Skip to content

Installation

The document is the entry point for anybody that is new to the NeXus data format and to FAIRmat/NOMAD. It serves as a guide to getting started with the pynxtools software.

What should you should know before this tutorial?

However, to get started, it does not hurt to the following explanations:

What you will know at the end of this tutorial?

You will know

  • how to install pynxtools
  • how to configure your pynxtools installation
  • how to install pynxtools together with NOMAD

Setup

It is recommended to use python 3.11 with a dedicated virtual environment for this package. Learn how to manage python versions and virtual environments.

There are many alternatives to managing virtual environments and package dependencies (requirements). We recommend using uv, an extremely fast manager Python package and project manager. In this tutorial, you will find paralleled descriptions, using either uv or a more classical approach using venv and pip.

Start by creating a virtual environment:

uv is capable of creating a virtual environment and install the required Python version at the same time.

uv venv --python 3.11

Note that you will need to install the Python version manually beforehand.

python -m venv .venv

That command creates a new virtual environment in a directory called .venv.

Installation

Install the latest stable version of this package from PyPI with

uv pip install pynxtools

pip install pynxtools

You can also install the latest development version with

uv pip install git+https://github.com/FAIRmat-NFDI/pynxtools.git

pip install git+https://github.com/FAIRmat-NFDI/pynxtools.git

Configuring your pynxtools installation

pynxtools comes with a list of built-in readers that can be used after after pip installation. In addition, pynxtools supports a plugin mechanism for adding file readers for different experimental techniques. The different FAIRmat-supported plugins can be installed together with pynxtools by passing the name of the plugin as an extra to the install call. For example, for the pynxtools-mpes plugin, you can run:

uv pip install pynxtools[mpes]

pip install pynxtools[mpes]

In addition, you can also install all of the pynxtools reader plugins which are maintained by FAIRmat by passing the [convert] extra to the install call:

uv pip install pynxtools[convert]

pip install pynxtools[convert]

Note that in this case, the latest version of the plugin(s) from PyPI are installed.

How to install pynxtools with NOMAD

To use pynxtools with NOMAD, simply install it in the same environment as the nomad-lab package. NOMAD will recognize pynxtools as a plugin automatically and offer automatic parsing of .nxs files. In addition, NOMAD will install a schema for NeXus application definitions.

Start using pynxtools

That's it! You can now use pynxtools and the plugins that you have installed!