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Add ecosystem package documentation page#1064

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xushenbo wants to merge 2 commits into
theislab:mainfrom
xushenbo:drug-screening-ecosystem-docs
Open

Add ecosystem package documentation page#1064
xushenbo wants to merge 2 commits into
theislab:mainfrom
xushenbo:drug-screening-ecosystem-docs

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PR Checklist

  • This comment contains a description of changes (with reason)
  • Referenced issue is linked
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Description of changes

This PR adds a small ecosystem documentation page to describe specialized packages that build on ehrapy without expanding the core API.

The immediate motivation is reviewer feedback on a self-controlled cohort drug-screening workflow based on Foundational Model-aided Automatic High-throughput Drug Screening Using Self-controlled Cohort Study. Rather than adding that setup-specific workflow directly into ehrapy.tools, the workflow now lives in the separate ehrapy-drug-screening ecosystem package with its own implementation, tests, documentation, and tutorial notebooks.

The new docs page explains that the future ecosystem package is intended to cover:

  • exposure episode construction
  • self-controlled cohort drug-screening analyses
  • grouped screening across drug hierarchy levels
  • indication mapping
  • post-processing
  • optional LLM-assisted review

Technical details

This PR intentionally keeps ehrapy focused on foundational EHR analysis. It does not add the full drug-screening implementation to ehrapy-main; that work is hosted separately in a standalone ecosystem package generated from the scverse package template.

Main changes:

  • Adds docs/ecosystem.md
  • Links the ecosystem page from docs/index.md

Validation performed locally:

  • git diff --check

Docs build note:

  • The ehrapy-main docs build was not rerun after this docs-only change because the local ehrapy-main environment is missing sphinx_tabs. The ecosystem package itself was validated with pytest and a Sphinx -W docs build.

Additional context

This PR is a scoped documentation update that aligns with the reviewer recommendation: keep the specialized drug-screening workflow in a dedicated ecosystem package, and reference that ecosystem expansion from ehrapy documentation.

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