Update research papers notebook and update the docs #2794
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*beep* *bop* 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): .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.
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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 ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ 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 ☔ View full report in Codecov by Sentry. |
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Sample Workflow Run: Sample PR: |
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*beep* *bop* Hi, human. The Click here to see your results. |
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*beep* *bop* Significantly changed benchmarks: | Change | Before [a054d743] <master> | After [bf40f942] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------|
| - | 3.01±0ms | 2.72±0ms | 0.9 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
All benchmarks: Benchmarks that have improved:
| Change | Before [a054d743] <master> | 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] <master> | 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 |
…ata if the owner is tardis-sn
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| - name: Approve pull request (I) | ||
| run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} | ||
| if: steps.create-pr.outputs.pull-request-operation == 'created' | ||
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| - name: Approve pull request (II) | ||
| run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.CORE_COORDINATOR_TOKEN }} | ||
| if: steps.create-pr.outputs.pull-request-operation == 'created' | ||
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| - name: Enable automerge | ||
| uses: peter-evans/enable-pull-request-automerge@v2 | ||
| with: | ||
| token: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} | ||
| pull-request-number: ${{ steps.create-pr.outputs.pull-request-number }} | ||
| merge-method: squash | ||
| if: steps.create-pr.outputs.pull-request-operation == 'created' |
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📝 Description
Type: 🪲
bugfix| 🚀feature| ☣️breaking change| 🚦testing| 📝documentation| 🎢infrastructureThis 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.
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
📌 Resources
Examples, notebooks, and links to useful references.
🚦 Testing
How did you test these changes?
☑️ Checklist
build_docslabel