v_inner convergence plots in docs

[erinvisser]

Based on #2981

📝 Description

Type: 📝 documentation

With the new store_plasma_state function in the v_inner workflow, we can now extract convergence information from the iterations. Using this, I added a cell to the workflow docs that plots this convergence information.

🚦 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

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[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (5dc751e).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

43	W291 	[*] Trailing whitespace
15	W293 	[*] Blank line contains whitespace
9	E999 	[ ] SyntaxError: Expected a statement
7	I001 	[*] Import block is un-sorted or un-formatted
3	G004 	[ ] Logging statement uses f-string
1	TD005	[ ] Missing issue description after `TODO`
1	W292 	[*] No newline at end of file
1	D202 	[*] No blank lines allowed after function docstring (found 1)
1	D210 	[*] No whitespaces allowed surrounding docstring text
1	F401 	[*] `tardis.visualization.shell_info_from_hdf` imported but unused

Complete output(might be large):

.github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression
.github/workflows/benchmarks.yml:20:5: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:91:49: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:121:81: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:122:54: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:209:1: W293 [*] Blank line contains whitespace
.github/workflows/benchmarks.yml:228:22: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:229:170: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:231:84: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:248:1: W293 [*] Blank line contains whitespace
.github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/lfs-cache.yml:1:12: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
.github/workflows/lfs-cache.yml:38:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:50:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:58:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:63:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:68:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:78:1: W293 [*] Blank line contains whitespace
.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
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:79:1: W293 [*] Blank line contains whitespace
docs/index.rst:103:1: W293 [*] Blank line contains whitespace
docs/io/visualization/demo_observed_spectrum.dat:1:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/io/visualization/how_to_generating_widgets.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/how_to_generating_widgets.ipynb:cell 5:3:5: F401 [*] `tardis.visualization.shell_info_from_hdf` imported but unused
docs/io/visualization/how_to_sdec_plot.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/how_to_sdec_plot.ipynb:cell 29:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/io/visualization/index.rst:33:68: W292 [*] No newline at end of file
docs/io/visualization/tardis_example.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/io/visualization/tutorial_convergence_plot.ipynb:cell 9:4:28: W291 [*] Trailing whitespace
docs/io/visualization/tutorial_convergence_plot.ipynb:cell 12:29:1: W293 [*] Blank line contains whitespace
docs/io/visualization/tutorial_convergence_plot.ipynb:cell 13:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/tutorial_montecarlo_packet_visualization.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/using_widgets.rst:1:1: E999 SyntaxError: Expected an expression
docs/io/visualization/using_widgets.rst:7:83: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:15:69: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:23:76: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:24:41: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:26:77: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:29:79: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:39:75: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:40:80: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:41:78: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:42:75: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:43:75: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:51:77: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:52:79: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:53:73: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:54:71: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:62:74: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:63:76: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:71:80: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:72:79: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:80:78: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:81:77: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:82:77: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:109:48: W291 [*] Trailing whitespace
docs/io/visualization/using_widgets.rst:161:77: W291 [*] Trailing whitespace
docs/workflows/v_inner_solver_workflow.ipynb:cell 1:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/workflows/v_inner_solver_workflow.ipynb:cell 4:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/workflows/v_inner_solver_workflow.ipynb:cell 11:14:45: W291 [*] Trailing whitespace
docs/workflows/v_inner_solver_workflow.ipynb:cell 11:21:28: W291 [*] Trailing whitespace
docs/workflows/v_inner_solver_workflow.ipynb:cell 11:52:30: W291 [*] Trailing whitespace
tardis/workflows/v_inner_solver.py:16:3: TD005 Missing issue description after `TODO`
tardis/workflows/v_inner_solver.py:56:9: D210 [*] No whitespaces allowed surrounding docstring text
tardis/workflows/v_inner_solver.py:56:45: W291 Trailing whitespace
tardis/workflows/v_inner_solver.py:57:53: W291 Trailing whitespace
tardis/workflows/v_inner_solver.py:84:1: W293 [*] Blank line contains whitespace
tardis/workflows/v_inner_solver.py:88:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/workflows/v_inner_solver.py:103:1: W293 [*] Blank line contains whitespace
tardis/workflows/v_inner_solver.py:220:17: G004 Logging statement uses f-string
tardis/workflows/v_inner_solver.py:247:17: G004 Logging statement uses f-string
tardis/workflows/v_inner_solver.py:355:17: G004 Logging statement uses f-string
tardis/workflows/v_inner_solver.py:415:1: W293 [*] Blank line contains whitespace
Found 82 errors.
[*] 67 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 16 lines in your changes missing coverage. Please review.

Project coverage is 69.10%. Comparing base (13c9a31) to head (5dc751e).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/workflows/v_inner_solver.py	0.00%	16 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2983      +/-   ##
==========================================
- Coverage   69.54%   69.10%   -0.44%     
==========================================
  Files         228      228              
  Lines       16429    16444      +15     
==========================================
- Hits        11425    11364      -61     
- Misses       5004     5080      +76     

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

[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 (cec8b53) and the latest commit (5dc751e).
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 [cec8b531] <master>   | After [5dc751ea]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 3.07±0.4μs                   | 4.14±1μs            | ~1.35   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 45.3±20μs                    | 56.9±20μs           | ~1.26   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 3.20±0.3μs                   | 3.67±0.6μs          | ~1.15   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 2.60±0.4ms                   | 2.88±0.4ms          | ~1.11   | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 36.9±0.01μs                  | 40.5±0.2μs          | 1.10    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 1.35±0.2μs                   | 1.46±0.4μs          | 1.08    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 561±100ns                    | 601±200ns           | 1.07    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 3.75±0ms                     | 3.99±0.1ms          | 1.06    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 40.4±20μs                    | 42.7±20μs           | 1.06    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 62.6±0.2ms                   | 65.1±0.1ms          | 1.04    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 3.06±0.2ms                   | 3.15±0.02ms         | 1.03    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 39.2±0.05s                   | 39.4±0.2s           | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 1.19±0μs                     | 1.21±0.02μs         | 1.01    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 730±0.2ns                    | 736±0.2ns           | 1.01    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 6.48±0.7μs                   | 6.54±0.8μs          | 1.01    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 641±200ns                    | 641±200ns           | 1.00    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 1.04±0m                      | 1.05±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                                 |
|          | 7.19±1μs                     | 7.16±2μs            | 1.00    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 570±200ns                    | 561±100ns           | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 1.79±0.02ms                  | 1.70±0ms            | 0.95    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 31.3±10μs                    | 29.7±9μs            | 0.95    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 217±0.09ns                   | 205±0.03ns          | 0.94    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 2.23±1μs                     | 2.05±1μs            | 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