pipeio_docs_collect produces duplicate notebook HTMLs alongside pipeio_nb_publish¶
When both pipeio_nb_publish and pipeio_docs_collect are used, the docs/pipelines/.../notebooks/ directory ends up with duplicates:
- nb-ttl_characterization_removal.html (from nb_publish)
- ttl_characterization_removal.html (from docs_collect copying .build/)
The generated index.md lists both. Deleting the non-prefixed copies from docs and .build doesn't help — docs_collect regenerates them.
Expected: docs_collect should either skip notebooks that already have a nb_publish export, or the two tools should use a consistent naming convention.
Source context: pixecog¶
PixEcog (pixecog): Neuropixels and ECoG dataset and analysis
Recent commits:
8110794 Add report frontmatter, regenerate deliverables index (1 report + 1 presentation)
28b18fe Add deliverables to nav, update docs-structure, collect pipeline + questio docs
7a9c0b2 Add TTL artifact characterization report, update meeting note links
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
Related Notes¶
- issue-arash-20260409-135103-976167.md — Same tool (pipeio_docs_collect) producing incorrect output; companion bug report
- issue-arash-20260408-041929-434391.md — pipeio docs_collect index generation — current note reports index.md listing duplicate entries
- issue-arash-20260408-041909-523276.md — pipeio docs_collect index behavior; same index.md output area
- issue-arash-20260409-163158-458231.md — pipeio docs_collect output path/link generation issues — same docs_collect output correctness theme
- issue-arash-20260410-000908-908952.md — pipeio_nb_exec output naming convention unclear — directly related to the nb_publish vs docs_collect naming inconsistency