diff --git a/.github/workflows/run_test.yml b/.github/workflows/run_test.yml index abd9db7..518dcf1 100644 --- a/.github/workflows/run_test.yml +++ b/.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 diff --git a/docs/source/index.rst b/docs/source/index.rst index 8d50bab..5ad006d 100644 --- a/docs/source/index.rst +++ b/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 `_. -If you have any question, please send E-mail to :email:`Yuanyue Li ` +Thank you for using the MS Entropy package, you can download the code from `MS Entropy Github repository `_. +If you encounter any issues, queries or need support, don't hesitate to contact :email:`Yuanyue Li ` -You can find the documentation of this package at `Read the Docs `_. +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 `_. +Additionally, you may find practical examples in the `examples `_ folder on our Github repository. -You can also find some examples in the `examples `_ folder. .. toctree:: :maxdepth: 2 diff --git a/examples/example-search_mona-with_read_write_functions-low_memory_usage.py b/examples/example-search_mona-with_read_write_functions-low_memory_usage.py index e19da6d..7b3bdde 100644 --- a/examples/example-search_mona-with_read_write_functions-low_memory_usage.py +++ b/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'