search

tardis-sn / tardis

TARDIS - Temperature And Radiative Diffusion In Supernovae
https://tardis-sn.github.io/tardis
201 stars 404 forks source link

Update research papers notebook and update the docs #2794

Closed KasukabeDefenceForce closed 3 weeks ago

KasukabeDefenceForce commented 1 month ago

:pencil: Description

Type: :beetle: bugfix | :rocket: feature | :biohazard: breaking change | :vertical_traffic_light: testing | :memo: documentation | :roller_coaster: infrastructure

This PR aims at improving the logic for fetching the research papers which use Tardis and updating them in the docs. Old Logic: We used to search for "Tardis" and "Kerzendorf" or "tardis" and "supernova" in the full text of the article and were published in the NATUR publication. The total number of articles with this logic were 50. image New Logic: We fetch all the papers which have cited this article. The total number of articles fetched with this logic are 132. You can have a look at these here

:pushpin: Resources

Examples, notebooks, and links to useful references.

:vertical_traffic_light: Testing

How did you test these changes?

:ballot_box_with_check: Checklist

Note: If you are not allowed to perform any of these actions, ping (@) a contributor.

review-notebook-app[bot] commented 1 month ago

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran ruff on the latest commit (bf40f9420eb99238617f66a377ce871e7647b4d8). Here are the outputs produced. Results can also be downloaded as artifacts here. Summarised output:

```diff 12 W291 [*] Trailing whitespace 8 W293 [*] Blank line contains whitespace 6 E999 [ ] SyntaxError: Expected ',', found ':' 3 F631 [ ] Assert test is a non-empty tuple, which is always `True` 2 S113 [ ] Probable use of requests call without timeout 2 B018 [ ] Found useless expression. Either assign it to a variable or remove it. 2 W292 [*] No newline at end of file 1 ANN205 [ ] Missing return type annotation for staticmethod `get_relative_path` 1 COM818 [ ] Trailing comma on bare tuple prohibited 1 RET506 [ ] Unnecessary `else` after `raise` statement 1 I001 [*] Import block is un-sorted or un-formatted 1 PLW0127 [ ] Self-assignment of variable `observed_spectrum` ```

Complete output(might be large):

```diff .github/workflows/tardis-research-papers.yml:3:4: E999 SyntaxError: Expected an expression .github/workflows/tardis-research-papers.yml:28:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:33:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:39:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:57:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:70:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:72:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:74:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:88:1: W293 [*] Blank line contains whitespace .github/workflows/tardis-research-papers.yml:116:82: W292 [*] No newline at end of file .zenodo.json:1:1: B018 Found useless expression. Either assign it to a variable or remove it. .zenodo.json:354:2: W292 [*] No newline at end of file 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 asv.conf.json:1:1: B018 Found useless expression. Either assign it to a variable or remove it. benchmarks/benchmark_base.py:29:9: ANN205 Missing return type annotation for staticmethod `get_relative_path` benchmarks/benchmark_base.py:75:9: RET506 Unnecessary `else` after `raise` statement docs/contributing/development/running_tests.rst:1:1: E999 SyntaxError: Expected a statement docs/contributing/development/running_tests.rst:8:90: COM818 Trailing comma on bare tuple prohibited docs/contributing/development/running_tests.rst:41:42: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:64:112: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:65:124: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:69:92: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:70:107: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:76:102: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:78:116: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:80:124: W291 [*] Trailing whitespace docs/contributing/development/running_tests.rst:92:62: W291 [*] Trailing whitespace docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement docs/resources/research_done_using_TARDIS/ads.ipynb:cell 1:1:1: I001 [*] Import block is un-sorted or un-formatted docs/resources/research_done_using_TARDIS/ads.ipynb:cell 2:2:39: W291 [*] Trailing whitespace docs/resources/research_done_using_TARDIS/ads.ipynb:cell 2:12:11: S113 Probable use of requests call without timeout docs/resources/research_done_using_TARDIS/ads.ipynb:cell 2:12:60: W291 [*] Trailing whitespace docs/resources/research_done_using_TARDIS/ads.ipynb:cell 2:28:23: S113 Probable use of requests call without timeout docs/resources/research_done_using_TARDIS/ads.ipynb:cell 2:28:76: W291 [*] Trailing whitespace tardis/visualization/tools/tests/test_sdec_plot.py:343:17: F631 Assert test is a non-empty tuple, which is always `True` tardis/visualization/tools/tests/test_sdec_plot.py:475:13: F631 Assert test is a non-empty tuple, which is always `True` tardis/visualization/tools/tests/test_sdec_plot.py:557:13: PLW0127 Self-assignment of variable `observed_spectrum` tardis/visualization/tools/tests/test_sdec_plot.py:618:13: F631 Assert test is a non-empty tuple, which is always `True` Found 40 errors. [*] 23 fixable with the `--fix` option. ```
KasukabeDefenceForce commented 1 month ago

I prefer to use requests over the ads package because the former is much faster. I could fetch all the papers in approx 2.5 minutes using requests while it took approx 7 minutes to do the same using ads.

codecov[bot] commented 1 month ago

Codecov Report

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

Project coverage is 69.37%. Comparing base (8a317dd) to head (bf40f94). Report is 8 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #2794 +/- ## ========================================== - Coverage 69.91% 69.37% -0.55% ========================================== Files 206 206 Lines 15523 15518 -5 ========================================== - Hits 10853 10765 -88 - Misses 4670 4753 +83 ```

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

KasukabeDefenceForce commented 1 month ago

Sample Workflow Run: https://github.com/KasukabeDefenceForce/tardis/actions/runs/10387669495

Sample PR: https://github.com/KasukabeDefenceForce/tardis/pull/44

tardis-bot commented 1 month ago

*beep* *bop*

Hi, human.

The docs workflow has succeeded :heavy_check_mark:

Click here to see your results.

tardis-bot commented 1 month ago

*beep* *bop* Hi human, I ran benchmarks as you asked comparing master (a054d743a0b35fd153e407a2f5df973b103bd32e) and the latest commit (bf40f9420eb99238617f66a377ce871e7647b4d8). Here are the logs produced by ASV. Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

```diff | Change | Before [a054d743] | After [bf40f942] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------| | - | 3.01±0ms | 2.72±0ms | 0.9 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | ```

All benchmarks:

```diff Benchmarks that have improved: | Change | Before [a054d743] | After [bf40f942] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------| | - | 3.01±0ms | 2.72±0ms | 0.9 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') | Benchmarks that have stayed the same: | Change | Before [a054d743] | After [bf40f942] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------| | | 41.7±20μs | 49.3±20μs | ~1.18 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission | | | 1.54±0.4μs | 1.30±0.3μs | ~0.84 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line | | | 66.8±30μs | 48.1±30μs | ~0.72 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter | | | 601±100ns | 651±200ns | 1.08 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation | | | 2.99±0.8μs | 3.20±0.5μs | 1.07 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell | | | 5.81±0.8μs | 6.17±0.8μs | 1.06 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket | | | 6.92±2μs | 7.34±1μs | 1.06 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley | | | 531±200ns | 551±100ns | 1.04 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation | | | 39.3±0s | 39.5±0.01s | 1.01 | run_tardis.BenchmarkRunTardis.time_run_tardis | | | 201±0.2ns | 203±0.3ns | 1.01 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body | | | 1.66±0.01ms | 1.67±0.01ms | 1.01 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop | | | 521±200ns | 521±100ns | 1.00 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation | | | 3.71±0.01ms | 3.71±0.01ms | 1.00 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') | | | 1.05±0m | 1.05±0m | 1.00 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking | | | 2.07±0m | 2.07±0m | 1.00 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions | | | 62.7±0.2ms | 62.6±0.02ms | 1.00 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe | | | 756±0.3ns | 745±0.3ns | 0.98 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter | | | 23.4±6μs | 23.0±6μs | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list | | | 30.5±0.05μs | 29.9±0.02μs | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list | | | 2.04±2μs | 1.96±2μs | 0.96 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators | | | 2.59±0.4ms | 2.49±0.4ms | 0.96 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop | | | 1.25±0μs | 1.19±0μs | 0.95 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary | | | 2.92±0.6μs | 2.76±0.3μs | 0.95 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket | ```

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