Update NumPy to 2.0.2[Do Not Merge]

[atharva-2001]

📝 Description

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

📌 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 (7e5b726).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

96	W293  	[*] Blank line contains whitespace
28	W291  	[*] Trailing whitespace
13	E999  	[ ] SyntaxError: Expected ',', found ':'
7	E902  	[ ] stream did not contain valid UTF-8
5	G004  	[ ] Logging statement uses f-string
4	E402  	[ ] Module level import not at top of file
4	W191  	[ ] Indentation contains tabs
3	FA100 	[ ] Add `from __future__ import annotations` to simplify `typing.Tuple`
3	F401  	[*] `numpy` imported but unused
2	RET505	[ ] Unnecessary `elif` after `return` statement
2	I001  	[*] Import block is un-sorted or un-formatted
2	W292  	[*] No newline at end of file
1	RET506	[ ] Unnecessary `else` after `raise` statement
1	E722  	[ ] Do not use bare `except`
1	PGH004	[ ] Use specific rule codes when using `noqa`

Complete output(might be large):

.github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression
.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/tests.yml:29:1: W293 [*] Blank line contains whitespace
.github/workflows/tests.yml:125:1: W293 [*] Blank line contains whitespace
CHANGELOG.md:4:15: E999 SyntaxError: Expected ',', found ':'
CITATION.cff:3:1: E999 SyntaxError: Invalid annotated assignment target
README.rst:1:1: E999 SyntaxError: Expected a statement
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
docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement
docs/workflows/state_linux.hdf:1:1: E902 stream did not contain valid UTF-8
docs/workflows/test1.npy:1:1: E902 stream did not contain valid UTF-8
j_blue_estimator.npy:1:1: E902 stream did not contain valid UTF-8
j_blue_large_raw.npy:1:1: E902 stream did not contain valid UTF-8
j_blue_normalized.npy:1:1: E902 stream did not contain valid UTF-8
j_blue_raw.npy:1:1: E902 stream did not contain valid UTF-8
j_blue_small_raw.npy:1:1: E902 stream did not contain valid UTF-8
jb.log:2:1: E999 SyntaxError: Expected a statement
jb.log:12:152: W291 [*] Trailing whitespace
jb.log:13:1: W191 Indentation contains tabs
jb.log:245:1: W293 [*] Blank line contains whitespace
jb.log:247:1: W293 [*] Blank line contains whitespace
jb.log:248:1: W293 [*] Blank line contains whitespace
jb.log:254:37: W291 [*] Trailing whitespace
jb.log:255:80: W291 [*] Trailing whitespace
jb.log:268:28: W291 [*] Trailing whitespace
jb.log:270:2: W291 [*] Trailing whitespace
jb.log:288:1: W293 [*] Blank line contains whitespace
jb.log:293:1: W293 [*] Blank line contains whitespace
jb.log:302:1: W293 [*] Blank line contains whitespace
jb.log:307:1: W293 [*] Blank line contains whitespace
jb.log:312:1: W293 [*] Blank line contains whitespace
jb.log:317:1: W293 [*] Blank line contains whitespace
jb.log:322:1: W293 [*] Blank line contains whitespace
jb.log:327:1: W293 [*] Blank line contains whitespace
jb.log:332:1: W293 [*] Blank line contains whitespace
jb.log:337:1: W293 [*] Blank line contains whitespace
jb.log:342:1: W293 [*] Blank line contains whitespace
jb.log:347:1: W293 [*] Blank line contains whitespace
jb.log:352:103: W291 [*] Trailing whitespace
jb3.log:2:1: E999 SyntaxError: Expected a statement
jb3.log:12:152: W291 [*] Trailing whitespace
jb3.log:13:1: W191 Indentation contains tabs
jb3.log:253:1: W293 [*] Blank line contains whitespace
jb3.log:255:1: W293 [*] Blank line contains whitespace
jb3.log:256:1: W293 [*] Blank line contains whitespace
jb3.log:262:37: W291 [*] Trailing whitespace
jb3.log:263:80: W291 [*] Trailing whitespace
jb3.log:276:28: W291 [*] Trailing whitespace
jb3.log:278:2: W291 [*] Trailing whitespace
jb3.log:296:1: W293 [*] Blank line contains whitespace
jb3.log:301:1: W293 [*] Blank line contains whitespace
jb3.log:310:1: W293 [*] Blank line contains whitespace
jb3.log:315:1: W293 [*] Blank line contains whitespace
jb3.log:320:1: W293 [*] Blank line contains whitespace
jb3.log:325:1: W293 [*] Blank line contains whitespace
jb3.log:330:1: W293 [*] Blank line contains whitespace
jb3.log:335:1: W293 [*] Blank line contains whitespace
jb3.log:340:1: W293 [*] Blank line contains whitespace
jb3.log:345:1: W293 [*] Blank line contains whitespace
jb3.log:350:1: W293 [*] Blank line contains whitespace
jb3.log:355:1: W293 [*] Blank line contains whitespace
jb3.log:360:103: W291 [*] Trailing whitespace
jb5.log:2:1: E999 SyntaxError: Expected a statement
jb5.log:12:152: W291 [*] Trailing whitespace
jb5.log:13:1: W191 Indentation contains tabs
jb5.log:982:1: W293 [*] Blank line contains whitespace
jb5.log:984:1: W293 [*] Blank line contains whitespace
jb5.log:985:1: W293 [*] Blank line contains whitespace
jb5.log:991:37: W291 [*] Trailing whitespace
jb5.log:992:80: W291 [*] Trailing whitespace
jb5.log:1005:28: W291 [*] Trailing whitespace
jb5.log:1007:2: W291 [*] Trailing whitespace
jb5.log:1025:1: W293 [*] Blank line contains whitespace
jb5.log:1030:1: W293 [*] Blank line contains whitespace
jb5.log:1039:1: W293 [*] Blank line contains whitespace
jb5.log:1044:1: W293 [*] Blank line contains whitespace
jb5.log:1049:1: W293 [*] Blank line contains whitespace
jb5.log:1054:1: W293 [*] Blank line contains whitespace
jb5.log:1059:1: W293 [*] Blank line contains whitespace
jb5.log:1064:1: W293 [*] Blank line contains whitespace
jb5.log:1069:1: W293 [*] Blank line contains whitespace
jb5.log:1074:1: W293 [*] Blank line contains whitespace
jb5.log:1079:1: W293 [*] Blank line contains whitespace
jb5.log:1084:1: W293 [*] Blank line contains whitespace
jb5.log:1089:103: W291 [*] Trailing whitespace
jb7.log:2:1: E999 SyntaxError: Expected a statement
jb7.log:12:152: W291 [*] Trailing whitespace
jb7.log:13:1: W191 Indentation contains tabs
jb7.log:401:1: W293 [*] Blank line contains whitespace
jb7.log:403:1: W293 [*] Blank line contains whitespace
jb7.log:404:1: W293 [*] Blank line contains whitespace
jb7.log:410:37: W291 [*] Trailing whitespace
jb7.log:411:80: W291 [*] Trailing whitespace
jb7.log:424:28: W291 [*] Trailing whitespace
jb7.log:426:2: W291 [*] Trailing whitespace
jb7.log:444:1: W293 [*] Blank line contains whitespace
jb7.log:449:1: W293 [*] Blank line contains whitespace
jb7.log:458:1: W293 [*] Blank line contains whitespace
jb7.log:463:1: W293 [*] Blank line contains whitespace
jb7.log:468:1: W293 [*] Blank line contains whitespace
jb7.log:473:1: W293 [*] Blank line contains whitespace
jb7.log:478:1: W293 [*] Blank line contains whitespace
jb7.log:483:1: W293 [*] Blank line contains whitespace
jb7.log:488:1: W293 [*] Blank line contains whitespace
jb7.log:493:1: W293 [*] Blank line contains whitespace
jb7.log:498:1: W293 [*] Blank line contains whitespace
jb7.log:503:1: W293 [*] Blank line contains whitespace
jb7.log:508:103: W291 [*] Trailing whitespace
tardis/__init__.py:6:31: PGH004 Use specific rule codes when using `noqa`
tardis/__init__.py:15:1: E402 Module level import not at top of file
tardis/__init__.py:16:1: E402 Module level import not at top of file
tardis/__init__.py:33:1: E402 Module level import not at top of file
tardis/__init__.py:33:25: F401 `tardis.base.run_tardis` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/__init__.py:34:1: E402 Module level import not at top of file
tardis/__init__.py:34:46: F401 `tardis.io.util.yaml_load_file` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/io/model/parse_radiation_field_configuration.py:118:13: G004 Logging statement uses f-string
tardis/io/model/parse_radiation_field_configuration.py:129:1: W293 [*] Blank line contains whitespace
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:155:50: W292 [*] No newline at end of file
tardis/plasma/radiation_field/planck_rad_field.py:36:1: W293 [*] Blank line contains whitespace
tardis/plasma/radiation_field/planck_rad_field.py:41:1: W293 [*] Blank line contains whitespace
tardis/plasma/radiation_field/planck_rad_field.py:82:44: FA100 Add `from __future__ import annotations` to simplify `typing.Union`
tardis/plasma/radiation_field/planck_rad_field.py:104:1: W293 [*] Blank line contains whitespace
tardis/plasma/radiation_field/planck_rad_field.py:165:44: FA100 Add `from __future__ import annotations` to simplify `typing.Union`
tardis/plasma/standard_plasmas.py:220:22: W291 [*] Trailing whitespace
tardis/plasma/standard_plasmas.py:323:9: RET506 Unnecessary `else` after `raise` statement
tardis/tests/test_tardis_full.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/tests/test_tardis_full.py:5:17: F401 [*] `numpy` imported but unused
tardis/tests/test_tardis_full.py:50:1: W293 [*] Blank line contains whitespace
tardis/tests/test_tardis_full.py:73:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/transport/montecarlo/estimators/j_blue_estimator.py:19:56: W291 [*] Trailing whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:24:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:29:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:32:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:38:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:42:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:44:49: W291 [*] Trailing whitespace
tardis/transport/montecarlo/estimators/j_blue_estimator.py:44:50: W292 [*] No newline at end of file
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:79:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:83:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:87:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:93:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:100:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:108:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:113:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:128:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:135:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:139:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:144:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/mc_rad_field_solver.py:148:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/radfield_estimator_calcs.py:117:1: W293 [*] Blank line contains whitespace
tardis/transport/montecarlo/estimators/radfield_estimator_calcs.py:121:1: W293 [*] Blank line contains whitespace
tardis/util/base.py:320:1: W293 [*] Blank line contains whitespace
tardis/util/base.py:324:1: W293 [*] Blank line contains whitespace
tardis/util/base.py:328:1: W293 [*] Blank line contains whitespace
tardis/util/base.py:359:5: RET505 Unnecessary `else` after `return` statement
tardis/util/base.py:533:5: E722 Do not use bare `except`
tardis/util/base.py:641:5: RET505 Unnecessary `elif` after `return` statement
tardis/workflows/simple_tardis_workflow.py:230:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:286:98: W291 [*] Trailing whitespace
tardis/workflows/simple_tardis_workflow.py:393:1: W293 [*] Blank line contains whitespace
tardis/workflows/simple_tardis_workflow.py:482:17: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:161:1: W293 [*] Blank line contains whitespace
tardis/workflows/standard_tardis_workflow.py:168:1: W293 [*] Blank line contains whitespace
tardis/workflows/standard_tardis_workflow.py:171:1: W293 [*] Blank line contains whitespace
tardis/workflows/standard_tardis_workflow.py:182:1: W293 [*] Blank line contains whitespace
tardis/workflows/standard_tardis_workflow.py:209:13: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:269:1: W293 [*] Blank line contains whitespace
tardis/workflows/standard_tardis_workflow.py:271:17: G004 Logging statement uses f-string
Found 172 errors.
[*] 129 fixable with the `--fix` option.

[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 (87e4ae1) and the latest commit (44fba2a).
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 [d73192c5] <master>   | After [44fba2ad]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 22.6±6μs                     | 45.4±20μs           | ~2.00   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 7.19±2μs                     | 9.62±7μs            | ~1.34   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 2.52±0.7μs                   | 3.22±0.4μs          | ~1.27   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 2.97±0.4μs                   | 3.39±0.6μs          | ~1.14   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 2.72±0ms                     | 2.89±0.04ms         | 1.06    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 2.54±0.4ms                   | 2.66±0.4ms          | 1.05    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 551±100ns                    | 572±100ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 3.59±0ms                     | 3.70±0.03ms         | 1.03    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 1.84±2μs                     | 1.90±1μs            | 1.03    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 1.66±0.01ms                  | 1.70±0.01ms         | 1.03    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 66.2±0.05ms                  | 68.6±0ms            | 1.03    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 38.2±0.01s                   | 38.8±0.1s           | 1.02    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 44.5±20μs                    | 45.5±30μs           | 1.02    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 1.04±0m                      | 1.05±0m             | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 205±0.01ns                   | 208±0.4ns           | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 42.7±20μs                    | 42.9±20μs           | 1.01    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 2.08±0m                      | 2.08±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.20±0μs                     | 1.19±0μs            | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 501±200ns                    | 491±200ns           | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 581±200ns                    | 561±100ns           | 0.97    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 739±0.9ns                    | 718±0.3ns           | 0.97    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 1.43±0.4μs                   | 1.37±0.3μs          | 0.96    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 40.0±0.05μs                  | 38.5±0.3μs          | 0.96    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 6.33±0.6μs                   | 5.76±0.8μs          | 0.91    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |

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