tests for composition #2944
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tests for composition #2944
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*beep* *bop* 31 W291 [*] Trailing whitespace
14 E999 [ ] SyntaxError: Expected ',', found ':'
10 E902 [ ] No such file or directory (os error 2)
7 G004 [ ] Logging statement uses f-string
7 I001 [*] Import block is un-sorted or un-formatted
6 W293 [*] Blank line contains whitespace
6 F401 [*] `tardis.io.model.parse_atom_data.parse_atom_data` imported but unused
5 INP001 [ ] File `tardis/analysis/opacities.py` is part of an implicit namespace package. Add an `__init__.py`.
4 RET505 [ ] Unnecessary `else` after `return` statement
3 W292 [*] No newline at end of file
2 PIE808 [*] Unnecessary `start` argument in `range`
2 PTH117 [ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
2 E712 [*] Avoid equality comparisons to `False`; use `if not ...:` for false checks
2 W605 [*] Invalid escape sequence: `\A`
2 F811 [ ] Redefinition of unused `monkeysession` from line 6
1 ANN204 [ ] Missing return type annotation for special method `__getitem__`
1 RET506 [ ] Unnecessary `else` after `raise` statement
1 E703 [*] Statement ends with an unnecessary semicolon
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/grid/how_to_TardisGridTutorial.ipynb:cell 2:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 7:2:74: W291 [*] Trailing whitespace
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 14:1:47: W291 [*] Trailing whitespace
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 14:4:46: E703 [*] Statement ends with an unnecessary semicolon
docs/io/grid/how_to_TardisGridTutorial.ipynb:cell 15:2:55: W291 [*] Trailing whitespace
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/analysis/opacities.py:1:1: INP001 File `tardis/analysis/opacities.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/grid/tests/test_grid.py:1:1: INP001 File `tardis/grid/tests/test_grid.py` is part of an implicit namespace package. Add an `__init__.py`.
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/io/model/readers/tests/test_arepo_parser.py:1:1: INP001 File `tardis/io/model/readers/tests/test_arepo_parser.py` is part of an implicit namespace package. Add an `__init__.py`.
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:9:45: F401 [*] `tardis.io.model.parse_atom_data.parse_atom_data` imported but unused
tardis/model/matter/tests/test_composition.py:51:1: 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/transport/montecarlo/tests/conftest.py:14:5: F811 Redefinition of unused `opacity_state_initialize` from line 7
tardis/visualization/tools/tests/test_convergence_plot.py:3:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/tools/tests/test_convergence_plot.py:6:36: F401 [*] `tardis.tests.test_util.monkeysession` imported but unused
tardis/visualization/tools/tests/test_convergence_plot.py:87:24: PIE808 [*] Unnecessary `start` argument in `range`
tardis/visualization/tools/tests/test_convergence_plot.py:111:22: PIE808 [*] Unnecessary `start` argument in `range`
tardis/visualization/tools/tests/test_convergence_plot.py:198:9: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
tardis/visualization/tools/tests/test_convergence_plot.py:215:9: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
tardis/visualization/tools/tests/test_convergence_plot.py:220:40: F811 Redefinition of unused `monkeysession` from line 6
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/standard_tardis_workflow.py:172:13: G004 Logging statement uses f-string
tardis/workflows/standard_tardis_workflow.py:212:17: 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 110 errors.
[*] 58 fixable with the `--fix` option (2 hidden fixes can be enabled with the `--unsafe-fixes` option).
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [13c9a314] <master> | After [766979a0] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 561±200ns | 501±100ns | ~0.89 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 671±100ns | 561±100ns | ~0.84 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 61.8±30μs | 45.1±30μs | ~0.73 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 39.9±10μs | 27.1±8μs | ~0.68 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 541±100ns | 572±200ns | 1.06 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 43.1±30μs | 45.0±30μs | 1.05 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 6.84±0.8μs | 7.16±0.8μs | 1.05 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 204±0.07ns | 212±0.6ns | 1.04 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 7.44±3μs | 7.63±2μs | 1.03 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 65.4±0.04ms | 66.1±0.1ms | 1.01 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 1.07±0m | 1.07±0m | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 2.12±0m | 2.11±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 734±1ns | 737±1ns | 1.00 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 38.6±0.07μs | 38.5±0.09μs | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 1.22±0μs | 1.21±0μs | 0.99 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 2.23±2μs | 2.21±2μs | 0.99 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 1.86±0.01ms | 1.84±0.01ms | 0.99 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 4.30±0ms | 4.22±0.01ms | 0.98 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 40.3±0.1s | 39.3±0.09s | 0.97 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 2.87±0.4ms | 2.77±0.5ms | 0.97 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 3.42±0.7μs | 3.29±0.4μs | 0.96 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 3.35±0.02ms | 3.15±0.02ms | 0.94 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 4.03±0.5μs | 3.76±0.7μs | 0.93 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 1.70±0.4μs | 1.56±0.4μs | 0.92 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
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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Hi, |
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can you use the regression data. |
Made the changes. Kindly take a look at my PR now. Edit: I made use of regression data fixture as asked. Before running the tests I ran the tests with generate reference. Its creating files in the regression data.
Thanks. |
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📝 Description
composition tests written and also added a small test for line info