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Add resolve_templates.py that loads YAML templates, walks the extends: chain, and produces resolved dicts with own, inherited, and merged columns. Includes comprehensive test suite (20 tests) covering all inheritance patterns and merge semantics. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add Jinja2 snippet and build script that resolves all templates, classifies them into organism/technology/experiment/sample groups, and injects the rendered section into site/index.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Replace dead adoc template loop with build_template_pages.py - Add index template section auto-generation step - Fix tool-support.adoc -> TOOLS.adoc filename mismatch - Add pip install pyyaml jinja2 to CI - Enable submodule checkout in CI for sdrf-templates access Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Sort columns by requirement: required > recommended > optional - Replace flat table with expandable detail rows (click to expand) - Fix documentation rendering for mixed paragraph/list blocks - Merge index template section into one unified table (remove redundant Organism/Technology card sections) - Remove broken metadata-guidelines section from index - Fix Jinja2 dict.values() conflict by renaming to allowed_values Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…adata into feat/yaml-driven-template-docs
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📝 WalkthroughWalkthroughA comprehensive refactoring consolidates the SDRF documentation build system from multiple shell scripts into Python-driven tooling, introduces a new sample-metadata template layer between base and technology/sample layers, replaces per-template README files with a centralized Templates Guide, and adds an interactive client-side SDRF Builder UI for configuring SDRF metadata. Changes
Sequence DiagramsequenceDiagram
participant User
participant Browser as Browser (quickstart.html)
participant Builder as SDRF Builder (sdrf-builder.js)
participant DataFile as sdrf-builder-data.json
participant TemplateResolved as Resolved Templates
User->>Browser: Load quickstart.html
Browser->>Builder: Load sdrf-builder.js
Builder->>DataFile: fetch('sdrf-builder-data.json')
DataFile-->>Builder: templates, combination_rules, terms
Builder->>TemplateResolved: resolveColumns(selections)
TemplateResolved-->>Builder: ordered column list
Builder->>Browser: Render technology options
User->>Builder: Select technology
Builder->>TemplateResolved: resolveColumns(+technology)
TemplateResolved-->>Builder: updated columns
Builder->>Browser: Render organism options
User->>Builder: Select organism
Builder->>TemplateResolved: resolveColumns(+organism)
TemplateResolved-->>Builder: resolved columns with organism overrides
Builder->>Browser: Live preview table
User->>Builder: Download TSV / Open in Editor
Builder->>Browser: Generate/export SDRF
Estimated code review effort🎯 4 (Complex) | ⏱️ ~60 minutes Possibly related PRs
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✨ Finishing Touches🧪 Generate unit tests (beta)
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Summary by CodeRabbit
New Features
Breaking Changes
Documentation
Bug Fixes