Remove atomic data from composition. #2992
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- Remove raw_isotope_abundance from Composition class - Update mass fraction parsing to conditionally apply isotope decay - Modify default model_isotope_time_0 to -1 s to allow skipping decay - Update test fixtures to explicitly set model_isotope_time_0 - Simplify mass fraction parsing functions by removing redundant returns
…updating methods for elemental number density calculations
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*beep* *bop* 38 W291 [*] Trailing whitespace
15 W293 [*] Blank line contains whitespace
14 E999 [ ] SyntaxError: Expected a statement
6 G004 [ ] Logging statement uses f-string
6 I001 [*] Import block is un-sorted or un-formatted
6 E902 [ ] stream did not contain valid UTF-8
3 F401 [*] `radioactivedecay.converters` imported but unused
2 RET505 [ ] Unnecessary `else` after `return` statement
2 PTH117 [ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
1 B020 [ ] Loop control variable `isotope_dict` overrides iterable it iterates
1 FA100 [ ] Add `from __future__ import annotations` to simplify `typing.Tuple`
1 G001 [ ] Logging statement uses `str.format`
1 INP001 [ ] File `tardis/io/model/readers/tests/test_artis_readers.py` is part of an implicit namespace package. Add an `__init__.py`.
1 PT009 [ ] Use a regular `assert` instead of unittest-style `assert_`
1 RET506 [ ] Unnecessary `else` after `raise` statement
1 NPY201 [ ] `np.recfromtxt` will be removed in NumPy 2.0. Use `np.genfromtxt` instead.
1 W292 [*] No newline at end of file
1 F631 [ ] Assert test is a non-empty tuple, which is always `True`
Complete output(might be large): .github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression
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.github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression
.github/workflows/benchmarks.yml:20:5: W291 [*] Trailing whitespace
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.github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/lfs-cache.yml:1:12: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
.github/workflows/lfs-cache.yml:38:1: W293 [*] Blank line contains whitespace
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.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
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-arm64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
docs/index.rst:1:1: E999 SyntaxError: Expected a statement
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docs/io/images/custom_abundance_widget.png:1:1: E902 stream did not contain valid UTF-8
docs/io/images/energy_level_widget_options.gif:1:1: E902 stream did not contain valid UTF-8
docs/io/images/line_info_widget_demo.gif:1:1: E902 stream did not contain valid UTF-8
docs/io/images/packet_diagram.jpg:1:1: E902 stream did not contain valid UTF-8
docs/io/images/sdec_ply_interaction.gif:1:1: E902 stream did not contain valid UTF-8
docs/io/images/shell_info_widget_demo.gif:1:1: E902 stream did not contain valid UTF-8
docs/io/visualization/demo_observed_spectrum.dat:1:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/io/visualization/how_to_generating_widgets.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/how_to_generating_widgets.ipynb:cell 5:3:5: F401 [*] `tardis.visualization.shell_info_from_hdf` imported but unused
docs/io/visualization/how_to_sdec_plot.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/how_to_sdec_plot.ipynb:cell 29:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/io/visualization/index.rst:33:68: W292 [*] No newline at end of file
docs/io/visualization/tardis_example.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/io/visualization/tutorial_convergence_plot.ipynb:cell 9:4:28: W291 [*] Trailing whitespace
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docs/io/visualization/tutorial_convergence_plot.ipynb:cell 13:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/tutorial_montecarlo_packet_visualization.ipynb:cell 5:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/io/visualization/using_widgets.rst:1:1: E999 SyntaxError: Expected an expression
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tardis/energy_input/tests/test_gamma_ray_channel.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/tests/test_gamma_ray_channel.py:8:30: F401 [*] `radioactivedecay.converters` imported but unused
tardis/energy_input/tests/test_gamma_ray_channel.py:13:5: F401 [*] `tardis.energy_input.energy_source.get_nuclear_lines_database` imported but unused
tardis/energy_input/tests/test_gamma_ray_channel.py:118:9: B020 Loop control variable `isotope_dict` overrides iterable it iterates
tardis/io/atom_data/base.py:197:34: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:259:17: G004 Logging statement uses f-string
tardis/io/atom_data/base.py:263:21: G001 Logging statement uses `str.format`
tardis/io/atom_data/base.py:702:17: G004 Logging statement uses f-string
tardis/io/configuration/schemas/model_definitions.yml:2:13: E999 SyntaxError: Expected an expression
tardis/io/configuration/schemas/model_definitions.yml:164:1: W293 [*] Blank line contains whitespace
tardis/io/configuration/schemas/model_definitions.yml:210:1: W293 [*] Blank line contains whitespace
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/generic_readers.py:20:6: FA100 Add `from __future__ import annotations` to simplify `typing.Tuple`
tardis/io/model/readers/generic_readers.py:47:12: NPY201 `np.recfromtxt` will be removed in NumPy 2.0. Use `np.genfromtxt` instead.
tardis/io/model/readers/tests/test_artis_readers.py:1:1: INP001 File `tardis/io/model/readers/tests/test_artis_readers.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/model/readers/tests/test_artis_readers.py:43:5: PT009 Use a regular `assert` instead of unittest-style `assert_`
tardis/io/model/readers/tests/test_artis_readers.py:61:5: F631 Assert test is a non-empty tuple, which is always `True`
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:177:9: RET505 Unnecessary `else` after `return` statement
tardis/plasma/standard_plasmas.py:316:9: RET506 Unnecessary `else` after `raise` statement
tardis/transport/montecarlo/packet_source.py:246:9: 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:451:17: G004 Logging statement uses f-string
Found 101 errors.
[*] 63 fixable with the `--fix` option.
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #2992 +/- ##
==========================================
- Coverage 69.54% 69.15% -0.39%
==========================================
Files 228 228
Lines 16429 16421 -8
==========================================
- Hits 11425 11356 -69
- Misses 5004 5065 +61 ☔ View full report in Codecov by Sentry. |
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [e0297c6a] <master> | After [4b8e818d] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 38.4±0.03μs | 44.9±3μs | ~1.17 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 591±200ns | 672±200ns | ~1.14 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 520±200ns | 581±100ns | ~1.12 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 46.9±30μs | 40.9±20μs | ~0.87 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 2.31±1μs | 1.98±1μs | ~0.85 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 54.6±30μs | 46.4±30μs | ~0.85 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 30.0±9μs | 23.4±6μs | ~0.78 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 1.84±0.3μs | 1.28±0.4μs | ~0.70 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 2.63±0ms | 2.83±0.02ms | 1.07 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 7.28±2μs | 7.61±8μs | 1.05 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 38.4±0.04s | 39.9±0.2s | 1.04 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 3.71±0.02ms | 3.80±0.02ms | 1.02 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 734±2ns | 749±0.4ns | 1.02 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 2.09±0m | 2.08±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 1.05±0m | 1.04±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 206±0.1ns | 205±0.4ns | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 1.22±0μs | 1.21±0μs | 0.99 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 67.9±0.2ms | 66.5±0.2ms | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 3.68±0.4μs | 3.62±0.5μs | 0.98 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 2.62±0.4ms | 2.54±0.5ms | 0.97 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 6.71±0.7μs | 6.52±1μs | 0.97 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 1.83±0.02ms | 1.71±0.02ms | 0.93 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 511±200ns | 471±200ns | 0.92 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 3.31±0.3μs | 3.01±0.3μs | 0.91 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
If you want to see the graph of the results, you can check it here |
DeerWhale
reviewed
Feb 24, 2025
| @@ -53,7 +53,7 @@ def __init__(self, configuration): | |||
| ) | |||
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| self.plasma_solver = plasma_solver_factory.assemble( | |||
| self.simulation_state.elemental_number_density, | |||
| self.simulation_state.calculate_elemental_number_density(), | |||
There was a problem hiding this comment.
This function requires element_masses as an input?
andrewfullard
requested changes
Feb 26, 2025
| nuclide_mass_fractions, | ||
| raw_isotope_mass_fractions, | ||
| ) = parse_mass_fractions_from_csvy( | ||
| (nuclide_mass_fractions) = parse_mass_fractions_from_csvy( |
| @@ -121,7 +121,7 @@ def assemble_plasma(config, simulation_state, atom_data=None): | |||
| kwargs = dict( | |||
| dilute_planckian_radiation_field=dilute_planckian_radiation_field, | |||
| abundance=simulation_state.abundance, | |||
| number_density=simulation_state.elemental_number_density, | |||
| number_density=simulation_state.calculate_elemental_number_density(), | |||
There was a problem hiding this comment.
Missing input argument here for elemental masses
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part of the restructure -> preceded by removal of raw_isotope_mass_fractions