bugfix: update ipynb

README.md

@@ -1,8 +1,19 @@
 # bdi-viz
 [![Tests](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/build.yml/badge.svg)](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/build.yml)
 [![Lint](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/lint.yml/badge.svg)](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/lint.yml)
+[![Documentation Status](https://readthedocs.org/projects/bdi-viz/badge/?version=latest)](https://bdi-viz.readthedocs.io/en/latest/)
 
-## Introduction
+
+## Contents
+
+- [1. Introduction](#sparkle-1-introduction)
+- [2. Installation](#package-2-installation)
+- [3. Quick Start](#rocket-3-quick-start)
+- [4. Documentation](#page_facing_up-4-documentation)
+  - [4.1 Read the Docs](#41-read-the-docs)
+  - [4.2 Demo Video](#42-demo-video)
+
+## :sparkle: 1. Introduction
 
 BDIViz is a powerful, interactive tool designed as an extension to [BDIKit](https://github.com/VIDA-NYU/bdi-kit) to assist biomedical researchers and domain experts in performing schema matching tasks. Built to address the challenges of matching complex biomedical datasets, BDIViz leverages a visual approach to streamline the process and enhance both speed and accuracy.
 
@@ -16,6 +27,44 @@ Key features of BDIViz include:
 
 BDIViz is designed to be integrated with Python notebooks, providing a flexible and easy-to-use tool for domain-specific schema matching in biomedical research and beyond.
 
-## Demo
+## :package: 2. Installation
+
+To use ``BDI-Viz``, install it using pip:
+
+```bash
+pip install bdi-viz
+```
+
+
+## :rocket: 3. Quick Start
+``BDI-Viz 1.0`` is built leveraging [Panel](https://panel.holoviz.org/). The application is designed to provide a user-friendly interface on jupyter notebooks. Where users can explore the schema matching recommandations, interact with the result, and pass them to the next step of the data integration process.
+
+```python
+import pandas as pd
+from bdiviz import BDISchemaMatchingHeatMap
+
+# Load the data
+source_df = pd.read_csv('data/source.csv')
+target_df = pd.read_csv('data/target.csv')
+
+# Render the BDI-Viz Heatmap
+heatmap_manager = BDISchemaMatchingHeatMap(
+    source=source_df,
+    target=target_df,
+    top_k=20,
+)
+heatmap_manager.plot_heatmap()
+```
+
+The following interface will be displayed in the jupyter notebook:
+![BDIViz Demo](docs/bdiviz-demo.png)
+
+
+## :page_facing_up: 4. Documentation
+
+### 4.1 Read the Docs
+For more information, please refer to the [documentation](https://bdi-viz.readthedocs.io/en/latest/).
+
+### 4.2 Demo Video
+[BDIViz Demo](https://drive.google.com/file/d/1eAbDicO0oXIbbVg56m3H8xdNDDsBGBLI/view?usp=drive_link)
 
-[BDIViz Demo](https://drive.google.com/file/d/1eAbDicO0oXIbbVg56m3H8xdNDDsBGBLI/view?usp=drive_link)

bdiviz/api.py

@@ -65,7 +65,7 @@ def __init__(
     ) -> None:
         """
         BDISchemaMatchingHeatMap is a class for generating and visualizing schema matching heatmaps between a source DataFrame and a target DataFrame or predefined dataset.
-        
+
         :param source: The source DataFrame containing the columns to be matched.
         :type source: pd.DataFrame
         :param target: The target DataFrame or a string identifier for a predefined dataset (default is "gdc").

docs/source/conf.py

@@ -3,54 +3,54 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath("../../"))
 
 # -- Project information
 
-project = 'BDI-Viz'
-copyright = '2024, NYU VIDA Lab'
-author = 'Eden Wu'
+project = "BDI-Viz"
+copyright = "2024, NYU VIDA Lab"
+author = "Eden Wu"
 
-release = '0.1'
-version = '0.1.0'
+release = "0.1"
+version = "0.1.0"
 
 # -- General configuration
 
 extensions = [
-    'sphinx.ext.duration',
-    'sphinx.ext.doctest',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.intersphinx',
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
     "nbsphinx",
 ]
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3/', None),
-    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
 }
-intersphinx_disabled_domains = ['std']
+intersphinx_disabled_domains = ["std"]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # -- Options for HTML output
 
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # -- Options for EPUB output
-epub_show_urls = 'footnote'
+epub_show_urls = "footnote"
 
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 
-autoclass_content = 'both'
+autoclass_content = "both"
 
 add_module_names = False
 
 autodoc_mock_imports = [
     "bdi-kit",
-    "bdikit", 
-    "bokeh", 
-    "datamart_profiler", 
+    "bdikit",
+    "bokeh",
+    "datamart_profiler",
     "sklearn",
     "pandas",
     "numpy",

docs/source/index.rst

@@ -15,12 +15,14 @@ how to :ref:`installation` the project.
 
    This project is under active development.
 
-.. disclaimer::
+
+Disclaimer
+----------
 
    This project is part of the ASKEM ARPA-H initiative and is funded by DARPA. It is a property of the NYU VIDA Lab.
 
 Contents
---------
+-----------
 
 .. toctree::
 

docs/source/installation.rst

@@ -1,5 +1,5 @@
 Installation
-=====
+==============
 
 
 To use ``BDI-Viz``, install it using pip: