Update documents.

.github/workflows/run_test.yml

@@ -13,15 +13,19 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install pytest
           pip install -r requirements.txt
+          pip install -e .
+
       - name: Test with pytest
         run: |
           pytest

docs/source/index.rst

@@ -3,15 +3,22 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to MS Entropy's documentation!
-======================================
+Introduction to MS Entropy!
+===========================
 
-Welcome to use this package, you can download the code from `MS Entropy Github repository <https://github.com/YuanyueLi/MSEntropy>`_.
-If you have any question, please send E-mail to :email:`Yuanyue Li <[email protected]>`
+Thank you for using the MS Entropy package, you can download the code from `MS Entropy Github repository <https://github.com/YuanyueLi/MSEntropy>`_.
+If you encounter any issues, queries or need support, don't hesitate to contact :email:`Yuanyue Li <[email protected]>`
 
-You can find the documentation of this package at `Read the Docs <https://msentropy.readthedocs.io>`_.
+This package comprises the following modules:
+
+1.  **Classical entropy calculation functions:** These functions are ideal for calculating the classical spectral entropy and entropy similarity for a small set of spectrum pairs.
+
+3.  **Flash Entropy Search Algorithm Functions:** If your task involves searching spectra against a large spectral library, this algorithm will significantly improve the speed of the search process.
+
+
+For a comprehensive understanding of the package, refer to our documentation hosted on `Read the Docs <https://msentropy.readthedocs.io>`_.
+Additionally, you may find practical examples in the `examples <https://github.com/YuanyueLi/MSEntropy/tree/main/examples>`_ folder on our Github repository.
 
-You can also find some examples in the `examples <https://github.com/YuanyueLi/MSEntropy/tree/main/examples>`_ folder.
 
 .. toctree::
    :maxdepth: 2

examples/example-search_mona-with_read_write_functions-low_memory_usage.py

@@ -7,7 +7,7 @@
 import numpy as np
 import zipfile
 
-from ms_entropy.flash_entropy_search import FlashEntropySearch
+from ms_entropy import FlashEntropySearch
 
 
 url_mona = r'https://mona.fiehnlab.ucdavis.edu/rest/downloads/retrieve/03d5a22c-c1e1-4101-ac70-9a4eae437ef5'