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Documentation site (MkDocs, GitHub Pages) with a JupyterLite demo - #57

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amjjbonvin merged 4 commits into
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50-docs-site
Nov 6, 2026
Merged

amjjbonvin merged 4 commits into
mainfrom
50-docs-site

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@amjjbonvin amjjbonvin commented Nov 6, 2026 •

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What does this PR do and why?

Adds a documentation site, https://www.bonvinlab.org/disvis, built with MkDocs Material and deployed to GitHub Pages, as for PowerFit and WHISCY.

  • Pages: home, installation, manual, example, performance, contributing, CLI reference, and "Try it in your browser". They include sections of README.md, INSTALLATION.md, CONTRIBUTING.md and test-cases/README.md (between <!-- --8<-- [start:x] --> markers, invisible on GitHub and PyPI), so nothing is duplicated.
  • New text: a recommended workflow and the web service (form and scanning modes, taken from the portal's help page and submit form).
  • The CLI reference is generated from the disvis arguments (mkdocs-rich-argparse); the example page links the reports of the CPU reference results (Write an HTML report with a Mol* view (--no-report to turn it off) #49).
  • A JupyterLite notebook runs the PRE5-PUP2 test case in the browser (quick scan, ~30 s) and shows the report with the Mol* view. The WebAssembly wheel is built from the source with cibuildwheel, as in pypi-publish.yml, since the 3.0.0 wheel on PyPI has no report.
  • docs extra, docs/Makefile (make -C docs, make -C docs serve) and .github/workflows/pages.yml (builds on PRs, deploys from main).
  • README: link to the site; the links to aidecl.yaml and CHANGELOG.md are now absolute (they were broken on PyPI). CONTRIBUTING.md explains how to build the site.

How was this tested?

  • make -C docs from a clean state: wheel, mkdocs build --strict, JupyterLite.
  • Pages and an example report checked in headless Chrome over HTTP.
  • WebAssembly wheel: the unit tests pass in Pyodide, and a 9.72° run gives output byte-identical to cpu/coarse.
  • Notebook: all cells run in headless Chrome, and checked by hand in a browser.
  • Manually checked a local version of the manual in a web browser

Not tested: the Pages workflow on GitHub (this PR runs its build job), and the deployment.

AI assistance

Written with Claude Code; checked as above.

Checklist

  • Tests cover the new and/or changed code
  • Documentation updated if needed (README.md, INSTALLATION.md)
  • Reference results in test-cases/*/example-results/ updated if the output changes (output unchanged)

Related issues

Closes #50

Notes for reviewers

  • GitHub Pages must be enabled for the repository (Settings → Pages → Source: GitHub Actions) before the first deployment.
  • jupyterlite-pyodide-kernel==0.8.7 and cibuildwheel==4.3.5 are pinned together: the Pyodide ABI of the wheel (2026_0) must match that of the JupyterLite kernel. PowerFit pins only the build side.
  • docs/test-cases is a symlink to test-cases/ (as WHISCY links example/), so the site can serve the example reports.

🤖 Generated with Claude Code

amjjbonvin and others added 2 commits November 6, 2026 21:42
- mkdocs.yml, docs/: MkDocs Material site, as for PowerFit. The pages
  include sections of README.md, INSTALLATION.md, CONTRIBUTING.md and
  test-cases/README.md (--8<-- markers), so nothing is duplicated.
- Manual with a recommended workflow and the web service; CLI reference
  generated from the arguments; the reports of the CPU reference results.
- JupyterLite notebook that runs DisVis in the browser with a WebAssembly
  wheel built from the source, and shows the report.
- docs extra, docs/Makefile and .github/workflows/pages.yml (deploys from
  main).
- README: link to the site; absolute links to aidecl.yaml and CHANGELOG.md.

Closes #50

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
amjjbonvin and others added 2 commits November 6, 2026 21:47
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@amjjbonvin
amjjbonvin marked this pull request as ready for review November 6, 2026 22:01
@amjjbonvin
amjjbonvin requested a review from a team as a code owner November 6, 2026 22:01
@amjjbonvin amjjbonvin self-assigned this Nov 6, 2026
@amjjbonvin
amjjbonvin merged commit d81081a into main Nov 6, 2026
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@amjjbonvin
amjjbonvin deleted the 50-docs-site branch November 6, 2026 22:01
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Documentation site (docs/, MkDocs, JupyterLite demo)

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