peppy
A python-based project metadata manager for portable encapsulated projects
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
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 · maintenance · safety
BSD2 (permissive) — BSD2 license is permissive; you can use, modify, and distribute peppy with minimal legal constraints, provided you include the license notice.
last release 2025-10-20 (298 days) · last repo commit 2026-08-07 · 40 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 117,880 downloads/mo, #12,144 on PyPI
Alternatives
Verify before relying
pip install peppy
import peppy
project = peppy.Project('path/to/pep.yaml')
samples = project.samples- Whether pephubclient dependency requires network access or external service connectivity
- Specific Python version floor (requires_python is unspecified in metadata)
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 on it.
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
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.samplesVerify before relying
- Whether pephubclient dependency requires network access or external service connectivity
- Specific Python version floor (requires_python is unspecified in metadata)
Package facts
| License | BSD2 permissive |
| Python support | Not specified |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 6 packagespandaspyyamlrichubiquergnumpypephubclient |
| Maintenance | Actively maintained 298 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 117,880 / month, #12,144 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaLicense :: OSI Approved :: BSD LicenseProgramming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.8Programming Language :: Python :: 3.9Topic :: Scientific/Engineering :: Bio-Informatics |
Evidence: peppy-0.40.8-py3-none-any.whl
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See also eido · pephubclient · piper · refgenie · refgenconf · biom-format · whey · pipestat · pefile · resdata