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update SS3 tests

Aperta
  • Qualcosa non va?
#441 4 commenti 0 reazioni 0 assegnatari Vedi su GitHub

I maintainer di solito rispondono entro 1 giorno

@Schiano-NOAA ci sta già lavorando.

Dal 19/10/2026.

  • #427 di @Schiano-NOAA — aperta

Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
35/100
Tipo di issue
Documentazione
Chiarezza
Abbastanza chiara
Stato di attività
Ferma
Stack tecnologico
r
Ambito
testing

Direzione di ricerca

Start with tests/testthat/test-convert_output.R, tests/testthat/fixtures/prepare_ss3_output_files.R, and the models in tests/testthat/fixtures/ss3_models. Compare the current r4ss::SS_output() workflow with the existing fixtures and tests, then decide where current SS3 outputs should live and how they should be prepared. Done means the tests cover all fixture models and save_all_plots() on their outputs; an open linked pull request indicates work is already underway.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Inspired by a conversation with @kellijohnson-NOAA yesterday, I've been trying out stockplotr with some SS3 models.
The package is making fast progress but there are still areas where I'm getting errors, and I think improving the tests would be a good first step to sorting out the issues.

Here are a few ways that the tests could be improved:

  • convert_output() now uses the output from r4ss::SS_output() but test-convert_output.R is still using the old method of parsing Report.sso and not testing the full set of test models in /tests/testthat/fixtures/ss3_models,
  • the Report.sso files in that fixtures folder are from 2024 and are out of date,
  • it would be good to integrate testing of the current r4ss::SS_output() into the tests of either stockplotr or r4ss, and
  • it would be good to test save_all_plots() on the output from the all of the SS3 test models, not just the example data.

The part that I'm not sure about is what should be dynamic and what files should be stored where. Here are a few options

  1. Run r4ss::SS_output() in https://github.com/nmfs-ost/stockplotr/blob/main/tests/testthat/fixtures/prepare_ss3_output_files.R and save the resulting list as a .rds or .rda to use instead of Report.sso
  2. Add more SS3 output files (like CompReport.sso which contains all the composition data) to fixtures/ss3_models and run the r4ss::SS_output() as a step in the testing process
  3. Add more SS3 output files to https://github.com/nmfs-ost/ss3-test-models instead of stockplotr and remove the files from fixtures/ss3_models

The 3rd option has the benefit of reducing the size of the stockplotr repo as well as always relying on the current SS3 files and the current version of r4ss. Adding r4ss to the 'Suggests:' field within DESCRIPTION will make it available for the tests without requiring all users to install it and its dependencies. Let me know what you think and I'm happy to work on a pull request if that would be helpful.

Lingua principale
R
Stelle
20
Fork
10
Merge medio
3g 9h
PR unite (30g)
21

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