Skip to content

pipeio_dag_export SVG: dot binary permission/PATH issues after install

After installing graphviz in the rag env, pipeio_dag_export(output_format="svg") failed with [Errno 13] Permission denied: 'dot' until the MCP server was restarted. The MCP server caches its PATH at startup and doesn't see newly installed binaries.

Additionally, the same tool hit 'FlowEntry' object has no attribute 'pipe' on the mermaid format (ontology migration leftover).

Both were fixed during the session, but the MCP server restart requirement for new binaries should be documented or handled gracefully.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

6b295b2 Update badlabel audit note: full pipeline comparison (85 new vs 7 legacy vs 71 TTL), zarr fix confirmed, 97.2% TTL catch rate
a532476 Fix zarr write bug in feature.py: include coordinate variables in chunk encoding
9cb9de5 Update badlabel audit result note with pipeline run findings: LNR useless after lowpass, zarr v3 write bug

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