Web docs

[calvinp0]

This pull request introduces several improvements and refinements across the ARC codebase and documentation. The main focus areas are enhanced documentation for the transition state (TS) search workflow, improved code clarity and type hinting, and updated documentation styling for a more polished appearance.

Documentation enhancements:

• Added a detailed section to the TS search documentation describing the new internal heuristics TS-guess adapter, including usage instructions, supported reaction families, and a workflow diagram. This helps users understand and leverage the new heuristic TS search capabilities. [1] [2]
• Improved explanations and formatting in various docstrings and documentation files for clarity and accuracy. [1] [2] [3] [4] [5] [6] [7] [8]

Type hinting and import updates:

• Added from __future__ import annotations to several modules to enable postponed evaluation of type hints, improving type checking and forward reference handling. [1] [2] [3]
• Updated type hints in class and method signatures for better code clarity and static analysis.

Documentation structure and style:

• Removed the rmgdb API documentation and its references, streamlining the API documentation. [1] [2]
• Added a custom CSS file for the documentation, providing a more modern and visually appealing style for the ARC docs. [1] [2]
• Enabled the sphinx.ext.graphviz extension and configured Sphinx to use the new style and logo, further enhancing documentation presentation. [1] [2] [3]

These changes improve both the user and developer experience by making ARC's documentation more comprehensive, visually appealing, and easier to maintain.

[Copilot]

Pull request overview

This PR refreshes ARC’s Sphinx “web docs” with a reorganized user guide, updated examples aligned with current input keys, and doc-build cleanup (autodoc + theming), alongside a few small typing/docstring maintenance tweaks in the Python codebase.

Changes:

• Rewrote/reshaped core docs pages (index, installation, running, examples, advanced) and added a custom CSS layer for the RTD theme.
• Updated example YAML inputs to use current top-level keys (bac_type, job_types.rotors) instead of removed/obsolete keys.
• Reduced Sphinx/autodoc noise and modernized type-hinting in a few modules (__future__.annotations, docstring/type fixes).

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
examples/Stationary/TS_with_xyz/input.yml	Updates example input keys to current schema (bac_type, job_types.rotors).
examples/Stationary/bde/input.yml	Replaces deprecated use_bac with bac_type: null in BDE example.
docs/web_docs_audit.md	Adds an audit note capturing findings during docs rebuild.
docs/source/index.rst	Replaces landing page copy and reorganizes toctrees (User Guide / API / Project).
docs/source/installation.rst	Rewrites installation/config guidance; adds modern “quick install” and per-user override workflow.
docs/source/running.rst	Rewrites run modes (YAML/Python) and local/SSH/HPC execution guidance.
docs/source/examples.rst	Replaces legacy examples with compact, current YAML + API patterns.
docs/source/advanced.rst	Rewrites advanced usage reference (job types, levels, routing, pipe mode, troubleshooting, etc.).
docs/source/conf.py	Enables _static, adds custom.css, disables autodoc type hints, sets html logo.
docs/source/_static/custom.css	Adds custom styling on top of sphinx_rtd_theme.
docs/source/links.txt	Updates a link target for examplesGitHub.
docs/source/api/index.rst	Drops rmgdb from API toctree.
docs/source/api/rmgdb.rst	Removes the arc.rmgdb API stub page.
arc/species/species.py	Docstring wrap + fixes TSGuess.arc_reaction type annotation.
arc/species/converter.py	Adds from __future__ import annotations.
arc/scheduler.py	Adds from __future__ import annotations.
arc/plotter.py	Adds from __future__ import annotations; minor docstring formatting.
arc/job/trsh.py	Docstring formatting/clarity tweaks in troubleshooting helper.
arc/job/local.py	Docstring whitespace cleanup.
arc/common.py	Docstring bullet formatting cleanup.

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[calvinp0]

To view this webpage locally:

1. Build the docs

   conda run -n arc_env sphinx-build -E -b html -d docs/build/doctrees docs/source docs/build/html

2. Change directory to the html build

   cd ~/code/ARC/docs/build/html
   

3. Host website

   python -m http.server 8000
   

4. Open webpage at http://localhost:8000

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 60.55%. Comparing base (be5c1c4) to head (c5c7e7e).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #893      +/-   ##
==========================================
+ Coverage   60.51%   60.55%   +0.03%     
==========================================
  Files         103      103              
  Lines       31186    31189       +3     
  Branches     8128     8128              
==========================================
+ Hits        18873    18886      +13     
+ Misses       9952     9948       -4     
+ Partials     2361     2355       -6     

Flag	Coverage Δ
functionaltests	60.55% <ø> (+0.03%)	⬆️
unittests	60.55% <ø> (+0.03%)	⬆️

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