Ruff tardis/io

[atharva-2001]

📝 Description

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

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Also, link issues affected by this pull request by using the keywords: close, closes, closed, fix, fixes, fixed, resolve, resolves or resolved.

📌 Resources

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🚦 Testing

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☑️ 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 (5a195c5).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

12	G004  	Logging statement uses f-string
7	INP001	File `tardis/io/configuration/tests/test_config_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
4	F401  	`tardis.io.atom_data.atom_web_download.download_atom_data` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
2	PT013 	Incorrect import of `pytest`; use `import pytest` instead
2	RET505	Unnecessary `else` after `return` statement
2	N812  	Lowercase `__path__` imported as non-lowercase `TARDIS_PATH`
1	B017  	`pytest.raises(Exception)` should be considered evil
1	FA100 	Add `from __future__ import annotations` to simplify `typing.Tuple`
1	G001  	Logging statement uses `str.format`
1	RET506	Unnecessary `else` after `raise` statement
1	RET508	Unnecessary `else` after `break` statement
1	NPY201	`np.recfromtxt` will be removed in NumPy 2.0. Use `np.genfromtxt` instead.
1	N999  	Invalid module name: 'test_HDFWriter'
1	F821  	Undefined name `basestring`

Complete output(might be large):

tardis/io/atom_data/__init__.py:5:51: F401 `tardis.io.atom_data.atom_web_download.download_atom_data` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/io/atom_data/__init__.py:6:38: F401 `tardis.io.atom_data.base.AtomData` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/io/atom_data/base.py:198:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:263:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:267:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:704:17: G004 Logging statement uses f-string
tardis/io/atom_data/util.py:35:13: G004 Logging statement uses f-string
tardis/io/configuration/config_internal.py:9:20: N812 Lowercase `__path__` imported as non-lowercase `TARDIS_PATH`
tardis/io/configuration/config_internal.py:25:13: G004 Logging statement uses f-string
tardis/io/configuration/config_internal.py:38:13: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:53:29: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:117:9: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:141:13: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:218:29: G004 Logging statement uses f-string
tardis/io/configuration/tests/test_config_reader.py:1:1: INP001 File `tardis/io/configuration/tests/test_config_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/configuration/tests/test_configuration_namespace.py:1:1: INP001 File `tardis/io/configuration/tests/test_configuration_namespace.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/logger/montecarlo_tracking.py:62:30: G004 Logging statement uses f-string
tardis/io/logger/montecarlo_tracking.py:63:30: G004 Logging statement uses f-string
tardis/io/model/__init__.py:2:44: F401 `tardis.io.model.readers.cmfgen.read_cmfgen_model` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/io/model/__init__.py:3:44: F401 `tardis.io.model.readers.stella.read_stella_model` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
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:47:12: NPY201 `np.recfromtxt` will be removed in NumPy 2.0. Use `np.genfromtxt` instead.
tardis/io/model/readers/stella.py:52:17: RET508 Unnecessary `else` after `break` statement
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/io/model/readers/tests/test_ascii_readers.py:1:1: INP001 File `tardis/io/model/readers/tests/test_ascii_readers.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_cmfgen_reader.py:1:1: INP001 File `tardis/io/model/readers/tests/test_cmfgen_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_cmfgen_reader.py:4:1: PT013 Incorrect import of `pytest`; use `import pytest` instead
tardis/io/model/readers/tests/test_csvy_reader.py:1:1: INP001 File `tardis/io/model/readers/tests/test_csvy_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_csvy_reader.py:48:10: B017 `pytest.raises(Exception)` should be considered evil
tardis/io/model/readers/tests/test_stella_reader.py:1:1: INP001 File `tardis/io/model/readers/tests/test_stella_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_stella_reader.py:5:1: PT013 Incorrect import of `pytest`; use `import pytest` instead
tardis/io/tests/test_HDFWriter.py:1:1: N999 Invalid module name: 'test_HDFWriter'
tardis/io/util.py:18:20: N812 Lowercase `__path__` imported as non-lowercase `TARDIS_PATH`
tardis/io/util.py:163:34: F821 Undefined name `basestring`
tardis/io/util.py:239:9: RET506 Unnecessary `else` after `raise` statement
tardis/io/util.py:328:21: G004 Logging statement uses f-string
tardis/io/util.py:412:13: G004 Logging statement uses f-string
Found 37 errors.

[codecov]

Codecov Report

Attention: Patch coverage is 89.18919% with 8 lines in your changes missing coverage. Please review.

Project coverage is 70.85%. Comparing base (71aad19) to head (5a195c5).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
tardis/io/logger/tests/test_logging.py	50.00%	3 Missing ⚠️
tardis/io/atom_data/util.py	50.00%	2 Missing ⚠️
tardis/io/model/readers/blondin_toymodel.py	0.00%	2 Missing ⚠️
tardis/io/configuration/config_internal.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2827      +/-   ##
==========================================
- Coverage   70.98%   70.85%   -0.14%     
==========================================
  Files         209      209              
  Lines       15654    15781     +127     
==========================================
+ Hits        11112    11181      +69     
- Misses       4542     4600      +58     

☔ 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 (71aad19) and the latest commit (5a195c5).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

| Change   | Before [e0382915] <master>   | After [5a195c58]    |   Ratio | Benchmark (Parameter)                                                                                   |
|----------|------------------------------|---------------------|---------|---------------------------------------------------------------------------------------------------------|
| -        | 2.02±0.02ms                  | 1.65±0.01ms         |    0.82 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |

All benchmarks:

Benchmarks that have improved:

| Change   | Before [e0382915] <master>   | After [5a195c58]    |   Ratio | Benchmark (Parameter)                                                                                   |
|----------|------------------------------|---------------------|---------|---------------------------------------------------------------------------------------------------------|
| -        | 2.02±0.02ms                  | 1.65±0.01ms         |    0.82 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |

Benchmarks that have stayed the same:

| Change   | Before [e0382915] <master>   | After [5a195c58]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 2.23±1μs                     | 1.98±1μs            | ~0.89   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 3.61±0.4μs                   | 3.09±0.5μs          | ~0.86   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 57.8±50μs                    | 44.0±30μs           | ~0.76   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 9.56±2μs                     | 7.16±2μs            | ~0.75   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 33.6±10μs                    | 20.4±4μs            | ~0.61   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 512±100ns                    | 531±200ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 551±100ns                    | 571±100ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 551±100ns                    | 571±200ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 725±0.1ns                    | 755±0.7ns           | 1.04    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 6.41±1μs                     | 6.60±0.7μs          | 1.03    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 1.19±0μs                     | 1.21±0μs            | 1.02    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 1.02±0m                      | 1.02±0m             | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.68±0ms                     | 2.67±0ms            | 1.00    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 36.9±0.01s                   | 36.8±0.01s          | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 203±0.1ns                    | 204±0.02ns          | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 32.0±0.04μs                  | 32.0±0.04μs         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.64±0.07ms                  | 3.55±0.01ms         | 0.97    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 2.16±0m                      | 2.08±0m             | 0.96    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 3.41±0.4μs                   | 3.23±0.3μs          | 0.95    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 1.44±0.3μs                   | 1.35±0.3μs          | 0.94    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 2.95±0.4ms                   | 2.78±0.4ms          | 0.94    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 43.0±50μs                    | 39.4±20μs           | 0.92    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 66.5±0.02ms                  | 60.8±0.03ms         | 0.91    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |

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