peppy

What it is and what it does

peppy is a Python library for reading and managing Portable Encapsulated Projects (PEPs), a standardized metadata format used in bioinformatics to organize project configuration, sample metadata, and workflow parameters. It parses PEP YAML files and provides programmatic access to project structure and sample information, making it useful for building reproducible bioinformatics pipelines and managing large-scale sequencing experiments.

The package depends on pandas, pyyaml, rich, ubiquerg, numpy, and pephubclient to handle data manipulation, YAML parsing, terminal output formatting, and integration with external project repositories. It targets bioinformatics workflows and is actively maintained, with support for Python 3.8 through 3.12.

Use it for:

• Load and parse PEP metadata files to configure bioinformatics analysis pipelines
• Access sample metadata and project configuration programmatically in workflow scripts
• Validate project structure and metadata consistency before running analyses
• Integrate project metadata into reproducible research workflows
• Build tools that manage large-scale sequencing experiments with standardized metadata

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

peppy reads and manages Portable Encapsulated Projects (PEPs)—a metadata format for organizing bioinformatics workflows and sequencing projects—providing Python access to project configuration and sample metadata.

Yes, if you work with bioinformatics projects using the PEP standard or need to manage project metadata in Python workflows. Low install friction, active maintenance, permissive license, and no known vulnerabilities make it a safe choice. Not relevant for non-bioinformatics use cases.

Install

peppy on PyPI

pip install peppy

uv add peppy

poetry add peppy

Installing peppy

Before you install

Low install friction; pure Python wheel with six runtime dependencies. Actively maintained as of August 2026, with a recent release in October 2025.

License in practice

BSD2 license is permissive; you can use, modify, and distribute peppy with minimal legal constraints, provided you include the license notice.

Quickstart

pip install peppy

import peppy
project = peppy.Project('path/to/pep.yaml')
samples = project.samples

Verify before relying

• Whether pephubclient dependency requires network access or external service connectivity
• Specific Python version floor (requires_python is unspecified in metadata)

Package facts

Evidence: peppy-0.40.8-py3-none-any.whl

Keywords: project, metadata, bioinformatics, sequencing, ngs, workflow

Tags

More Bio-Informatics packages