update README and pyproject.toml

README.md

@@ -1,33 +1,61 @@
-# PPI-net-builder v0.1.0
-Protein-Protein Interaction (PPI) network construction and analysis using STRING-db (https://string-db.org/) in Python.
 
+# PPI-net-builder
+![PyPI version](https://img.shields.io/pypi/v/ppi-net-builder)
+![Python version](https://img.shields.io/badge/python-3.9%2B-blue)
+![License](https://img.shields.io/pypi/l/ppi-net-builder)
+
+**PPI-net-builder** is a Python package for constructing and analyzing protein-protein interaction (PPI) networks using the [STRING-db](https://string-db.org/) database.
+
+## Features
+- Construct PPI networks from a list of genes.
+- Extract high-modality subnetworks.
+- Perform enrichment analysis on the main network or its subnetworks.
+- Save enrichment plots for visualization.
 
 ## Installation
+Install the package using pip:
+
 ```bash
 pip install ppi-net-builder
 ```
 
 ## Usage
+Here is an example demonstrating how to use **PPI-net-builder**:
+
 ```python
 from ppi_net_builder import NetworkBuilder
 
+# List of genes to construct the network
 genes = ["p53", "BRCA1", "cdk2", "Q99835"]
-annot_file_name = "./annotation.csv"  # this will be created later
+
+# Specify the annotation file name (this will be created later)
+annot_file_name = "./annotation.csv"
+
+# Initialize the NetworkBuilder
 nb = NetworkBuilder(genes,
                     annot_file_name=annot_file_name,
                     add_color_nodes=10)
 
-# construct a ppi network, and find high-modality subnetworks
+# Construct a PPI network and find high-modality subnetworks
 nb.construct_network()
 nb.extract_subnets()
 print(nb.subnets)
 
-# do enrichment analysis on the main network or subnets
+# Perform enrichment analysis on the main network or subnetworks
 enrich_df = nb.get_enrichment_table()
 print(enrich_df.head())
 
-
+# Save enrichment analysis plots
 nb.save_enrichment_plot(img_file_name="enrichment.png")
-
 ```
 
+## Requirements
+- Python 3.9 or higher
+- Dependencies are automatically installed with the package.
+
+## Contributing
+Contributions are welcome! Feel free to submit issues or pull requests to improve the package.
+
+## License
+This project is licensed under the MIT License. See the LICENSE file for details.
+

pyproject.toml

@@ -42,8 +42,6 @@ push = true
 "pyproject.toml" = [
     'current_version = "{version}"',
 ]
-"README.md" = [
-    "{version}",
-    "{pep440_version}",
-]
-
+"ppi_net_builder/__init__.py" = [
+    '^__version__ = "{version}"$',
+]