Auto3D v3.0.0

What's New

Modern CLI

• Beautiful terminal output with Rich
• Typer-based subcommand structure: run, config, models, validate
• Progress bars and helpful error messages
• Shell completion support (bash, zsh, fish)

Improved Architecture

• Strategy patterns for isomer engines
• Cleaner separation of concerns
• Structured logging throughout workflow
• Full type hints and Pydantic validation

New Commands

auto3d run input.smi --k=5        # Generate conformers
auto3d config init                 # Create config template
auto3d config show config.yaml     # Display with syntax highlighting
auto3d models list                 # List available NNP models
auto3d models info AIMNET          # Show model details
auto3d validate input.smi          # Validate input files

Quality

• 523 tests passing
• mypy type checking
• ruff linting
• Comprehensive documentation

Breaking Changes

• Requires Python 3.10+
• CLI syntax changed to subcommand structure (legacy YAML mode still supported)

Installation

# Using uv (fastest)
uv pip install Auto3D

# Using pip
pip install Auto3D

# Using conda
conda install -c conda-forge auto3d

Full Changelog: v2.3.1...v3.0.0

v2.3.1 released

fix thermo calc naming

v2.3.0 is public

Generalize to any machine learning potential;
Fix the large number of conformers in some cases.

v2.2.7 is available

• Swap date and name in the folder name
• handle IDs with underscore
• remove unnecessary variables atom_list and num_atomsin https://github.com/isayevlab/Auto3D_pkg/blob/3e685283db73c89d1fb87f141042d6803564fe49/src/Auto3D/isomer_engine.py#L156

v2.1.0

support SDF input
Enumerate SDF using RDKit;
Enumerate SDF using Omega.

v2.0.1

• Replace OpenBabel with RDKit to be compatible with more platforms;
• Optimize a few details.