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Move visualization section to analysing tardis output #2967

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Move visualization section to analysing tardis output #2967

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KasukabeDefenceForce
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📝 Description

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

This PR aims at shifting the visualization section from input/output to analysing tardis outputs section
Also, link issues affected by this pull request by using the keywords: close, closes, closed, fix, fixes, fixed, resolve, resolves or resolved.

📌 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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*beep* *bop*
Hi human,
I ran ruff on the latest commit (9377df4).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

31	W291	[*] Trailing whitespace
5	I001	[*] Import block is un-sorted or un-formatted
5	E999	[ ] SyntaxError: Expected a statement
4	W293	[*] Blank line contains whitespace
1	W292	[*] No newline at end of file
1	F401	[*] `tardis.visualization.shell_info_from_hdf` imported but unused

Complete output(might be large):

docs/analysing_tardis_outputs/visualization/demo_observed_spectrum.dat:1:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/analysing_tardis_outputs/visualization/how_to_generating_widgets.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/analysing_tardis_outputs/visualization/how_to_generating_widgets.ipynb:cell 5:3:5: F401 [*] `tardis.visualization.shell_info_from_hdf` imported but unused
docs/analysing_tardis_outputs/visualization/how_to_sdec_plot.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted
docs/analysing_tardis_outputs/visualization/how_to_sdec_plot.ipynb:cell 29:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/analysing_tardis_outputs/visualization/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/analysing_tardis_outputs/visualization/index.rst:33:68: W292 [*] No newline at end of file
docs/analysing_tardis_outputs/visualization/tardis_example.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/analysing_tardis_outputs/visualization/tutorial_convergence_plot.ipynb:cell 9:4:28: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/tutorial_convergence_plot.ipynb:cell 12:29:1: W293 [*] Blank line contains whitespace
docs/analysing_tardis_outputs/visualization/tutorial_convergence_plot.ipynb:cell 13:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/analysing_tardis_outputs/visualization/tutorial_montecarlo_packet_visualization.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/analysing_tardis_outputs/visualization/using_widgets.rst:1:1: E999 SyntaxError: Expected an expression
docs/analysing_tardis_outputs/visualization/using_widgets.rst:7:83: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:15:69: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:23:76: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:24:41: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:26:77: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:29:79: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:39:75: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:40:80: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:41:78: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:42:75: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:43:75: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:51:77: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:52:79: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:53:73: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:54:71: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:62:74: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:63:76: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:71:80: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:72:79: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:80:78: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:81:77: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:82:77: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:109:48: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/using_widgets.rst:161:77: W291 [*] Trailing whitespace
docs/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/index.rst:21:51: W291 [*] Trailing whitespace
docs/index.rst:43:76: W291 [*] Trailing whitespace
docs/index.rst:44:64: W291 [*] Trailing whitespace
docs/index.rst:45:71: W291 [*] Trailing whitespace
docs/index.rst:46:69: W291 [*] Trailing whitespace
docs/index.rst:47:68: W291 [*] Trailing whitespace
docs/index.rst:66:1: W293 [*] Blank line contains whitespace
docs/index.rst:87:1: W293 [*] Blank line contains whitespace
docs/index.rst:111:1: W293 [*] Blank line contains whitespace
Found 47 errors.
[*] 42 fixable with the `--fix` option.

@codecov Codecov
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codecov bot commented Feb 10, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.17%. Comparing base (304154a) to head (9377df4).

Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #2967      +/-   ##
==========================================
- Coverage   69.54%   69.17%   -0.37%     
==========================================
  Files         228      228              
  Lines       16429    16429              
==========================================
- Hits        11425    11365      -60     
- Misses       5004     5064      +60

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

@tardis-bot
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*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

@tardis-bot
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*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (304154a) and the latest commit (9377df4).
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 [304154a2] <release-2025.02.09>   | After [9377df4b]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 21.2±5μs                                 | 24.0±6μs            | ~1.13   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 7.68±2μs                                 | 6.42±1μs            | ~0.84   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 2.35±2μs                                 | 1.96±2μs            | ~0.83   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 1.84±0.3μs                               | 1.49±0.3μs          | ~0.81   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 56.2±20μs                                | 42.9±20μs           | ~0.76   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 581±200ns                                | 632±200ns           | 1.09    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 41.1±20μs                                | 44.4±20μs           | 1.08    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 2.80±0.4μs                               | 3.00±0.4μs          | 1.07    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 6.05±0.6μs                               | 6.24±0.5μs          | 1.03    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 729±0.3ns                                | 740±0.3ns           | 1.02    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 2.61±0.01ms                              | 2.64±0ms            | 1.01    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 1.68±0.01ms                              | 1.70±0.02ms         | 1.01    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 621±200ns                                | 621±100ns           | 1.00    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 3.78±0.01ms                              | 3.77±0ms            | 1.00    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 1.05±0m                                  | 1.04±0m             | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.08±0m                                  | 2.08±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.21±0μs                                 | 1.21±0μs            | 1.00    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 62.7±0.01ms                              | 62.5±0.2ms          | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 38.6±0.1s                                | 38.4±0.1s           | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.67±0.4ms                               | 2.63±0.5ms          | 0.99    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 206±0.1ns                                | 203±0.8ns           | 0.98    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 40.9±0.07μs                              | 38.7±0.05μs         | 0.95    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.35±0.6μs                               | 3.16±0.6μs          | 0.94    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 561±100ns                                | 521±200ns           | 0.93    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |





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

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    
















  
  

    

      

  




    


    

      

              

  
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