tests for composition #2944
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tests for composition #2944
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*beep* *bop* 28 W291 [*] Trailing whitespace
14 E999 [ ] SyntaxError: Expected ',', found ':'
10 E902 [ ] No such file or directory (os error 2)
8 W293 [*] Blank line contains whitespace
5 G004 [ ] Logging statement uses f-string
5 I001 [*] Import block is un-sorted or un-formatted
5 F401 [*] `tardis.io.model.parse_atom_data.parse_atom_data` imported but unused
4 RET505 [ ] Unnecessary `else` after `return` statement
3 W292 [*] No newline at end of file
2 INP001 [ ] File `tardis/model/matter/tests/test_composition.py` is part of an implicit namespace package. Add an `__init__.py`.
2 PTH117 [ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
2 W605 [*] Invalid escape sequence: `\A`
1 ANN204 [ ] Missing return type annotation for special method `__getitem__`
1 RET506 [ ] Unnecessary `else` after `raise` statement
1 D202 [*] No blank lines allowed after function docstring (found 1)
1 D406 [*] Section name should end with a newline ("Returns")
1 D407 [*] Missing dashed underline after section ("Returns")
1 F541 [*] f-string without any placeholders
Complete output(might be large): .github/actions/setup_env/action.yml:4:8: E999 SyntaxError: Expected an expression
.github/actions/setup_env/action.yml:17:1: W293 [*] Blank line contains whitespace
.github/actions/setup_env/action.yml:19:15: W291 [*] Trailing whitespace
.github/actions/setup_env/action.yml:24:1: W293 [*] Blank line contains whitespace
.github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression
.github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression
.github/workflows/benchmarks.yml:20:5: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:87:49: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:117:81: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:118:54: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:205:1: W293 [*] Blank line contains whitespace
.github/workflows/benchmarks.yml:224:22: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:225:170: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:227:84: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:244:1: W293 [*] Blank line contains whitespace
.github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/lfs-cache.yml:1:1: E902 No such file or directory (os error 2)
.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
.mailmap:1:38: E999 SyntaxError: Expected an expression
.mailmap:294:39: W292 [*] No newline at end of file
CHANGELOG.md:4:15: E999 SyntaxError: Expected ',', found ':'
CITATION.cff:3:1: E999 SyntaxError: Invalid annotated assignment target
README.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/benchmarks.rst:1:1: E999 SyntaxError: Expected a statement
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/running_tests.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/running_tests.rst:59:112: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:60:124: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:64:92: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:65:107: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:75:62: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:76:85: W292 [*] No newline at end of file
docs/io/output/how_to_rpacket_tracking.ipynb:cell 12:1:62: W291 [*] Trailing whitespace
docs/physics/plasma/equilibrium/tardis_solver_cmfgen.ipynb:1:1: E902 No such file or directory (os error 2)
docs/physics/setup/model.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/setup/model.ipynb:cell 25:19:12: F541 [*] f-string without any placeholders
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/credits.rst:1:1: E999 SyntaxError: Expected a statement
docs/workflows/v_inner_solver_workflow.ipynb:1:1: E902 No such file or directory (os error 2)
tardis/io/configuration/config_reader.py:53:29: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:117:9: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:141:13: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:218:29: G004 Logging statement uses f-string
tardis/io/configuration/schemas/montecarlo_definitions.yml:1:13: E999 SyntaxError: Expected an expression
tardis/io/model/parse_geometry_configuration.py:50:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/model/base.py:340:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/model/base.py:375:21: G004 Logging statement uses f-string
tardis/model/matter/tests/test_composition.py:1:1: INP001 File `tardis/model/matter/tests/test_composition.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/model/matter/tests/test_composition.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/model/matter/tests/test_composition.py:7:45: F401 [*] `tardis.io.model.parse_atom_data.parse_atom_data` imported but unused
tardis/model/matter/tests/test_composition.py:39:1: W293 [*] Blank line contains whitespace
tardis/model/matter/tests/test_composition.py:44:1: W293 [*] Blank line contains whitespace
tardis/model/matter/tests/test_composition.py:60:1: W293 [*] Blank line contains whitespace
tardis/opacities/macro_atom/macroatom_state.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/opacity_state.py:210:9: ANN204 Missing return type annotation for special method `__getitem__`
tardis/opacities/opacity_state.py:216:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/opacities/opacity_state.py:216:9: D406 [*] Section name should end with a newline ("Returns")
tardis/opacities/opacity_state.py:251:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/opacities/tests/test_opacity_state_numba.py:1:1: INP001 File `tardis/opacities/tests/test_opacity_state_numba.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/opacities/tests/test_opacity_state_numba.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/plasma/equilibrium/rates/__init__.py:2:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonCMFGENSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:3:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonRegemorterSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:6:5: F401 `tardis.plasma.equilibrium.rates.collisional_rates.ThermalCollisionalRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:9:5: F401 `tardis.plasma.equilibrium.rates.radiative_rates.RadiativeRatesSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/collisional_ionization_rates.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/collisional_ionization_strengths.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/photoionization_rates.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/photoionization_strengths.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral.py:358:13: RET506 Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral.py:698:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:734:5: RET505 Unnecessary `else` after `return` statement
tardis/workflows/simple_tardis_workflow.py:230:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:449:17: G004 Logging statement uses f-string
tardis/workflows/util.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/v_inner_solver.py:1:1: E902 No such file or directory (os error 2)
Found 94 errors.
[*] 51 fixable with the `--fix` option.
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [5e2d0bb3] <master> | After [665a7f24] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 43.7±30μs | 48.8±20μs | ~1.12 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 601±100ns | 541±100ns | ~0.90 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 3.53±0.2μs | 3.18±0.4μs | ~0.90 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 1.70±0.4μs | 1.51±0.4μs | ~0.89 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 7.66±1μs | 6.83±0.6μs | ~0.89 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 59.0±30μs | 51.7±30μs | ~0.88 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 691±200ns | 561±200ns | ~0.81 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 511±100ns | 551±200ns | 1.08 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 2.74±0.03ms | 2.92±0.02ms | 1.07 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 2.21±1μs | 2.32±1μs | 1.05 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 735±0.8ns | 748±0.2ns | 1.02 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 37.5±0.06μs | 38.4±0.04μs | 1.02 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 39.2±0.09s | 39.0±0.03s | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 1.06±0m | 1.06±0m | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 2.08±0m | 2.08±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 206±0.3ns | 207±0.09ns | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 1.22±0μs | 1.22±0μs | 1.00 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 65.1±0.01ms | 65.4±0.5ms | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 2.77±0.5ms | 2.76±0.5ms | 1.00 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 7.41±2μs | 7.32±1μs | 0.99 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 1.70±0.01ms | 1.66±0ms | 0.98 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 3.88±0.02ms | 3.74±0ms | 0.96 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 3.33±0.4μs | 3.16±0.4μs | 0.95 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 22.7±6μs | 20.9±4μs | 0.92 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
If you want to see the graph of the results, you can check it here |
| def test_elemental_mass_fraction(composition_instance): | ||
| elemental_mass_fraction = composition_instance.elemental_mass_fraction | ||
| assert isinstance(elemental_mass_fraction, pd.DataFrame) | ||
| np.testing.assert_allclose(elemental_mass_fraction.sum(), 1.0, rtol=1e-3) |
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Why only a tolerance of 1e-3? That seems large.
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No specific reason why exactly 1e-3. thought it would be acceptable tolerance. Will remove.
| mass_fractions.index | ||
| ) | ||
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| expected_density = mass_fractions.multiply(density_value).divide( |
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rename to expected_number_density
| @@ -53,6 +53,13 @@ def test_get_species_interactions( | |||
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| assert species_interactions_df.shape == (expected_df_length, 1) | |||
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| def test_get_middle_half_edges(self, wavelength_range, filter_mode): | |||
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Why is this part of this PR?
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Thought a separate PR for this small test wouldnt look good. I'll create a separate one for this to keep everything clean 👍
jvshields
reviewed
Jan 27, 2025
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| @pytest.fixture(scope="function") | ||
| def composition_instance(config_verysimple): |
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Take a look at some of the other fixtures we have defined throughout the code. We would prefer a more consistent naming scheme than this.
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Have made changes. Kindly take a look. Thanks.
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📝 Description
composition tests written and also added a small test for line info