lllin000_PaperForge/docs/INSTALLATION.md

Installation Guide

For LLM Agents

If you're an LLM Agent helping set up this literature workflow, welcome. You'll help your user install the pipeline and configure their Zotero/Obsidian integration.

Tell the user: Paste this to your agent to auto-configure:

Install and configure the literature workflow by following the instructions here:
https://raw.githubusercontent.com/YOUR-USERNAME/YOUR-REPO/main/docs/INSTALLATION.md

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Step 0: Ask User About Their Setup

Ask the user these questions to determine configuration:

1. Do you have Zotero installed?

   • If yes: Where is your Zotero data directory? (usually C:\Users\<User>\Zotero on Windows or ~/Zotero on macOS/Linux)
   • If no: Install Zotero first from https://www.zotero.org/download/ and install the Better BibTeX plugin

2. Is your Zotero storage directory in a different location?

   • Default: same as data directory
   • If different path: ask for the full path to the storage folder

3. Do you have Obsidian installed?

   • If yes: Where is your vault located? (e.g., D:\L\Med\Research)
   • If no: Ask them to install Obsidian and create a vault first

4. Do you have a PaddleOCR API key?

   • If yes: ask for the API key
   • If no: Direct them to https://paddleocr.baidu.com/ to apply for one

5. Do you have Python 3.10+ installed?

   • If yes: proceed
   • If no: Ask them to install Python 3.10+ from https://python.org

Configuration summary:

• Zotero path: {zotero_path}
• Zotero storage path: {storage_path} (may equal zotero_path)
• Obsidian vault path: {vault_path}
• PaddleOCR API key: {ocr_api_key}

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Step 1: Install Dependencies

Run in the terminal (spawn a subagent if needed):

pip install requests pymupdf pillow pytest

If using Poetry:

poetry add requests pymupdf pillow pytest

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Step 2: Create Directory Structure

Create the following directories in the Obsidian vault:

mkdir -p "{vault_path}/99_System/PaperForge/ocr"
mkdir -p "{vault_path}/99_System/PaperForge/worker/scripts"
mkdir -p "{vault_path}/99_System/Zotero"
mkdir -p "{vault_path}/03_Resources/Literature"
mkdir -p "{vault_path}/00_Inbox"

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Step 3: Configure Zotero Integration

Option A: Junction/Symlink (Recommended)

Windows (admin terminal):

mklink /J "{vault_path}\99_System\Zotero" "{zotero_path}"

macOS/Linux:

ln -s "{zotero_path}" "{vault_path}/99_System/Zotero"

Option B: Config file (if symlink not possible)

Create {vault_path}/.env:

ZOTERO_DATA_DIR={zotero_path}
ZOTERO_STORAGE_DIR={storage_path}

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Step 4: Configure OCR Pipeline

Create {vault_path}/.env (or append if exists):

PADDLEOCR_API_KEY={ocr_api_key}
PADDLEOCR_API_URL=https://paddleocr.baidu.com/api/v1/ocr

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Step 5: Install Workflow Scripts

Copy the following files from the repository to your vault:

# Copy scripts
cp -r scripts/* "{vault_path}/99_System/PaperForge/worker/scripts/"

# Copy templates
cp -r templates/* "{vault_path}/99_System/Template/"

# Copy AGENTS.md
cp AGENTS.md "{vault_path}/AGENTS.md"

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Step 6: Verify Setup

Run validation:

cd "{vault_path}"
python 99_System/PaperForge/worker/scripts/validate_setup.py

This checks:

• Zotero SQLite accessible
• OCR directory writable
• Required Python packages installed
• AGENTS.md exists
• Directory structure correct

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Step 7: Configure AGENTS.md

Edit {vault_path}/AGENTS.md:

1. Update the vault path references
2. Set your preferred output language (default: Simplified Chinese)
3. Configure any custom collection paths

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For Humans

Quick Start

1. Prerequisites:

   • Python 3.10+
   • Zotero + Better BibTeX plugin
   • Obsidian
   • PaddleOCR API key

2. Run the installer:

   python setup.py
   

   This interactive script will ask you the same questions as above and configure everything automatically.

3. Verify:

   python 99_System/PaperForge/worker/scripts/validate_setup.py
   

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Troubleshooting

Zotero not found

• Ensure Zotero is installed
• Check the data directory path (Edit → Preferences → Advanced → Files and Folders)

Permission denied on Windows

• Run terminal as Administrator for junction creation
• Or use Option B (config file) instead

Better BibTeX not installed

• In Zotero: Tools → Plugins → Install plugin from file
• Download from https://github.com/retorquere/zotero-better-bibtex/releases

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Next Steps

After installation:

1. Index your library: Run the index-refresh worker to create formal notes for existing papers
2. Queue papers for analysis: Use the Base system to mark papers for deep reading
3. Run OCR: The OCR worker processes queued papers automatically
4. Start deep reading: Use /LD-deep <zotero_key> to generate structured reading notes

Read the Workflow Guide for detailed usage instructions.