Simple Atom data refactor

[andrewfullard]

:pencil: Description

Type: :roller_coaster: infrastructure

This uses dataclasses to begin simplifying the atom data.

:vertical_traffic_light: Testing

How did you test these changes?

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

:ballot_box_with_check: Checklist

• [x] 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 (a0a1566660991fbcd21770db2e90dce81d83a223). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 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):

```diff 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[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ 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 ```

:umbrella: View full report in Codecov by Sentry.
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[tardis-bot]

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (8a317dd9eead8acab8d9c17d290863e05f5a27f2) and the latest commit (a0a1566660991fbcd21770db2e90dce81d83a223). Here are the logs produced by ASV. Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

```diff ```

All benchmarks:

```diff Benchmarks that have stayed the same: | Change | Before [8a317dd9] | 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