scope-qc 0.9.3

SCOPE: Chemically-aware workflow automation for molecules and molecular crystals. Core package

scope

scope is the core SCOPE package: a chemically aware workflow-automation toolkit for molecules and molecular crystals.

It provides the main object model and workflow engine used across the SCOPE project:

• chemistry-aware classes for molecules, ligands, atoms, bonds, and cells
• workflow orchestration for preparing, submitting, and tracking computations
• parsing and registration of Gaussian and Quantum Espresso results
• environment, path, and queue management for HPC execution
• a CLI for configuring projects, creating systems, and running tasks

Optional add-ons such as scope-azo and scope-sco build on top of this core package.

Documentation

• Repository and source code: https://github.com/QTC-IQAC/Scope
• Preprint: https://doi.org/10.26434/chemrxiv.15001415/v1
• Tutorials: https://github.com/QTC-IQAC/Scope_Tutorials

Installation

create and activate conda environment and install pip:

conda create --name scope python=3.12 
conda activate scope
conda install pip

# `cell2mol` is an external dependency and must currently be installed separately from its source repository.
pip install git+https://github.com/lcmd-epfl/cell2mol.git

Option 1: from PyPI

pip install scope-qc    # Core Modules

Option 2: from repository

git clone https://github.com/QTC-IQAC/Scope.git
cd Scope
pip install -e core

Option 3: from TestPyPi:

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ scope-qc

Dependencies

The core package depends on:

• numpy
• networkx < 3.3
• scipy
• rdkit
• ipykernel
• plotly
• nbformat
• jupyter
• matplotlib
• platformdirs

External prerequisite:

• cell2mol, installed separately from https://github.com/lcmd-epfl/cell2mol.git

Python requirement:

• Python 3.12

Command Line Interface

The core package provides the scope command with subcommands for configuring SCOPE environments, creating systems, and running tasks.

For help:

scope -h

Usage

SCOPE is typically used through the command line to:

• configure environments: scope config
• create systems: scope create_single and scope create_many
• execute workflows: scope run

System objects are saved in binary files that can then be inspected later in notebooks or other interactive sessions.

License

See the repository-level LICENSE file for licensing information.