacket.py

@@ -31,7 +31,8 @@ class GXPacketStatus(IntEnum):
    ("nu_cmf", float64),
    ("status", int64),
    ("shell", int64),
-    ("time_current", float64),
+    ("time_start", float64),


I don't think this is a good name for a variable that is updated once the packet has travelled a distance.

andrewfullard · 2024-12-09T15:41:54Z

tardis/energy_input/gamma_packet_loop.py

-    print("Escaped packets:", escaped_packets)
-    print("Scattered packets:", scattered_packets)
+    print("Number of escaped packets:", escaped_packets)
+    print("Number of scattered packets:", scattered_packets)


See note about print statements above

I think these print statements are useful diagnostics. I am not sure how to use logging here.

andrewfullard · 2024-12-09T15:44:42Z

tardis/energy_input/gamma_ray_channel.py

+        dataframe of isotopes for each shell with their decay mode, number of decays, radiation type,
+        radiation energy and radiation intensity at each time step.
+
+    """


This function duplicates some code from the function above that could be factored out into a different function

jvshields · 2024-12-09T15:46:45Z

tardis/energy_input/gamma_ray_channel.py

@@ -167,3 +169,98 @@ def create_isotope_decay_df(cumulative_decay_df, gamma_ray_lines):
    )

    return isotope_decay_df
+
+
+def time_evolve_mass_fraction(raw_isotope_mass_fraction, time_array):


Maybe combine this with the time_evolve_cumilative_decay function below, and just have the combined function return both the new mass fractions and cumulative decays.

jvshields · 2024-12-09T15:49:48Z

tardis/energy_input/gamma_ray_packet_source.py

    get_index,
    get_random_unit_vector,
 )
 from tardis.transport.montecarlo.packet_source import BasePacketSource

+POSITRON_ANNIHILATION_LINE = 511.0


Perhaps have a comment here adding "in KeV"

jvshields · 2024-12-09T15:58:05Z

tardis/energy_input/gamma_ray_packet_source.py

+        # annihilation line of positrons
+        annihilation_line = packets["radiation_energy_keV"] == POSITRON_ANNIHILATION_LINE
+        # three photon decay of positronium
+        three_photon_decay = np.random.random(number_of_packets) > PARA_TO_ORTHO_RATIO


Probably just use np.random.uniform instead of np.random.random? Weird to use different functions between this line and above in 601.

jvshields · 2024-12-09T16:09:41Z

tardis/energy_input/gamma_ray_packet_source.py

-        positronium_energy, positronium_intensity = positronium_continuum()
+        # sample packets from the gamma-ray lines only (include X-rays!)
+        sampled_packets_df_gamma = decays_per_isotope[
+            decays_per_isotope["radiation"] == "g"


This is a pretty weird operation, especially considering the documentation says that decays_per_isotope is an array of int64s. Is the documentation wrong?

Anirban Dutta added 10 commits August 5, 2024 15:29

Changed GX_packet to accommodate positron_fraction

ddc060c

Added tardis like string

cc6a1e5

Added positronium sampler

1be314c

Added time evolution of decays as the composition changes

82dc7de

Added 3D Doppler function for all packets

cf0258d

changed name of root to discriminant-helps in understanding

05f09f5

Added sampling frequencies and positronium fraction

6e5f459

Modified energy deposition

8d2179d

Added tests and changed main loop

0ab1571

Added changes to get deposition

6dd1c54

Knights-Templars marked this pull request as draft August 13, 2024 13:55

andrewfullard reviewed Aug 13, 2024

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Knights-Templars commented Aug 14, 2024

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andrewfullard reviewed Aug 14, 2024

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andrewfullard added the nebular label Aug 14, 2024

wkerzendorf reviewed Aug 14, 2024

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Anirban Dutta added 5 commits August 19, 2024 08:08

Modified how times and effective times are used

ca8c054

Changed mailmap

9e8c19a

Black formatting

101c037

changed GXpacket attribute

8484acd

Fixed test

1d0398e

Added a note to change appending to dataframes

76115ad

andrewfullard previously approved these changes Aug 19, 2024

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andrewfullard marked this pull request as ready for review August 19, 2024 18:25

Knights-Templars commented Aug 30, 2024

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DeerWhale reviewed Aug 30, 2024

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Merged updates into working branch

8d39eb0

Knights-Templars added gamma-ray and removed nebular labels Nov 28, 2024

Added corrections to comments

0a5ac59

Knights-Templars dismissed andrewfullard’s stale review via 0a5ac59 December 2, 2024 12:44

Comments addressed

8fb6f48

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Knights-Templars added 3 commits December 2, 2024 15:05

Added review suggestions and small changes to the GX packet

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984b95e

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andrewfullard requested review from jvshields, DeerWhale and wkerzendorf and removed request for Rodot- December 3, 2024 16:01

Knights-Templars added 3 commits December 3, 2024 13:54

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Gamma ray spectra dep #2793

Gamma ray spectra dep #2793

Knights-Templars commented Aug 13, 2024

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Gamma ray spectra dep #2793

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Gamma ray spectra dep #2793

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Knights-Templars commented Aug 13, 2024

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