Restructure/gamma rays code1 #2976
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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
- Implement `get_radioactive_isotopes()` in energy_source.py to track decay chains - Add `get_decay_radiation_data()` in gamma_ray_transport.py to process radiation data - Enhance `IsotopicMassFraction` in decay.py with `calculate_decayed_mass_fractions()` and `calculate_number_of_decays()` - Refactor decay-related methods to improve clarity and functionality
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*beep* *bop* 38 W291 [*] Trailing whitespace
15 E999 [ ] SyntaxError: Expected a statement
15 W293 [*] Blank line contains whitespace
7 I001 [*] Import block is un-sorted or un-formatted
6 E902 [ ] stream did not contain valid UTF-8
4 G004 [ ] Logging statement uses f-string
4 RET505 [ ] Unnecessary `elif` after `return` statement
4 F401 [*] `radioactivedecay.converters` imported but unused
2 W292 [*] No newline at end of file
1 B020 [ ] Loop control variable `isotope_dict` overrides iterable it iterates
1 C416 [*] Unnecessary `list` comprehension (rewrite using `list()`)
1 FA100 [ ] Add `from __future__ import annotations` to simplify `typing.Tuple`
1 G001 [ ] Logging statement uses `str.format`
1 PTH117 [ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
1 NPY201 [ ] `np.recfromtxt` will be removed in NumPy 2.0. Use `np.genfromtxt` instead.
1 PERF102 [*] When using only the values of a dict use the `values()` method
1 E722 [ ] Do not use bare `except`
1 D202 [*] No blank lines allowed after function docstring (found 1)
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
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.github/workflows/benchmarks.yml:248:1: W293 [*] Blank line contains whitespace
.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/how_to_guides.rst:1:8: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/how_to_guides.rst:18:43: W292 [*] No newline at end of file
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
docs/io/visualization/using_widgets.rst:7:83: W291 [*] Trailing whitespace
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tardis/energy_input/energy_source.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/energy_source.py:113:16: C416 Unnecessary `list` comprehension (rewrite using `list()`)
tardis/energy_input/energy_source.py:256:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/gamma_ray_packet_source.py:14:5: F401 [*] `tardis.energy_input.util.get_index` imported but unused
tardis/energy_input/gamma_ray_transport.py:457:39: PERF102 When using only the values of a dict use the `values()` method
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/model/matter/composition.py:204:9: RET505 Unnecessary `else` after `return` statement
tardis/model/matter/decay.py:101:21: G004 Logging statement uses f-string
tardis/transport/montecarlo/packet_source.py:246:9: RET505 Unnecessary `else` after `return` statement
tardis/util/base.py:337:5: RET505 Unnecessary `else` after `return` statement
tardis/util/base.py:511:5: E722 Do not use bare `except`
tardis/util/base.py:619:5: RET505 Unnecessary `elif` after `return` statement
Found 104 errors.
[*] 67 fixable with the `--fix` option (2 hidden fixes can be enabled with the `--unsafe-fixes` option).
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*beep* *bop* Hi, human. The Click here to see the build log. |
jvshields
reviewed
Feb 17, 2025
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There was a problem hiding this comment.
Is this a rebasing issue? Doesn't seem like part of the PR
DeerWhale
reviewed
Feb 17, 2025
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There was a problem hiding this comment.
Line #6. decayed_mass_fractions = model.composition.isotopic_mass_fraction.calculate_decayed_mass_fractions(time_interval.to(u.s).value)
The issue might be double converting day to seconds here? The alculate_decayed_mass_fractions function takes in time_decay assuming units of days.
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [b53686a4] <master> | After [41e02b01] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 21.7±5μs | 28.8±8μs | ~1.33 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 44.5±30μs | 54.6±30μs | ~1.23 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 3.75±0ms | 4.30±0.04ms | ~1.15 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 41.6±20μs | 46.6±20μs | ~1.12 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 561±100ns | 500±100ns | ~0.89 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 1.76±0.3μs | 1.57±0.3μs | ~0.89 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 601±100ns | 501±100ns | ~0.83 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 9.42±2μs | 7.57±2μs | ~0.80 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 4.29±0.5μs | 3.28±0.6μs | ~0.76 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 1.91±1μs | 2.06±2μs | 1.08 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 582±200ns | 611±200ns | 1.05 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 2.62±0ms | 2.67±0.03ms | 1.02 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 206±0.3ns | 211±0.3ns | 1.02 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 38.5±0.02s | 38.7±0.06s | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 1.05±0m | 1.05±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 |
| | 1.74±0ms | 1.74±0.02ms | 1.00 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 3.01±0.5μs | 2.98±0.2μs | 0.99 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 740±1ns | 726±1ns | 0.98 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 38.1±0μs | 36.9±0.01μs | 0.97 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 2.96±0.5ms | 2.86±0.5ms | 0.96 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 6.43±0.9μs | 6.18±1μs | 0.96 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 67.0±0.02ms | 63.9±0.3ms | 0.95 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 1.29±0μs | 1.20±0μs | 0.93 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
If you want to see the graph of the results, you can check it here |
- Update docstring for `create_inventories_dict_old()` in gamma_ray_transport.py - Increment notebook execution count in decay_radiation.ipynb e
…ys and beta particles
…ay radiation data extraction function
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There is already an existing PR #2793 |
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