versionix 0.99.5

Overview

Many standalone tools expose their version in different ways:

• Some require --version, some -v, and some no argument at all.

• Some write to stdout, others to stderr.

• Version strings come in many formats (1.2.3, v1.2.3, tool 1.2.3 (build ...), …).

Versionix handles all of these cases automatically. For ~80 % of tools the built-in regular-expression heuristic is enough; for the rest a curated registry of metadata ensures the right command is run and the right output channel is parsed.

Installation

Install from PyPI with pip:

pip install versionix --upgrade

No extra dependencies are required beyond the Python standard library and a handful of small pure-Python packages.

Usage

Command line

Just type versionix followed by the name of any executable on your $PATH:

versionix ls          # any system command
versionix fastqc      # common bioinformatics tool
versionix bwa

versionix prints a clean X.Y.Z version string to the terminal.

List all registered tools:

versionix --registered

Full help:

versionix --help

versionix sniffles --from sniffles_2.7.3.img
versionix fastqc --from fastqc.sif

from versionix import get_version

version = get_version("fastqc")
print(version)  # e.g. "0.11.9"

from versionix import get_version

version = get_version("sniffles", container="sniffles_2.7.3.img")

How it works

The first difficulty is that standalone applications have different ways to obtain their version information. Some require the use of a long or short argument (--version or -v), while others do not require any argument at all. In addition, the display channel (stdout or stderr) and the format of the version output differ between applications.

To handle these various cases, Versionix uses a regular expression that covers the majority of applications. For non-standard cases, a dictionary of metadata for each registered standalone is available. These metadata specify:

• the command and options to run,

• whether to read stdout or stderr, and

• how to parse the output to extract the version string.

Versionix is designed to be used with all Sequana pipelines and is not intended to be universal. You can add support for your own tool by editing versionix/registry.py and opening a Pull Request.

Contributing

Contributions are very welcome! Please:

1. Fork the repository and create a feature branch.

2. Add or update tests as appropriate.

3. Open a Pull Request against main.

Run the test suite locally with:

pytest -v --cov versionix

Changelog