Implementation of refactored rates in plasma #2896
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*beep* *bop* Details2218 [ ] syntax-error
84 F405 [ ] undefined-local-with-import-star-usage
33 I001 [*] unsorted-imports
33 W293 [ ] blank-line-with-whitespace
32 W291 [ ] trailing-whitespace
16 F401 [*] unused-import
10 S108 [ ] hardcoded-temp-file
10 E701 [ ] multiple-statements-on-one-line-colon
10 W605 [*] invalid-escape-sequence
9 E402 [ ] module-import-not-at-top-of-file
7 D202 [*] blank-line-after-function
4 ICN001 [ ] unconventional-import-alias
4 G004 [ ] logging-f-string
4 W292 [ ] missing-newline-at-end-of-file
4 F821 [ ] undefined-name
3 E902 [ ] io-error
3 UP015 [*] redundant-open-modes
3 UP032 [*] f-string
2 C416 [ ] unnecessary-comprehension
2 RET505 [*] superfluous-else-return
2 E702 [ ] multiple-statements-on-one-line-semicolon
2 E703 [*] useless-semicolon
1 EXE001 [ ] shebang-not-executable
1 EXE003 [ ] shebang-missing-python
1 G001 [ ] logging-string-format
1 RET506 [*] superfluous-else-raise
1 F403 [ ] undefined-local-with-import-star
1 F541 [*] f-string-missing-placeholders
1 F811 [*] redefined-while-unused
1 RUF022 [*] unsorted-dunder-all
Found 2503 errors.
[*] 121 fixable with the `--fix` option (13 hidden fixes can be enabled with the `--unsafe-fixes` option).
Complete output(might be large): Detailsbenchmarks/benchmark_base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
benchmarks/benchmark_base.py:74:9: RET506 [*] Unnecessary `else` after `raise` statement
tardis/io/atom_data/base.py:197:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:259:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:263:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:707:17: G004 Logging statement uses f-string
tardis/plasma/properties/partition_function.py:21:11: RUF022 [*] `__all__` is not sorted
tardis/plasma/properties/partition_function.py:154:9: RET505 [*] Unnecessary `elif` after `return` statement
tardis/plasma/properties/partition_function.py:190:25: G004 Logging statement uses f-string
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:54:9: F405 `PreviousBetaSobolev` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:58:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:58:23: F405 `NLTEPopulationSolverRoot` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:61:6: F405 `NLTEIndexHelper` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:61:23: F405 `NLTEPopulationSolverLU` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:65:9: F405 `HeliumNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:66:9: F405 `RadiationFieldCorrection` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:67:9: F405 `ZetaData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:68:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:69:9: F405 `LevelNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:70:9: F405 `IonNumberDensityHeNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:74:6: F405 `LevelNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:74:26: F405 `IonNumberDensity` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:77:6: F405 `HeliumNumericalNLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:81:9: F405 `PhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:82:9: F405 `StimRecombRateFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:83:9: F405 `BfHeatingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:84:9: F405 `StimRecombCoolingRateCoeffEstimator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:85:9: F405 `YgData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:90:9: F405 `StimRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:91:9: F405 `PhotoIonizationData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:92:9: F405 `SpontRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:93:9: F405 `ThermalLevelBoltzmannFactorLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:94:9: F405 `ThermalLTEPartitionFunction` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:95:9: F405 `BetaElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:96:9: F405 `ThermalGElectron` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:97:9: F405 `ThermalPhiSahaLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:98:9: F405 `SahaFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:99:9: F405 `CorrPhotoIonRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:100:9: F405 `SpontRecombCoolingRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:101:9: F405 `YgInterpolator` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:102:9: F405 `CollExcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:103:9: F405 `CollDeexcRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:104:9: F405 `RawCollisionTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:105:9: F405 `MarkovChainIndex` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:106:9: F405 `FreeFreeCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:107:9: F405 `FreeBoundCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:108:9: F405 `LevelNumberDensityLTE` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:109:9: F405 `PhotoIonBoltzmannFactor` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:110:9: F405 `FreeBoundEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:111:9: F405 `LevelIdxs2LineIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:112:9: F405 `LevelIdxs2TransitionIdx` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:113:9: F405 `CollIonRateCoeffSeaton` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:114:9: F405 `CollRecombRateCoeff` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:115:9: F405 `ContinuumInteractionHandler` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:118:58: F405 `AdiabaticCoolingRate` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:121:9: F405 `RawTwoPhotonTransProbs` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:122:9: F405 `TwoPhotonData` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:123:9: F405 `TwoPhotonEmissionCDF` may be undefined, or defined from star imports
tardis/plasma/properties/property_collections.py:124:9: F405 `TwoPhotonFrequencySampler` may be undefined, or defined from star imports
Found 94 errors.
[*] 4 fixable with the `--fix` option.
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Contributor
Author
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This requires updated default atomic data to function correctly, using the full set of Chianti collisional strength values (and not the Carsus pre-calculated values). |
Contributor
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*beep* *bop* Hi, human. The Click here to see the build log. |
Contributor
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*beep* *bop* Significantly changed benchmarks: Details| Change | Before [5e2d0bb3] <master> | After [524968d7] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|---------------------------------------------------------------------------------------------------|
| + | 4.09±0.01ms | 6.27±0.01ms | 1.53 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
All benchmarks: DetailsBenchmarks that have stayed the same:
| Change | Before [5e2d0bb3] <master> | After [524968d7] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 1.31±0.3μs | 1.89±0.4μs | ~1.44 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 591±200ns | 782±300ns | ~1.32 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 3.08±0.01ms | 3.56±0.03ms | ~1.16 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 2.02±1μs | 2.34±1μs | ~1.16 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 3.05±0.5μs | 3.52±0.2μs | ~1.15 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 2.62±0.5ms | 2.86±0.4ms | 1.09 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 43.8±20μs | 46.8±20μs | 1.07 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 45.2±20μs | 46.3±20μs | 1.02 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 63.4±0.1ms | 64.5±0.2ms | 1.02 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 38.9±0.3s | 39.3±0.1s | 1.01 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 3.19±0.5μs | 3.23±0.7μs | 1.01 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 592±200ns | 591±500ns | 1.00 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 2.08±0m | 2.08±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 203±0.2ns | 203±0.03ns | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 1.69±0.2ms | 1.69±0.01ms | 1.00 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 6.32±0.8μs | 6.35±1μs | 1.00 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 1.05±0.01m | 1.04±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 735±0.8ns | 726±0.08ns | 0.99 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 39.4±0.02μs | 38.5±0.02μs | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 601±100ns | 581±200ns | 0.97 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 21.2±5μs | 20.6±5μs | 0.97 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 1.27±0μs | 1.22±0μs | 0.96 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 7.97±2μs | 7.38±2μs | 0.93 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
Benchmarks that have got worse:
| Change | Before [5e2d0bb3] <master> | After [524968d7] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|---------------------------------------------------------------------------------------------------|
| + | 4.09±0.01ms | 6.27±0.01ms | 1.53 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
If you want to see the graph of the results, you can check it here |
6 tasks
Contributor
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We need to change the new atomic data (version 2.0) to have |
Contributor
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Double check where interpolation is happening |
Contributor
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Interpolation is only happening for Chianti data in the |
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TODO:
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6 tasks
jvshields
reviewed
May 7, 2025
jvshields
reviewed
May 7, 2025
jvshields
reviewed
May 29, 2025
|
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||
| # A fake electron distribution. Will eventually be a direct input | ||
| # to the plasma property. | ||
| electron_distribution = ThermalElectronEnergyDistribution( |
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Is this still correct or was this a placeholder?
Or is this just needed to initialize the solver as a first guess?
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This is a placeholder. Eventually t_electrons and previous_electron_densities should be in a ThermalElectronEnergyDistribution object and passed around together instead of as separate items. Ideally with a nonzero energy.
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Pull Request Overview
This PR updates the references to the atomic data file throughout the documentation, configuration examples, notebooks, benchmarks, and CI workflows to use the new file "kurucz_cd23_chianti_H_He_latest.h5" for the refactored plasma rates solver implementation.
- Updated file paths and download commands in various documentation and configuration files
- Adjusted references in CI workflows and benchmarking scripts for consistent use of the new atomic data filename
Reviewed Changes
Copilot reviewed 86 out of 86 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| docs/io/configuration/components/models/densitycust/test_config.yml | Updated atomic data filename |
| docs/io/configuration/components/models/data/config_no_init_trad.yml | Updated atomic data filename |
| docs/io/configuration/components/models/data/config_init_trad.yml | Updated atomic data filename |
| docs/io/configuration/components/models/Custom_TARDIS_Model_Tutorial.ipynb | Updated atomic data filename in log messages |
| docs/io/configuration/components/atomic/current_public_table.rst | Updated atomic data hyperlink and table entry |
| docs/contributing/tools/profiling/tardis_profiling_threads.ipynb | Updated filename in sample code |
| docs/contributing/tools/profiling/profiling_example.ipynb | Updated filename in sample code |
| docs/contributing/tools/benchmark.ipynb | Updated filename in sample code |
| docs/contributing/in_progress/nebular_phase/gammaray_deposition.ipynb | Updated atomic data configuration |
| docs/analyzing_tardis/visualization/tutorial_montecarlo_packet_visualization.ipynb | Updated download command |
| docs/analyzing_tardis/visualization/tutorial_convergence_plot.ipynb | Updated download command |
| docs/analyzing_tardis/visualization/how_to_sdec_plot.ipynb | Updated download command |
| docs/analyzing_tardis/visualization/how_to_liv_plot.ipynb | Updated download command |
| docs/analyzing_tardis/visualization/how_to_generating_widgets.ipynb | Updated log messages and download command |
| docs/analyzing_tardis/liv_plot_notebook.ipynb | Updated dataset recommendation and download command |
| benchmarks/data/tardis_configv1_benchmark.yml | Updated atomic data filename |
| benchmarks/benchmark_base.py | Updated atomic data import, check variable, and file path |
| .github/workflows/lfs-cache.yml | Updated sparse checkout and LFS pull commands |
| .github/actions/setup_lfs/action.yml | Updated sparse checkout and LFS checkout commands |
| .ci-helpers/download_reference_data.sh | Updated atomic data filename in file list |
wkerzendorf
reviewed
May 29, 2025
wkerzendorf
reviewed
May 29, 2025
jvshields
reviewed
May 29, 2025
| @@ -0,0 +1,373 @@ | |||
| { | |||
Contributor
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Might be a hassle, but is there anything that could be added to this plot to show that the NLTE species are doing something? Like also running a workflow without the NLTE balances and just showing that's it's different at all, or doing it from the number densities directly.
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wkerzendorf
reviewed
May 29, 2025
| nlte_data, | ||
| t_electrons, | ||
| j_blues, | ||
| dilute_planckian_radiation_field, |
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that should be any radiation field - or direct mean_intensities which @jvshields suggests
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This cannot be any radiation field in the current plasma, because this is a standard plasma input. The function that this is passed to takes a generic radiation field. The current plasma does not have a mean intensities property. Changes like that are outside the scope of this PR
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|
Sparse checkout of the cache (only pulling the atomic data) isn't working, because the workflows are not pulling the |
Now matches the master branch and passes tests
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2896 +/- ##
==========================================
- Coverage 69.63% 69.02% -0.62%
==========================================
Files 232 232
Lines 16964 16917 -47
==========================================
- Hits 11813 11677 -136
- Misses 5151 5240 +89 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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jvshields
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May 30, 2025
atharva-2001
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Jul 2, 2025
* Implementation of the rates matrix and level pop solvers into plasma * Demonstration notebook * Fixes missing property for radiative NLTE and workflow notebook * Fix legacy test * Rename to use _latest atomic data file * Resolve a couple of comments * Correct Carsus read-in for new data files * Locked in demo notebook * Fix broken tests - Corrected MD5 hash for the atomic data - Renamed global because it is MD5 not UUID - Removed legacy tests (not compatible with new data) * Magic number change due to a change in atomic data * Fix some more magic numbers * Correct atomic data hash * Fix hardcoded paths in notebooks * Revert magic number change Now matches the master branch and passes tests * Revert another magic number change * Revert magic number changes * Fixes some docs pointing to the old data
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📝 Description
Type: 🚀
featureInitial implementation of the new rates solver, level pop solver, and atomic data parsing into the plasma.
Relies on PRs tardis-sn/carsus#414 tardis-sn/carsus-regression-data#2 tardis-sn/tardis-regression-data#45
🚦 Testing
How did you test these changes?
☑️ Checklist
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