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tardis-sn / tardis

TARDIS - Temperature And Radiative Diffusion In Supernovae
https://tardis-sn.github.io/tardis
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Rates matrix solver #2865

Open andrewfullard opened 1 month ago

andrewfullard commented 1 month ago

:pencil: Description

Type: :rocket: feature

Initial plans for replacing the old "NLTE" setup with a hopefully cleaner structure.

:vertical_traffic_light: Testing

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tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran ruff on the latest commit (4bd4206c61714e81e948ff59c3e37c3c5568b16b). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 21 E999 [ ] SyntaxError: Expected ',', found ':' 8 W293 [*] Blank line contains whitespace 7 F401 [*] `astropy.constants` imported but unused 5 RET505 [ ] Unnecessary `else` after `return` statement 3 G004 [ ] Logging statement uses f-string 2 E902 [ ] No such file or directory (os error 2) 1 ICN001 [*] `matplotlib` should be imported as `mpl` 1 G001 [ ] Logging statement uses `str.format` 1 RET506 [ ] Unnecessary `else` after `raise` statement 1 I001 [*] Import block is un-sorted or un-formatted 1 E701 [ ] Multiple statements on one line (colon) 1 W291 [*] Trailing whitespace 1 W292 [*] No newline at end of file 1 F811 [ ] Redefinition of unused `opacity_state_initialize` from line 13 1 F821 [ ] Undefined name `tardis_githash` ```

Complete output(might be large):

```diff .github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/post-release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/post-release.yml:124:37: W291 [*] Trailing whitespace .github/workflows/pre-release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/release.yml:16:7: E701 Multiple statements on one line (colon) .github/workflows/release.yml:48:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:51:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:58:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:61:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:64:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:69:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:73:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:89:1: W293 [*] Blank line contains whitespace .github/workflows/release.yml:97:23: W292 [*] No newline at end of file .mailmap:1:38: E999 SyntaxError: Expected an expression 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/physics/plasma/equilibrium/collisional_rate_coefficients.hdf:1:1: E902 stream did not contain valid UTF-8 docs/physics/plasma/equilibrium/comparison.ipynb:cell 31:1:1: I001 [*] Import block is un-sorted or un-formatted docs/physics/plasma/equilibrium/tardis_solver.ipynb:cell 11:1:29: F401 [*] `astropy.constants` imported but unused docs/physics/plasma/equilibrium/test_continuum_template_wkerzen_rate_coeffs.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement 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/plasma/detailed_balance/rates/__init__.py:1:1: E902 No such file or directory (os error 2) tardis/plasma/electron_energy_distribution/__init__.py:2:5: F401 `tardis.plasma.electron_energy_distribution.base.ElectronEnergyDistribution` imported but unused; consider removing, adding to `__all__`, or using a redundant alias tardis/plasma/electron_energy_distribution/__init__.py:3:5: F401 `tardis.plasma.electron_energy_distribution.base.ThermalElectronEnergyDistribution` imported but unused; consider removing, adding to `__all__`, or using a redundant alias 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/spectrum/formal_integral.py:23:5: F811 Redefinition of unused `opacity_state_initialize` from line 13 tardis/spectrum/formal_integral.py:340:13: RET506 Unnecessary `else` after `raise` statement tardis/spectrum/formal_integral.py:681:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral.py:717:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral_cuda.py:375:5: RET505 Unnecessary `else` after `return` statement tardis/spectrum/formal_integral_cuda.py:420:5: RET505 Unnecessary `else` after `return` statement tardis/tests/integration_tests/at/abundances.dat:2:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/at/config.yml:2:7: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/at/densities.dat:1:10: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/tests/integration_tests/conftest.py:43:13: F821 Undefined name `tardis_githash` tardis/tests/integration_tests/conftest.py:88:5: RET505 Unnecessary `else` after `return` statement tardis/tests/integration_tests/paper1_downbranch/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/paper1_macroatom/abundances.dat:1:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/paper1_macroatom/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/paper1_macroatom/densities.dat:1:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/paper1_scatter/config.yml:7:4: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/test_integration.py:3:8: ICN001 `matplotlib` should be imported as `mpl` tardis/tests/integration_tests/w7/abundances.dat:2:1: E999 SyntaxError: Unexpected indentation tardis/tests/integration_tests/w7/config.yml:2:7: E999 SyntaxError: Expected an expression tardis/tests/integration_tests/w7/densities.dat:1:11: E999 SyntaxError: Simple statements must be separated by newlines or semicolons Found 55 errors. [*] 12 fixable with the `--fix` option (1 hidden fix can be enabled with the `--unsafe-fixes` option). ```
tardis-bot commented 1 month ago

*beep* *bop*

Hi, human.

The docs workflow has failed :x:

Click here to see the build log.

tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (a1f621f6d909cbc6e54a220d16648ce2548fab6d) and the latest commit (4bd4206c61714e81e948ff59c3e37c3c5568b16b). Here are the logs produced by ASV. Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

```diff ```

All benchmarks:

```diff Benchmarks that have stayed the same: | Change | Before [6ee870e0] | After [4bd4206c] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------| | | 7.07±2μs | 9.50±0.3μs | ~1.34 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley | | | 45.0±30μs | 52.9±30μs | ~1.17 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter | | | 3.12±1μs | 1.94±0.9μs | ~0.62 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators | | | 4.99±1μs | 2.54±0.7μs | ~0.51 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket | | | 1.45±0.4μs | 1.59±0.3μs | 1.10 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line | | | 5.60±1μs | 6.08±1μs | 1.09 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket | | | 501±100ns | 541±100ns | 1.08 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation | | | 1.17±0μs | 1.24±0μs | 1.06 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary | | | 601±100ns | 631±100ns | 1.05 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation | | | 62.6±0.3ms | 65.8±0.3ms | 1.05 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe | | | 621±200ns | 641±100ns | 1.03 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation | | | 40.9±20μs | 41.7±20μs | 1.02 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission | | | 1.64±0ms | 1.66±0.02ms | 1.01 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop | | | 1.05±0m | 1.06±0m | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking | | | 2.08±0m | 2.07±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions | | | 206±0.1ns | 206±0.2ns | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body | | | 30.8±0.03μs | 30.9±0.01μs | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list | | | 3.23±0.6μs | 3.23±0.5μs | 1.00 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell | | | 40.0±0.05s | 39.8±0.06s | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis | | | 2.49±0.4ms | 2.47±0.4ms | 0.99 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop | | | 3.52±0.02ms | 3.44±0.01ms | 0.98 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') | | | 758±2ns | 725±1ns | 0.96 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter | | | 23.1±6μs | 21.8±5μs | 0.94 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list | | | 2.73±0.01ms | 2.50±0.01ms | 0.92 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | ```

If you want to see the graph of the results, you can check it here

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 95.58824% with 6 lines in your changes missing coverage. Please review.

Project coverage is 70.18%. Comparing base (a1f621f) to head (4bd4206). Report is 5 commits behind head on master.

Files with missing lines Patch % Lines
tardis/io/atom_data/base.py 78.94% 4 Missing :warning:
...rdis/plasma/equilibrium/rates/collisional_rates.py 80.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #2865 +/- ## ========================================== + Coverage 69.97% 70.18% +0.20% ========================================== Files 216 219 +3 Lines 16077 16094 +17 ========================================== + Hits 11250 11295 +45 + Misses 4827 4799 -28 ```

:umbrella: View full report in Codecov by Sentry.
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wkerzendorf commented 1 week ago

adding more tests to get coverage up probably

andrewfullard commented 4 days ago

Note to self: make sure the tests pull the extra atom data file from the regression data repo