Plan to document the software using Material for MkDocs and publish with GitHub Actions

[yulewu]

We plan to document the UELer software using Material for MkDocs. The documentation will be published automatically using GitHub Actions, making it easy to keep the docs up to date with the latest changes. This approach will ensure that our documentation is structured, navigable, visually appealing, and always current.

Further updates, including the workflow setup and publishing instructions, will be provided in this issue.

Please share any suggestions or requirements you have for the documentation process.

[yulewu]

Update Summary: Material for MkDocs documentation site (#80) (commit 0b13d7a)

Created a full MkDocs Material documentation site for UELer, covering all user-facing and developer-facing content, with a GitHub Actions workflow for automatic publishing.

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Actions Taken

• Created mkdocs.yml:
  Configured Material for MkDocs with light/dark theme, teal/cyan palette, navigation tabs, search, code copy, and all required Markdown extensions. Nav structure: Home, Installation, Get Started, Tutorials (4 pages), FAQ, Developer Notes (7 pages).
• Created docs/ directory with all content pages:
  • index.md — Landing page with feature summary, Binder badge, quick-nav cards, and supported data formats.
  • installation.md — Step-by-step installation (micromamba/conda, clone, pip install, update, dev extras, MkDocs preview).
  • getting-started.md — First-run guide: open notebook, configure paths, expected folder structure.
  • tutorials/index.md — Tutorial index table.
  • tutorials/basic-usage.md — FOV navigation, channel selection, marker sets, contrast, overlays.
  • tutorials/user-interface.md — Four-panel layout, left/main/right/footer regions, all controls.
  • tutorials/map-mode.md — Enabling/disabling map mode, navigation, ROI capture, export.
  • tutorials/export.md — Full FOV, ROI, single-cell, and map-mode ROI export; marker set dropdown; scale bar.
  • faq.md — Common questions on installation, viewer behavior, ROI bugs, and export issues.
  • develop-notes/index.md — Developer notes index with topic table.
  • develop-notes/packaging.md — Package layout, shims, editable install.
  • develop-notes/viewer-runtime.md — FOV load cycle, downsampling, channel controls, VS Code fallback.
  • develop-notes/map-mode.md — Coordinate systems, tile rendering pipeline, plugin hooks.
  • develop-notes/export-pipeline.md — Job runner, rendering pipeline diagram, NaN sanitization.
  • develop-notes/roi-gallery.md — ROI record schema, gallery pagination, map-mode thumbnails.
  • develop-notes/heatmap.md — Heatmap plugin, meta-cluster registry, planned cell annotation workflow.
  • develop-notes/ome-tiff.md — Auto-detection, OMEFovWrapper, pyramid level selection.
• Created .github/workflows/docs.yml:
  GitHub Actions workflow that builds the MkDocs site on every push to main and deploys it to GitHub Pages using the official actions/deploy-pages action.
• Updated pyproject.toml:
  Added [project.optional-dependencies] docs = ["mkdocs-material>=9.5"] and updated the documentation URL to https://hartmannlab.github.io/UELer/.

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Files Changed

• mkdocs.yml — new MkDocs site configuration
• docs/index.md — home page
• docs/installation.md — installation guide
• docs/getting-started.md — quick start guide
• docs/faq.md — FAQ
• docs/tutorials/index.md — tutorial index
• docs/tutorials/basic-usage.md — basic usage tutorial
• docs/tutorials/user-interface.md — UI walkthrough
• docs/tutorials/map-mode.md — map mode tutorial
• docs/tutorials/export.md — batch export tutorial
• docs/develop-notes/index.md — developer notes index
• docs/develop-notes/packaging.md — packaging notes
• docs/develop-notes/viewer-runtime.md — viewer runtime notes
• docs/develop-notes/map-mode.md — map mode internals
• docs/develop-notes/export-pipeline.md — export pipeline notes
• docs/develop-notes/roi-gallery.md — ROI workflow notes
• docs/develop-notes/heatmap.md — heatmap & cell annotation notes
• docs/develop-notes/ome-tiff.md — OME-TIFF loading notes
• .github/workflows/docs.yml — GitHub Actions deploy workflow
• pyproject.toml — added docs optional dependency group; updated documentation URL

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Tests

pip install mkdocs-material
mkdocs build --strict

• ✅ Site builds without errors (verify locally before merging)