[parashardhapola]

Add the tool logo to the README and use shared Nygen logos, favicons, styles and navigation assets throughout the documentation. Pin the MyST version and book theme, label the landing page Overview, and add a link to the documentation hub.

Reviewed existing generated output and verified the deployed shared assets. Fresh documentation builds should pass before merging.

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PR Summary by Qodo

Apply shared Nygen branding across CyteType documentation

📝 Documentation ✨ Enhancement ⚙️ Configuration changes 🕐 20-40 Minutes

AI Description

• Add CyteType and Nygen branding to the README, documentation site, and API reference.
• Link generated pages to shared brand assets and add a documentation-hub link.
• Pin MyST and the book theme to stabilize branded documentation builds.

Diagram

graph TD
  A["Shared brand assets"] --> C["MyST config"] --> B["MyST build"] --> D["Discovery links"] --> R["Asset relinker"] --> P["Published docs"]
  A --> S["Sphinx API"] --> B

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High-Level Assessment

The following are alternative approaches to this PR:

1. Maintain a branded book-theme fork

• ➕ Could replace generated-JavaScript rewriting with theme-level asset links.
• ➖ Adds a theme fork and an ongoing synchronization burden.

2. Keep build-local asset copies

• ➕ Avoids post-build asset rewriting and dependence on the shared asset host.
• ➖ Duplicates branding assets and can let documentation sites drift apart.

Recommendation: The shared-asset approach avoids duplicating branding or maintaining a theme fork. Its generated-output rewriting depends on the pinned theme structure, so a fresh MyST and Sphinx build should be verified before merging.

Files changed (6) +90 / -5

Enhancement (1) +75 / -0

build_docs.pyLink generated documentation to shared brand assets +75/-0

Link generated documentation to shared brand assets

• Injects the shared documentation script into MyST pages and rewrites generated HTML, JSON, and theme JavaScript to reference shared assets. Rehashes affected JavaScript filenames, updates references, and removes copied brand files.

docs/build_docs.py

Documentation (1) +1 / -2

README.mdAdd the CyteType logo to the README heading +1/-2

Add the CyteType logo to the README heading

• Places the shared CyteType SVG beside the README title.

README.md

Other (4) +14 / -3

myst.ymlConfigure branded MyST theme and navigation +8/-1

Configure branded MyST theme and navigation

• Pins the book-theme archive, labels the landing page Overview, and adds shared logos, favicon, and stylesheet. Adds a navbar link to the Nygen documentation hub.

docs/source/myst.yml

conf.pyBrand the Sphinx API reference +4/-0

Brand the Sphinx API reference

• Configures the API reference to use shared Nygen CSS, the CyteType logo and favicon, and logo text.

docs/source/reference/api/conf.py

pyproject.tomlPin the MyST documentation dependency +1/-1

Pin the MyST documentation dependency

• Changes the docs dependency from a minimum MyST version to exactly 1.11.0 for reproducible theme output.

pyproject.toml

uv.lockSynchronize the MyST dependency constraint +1/-1

Synchronize the MyST dependency constraint

• Records the exact MyST 1.11.0 requirement in the docs dependency group.

uv.lock