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Ruff tardis/visualization #2846

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📝 Description

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

Write a complete description of your changes, including the necessary context or any piece of information required to understand your work.

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

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🚦 Testing

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  • 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 commented Oct 8, 2024

*beep* *bop*
Hi human,
I ran ruff on the latest commit (5f3b5ae).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

36	W293  	[*] Blank line contains whitespace
31	F401  	[*] `astropy.units` imported but unused
23	E999  	[ ] SyntaxError: Expected ',', found ':'
22	W291  	[*] Trailing whitespace
18	G004  	[ ] Logging statement uses f-string
18	UP008 	[*] Use `super()` instead of `super(__class__, self)`
14	RET505	[ ] Unnecessary `elif` after `return` statement
14	E902  	[ ] No such file or directory (os error 2)
13	I001  	[*] Import block is un-sorted or un-formatted
7	ISC003	[ ] Explicitly concatenated string should be implicitly concatenated
6	E402  	[ ] Module level import not at top of cell
6	D202  	[*] No blank lines allowed after function docstring (found 1)
5	RET506	[ ] Unnecessary `elif` after `raise` statement
5	E722  	[ ] Do not use bare `except`
5	F821  	[ ] Undefined name `display`
5	UP032 	[*] Use f-string instead of `format` call
4	E701  	[ ] Multiple statements on one line (colon)
4	F811  	[ ] Redefinition of unused `input_d_time_0_eventhandler` from line 1713
3	E712  	[*] Avoid equality comparisons to `True`; use `if latex_label:` for truth checks
3	F403  	[ ] `from tardis.plasma.properties.base import *` used; unable to detect undefined names
3	F405  	[ ] `HiddenPlasmaProperty` may be undefined, or defined from star imports
3	UP015 	[*] Unnecessary open mode parameters
2	C416  	[*] Unnecessary `list` comprehension (rewrite using `list()`)
2	FLY002	[*] Consider `f"{hash_string}_{nlte_prop}"` instead of string join
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	G001  	[ ] Logging statement uses `str.format`
1	PIE808	[*] Unnecessary `start` argument in `range`
1	W292  	[*] No newline at end of file
1	PGH004	[ ] Use specific rule codes when using `noqa`
1	UP004 	[*] Class `NLTEExcitationData` inherits from `object`
1	UP034 	[*] Avoid extraneous parentheses
1	RUF015	[*] Prefer `next(iter(unique_v))` over single element slice
1	TRY300	[ ] Consider moving this statement to an `else` block

Complete output(might be large):

.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/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
.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
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/contributing/development/code_quality.rst:1:1: E999 SyntaxError: Expected an expression
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/known_projects.inc:1:1: E999 SyntaxError: Expected a statement
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/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/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
tardis/conftest.py:12:1: F403 `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names
tardis/conftest.py:14:36: F401 [*] `tardis.tests.test_util.monkeysession` imported but unused
tardis/conftest.py:31:49: PGH004 Use specific rule codes when using `noqa`
tardis/conftest.py:33:9: F821 Undefined name `pytest_report_header`
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/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/__init__.py:1:1: E902 No such file or directory (os error 2)
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/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/visualization/__init__.py:3:57: F401 `tardis.visualization.tools.convergence_plot.ConvergencePlots` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:4:49: F401 `tardis.visualization.tools.liv_plot.LIVPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:5:53: F401 `tardis.visualization.tools.rpacket_plot.RPacketPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:6:50: F401 `tardis.visualization.tools.sdec_plot.SDECPlotter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:7:59: F401 `tardis.visualization.widgets.custom_abundance.CustomAbundanceWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:8:51: F401 `tardis.visualization.widgets.grotrian.GrotrianWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:9:52: F401 `tardis.visualization.widgets.line_info.LineInfoWidget` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:11:5: F401 `tardis.visualization.widgets.shell_info.shell_info_from_hdf` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/__init__.py:12:5: F401 `tardis.visualization.widgets.shell_info.shell_info_from_simulation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/visualization/plot_util.py:43:5: RET505 Unnecessary `else` after `return` statement
tardis/visualization/tools/convergence_plot.py:320:13: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/tools/liv_plot.py:339:13: RET506 Unnecessary `elif` after `raise` statement
tardis/visualization/tools/rpacket_plot.py:100:13: RET505 Unnecessary `else` after `return` statement
tardis/visualization/tools/rpacket_plot.py:229:35: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/tools/rpacket_plot.py:612:35: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/tools/tests/test_liv_plot.py:352:29: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/tools/tests/test_sdec_plot.py:326:29: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/tools/tests/test_sdec_plot.py:381:9: F811 Redefinition of unused `test_generate_plot_mpl` from line 292
tardis/visualization/widgets/custom_abundance.py:1130:9: RET505 Unnecessary `else` after `return` statement
tardis/visualization/widgets/custom_abundance.py:1421:9: RET506 Unnecessary `else` after `raise` statement
tardis/visualization/widgets/custom_abundance.py:1724:9: F811 Redefinition of unused `input_d_time_0_eventhandler` from line 1713
tardis/visualization/widgets/custom_abundance.py:1754:13: F821 Undefined name `display`
tardis/visualization/widgets/custom_abundance.py:1756:13: F821 Undefined name `display`
tardis/visualization/widgets/custom_abundance.py:1758:13: F821 Undefined name `display`
tardis/visualization/widgets/grotrian.py:612:35: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/widgets/grotrian.py:757:35: ISC003 Explicitly concatenated string should be implicitly concatenated
tardis/visualization/widgets/grotrian.py:1180:9: RET505 Unnecessary `elif` after `return` statement
tardis/visualization/widgets/tests/test_custom_abundance.py:224:37: RUF015 Prefer `next(iter(unique_v))` over single element slice
tardis_env3.yml:3:10: E999 SyntaxError: Expected an expression
Found 262 errors.
[*] 95 fixable with the `--fix` option (39 hidden fixes can be enabled with the `--unsafe-fixes` option).

@andrewfullard
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Some interesting test failures in test_line_info

@tardis-bot
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tardis-bot commented Oct 8, 2024

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (4341331) and the latest commit (5f3b5ae).
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 [81ec6e8e] <master>   | After [5f3b5ae4]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 7.65±2μs                     | 6.76±2μs            | ~0.88   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 25.9±7μs                     | 20.9±5μs            | ~0.81   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 3.46±0.6μs                   | 2.82±0.4μs          | ~0.81   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 69.4±20μs                    | 42.8±30μs           | ~0.62   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 6.33±0.6μs                   | 6.43±1μs            | 1.02    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 37.4±0.07s                   | 37.5±0.01s          | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.08±0m                      | 2.08±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 204±0.01ns                   | 204±0.1ns           | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 2.02±0.9μs                   | 2.01±1μs            | 1.00    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 1.22±0μs                     | 1.21±0μs            | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 1.69±0ms                     | 1.68±0.01ms         | 0.99    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 541±100ns                    | 531±200ns           | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 1.03±0m                      | 1.01±0m             | 0.98    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 41.0±20μs                    | 40.1±20μs           | 0.98    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 723±0.9ns                    | 704±0.2ns           | 0.97    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 31.2±0.01μs                  | 30.3±0.02μs         | 0.97    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.28±0.3μs                   | 3.19±0.8μs          | 0.97    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 551±200ns                    | 531±100ns           | 0.96    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 1.45±0.4μs                   | 1.39±0.3μs          | 0.96    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 2.50±0.4ms                   | 2.41±0.5ms          | 0.96    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 63.9±0.3ms                   | 60.9±0.1ms          | 0.95    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 3.74±0.03ms                  | 3.51±0.03ms         | 0.94    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 2.66±0.01ms                  | 2.50±0ms            | 0.94    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 601±100ns                    | 561±200ns           | 0.93    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |

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

@atharva-2001 atharva-2001 marked this pull request as draft October 14, 2024 14:50
@atharva-2001 atharva-2001 marked this pull request as ready for review October 16, 2024 11:11
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codecov bot commented Oct 16, 2024

Codecov Report

Attention: Patch coverage is 91.66667% with 5 lines in your changes missing coverage. Please review.

Project coverage is 70.67%. Comparing base (4341331) to head (5f3b5ae).
Report is 12 commits behind head on master.

Files with missing lines Patch % Lines
tardis/visualization/widgets/grotrian.py 70.00% 3 Missing ⚠️
...sualization/widgets/tests/test_custom_abundance.py 50.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #2846      +/-   ##
==========================================
- Coverage   70.87%   70.67%   -0.21%     
==========================================
  Files         209      213       +4     
  Lines       15589    15804     +215     
==========================================
+ Hits        11049    11169     +120     
- Misses       4540     4635      +95     

☔ View full report in Codecov by Sentry.
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@@ -1154,8 +1158,8 @@ def _wavelength_change_handler(self, change):
"""
min_wavelength, max_wavelength = change["new"]
index = self.fig.children.index(self.plot.fig)
setattr(self.plot, "min_wavelength", min_wavelength)
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@atharva-2001 can you test that.

@atharva-2001 atharva-2001 marked this pull request as draft November 4, 2024 15:06
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