Refactor isotope mass fraction handling and configuration

[wkerzendorf]

• Remove raw_isotope_abundance from Composition class
• Update mass fraction parsing to conditionally apply isotope decay
• Modify default model_isotope_time_0 to -1 s to allow skipping decay
• Update test fixtures to explicitly set model_isotope_time_0
• Simplify mass fraction parsing functions by removing redundant returns

[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (7c2e477).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

2	W293  	[*] Blank line contains whitespace
2	F401  	[*] `radioactivedecay.converters` imported but unused
1	B020  	[ ] Loop control variable `isotope_dict` overrides iterable it iterates
1	RET505	[ ] Unnecessary `else` after `return` statement
1	PTH117	[ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
1	I001  	[*] Import block is un-sorted or un-formatted
1	E999  	[ ] SyntaxError: Expected an expression

Complete output(might be large):

tardis/energy_input/tests/test_gamma_ray_channel.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/tests/test_gamma_ray_channel.py:8:30: F401 [*] `radioactivedecay.converters` imported but unused
tardis/energy_input/tests/test_gamma_ray_channel.py:13:5: F401 [*] `tardis.energy_input.energy_source.get_nuclear_lines_database` imported but unused
tardis/energy_input/tests/test_gamma_ray_channel.py:118:9: B020 Loop control variable `isotope_dict` overrides iterable it iterates
tardis/io/configuration/schemas/model_definitions.yml:2:13: E999 SyntaxError: Expected an expression
tardis/io/configuration/schemas/model_definitions.yml:164:1: W293 [*] Blank line contains whitespace
tardis/io/configuration/schemas/model_definitions.yml:210:1: W293 [*] Blank line contains whitespace
tardis/io/model/parse_mass_fraction_configuration.py:62:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/model/matter/composition.py:204:9: RET505 Unnecessary `else` after `return` statement
Found 9 errors.
[*] 5 fixable with the `--fix` option.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.18%. Comparing base (13c9a31) to head (7c2e477).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2974      +/-   ##
==========================================
- Coverage   69.54%   69.18%   -0.36%     
==========================================
  Files         228      228              
  Lines       16429    16433       +4     
==========================================
- Hits        11425    11369      -56     
- Misses       5004     5064      +60     

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[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (13c9a31) and the latest commit (7c2e477).
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 [13c9a314] <release-2025.02.16>   | After [7c2e4778]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 521±100ns                                | 581±90ns            | ~1.12   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 1.68±0.5μs                               | 1.51±0.2μs          | ~0.90   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 3.87±0.6μs                               | 3.41±0.6μs          | ~0.88   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 581±100ns                                | 491±100ns           | ~0.85   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 3.18±0.6ms                               | 2.64±0.4ms          | ~0.83   | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 4.01±0.5ms                               | 3.06±0.07ms         | ~0.76   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 66.6±20μs                                | 42.7±20μs           | ~0.64   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 64.7±0.4ms                               | 69.4±2ms            | 1.07    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 2.62±0.7μs                               | 2.74±0.5μs          | 1.05    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 7.07±2μs                                 | 7.39±2μs            | 1.05    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 38.6±0.02s                               | 39.9±0.2s           | 1.04    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 40.9±20μs                                | 42.4±20μs           | 1.04    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 3.98±0.02ms                              | 4.10±0.04ms         | 1.03    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 1.05±0m                                  | 1.06±0m             | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 206±0.1ns                                | 207±0.2ns           | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 581±200ns                                | 581±200ns           | 1.00    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 2.08±0m                                  | 2.09±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.21±0μs                                 | 1.20±0μs            | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 742±80ns                                 | 731±0.4ns           | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 27.8±8μs                                 | 27.5±8μs            | 0.99    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 2.40±1μs                                 | 2.33±1μs            | 0.97    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 39.9±0.03μs                              | 38.7±0.04μs         | 0.97    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 1.76±0ms                                 | 1.68±0ms            | 0.95    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 6.90±0.9μs                               | 6.39±0.7μs          | 0.93    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |

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

[jvshields]

Why -1? Doesn't that mean something different?

[wkerzendorf]

it mens we are using the exact same time as time_explosion. Can put in the description if that helps.