[MansurJisan-NCO]

Description

The README and the Read the Docs pages were last refreshed in April 2026. This PR brings them up to date with the code. It changes docs only; there are no code or test changes.

• README.md: rewritten short, in the style of the nos-workflow README.
  • It covers the systems nos-utils serves through nos-workflow: SECOFS (SCHISM, DATM+SCHISM, DATM+SCHISM+WW3), STOFS-3D-ATL (standalone and DATM-coupled) and STOFS-2D-Global (GFS meteorology for ADCIRC).
  • It has a module table grouped by purpose, install and test commands (.[full,dev]), the docs link and the NOAA disclaimer.
• docs/index.rst:
  • Current systems and features. STOFS-3D-ATL is no longer "work in progress", and WW3 and ADCIRC support are added.
  • Ensemble moves to features.
  • No hard test count.
  • Performance figures that did not say what they were measured on are dropped.
• docs/api/:
  • Every public module is now autodocumented exactly once. That adds about 10 nos_utils.forcing modules, a new post.rst for nos_utils.post, and coords.rst.
  • The package-level automodules use :no-members:, to stop duplicate entries.
  • Cross-references point at the defining modules, so they resolve.
• docs/usage.rst, interp.rst, installation.rst, contributing.rst: fixes to statements that no longer matched the code.
  • PrepOrchestrator(..., skip_legacy=False) runs the SECOFS RTOFS and NWM steps. The nos-utils prep CLI keeps the default, which skips them.
  • The RTOFS SSH weights lookup ($FIXofs/$FIXstofs3d, exact file names) is described correctly.
  • SECOFS rivers come from NWMProcessor (analysis_assim).
  • The STOFS-3D-ATL forecast length is 96 h.
  • build_npz replaces the name build_ssh_npz, which does not exist.
  • There is no hard test count.
• docs/conf.py: numpy is removed from autodoc_mock_imports. It is a core dependency, and mocking it broke the import of nudge_ops on Read the Docs.

This PR does not touch the clone-URL lines that #75 edits; a test merge with #75 is clean.

Type of change

• Maintenance (refactor, cleanup, CI, comments)

Change characteristics

• Changes outputs (values, COMOUT files or names, archives)? NO
• Breaking change to existing functionality? NO
• Requires a nos-utils submodule bump (nos-workflow) or a paired nos-workflow change (nos-utils)? NO
• Requires new or regenerated fix files on the machine? NO
• Requires a re-prep or a new hotstart before the next cycle? NO
• Machines affected: none (docs only)

How has this been tested?

• Sphinx build in a venv that mirrors Read the Docs (pip install .[docs] only): 0 autodoc import failures. The 7 remaining warnings are existing docstring formatting.
• The build also passes with .[full,docs], as the GitHub Docs workflow installs.
• The edited cross-references render as links in the built HTML.
• The new text was checked against the code (orchestrator, rtofs, config, wave_boundary, ufs_config) by an independent review.

Checklist

• Dependent PRs merged and published (nos-utils before any submodule bump)
• pytest suite passes
• Existing operational behavior preserved, or the change is called out above
• No edits to a shared FIXofs while it is cycling
• Self-review done; yaml comments and docstrings updated where behavior changed
• No markdown files added to the repo (this template is the only exception)