Update docs with regression data #2842
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*beep* *bop* 44 W291 [*] Trailing whitespace
37 W293 [*] Blank line contains whitespace
30 E999 [ ] SyntaxError: Expected ',', found ':'
25 F401 [*] `astropy.units` imported but unused
18 G004 [ ] Logging statement uses f-string
18 UP008 [*] Use `super()` instead of `super(__class__, self)`
16 E902 [ ] No such file or directory (os error 2)
15 I001 [*] Import block is un-sorted or un-formatted
10 RET505 [ ] Unnecessary `elif` after `return` statement
6 E402 [ ] Module level import not at top of cell
6 D202 [*] No blank lines allowed after function docstring (found 1)
5 E722 [ ] Do not use bare `except`
5 UP032 [*] Use f-string instead of `format` call
4 E701 [ ] Multiple statements on one line (colon)
4 W292 [*] No newline at end of file
3 RET506 [ ] Unnecessary `else` after `raise` statement
3 E712 [*] Avoid equality comparisons to `True`; use `if latex_label:` for truth checks
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 PIE808 [*] Unnecessary `start` argument in `range`
2 FLY002 [*] Consider `f"{hash_string}_{nlte_prop}"` instead of string join
2 W605 [*] Invalid escape sequence: `\A`
2 F403 [ ] `from tardis.plasma.properties.base import *` used; unable to detect undefined names
2 F811 [*] Redefinition of unused `npt` from line 2
1 S605 [ ] Starting a process with a shell: seems safe, but may be changed in the future; consider rewriting without `shell`
1 COM818 [ ] Trailing comma on bare tuple prohibited
1 FA102 [*] Missing `from __future__ import annotations`, but uses PEP 604 union
1 G001 [ ] Logging statement uses `str.format`
1 F821 [ ] Undefined name `s1`
1 UP004 [*] Class `NLTEExcitationData` inherits from `object`
1 UP034 [*] Avoid extraneous parentheses
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
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/contributing/development/azure_links.inc: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/continuous_integration.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/continuous_integration.rst:16:76: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:18:68: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:21:92: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:22:86: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:48:1: W293 [*] Blank line contains whitespace
docs/contributing/development/continuous_integration.rst:82:70: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:97:78: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:98:94: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:99:83: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:100:96: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:102:97: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:103:62: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:110:90: W291 [*] Trailing whitespace
docs/contributing/development/continuous_integration.rst:111:19: W292 [*] No newline at end of file
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:5:30: 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:37:42: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:60:112: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:61:124: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:65:92: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:66:107: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:76:62: W291 [*] Trailing whitespace
docs/contributing/development/update_refdata.rst:1:1: E902 No such file or directory (os error 2)
docs/contributing/development/update_regression_data.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/update_regression_data.rst:27:151: W292 [*] No newline at end of file
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
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/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_env3.yml:3:10: E999 SyntaxError: Expected an expression
Found 275 errors.
[*] 129 fixable with the `--fix` option (38 hidden fixes can be enabled with the `--unsafe-fixes` option).
|
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #2842 +/- ##
==========================================
- Coverage 70.87% 70.70% -0.17%
==========================================
Files 209 213 +4
Lines 15589 15823 +234
==========================================
+ Hits 11049 11188 +139
- Misses 4540 4635 +95 ☔ View full report in Codecov by Sentry. |
atharva-2001
requested changes
Oct 8, 2024
|
*beep* *bop* Hi, human. The Click here to see your results. |
|
*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [81ec6e8e] <master> | After [34b63072] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 46.5±20μs | 67.4±20μs | ~1.45 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 7.06±2μs | 7.98±1μs | ~1.13 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 3.25±0.6μs | 2.91±0.3μs | ~0.90 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 2.42±1μs | 2.04±1μs | ~0.84 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 1.89±0.3μs | 1.31±0.6μs | ~0.69 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 521±100ns | 571±100ns | 1.10 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 2.54±0.01ms | 2.74±0ms | 1.07 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 62.0±0.1ms | 65.7±0.2ms | 1.06 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 581±200ns | 612±100ns | 1.05 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 3.53±0.01ms | 3.68±0.01ms | 1.04 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 6.20±1μs | 6.45±0.7μs | 1.04 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 561±200ns | 571±100ns | 1.02 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 2.08±0m | 2.08±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 204±0.03ns | 204±0.1ns | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 1.19±0μs | 1.19±0μs | 1.00 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 42.1±20μs | 42.3±10μs | 1.00 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 20.9±5μs | 20.9±5μs | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 1.04±0m | 1.03±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 1.69±0ms | 1.67±0.01ms | 0.99 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 38.1±0.02s | 37.5±0.01s | 0.98 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 738±0.5ns | 705±0.7ns | 0.96 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 32.0±0.01μs | 30.9±0.01μs | 0.96 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 2.67±0.5ms | 2.57±0.4ms | 0.96 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 3.41±0.3μs | 3.24±0.5μs | 0.95 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
If you want to see the graph of the results, you can check it here |
atharva-2001
reviewed
Oct 9, 2024
atharva-2001
requested changes
Oct 9, 2024
| It runs the "Bridge" and sends an artifact containing the generated atomic data file | ||
| and the comparison notebook to Moria. This workflow has a separate job to indicate if the | ||
| bridge has failed. | ||
| Publishes a new release of TARDIS every sunday at 00:00 UTC. |
There was a problem hiding this comment.
We should document the pre and post release workflows too but perhaps in a different pull request
| @@ -292,8 +44,7 @@ Testing pipeline | |||
| ================ | |||
|
|
|||
| The `testing pipeline`_ (CI) consists basically in the same job running twice | |||
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6 jobs in parallel(continuum and non continuum tests each times 3 different OS platforms)
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which is the third os?
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My apologies, there are just two platforms, osx-arm and linux. The rpacket_tracking tests would soon be removed. We don't test on osx intel.
So it would be- The testing pipeline_ (CI) comprises of four concurrent jobs, since there are two types of tests(continuum and non-continuum) for each platform, osx-arm and linux. Additionally...
atharva-2001
requested changes
Oct 14, 2024
| The `testing pipeline`_ (CI) consists basically in the same job running twice | ||
| in parallel (one for each OS) with the steps from the default template, plus | ||
| extra steps to run the tests and upload the coverage results. | ||
| The `testing pipeline`_ (CI) comprises of six concurrent jobs. Each of these jobs runs three types of tests across two distinct categories—continuum and non-continuum—and supports three different operating system platforms. Additionally, there are extra steps involved in executing the tests and uploading the coverage results |
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six different jobs- three test types for two test platforms
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yes continuum not rpacket
not continuum not rpacket
not continuum yes rpacket
jvshields
previously approved these changes
Oct 14, 2024
wkerzendorf
reviewed
Oct 14, 2024
andrewfullard
approved these changes
Oct 16, 2024
atharva-2001
approved these changes
Oct 21, 2024
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📝 Description
Type: 🪲
bugfix| 🚀feature| ☣️breaking change| 🚦testing| 📝documentation| 🎢infrastructureThis PR aims at updating the docs with the new regression data and remove the outdated refdata content.
📌 Resources
Examples, notebooks, and links to useful references.
🚦 Testing
How did you test these changes?
☑️ Checklist
build_docslabel