pkg-mgmt

name	pkg-mgmt
description	Python package and environment management using uv and mamba. Use when installing packages, creating virtual environments, setting up new projects, or managing dependencies. NOT for general Python coding questions.

Python Environment Skill (Comp Chem & AI Edition)

Default to uv for speed/ML; use mamba for heavy C++/Fortran binaries (e.g., OpenMM).

uv — Fast Project Management (Primary)

Best for: New projects, PyTorch/JAX, RDKit, CI/CD.

uv is an extremely fast Python package installer and resolver written in Rust.

Installation

# macOS/Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# Or with Homebrew
brew install uv

Modern Workflow (Replaces pip/venv)

# Initialize project
uv init my-project && cd my-project

# (Optional) Pin Python version — uv downloads it automatically if missing
uv python pin 3.11

# Add dependencies (updates pyproject.toml & uv.lock)
uv add rdkit pandas torch
uv add --dev pytest ruff

# Sync environment (guarantees reproducibility)
uv sync

# Run commands in the environment
uv run python train_model.py
uv run pytest

The "Quick Experiment"

Run a script with dependencies ephemerally (no permanent env created):

uv run --with rdkit --with matplotlib molecular_vis.py

Legacy Workflow (pip-style)

# Create a virtual environment
uv venv
uv venv --python 3.11  # specific version

# Activate
source .venv/bin/activate

# Install packages
uv pip install rdkit scikit-learn pandas
uv pip install -r requirements.txt
uv pip install -e .

mamba — Complex Binaries (Secondary)

Best for: OpenMM, AmberTools, legacy projects, or strict system library requirements.

mamba is a fast, drop-in replacement for conda.

Installation

# Install miniforge (includes mamba)
# macOS ARM
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh"
bash Miniforge3-MacOSX-arm64.sh

# macOS Intel
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh"
bash Miniforge3-MacOSX-x86_64.sh

# Linux
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
bash Miniforge3-Linux-x86_64.sh

Reproducible Workflow

Always use environment.yml with conda-forge:

# environment.yml
name: md-sim
channels:
  - conda-forge
dependencies:
  - python=3.11
  - openmm
  - ambertools
  - rdkit
  - numpy
  - pandas
  - pip  # Allow pip for pure python packages if needed

# Create from file
mamba env create -f environment.yml

# Update (use --prune to remove deleted deps)
mamba env update -f environment.yml --prune

# Export environment
mamba env export --no-builds > environment.yml

Quick Commands

# Create environment
mamba create -n myenv python=3.11

# Activate/deactivate
mamba activate myenv
mamba deactivate

# Install packages
mamba install rdkit numpy pandas

Decision Matrix: Chemist Edition

Scenario	Tool	Reasoning
General ML / PyTorch	uv	100x faster, handles wheels perfectly
Cheminformatics (RDKit)	uv	RDKit PyPI wheels are now stable
MD Sims (OpenMM/Amber)	mamba	Complex CUDA/C++ bindings are fragile on PyPI
Publishing/Sharing	uv	pyproject.toml is the modern standard (PEP 621)
Quick Scripts	uv	uv run --with enables single-file reproducibility
Legacy Projects	mamba	If it already uses Conda, stick with it

The Hybrid Approach

Need mamba binaries (e.g., OpenMM) but want uv speed for everything else? Create the env with mamba, then use uv pip inside it:

mamba create -n hybrid-env openmm python=3.11 -c conda-forge
mamba activate hybrid-env
uv pip install torch rdkit scikit-learn  # Installs into the active Conda env

Best Practices

1. Lockfiles are Mandatory

# uv does this automatically (uv.lock)
uv lock

# For mamba, export without build strings for portability
mamba env export --no-builds > environment.yml

2. pyproject.toml is Truth

Stop using requirements.txt. Define deps in pyproject.toml:

[project]
name = "my-project"
version = "0.1.0"
dependencies = [
    "rdkit",
    "numpy>=1.24",
    "pandas>=2.0",
]

[project.optional-dependencies]
dev = ["pytest", "ruff"]

3. Strict Channels for Mamba

Avoid ABI conflicts by strictly prioritizing conda-forge:

conda config --add channels conda-forge
conda config --set channel_priority strict

4. Never Install to System Python

# Bad
pip install rdkit

# Good
uv venv && source .venv/bin/activate && uv pip install rdkit

CI/CD Pipeline

# GitHub Actions example
- uses: astral-sh/setup-uv@v4
- run: uv sync
- run: uv run pytest