Numpy v2 Upgrade PR 2 #2935

atharva-2001 · 2025-01-10T13:09:59Z

📝 Description

Based on #2934
Tested on my own Reference Data- https://github.com/tardis-sn/tardis/actions/runs/12789863418?pr=2935

This is the new regression data- tardis-sn/tardis-regression-data#42

📌 Resources

Examples, notebooks, and links to useful references.

🚦 Testing

How did you test these changes?

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☑️ Checklist

I requested two reviewers for this pull request
I updated the documentation according to my changes
I built the documentation by applying the build_docs label

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tardis-bot · 2025-01-10T13:12:03Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (12fe439).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

7	W293 	[*] Blank line contains whitespace
6	W291 	[*] Trailing whitespace
5	E999 	[ ] SyntaxError: Expected an expression
3	G004 	[ ] Logging statement uses f-string
1	FA100	[ ] Add `from __future__ import annotations` to simplify `typing.Tuple`
1	G001 	[ ] Logging statement uses `str.format`

Complete output(might be large):

.github/actions/setup_lfs/action.yml:5:8: E999 SyntaxError: Expected an expression
.github/actions/setup_lfs/action.yml:37:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:1:12: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
.github/workflows/lfs-cache.yml:43:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:62:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:65:78: W291 [*] Trailing whitespace
.github/workflows/lfs-cache.yml:70:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:73:45: W291 [*] Trailing whitespace
.github/workflows/lfs-cache.yml:74:78: W291 [*] Trailing whitespace
.github/workflows/lfs-cache.yml:78:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:81:46: W291 [*] Trailing whitespace
.github/workflows/lfs-cache.yml:82:78: W291 [*] Trailing whitespace
.github/workflows/lfs-cache.yml:86:1: W293 [*] Blank line contains whitespace
.github/workflows/lfs-cache.yml:96:1: W293 [*] Blank line contains whitespace
conda-linux-64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
conda-lock.yml:14:10: E999 SyntaxError: Expected an expression
conda-osx-arm64.lock:5:1: E999 SyntaxError: Expected class, function definition or async function definition after decorator
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:705:17: G004 Logging statement uses f-string
tardis/io/model/readers/generic_readers.py:20:6: FA100 Add `from __future__ import annotations` to simplify `typing.Tuple`
tardis/io/model/readers/generic_readers.py:51:72: W291 [*] Trailing whitespace
Found 23 errors.
[*] 13 fixable with the `--fix` option.

codecov · 2025-01-15T14:21:28Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.17%. Comparing base (6e790c6) to head (12fe439).
Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2935      +/-   ##
==========================================
- Coverage   69.53%   69.17%   -0.37%     
==========================================
  Files         228      228              
  Lines       16429    16430       +1     
==========================================
- Hits        11424    11365      -59     
- Misses       5005     5065      +60

☔ View full report in Codecov by Sentry.
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tardis-bot · 2025-01-15T15:25:28Z

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (6e790c6) and the latest commit (12fe439).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [6e790c66] <release-2025.02.23>   | After [12fe439e]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 66.4±40μs                                | 87.8±40μs           | ~1.32   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 2.09±0.05ms                              | 2.59±0.1ms          | ~1.24   | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 662±200ns                                | 572±200ns           | ~0.86   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 5.79±0.3ms                               | 4.99±0.2ms          | ~0.86   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 56.3±30μs                                | 42.8±30μs           | ~0.76   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 872±200ns                                | 591±100ns           | ~0.68   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 4.29±0.07ms                              | 2.83±0.08ms         | ~0.66   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 52.1±20μs                                | 25.5±6μs            | ~0.49   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 39.9±0.3μs                               | 41.6±0.4μs          | 1.04    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.73±0.4μs                               | 3.81±0.4μs          | 1.02    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 719±0.3ns                                | 728±0.3ns           | 1.01    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 2.92±0.4ms                               | 2.94±0.5ms          | 1.01    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 206±0.1ns                                | 205±0.1ns           | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 66.4±0.1ms                               | 66.7±0.04ms         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 8.70±2μs                                 | 8.68±2μs            | 1.00    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 41.9±0.1s                                | 41.4±0.03s          | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.18±0m                                  | 2.16±0m             | 0.99    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.22±0μs                                 | 1.21±0μs            | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 1.14±0m                                  | 1.11±0m             | 0.98    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 551±100ns                                | 531±100ns           | 0.96    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 7.00±0.8μs                               | 6.67±0.8μs          | 0.95    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 4.15±0.3μs                               | 3.95±1μs            | 0.95    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 1.64±0.5μs                               | 1.55±0.3μs          | 0.94    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 2.67±2μs                                 | 2.48±2μs            | 0.93    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |

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

tardis-bot · 2025-01-27T14:39:26Z

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

andrewfullard · 2025-01-27T15:09:07Z

.github/actions/setup_lfs/action.yml

      uses: actions/checkout@v4
      with:
-        repository: ${{ inputs.regression-data-repo }}
+        repository: atharva-2001/tardis-regression-data


Revert changes in this file

Still needs doing

andrewfullard · 2025-02-21T15:04:16Z

Please resolve the merge conflicts

atharva-2001 force-pushed the numpy_v2_2 branch from 356c0d3 to dd6d499 Compare January 15, 2025 13:55

atharva-2001 added build-docs benchmarks labels Jan 15, 2025

atharva-2001 force-pushed the numpy_v2_2 branch from 4c85ee7 to 5b1c4a7 Compare January 17, 2025 11:16

atharva-2001 marked this pull request as ready for review January 27, 2025 14:13

andrewfullard reviewed Jan 27, 2025

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atharva-2001 mentioned this pull request Feb 12, 2025

NumPy v2 changes tardis-sn/tardis-regression-data#39

Closed

6 tasks

Atharva Arya and others added 7 commits February 24, 2025 06:42

Add linux based conda lock files

8663a47

osx arm changes

ac6f4c7

Use genfromtxt instead of recfromtxt

e295883

Keep the dtype the same as in recfromtxt

8564830

Sort lines dataframe with line id and kind stable

63512c4

Do not hard code largest size of boundary interaction array

5c20ba8

Workflow tests

355e4eb

atharva-2001 mentioned this pull request Feb 24, 2025

NumPy v2 changes tardis-sn/tardis-regression-data#42

Merged

6 tasks

atharva-2001 force-pushed the numpy_v2_2 branch from 5b1c4a7 to 355e4eb Compare February 24, 2025 13:33

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andrewfullard added the git-lfs-pull Allow git lfs pull in PRs label Feb 24, 2025

LFS key changes

12fe439

atharva-2001 dismissed stale reviews from DeerWhale and andrewfullard via 12fe439 February 24, 2025 15:37

andrewfullard requested review from andrewfullard and removed request for andrewfullard February 24, 2025 15:56

andrewfullard requested a review from DeerWhale February 24, 2025 15:56

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andrewfullard merged commit e0297c6 into tardis-sn:master Feb 24, 2025
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Numpy v2 Upgrade PR 2 #2935

Numpy v2 Upgrade PR 2 #2935

atharva-2001 commented Jan 10, 2025 •

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tardis-bot commented Jan 27, 2025

andrewfullard Jan 27, 2025

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andrewfullard commented Feb 21, 2025

Numpy v2 Upgrade PR 2 #2935

Numpy v2 Upgrade PR 2 #2935

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atharva-2001 commented Jan 10, 2025 • edited Loading

📝 Description

📌 Resources

🚦 Testing

☑️ Checklist

tardis-bot commented Jan 10, 2025 • edited Loading

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Codecov Report

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