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tardis-sn / tardis

TARDIS - Temperature And Radiative Diffusion In Supernovae
https://tardis-sn.github.io/tardis
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Migrate to Regression Data Completely #2808

Closed atharva-2001 closed 2 days ago

atharva-2001 commented 3 weeks ago

:pencil: Description

Type: :biohazard: breaking change | :vertical_traffic_light: testing | :roller_coaster: infrastructure

This PR aims to remove references of refdata from the tardis repo. https://github.com/tardis-sn/tardis-regression-data/pull/21 and https://github.com/tardis-sn/tardis-regression-data/pull/22 will need to be merged before in order for tests to pass.

:pushpin: Resources

Examples, notebooks, and links to useful references.

:vertical_traffic_light: Testing

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tardis-bot commented 3 weeks ago

*beep* *bop* Hi human, I ran ruff on the latest commit (8b6fda302664b83f6dacc5d2b1f0b16a337ff49a). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 23 E999 [ ] SyntaxError: Expected an expression 6 UP015 [*] Unnecessary open mode parameters 5 W291 [*] Trailing whitespace 4 I001 [*] Import block is un-sorted or un-formatted 4 F401 [*] `astropy.constants` imported but unused 2 FLY002 [*] Consider `f"{hash_string}_{nlte_prop}"` instead of string join 1 B018 [ ] Found useless expression. Either assign it to a variable or remove it. 1 G004 [ ] Logging statement uses f-string 1 INP001 [ ] File `tardis/io/model/readers/tests/test_arepo_parser.py` is part of an implicit namespace package. Add an `__init__.py`. 1 W292 [*] No newline at end of file 1 W605 [*] Invalid escape sequence: `\g` 1 F403 [ ] `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names 1 F821 [ ] Undefined name `pytest_report_header` 1 PGH004 [ ] Use specific rule codes when using `noqa` ```

Complete output(might be large):

```diff .github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression .github/workflows/archive/dispatcher.yml:2:4: E999 SyntaxError: Expected an expression .github/workflows/build-docs.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/pre-release.yml:7:4: E999 SyntaxError: Expected an expression .github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression asv.conf.json:1:1: B018 Found useless expression. Either assign it to a variable or remove it. asv.conf.json:32:2: W292 [*] No newline at end of file docs/io/configuration/components/models/data/config_init_trad.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons docs/io/configuration/components/models/data/config_no_init_trad.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons docs/resources/code_comparison/plasma_compare/tardis_example.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/conftest.py:12:1: F403 `from tardis.tests.fixtures.atom_data import *` used; unable to detect undefined names tardis/conftest.py:30:49: PGH004 Use specific rule codes when using `noqa` tardis/conftest.py:32:9: F821 Undefined name `pytest_report_header` tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 1:2:1: I001 [*] Import block is un-sorted or un-formatted tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 1:3:18: F401 [*] `pandas` imported but unused tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 1:6:29: F401 [*] `astropy.constants` imported but unused tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 1:7:25: F401 [*] `astropy.units` imported but unused tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 7:5:70: W291 [*] Trailing whitespace tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 9:3:96: W291 [*] Trailing whitespace tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 9:4:99: W291 [*] Trailing whitespace tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 9:6:78: W291 [*] Trailing whitespace tardis/energy_input/docs/working_gamma_ray_test.ipynb:cell 10:2:65: W605 [*] Invalid escape sequence: `\g` tardis/io/model/parse_atom_data.py:40:21: G004 Logging statement uses f-string tardis/io/model/readers/tests/data/csvy_test_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons 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_arepo_parser.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/io/model/readers/tests/test_arepo_parser.py:16:10: UP015 [*] Unnecessary open mode parameters tardis/io/model/readers/tests/test_arepo_parser.py:48:10: UP015 [*] Unnecessary open mode parameters tardis/io/model/readers/tests/test_arepo_parser.py:59:10: UP015 [*] Unnecessary open mode parameters tardis/io/model/readers/tests/test_arepo_parser.py:89:10: UP015 [*] Unnecessary open mode parameters tardis/io/model/readers/tests/test_arepo_parser.py:99:10: UP015 [*] Unnecessary open mode parameters tardis/io/model/readers/tests/test_arepo_parser.py:109:10: UP015 [*] Unnecessary open mode parameters tardis/model/tests/data/branch85_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/branch85_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/csvy_model_to_test_abundances.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/exponential_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/exponential_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/model_full_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/model_full_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/powerlaw_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/powerlaw_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/radiative_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/radiative_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/uniform_csvy.yml:1:69: W291 [*] Trailing whitespace tardis/model/tests/data/uniform_csvy.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/model/tests/data/uniform_old_config.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/plasma/tests/data/config_init_trad.yml:2:26: E999 SyntaxError: Simple statements must be separated by newlines or semicolons tardis/plasma/tests/test_complete_plasmas.py:149:27: FLY002 Consider `f"{hash_string}_{prop}"` instead of string join tardis/plasma/tests/test_complete_plasmas.py:154:39: FLY002 Consider `f"{hash_string}_{nlte_prop}"` instead of string join tardis/tests/fixtures/atom_data.py:1:1: I001 [*] Import block is un-sorted or un-formatted tardis/tests/fixtures/atom_data.py:2:21: F401 [*] `pathlib.Path` imported but unused Found 52 errors. [*] 21 fixable with the `--fix` option (2 hidden fixes can be enabled with the `--unsafe-fixes` option). ```
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tardis-bot commented 3 weeks ago

*beep* *bop*

Hi, human.

The docs workflow has failed :x:

Click here to see the build log.

andrewfullard commented 1 week ago

Can you fix the benchmarks? Docs as well.

tardis-bot commented 1 week ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (260207cb7cee6829390d77fbf48de53843818f09) and the latest commit (8b6fda302664b83f6dacc5d2b1f0b16a337ff49a). 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 [260207cb] | After [8b6fda30] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------| | | 2.03±1μs | 2.50±1μs | ~1.23 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators | | | 3.10±0.5μs | 3.80±0.6μs | ~1.23 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket | | | 44.2±20μs | 51.8±30μs | ~1.17 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter | | | 1.73±0.02ms | 1.95±0.01ms | ~1.13 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop | | | 491±200ns | 551±100ns | ~1.12 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation | | | 1.58±0.3μs | 1.38±0.4μs | ~0.87 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line | | | 3.46±0.01ms | 2.77±0.03ms | ~0.80 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | | | 11.0±3μs | 7.30±2μs | ~0.66 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley | | | 6.50±0.8μs | 6.87±0.6μs | 1.06 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket | | | 23.2±6μs | 23.9±6μs | 1.03 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list | | | 2.77±0.4ms | 2.81±0.5ms | 1.02 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop | | | 2.07±0m | 2.10±0.01m | 1.01 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions | | | 204±0.2ns | 206±0.6ns | 1.01 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body | | | 1.17±0μs | 1.18±0μs | 1.01 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary | | | 63.2±0.2ms | 64.1±0.06ms | 1.01 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe | | | 601±100ns | 601±100ns | 1.00 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation | | | 30.6±0.01μs | 30.6±0.06μs | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list | | | 3.26±0.5μs | 3.25±0.4μs | 1.00 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell | | | 3.92±0.03ms | 3.79±0.02ms | 0.97 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') | | | 561±100ns | 541±200ns | 0.96 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation | | | 40.8±0.05s | 39.2±0.08s | 0.96 | run_tardis.BenchmarkRunTardis.time_run_tardis | | | 1.09±0m | 1.05±0m | 0.96 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking | | | 44.8±20μs | 42.1±20μs | 0.94 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission | | | 742±0.5ns | 697±1ns | 0.94 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter | ```

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

codecov[bot] commented 1 week ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 70.79%. Comparing base (be4ec9a) to head (8b6fda3). Report is 3 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #2808 +/- ## ========================================== - Coverage 70.96% 70.79% -0.18% ========================================== Files 209 209 Lines 15638 15637 -1 ========================================== - Hits 11098 11070 -28 - Misses 4540 4567 +27 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

andrewfullard commented 1 week ago

Do you know why docs are failing?

atharva-2001 commented 1 week ago

I think it is because of the YAML file not being updated because it is a pull request target event. The YAML file was picked up from the master branch instead of this branch.

On Fri, 6 Sep 2024 at 7:46 PM, Andrew @.***> wrote:

Do you know why docs are failing?

— Reply to this email directly, view it on GitHub https://github.com/tardis-sn/tardis/pull/2808#issuecomment-2334162066, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKOCXAKNDMI54URPKGDUQDZVG2LJAVCNFSM6AAAAABM7N3M7GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZUGE3DEMBWGY . You are receiving this because you authored the thread.Message ID: @.***>

atharva-2001 commented 1 week ago

I think it should all work once the PR is merged!

On Fri, 6 Sep 2024 at 10:21 PM, Atharva Arya @.***> wrote:

I think it is because of the YAML file not being updated because it is a pull request target event. The YAML file was picked up from the master branch instead of this branch.

On Fri, 6 Sep 2024 at 7:46 PM, Andrew @.***> wrote:

Do you know why docs are failing?

— Reply to this email directly, view it on GitHub https://github.com/tardis-sn/tardis/pull/2808#issuecomment-2334162066, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKOCXAKNDMI54URPKGDUQDZVG2LJAVCNFSM6AAAAABM7N3M7GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZUGE3DEMBWGY . You are receiving this because you authored the thread.Message ID: @.***>