Hoodini Colab API Reference

Python API for running Hoodini in Google Colab notebooks.

Version: '0.1.2'

Hoodini Colab provides an interactive widget interface for running Hoodini analysis directly in Google Colab. It handles installation, parameter configuration, and execution in a user-friendly way.

Usage:

from hoodini_colab import create_launcher
launcher = create_launcher()
display(launcher)

Launcher Widget

Interactive widget for running Hoodini in Google Colab notebooks.

widget

Hoodini Launcher widget - Interactive parameter configurator for Hoodini CLI.

HoodiniLauncher

Interactive Hoodini CLI launcher widget with Sidebar and Modes.

This widget provides an interactive interface for configuring and launching Hoodini genomic neighborhood analysis with various input modes:

• Single Input: Single protein ID or FASTA
• Input List: Multiple IDs or files
• Input Sheet: Tabular data with multiple columns

Attributes: command: The generated command line string. run_requested: Trigger for running the command. status_state: Current status (idle, installing, running, finished, error). status_message: Status message to display.

Methods:

• keep_alive()

  def keep_alive(interval_seconds: int = 30)

  Start a background heartbeat to keep Colab alive without blocking UI.

create_launcher()

def create_launcher() -> HoodiniLauncher

Create and configure a HoodiniLauncher widget with execution handler.

This function sets up the launcher widget and attaches the execution handler that manages installation checks and command execution.

Returns: HoodiniLauncher: Configured launcher widget ready to be displayed.

Example:

from hoodini_colab import create_launcher launcher = create_launcher() display(launcher)

Installation Utilities

Functions for installing and managing Hoodini in Colab environments.

utils

Utility functions for hoodini installation and package management.

check_launcher_packages()

def check_launcher_packages() -> bool

Check if launcher dependencies are installed.

Returns: bool: True if all dependencies are installed, False otherwise.

install_launcher_packages()

def install_launcher_packages() -> bool

Install launcher dependencies.

Returns: bool: True if installation succeeded, False otherwise.

check_hoodini_installed()

def check_hoodini_installed() -> bool

Check if hoodini is available in PATH or via pixi.

Returns: bool: True if hoodini is installed, False otherwise.

run_cmd()

def run_cmd(cmd: str, shell: bool = True) -> int

Run command and stream output.

Args: cmd: Command to run. shell: Whether to run command in shell.

Returns: int: Return code of the command.

install_hoodini()

def install_hoodini(command: str = '', launcher = None) -> bool

Install pixi and hoodini environment.

Args: command: The hoodini command to be executed, used to determine which databases to download. launcher: Optional HoodiniLauncher widget to update status.

Returns: bool: True if installation succeeded, False otherwise.