Skip to content

pipeio_registry_scan should support mod grouping hints

Observed: pipeio_registry_scan creates 1:1 rule→mod mappings (every Snakemake rule becomes its own mod). This is wrong for flows where multiple rules form a conceptual group (e.g., parse+clean = "parse" mod, preprocess+epochs+summary = "preprocess" mod).

During the preprocess_motion flow creation, the scanner generated 12 mods from 12 rules. Had to manually edit registry.yml to consolidate into 5 mods (detect, parse, kinematics, preprocess, plot).

Expected: Either: 1. Support a mods.yml or mods: section in config.yml that declares the grouping, which registry_scan respects 2. Or infer grouping from rules/*.smk files (rules in the same .smk = one mod) 3. Or at minimum, don't overwrite manually edited mod groupings on re-scan

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

0f7168f [DATALAD] Added subdataset
740ebbb [DATALAD] Recorded changes
9ca941d [DATALAD] Recorded changes

README:

type: readme

Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha