purrito-catgt-wrapper 0.1.0

A Python wrapper for the CatGt command-line tool

purrito

A Python wrapper for CatGt, providing a human-readable interface to generate command-line arguments for the CatGt tool.

Overview

CatGt is a command-line tool for preprocessing SpikeGLX data from Neuropixels probes. This wrapper simplifies the process of creating CatGt commands by allowing users to specify options in Python.

Installation

pip install purrito-catgt-wrapper

Import it in Python as:

from purrito import CatGt

For development:

pip install -e .

Usage

Basic Example

from purrito import CatGt

# Create a CatGt instance with basic parameters
catgt = CatGt(
    basepath="/path/to/data",
    run="g0",
    gate=0,
    trigger=0
)

# Check the command that will be executed
catgt.dry_run()

# Output: CatGt -dir=/path/to/data -run=g0 -g=0 -t=0


# Run catgt
catgt.run()
# Generate the command line string

Advanced Example with Options

from purrito import CatGt

# Create a CatGt instance with preprocessing options
catgt = CatGt(
    basepath="/data/neuropixels",
    run="g0",
    gate=0,
    trigger=0,
    ap=True,           # Process AP band
    lf=True,           # Process LF band
    prb=0,             # Probe index
    prb_fld=True,         # Probe folder
    dest="/data/processed",  # Output destination
)

cmd = catgt.build_command()
print(cmd)

Using with subprocess

import subprocess
from purrito import CatGt

catgt = CatGt(
    basepath="/data/test",
    run="g0",
    gate=0,
    ap=True
)

# Get command as list for subprocess
args = catgt.get_command_args(catgt_path="/usr/local/bin/CatGt")

# Run the command
# subprocess.run(args)

Features

• Intuitive Python API: Specify options using Python arguments
• Flexible Options: Support for boolean flags, string values, numeric values, and lists
• Native CatGt Flags: Uses CatGt's underscore-based option names such as prb_fld
• Path Handling: Automatically converts relative paths to absolute paths
• Command Generation: Generate command strings for direct use or subprocess execution

API Reference

CatGt Class

CatGt(basepath, run=None, gate=None, trigger=None, catgt_path="CatGt", **options)

Parameters:

• basepath (str): Base directory path containing the SpikeGLX data
• run (str, optional): Run name (e.g., "g0", "g0_t0"). If omitted, it is inferred from basepath
• gate (int, optional): Gate index
• trigger (int, optional): Trigger index
• catgt_path (str, optional): Path to the CatGt executable. Defaults to CatGt
• **options: Additional CatGt options as keyword arguments

Methods:

• build_command(catgt_path="CatGt"): Build the complete command line string
• get_command_args(catgt_path="CatGt"): Get command and arguments as a list for subprocess

Testing

Run tests using unittest:

python -m unittest discover tests

Or with pytest (if installed):

pytest tests/

Releasing to PyPI

This package is automatically published to PyPI when a new GitHub release is created. To create a new release:

1. Update the version number in:

   • purrito/__init__.py

2. Create a new GitHub release:

   • Go to the repository's Releases page
   • Click "Draft a new release"
   • Create a new tag (e.g., v0.1.1)
   • Fill in the release title and description
   • Click "Publish release"

3. The GitHub Actions workflow will automatically:

   • Build the package
   • Run quality checks
   • Publish to PyPI

PyPI Setup (One-time)

Before the first release, you need to configure PyPI trusted publishing:

1. Go to PyPI and create an account if you don't have one
2. Create the purrito-catgt-wrapper project on PyPI (or wait for the first upload)
3. Go to your project's settings on PyPI
4. Under "Publishing", add a new "trusted publisher"
5. Configure it with:
   • Owner: eliezyer
   • Repository: purrito
   • Workflow: publish-to-pypi.yml
   • Environment: (leave empty)

This allows GitHub Actions to publish directly to PyPI without needing API tokens.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Developed in Rajasethupathy Lab