bio-learn/biolearn

enhancement: surface required CpG sites in docs for models without a coefficients file

Open

#200 opened on Mar 25, 2026

View on GitHub
 (0 comments) (0 reactions) (0 assignees)Python (35 forks)auto 404
good first issue

Repository metrics

Stars
 (87 stars)
PR merge metrics
 (PR metrics pending)

Description

Models like HurdleInflammAge don't have a model.file entry but do expose their required sites via methylation_sites(). The doc generator currently shows "N/A" for these models.

A future improvement could instantiate the model (or extract sites statically) to populate the coefficients column. This would require reworking how doc/generate.py accesses model info since it currently only reads static definition dicts, not instantiated objects.

Ref: https://github.com/bio-learn/biolearn/pull/197#pullrequestreview-2710853685

Contributor guide

Research direction
Examine the current doc generator in doc/generate.py to understand how it accesses model info. Identify how to instantiate models or statically extract methylation sites for models lacking a coefficients file. Implement code to call methylation sites() on the model object and populate the coefficients column in the documentation.
Tech stack
python
Domain
documentation
Issue type
Documentation
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Half day
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Python
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
50