Quickstart Instructions

This guide provides a quick overview of how to get started with peakipy. Follow these instructions to set up your environment, install the necessary components, and execute basic commands.

Inputs

To work with peakipy, you will need the following input files: 1. Peak List: A formatted file that describes the peaks of interest. Refer to the instructions for formatting guidance. 2. NMRPipe Frequency Domain Dataset: This can be a 2D or pseudo 3D dataset for processing.

Main Commands

peakipy provides four main commands to facilitate peak analysis:

peakipy read
Converts your peak list into a .csv file while selecting clusters of peaks.
Usage:
```
peakipy read [PEAK_LIST_FILE] [NMR_DATA_FILE] [OUTPUT_FORMAT] [OPTIONS]
```
peakipy edit
Interactively checks and adjusts fit parameters (i.e., clusters and mask radii) if the initial clustering is not satisfactory.
Usage:
```
peakipy edit [PEAK_LIST_FILE] [NMR_DATA_FILE] [OPTIONS]
```
peakipy fit
Fits clusters of peaks using the .csv peak list generated (or edited) by the read (or edit) command(s).
Usage:
```
peakipy fit [PEAK_LIST_FILE] [NMR_DATA_FILE] [OUTPUT_FILE] [OPTIONS]
```
peakipy check
Checks individual fits or groups of fits and generates plots.
Usage:
```
peakipy check [OUTPUT_FILE] [NMR_DATA_FILE] [OPTIONS]
```

For more details on how to run these scripts, check the instructions. You can also use the --help flag for further guidance on running each command (e.g., peakipy read --help).

How to Install `peakipy`

Using `uv` (recommended)

Either of the following approaches should work:

Clone the peakipy repository:

git clone https://github.com/j-brady/peakipy.git
cd peakipy
uv sync

The uv sync command will automatically create a virtual environment for you in .venv which you can then activate with the usual source .venv/bin/activate.

Install from PyPI:

uv venv --python 3.12
source .venv/bin/activate
uv pip install peakipy

Using pip

Install peakipy using pip:
```
pip install peakipy
```

Example Bash Script

Below is an example of an installation script and a basic use case:

#!/bin/bash
# Create a virtual environment and activate it
uv venv --python 3.12
source .venv/bin/activate

# Install peakipy
uv pip install peakipy

# Process some data using peakipy
peakipy read peaks.a2 test.ft2 a2 --y-radius-ppm 0.213 --show
peakipy edit peaks.csv test.ft2  # Adjust fitting parameters
peakipy fit peaks.csv test.ft2 fits.csv --vclist vclist --max-cluster-size 15
peakipy check fits.csv test.ft2 --clusters 1 --clusters 2 --clusters 3 --colors purple green --show --outname tmp.pdf

Run this script by sourcing the file:

source file_containing_commands

Note: It is recommended to use a virtual environment:

uv venv --python 3.12
source .venv/bin/activate
# or for csh:
source .venv/bin/activate.csh

Requirements

Latest

The latest version (2.1.2) of peakipy requires Python 3.11 or above (see pyproject.toml for details).

Legacy Version (0.2.0)

peakipy version 0.2.0, which runs on Python 3.8, can be installed as follows:

git clone --branch v0.2 https://github.com/j-brady/peakipy.git
cd peakipy
poetry install

Or:

pip install peakipy==0.2.0