Publish documentation links and GitHub Pages

[mtap-research]

Summary

• replace the obsolete Chung Research Group Google Sites URL with the current official GitHub Pages website
• make the new Read the Docs deployment the primary README documentation link
• retain the GitHub Pages mirror as a secondary documentation link
• publish the modern PyData/Sphinx documentation into docs/ so GitHub Pages serves the same content
• remove stale uppercase generated pages and build-time doctrees that caused case-insensitive collisions
• trim unneeded source maps, TTF fallbacks, and generated Font Awesome JavaScript from the committed Pages bundle

Verified destinations

• Read the Docs: https://aim-adsorption.readthedocs.io/en/latest/
• GitHub Pages mirror: https://chung-research-group.github.io/AIM/
• Chung Research Group: https://chung-research-group.github.io/

Validation

• Read the Docs returns HTTP 200 and exposes the PyData theme, tutorials, and input/output guide
• all 14 generated GitHub Pages HTML files have valid local links and assets
• all root README relative links exist
• every external README link and badge returned HTTP 200 after redirects
• git diff --check
• python ci/check_repository.py
• warning-free Sphinx build of all 12 source pages

Summary by CodeRabbit

• Documentation
  • Refreshed the documentation site with a modern, responsive layout, improved navigation, search, theme switching, and readable tables and equations.
  • Added or restored guidance for installation, module workflows, input/output files, tutorials, development, examples, citation, and licensing.
  • Clarified supported file formats, metadata tags, pressure requirements, output files, reproducibility steps, and contribution checks.
  • Corrected terminology, formatting, image links, and mathematical presentation across module documentation.
  • Updated project, support, and documentation links.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: db99efc1-1796-4065-9054-ed2026f75012

📥 Commits

Reviewing files that changed from the base of the PR and between 8b5997f and 3c8ef86.

⛔ Files ignored due to path filters (6)

• docs/.doctrees/environment.pickle is excluded by !**/*.pickle
• docs/_sphinx_design_static/sphinx-design.min.css is excluded by !**/*.min.css
• docs/_static/sphinx-design.min.css is excluded by !**/*.min.css
• docs/_static/vendor/fontawesome/webfonts/fa-brands-400.woff2 is excluded by !**/*.woff2
• docs/_static/vendor/fontawesome/webfonts/fa-regular-400.woff2 is excluded by !**/*.woff2
• docs/_static/vendor/fontawesome/webfonts/fa-solid-900.woff2 is excluded by !**/*.woff2

📒 Files selected for processing (62)

• README.md
• docs/.buildinfo
• docs/.doctrees/AIM Modules.doctree
• docs/.doctrees/BreakLab.doctree
• docs/.doctrees/Citation.doctree
• docs/.doctrees/HeatFit.doctree
• docs/.doctrees/Input-Output Data Files.doctree
• docs/.doctrees/Installation.doctree
• docs/.doctrees/IsoFit.doctree
• docs/.doctrees/MixPred.doctree
• docs/.doctrees/Tutorials.doctree
• docs/.doctrees/index.doctree
• docs/AIM Modules.html
• docs/Citation.html
• docs/Input-Output Data Files.html
• docs/Installation.html
• docs/IsoFit.html
• docs/MixPred.html
• docs/Tutorials.html
• docs/_sources/AIM Modules.rst.txt
• docs/_sources/Citation.rst.txt
• docs/_sources/Installation.rst.txt
• docs/_sources/Tutorials.rst.txt
• docs/_sources/breaklab.rst.txt
• docs/_sources/citation.rst.txt
• docs/_sources/development.rst.txt
• docs/_sources/examples.rst.txt
• docs/_sources/heatfit.rst.txt
• docs/_sources/index.rst.txt
• docs/_sources/input-output.rst.txt
• docs/_sources/installation.rst.txt
• docs/_sources/isofit.rst.txt
• docs/_sources/mixpred.rst.txt
• docs/_sources/modules.rst.txt
• docs/_sources/tutorials.rst.txt
• docs/_sphinx_design_static/design-tabs.js
• docs/_static/aim.css
• docs/_static/design-tabs.js
• docs/_static/documentation_options.js
• docs/_static/pygments.css
• docs/_static/scripts/bootstrap.js
• docs/_static/scripts/bootstrap.js.LICENSE.txt
• docs/_static/scripts/pydata-sphinx-theme.js
• docs/_static/styles/pydata-sphinx-theme.css
• docs/_static/styles/theme.css
• docs/_static/webpack-macros.html
• docs/breaklab.html
• docs/citation.html
• docs/development.html
• docs/examples.html
• docs/genindex.html
• docs/heatfit.html
• docs/index.html
• docs/input-output.html
• docs/installation.html
• docs/isofit.html
• docs/mixpred.html
• docs/modules.html
• docs/objects.inv
• docs/search.html
• docs/searchindex.js
• docs/tutorials.html

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📝 Walkthrough

Walkthrough

AIM’s documentation is reorganized with new source pages, updated module and workflow content, a PyData Sphinx theme, custom styling and scripts, regenerated HTML output, and refreshed search/build metadata. README documentation links and project attribution are also updated.

Changes

Documentation refresh

Layer / File(s)	Summary
Documentation source and content updates README.md, docs/_sources/*	Adds installation, development, citation, examples, module workflow, and video tutorial guidance; revises input/output and module documentation; and corrects formatting, image paths, terminology, and equations.
Theme assets and interactive behavior docs/_static/*, docs/_sphinx_design_static/*, docs/_static/webpack-macros.html	Adds PyData Sphinx and Bootstrap assets, AIM-specific CSS, theme-aware syntax highlighting, synchronized tabs, navigation options, and asset-loading macros.
Regenerated documentation pages docs/*.html	Adds or regenerates documentation pages with the new responsive theme, navigation, rendered content, tables, formulas, tutorials, and footer structure.
Documentation metadata and indexes docs/.buildinfo, docs/objects.inv, docs/searchindex.js	Refreshes the build fingerprint, project inventory metadata, and search index for the updated documentation set.

Estimated code review effort: 4 (Complex) | ~45 minutes

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch agent/readme-link-refresh

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