paper-pipeline

name	paper-pipeline
description	End-to-end paper workflow: resolve a paper reference, acquire the canonical raw bundle, discover and clone repository. Generate reading notes if user requests ("笔记", "reading notes", "--with-notes").
argument-hint	<paper_reference> [--skip-repo] [--with-notes] [--output <note_path>]
allowed-tools	Skill, Read, Bash

Paper Pipeline

End-to-end paper workflow. Calls other paper-* skills sequentially.

Storage

Canonical store: ~/docs/papers/{folder_slug}/

Example: ~/docs/papers/iclr2017-gcn-kipf/

Pipeline

Default: resolve → acquire → repo

Notes: Only if user requests ("笔记", "reading notes", "--with-notes")

Execution Steps

Parse user arguments first:

Flag	Effect
--skip-repo	Skip Step 3
--with-notes	Run Step 4 after Step 3
--output <path>	Pass to paper-reading-notes
--refresh	Re-run completed steps

Step 1: paper-resolve

Call: Skill(skill="paper-resolve", args="<paper_reference>")

Output: ~/docs/papers/{folder_slug}/metadata.yaml

Skip if: metadata.yaml already exists and --refresh not set.

Step 2: paper-acquire

Call: Skill(skill="paper-acquire", args="{folder_slug}")

Output: ~/docs/papers/{folder_slug}/paper/paper.pdf, paper.md

Skip if: paper.md already exists and --refresh not set.

Step 3: paper-repo

Call: Skill(skill="paper-repo", args="{folder_slug}")

Output: ~/docs/papers/{folder_slug}/repo/ (if found)

Skip if: --skip-repo or repo already exists and --refresh not set.

Step 4: paper-reading-notes

Call: Skill(skill="paper-reading-notes", args="{folder_slug} --output {path}")

Output: reading-note.md

Only runs if user requests notes.

Example

User: "SpaMI spatial multi-omics --with-notes"

Execute:

1. Skill(skill="paper-resolve", args="SpaMI spatial multi-omics")
2. Skill(skill="paper-acquire", args="preprint2024-spami-pei")
3. Skill(skill="paper-repo", args="preprint2024-spami-pei")
4. Skill(skill="paper-reading-notes", args="preprint2024-spami-pei")