Address pytest warnings

[atharva-2001]

📝 Description

Type: 🪲 bugfix | 🚀 feature | ☣️ breaking change | 🚦 testing | 📝 documentation | 🎢 infrastructure

Addresses pytest warnings.

📌 Resources

Examples, notebooks, and links to useful references.

🚦 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]

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Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

[codecov]

Codecov Report

Attention: Patch coverage is 65.62500% with 11 lines in your changes missing coverage. Please review.

Project coverage is 69.83%. Comparing base (bcbe40d) to head (ea84805).
Report is 9 commits behind head on master.

Files	Patch %	Lines
tardis/visualization/widgets/custom_abundance.py	18.18%	9 Missing ⚠️
tardis/io/model/readers/blondin_toymodel.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2745      +/-   ##
==========================================
+ Coverage   69.65%   69.83%   +0.17%     
==========================================
  Files         188      191       +3     
  Lines       14930    15022      +92     
==========================================
+ Hits        10400    10490      +90     
- Misses       4530     4532       +2     

☔ 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 (bcbe40d) and the latest commit (ea84805).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

All benchmarks:

| Change   | Before [17ee2872] <master>   | After [ea848050]    | Ratio   | Benchmark (Parameter)                                                                                                                                                                                                                              |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|          | 2.76±0.9μs                   | 2.78±0.9μs          | 1.01    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000.0, 255.5)                                                                                                                                    |
|          | 2.57±0.8μs                   | 2.44±0.8μs          | 0.95    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000.0, 511.0)                                                                                                                                    |
|          | 2.84±1μs                     | 2.80±0.9μs          | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000.0, 5110000000.0)                                                                                                                             |
|          | 3.65±1μs                     | 2.88±0.9μs          | ~0.79   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000000000.0, 255.5)                                                                                                                              |
|          | 2.83±0.9μs                   | 2.48±0.8μs          | ~0.88   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000000000.0, 511.0)                                                                                                                              |
|          | 2.78±0.9μs                   | 2.57±0.8μs          | 0.93    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(100000000000.0, 5110000000.0)                                                                                                                       |
|          | 2.72±0.9μs                   | 3.14±1μs            | ~1.15   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(1000000000000000.0, 255.5)                                                                                                                          |
|          | 2.83±1μs                     | 2.60±0.9μs          | 0.92    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(1000000000000000.0, 511.0)                                                                                                                          |
|          | 2.56±0.8μs                   | 2.77±0.9μs          | 1.08    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation(1000000000000000.0, 5110000000.0)                                                                                                                   |
|          | 3.03±1μs                     | 5.23±2μs            | ~1.73   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 255.5, 'Iron_group_fraction': 0.0})                                                                        |
|          | 2.91±0.9μs                   | 6.86±3μs            | ~2.36   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 255.5, 'Iron_group_fraction': 0.5})                                                                        |
|          | 2.71±0.8μs                   | 5.25±2μs            | ~1.94   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 511.0, 'Iron_group_fraction': 0.5})                                                                        |
|          | 3.80±1μs                     | 4.01±2μs            | 1.06    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 5110000000.0, 'Iron_group_fraction': 0.0})                                                                 |
|          | 2.70±0.8μs                   | 3.89±1μs            | ~1.44   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation({'Ejecta_density': 100000.0, 'Energy': 255.5, 'Iron_group_fraction': 1.0})                                                                    |
|          | 3.65±0.8μs                   | 4.55±2μs            | ~1.25   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 255.5, 'Iron_group_fraction': 0.0})                                                                      |
|          | 2.98±1μs                     | 4.48±2μs            | ~1.51   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 255.5, 'Iron_group_fraction': 0.5})                                                                      |
|          | 3.07±1μs                     | 4.19±2μs            | ~1.36   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 511.0, 'Iron_group_fraction': 0.5})                                                                      |
|          | 3.01±0.9μs                   | 4.44±2μs            | ~1.48   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation({'Ejecta_density': 0.01, 'Energy': 5110000000.0, 'Iron_group_fraction': 0.0})                                                               |
|          | 3.76±1μs                     | 5.60±2μs            | ~1.49   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation({'Ejecta_density': 100000.0, 'Energy': 255.5, 'Iron_group_fraction': 1.0})                                                                  |
|          | 1.45±0.01s                   | 1.44±0.01s          | 0.99    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                                                                                                                                  |
|          | 1.47±0.01s                   | 1.47±0s             | 1.00    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                                                                                                                                    |
|          | 40.6±0.08s                   | 40.0±0.02s          | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                                                                                                                                      |
|          | 2.14±0m                      | 2.14±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                                                                                                                                |
|          | 3.47±1μs                     | 4.38±2μs            | ~1.26   | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body({'nu': 100000000000000.0, 'temperature': 10000.0})                                                                                                   |
|          | 67.0±20μs                    | 61.6±20μs           | 0.92    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                                                                                                                               |
|          | 73.3±10μs                    | 73.7±10μs           | 1.01    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line({'packet': {'nu_line': 0.1, 'is_last_line': True}, 'enable_full_relativity': True})                                               |
|          | 72.5±10μs                    | 71.5±10μs           | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line({'packet': {'nu_line': 0.2, 'is_last_line': False}, 'enable_full_relativity': True})                                              |
|          | 80.7±20μs                    | 89.7±20μs           | ~1.11   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators({'cur_line_id': 0, 'distance_trace': 0, 'time_explosion': 52000000.0, 'enable_full_relativity': True})               |
|          | 81.1±20μs                    | 85.2±20μs           | 1.05    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators({'cur_line_id': 0, 'distance_trace': 1000000000000.0, 'time_explosion': 52000000.0, 'enable_full_relativity': True}) |
|          | 83.2±20μs                    | 79.5±20μs           | 0.96    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators({'cur_line_id': 1, 'distance_trace': 100000.0, 'time_explosion': 10000000000.0, 'enable_full_relativity': False})    |
|          | 7.84±0.04s                   | 7.65±0.02s          | 0.98    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission({'mu': 0.8599443103322428, 'emission_line_id': 1000, 'energy': 0.9114437898710559})                                                                    |
|          | 7.80±0.01s                   | 7.68±0s             | 0.98    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter(<LineInteractionType.MACROATOM: 2>)                                                                                                                     |
|          | 7.81±0.04s                   | 7.72±0.01s          | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter(<LineInteractionType.SCATTER: 0>)                                                                                                                       |
|          | 3.63±0.03s                   | 3.57±0.04s          | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                                                                                                                                      |
|          | 4.34±0.02s                   | 4.46±0.01s          | 1.03    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                                                                                                                                            |
|          | 1.44±0s                      | 1.44±0s             | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                                                                                                                                 |
|          | 6.41±0.02s                   | 6.36±0.01s          | 0.99    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                                                                                                                                       |
|          | 5.11±0.07s                   | 4.99±0s             | 0.98    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                                                                                                                                      |
|          | 4.97±0.04s                   | 4.88±0.01s          | 0.98    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                                                                                                                                          |
|          | 5.02±0.02s                   | 4.92±0.01s          | 0.98    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley({'tau_russian': 10.0, 'survival_possibility': 0.0})                                                                                               |
|          | 4.98±0.01s                   | 4.93±0s             | 0.99    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley({'tau_russian': 15.0, 'survival_possibility': 0.1})                                                                                               |
|          | 3.72±0.03s                   | 3.58±0.01s          | 0.96    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                                                                                                                                             |

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

[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (ea84805).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

Complete output(might be large):