Add molecular data exposure to tardis atom data

[jvshields]

Needed for STARDIS to access the molecular information ingested by carsus added in tardis-sn/carsus#396

Currently I don't think it's worth adding a molecular_data class, but if we ever want to do more complex handling of molecules, calculating them in a similar way to atomic number densities instead of just using equilibrium constants, then it might be worth reconsidering.

[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (ec4d62a).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

5	I001  	[*] Import block is un-sorted or un-formatted
4	G004  	[ ] Logging statement uses f-string
3	F405  	[ ] `deepcopy` may be undefined, or defined from star imports
2	RET505	[ ] Unnecessary `else` after `return` statement
2	D202  	[*] No blank lines allowed after function docstring (found 1)
1	G001  	[ ] Logging statement uses `str.format`
1	PT020 	[ ] `@pytest.yield_fixture` is deprecated, use `@pytest.fixture`
1	RET506	[ ] Unnecessary `elif` after `raise` statement
1	E902  	[ ] No such file or directory (os error 2)
1	F401  	[*] `astropy.units` imported but unused
1	F403  	[ ] `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names
1	F821  	[ ] Undefined name `pytest_report_header`
1	PGH004	[ ] Use specific rule codes when using `noqa`
1	UP030 	[*] Use implicit references for positional format fields

Complete output(might be large):

tardis/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/conftest.py:11:1: F403 `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names
tardis/conftest.py:30:49: PGH004 Use specific rule codes when using `noqa`
tardis/conftest.py:32:9: F821 Undefined name `pytest_report_header`
tardis/conftest.py:145:5: RET505 Unnecessary `else` after `return` statement
tardis/conftest.py:169:1: PT020 `@pytest.yield_fixture` is deprecated, use `@pytest.fixture`
tardis/conftest.py:240:19: F405 `deepcopy` may be undefined, or defined from star imports
tardis/conftest.py:249:19: F405 `deepcopy` may be undefined, or defined from star imports
tardis/conftest.py:278:19: F405 `deepcopy` may be undefined, or defined from star imports
tardis/gui/tests/test_gui.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/gui/tests/test_gui.py:5:25: F401 [*] `astropy.units` imported but unused
tardis/gui/tests/test_gui.py:8:1: I001 [*] Import block is un-sorted or un-formatted
tardis/io/atom_data/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
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: UP030 Use implicit references for positional format fields
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/tests/test_tardis_full_formal_integral.py:61:9: RET505 Unnecessary `else` after `return` statement
tardis/visualization/tools/liv_plot.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/tools/liv_plot.py:25:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/visualization/tools/liv_plot.py:48:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/visualization/tools/liv_plot.py:247:17: G004 Logging statement uses f-string
tardis/visualization/tools/liv_plot.py:357:13: RET506 Unnecessary `elif` after `raise` statement
tardis/visualization/tools/tests/test_liv_plot.py:1:1: E902 No such file or directory (os error 2)
Found 25 errors.
[*] 8 fixable with the `--fix` option (1 hidden fix can be enabled with the `--unsafe-fixes` option).

[andrewfullard]

Seems reasonable. Should definitely become a class eventually.

[codecov]

Codecov Report

Attention: Patch coverage is 70.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 70.79%. Comparing base (5fe6806) to head (ec4d62a).
Report is 3 commits behind head on master.

Files	Patch %	Lines
tardis/io/atom_data/base.py	70.00%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2806      +/-   ##
==========================================
+ Coverage   69.88%   70.79%   +0.91%     
==========================================
  Files         208      209       +1     
  Lines       15453    15638     +185     
==========================================
+ Hits        10799    11071     +272     
+ Misses       4654     4567      -87     

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

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (5fe6806) and the latest commit (ec4d62a).
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 [b6f11851] <master>   | After [ec4d62ad]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 491±100ns                    | 1.09±0.3μs          | ~2.22   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 2.87±0.5μs                   | 3.24±0.3μs          | ~1.13   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 601±200ns                    | 521±100ns           | ~0.87   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 28.8±8μs                     | 24.8±7μs            | ~0.86   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 2.33±1μs                     | 1.98±2μs            | ~0.85   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 3.92±0.6μs                   | 3.20±0.3μs          | ~0.82   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 63.6±0.06ms                  | 69.1±2ms            | 1.09    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 6.05±0.9μs                   | 6.37±0.8μs          | 1.05    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 39.3±0.02s                   | 39.2±0.07s          | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.07±0m                      | 2.07±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.44±0.3μs                   | 1.44±0.4μs          | 1.00    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 1.05±0m                      | 1.04±0m             | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 211±0.1ns                    | 208±0.3ns           | 0.99    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 735±0.2ns                    | 728±5ns             | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 30.7±0.03μs                  | 30.4±0.05μs         | 0.99    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 4.16±0.04ms                  | 4.09±0.03ms         | 0.98    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 1.73±0.02ms                  | 1.70±0.02ms         | 0.98    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 7.40±2μs                     | 7.28±2μs            | 0.98    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 581±200ns                    | 561±200ns           | 0.97    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 2.69±0.4ms                   | 2.60±0.5ms          | 0.97    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 1.24±0μs                     | 1.19±0.1μs          | 0.96    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 44.0±20μs                    | 42.3±20μs           | 0.96    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 46.8±20μs                    | 44.1±30μs           | 0.94    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 2.95±0.02ms                  | 2.71±0.02ms         | 0.92    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |

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

[wkerzendorf]

Seems reasonable. Should definitely become a class eventually.

I think make it a dataclass now to put all of these together in one.