https://github.com/tskit-dev/tszip

Gzip-like compression for tskit tree sequences
https://github.com/tskit-dev/tszip

compression tree-sequence tskit

Last synced: about 2 months ago
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Gzip-like compression for tskit tree sequences

• Host: GitHub
• URL: https://github.com/tskit-dev/tszip
• Owner: tskit-dev
• License: mit
• Created: 2019-04-30T14:09:17.000Z (almost 7 years ago)
• Default Branch: main
• Last Pushed: 2026-03-02T13:05:29.000Z (about 2 months ago)
• Last Synced: 2026-03-02T13:19:05.261Z (about 2 months ago)
• Topics: compression, tree-sequence, tskit
• Language: Python
• Homepage: https://tskit.dev/tszip/docs/
• Size: 435 KB
• Stars: 5
• Watchers: 4
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.rst
  • License: LICENSE

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README

          
# tszip

[![License](https://img.shields.io/github/license/tskit-dev/tszip)](https://github.com/tskit-dev/tszip/blob/main/LICENSE) [![PyPI version](https://img.shields.io/pypi/v/tszip.svg)](https://pypi.org/project/tszip/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/tszip.svg)](https://pypi.org/project/tszip/) [![Docs Build](https://github.com/tskit-dev/tszip/actions/workflows/docs.yml/badge.svg)](https://github.com/tskit-dev/tszip/actions/workflows/docs.yml) [![Binary wheels](https://github.com/tskit-dev/tszip/actions/workflows/wheels.yml/badge.svg)](https://github.com/tskit-dev/tszip/actions/workflows/wheels.yml) [![Tests](https://github.com/tskit-dev/tszip/actions/workflows/tests.yml/badge.svg)](https://github.com/tskit-dev/tszip/actions/workflows/tests.yml) [![codecov](https://codecov.io/gh/tskit-dev/tszip/branch/main/graph/badge.svg)](https://codecov.io/gh/tskit-dev/tszip)

Gzip-like compression for [tskit](https://tskit.dev/software/tskit.html) tree sequences. Compression is lossless for supported tskit tree sequences.

Please see the [documentation](https://tskit.dev/tszip/docs/stable/) ([latest](https://tskit.dev/tszip/docs/latest/)) for more details

and [installation instructions](https://tskit.dev/tszip/docs/stable/installation.html).

## Installation

Install from PyPI or conda-forge:

```

python -m pip install tszip

# or

conda install -c conda-forge tszip

```

## Quickstart

CLI usage:

```bash

# Compress a .trees file to a .tsz archive

tszip data.trees

# Decompress back to .trees

tsunzip data.trees.tsz

```

Along with the CLI, tszip can be used directly from Python:

```python

import tskit

import tszip

ts = tskit.load("data.trees")

tszip.compress(ts, "data.trees.tsz")  # write compressed archive

# load handles .tsz archives and plain .trees files

restored = tszip.load("data.trees.tsz")

print(restored.equals(ts))  # True

```