<div align="center">
<img src="https://raw.githubusercontent.com/Lexi-BU/lexi/stable/images/lexi_logo.png" alt="LEXI Logo" width="200" height="131">
</div>
[](https://doi.org/10.5281/zenodo.14582916)
A python package for data analysis related to [LEXI](https://lexi-bu.github.io/).
# 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:
```bash
python3 -m venv lexi_venv
```
You can activate the virtual environment by running the following command:
#### on Linux/MacOS:
```bash
source lexi_venv/bin/activate
```
#### on Windows:
```bash
.\lexi_venv\Scripts\activate
```
You can deactivate the virtual environment by running the following command:
```bash
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:
```bash
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:
```bash
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:
```bash
pip install git+https://github.com/Lexi-BU/lexi@0.3.1
```
## Verifying the installation
You can verify that `lexi` was installed by running the following command:
```bash
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: qudsiramiz@gmail.com
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:
```bash
pip list
```
which should produce output similar to the following:
```bash
Package Version
--------------- -------
.....................
kiwisolver 1.4.5
lexi_xray 0.4.1
matplotlib 3.8.2
numpy 1.26.4
.....................
```
You can open a Python shell and import `lexi` by running the following command:
```bash
python
from lexi_xray import lexi as lexi
import lexi_xray
lexi_xray.__version__
```
which should produce output similar to the following:
```bash
'0.4.1'
```
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 Google Colab Notebook
1. 1. If you haven't already, download the example notebook from the following link:
[Concise
Tutorial](https://colab.research.google.com/drive/1Q0dmH7QrwRXZh8ZrzfOQbshBA-B86y6T?usp=sharing)
[Detailed Tutorial](https://colab.research.google.com/drive/1rVOE_INV3bO2O_s0K7u58zHxbNhawELt?usp=sharing)
2. Open the notebook in Google Colab by clicking on the link above.
3. The notebook will then guide you through the process of using `lexi` to analyze data from LEXI.
4. If you want to run the notebook on your local machine, you can download the notebook from the link
above and run it in a Jupyter Notebook environment.
5. If you encounter any issues, please report them to us by creating an issue on our GitHub
repository [here](https://github.com/Lexi-BU/lexi/issues).
## Citation
If you use `lexi` in your research, please cite the following paper:
```
@Software{Qudsi2025,
author = {Qudsi, Ramiz and Chitty, Zoe and Connor, Cadin and Walsh, Brian},
title = {Lexi-BU/lexi: v0.4.0},
doi = {10.5281/zenodo.14606885},
url = {https://doi.org/10.5281/zenodo.14606885},
version = {v0.4.0},
month = jan,
publisher = {Zenodo},
path=Lexi-BU-lexi-e01a2a4 },
year = {2025},
}
```
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"description": "<div align=\"center\">\n <img src=\"https://raw.githubusercontent.com/Lexi-BU/lexi/stable/images/lexi_logo.png\" alt=\"LEXI Logo\" width=\"200\" height=\"131\">\n</div>\n\n\n[](https://doi.org/10.5281/zenodo.14582916)\n\nA python package for data analysis related to [LEXI](https://lexi-bu.github.io/).\n\n# Installation Guide\n\nThe next section of this document will guide you through the installation process of `lexi`.\n\nThough it is not necessary, we strongly recommend that you install `lexi` in a virtual environment.\nThis will prevent any conflicts with other Python packages you may have installed.\n\nA virtual environment is a self-contained directory tree that contains a Python installation for a\nparticular version of Python, plus a number of additional packages. You can install packages into a\nvirtual environment without affecting the system's Python installation. This is especially useful when\nyou need to install packages that might conflict with other packages you have installed.\n\n## Creating a virtual environment\nThere are several ways to create a virtual environment. We recommend using `python3` to do so.\n\nFor this exercise, we will assume that you have a directory called `Documents/lexi` where you will\ninstall `lexi` and create your virtual environment. Please replace `Documents/lexi` with the actual\npath to the directory where you want to install `lexi` and create your virtual environment.\n\n- cd into `Documents/lexi`\n\n### Using python3\nYou can create a virtual environment called `lexi_venv` (or any other name you might like) using \n`python3` by running the following command:\n\n```bash\n python3 -m venv lexi_venv\n```\n\nYou can activate the virtual environment by running the following command:\n\n#### on Linux/MacOS:\n\n```bash\n source lexi_venv/bin/activate\n```\n\n#### on Windows:\n\n```bash\n .\\lexi_venv\\Scripts\\activate\n```\n\nYou can deactivate the virtual environment by running the following command:\n\n```bash\n deactivate\n```\n\n## Installing `lexi`\n\n### Installing from PyPI\nAfter you have created and activated your virtual environment, you can install `lexi` from PyPI by running the following command:\n\n```bash\n pip install lexi_xray\n```\n\n### Installing from source\nAfter you have created and activated your virtual environment, you can install `lexi` directly from\nGitHub by running the following command:\n\n```bash\n pip install git+https://github.com/Lexi-BU/lexi\n```\nNOTE: This will install the latest version of `lexi` from the main branch. 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You have successfully installed `lexi`.\n\n\n# Using LEXI Software\n\nNOTE: We will add more examples and tutorials in the future. For now, we will use a Jupyter Notebook\nto demonstrate how to use `lexi` to analyze data from LEXI.\n\n## Using the Example Google Colab Notebook\n1. 1. If you haven't already, download the example notebook from the following link:\n [Concise\n Tutorial](https://colab.research.google.com/drive/1Q0dmH7QrwRXZh8ZrzfOQbshBA-B86y6T?usp=sharing)\n\n [Detailed Tutorial](https://colab.research.google.com/drive/1rVOE_INV3bO2O_s0K7u58zHxbNhawELt?usp=sharing)\n2. Open the notebook in Google Colab by clicking on the link above.\n\n3. The notebook will then guide you through the process of using `lexi` to analyze data from LEXI.\n\n4. If you want to run the notebook on your local machine, you can download the notebook from the link\n above and run it in a Jupyter Notebook environment.\n\n5. 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