peppy

library0.40.8pypypi✓ verified 85d ago

peppy is the official Python package for reading Portable Encapsulated Projects (PEPs). It provides a Python interface for managing project metadata, including samples and their attributes. The library facilitates loading, validating, and interacting with PEP-formatted metadata. The current stable version is 0.40.8, with significant breaking changes anticipated in the upcoming 0.50.0aX releases. It maintains an active development and release cadence.

data serialization workflow

pip install peppy

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · PEPPY

peppy

datapythonv0.40.8

Install

11.7s avg

Import

1217ms

Disk

196MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.40.8 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.920 runs

installs and imports cleanly · install 0.0s · import 1.248s · 195.6MB

glibc

py 3.10–3.920 runs

installs and imports cleanly · install 11.7s · import 1.186s · 188MB

196MB installed

● package 196MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Project

✓ from peppy import Project

Demonstrates how to initialize a `peppy.Project` object from a configuration file and access its samples and their attributes. Users should provide their own PEP configuration file.

import os from peppy import Project # For a runnable example, clone the example_peps repository: # git clone https://github.com/pepkit/example_peps.git # and adjust the path below to 'example_peps/example_basic/project_config.yaml' # Placeholder for a project configuration file (YAML or CSV). # In a real scenario, replace with the actual path to your PEP config. project_path = os.environ.get('PEPPY_PROJECT_CONFIG', 'path/to/your/project_config.yaml') try: # Instantiate an in-memory Project representation prj = Project(cfg=project_path) print(f"Successfully loaded Project: '{prj.name}'") print(f"Number of samples: {len(prj.samples)}") if prj.samples: first_sample = prj.samples[0] print(f"\nFirst sample name: {first_sample.sample_name}") # Access a sample attribute, e.g., 'protocol' or 'file' if 'protocol' in first_sample: print(f"First sample's protocol: {first_sample.protocol}") else: print("No samples found in the project.") except FileNotFoundError: print(f"Error: Project configuration file not found at '{project_path}'.") print("Please ensure the path is correct or clone a PEP example.") except Exception as e: print(f"An error occurred during project loading: {e}")

peppy --version

Debug

Known issues

breakingStarting from version 0.50.0a1, functionality previously provided by external `pephubclient` and `eido` libraries has been merged directly into `peppy`. Code relying on direct imports or usage of these separate packages for PEP-related operations will break.

fix

Review the `peppy` documentation for 0.50.0aX to understand how merged functionalities are accessed internally. Remove direct `pephubclient` and `eido` imports related to PEP processing.

affects: >=0.50.0a1

breakingThe command-line interface (CLI) in `peppy` has been completely revamped and switched to `typer` in version 0.50.0a1. Existing CLI commands will no longer work as before.

fix

Consult the updated CLI documentation for version 0.50.0aX to learn the new command structure and usage with `typer`.

affects: >=0.50.0a1

gotchaProject initialization (`peppy.Project(cfg=...)`) requires a correctly formatted PEP configuration file (typically YAML) that points to a sample table. Incorrect paths, malformed YAML, or missing files are common issues leading to errors.

fix

Ensure the `cfg` path is absolute or correctly relative to the current working directory. Validate your YAML file for syntax errors and confirm that all referenced files (like `sample_table.csv`) exist and are accessible. Refer to the PEP specification for correct format.

affects: <0.50.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'peppy'

The 'peppy' library is not installed in the current Python environment.

fix

Install the library using pip: `pip install peppy`

FileNotFoundError: [Errno 2] No such file or directory: 'path/to/project_config.yaml'

The configuration file specified during `Project` initialization either does not exist or the provided path is incorrect.

fix

Verify that the `project_config.yaml` file exists at the specified path. Use an absolute path or ensure the relative path is correct from where your script is run. Consider cloning the `pepkit/example_peps` repository for test data.

AttributeError: 'Project' object has no attribute 'samples' (or similar errors when accessing project/sample data)

This often occurs if the project configuration (e.g., `sample_table.csv`) is empty, malformed, or if `defer_samples_creation=True` was used without subsequently creating samples.

fix

Review your `project_config.yaml` and associated sample table(s) to ensure they correctly define samples. If you initialized with `defer_samples_creation=True`, call `prj.create_samples()` before attempting to access `prj.samples`.

Upgrade

Version history

0.40.8latest on PyPI · released Oct 20, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

21 hits · last 30 days

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OpenAI (training)

Resources

githubhttps://github.com/pepkit/peppy ↗

packagehttps://pypi.org/project/peppy/ ↗

homepagehttps://pepkit.github.io/peppy/ ↗