Tests for workflows: Simple, Standard, and Inner Velocity Solver #3050
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*beep* *bop* Details6631 [ ] syntax-error
35 E902 [ ] io-error
26 W293 [ ] blank-line-with-whitespace
26 I001 [*] unsorted-imports
25 F821 [ ] undefined-name
24 F401 [ ] unused-import
24 G004 [ ] logging-f-string
14 E701 [ ] multiple-statements-on-one-line-colon
14 RET505 [*] superfluous-else-return
13 F405 [ ] undefined-local-with-import-star-usage
12 W605 [*] invalid-escape-sequence
11 W291 [ ] trailing-whitespace
8 D202 [*] blank-line-after-function
8 UP008 [ ] super-call-with-parameters
6 E402 [ ] module-import-not-at-top-of-file
6 UP031 [ ] printf-string-formatting
4 E702 [ ] multiple-statements-on-one-line-semicolon
4 B011 [ ] assert-false
4 PT015 [ ] pytest-assert-always-false
4 UP015 [*] redundant-open-modes
3 W292 [ ] missing-newline-at-end-of-file
3 C408 [ ] unnecessary-collection-call
3 D209 [*] new-line-after-last-paragraph
3 NPY201 [ ] numpy2-deprecation
3 PTH117 [ ] os-path-isabs
2 E712 [ ] true-false-comparison
2 D411 [*] no-blank-line-before-section
2 F403 [ ] undefined-local-with-import-star
2 F811 [ ] redefined-while-unused
2 INP001 [ ] implicit-namespace-package
2 PGH004 [ ] blanket-noqa
2 RET506 [*] superfluous-else-raise
1 E722 [ ] bare-except
1 B017 [ ] assert-raises-exception
1 B019 [ ] cached-instance-method
1 B020 [ ] loop-variable-overrides-iterator
1 C416 [ ] unnecessary-comprehension
1 D406 [*] missing-new-line-after-section-name
1 D407 [*] missing-dashed-underline-after-section
1 ICN001 [ ] unconventional-import-alias
1 LOG015 [ ] root-logger-call
1 N812 [ ] lowercase-imported-as-non-lowercase
1 N999 [ ] invalid-module-name
1 PERF102 [ ] incorrect-dict-iterator
1 PERF403 [ ] manual-dict-comprehension
1 PIE790 [*] unnecessary-placeholder
1 PT021 [ ] pytest-fixture-finalizer-callback
1 RUF021 [*] parenthesize-chained-operators
1 S604 [ ] call-with-shell-equals-true
1 TRY300 [ ] try-consider-else
1 UP004 [*] useless-object-inheritance
1 UP009 [*] utf8-encoding-declaration
1 UP024 [*] os-error-alias
1 UP030 [ ] format-literals
1 UP032 [*] f-string
Found 6951 errors.
[*] 113 fixable with the `--fix` option (37 hidden fixes can be enabled with the `--unsafe-fixes` option).
Complete output(might be large): Detailsbenchmarks/spectrum_formal_integral.py:22:5: B019 Use of `functools.lru_cache` or `functools.cache` on methods can lead to memory leaks
docs/conf.py:1:1: UP009 [*] UTF-8 encoding declaration is unnecessary
docs/conf.py:27:1: I001 [*] Import block is un-sorted or un-formatted
docs/conf.py:30:8: F401 [*] `tardis` imported but unused
docs/conf.py:37:43: PGH004 Use specific rule codes when using `noqa`
docs/conf.py:47:27: UP015 [*] Unnecessary mode argument
docs/conf.py:68:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:69:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:70:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:71:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:72:1: F405 `exclude_patterns` may be undefined, or defined from star imports
docs/conf.py:142:1: W293 Blank line contains whitespace
docs/conf.py:177:1: W293 Blank line contains whitespace
docs/conf.py:194:13: UP030 Use implicit references for positional format fields
docs/conf.py:194:13: UP032 [*] Use f-string instead of `format` call
docs/conf.py:221:1: E402 Module level import not at top of file
docs/conf.py:294:4: E712 Avoid equality comparisons to `True`; use `toml_config_tool_dict["tardis"]['edit_on_github']:` for truth checks
docs/conf.py:316:1: E402 Module level import not at top of file
docs/conf.py:368:1: E402 Module level import not at top of file
docs/conf.py:383:37: UP015 [*] Unnecessary modes, use `w`
docs/conf.py:398:41: UP015 [*] Unnecessary modes, use `w`
docs/conf.py:408:55: W291 [*] Trailing whitespace
docs/conf.py:413:37: UP015 [*] Unnecessary modes, use `w`
docs/physics/pyplot/lte_ionization_balance.py:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/pyplot/lte_ionization_balance.py:1:8: F401 [*] `os` imported but unused
docs/physics/pyplot/lte_ionization_balance.py:22:31: F821 Undefined name `atom_fname`
docs/physics/pyplot/lte_ionization_balance.py:73:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/lte_ionization_balance.py:74:15: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/pyplot/nebular_ionization_balance.py:33:18: F821 Undefined name `plasma`
docs/physics/pyplot/nebular_ionization_balance.py:71:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:72:15: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:117:9: UP031 Use format specifiers instead of percent format
docs/physics/pyplot/nebular_ionization_balance.py:118:15: UP031 Use format specifiers instead of percent format
tardis/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/conftest.py:12:1: F403 `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names
tardis/conftest.py:15:36: F401 [*] `tardis.tests.test_util.monkeysession` imported but unused
tardis/conftest.py:18:12: F401 `tardisbase` imported but unused; consider using `importlib.util.find_spec` to test for availability
tardis/conftest.py:39:49: PGH004 Use specific rule codes when using `noqa`
tardis/conftest.py:41:9: F821 Undefined name `pytest_report_header`
tardis/energy_input/GXPacket.py:1:1: N999 Invalid module name: 'GXPacket'
tardis/energy_input/GXPacket.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/GXPacket.py:41:16: UP004 [*] Class `GXPacket` inherits from `object`
tardis/energy_input/GXPacket.py:75:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/energy_input/GXPacket.py:75:9: D406 [*] Section name should end with a newline ("Returns")
tardis/energy_input/GXPacket.py:202:13: F821 Undefined name `get_chain_decay_power_per_ejectamass`
tardis/energy_input/GXPacket.py:203:17: F821 Undefined name `inventory`
tardis/energy_input/decay_radiation.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/energy_source.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/energy_source.py:96:11: E712 Avoid equality comparisons to `True`; use `check:` for truth checks
tardis/energy_input/energy_source.py:112:16: C416 Unnecessary list comprehension (rewrite using `list()`)
tardis/energy_input/energy_source.py:198:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/gamma_ray_packet_source.py:1:25: F401 [*] `astropy.units` imported but unused
tardis/energy_input/gamma_ray_packet_source.py:294:53: F821 Undefined name `positronium_continuum`
tardis/energy_input/gamma_ray_transport.py:231:9: PERF403 Use a dictionary comprehension instead of a for-loop
tardis/energy_input/gamma_ray_transport.py:456:39: PERF102 When using only the values of a dict use the `values()` method
tardis/energy_input/main_gamma_ray_loop.py:166:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:167:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:211:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:234:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:235:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:295:17: G004 Logging statement uses f-string
tardis/energy_input/tests/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/tests/conftest.py:16:12: S604 Function call with truthy `shell` parameter identified, security issue
tardis/energy_input/tests/test_gamma_ray_channel.py:119:9: B020 Loop control variable `isotope_dict` overrides iterable it iterates
tardis/energy_input/tests/test_gamma_ray_grid.py:12:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:12:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_packet_source_minimal.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/transport/GXPacket.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/transport/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/util.py:409:5: RET505 [*] Unnecessary `elif` after `return` statement
tardis/energy_input/util.py:420:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/util.py:422:5: D411 [*] Missing blank line before section ("Parameters")
tardis/gui/widgets.py:6:5: I001 [*] Import block is un-sorted or un-formatted
tardis/gui/widgets.py:8:5: I001 [*] Import block is un-sorted or un-formatted
tardis/gui/widgets.py:16:1: I001 [*] Import block is un-sorted or un-formatted
tardis/gui/widgets.py:16:8: ICN001 `matplotlib` should be imported as `mpl`
tardis/gui/widgets.py:17:1: F403 `from matplotlib.figure import *` used; unable to detect undefined names
tardis/gui/widgets.py:24:32: F401 [*] `matplotlib.patches.Circle` imported but unused
tardis/gui/widgets.py:29:30: F401 [*] `tardis.util` imported but unused
tardis/gui/widgets.py:36:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/gui/widgets.py:43:23: F405 `Figure` may be undefined, or defined from star imports
tardis/gui/widgets.py:54:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:55:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:58:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:164:27: C408 Unnecessary `dict()` call (rewrite as a literal)
tardis/gui/widgets.py:167:26: C408 Unnecessary `dict()` call (rewrite as a literal)
tardis/gui/widgets.py:168:23: C408 Unnecessary `dict()` call (rewrite as a literal)
tardis/gui/widgets.py:186:9: RET505 [*] Unnecessary `elif` after `return` statement
tardis/gui/widgets.py:198:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:226:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:229:22: F405 `yaml` may be undefined, or defined from star imports
tardis/gui/widgets.py:229:61: F405 `yaml` may be undefined, or defined from star imports
tardis/gui/widgets.py:353:24: F405 `TreeModel` may be undefined, or defined from star imports
tardis/gui/widgets.py:358:38: F405 `TreeDelegate` may be undefined, or defined from star imports
tardis/gui/widgets.py:429:35: UP024 [*] Replace aliased errors with `OSError`
tardis/gui/widgets.py:444:9: PIE790 [*] Unnecessary `pass` statement
tardis/gui/widgets.py:528:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/gui/widgets.py:646:41: F405 `np` may be undefined, or defined from star imports
tardis/gui/widgets.py:657:9: D209 [*] Multi-line docstring closing quotes should be on a separate line
tardis/gui/widgets.py:660:41: F405 `np` may be undefined, or defined from star imports
tardis/gui/widgets.py:688:41: F405 `np` may be undefined, or defined from star imports
tardis/gui/widgets.py:815:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:851:9: D209 [*] Multi-line docstring closing quotes should be on a separate line
tardis/gui/widgets.py:927:9: D209 [*] Multi-line docstring closing quotes should be on a separate line
tardis/gui/widgets.py:929:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:1124:14: UP008 Use `super()` instead of `super(__class__, self)`
tardis/gui/widgets.py:1231:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/io/atom_data/util.py:35:13: G004 Logging statement uses f-string
tardis/io/configuration/config_internal.py:9:20: N812 Lowercase `__path__` imported as non-lowercase `TARDIS_PATH`
tardis/io/configuration/config_internal.py:25:13: G004 Logging statement uses f-string
tardis/io/configuration/config_internal.py:37:9: LOG015 `critical()` call on root logger
tardis/io/configuration/config_internal.py:38:13: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/io/configuration/config_reader.py:54:29: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:118:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:142:13: RET505 [*] Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:219:29: G004 Logging statement uses f-string
tardis/io/configuration/tests/test_configuration_namespace.py:1:1: INP001 File `tardis/io/configuration/tests/test_configuration_namespace.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/parse_geometry_configuration.py:50:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/io/model/parse_mass_fraction_configuration.py:4:25: F401 [*] `astropy.units` imported but unused
tardis/io/model/parse_mass_fraction_configuration.py:62:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/io/model/readers/tests/test_csvy_reader.py:1:1: INP001 File `tardis/io/model/readers/tests/test_csvy_reader.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_csvy_reader.py:48:10: B017 Do not assert blind exception: `Exception`
tardis/io/util.py:20:20: F401 [*] `tardis.__version__` imported but unused
tardis/model/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/model/base.py:336:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/model/base.py:371:21: G004 Logging statement uses f-string
tardis/model/matter/composition.py:173:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/model/matter/decay.py:101:21: G004 Logging statement uses f-string
tardis/model/matter/decay.py:104:17: G004 Logging statement uses f-string
tardis/opacities/macro_atom/macroatom_solver.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/macro_atom/macroatom_solver.py:18:34: F401 [*] `astropy.constants` imported but unused
tardis/opacities/macro_atom/macroatom_solver.py:177:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/macro_atom/macroatom_solver.py:180:9: D411 [*] Missing blank line before section ("Parameters")
tardis/scripts/cmfgen2tardis.py:13:27: F821 Undefined name `atomic_dataset`
tardis/scripts/cmfgen2tardis.py:68:34: F821 Undefined name `atomic_dataset`
tardis/simulation/base.py:245:17: G004 Logging statement uses f-string
tardis/simulation/base.py:418:13: G004 Logging statement uses f-string
tardis/simulation/base.py:519:13: G004 Logging statement uses f-string
tardis/simulation/base.py:599:13: G004 Logging statement uses f-string
tardis/simulation/base.py:604:13: G004 Logging statement uses f-string
tardis/simulation/base.py:655:13: TRY300 Consider moving this statement to an `else` block
tardis/simulation/base.py:657:26: G004 Logging statement uses f-string
tardis/simulation/tests/test_simulation.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/simulation/tests/test_simulation.py:5:18: F401 [*] `copy.deepcopy` imported but unused
tardis/spectrum/formal_integral.py:12:56: F401 [*] `tardis.opacities.continuum.continuum_state.ContinuumState` imported but unused
tardis/spectrum/formal_integral.py:14:5: F401 [*] `tardis.opacities.opacity_state.OpacityState` imported but unused
tardis/spectrum/formal_integral.py:358:13: RET506 [*] Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral.py:423:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral.py:716:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:752:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:814:12: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/spectrum/formal_integral/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/base.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/formal_integral.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/formal_integral_numba.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/source_function.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/tests/test_formal_integral.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral/tests/test_source_function.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral_cuda.py:375:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral_cuda.py:420:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/tests/test_numba_formal_integral.py:35:16: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/tests/test_tardis_full_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/transport/montecarlo/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/transport/montecarlo/base.py:10:56: F401 [*] `tardis.opacities.continuum.continuum_state.ContinuumState` imported but unused
tardis/transport/montecarlo/base.py:12:5: F401 [*] `tardis.opacities.opacity_state.OpacityState` imported but unused
tardis/transport/montecarlo/packet_source.py:246:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/transport/montecarlo/tests/test_montecarlo.py:27:1: E402 Module level import not at top of file
tardis/transport/montecarlo/tests/test_montecarlo.py:32:1: E402 Module level import not at top of file
tardis/transport/montecarlo/tests/test_montecarlo.py:48:5: PT021 Use `yield` instead of `request.addfinalizer`
tardis/transport/montecarlo/tests/test_montecarlo.py:204:5: F811 Redefinition of unused `test_get_random_mu_different_output` from line 195
tardis/transport/montecarlo/tests/test_montecarlo.py:484:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:570:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:571:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:579:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:596:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:601:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:624:9: F821 Undefined name `transport`
tardis/transport/montecarlo/tests/test_montecarlo.py:625:9: F821 Undefined name `transport`
tardis/transport/montecarlo/tests/test_montecarlo.py:626:9: F821 Undefined name `transport`
tardis/transport/montecarlo/tests/test_montecarlo.py:627:9: F821 Undefined name `transport`
tardis/transport/montecarlo/tests/test_montecarlo.py:629:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:642:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:666:5: F821 Undefined name `mc`
tardis/transport/montecarlo/tests/test_montecarlo.py:679:5: F821 Undefined name `mc`
tardis/util/base.py:188:20: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/util/base.py:341:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/util/base.py:515:5: E722 Do not use bare `except`
tardis/util/base.py:623:5: RET505 [*] Unnecessary `elif` after `return` statement
tardis/visualization/plot_util.py:54:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/visualization/tests/test_plot_util.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/widgets/custom_abundance.py:740:16: RUF021 [*] Parenthesize `a and b` expressions when chaining `and` and `or` together, to make the precedence clear
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/tests/test_line_info.py:10:1: E402 Module level import not at top of file
tardis/workflows/high_energy/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/conftest.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/test_tardis_he_workflow.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/simple_tardis_workflow.py:249:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:466:17: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:170:13: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:210:17: G004 Logging statement uses f-string
tardis/workflows/tardis_he_workflow.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/workflows/tardis_he_workflow.py:2:17: F401 [*] `numpy` imported but unused
tardis/workflows/tardis_he_workflow.py:4:25: F401 [*] `astropy.units` imported but unused
tardis/workflows/tardis_he_workflow.py:5:29: F401 [*] `astropy.constants` imported but unused
tardis/workflows/tardis_he_workflow.py:8:47: F401 [*] `tardis.energy_input.energy_source.get_nuclear_lines_database` imported but unused
tardis/workflows/tardis_he_workflow.py:72:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:84:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:93:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:103:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:107:90: W291 Trailing whitespace
tardis/workflows/tardis_he_workflow.py:112:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:127:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:134:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:139:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:169:44: W291 [*] Trailing whitespace
tardis/workflows/tardis_he_workflow.py:170:54: W291 [*] Trailing whitespace
tardis/workflows/tardis_he_workflow.py:193:34: W292 [*] No newline at end of file
tardis/workflows/tests/test_workflows.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/workflows/tests/test_workflows.py:2:21: F401 [*] `pathlib.Path` imported but unused
tardis/workflows/tests/test_workflows.py:7:51: F401 [*] `tardis.io.configuration.config_reader.Configuration` imported but unused
Found 235 errors.
[*] 87 fixable with the `--fix` option (37 hidden fixes can be enabled with the `--unsafe-fixes` option).
|
jvshields
reviewed
Apr 16, 2025
| def test_simple_tardis_workflow(key, simulation_simple_workflow, simulation_verysimple): | ||
| actual = getattr(simulation_simple_workflow.simulation_state, key) | ||
| actual = actual.to_value() if hasattr(actual, "to_value") else actual | ||
| expected = getattr(simulation_verysimple.simulation_state, key) |
Contributor
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I don't think expected vs actual is a great way of phrasing these things. That makes more sense comparing something like a new value to regression data. Here I think you're comparing different workflows together, which is a useful test, but they're both freshly calculated.
Contributor
There was a problem hiding this comment.
Updated the phrasing to be more informative.
jvshields
reviewed
Apr 16, 2025
| from tardis.workflows.standard_tardis_workflow import StandardTARDISWorkflow | ||
|
|
||
| @pytest.fixture(scope="module") | ||
| def simulation_simple_workflow(config_verysimple, atomic_data_fname): |
Contributor
There was a problem hiding this comment.
Maybe this should be called something like "workflow_simple" rather than "simulation_simple_workflow" They can have different attributes so keying in somebody else who might use this object that it is a different thing than a simulation object is important.
Similarly I'd probably rename sim to workflow as well.
These comments apply to all of these tests too, but should be an easy enough find and replace
Contributor
There was a problem hiding this comment.
Updated the naming to emphasize the workflow.
Contributor
|
The tests seem to be failing to find the atomic data. Not sure if this is an issue with the workflows or the tests. I also wonder if we can just compare to the simulation regression data instead of the verysimple fixture (or if that is already happening anyway) |
Contributor
|
Should investigate why the tests are failing because they can't find the atom data. |
Contributor
|
*beep* *bop* Hi, human. I'm the @tardis-bot and I noticed that your email is not associated with an ORCID ID in our database. Please add your email and ORCID ID to the If you don't have an ORCID ID yet, you can create one for free at orcid.org. ORCID IDs help ensure you get proper credit for your scientific contributions. The format should be: |
Contributor
That's a good idea, now the standard_workflow is compared to the regression data produced for the test_simulation.py, the iteration values are consistent, but the estimators and output energies are somewhere different, looks like the run_tardis recompute the opacity state in the run_final while the workflow only recompute the MC state after convergence. To match with the run_tardis, added the step recompute the opacity state in simple and standard workflow after convergence, now all test pass comparing the simulation regression data. Since the simple workflow doesn't have iteration values logged by default, it is currently cross compared with the standard workflow results. The v_inner test will fail for now till the newly generated regression data PR is merged. |
Contributor
|
*beep* *bop* Significantly changed benchmarks: Details| Change | Before [7aee1a91] <master> | After [c8ec5a42] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------|
| + | 1.14±0μs | 1.28±0μs | 1.12 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
All benchmarks: DetailsBenchmarks that have stayed the same:
| Change | Before [7aee1a91] <master> | After [c8ec5a42] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 45.8±30μs | 50.5±30μs | ~1.10 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 3.30±0.3μs | 2.90±0.5μs | ~0.88 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 571±100ns | 491±100ns | ~0.86 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 551±100ns | 471±200ns | ~0.85 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 541±200ns | 581±100ns | 1.07 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 2.95±0.5ms | 3.14±0.4ms | 1.06 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 3.34±0.02ms | 3.50±0.04ms | 1.05 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 58.7±0.06ms | 61.3±0.03ms | 1.05 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 2.11±0m | 2.13±0m | 1.01 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 31.2±9μs | 31.4±9μs | 1.01 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 3.43±0.5μs | 3.48±7μs | 1.01 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 39.2±0.06s | 38.8±0.04s | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 1.01±0m | 1.00±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 199±0.1ns | 198±0.02ns | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 686±0.7ns | 681±2ns | 0.99 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 7.03±3μs | 6.98±2μs | 0.99 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 41.1±0.03μs | 39.1±0.2μs | 0.95 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 6.68±1μs | 6.34±1μs | 0.95 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 2.35±2μs | 2.22±1μs | 0.94 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 45.8±30μs | 43.3±30μs | 0.94 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 4.46±0.01ms | 4.16±0ms | 0.93 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 1.48±0.6μs | 1.36±0.4μs | 0.92 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 2.81±0.01ms | 2.60±0.03ms | 0.92 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
Benchmarks that have got worse:
| Change | Before [7aee1a91] <master> | After [c8ec5a42] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------|
| + | 1.14±0μs | 1.28±0μs | 1.12 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
If you want to see the graph of the results, you can check it here |
andrewfullard
previously approved these changes
Jul 1, 2025
… and test workflow
andrewfullard
previously approved these changes
Jul 11, 2025
jvshields
reviewed
Jul 14, 2025
jvshields
reviewed
Jul 14, 2025
jvshields
reviewed
Jul 14, 2025
jvshields
reviewed
Jul 14, 2025
jvshields
reviewed
Jul 14, 2025
Contributor
|
The test still failing because silly me generated the regression data in the wrong path, should be passing after merging this PR on regression-data repo: tardis-sn/tardis-regression-data#60 |
Contributor
|
Weirdly Mac is failing, but Ubuntu passing |
Contributor
|
Likely an issue in a sort function somewhere. Need to use |
6 tasks
Contributor
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Pull Request Overview
This PR adds comprehensive test coverage for TARDIS workflows and improves code consistency. The changes primarily focus on testing the Simple and Standard TARDIS workflows against reference data, and introducing tests for the Inner Velocity Solver workflow with proper regression testing.
- Adds test suite for Simple, Standard, and Inner Velocity Solver workflows
- Refactors simulation tests to use shared configuration fixtures
- Makes opacity_states an instance variable for better state management
Reviewed Changes
Copilot reviewed 7 out of 8 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| tardis/workflows/tests/test_workflows.py | New comprehensive test suite for all three workflow types with regression testing |
| tardis/workflows/util.py | Adds stable sorting to ensure deterministic behavior |
| tardis/workflows/standard_tardis_workflow.py | Converts opacity_states to instance variable and minor formatting fixes |
| tardis/workflows/simple_tardis_workflow.py | Converts opacity_states to instance variable for consistency |
| tardis/simulation/tests/test_simulation.py | Refactors to use shared configuration fixture |
| tardis/conftest.py | Adds reusable configuration fixture for simulation tests |
| .orcid.csv | Adds ORCID identifiers for new contributors |
Comment on lines
+73
to
+107
| / f"test_{attr_type}__{attr}__.h5" | ||
| ) | ||
| ref_data = pd.read_hdf(ref_file) | ||
| if attr_type == "plasma_estimates": | ||
| if attr in ["nu_bar_estimator", "j_estimator"]: | ||
| attr_data = getattr( | ||
| standard_workflow_one_loop.transport_state.radfield_mc_estimators, | ||
| attr, | ||
| ) | ||
| elif attr in ["output_nus", "output_energies"]: | ||
| attr_data = getattr( | ||
| standard_workflow_one_loop.transport_state.packet_collection, | ||
| attr, | ||
| ) | ||
| else: | ||
| raise ValueError(f"Unknown plasma_estimates attr: {attr}") | ||
| if hasattr(attr_data, "value"): | ||
| attr_data = attr_data.value | ||
| attr_data = pd.Series(attr_data) | ||
| pd.testing.assert_series_equal( | ||
| attr_data, ref_data, check_exact=False, rtol=1e-6 | ||
| ) | ||
| elif attr_type == "plasma_state_iterations": | ||
| attr_data = getattr(standard_workflow_one_loop, attr) | ||
| if hasattr(attr_data, "value"): | ||
| attr_data = attr_data.value | ||
| attr_data = pd.DataFrame(attr_data) | ||
| pd.testing.assert_frame_equal(attr_data, ref_data, atol=0, rtol=1e-14) | ||
| else: | ||
| raise ValueError(f"Unknown attr_type: {attr_type}") | ||
|
|
||
|
|
||
| @pytest.mark.parametrize( | ||
| "attr", | ||
| [ |
There was a problem hiding this comment.
The test function 'test_standard_tardis_workflow_against_run_tardis' has complex nested conditional logic that makes it difficult to maintain. Consider splitting this into separate test functions for 'plasma_estimates' and 'plasma_state_iterations' to improve readability and maintainability.
Suggested change
| / f"test_{attr_type}__{attr}__.h5" | |
| ) | |
| ref_data = pd.read_hdf(ref_file) | |
| if attr_type == "plasma_estimates": | |
| if attr in ["nu_bar_estimator", "j_estimator"]: | |
| attr_data = getattr( | |
| standard_workflow_one_loop.transport_state.radfield_mc_estimators, | |
| attr, | |
| ) | |
| elif attr in ["output_nus", "output_energies"]: | |
| attr_data = getattr( | |
| standard_workflow_one_loop.transport_state.packet_collection, | |
| attr, | |
| ) | |
| else: | |
| raise ValueError(f"Unknown plasma_estimates attr: {attr}") | |
| if hasattr(attr_data, "value"): | |
| attr_data = attr_data.value | |
| attr_data = pd.Series(attr_data) | |
| pd.testing.assert_series_equal( | |
| attr_data, ref_data, check_exact=False, rtol=1e-6 | |
| ) | |
| elif attr_type == "plasma_state_iterations": | |
| attr_data = getattr(standard_workflow_one_loop, attr) | |
| if hasattr(attr_data, "value"): | |
| attr_data = attr_data.value | |
| attr_data = pd.DataFrame(attr_data) | |
| pd.testing.assert_frame_equal(attr_data, ref_data, atol=0, rtol=1e-14) | |
| else: | |
| raise ValueError(f"Unknown attr_type: {attr_type}") | |
| @pytest.mark.parametrize( | |
| "attr", | |
| [ | |
| / f"test_plasma_estimates__{attr}__.h5" | |
| ) | |
| ref_data = pd.read_hdf(ref_file) | |
| if attr in ["nu_bar_estimator", "j_estimator"]: | |
| attr_data = getattr( | |
| standard_workflow_one_loop.transport_state.radfield_mc_estimators, | |
| attr, | |
| ) | |
| elif attr in ["output_nus", "output_energies"]: | |
| attr_data = getattr( | |
| standard_workflow_one_loop.transport_state.packet_collection, | |
| attr, | |
| ) | |
| else: | |
| raise ValueError(f"Unknown plasma_estimates attr: {attr}") | |
| if hasattr(attr_data, "value"): | |
| attr_data = attr_data.value | |
| attr_data = pd.Series(attr_data) | |
| pd.testing.assert_series_equal( | |
| attr_data, ref_data, check_exact=False, rtol=1e-6 | |
| ) | |
| @pytest.mark.parametrize( | |
| "attr", | |
| [ | |
| "iterations_w", | |
| "iterations_t_rad", | |
| "iterations_electron_densities", | |
| "iterations_t_inner", | |
| ], | |
| ) | |
| def test_standard_tardis_workflow_plasma_state_iterations( | |
| standard_workflow_one_loop, attr, regression_data | |
| ): | |
| ref_file = ( | |
| regression_data.regression_data_path | |
| / "tardis" | |
| / "simulation" | |
| / "tests" | |
| / "test_simulation" | |
| / f"test_plasma_state_iterations__{attr}__.h5" | |
| ) | |
| ref_data = pd.read_hdf(ref_file) | |
| attr_data = getattr(standard_workflow_one_loop, attr) | |
| if hasattr(attr_data, "value"): | |
| attr_data = attr_data.value | |
| attr_data = pd.DataFrame(attr_data) | |
| pd.testing.assert_frame_equal(attr_data, ref_data, atol=0, rtol=1e-14) | |
| @pytest.mark.parametrize( | |
| "attr", | |
| [ |
andrewfullard
approved these changes
Aug 6, 2025
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📝 Description
Type: 🚦
testingAdded tests to cover the Simple and Standard TARDIS Workflows using the config_verysimple and simulation_verysimple as defined in conftest.py.
Added tests to cover the v_inner_solver workflow. Created regression data needed for the test in this PR on the tardis-regression-data repo. .
🚦 Testing
How did you test these changes?
☑️ Checklist
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