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Rebuild the documentation on Zensical - #214

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lorenzocerrone merged 15 commits into
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fix/docs_refactor
Jul 30, 2026
Merged

Rebuild the documentation on Zensical#214
lorenzocerrone merged 15 commits into
mainfrom
fix/docs_refactor

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@lorenzocerrone

@lorenzocerrone lorenzocerrone commented Jul 29, 2026

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Full refactor of the documentation site.

Summary

  • Rebuild the docs on Zensical instead of MkDocs + Material, and move every executed code block out of the Markdown into standalone scripts under docs/snippets/, included via pymdownx.snippets and run at build time. The five tutorial notebooks become Markdown pages, and CI builds with --strict (a plain build exits 0 even when a code block raised).
  • Apply the commissioned design system: the mark-G logo set, a contrast-audited teal palette and full theme layer in docs/stylesheets/ngio.css, and six explanatory figures authored as inline SVG so they follow the light/dark toggle.
  • Rewrite the copy to the design system's content conventions: sentence case, British spelling, second person, openers that lead with what the reader does. Adds a landing page, a 14-term glossary, "Next steps" footers and API cross-references.
  • Add CODE_OF_CONDUCT.md and CITATION.cff, and move CONTRIBUTING.md to the repository root, single-sourced into the docs.
  • Fix defects found along the way: silently dropped Markdown extensions, invalid YAML front matter on six pages, wrong site_url, tables rendering as literal |---|, and per-page snippet state under Zensical's fresh per-page markdown-exec sessions.

Checklist before merging

  • I added an appropriate entry to CHANGELOG.md

@lorenzocerrone lorenzocerrone changed the title Fix/docs refactor Rebuild the documentation on Zensical Jul 29, 2026
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Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

lorenzocerrone and others added 9 commits July 30, 2026 08:35
ngio is an acronym: n(ext) g(eneration file format) IO, after the OME-NGFF
specification the library reads and writes. The site title expands it again,
while the descriptive "a Python library for OME-Zarr bioimage analysis" moves
to the site description and the landing-page, README and llms.txt openers.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The rewritten opener led with second-person imperatives ("Open an image, reach
for the resolution level you need"), a register that belongs to task pages
rather than to a project's front door — zarr, napari, anndata, spatialdata and
scikit-image all open with "X is a Y that does Z". Restore that form, tightened
to drop the "mission is to streamline" and "comprehensive support" framing.

Also drop the sentence explaining where the name comes from (the title already
carries the acronym) and the changelog entry for the title, which reverted to
what main already had.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
@lorenzocerrone
lorenzocerrone merged commit 7bb4aed into main Jul 30, 2026
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@lorenzocerrone
lorenzocerrone deleted the fix/docs_refactor branch July 30, 2026 11:57
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