docs: Add MkDocs Material documentation site#62
Merged
ericchansen merged 3 commits intomasterfrom Mar 19, 2026
Merged
Conversation
- Add mkdocs.yml with Material theme, mermaid, code highlighting - Add GitHub Actions workflow for auto-deploy to gh-pages - Create docs: index, getting-started, tutorial, API, references - Integrate existing performance.md into nav - Slim README to focus on motivation, quick start, and docs link - Add docs extra and Documentation URL to pyproject.toml Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
There was a problem hiding this comment.
Pull request overview
Adds a MkDocs Material documentation site for Q2MM and wires up GitHub Pages deployment, while slimming the top-level README to emphasize motivation and quick start and moving long-form guidance into docs/.
Changes:
- Introduces a Material-for-MkDocs site (
mkdocs.yml+ newdocs/*.mdpages) and a GitHub Actions workflow to deploy togh-pages. - Adds a
docsoptional dependency extra and a Documentation URL inpyproject.toml. - Refactors
README.mdto link out to the new docs site and reduces in-repo long-form content.
Reviewed changes
Copilot reviewed 9 out of 10 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
pyproject.toml |
Adds docs extra (mkdocs-material) and a Documentation project URL. |
mkdocs.yml |
Configures Material theme, nav, and markdown extensions (incl. Mermaid fences). |
docs/index.md |
New docs landing page with architecture diagram and “What’s New”. |
docs/getting-started.md |
Installation/backends overview + basic usage and dev commands. |
docs/tutorial.md |
End-to-end tutorial workflow (QM → Seminario → optimization → export). |
docs/api.md |
API overview page describing key models/optimizers/backends/parsers. |
docs/references.md |
References page with grouped citations and summaries. |
README.md |
Slimmed README with docs link and condensed quick-start/backends table. |
.github/workflows/docs.yml |
Deploys docs to GitHub Pages on push to master. |
.gitignore |
Ignores generated site/ output. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
You can also share your feedback on Copilot code review. Take the survey.
Correct 9 issues caught by Gemini 3 Pro and Opus 4.6 code reviews: - Fix backend import paths (openmm_engine -> openmm, tinker_engine -> tinker) - Fix TinkerEngine param name (tinker_path -> tinker_dir) - Fix OptimizationResult attributes (.x/.score -> .final_params/.final_score) - Fix GaussLog attributes (.energies/.geometries -> .structures/.evals/.evecs) - Fix ObjectiveFunction param name (reference_data -> reference) and add missing molecules arg - Add required data_idx to ReferenceData.add_frequency() example - Fix atom_types type (list[int] -> list[str]) and bond_tolerance default (1.2 -> 1.3) - Note estimate_force_constants accepts single molecule or list Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
- Make README Quick Start self-contained and copy-pasteable - Add matplotlib install note in tutorial convergence plot - Add README.md for examples/sn2-test/ (scripts, data, execution order) - Add README.md for examples/rh-enamide/ (system description, files, quick start) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Add a full MkDocs Material documentation site with GitHub Pages auto-deployment. Slims the README to focus on motivation and quick start, moving detailed content to the docs site.
Pages
index.md)Changes
mkdocs.yml-- Material theme with mermaid, code highlighting, admonitions.github/workflows/docs.yml-- Auto-deploy to gh-pages on push to masterpyproject.toml-- Addeddocsextra (mkdocs-material), Documentation URLREADME.md-- Slimmed from 158 to 63 lines; keeps motivation, quick start, backends table, docs link.gitignore-- Addedsite/Testing
mkdocs build --strictpasses with no warningsruff check+ruff format --checkcleanpytest -q: 153 passed, 8 skipped, 1 xfailedSite will be live at https://ericchansen.github.io/q2mm/ after merge.