Add sdec visualisation notebook

[KasukabeDefenceForce]

📝 Description

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

This PR aims at adding a notebook which analyses the sdec data and provides a simple way to plot that data

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

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• 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

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[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (b979a4f).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

34	W291  	[*] Trailing whitespace
7	I001  	[*] Import block is un-sorted or un-formatted
7	E999  	[ ] SyntaxError: Expected a statement
7	W293  	[*] Blank line contains whitespace
3	INP001	[ ] File `tardis/analysis/opacities.py` is part of an implicit namespace package. Add an `__init__.py`.
2	PIE808	[*] Unnecessary `start` argument in `range`
2	RET506	[ ] Unnecessary `else` after `raise` statement
2	E712  	[*] Avoid equality comparisons to `False`; use `if not ...:` for false checks
2	F401  	[*] `tardis.tests.test_util.monkeysession` imported but unused
2	F811  	[ ] Redefinition of unused `monkeysession` from line 6
1	E703  	[*] Statement ends with an unnecessary semicolon

Complete output(might be large):

docs/analysing_tardis_outputs/index.rst:1:1: E999 SyntaxError: Expected an expression
docs/analysing_tardis_outputs/index.rst:12:1: W293 [*] Blank line contains whitespace
docs/analysing_tardis_outputs/spectrum/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/analysing_tardis_outputs/spectrum/index.rst:7:1: W293 [*] Blank line contains whitespace
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:25:1: W293 [*] Blank line contains whitespace
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:88:1: W293 [*] Blank line contains whitespace
docs/index.rst:112:1: W293 [*] Blank line contains whitespace
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 2:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 7:2:74: W291 [*] Trailing whitespace
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 14:1:47: W291 [*] Trailing whitespace
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 14:4:46: E703 [*] Statement ends with an unnecessary semicolon
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 15:2:55: W291 [*] Trailing whitespace
tardis/analysis/opacities.py:1:1: INP001 File `tardis/analysis/opacities.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/grid/tests/test_grid.py:1:1: INP001 File `tardis/grid/tests/test_grid.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_arepo_parser.py:1:1: INP001 File `tardis/io/model/readers/tests/test_arepo_parser.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/transport/montecarlo/tests/conftest.py:14:5: F811 Redefinition of unused `opacity_state_initialize` from line 7
tardis/visualization/sdec/util.py:115:9: RET506 Unnecessary `else` after `raise` statement
tardis/visualization/sdec/util.py:273:9: RET506 Unnecessary `else` after `raise` statement
tardis/visualization/tools/tests/test_convergence_plot.py:3:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/tools/tests/test_convergence_plot.py:6:36: F401 [*] `tardis.tests.test_util.monkeysession` imported but unused
tardis/visualization/tools/tests/test_convergence_plot.py:87:24: PIE808 [*] Unnecessary `start` argument in `range`
tardis/visualization/tools/tests/test_convergence_plot.py:111:22: PIE808 [*] Unnecessary `start` argument in `range`
tardis/visualization/tools/tests/test_convergence_plot.py:198:9: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
tardis/visualization/tools/tests/test_convergence_plot.py:215:9: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
tardis/visualization/tools/tests/test_convergence_plot.py:220:40: F811 Redefinition of unused `monkeysession` from line 6
Found 69 errors.
[*] 53 fixable with the `--fix` option (2 hidden fixes can be enabled with the `--unsafe-fixes` option).

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 96 lines in your changes missing coverage. Please review.

Project coverage is 68.77%. Comparing base (304154a) to head (b979a4f).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/visualization/sdec/util.py	0.00%	96 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2968      +/-   ##
==========================================
- Coverage   69.54%   68.77%   -0.77%     
==========================================
  Files         228      229       +1     
  Lines       16429    16525      +96     
==========================================
- Hits        11425    11365      -60     
- Misses       5004     5160     +156     

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

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (13c9a31) and the latest commit (b979a4f).
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] <master>   | After [b979a4fb]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 41.9±20μs                    | 57.5±20μs           | ~1.37   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 2.70±0ms                     | 3.15±0.02ms         | ~1.17   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 1.32±0.4μs                   | 1.51±0.3μs          | ~1.14   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 47.6±30μs                    | 53.9±30μs           | ~1.13   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 601±80ns                     | 541±100ns           | ~0.90   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 7.31±0.8μs                   | 6.26±1μs            | ~0.86   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 3.93±0.6μs                   | 2.86±0.3μs          | ~0.73   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 36.2±0.9μs                   | 23.2±6μs            | ~0.64   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 37.8±0.03μs                  | 39.8±0.05μs         | 1.06    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.73±0.01ms                  | 3.93±0.04ms         | 1.05    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 562±100ns                    | 572±100ns           | 1.02    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 1.20±0.06μs                  | 1.22±0.01μs         | 1.02    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 38.6±0.05s                   | 38.6±0.04s          | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.08±0m                      | 2.08±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 209±0.5ns                    | 208±0.03ns          | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 726±1ns                      | 715±0.3ns           | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 1.74±0.02ms                  | 1.73±0.02ms         | 0.99    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 561±200ns                    | 552±100ns           | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 1.08±0.02m                   | 1.05±0m             | 0.96    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 66.2±0ms                     | 63.4±0.2ms          | 0.96    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 7.70±2μs                     | 7.33±2μs            | 0.95    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 2.76±0.4ms                   | 2.61±0.5ms          | 0.94    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 3.77±0.8μs                   | 3.55±0.3μs          | 0.94    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 2.32±2μs                     | 2.14±0.9μs          | 0.92    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |

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