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tardis-sn / tardis

TARDIS - Temperature And Radiative Diffusion In Supernovae
https://tardis-sn.github.io/tardis
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Update docs with regression data #2842

Closed KasukabeDefenceForce closed 1 month ago

KasukabeDefenceForce commented 1 month ago

:pencil: Description

Type: :beetle: bugfix | :rocket: feature | :biohazard: breaking change | :vertical_traffic_light: testing | :memo: documentation | :roller_coaster: infrastructure

This PR aims at updating the docs with the new regression data and remove the outdated refdata content.

:pushpin: Resources

Examples, notebooks, and links to useful references.

:vertical_traffic_light: Testing

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review-notebook-app[bot] commented 1 month ago

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tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran ruff on the latest commit (34b63072ed777f1018be8a922abf65032e14f457). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 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):

```diff .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[bot] commented 1 month ago

Codecov Report

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

Project coverage is 70.70%. Comparing base (4341331) to head (34b6307). Report is 19 commits behind head on master.

Additional details and impacted files ```diff @@ 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 ```

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

tardis-bot commented 1 month ago

*beep* *bop*

Hi, human.

The docs workflow has succeeded :heavy_check_mark:

Click here to see your results.

tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (434133196adc18ca360c71779204bee9d37cd6c5) and the latest commit (34b63072ed777f1018be8a922abf65032e14f457). 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 [81ec6e8e] | 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