Fix codespell

[KasukabeDefenceForce]

📝 Description

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

This PR aims at fixing the codespell workflow by adding it to the conda lock file instead of installing it in the workflow.

📌 Resources

Sample Run: https://github.com/KasukabeDefenceForce/tardis/actions/runs/11287836606/job/31394460157

🚦 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]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (66367f8).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

6	E999	[ ] SyntaxError: Expected an expression
1	E701	[ ] Multiple statements on one line (colon)
1	W292	[*] No newline at end of file
1	W293	[*] Blank line contains whitespace

Complete output(might be large):

.github/workflows/codespell.yml:3:4: E999 SyntaxError: Expected an expression
.github/workflows/codespell.yml:22:11: E701 Multiple statements on one line (colon)
.github/workflows/codespell.yml:35:1: W293 [*] Blank line contains whitespace
.github/workflows/codespell.yml:38:26: W292 [*] No newline at end of file
conda-linux-64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
conda-lock.yml:14:10: E999 SyntaxError: Expected an expression
conda-osx-64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
conda-osx-arm64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
tardis_env3.yml:3:10: E999 SyntaxError: Expected an expression
Found 9 errors.
[*] 2 fixable with the `--fix` option.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 70.49%. Comparing base (b3af245) to head (66367f8).
Report is 4 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2851      +/-   ##
==========================================
- Coverage   70.87%   70.49%   -0.39%     
==========================================
  Files         209      209              
  Lines       15580    15580              
==========================================
- Hits        11043    10983      -60     
- Misses       4537     4597      +60     

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

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (b3af245) and the latest commit (66367f8).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

| Change   | Before [e3aac0d5] <master>   | After [66367f85]    |   Ratio | Benchmark (Parameter)                                                                         |
|----------|------------------------------|---------------------|---------|-----------------------------------------------------------------------------------------------|
| +        | 208±0.2ns                    | 240±0.05ns          |    1.15 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [e3aac0d5] <master>   | After [66367f85]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 44.9±30μs                    | 62.2±30μs           | ~1.39   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 521±200ns                    | 601±200ns           | ~1.15   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 41.6±20μs                    | 47.7±10μs           | ~1.15   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 2.76±0.6μs                   | 3.11±0.4μs          | ~1.12   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 1.67±0.4μs                   | 1.45±0.4μs          | ~0.87   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 6.92±0.8μs                   | 5.95±0.9μs          | ~0.86   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 2.68±2μs                     | 1.97±0.9μs          | ~0.73   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 20.3±5μs                     | 22.1±6μs            | 1.09    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 2.86±0.01ms                  | 3.06±0.01ms         | 1.07    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 641±100ns                    | 682±100ns           | 1.06    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 4.06±0.1ms                   | 4.32±0ms            | 1.06    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 6.91±1μs                     | 7.31±2μs            | 1.06    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 1.21±0μs                     | 1.26±0μs            | 1.04    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 572±100ns                    | 581±100ns           | 1.02    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 37.6±0.04s                   | 37.9±0.01s          | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 3.26±0.2μs                   | 3.28±0.7μs          | 1.01    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 1.03±0m                      | 1.03±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                                 |
|          | 1.67±0.01ms                  | 1.67±0.01ms         | 1.00    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 31.8±0.1μs                   | 31.7±0.06μs         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 62.3±0.2ms                   | 62.3±0.3ms          | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 2.69±0.5ms                   | 2.66±0.5ms          | 0.99    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 747±0.6ns                    | 728±1ns             | 0.97    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |

Benchmarks that have got worse:

| Change   | Before [e3aac0d5] <master>   | After [66367f85]    |   Ratio | Benchmark (Parameter)                                                                         |
|----------|------------------------------|---------------------|---------|-----------------------------------------------------------------------------------------------|
| +        | 208±0.2ns                    | 240±0.05ns          |    1.15 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |

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