---
id: pephubclient
version: "0.6.0"
license: BSD2
license_treatment: permissive
maintenance: active
---

# pephubclient — PEPhub command line interface.

License: permissive · Maintenance: active · Downloads: 118.1K/mo

## What it is and what it does

PEPHubClient is a client library and command-line tool for interacting with PEPhub, a bioinformatics project metadata repository. It lets you push (upload) and pull (download) project configurations and sample metadata to and from PEPhub, with built-in support for authentication via device-code flow or JWT tokens. The tool is designed for bioinformatics workflows where project metadata needs to be centrally managed and shared.

The package wraps HTTP requests to PEPhub behind a Python API and CLI commands, handling credential caching in a local directory and supporting both public and private projects. It depends on typer for CLI scaffolding, peppy for project parsing, pydantic for validation, and pandas for data handling. Authentication is optional for public projects but required to upload or access private projects.

Use it for:

- Upload bioinformatics project configurations and sample metadata to a shared PEPhub repository for team collaboration.
- Download project metadata from PEPhub to a local machine for reproducible analysis workflows.
- Authenticate and manage private project access using device-code or token-based login.
- Integrate project metadata synchronization into bioinformatics pipelines via Python API calls.
- Switch between multiple PEPhub instances by setting environment variables or login URLs.

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

PEPHubClient provides a Python API and command-line interface to upload and download bioinformatics project metadata to and from PEPhub, with support for authentication and private projects.

Yes, if you work with PEPhub or bioinformatics project metadata management. The package is actively maintained, has low install friction, carries a permissive BSD2 license, and has no known vulnerabilities. It is in alpha status, so expect potential API changes; verify that the CLI and Python API meet your integration needs before committing to production use.

## Install

pip install pephubclient
uv add pephubclient
poetry add pephubclient

## Installing pephubclient

Before you install: Low install friction with a pure-wheel distribution. Actively maintained with a release 9 days ago. Depends on 8 runtime packages including typer for CLI, peppy for project handling, and pydantic for validation.

License in practice: BSD2 license is permissive, allowing commercial use, modification, and redistribution with minimal restrictions.

Quickstart:

pip install pephubclient

from pephubclient import PEPHubClient

client = PEPHubClient()
client.pull('namespace/project_name')

Requires authentication via device-code flow or JWT token to access private projects; set PEPHUB_BASE_URL environment variable to use a custom PEPhub instance.

Verify before relying:

- Whether the Python API is fully documented or if CLI is the primary interface.
- Performance characteristics when working with large project metadata or many projects.
- Compatibility with different PEPhub instance versions.

## Package facts

- License: BSD2 (permissive)
- Python support: unspecified
- Install friction: low
- Maintenance: active
- Downloads: 118.1K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

bioinformatics project metadata management, pephub client cli, upload download project config, bioinformatics data repository, project registry sync tool, bioinformatics, metadata-management, cli-tool

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