Numpy v2 Upgrade PR 2

[atharva-2001]

📝 Description

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

Based on #2934
Tested on my own Reference Data- https://github.com/tardis-sn/tardis/actions/runs/12789863418?pr=2935

📌 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]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (5b1c4a7).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

4	E999 	[ ] SyntaxError: Expected an expression
3	G004 	[ ] Logging statement uses f-string
1	FA100	[ ] Add `from __future__ import annotations` to simplify `typing.Tuple`
1	G001 	[ ] Logging statement uses `str.format`
1	W291 	[*] Trailing whitespace

Complete output(might be large):

.github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression
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-arm64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
tardis/io/atom_data/base.py:197:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:259:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:263:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:705:17: G004 Logging statement uses f-string
tardis/io/model/readers/generic_readers.py:20:6: FA100 Add `from __future__ import annotations` to simplify `typing.Tuple`
tardis/io/model/readers/generic_readers.py:51:72: W291 [*] Trailing whitespace
Found 10 errors.
[*] 1 fixable with the `--fix` option.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.38%. Comparing base (5e2d0bb) to head (5b1c4a7).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2935      +/-   ##
==========================================
- Coverage   69.74%   69.38%   -0.36%     
==========================================
  Files         224      224              
  Lines       16313    16314       +1     
==========================================
- Hits        11377    11320      -57     
- Misses       4936     4994      +58     

☔ 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 (5e2d0bb) and the latest commit (5b1c4a7).
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 [5e2d0bb3] <master>   | After [5b1c4a78]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 42.5±20μs                    | 61.0±40μs           | ~1.43   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 2.62±0.01ms                  | 2.93±0ms            | ~1.12   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 2.39±2μs                     | 2.64±1μs            | ~1.10   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 7.68±3μs                     | 6.87±2μs            | ~0.89   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 2.92±0.4μs                   | 3.21±0.5μs          | 1.10    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 530±200ns                    | 570±200ns           | 1.08    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 2.56±0.4ms                   | 2.76±0.5ms          | 1.07    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 21.9±5μs                     | 23.2±6μs            | 1.06    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 63.3±0.07ms                  | 65.9±0.3ms          | 1.04    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 1.50±0.3μs                   | 1.55±0.5μs          | 1.03    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 501±200ns                    | 511±200ns           | 1.02    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 38.4±0.06s                   | 38.7±0.06s          | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.08±0m                      | 2.10±0m             | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 203±0.2ns                    | 205±0.3ns           | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 6.22±1μs                     | 6.30±1μs            | 1.01    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 531±200ns                    | 531±100ns           | 1.00    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 38.1±0.01μs                  | 38.1±0.01μs         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 1.05±0m                      | 1.05±0m             | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 750±0.3ns                    | 744±1ns             | 0.99    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 1.66±0ms                     | 1.65±0ms            | 0.99    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 1.23±0μs                     | 1.20±0μs            | 0.98    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 3.76±0.5μs                   | 3.69±0.4μs          | 0.98    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 3.96±0ms                     | 3.73±0.03ms         | 0.94    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 41.9±20μs                    | 39.3±20μs           | 0.94    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |

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