Docs + Schema Fixes#129

Merged

aditigopalan merged 89 commits intomainfrom

Jan 20, 2026

Commits on Jan 6, 2026

Commits on Jan 7, 2026

Clinical: Rename to Manifests, add conditional requirements, clean enum representation
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Clinical: Use 'Required IF' for conditionals, add Common Attributes section, show patterns
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Fix pattern extraction and improve conditional requirement clarity
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Fix pattern extraction for all attributes and improve conditional requirement clarity
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Improve conditional requirement clarity and ensure patterns are captured for all attributes
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Further improve conditional requirement clarity
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Remove Pattern column, show patterns in Type column instead
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Escape pipe characters in patterns to prevent markdown table breakage
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Add home page with architecture overview from README
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Add image path to Sphinx configuration
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Escape backticks in patterns to fix markdown table rendering
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Use HTML code tags instead of backticks for patterns in markdown tables
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Implement Option B: self-contained module pages with all inherited attributes
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Fix documentation issues: remove duplicate Enums, add identifier page, add getting started to menu
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Refactor generate_class_table to use write_attribute_row for consistent pattern display
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Add HTAN Centers RFC statement and Curator link to index page, add index to sidebar menu
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Remove Data Model Architecture section and image, clean up Contents/Reference sections
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Restructure docs: remove Classes/Enums headings, create landing pages and separate level pages for multi-level modules
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Add README overview to scRNA-seq landing page
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Fix level page links by using toctree instead of :doc: directive
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Fix SpatialOmics schema name check and MultiplexMicroscopy links
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Fix level page links to use markdown links instead of toctree
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Fix level pages: add Core File attributes and use toctree for sidebar menu
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Add level pages to sidebar menu in index.rst
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Use MyST toctree syntax for nested level pages in sidebar
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Remove unused docs/index.md file
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Remove Modules section and Reference caption from index.rst
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Add Modules section back to index.rst
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Adjust toctree maxdepth values in index.rst
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Fix DigitalPathology module, add submission guidance to level pages, remove duplicates
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Fix enum anchor links to use full enum name (tumorgradeenum instead of tumorgrade)
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Remove explicit anchor syntax from enum headings and fix enum links to match Sphinx auto-generated anchors
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Fix enum links to use simple anchor format matching MyST auto-generated anchors
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Add enum sections to level pages (WES, scRNA-seq, etc.) and ensure enum links work correctly
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Remove identifiers page entirely
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Add custom CSS to increase documentation content width
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Fix content width: use RTD theme option and improved CSS selectors
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Add CSV export functionality for all modules and levels
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Fix CSV generation: include all attributes from all classes for Clinical module
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Commits on Jan 15, 2026