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tardis-sn / tardis

TARDIS - Temperature And Radiative Diffusion In Supernovae
https://tardis-sn.github.io/tardis
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moved _parse_species_list function to tardis.io.util.py #2837

Open rudrakshnalbalwar opened 1 month ago

rudrakshnalbalwar commented 1 month ago

:pencil: Description

Type: :roller_coaster: infrastructure

Relocated species list parsing logic from liv_plot.py to util.py to improve file organization and maintainability. No changes to functionality were made; the parsing logic remains the same but is now centralized in a more appropriate file.

:pushpin: Resources

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:vertical_traffic_light: Testing

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tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran ruff on the latest commit (8b00774ed53b81498e21f40e200c3207d947d10d). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 65 W291 [*] Trailing whitespace 50 W293 [*] Blank line contains whitespace 50 F401 [*] `astropy.units` imported but unused 48 E999 [ ] SyntaxError: Expected ',', found ':' 36 I001 [*] Import block is un-sorted or un-formatted 20 G004 [ ] Logging statement uses f-string 20 E902 [ ] No such file or directory (os error 2) 19 RET505 [ ] Unnecessary `elif` after `return` statement 18 UP008 [*] Use `super()` instead of `super(__class__, self)` 13 D202 [*] No blank lines allowed after function docstring (found 1) 8 E402 [ ] Module level import not at top of cell 8 F405 [ ] `HiddenPlasmaProperty` may be undefined, or defined from star imports 7 RET506 [ ] Unnecessary `elif` after `raise` statement 7 UP015 [*] Unnecessary open mode parameters 6 UP032 [*] Use f-string instead of `format` call 5 E722 [ ] Do not use bare `except` 5 F811 [ ] Redefinition of unused `OpacityState` from line 14 5 UP004 [*] Class `CudaFormalIntegrator` inherits from `object` 4 E701 [ ] Multiple statements on one line (colon) 4 E712 [*] Avoid equality comparisons to `True`; use `if latex_label:` for truth checks 4 F821 [ ] Undefined name `atomic_dataset` 3 FLY002 [*] Consider `f"{filename}.csv"` instead of string join 3 W292 [*] No newline at end of file 2 COM818 [ ] Trailing comma on bare tuple prohibited 2 C416 [*] Unnecessary `list` comprehension (rewrite using `list()`) 2 ISC003 [ ] Explicitly concatenated string should be implicitly concatenated 2 PIE808 [*] Unnecessary `start` argument in `range` 2 W605 [*] Invalid escape sequence: `\A` 2 D209 [*] Multi-line docstring closing quotes should be on a separate line 2 F403 [ ] `from tardis.plasma.properties.base import *` used; unable to detect undefined names 2 PGH004 [ ] Use specific rule codes when using `noqa` 2 UP024 [*] Replace aliased errors with `OSError` 1 S605 [ ] Starting a process with a shell: seems safe, but may be changed in the future; consider rewriting without `shell` 1 FA102 [*] Missing `from __future__ import annotations`, but uses PEP 604 union 1 ICN001 [*] `matplotlib` should be imported as `mpl` 1 G001 [ ] Logging statement uses `str.format` 1 PIE790 [*] Unnecessary `pass` statement 1 TD006 [*] Invalid TODO capitalization: `todo` should be `TODO` 1 N812 [ ] Lowercase `__path__` imported as non-lowercase `TARDIS_PATH` 1 E713 [*] Test for membership should be `not in` 1 PLW0127 [ ] Self-assignment of variable `atom_data` 1 UP009 [*] UTF-8 encoding declaration is unnecessary 1 UP030 [*] Use implicit references for positional format fields 1 UP034 [*] Avoid extraneous parentheses 1 TRY300 [ ] Consider moving this statement to an `else` block ```

Complete output(might be large):

```diff .github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression .github/workflows/benchmarks.yml:20:5: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:81:49: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:111:81: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:112:54: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:199:1: W293 [*] Blank line contains whitespace .github/workflows/benchmarks.yml:218:22: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:219:170: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:221:84: W291 [*] Trailing whitespace .github/workflows/benchmarks.yml:238:1: W293 [*] Blank line contains whitespace .github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/codespell.yml:3:4: E999 SyntaxError: Expected an expression .github/workflows/codespell.yml:18:11: E701 Multiple statements on one line (colon) .github/workflows/codespell.yml:39:26: W292 [*] No newline at end of file .github/workflows/codestyle.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/codestyle.yml:25:11: E701 Multiple statements on one line (colon) .github/workflows/codestyle.yml:30:11: E701 Multiple statements on one line (colon) .github/workflows/codestyle.yml:46:8: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:63:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:65:15: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:69:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:78:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:82:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:90:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:102:26: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:106:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:114:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:125:22: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:126:89: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:128:84: W291 [*] Trailing whitespace .github/workflows/codestyle.yml:144:1: W293 [*] Blank line contains whitespace .github/workflows/codestyle.yml:148:1: W293 [*] Blank line contains whitespace .github/workflows/post-release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/post-release.yml:124:37: W291 [*] Trailing whitespace .github/workflows/pre-release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/release.yml:16:7: E701 Multiple statements on one line (colon) .github/workflows/release.yml:57:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:59:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:3:4: E999 SyntaxError: Expected an expression .github/workflows/stardis-tests.yml:22:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:39:11: W291 [*] Trailing whitespace .github/workflows/stardis-tests.yml:51:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:58:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:64:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:69:1: W293 [*] Blank line contains whitespace .github/workflows/stardis-tests.yml:75:32: W291 [*] Trailing whitespace .github/workflows/stardis-tests.yml:76:20: W292 [*] No newline at end of file .github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression .mailmap:1:38: E999 SyntaxError: Expected an expression CHANGELOG.md:4:15: E999 SyntaxError: Expected ',', found ':' CITATION.cff:3:1: E999 SyntaxError: Invalid annotated assignment target CODE_OF_CONDUCT.md:4:5: E999 SyntaxError: Simple statements must be separated by newlines or semicolons CODE_OF_CONDUCT.md:6:28: COM818 Trailing comma on bare tuple prohibited CODE_OF_CONDUCT.md:13:257: W291 [*] Trailing whitespace GOVERNANCE.md:3:8: E999 SyntaxError: Simple statements must be separated by newlines or semicolons README.rst:1:1: E999 SyntaxError: Expected a statement README_TEMPLATE.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-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 docs/_static/ruff_badge.json:1:1: E902 No such file or directory (os error 2) 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/azure_links.inc:2:1: E999 SyntaxError: Expected a statement docs/contributing/development/code_quality.rst:1:1: E999 SyntaxError: Expected an expression docs/contributing/development/continuous_integration.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/continuous_integration.rst:43:71: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:47:76: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:49:68: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:67:11: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:150:68: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:187:78: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:267:24: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:308:70: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:318:61: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:333:85: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:336:53: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:353:90: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:360:78: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:361:94: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:362:83: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:363:96: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:365:97: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:366:62: W291 [*] Trailing whitespace docs/contributing/development/continuous_integration.rst:373:90: W291 [*] Trailing whitespace docs/contributing/development/developer_faq.rst:1:1: E999 SyntaxError: Expected an expression docs/contributing/development/developer_faq.rst:13:40: W291 [*] Trailing whitespace docs/contributing/development/index.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/known_projects.inc:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/links.inc:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/links.inc:6:30: W292 [*] No newline at end of file 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:80:62: W291 [*] Trailing whitespace docs/contributing/development/update_refdata.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/update_refdata.rst:12:105: W291 [*] Trailing whitespace docs/contributing/development/update_regression_data.rst:1:1: E902 No such file or directory (os error 2) docs/contributing/tools/hdf_writer.ipynb:cell 3:9:1: W293 [*] Blank line contains whitespace docs/contributing/tools/hdf_writer.ipynb:cell 8:3:11: E999 SyntaxError: Simple statements must be separated by newlines or semicolons docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:1:1: I001 [*] Import block is un-sorted or un-formatted docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:1:8: F401 [*] `tardis` imported but unused docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:5:38: F401 [*] `tardis.io.atom_data.base.AtomData` imported but unused docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:7:20: F811 [*] Redefinition of unused `run_tardis` from cell 2, line 2 docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:11:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:11:1: I001 [*] Import block is un-sorted or un-formatted docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:12:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:13:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:13:30: F401 [*] `astropy.units` imported but unused docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:14:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:15:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 2:16:1: E402 Module level import not at top of cell docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:2:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:8:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:12:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:17:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:22:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:24:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:26:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:32:21: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:35:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:37:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:44:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:54:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:57:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:63:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:68:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 4:75:5: RET505 Unnecessary `elif` after `return` statement docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:1:32: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:2:35: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:3:37: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:4:41: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:5:31: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:6:31: W291 [*] Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:8:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:11:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:13:112: W291 Trailing whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:15:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:49:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:54:33: UP032 [*] Use f-string instead of `format` call docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:56:33: UP032 [*] Use f-string instead of `format` call docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 7:57:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 8:9:6: UP015 [*] Unnecessary open mode parameters docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 8:12:6: UP015 [*] Unnecessary open mode parameters docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 8:16:19: C416 Unnecessary `list` comprehension (rewrite using `list()`) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 8:17:23: C416 Unnecessary `list` comprehension (rewrite using `list()`) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 9:2:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 9:4:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 9:11:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:2:5: D202 [*] No blank lines allowed after function docstring (found 1) docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:4:1: W293 Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:18:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:30:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:44:1: W293 [*] Blank line contains whitespace docs/contributing/tools/profiling/tardis_profiling_threads.ipynb:cell 10:45:43: UP032 [*] Use f-string instead of `format` call docs/index.rst:1:1: E999 SyntaxError: Expected a statement docs/index.rst:21:51: W291 [*] Trailing whitespace docs/index.rst:43:76: W291 [*] Trailing whitespace docs/index.rst:44:64: W291 [*] Trailing whitespace docs/index.rst:45:71: W291 [*] Trailing whitespace docs/index.rst:46:69: W291 [*] Trailing whitespace docs/index.rst:47:68: W291 [*] Trailing whitespace docs/index.rst:66:1: W293 [*] Blank line contains whitespace docs/index.rst:79:1: W293 [*] Blank line contains whitespace docs/index.rst:102:1: W293 [*] Blank line contains whitespace docs/io/configuration/components/models/converters/arepo_to_tardis.ipynb:cell 6:1:1: I001 [*] Import block is un-sorted or un-formatted docs/io/configuration/components/models/converters/arepo_to_tardis.ipynb:cell 6:1:17: F401 [*] `numpy` imported but unused docs/io/configuration/components/models/converters/arepo_to_tardis.ipynb:cell 6:4:8: F401 [*] `json` imported but unused docs/io/configuration/components/models/csvy_full_rad.csvy:1:4: E999 SyntaxError: Expected an expression docs/multiindex_isotope_decay_data.ipynb:cell 1:2:1: I001 [*] Import block is un-sorted or un-formatted docs/multiindex_isotope_decay_data.ipynb:cell 1:2:21: F401 [*] `pathlib.Path` imported but unused docs/multiindex_isotope_decay_data.ipynb:cell 7:5:70: W291 [*] Trailing whitespace docs/physics/plasma/detailed_balance/collisional_rate_coefficients.hdf:1:1: E902 No such file or directory (os error 2) docs/physics/plasma/detailed_balance/comparison.ipynb:1:1: E902 No such file or directory (os error 2) docs/physics/plasma/detailed_balance/rates.ipynb:1:1: E902 No such file or directory (os error 2) docs/physics/plasma/detailed_balance/test_continuum_template_wkerzen_rate_coeffs.yml:1:1: E902 No such file or directory (os error 2) docs/physics/tardisgamma/index.rst:1:1: E902 No such file or directory (os error 2) docs/physics/tardisgamma/packetinitialization.rst:1:1: E902 No such file or directory (os error 2) docs/quickstart.ipynb:cell 12:1:39: W291 [*] Trailing whitespace docs/quickstart.ipynb:cell 12:5:35: W291 [*] Trailing whitespace docs/quickstart.ipynb:cell 16:10:26: W605 [*] Invalid escape sequence: `\A` docs/quickstart.ipynb:cell 16:11:40: W605 [*] Invalid escape sequence: `\A` docs/resources/code_comparison/toy_models/blondin_compare.csvy:1:4: E999 SyntaxError: Expected an expression docs/resources/code_comparison/toy_models/blondin_compare_01.csvy:1:4: E999 SyntaxError: Expected an expression docs/resources/code_comparison/toy_models/blondin_compare_06.csvy:1:4: E999 SyntaxError: Expected an expression docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement docs/workflows/simple_workflow.ipynb:1:1: E902 No such file or directory (os error 2) docs/workflows/standard_workflow.ipynb:1:1: E902 No such file or directory (os error 2) tardis/__init__.py:6:31: PGH004 Use specific rule codes when using `noqa` tardis/__init__.py:25:1: I001 [*] Import block is un-sorted or un-formatted tardis/__init__.py:32:25: F401 `tardis.base.run_tardis` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/__init__.py:33:46: F401 `tardis.io.util.yaml_load_file` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/_astropy_init.py:12:1: I001 [*] Import block is un-sorted or un-formatted tardis/base.py:5:1: I001 [*] Import block is un-sorted or un-formatted tardis/base.py:73:1: I001 [*] Import block is un-sorted or un-formatted tardis/base.py:101:13: PLW0127 Self-assignment of variable `atom_data` tardis/energy_input/util.py:383:5: RET505 Unnecessary `elif` after `return` statement tardis/io/model/parse_radiation_field_configuration.py:118:13: G004 Logging statement uses f-string tardis/io/util.py:18:20: N812 Lowercase `__path__` imported as non-lowercase `TARDIS_PATH` tardis/io/util.py:190:60: W291 [*] Trailing whitespace tardis/io/util.py:191:1: W293 [*] Blank line contains whitespace tardis/io/util.py:290:9: RET506 Unnecessary `else` after `raise` statement tardis/io/util.py:383:21: G004 Logging statement uses f-string tardis/io/util.py:467:13: G004 Logging statement uses f-string tardis/model/matter/composition.py:206:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/__init__.py:2:63: W291 Trailing whitespace tardis/plasma/__init__.py:5:32: F401 `tardis.plasma.base.BasePlasma` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/assembly/base.py:132:22: FA102 Missing `from __future__ import annotations`, but uses PEP 604 union tardis/plasma/base.py:11:1: F403 `from tardis.plasma.properties.base import *` used; unable to detect undefined names tardis/plasma/base.py:45:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/base.py:46:18: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/base.py:53:9: RET506 Unnecessary `else` after `raise` statement tardis/plasma/base.py:54:18: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/base.py:111:17: E722 Do not use bare `except` tardis/plasma/base.py:144:44: F405 `PreviousIterationProperty` may be undefined, or defined from star imports tardis/plasma/base.py:153:46: F405 `Input` may be undefined, or defined from star imports tardis/plasma/base.py:273:13: G004 Logging statement uses f-string tardis/plasma/base.py:296:20: F401 [*] `pygraphviz` imported but unused tardis/plasma/base.py:297:9: E722 Do not use bare `except` tardis/plasma/base.py:306:16: E712 Avoid equality comparisons to `True`; use `if latex_label:` for truth checks tardis/plasma/base.py:327:16: E712 Avoid equality comparisons to `True`; use `if latex_label:` for truth checks tardis/plasma/base.py:333:16: E712 Avoid equality comparisons to `True`; use `if latex_label:` for truth checks tardis/plasma/base.py:383:9: E722 Do not use bare `except` tardis/plasma/base.py:429:35: F405 `HiddenPlasmaProperty` may be undefined, or defined from star imports tardis/plasma/base.py:447:29: E722 Do not use bare `except` tardis/plasma/detailed_balance/rates/__init__.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/detailed_balance/rates/collision_strengths.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/detailed_balance/rates/collisional_rates.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/detailed_balance/rates/radiative_rates.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/detailed_balance/tests/__init__.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/detailed_balance/tests/test_collisional_transitions.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/properties/atomic.py:6:28: F401 [*] `radioactivedecay` imported but unused tardis/plasma/properties/atomic.py:11:33: F401 [*] `tardis.constants` imported but unused tardis/plasma/properties/atomic.py:379:17: UP032 [*] Use f-string instead of `format` call tardis/plasma/properties/atomic.py:558:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/properties/atomic.py:589:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/properties/atomic.py:602:17: G004 Logging statement uses f-string tardis/plasma/properties/atomic.py:643:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/properties/base.py:78:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/base.py:117:25: G004 Logging statement uses f-string tardis/plasma/properties/base.py:135:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/base.py:163:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/base.py:178:9: RET505 Unnecessary `else` after `return` statement tardis/plasma/properties/continuum_processes/__init__.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/properties/continuum_processes/__init__.py:2:5: F401 `tardis.plasma.properties.continuum_processes.photo_ion_rate_coeff.PhotoIonRateCoeff` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/properties/continuum_processes/__init__.py:4:1: F403 `from tardis.plasma.properties.continuum_processes.rates import *` used; unable to detect undefined names tardis/plasma/properties/continuum_processes/__init__.py:6:5: F401 `tardis.plasma.properties.continuum_processes.recomb_rate_coeff.StimRecombRateFactor` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/properties/continuum_processes/__init__.py:7:5: F401 `tardis.plasma.properties.continuum_processes.recomb_rate_coeff.SpontRecombRateCoeff` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/properties/continuum_processes/__init__.py:8:5: F401 `tardis.plasma.properties.continuum_processes.recomb_rate_coeff.StimRecombRateCoeff` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/properties/continuum_processes/fast_array_util.py:3:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/properties/general.py:4:30: F401 [*] `astropy.units` imported but unused tardis/plasma/properties/general.py:33:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/general.py:74:21: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/general.py:118:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/helium_nlte.py:53:13: UP034 [*] Avoid extraneous parentheses tardis/plasma/properties/helium_nlte.py:130:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/helium_nlte.py:182:21: E722 Do not use bare `except` tardis/plasma/properties/helium_nlte.py:185:29: G004 Logging statement uses f-string tardis/plasma/properties/helium_nlte.py:218:23: S605 Starting a process with a shell: seems safe, but may be changed in the future; consider rewriting without `shell` tardis/plasma/properties/helium_nlte.py:235:18: UP015 [*] Unnecessary open mode parameters tardis/plasma/properties/helium_nlte.py:238:36: PIE808 [*] Unnecessary `start` argument in `range` tardis/plasma/properties/helium_nlte.py:261:69: F821 Undefined name `s1` tardis/plasma/properties/ion_population.py:206:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/ion_population.py:291:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/ion_population.py:370:25: G004 Logging statement uses f-string tardis/plasma/properties/ion_population.py:424:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/ion_population.py:495:25: G004 Logging statement uses f-string tardis/plasma/properties/level_population.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/properties/level_population.py:28:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/nlte.py:2:8: F401 [*] `os` imported but unused tardis/plasma/properties/nlte.py:4:17: F401 [*] `numpy` imported but unused tardis/plasma/properties/nlte.py:10:53: F401 [*] `tardis.plasma.properties.ion_population.PhiSahaNebular` imported but unused tardis/plasma/properties/nlte_excitation_data.py:8:26: UP004 [*] Class `NLTEExcitationData` inherits from `object` tardis/plasma/properties/nlte_rate_equation_solver.py:302:25: UP032 [*] Use f-string instead of `format` call tardis/plasma/properties/nlte_rate_equation_solver.py:302:25: G001 Logging statement uses `str.format` tardis/plasma/properties/nlte_rate_equation_solver.py:311:25: G004 Logging statement uses f-string tardis/plasma/properties/partition_function.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/properties/partition_function.py:145:9: RET505 Unnecessary `elif` after `return` statement tardis/plasma/properties/partition_function.py:161:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/partition_function.py:181:25: G004 Logging statement uses f-string tardis/plasma/properties/partition_function.py:192:21: G004 Logging statement uses f-string tardis/plasma/properties/partition_function.py:199:21: G004 Logging statement uses f-string tardis/plasma/properties/partition_function.py:252:21: RET506 Unnecessary `else` after `raise` statement tardis/plasma/properties/partition_function.py:395:21: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/plasma_input.py:2:5: F401 [*] `tardis.plasma.properties.base.ArrayInput` imported but unused tardis/plasma/properties/radiative_properties.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/properties/radiative_properties.py:42:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/radiative_properties.py:178:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/plasma/properties/rate_matrix_index.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/radiation_field/__init__.py:2:5: F401 `tardis.plasma.radiation_field.planck_rad_field.DilutePlanckianRadiationField` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/tests/test_complete_plasmas.py:149:27: FLY002 Consider `f"{hash_string}_{prop}"` instead of string join tardis/plasma/tests/test_complete_plasmas.py:154:39: FLY002 Consider `f"{hash_string}_{nlte_prop}"` instead of string join tardis/plasma/tests/test_hdf_plasma.py:1:17: F401 [*] `numpy` imported but unused tardis/plasma/tests/test_nlte_excitation.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/tests/test_nlte_excitation.py:5:27: F401 [*] `numpy.testing.assert_allclose` imported but unused tardis/plasma/tests/test_nlte_solver.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/plasma/tests/test_nlte_solver.py:5:25: F811 [*] Redefinition of unused `npt` from line 2 tardis/plasma/tests/test_plasma_continuum.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/scripts/cmfgen2tardis.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/scripts/cmfgen2tardis.py:2:8: F401 [*] `sys` imported but unused tardis/scripts/cmfgen2tardis.py:7:33: F401 [*] `tardis.io.atom_data.AtomData` imported but unused tardis/scripts/cmfgen2tardis.py:15:27: F821 Undefined name `atomic_dataset` tardis/scripts/cmfgen2tardis.py:43:10: UP015 [*] Unnecessary open mode parameters tardis/scripts/cmfgen2tardis.py:70:34: F821 Undefined name `atomic_dataset` tardis/scripts/cmfgen2tardis.py:105:18: FLY002 Consider `f"{filename}.csv"` instead of string join tardis/simulation/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/simulation/base.py:155:14: UP008 Use `super()` instead of `super(__class__, self)` tardis/simulation/base.py:199:13: RET506 Unnecessary `else` after `raise` statement tardis/simulation/base.py:263:17: G004 Logging statement uses f-string tardis/simulation/base.py:270:9: RET505 Unnecessary `else` after `return` statement tardis/simulation/base.py:451:13: G004 Logging statement uses f-string tardis/simulation/base.py:549:13: G004 Logging statement uses f-string tardis/simulation/base.py:656:25: G004 Logging statement uses f-string tardis/simulation/base.py:659:13: G004 Logging statement uses f-string tardis/simulation/base.py:664:13: G004 Logging statement uses f-string tardis/simulation/base.py:715:13: TRY300 Consider moving this statement to an `else` block tardis/simulation/base.py:717:26: G004 Logging statement uses f-string tardis/spectrum/formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/spectrum/formal_integral.py:9:25: F401 [*] `numba.char` imported but unused tardis/spectrum/formal_integral.py:9:31: F401 [*] `numba.float64` imported but unused tardis/spectrum/formal_integral.py:9:40: F401 [*] `numba.int64` imported but unused tardis/spectrum/formal_integral.py:9:47: F401 [*] `numba.typeof` imported but unused tardis/spectrum/formal_integral.py:9:55: F401 [*] `numba.byte` imported but unused tardis/spectrum/formal_integral.py:10:32: F401 [*] `numba.experimental.jitclass` imported but unused tardis/spectrum/formal_integral.py:21:5: F811 Redefinition of unused `opacity_state_initialize` from line 15 tardis/spectrum/formal_integral.py:22:5: F811 Redefinition of unused `OpacityState` from line 14 tardis/spectrum/formal_integral.py:22:5: F401 [*] `tardis.transport.montecarlo.numba_interface.OpacityState` imported but unused tardis/spectrum/formal_integral.py:55:5: D202 [*] No blank lines allowed after function docstring (found 1) tardis/spectrum/formal_integral.py:65:7: TD006 [*] Invalid TODO capitalization: `todo` should be `TODO` tardis/spectrum/formal_integral.py:218:29: UP004 [*] Class `NumbaFormalIntegrator` inherits from `object` tardis/spectrum/formal_integral.py:261:24: UP004 [*] Class `FormalIntegrator` inherits from `object` tardis/spectrum/formal_integral.py:299:9: D209 [*] Multi-line docstring closing quotes should be on a separate line tardis/spectrum/formal_integral.py:344:13: RET506 Unnecessary `else` after `raise` statement tardis/spectrum/formal_integral.py:356:16: E713 [*] Test for membership should be `not in` tardis/spectrum/formal_integral.py:615:9: D209 [*] Multi-line docstring closing quotes should be on a separate line tardis/spectrum/formal_integral.py:684:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral.py:720:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral_cuda.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/spectrum/formal_integral_cuda.py:1:8: F401 [*] `sys` imported but unused tardis/spectrum/formal_integral_cuda.py:3:30: F401 [*] `astropy.units` imported but unused tardis/spectrum/formal_integral_cuda.py:4:19: F401 [*] `numba.float64` imported but unused tardis/spectrum/formal_integral_cuda.py:4:28: F401 [*] `numba.int64` imported but unused tardis/spectrum/formal_integral_cuda.py:17:5: D202 [*] No blank lines allowed after function docstring (found 1) tardis/spectrum/formal_integral_cuda.py:58:5: D202 [*] No blank lines allowed after function docstring (found 1) tardis/spectrum/formal_integral_cuda.py:237:28: UP004 [*] Class `CudaFormalIntegrator` inherits from `object` tardis/spectrum/formal_integral_cuda.py:378:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral_cuda.py:423:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral_cuda.py:433:5: PIE790 [*] Unnecessary `pass` statement tardis/spectrum/formal_integral_cuda.py:513:5: D202 [*] No blank lines allowed after function docstring (found 1) tardis/spectrum/formal_integral_cuda.py:555:5: D202 [*] No blank lines allowed after function docstring (found 1) tardis/spectrum/tests/test_cuda_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/spectrum/tests/test_cuda_formal_integral.py:15:46: F401 [*] `tardis.transport.montecarlo.base.MonteCarloTransportSolver` imported but unused tardis/spectrum/tests/test_numba_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/spectrum/tests/test_numba_formal_integral.py:5:18: F401 [*] `copy.deepcopy` imported but unused tardis/spectrum/tests/test_spectrum.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/fixtures/atom_data.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/fixtures/atom_data.py:2:21: F401 [*] `pathlib.Path` imported but unused tardis/tests/integration_tests/at/abundances.dat:2:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/at/config.yml:2:7: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/at/densities.dat:1:10: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/tests/integration_tests/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/integration_tests/conftest.py:42:13: F821 Undefined name `tardis_githash` tardis/tests/integration_tests/conftest.py:87:5: RET505 Unnecessary `else` after `return` statement tardis/tests/integration_tests/conftest.py:90:16: UP024 [*] Replace aliased errors with `OSError` tardis/tests/integration_tests/conftest.py:91:19: UP024 [*] Replace aliased errors with `OSError` tardis/tests/integration_tests/paper1_downbranch/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/paper1_macroatom/abundances.dat:1:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/paper1_macroatom/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/paper1_macroatom/densities.dat:1:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/paper1_scatter/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/test_integration.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/integration_tests/test_integration.py:5:8: ICN001 `matplotlib` should be imported as `mpl` tardis/tests/integration_tests/test_integration.py:8:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/integration_tests/test_integration.py:74:23: UP004 [*] Class `TestIntegration` inherits from `object` tardis/tests/integration_tests/w7/abundances.dat:2:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/w7/config.yml:2:7: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/w7/densities.dat:1:11: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/tests/test_util.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/test_util.py:3:25: F401 [*] `numpy.testing` imported but unused tardis/tests/test_util.py:15:5: F401 [*] `tardis.util.base.create_synpp_yaml` imported but unused tardis/visualization/tools/liv_plot.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/tools/liv_plot.py:3:25: F401 [*] `matplotlib.cm` imported but unused tardis/visualization/tools/liv_plot.py:26:9: D202 [*] No blank lines allowed after function docstring (found 1) tardis/visualization/tools/liv_plot.py:49:9: D202 [*] No blank lines allowed after function docstring (found 1) tardis/visualization/tools/liv_plot.py:305:13: RET506 Unnecessary `elif` after `raise` statement tardis/visualization/tools/sdec_plot.py:8:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/tools/sdec_plot.py:21:5: F401 [*] `tardis.util.base.element_symbol2atomic_number` imported but unused tardis/visualization/tools/sdec_plot.py:23:5: F401 [*] `tardis.util.base.roman_to_int` imported but unused tardis/visualization/tools/sdec_plot.py:24:5: F401 [*] `tardis.util.base.species_string_to_tuple` imported but unused tardis/visualization/tools/sdec_plot.py:202:9: RET505 Unnecessary `elif` after `return` statement tardis/visualization/tools/sdec_plot.py:343:13: RET505 Unnecessary `elif` after `return` statement tardis/visualization/tools/sdec_plot.py:460:9: RET505 Unnecessary `else` after `return` statement tardis/visualization/tools/sdec_plot.py:496:9: RET505 Unnecessary `elif` after `return` statement tardis/visualization/tools/sdec_plot.py:611:13: RET506 Unnecessary `else` after `raise` statement tardis/visualization/tools/sdec_plot.py:1131:11: W291 [*] Trailing whitespace tardis/visualization/tools/sdec_plot.py:1536:10: W291 [*] Trailing whitespace tardis/visualization/tools/tests/test_liv_plot.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/tools/tests/test_liv_plot.py:128:1: W293 [*] Blank line contains whitespace tardis/visualization/tools/tests/test_liv_plot.py:132:1: W293 [*] Blank line contains whitespace tardis/visualization/tools/tests/test_liv_plot.py:143:1: W293 [*] Blank line contains whitespace tardis/visualization/tools/tests/test_liv_plot.py:363:29: ISC003 Explicitly concatenated string should be implicitly concatenated tardis/visualization/tools/tests/test_rpacket_plot.py:3:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/tools/tests/test_sdec_plot.py:2:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/tools/tests/test_sdec_plot.py:182:1: W293 [*] Blank line contains whitespace tardis/visualization/tools/tests/test_sdec_plot.py:333:29: ISC003 Explicitly concatenated string should be implicitly concatenated tardis/visualization/tools/tests/test_sdec_plot.py:388:9: F811 Redefinition of unused `test_generate_plot_mpl` from line 299 tardis/visualization/widgets/shell_info.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/visualization/widgets/shell_info.py:1:25: F401 [*] `tardis.base.run_tardis` imported but unused tardis/visualization/widgets/shell_info.py:2:51: F401 [*] `tardis.io.atom_data.atom_web_download.download_atom_data` imported but unused tardis/visualization/widgets/shell_info.py:12:17: F401 [*] `numpy` imported but unused tardis/visualization/widgets/shell_info.py:299:25: PIE808 [*] Unnecessary `start` argument in `range` tardis/workflows/__init__.py:1:1: E902 No such file or directory (os error 2) tardis/workflows/simple_tardis_workflow.py:1:1: E902 No such file or directory (os error 2) tardis/workflows/standard_tardis_workflow.py:1:1: E902 No such file or directory (os error 2) tardis/workflows/workflow_logging.py:1:1: E902 No such file or directory (os error 2) tardis_env3.yml:3:10: E999 SyntaxError: Expected an expression Found 439 errors. [*] 228 fixable with the `--fix` option (44 hidden fixes can be enabled with the `--unsafe-fixes` option). ```
tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (3b6084f275342c30b5be913a11a76690cc56e1ff) and the latest commit (8b00774ed53b81498e21f40e200c3207d947d10d). 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 [6ee870e0] | After [8b00774e] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------| | | 531±200ns | 651±100ns | ~1.23 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation | | | 1.89±1μs | 2.32±1μs | ~1.23 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators | | | 501±100ns | 591±200ns | ~1.18 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation | | | 2.95±0.6μs | 3.29±0.6μs | ~1.12 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket | | | 45.0±20μs | 49.9±30μs | ~1.11 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter | | | 1.45±0.4μs | 1.23±0.4μs | ~0.85 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line | | | 3.79±0ms | 4.09±0.01ms | 1.08 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') | | | 6.58±0.5μs | 7.07±3μs | 1.07 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket | | | 1.17±0μs | 1.22±0.08μs | 1.04 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary | | | 30.3±0μs | 30.7±0.04μs | 1.02 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list | | | 40.3±0.02s | 40.5±0.06s | 1.01 | run_tardis.BenchmarkRunTardis.time_run_tardis | | | 1.06±0m | 1.07±0m | 1.01 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking | | | 2.06±0m | 2.07±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions | | | 2.69±0.5ms | 2.68±0.5ms | 1.00 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop | | | 41.7±20μs | 41.4±20μs | 0.99 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission | | | 511±100ns | 500±100ns | 0.98 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation | | | 206±0.1ns | 203±0.4ns | 0.98 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body | | | 1.68±0.02ms | 1.65±0ms | 0.98 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop | | | 65.0±0.5ms | 62.8±0.2ms | 0.97 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe | | | 22.4±6μs | 21.5±5μs | 0.96 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list | | | 7.32±2μs | 7.02±2μs | 0.96 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley | | | 3.43±0.4μs | 3.25±0.7μs | 0.95 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell | | | 2.81±0.02ms | 2.63±0.02ms | 0.94 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | | | 746±6ns | 704±0.3ns | 0.94 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter | ```

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

jvshields commented 1 month ago

Thanks for the contribution! This is a good change, but I think you need to double check where this function is used in the codebase, and change any imports or function calls to point to the right location. I believe that this function is used in the LIV and SDEC plot classes. https://github.com/search?q=repo%3Atardis-sn%2Ftardis%20_parse_species_list&type=code

rudrakshnalbalwar commented 1 month ago

@jvshields I made the changes as you mentioned , I’ve removed the underscore from the parse_species_list function name as requested. However, I did not change the name of the test function test_parse_species_list, since it already follows the convention for testing this function. And I noticed that there were no explicit imports for the _parse_species_list function previously. Since the function is used within the same class/module, an import doesn't seem necessary in this case. Therefore, I haven't added an import for parse_species_list either.

rudrakshnalbalwar commented 1 month ago

Also one more thing do I have to make changes here too ? tardis/.pytest_cache/v/cache/nodeids @jvshields , @atharva-2001 , @andrewfullard

jvshields commented 1 month ago

Please double check that the tests are passing.

I believe that the full refactor here should look like this.

First, move the parse_species_list() function to the util file. (You have done this and it looks good)

Next, remove the function definition from the sdec plot and liv plot classes. Import the more generic function from the util file.

Finally, wherever the function is used in those classes, make sure that it's working properly with the new imported function. The tests here will tell you if everything is hooked up correctly.

Thanks.

rudrakshnalbalwar commented 2 weeks ago

Please double check that the tests are passing.

I believe that the full refactor here should look like this.

First, move the parse_species_list() function to the util file. (You have done this and it looks good)

Next, remove the function definition from the sdec plot and liv plot classes. Import the more generic function from the util file.

Finally, wherever the function is used in those classes, make sure that it's working properly with the new imported function. The tests here will tell you if everything is hooked up correctly.

Thanks.

As you mentioned, I've implemented those changes, and I ran all the tests locally on my device. They are all passing successfully. Could you please review the changes?

codecov[bot] commented 2 weeks ago

Codecov Report

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

Project coverage is 69.62%. Comparing base (3b6084f) to head (f3b31dd). Report is 26 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #2837 +/- ## ========================================== - Coverage 70.89% 69.62% -1.27% ========================================== Files 209 216 +7 Lines 15589 16090 +501 ========================================== + Hits 11052 11203 +151 - Misses 4537 4887 +350 ```

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rudrakshnalbalwar commented 4 days ago

Hey @atharva-2001 and Prof. @wkerzendorf, I've made the necessary changes to both sdec_plot.py and test_sdec_plot.py files as part of refactoring the parse_species_list functionality. The function is now correctly imported from util.py after being moved from liv_plot.py. Could you please review the changes and let me know if everything looks good or if any further adjustments are needed?