Simple Atom data refactor

[andrewfullard]

📝 Description

Type: 🎢 infrastructure

This uses dataclasses to begin simplifying the atom 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.

[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (a0a1566).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

3	G004 	[ ] Logging statement uses f-string
1	G001 	[ ] Logging statement uses `str.format`
1	E902 	[ ] No such file or directory (os error 2)
1	UP030	[*] Use implicit references for positional format fields

Complete output(might be large):

tardis/io/atom_data/base.py:182:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:236:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:240:21: UP030 Use implicit references for positional format fields
tardis/io/atom_data/base.py:240:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:670:17: G004 Logging statement uses f-string
tardis/plasma/nlte/__init__.py:1:1: E902 No such file or directory (os error 2)
Found 6 errors.
No fixes available (1 hidden fix can be enabled with the `--unsafe-fixes` option).

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.68%. Comparing base (8a317dd) to head (a0a1566).
Report is 9 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2783      +/-   ##
==========================================
- Coverage   69.91%   69.68%   -0.24%     
==========================================
  Files         206      208       +2     
  Lines       15523    15490      -33     
==========================================
- Hits        10853    10794      -59     
- Misses       4670     4696      +26     

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

[Rodot-]

Could you expand a bit on the broader design goals of this PR?

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (8a317dd) and the latest commit (a0a1566).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [8a317dd9] <master>   | After [a0a15666]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 6.75±0.6μs                   | 6.05±1μs            | ~0.90   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 551±100ns                    | 491±100ns           | ~0.89   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 52.0±20μs                    | 45.9±20μs           | ~0.88   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 48.8±20μs                    | 42.4±20μs           | ~0.87   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 671±200ns                    | 551±100ns           | ~0.82   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 3.07±0.5μs                   | 3.36±0.5μs          | 1.09    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 7.13±2μs                     | 7.60±1μs            | 1.07    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 1.64±0.2μs                   | 1.72±0.3μs          | 1.05    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 769±0.7ns                    | 801±2ns             | 1.04    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 2.12±2μs                     | 2.15±1μs            | 1.01    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 1.05±0m                      | 1.04±0m             | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.07±0m                      | 2.07±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 206±0.5ns                    | 207±0.1ns           | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 30.4±0.06μs                  | 30.4±0.07μs         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 39.3±0.07s                   | 39.0±0.02s          | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.58±0.5ms                   | 2.56±0.5ms          | 0.99    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 1.69±0.01ms                  | 1.66±0ms            | 0.98    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 64.1±0ms                     | 63.0±0.3ms          | 0.98    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 3.72±0.01ms                  | 3.61±0.01ms         | 0.97    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 1.21±0.04μs                  | 1.16±0μs            | 0.96    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 571±200ns                    | 541±100ns           | 0.95    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 2.79±0.02ms                  | 2.64±0.01ms         | 0.95    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 23.5±6μs                     | 22.2±5μs            | 0.94    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 2.99±0.4μs                   | 2.79±0.7μs          | 0.93    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |

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

[wkerzendorf]

I don't think that is quite right. I'm pretty sure the yg_data stores it as part of the columns. Or ChiantiCollisionData. have a quick look in the plasma

[andrewfullard]

Looking at the plasma YgData class, it uses both yg_data and collision_data_temperatures. See https://github.com/andrewfullard/tardis/blob/atom-data-refactor-v2/tardis/plasma/properties/atomic.py#L676 and https://github.com/andrewfullard/tardis/blob/atom-data-refactor-v2/tardis/plasma/properties/atomic.py#L687. For the Chianti-source collision_data, it is used in NLTEData, see https://github.com/andrewfullard/tardis/blob/atom-data-refactor-v2/tardis/io/atom_data/nlte_data.py#L18-L19 and https://github.com/andrewfullard/tardis/blob/atom-data-refactor-v2/tardis/io/atom_data/nlte_data.py#L86.

Oddly in the from_hdf method in this class, collision_data is set to "dummy value" if the data is sourced from CMFGen, see https://github.com/andrewfullard/tardis/blob/atom-data-refactor-v2/tardis/io/atom_data/base.py#L199. That is why I did not include it in the CMFGen dataclass.