TODO.md

The Gold: migrate get_domain_specific_options() to use gecioptparse

Design decisions

Option definitions

Option	Short flag	Type	Default	Help text
--data-path	-d	character_option	/workdir/data/weather_station_data.csv	"File path of the weather station data"
--roni-path	-r	character_option	/workdir/data/external/roni_data.csv	"File path of the ONI data (regional ocean climate data)"
--output-path	-o	character_option	/workdir/data/processed/weather_classified_data.csv	"File path of the classified weather data output"

• No additional options beyond these three.
• Return value changes from named character vector to named list (optparse::parse_args() output).

DESCRIPTION changes

• Add gecioptparse to Imports: (alphabetical order).
• Add IslasGECI/gecioptparse to Remotes: (follows bycatch_code pattern).

TDD plan

1. RED — write failing test

Update tests/testthat/test_get_domain_specific_options.R:

• Keep existing name-check assertion.
• Add it("has the expected default values") block that asserts the three new defaults.

Expected failure: current stub returns "" for all values, not the new defaults.

2. GREEN — implement using gecioptparse

Rewrite R/get_domain_specific_options.R:

• Build each option with gecioptparse::character_option(name, default, help).
• Combine into a vector.
• Pass to gecioptparse::get_options_from_vec().
• Update DESCRIPTION (Imports + Remotes).
• Run make setup to regenerate NAMESPACE (adds gecioptparse import).

3. REFACTOR

• Verify help strings render correctly.
• Check make check (styler format) passes.
• Confirm make tests passes.
• Update DOCS.md if return-type description needs adjustment.