Io artis reader #2973
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Io artis reader #2973
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- Enhance ARTIS model reading with more detailed isotope and elemental mass fraction handling - Add `to_geometry()` method to convert ArtisModelData to HomologousRadial1DGeometry - Improve documentation in Jupyter notebook example - Update mass fraction reading to support normalization and multi-index - Add index and column names for better data clarity
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*beep* *bop* 41 W291 [*] Trailing whitespace
12 E999 [ ] SyntaxError: Expected a statement
12 W293 [*] Blank line contains whitespace
7 I001 [*] Import block is un-sorted or un-formatted
6 E902 [ ] stream did not contain valid UTF-8
5 INP001 [ ] File `tardis/analysis/opacities.py` is part of an implicit namespace package. Add an `__init__.py`.
3 F401 [*] `tardis.io.model.readers.artis.read_artis_density` imported but unused
2 PIE808 [*] Unnecessary `start` argument in `range`
2 RET505 [ ] Unnecessary `else` after `return` statement
2 E712 [*] Avoid equality comparisons to `False`; use `if not ...:` for false checks
2 W292 [*] No newline at end of file
2 F811 [ ] Redefinition of unused `monkeysession` from line 6
1 PT009 [ ] Use a regular `assert` instead of unittest-style `assert_`
1 E402 [ ] Module level import not at top of file
1 E703 [*] Statement ends with an unnecessary semicolon
1 W605 [*] Invalid escape sequence: `\s`
1 F631 [ ] Assert test is a non-empty tuple, which is always `True`
Complete output(might be large): .github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression
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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
docs/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/index.rst:21:51: W291 [*] Trailing whitespace
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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/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/model/data/artis_abundances.dat:1:1: E999 SyntaxError: Unexpected indentation
docs/io/model/data/artis_model.dat:1:1: E999 SyntaxError: Unexpected indentation
docs/io/model/index.rst:1:1: E999 SyntaxError: Expected an expression
docs/io/model/index.rst:12:34: W292 [*] No newline at end of file
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/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/model/readers/artis.py:119:5: RET505 Unnecessary `else` after `return` statement
tardis/io/model/readers/artis.py:144:34: W605 [*] Invalid escape sequence: `\s`
tardis/io/model/readers/artis.py:197:1: E402 Module level import not at top of file
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/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/io/model/readers/tests/test_ascii_readers.py:1:1: INP001 File `tardis/io/model/readers/tests/test_ascii_readers.py` is part of an implicit namespace package. Add an `__init__.py`.
tardis/io/tests/test_model_reader.py:6:43: F401 [*] `tardis.io.model.readers.artis.read_artis_density` imported but unused
tardis/transport/montecarlo/packet_source.py:246:9: 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
Found 101 errors.
[*] 69 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 your results. |
- Remove unnecessary slice indexing on mean density array - Ensure full density array is preserved when reading ARTIS model files
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [6e790c66] <release-2025.02.23> | After [a370960e] | Ratio | Benchmark (Parameter) |
|----------|------------------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 21.5±5μs | 29.9±8μs | ~1.39 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 45.4±30μs | 59.5±40μs | ~1.31 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 2.16±1μs | 2.42±1μs | ~1.12 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 3.76±0.5μs | 3.38±0.5μs | ~0.90 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 601±100ns | 511±100ns | ~0.85 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 6.44±1μs | 7.08±1μs | 1.10 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 601±100ns | 651±200ns | 1.08 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 1.71±0.03ms | 1.85±0.01ms | 1.08 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 3.53±0.4μs | 3.63±0.5μs | 1.03 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 710±1ns | 725±0.8ns | 1.02 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 40.5±0.1s | 40.3±0.07s | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 1.08±0m | 1.08±0m | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 2.11±0m | 2.12±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 7.54±2μs | 7.55±2μs | 1.00 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 206±0.2ns | 203±0.3ns | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 1.20±0μs | 1.19±0μs | 0.99 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 66.4±0.2ms | 65.8±0.2ms | 0.99 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 1.56±0.4μs | 1.52±0.3μs | 0.97 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
| | 40.4±0.2μs | 39.0±0.2μs | 0.97 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 45.9±30μs | 44.3±20μs | 0.96 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 2.89±0.4ms | 2.76±0.4ms | 0.96 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 4.55±0.02ms | 4.29±0.02ms | 0.94 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 3.45±0.04ms | 3.23±0.01ms | 0.94 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 602±100ns | 552±100ns | 0.92 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
If you want to see the graph of the results, you can check it here |
| mean_density=mean_density, | ||
| mass_fractions=mass_fractions, | ||
| ) | ||
| from tardis.model.geometry.radial1d import HomologousRadial1DGeometry |
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Import at end of file?
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to avoid circular import - do you want me to fix?
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The |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2973 +/- ##
==========================================
- Coverage 69.54% 69.26% -0.28%
==========================================
Files 228 229 +1
Lines 16429 16487 +58
==========================================
- Hits 11425 11420 -5
- Misses 5004 5067 +63 ☔ View full report in Codecov by Sentry. |
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New IO ARTIS reader. Making way for more changes down the line.