lexi-xray 0.4.0

Data analysis tools for the Lexi project

A python package for data analysis related to LEXI.

Installation Guide

The next section of this document will guide you through the installation process of lexi.

Though it is not necessary, we strongly recommend that you install lexi in a virtual environment. This will prevent any conflicts with other Python packages you may have installed.

A virtual environment is a self-contained directory tree that contains a Python installation for a particular version of Python, plus a number of additional packages. You can install packages into a virtual environment without affecting the system's Python installation. This is especially useful when you need to install packages that might conflict with other packages you have installed.

Creating a virtual environment

There are several ways to create a virtual environment. We recommend using python3 to do so.

For this exercise, we will assume that you have a directory called Documents/lexi where you will install lexi and create your virtual environment. Please replace Documents/lexi with the actual path to the directory where you want to install lexi and create your virtual environment.

• cd into Documents/lexi

Using python3

You can create a virtual environment called lexi_venv (or any other name you might like) using python3 by running the following command:

    python3 -m venv lexi_venv

You can activate the virtual environment by running the following command:

on Linux/MacOS:

    source lexi_venv/bin/activate

on Windows:

    .\lexi_venv\Scripts\activate

You can deactivate the virtual environment by running the following command:

    deactivate

Installing lexi

Installing from PyPI

After you have created and activated your virtual environment, you can install lexi from PyPI by running the following command:

    pip install lexi_xray

Installing from source

After you have created and activated your virtual environment, you can install lexi directly from GitHub by running the following command:

    pip install git+https://github.com/Lexi-BU/lexi

NOTE: This will install the latest version of lexi from the main branch. If you want to install a specific version, please append the version number to the URL. For example, if you want to install version 0.3.1, you can run the following command:

    pip install git+https://github.com/Lexi-BU/lexi@0.3.1

Installing from a local copy

We don't recommend this, however if you must, here are the details.

After you have created and activated your virtual environment, you can install lexi from a local copy by following these steps:

NOTE: We will use version 0.3.4 as an example. Please replace 0.3.4 with the actual version number you want to install.

1. Download lexi-0.3.4.tar.gz directory from the following link: Download LEXI Software

2. Copy the lexi-0.3.4.tar.gz file into Documents/lexi (or any other directory where you want to install lexi in).

3. Activate your virtual environment using the instructions above.

4. Install lexi by running the following command (NOTE: replace lexi-0.3.4.tar.gz with the actual name of the file you downloaded):

       pip install lexi-0.3.4.tar.gz
   

This will install lexi and all its dependencies.

Verifying the installation

You can verify that lexi was installed by running the following command:

    pip show lexi_xray

which should produce output similar to the following:

    Name: lexi_xray
    Version: 0.0.1
    Summary: Main repository for all data analysis related to LEXI
    Home-page: 
    Author: qudsiramiz
    Author-email: [e-mail]
    License: GNU GPLv3
    Location: /home/cephadrius/Desktop/lexi_code_test_v2/lexi_test_v2/lib/python3.10/site-packages
    Requires: cdflib, matplotlib, pandas, pytest, toml
    Required-by: 

You can also verify that lexi was installed by running the following command:

    pip list

which should produce output similar to the following:

    Package         Version
    --------------- -------
    .....................
    kiwisolver      1.4.5
    lexi_xray         0.0.1
    matplotlib      3.8.2
    numpy           1.26.4
    .....................

You can open a Python shell and import lexi by running the following command:

    python
    from lexi_xray import lexi as lexi
    import lexi_xray
    lexi_xray.__version__

which should produce output similar to the following:

'0.0.1'

If that worked, congratulations! You have successfully installed lexi.

Using LEXI Software

NOTE: We will add more examples and tutorials in the future. For now, we will use a Jupyter Notebook to demonstrate how to use lexi to analyze data from LEXI.

Using the Example Jupyter Notebook

1. If you haven't already, download the example folder from the following link: Download LEXI Examples and extract it to a directory of your choice. We will refer to this directory as examples for the rest of this document.

2. Activate your virtual environment. If you haven't already created a virtual environment, please refer to the creating a virtual environment section for instructions on how to do so. Remember that you can activate your virtual environment by running the following command:

on Linux/MacOS:

    source lexi_venv/bin/activate

on Windows:

    .\lexi_venv\Scripts\activate

3. cd into the examples directory and

4. If you haven't already, install Jupyter Notebook by running the following command:

    pip install jupyter

5. Open the Jupyter Notebook by running the following command:

    jupyter notebook lexi_tutorial.ipynb

6. This will open a new tab in your web browser and will look like the image below:

7. You can now run the cells in the Jupyter Notebook to see how to use lexi to analyze data from LEXI.

Citation

If you use lexi in your research, please cite the following paper:

    @software{ramiz_qudsi_2025_14585868,
                author       = {Ramiz Qudsi and
                                Zoe Chitty and
                                Cadin Connor and
                                Brian Walsh},
                  title        = {Lexi-BU/lexi: v0.3.4},
                  month        = jan,
                  year         = 2025,
                  publisher    = {Zenodo},
                  version      = {v0.3.4},
                  doi          = {10.5281/zenodo.14585868},
                  url          = {https://doi.org/10.5281/zenodo.14585868},
                  swhid        = {swh:1:dir:0f71ede7ba2db5f1548c45f330b2c945af59794b
                                   ;origin=https://doi.org/10.5281/zenodo.14582915;vi
                                   sit=swh:1:snp:6552c7107029bb957e1e2592742d13109209
                                   1a11;anchor=swh:1:rel:5ca1c846400ca145a0d2599c9951
                                   04421046558a;path=Lexi-BU-lexi-74dd3c2
                                  },
}