Pixi Package Manager for Scientific Python

pixi is a package manager that unifies the conda and PyPI ecosystems for reproducible scientific Python development. Use it to manage scientific dependencies, create isolated environments, and build reproducible workflows via pyproject.toml integration.

Official Documentation: https://pixi.sh GitHub: https://github.com/prefix-dev/pixi

Quick Reference Card

Installation & Setup

# Install pixi (macOS/Linux)
curl -fsSL https://pixi.sh/install.sh | bash

# Install pixi (Windows)
irm -useb https://pixi.sh/install.ps1 | iex

# Initialize new project with pyproject.toml
pixi init --format pyproject

# Import from an existing environment.yml
pixi init --format pyproject --import environment.yml

Essential Commands

# Add dependencies
pixi add numpy scipy pandas              # conda packages
pixi add --pypi pytest-cov               # PyPI-only packages
pixi add --feature dev pytest ruff       # dev environment

# Install all dependencies
pixi install

# Run commands in environment
pixi run python script.py
pixi run pytest

# Shell with environment activated
pixi shell

# Add tasks
pixi task add test "pytest tests/"
pixi task add docs "sphinx-build docs/ docs/_build"

# Run tasks
pixi run test
pixi run docs

# Update dependencies
pixi update numpy                         # update specific
pixi update                              # update all

# List packages
pixi list
pixi tree numpy                          # show dependency tree

# Global tools (replaces pipx / condax for CLI utilities)
pixi global install ruff                  # install a CLI tool globally
pixi global list                          # list globally installed tools

# Run a tool in a temporary throwaway environment (no project needed)
pixi exec ruff check .                    # run ruff without installing it
pixi exec --spec python=3.12 python -V    # one-off env with a pinned spec

# Print activation for use in scripts / CI without a subshell
pixi shell-hook                           # emit activation commands

Core Concepts

Pixi uses the [tool.pixi.workspace] table (formerly project; still a deprecated alias). For pixi.toml vs pyproject.toml, pyproject integration, and pixi-vs-uv guidance, see [references/manifest-and-tooling.md](references/manifest-and-tooling.md).

1. Unified Package Management (conda + PyPI)

Conda-forge and PyPI packages resolve in one graph:

[project]
name = "my-science-project"
dependencies = [
    "numpy>=1.24",      # from conda-forge (optimized builds)
    "pandas>=2.0",      # from conda-forge
]

[tool.pixi.pypi-dependencies]
my-custom-pkg = ">=1.0"        # PyPI-only package

2. Multi-Platform Lockfiles

Commit pixi.lock (covers linux-64, osx-64/arm64, win-64) so collaborators and CI resolve identical versions.

3. Feature-Based Environments

Compose environments from features without duplicating dependencies:

[tool.pixi.feature.test.dependencies]
pytest = ">=7.0"
pytest-cov = ">=4.0"

[tool.pixi.feature.gpu.dependencies]
pytorch-cuda = "11.8.*"

[tool.pixi.environments]
test = ["test"]
gpu = ["gpu"]
gpu-test = ["gpu", "test"]  # combines features

4. Task Automation

Define reusable commands as tasks:

[tool.pixi.tasks]
test = "pytest tests/ -v"
format = "ruff format src/ tests/"
lint = "ruff check src/ tests/"
docs = "sphinx-build docs/ docs/_build"
analyse = { cmd = "python scripts/analyze.py", depends-on = ["test"] }

5. Global Tools and One-Off Execution

Not every tool belongs in a project environment — install persistent CLI tools, run throwaway one-offs, or emit a subshell-free activation script for CI using the global / exec / shell-hook commands in the Quick Reference Card above.

Quick Start

Minimal Example: Data Analysis Project

# Create new project
mkdir climate-analysis && cd climate-analysis
pixi init --format pyproject

# Add scientific stack
pixi add python=3.11 numpy pandas matplotlib xarray

# Add development tools
pixi add --feature dev pytest ipython ruff

# Create analysis script
cat > analyze.py << 'EOF'
import pandas as pd
import matplotlib.pyplot as plt

# Your analysis code
data = pd.read_csv("data.csv")
data.plot()
plt.savefig("output.png")
EOF

# Run in pixi environment
pixi run python analyze.py

# Verify the environment and lockfile
pixi list                 # confirm packages installed
ls pixi.lock              # confirm lockfile was generated

# Or activate shell
pixi shell
python analyze.py

Deeper References

• [references/manifest-and-tooling.md](references/manifest-and-tooling.md) — pixi.toml vs pyproject.toml, the workspace terminology, pyproject integration, and pixi-vs-uv selection.
• [references/patterns.md](references/patterns.md) — migrating existing projects, multi-environment workflows, library development, conda + PyPI strategy, reproducible research, task pipelines.
• assets/ — ready-to-use templates: pyproject-pixi-example.toml, pyproject-multi-env.toml, and a SHA-pinned github-actions-pixi.yml CI workflow.

Troubleshooting

Quick fixes for the most common failures (full guide in [references/common-issues.md](references/common-issues.md)):

• pixi add fails with "package not found" → it may be PyPI-only; retry with

pixi add --pypi <pkg> (or check the conda name with pixi search <pkg>), then run pixi list to confirm it installed.

• Solver reports a conflict → inspect with pixi tree <pkg>, relax pins

(numpy>=1.24,<2 instead of ==) or isolate the environment with its own solve-group, then re-run pixi install and confirm it resolves cleanly.

• Lockfile didn't generate / is stale → run pixi install to regenerate

pixi.lock, then verify with ls pixi.lock; after a git merge conflict, take one side and re-run pixi install.

• Works on one OS, fails on another → guard OS-specific deps under

[tool.pixi.target.<platform>.dependencies], confirm the platform is listed in [tool.pixi.workspace].platforms, then re-run pixi install on that platform.

See the reference for editable local installs, slow environment creation, and PyPI build failures.

Best Practices

See [references/best-practices.md](references/best-practices.md) for checklists covering project setup, dependency management, reproducibility, performance, and development workflow — including SHA-pinning GitHub Actions in CI (see [assets/github-actions-pixi.yml](assets/github-actions-pixi.yml)).

Resources

• Documentation: https://pixi.sh/latest/ · GitHub: https://github.com/prefix-dev/pixi
• Configuration reference: https://pixi.sh/latest/reference/project_configuration/
• Building packages (pixi build): https://pixi.sh/latest/build/getting_started/
• Migration guides (conda, poetry, uv): https://pixi.sh/latest/switching_from/conda/