doc: improve readme

Author: gautierdag

README.md

@@ -1,5 +1,7 @@
 # bibextract
 
+[![codecov](https://codecov.io/gh/gautierdag/bibextract/branch/main/graph/badge.svg?token=NWHDJ22L8I)](https://codecov.io/gh/gautierdag/bibextract) [![tests](https://github.com/gautierdag/bibextract/actions/workflows/test.yml/badge.svg)](https://github.com/gautierdag/bibextract/actions/workflows/bibextract.yml) [![image](https://img.shields.io/pypi/l/bibextract.svg)](https://pypi.python.org/pypi/bibextract) [![image](https://img.shields.io/pypi/pyversions/bibextract.svg)](https://pypi.python.org/pypi/bibextract) [![PyPI version](https://badge.fury.io/py/bibextract.svg)](https://badge.fury.io/py/bibextract)
+
 A Python package (with Rust backend) for extracting survey content and bibliography from arXiv papers.
 
 ## Features
@@ -13,34 +15,40 @@ A Python package (with Rust backend) for extracting survey content and bibliogra
 
 ## Installation
 
-### From PyPI (when published)
+### MCP server implementation
+
+```bash
+uv run bibextract_mcp.py
+```
+
+### From PyPI
 
 ```bash
-pip install bibextract
+uv add bibextract
 ```
 
 ### From Source
 
 1. Install Rust (if not already installed):
 
-```bash
-curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
-source ~/.cargo/env
-```
+    ```bash
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+    source ~/.cargo/env
+    ```
 
 2. Install maturin:
 
-```bash
-pip install maturin
-```
+    ```bash
+    pip install maturin
+    ```
 
 3. Clone and build:
 
-```bash
-git clone https://github.com/your-username/bibextract.git
-cd bibextract
-maturin develop
-```
+    ```bash
+    git clone https://github.com/gautier/bibextract.git
+    cd bibextract
+    maturin develop
+    ```
 
 ## Usage
 
@@ -74,290 +82,15 @@ cargo build --release
 ./target/release/bibextract --paper-ids 2104.08653 1912.02292 --output survey.tex
 ```
 
-## Example Output
-
-The package will generate:
-
-1. **Survey Text** (`survey_text`): LaTeX content with normalized sections:
-
-```latex
-\section{Related Work}
-
-Recent advances in machine learning have shown...
-\cite{author2021paper, smith2020method}
-
-\section{Background}
-
-The foundations of this work build upon...
-\cite{jones2019foundation}
-```
-
-2. **BibTeX Bibliography** (`bibtex`): Properly formatted citations:
-
-```bibtex
-@article{author2021paper,
-  title = {A Novel Approach to Machine Learning},
-  author = {Author, First and Author, Second},
-  journal = {Journal of ML},
-  year = {2021},
-}
-
-@inproceedings{smith2020method,
-  title = {Efficient Methods for Deep Learning},
-  author = {Smith, John},
-  booktitle = {Conference on AI},
-  year = {2020},
-}
-```
-
-## API Reference
-
-### `extract_survey(arxiv_ids)`
-
-Extract survey content from arXiv papers.
-
-**Parameters:**
-
-- `arxiv_ids` (list): List of arXiv paper IDs (e.g., `['2104.08653', '1912.02292']`)
-
-**Returns:**
-
-- `dict` with keys:
-  - `'survey_text'`: Raw LaTeX text with extracted sections and normalized citations
-  - `'bibtex'`: BibTeX bibliography entries for all cited works
-
-**Raises:**
-
-- `TypeError`: If `arxiv_ids` is not a list
-- `ValueError`: If `arxiv_ids` is empty or contains no valid IDs
-- `RuntimeError`: If there's an error processing the papers
-
 ## Development
 
 ### Running Tests
 
 ```bash
 cargo test
+pytest tests
 ```
 
-### Building Documentation
-
-```bash
-cargo doc --open
-```
-
-### Contributing
-
-1. Fork the repository
-2. Create a feature branch
-3. Make your changes
-4. Add tests if applicable
-5. Submit a pull request
-
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
-
-## Acknowledgments
-
-- Built with [PyO3](https://pyo3.rs/) for Python-Rust integration
-- Uses [reqwest](https://github.com/seanmonstar/reqwest) for HTTP requests
-- Bibliography verification via DBLP and arXiv APIs
-- **Parallel Processing**: Uses parallel verification for improved performance
-- **Multiple Paper Support**: Processes multiple papers and consolidates their bibliographies
-
-## Installation
-
-### Prerequisites
-
-- Rust (latest stable version)
-- Internet connection for downloading papers and verifying citations
-
-### Building from Source
-
-```bash
-git clone https://github.com/yourusername/bibextract.git
-cd bibextract
-cargo build --release
-```
-
-The binary will be available at `target/release/bibextract`.
-
-## Usage
-
-### Basic Usage
-
-Extract related work sections from a single arXiv paper:
-
-```bash
-bibextract --paper-ids 2104.08653
-```
-
-### Multiple Papers
-
-Process multiple papers at once:
-
-```bash
-bibextract --paper-ids 2104.08653 2203.15556 2307.09288
-```
-
-### Save to File
-
-Save the output to a LaTeX file:
-
-```bash
-bibextract --paper-ids 2104.08653 2203.15556 --output survey.tex
-```
-
-### Verbose Logging
-
-Enable detailed logging to see the processing steps:
-
-```bash
-bibextract --paper-ids 2104.08653 --verbose
-```
-
-### Command Line Options
-
-- `--paper-ids` or `-p`: List of arXiv paper IDs (e.g., 2104.08653)
-- `--output` or `-o`: Output file path (prints to stdout if not specified)
-- `--verbose` or `-v`: Enable verbose logging
-
-## How It Works
-
-### 1. Paper Download and Extraction
-
-The tool downloads LaTeX source files from arXiv and extracts them:
-
-- Supports both ZIP and TAR.GZ archives
-- Finds the main LaTeX file automatically
-- Processes `\input` and `\include` commands recursively
-
-### 2. Section Detection
-
-Identifies relevant sections based on common patterns:
-
-- "Related Work"
-- "Background"
-- "Literature Review"
-- "Prior Work"
-- "State of the Art"
-- And many more variants
-
-### 3. Bibliography Processing
-
-Parses `.bbl` files to extract bibliography entries:
-
-- Handles standard BibTeX formats
-- Extracts author, title, year, and other metadata
-- Supports both `\bibitem` and `\citeauthoryear` formats
-
-### 4. Citation Verification
-
-Verifies bibliography entries using external APIs:
-
-- **DBLP API**: For academic paper verification
-- **arXiv API**: For arXiv preprint verification
-- **Parallel Processing**: Verifies multiple entries simultaneously
-- **Smart Matching**: Uses title, author, and year for accurate matching
-
-### 5. Output Generation
-
-Produces clean LaTeX output:
-
-- Normalized citation keys
-- Consolidated bibliography
-- Ready-to-use LaTeX sections
-
-## Output Format
-
-The tool generates LaTeX output with:
-
-```latex
-\section{Related Work}
-...section content with normalized citations...
-
-\section{Background}
-...section content with normalized citations...
-
-% Consolidated bibliography
-Bibliography {
-  smith_machine_learning_2020: article {
-    author: "John Smith",
-    title: "Machine Learning Approaches",
-    year: "2020",
-    verified_source: "DBLP",
-  }
-  ...
-}
-```
-
-## Example
-
-```bash
-# Extract related work from a few machine learning papers
-bibextract --paper-ids 2104.08653 2203.15556 2307.09288 --output ml_survey.tex --verbose
-```
-
-This will:
-
-1. Download and extract LaTeX sources for each paper
-2. Parse bibliography files
-3. Verify citations using DBLP and arXiv APIs
-4. Extract related work sections
-5. Normalize citation keys
-6. Consolidate bibliographies
-7. Save the result to `ml_survey.tex`
-
-## Architecture
-
-The project is organized into several modules:
-
-- `latex::bibliography`: Bibliography parsing and management
-- `latex::citation`: Citation extraction and normalization
-- `latex::parser`: LaTeX file parsing and archive extraction
-- `latex::verification`: Bibliography verification using external APIs
-
-## Dependencies
-
-- `anyhow`: Error handling
-- `clap`: Command line argument parsing
-- `reqwest`: HTTP client for API requests
-- `regex`: Regular expression support
-- `rayon`: Parallel processing
-- `serde_json`: JSON parsing for API responses
-- `tempfile`: Temporary file management
-- `zip`: ZIP archive extraction
-- `tar` + `flate2`: TAR.GZ archive extraction
-
-## Logging
-
-The tool uses structured logging to show progress:
-
-```
-INFO Processing arXiv paper with ID: 2104.08653
-INFO Downloading source files from arXiv for paper: 2104.08653
-INFO Extracting ZIP archive
-INFO Verifying bibliography entries for paper 2104.08653
-INFO Verified entry: smith2020 (progress: 1/25)
-INFO Found 3 sections with bibliography entries
-INFO Output written to "survey.tex"
-```
-
-## Error Handling
-
-The tool handles various error conditions gracefully:
-
-- Invalid arXiv IDs
-- Missing or corrupted source files
-- Network failures during verification
-- Malformed LaTeX files
-- Missing bibliography files
-
-## Contributing
-
-Contributions are welcome! Please feel free to submit issues and pull requests.
-
-## License
-
-This project is licensed under the MIT License - see the LICENSE file for details.

bibextract_mcp.py

@@ -0,0 +1,31 @@
+# /// script
+# dependencies = ["fastmcp", "bibextract"]
+# ///
+
+from fastmcp import FastMCP
+
+mcp = FastMCP("Get arvix paper related work and bibliography")
+
+
+@mcp.tool(
+    name="arvix_survey", description="Get arvix paper related work and bibliography"
+)
+def arvix_survey(arvix_id: str) -> str:
+    """
+    Get arvix paper related work and bibliography.
+    Args:
+        arvix_id (str): The ID of the arXiv paper to process.
+    Returns:
+        str: related work and cited work bibliography
+    """
+    try:
+        from bibextract import extract_survey
+
+        result = extract_survey([arvix_id])
+        return f"Related work:\n{result['survey_text']}\n\nBibliography:\n{result['bibtex']}"
+    except Exception as e:
+        return f"Error processing arXiv paper {arvix_id}: {e}"
+
+
+if __name__ == "__main__":
+    mcp.run()