Remove deprecated setup.py

KasukabeDefenceForce commented 2 months ago

:pencil: Description

This PR aims at removing setup.py from the codebase as it is deprecated.

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

:pushpin: Resources

Examples, notebooks, and links to useful references.

:vertical_traffic_light: Testing

How did you test these changes?

[ ] Testing pipeline
[ ] Other method (describe)
[ ] My changes can't be tested (explain why)

:ballot_box_with_check: 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 commented 2 months ago

*beep* *bop* Hi human, I ran ruff on the latest commit (c49bf268794cbf6a859056d6af4e4cd761c61d2a). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 77 W191 [ ] Indentation contains tabs 17 W291 [*] Trailing whitespace 9 E999 [ ] SyntaxError: Expected ',', found ':' 6 W293 [*] Blank line contains whitespace 5 F405 [ ] `exclude_patterns` may be undefined, or defined from star imports 4 E101 [ ] Indentation contains mixed spaces and tabs 3 F631 [ ] Assert test is a non-empty tuple, which is always `True` 3 UP015 [*] Unnecessary open mode parameters 2 B018 [ ] Found useless expression. Either assign it to a variable or remove it. 2 E402 [ ] Module level import not at top of file 1 ANN205 [ ] Missing return type annotation for staticmethod `get_relative_path` 1 COM818 [ ] Trailing comma on bare tuple prohibited 1 RET506 [ ] Unnecessary `else` after `raise` statement 1 I001 [*] Import block is un-sorted or un-formatted 1 E712 [*] Avoid equality comparisons to `True`; use `if toml_config_tool_dict["tardis"]['edit_on_github']:` for truth checks 1 E902 [ ] No such file or directory (os error 2) 1 W292 [*] No newline at end of file 1 F401 [*] `tardis` imported but unused 1 PGH004 [ ] Use specific rule codes when using `noqa` 1 PLW0127 [ ] Self-assignment of variable `observed_spectrum` 1 UP009 [*] UTF-8 encoding declaration is unnecessary 1 UP030 [*] Use implicit references for positional format fields 1 UP032 [*] Use f-string instead of `format` call ```

Complete output(might be large):

```diff .zenodo.json:1:1: B018 Found useless expression. Either assign it to a variable or remove it. .zenodo.json:354:2: W292 [*] No newline at end of file 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 asv.conf.json:1:1: B018 Found useless expression. Either assign it to a variable or remove it. benchmarks/benchmark_base.py:29:9: ANN205 Missing return type annotation for staticmethod `get_relative_path` benchmarks/benchmark_base.py:75:9: RET506 Unnecessary `else` after `raise` statement docs/Makefile:5:16: E999 SyntaxError: Expected an expression docs/Makefile:22:1: W191 Indentation contains tabs docs/Makefile:23:1: W191 Indentation contains tabs docs/Makefile:24:1: W191 Indentation contains tabs docs/Makefile:25:1: W191 Indentation contains tabs docs/Makefile:26:1: W191 Indentation contains tabs docs/Makefile:27:1: W191 Indentation contains tabs docs/Makefile:28:1: W191 Indentation contains tabs docs/Makefile:29:1: W191 Indentation contains tabs docs/Makefile:30:1: W191 Indentation contains tabs docs/Makefile:31:1: W191 Indentation contains tabs docs/Makefile:32:1: W191 Indentation contains tabs docs/Makefile:33:1: W191 Indentation contains tabs docs/Makefile:34:1: W191 Indentation contains tabs docs/Makefile:35:1: W191 Indentation contains tabs docs/Makefile:36:1: W191 Indentation contains tabs docs/Makefile:37:1: W191 Indentation contains tabs docs/Makefile:40:1: W191 Indentation contains tabs docs/Makefile:41:1: W191 Indentation contains tabs docs/Makefile:42:1: W191 Indentation contains tabs docs/Makefile:45:1: W191 Indentation contains tabs docs/Makefile:46:1: W191 Indentation contains tabs docs/Makefile:47:1: W191 Indentation contains tabs docs/Makefile:50:1: W191 Indentation contains tabs docs/Makefile:51:1: W191 Indentation contains tabs docs/Makefile:52:1: W191 Indentation contains tabs docs/Makefile:55:1: W191 Indentation contains tabs docs/Makefile:56:1: W191 Indentation contains tabs docs/Makefile:57:1: W191 Indentation contains tabs docs/Makefile:60:1: W191 Indentation contains tabs docs/Makefile:61:1: W191 Indentation contains tabs docs/Makefile:62:1: W191 Indentation contains tabs docs/Makefile:65:1: W191 Indentation contains tabs docs/Makefile:66:1: W191 Indentation contains tabs docs/Makefile:67:1: W191 Indentation contains tabs docs/Makefile:70:1: W191 Indentation contains tabs docs/Makefile:71:1: W191 Indentation contains tabs docs/Makefile:72:1: W191 Indentation contains tabs docs/Makefile:73:1: W191 Indentation contains tabs docs/Makefile:73:1: E101 Indentation contains mixed spaces and tabs docs/Makefile:76:1: W191 Indentation contains tabs docs/Makefile:77:1: W191 Indentation contains tabs docs/Makefile:78:1: W191 Indentation contains tabs docs/Makefile:79:1: W191 Indentation contains tabs docs/Makefile:79:1: E101 Indentation contains mixed spaces and tabs docs/Makefile:80:1: W191 Indentation contains tabs docs/Makefile:81:1: W191 Indentation contains tabs docs/Makefile:82:1: W191 Indentation contains tabs docs/Makefile:85:1: W191 Indentation contains tabs docs/Makefile:86:1: W191 Indentation contains tabs docs/Makefile:87:1: W191 Indentation contains tabs docs/Makefile:88:1: W191 Indentation contains tabs docs/Makefile:89:1: W191 Indentation contains tabs docs/Makefile:90:1: W191 Indentation contains tabs docs/Makefile:91:1: W191 Indentation contains tabs docs/Makefile:94:1: W191 Indentation contains tabs docs/Makefile:95:1: W191 Indentation contains tabs docs/Makefile:96:1: W191 Indentation contains tabs docs/Makefile:99:1: W191 Indentation contains tabs docs/Makefile:100:1: W191 Indentation contains tabs docs/Makefile:101:1: W191 Indentation contains tabs docs/Makefile:102:1: W191 Indentation contains tabs docs/Makefile:103:1: W191 Indentation contains tabs docs/Makefile:103:1: E101 Indentation contains mixed spaces and tabs docs/Makefile:106:1: W191 Indentation contains tabs docs/Makefile:107:1: W191 Indentation contains tabs docs/Makefile:108:1: W191 Indentation contains tabs docs/Makefile:109:1: W191 Indentation contains tabs docs/Makefile:112:1: W191 Indentation contains tabs docs/Makefile:113:1: W191 Indentation contains tabs docs/Makefile:114:1: W191 Indentation contains tabs docs/Makefile:117:1: W191 Indentation contains tabs docs/Makefile:118:1: W191 Indentation contains tabs docs/Makefile:119:1: W191 Indentation contains tabs docs/Makefile:122:1: W191 Indentation contains tabs docs/Makefile:123:1: W191 Indentation contains tabs docs/Makefile:124:1: W191 Indentation contains tabs docs/Makefile:127:1: W191 Indentation contains tabs docs/Makefile:128:1: W191 Indentation contains tabs docs/Makefile:129:1: W191 Indentation contains tabs docs/Makefile:130:1: W191 Indentation contains tabs docs/Makefile:130:1: E101 Indentation contains mixed spaces and tabs docs/conf.py:1:1: UP009 [*] UTF-8 encoding declaration is unnecessary docs/conf.py:27:1: I001 [*] Import block is un-sorted or un-formatted docs/conf.py:30:8: F401 [*] `tardis` imported but unused docs/conf.py:36:43: PGH004 Use specific rule codes when using `noqa` docs/conf.py:46:6: UP015 [*] Unnecessary open mode parameters docs/conf.py:67:1: F405 `exclude_patterns` may be undefined, or defined from star imports docs/conf.py:68:1: F405 `exclude_patterns` may be undefined, or defined from star imports docs/conf.py:69:1: F405 `exclude_patterns` may be undefined, or defined from star imports docs/conf.py:70:1: F405 `exclude_patterns` may be undefined, or defined from star imports docs/conf.py:71:1: F405 `exclude_patterns` may be undefined, or defined from star imports docs/conf.py:138:1: W293 Blank line contains whitespace docs/conf.py:173:1: W293 Blank line contains whitespace docs/conf.py:190:13: UP030 Use implicit references for positional format fields docs/conf.py:190:13: UP032 [*] Use f-string instead of `format` call docs/conf.py:217:1: E402 Module level import not at top of file docs/conf.py:290:4: E712 Avoid equality comparisons to `True`; use `if toml_config_tool_dict["tardis"]['edit_on_github']:` for truth checks docs/conf.py:351:1: E402 Module level import not at top of file docs/conf.py:366:10: UP015 [*] Unnecessary open mode parameters, use ""w"" docs/conf.py:381:10: UP015 [*] Unnecessary open mode parameters, use ""w"" docs/contributing/development/documentation_guidelines.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/documentation_guidelines.rst:44:1: W293 [*] Blank line contains whitespace docs/contributing/development/documentation_guidelines.rst:58:10: W291 [*] Trailing whitespace docs/contributing/development/git_workflow.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/running_tests.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/running_tests.rst:8:90: COM818 Trailing comma on bare tuple prohibited docs/contributing/development/running_tests.rst:41:42: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:64:112: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:65:124: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:69:92: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:70:107: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:76:102: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:78:116: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:80:124: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:92:62: W291 [*] Trailing whitespace docs/installation.rst:1:1: E999 SyntaxError: Expected a statement docs/installation.rst:9:1: W293 [*] Blank line contains whitespace docs/installation.rst:10:84: W291 [*] Trailing whitespace docs/installation.rst:11:109: W291 [*] Trailing whitespace docs/installation.rst:14:116: W291 [*] Trailing whitespace docs/installation.rst:15:133: W291 [*] Trailing whitespace docs/installation.rst:27:67: W291 [*] Trailing whitespace docs/installation.rst:59:1: W293 [*] Blank line contains whitespace docs/installation.rst:66:19: W291 [*] Trailing whitespace docs/installation.rst:69:1: W293 [*] Blank line contains whitespace docs/installation.rst:86:102: W291 [*] Trailing whitespace docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement setup.py:1:1: E902 No such file or directory (os error 2) tardis/visualization/tools/tests/test_sdec_plot.py:343:17: F631 Assert test is a non-empty tuple, which is always `True` tardis/visualization/tools/tests/test_sdec_plot.py:475:13: F631 Assert test is a non-empty tuple, which is always `True` tardis/visualization/tools/tests/test_sdec_plot.py:557:13: PLW0127 Self-assignment of variable `observed_spectrum` tardis/visualization/tools/tests/test_sdec_plot.py:618:13: F631 Assert test is a non-empty tuple, which is always `True` Found 141 errors. [*] 29 fixable with the `--fix` option (4 hidden fixes can be enabled with the `--unsafe-fixes` option). ```

codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 69.37%. Comparing base (8a317dd) to head (c49bf26). Report is 7 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #2798 +/- ## ========================================== - Coverage 69.91% 69.37% -0.55% ========================================== Files 206 206 Lines 15523 15518 -5 ========================================== - Hits 10853 10765 -88 - Misses 4670 4753 +83 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

tardis-bot commented 2 months ago

*beep* *bop*

Hi, human.

The docs workflow has succeeded :heavy_check_mark:

Click here to see your results.

tardis-bot commented 2 months ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (8a317dd9eead8acab8d9c17d290863e05f5a27f2) and the latest commit (c49bf268794cbf6a859056d6af4e4cd761c61d2a). Here are the logs produced by ASV. Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

```diff ```

All benchmarks:

```diff Benchmarks that have stayed the same: | Change | Before [a054d743] | After [c49bf268] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------| | | 2.04±1μs | 2.28±1μs | ~1.12 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators | | | 561±200ns | 501±100ns | ~0.89 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation | | | 671±100ns | 571±100ns | ~0.85 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation | | | 3.44±0.4μs | 2.80±0.8μs | ~0.81 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket | | | 44.5±30μs | 47.3±30μs | 1.06 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter | | | 42.2±20μs | 43.7±20μs | 1.04 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission | | | 2.69±0.03ms | 2.75±0.01ms | 1.02 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | | | 1.69±0.01ms | 1.72±0.01ms | 1.02 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop | | | 31.1±0.02μs | 31.5±0.01μs | 1.01 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list | | | 2.86±0.5ms | 2.90±0.4ms | 1.01 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop | | | 7.33±2μs | 7.42±1μs | 1.01 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley | | | 39.3±0.07s | 39.4±0.04s | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis | | | 2.07±0m | 2.07±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions | | | 1.05±0m | 1.05±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking | | | 206±0.1ns | 203±0.05ns | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body | | | 1.53±0.5μs | 1.51±0.4μs | 0.99 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line | | | 64.5±0.1ms | 63.7±0.07ms | 0.99 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe | | | 571±200ns | 561±200ns | 0.98 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation | | | 1.23±0μs | 1.21±0μs | 0.98 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary | | | 764±0.7ns | 731±0.4ns | 0.96 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter | | | 3.89±0.01ms | 3.62±0.02ms | 0.93 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') | | | 3.47±0.3μs | 3.23±0.4μs | 0.93 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell | | | 24.9±7μs | 22.8±6μs | 0.92 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list | | | 6.94±0.4μs | 6.35±0.7μs | 0.91 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket | ```

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

tardis-sn / tardis