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update SS3 tests

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  • ¿Algo no está bien?
#441 4 comentarios 0 reacciones 0 asignados Ver en GitHub

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@Schiano-NOAA ya está trabajando en esto.

Desde el 19/10/2026.

  • #427 de @Schiano-NOAA — abierto

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Documentación
Claridad
Bastante claro
Estado de actividad
Estancado
Stack tecnológico
r
Área
testing

Línea de trabajo

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.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

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  • the Report.sso files in that fixtures folder are from 2024 and are out of date,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.

Lenguaje dominante
R
Estrellas
20
Forks
10
Merge medio
3 d 9 h
PR fusionados (30 d)
21

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