Added obindices function

[spiani]

No description provided.

[Copilot]

Pull request overview

This PR introduces a new ob_indices CLI subcommand under mitgcm_inputs intended to generate MITgcm open-boundary indices (and optional sponge/nudging indices), and wires it into the main CLI + a launcher script; it also includes dependency / tooling updates and some formatting cleanups.

Changes:

• Added mitgcm_inputs.ob_indices package with logic to compute OB indices + CLI entrypoint.
• Registered the new ob_indices command in src/mitgcm_inputs/__main__.py and updated a domain-generation launcher to call it.
• Updated dependencies/lockfile and pre-commit hook versions; performed small whitespace/formatting cleanups.

Reviewed changes

Copilot reviewed 17 out of 18 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
src/mitgcm_inputs/ob_indices/ob_indices.py	New OB-index generation logic (boundary slicing, component detection, MITgcm run-length encoding).
src/mitgcm_inputs/ob_indices/init.py	New CLI subcommand definition and I/O plumbing for ob_indices.
src/mitgcm_inputs/main.py	Registers ob_indices subcommand and adjusts logging noise filtering.
launcers/all_statics/generate_mer_statics.sh	Runs mitgcm_inputs ob_indices for each domain and adds GNU parallel execution.
pyproject.toml	Adds numba dependency and deptry ignore entry.
poetry.lock	Updates lockfile (bitsea ref bump and multiple package version bumps; adds numba/llvmlite).
.pre-commit-config.yaml	Updates hook versions and removes ruff-format hook.
src/mitgcm_inputs/rbcs/scarichi_json_gen.py	Argparse help formatting change only.
src/mitgcm_inputs/rbcs/rbcs_gen.py	Argparse help formatting change + whitespace cleanup.
src/mitgcm_inputs/rbcs/fiumi_json_gen.py	Argparse help formatting change only.
src/mitgcm_inputs/rbcs/init.py	Whitespace cleanup only.
src/mitgcm_inputs/surface_deposition/surface_deposition.py	Whitespace cleanup only.
src/mitgcm_inputs/surface_deposition/init.py	Whitespace cleanup only.
src/mitgcm_inputs/k_extinction/k_extinction.py	Whitespace cleanup only.
src/mitgcm_inputs/k_extinction/init.py	Whitespace cleanup only.
src/mitgcm_inputs/bottom_fluxes/bottom_fluxes.py	Whitespace cleanup only.
src/mitgcm_inputs/bottom_fluxes/init.py	Whitespace cleanup only.

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[Copilot]

open_on_boundary uses mask.shape[domain_index + 1], but the boundary coordinate that needs to be reported for EAST/NORTH is the sponge axis size (x for EAST, y for NORTH). With the current indexing, NORTH uses Nx and EAST uses Ny, producing incorrect boundary indices. Use mask.shape[sponge_index + 1] (still +1 to skip the depth dimension) for the end-boundary value.

Suggested change

	open_on_boundary = mask.shape[domain_index + 1]
	open_on_boundary = mask.shape[sponge_index + 1]