Installation & Getting Started

Prerequisites

  • Python 3.11 or later (3.13 recommended)

  • A conda or virtual environment is recommended to avoid dependency conflicts

Installing from Source

Clone the repository and install in development mode:

git clone -b dev https://github.com/hjibarram/3DCubeGen.git
cd 3DCubeGen
pip install -e .

Verify the installation by checking that the three CLI entry points are available:

3dcubegen --help      # LVM pipeline
pipemegara --help     # MEGARA pipeline
vpcubetools --help    # VirusP tools

Core Dependencies

The following packages are installed automatically by pip install:

Package

Purpose

astropy

FITS I/O, WCS transformations, coordinate handling

numpy

Array operations throughout the codebase

scipy

Spatial distance calculations, interpolation

matplotlib

Plotting utilities

pyyaml

YAML configuration file parsing

click / cloup

Command-line interface framework

tqdm

Progress bars during cube reconstruction

sdeconv

Richardson-Lucy deconvolution for map sharpening

Optional Dependencies

These are not installed automatically and are only needed for specific pipelines:

MEGARA pipeline – requires the numina framework and megaradrp (MEGARA Data Reduction Pipeline):

pip install numina megaradrp

Deconvolution – the scikit-image package provides additional deconvolution routines:

pip install scikit-image

Quick Verification

After installation, a quick way to confirm everything works is to generate the help text for each command:

# LVM commands
3dcubegen sincube --help
3dcubegen pipecube --help
3dcubegen sinmap --help
3dcubegen pipemap --help

# MEGARA commands
pipemegara rundrp --help
pipemegara runfulldrp --help

# VirusP commands
vpcubetools vpcube --help