nomad-analysis 0.0.0

A NOMAD plugin for analysis of FAIR data.

NOMAD's Analysis plugin

This is a plugin for NOMAD to facilitate analysis of processed entry archives using classes and functions. The plugin also supports ELN schemas which allow the use of these functions in Jupyter notebooks and persist the analysis workflow.

Getting started

Install the dependencies

Clone the project and, in the workspace folder, create a virtual environment (note this project uses Python 3.9):

git clone https://github.com/FAIRmat-NFDI/nomad-analysis.git
cd nomad-analysis
python3.9 -m venv .pyenv

Install the nomad-lab package:

pip install --upgrade pip
pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple

Note: Until we have an official PyPI NOMAD release with the plugin functionality, make sure to include NOMAD's internal package registry (via --index-url in the above command).

Run the tests

You can run the unit testing using the pytest package:

python -m pytest -sv

We recommend to install the coverage and coveralls packages for a more comprehensive output of the testing:

pip install coverage coveralls
python -m coverage run -m pytest -sv

Development

The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added -e flag) with the development dependencies:

pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple

Setting up the plugin on your local installation

Read the NOMAD plugin documentation for all details on how to deploy the plugin on your local NOMAD installation. In summary:

1. Install the plugin repo in your local installation environment

   pip install -e <path to the plugin repo>
   

2. From the following available entry points, include the ones you want (or all) in the nomad.yaml of your local installation:

   plugins:
     include:
       - nomad_analysis.general:schema
       - nomad_analysis.jupyter:schema
   

Run linting and auto-formatting

Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request to add your contributions to this repo, the following commands run in your local without any errors otherwise the workflow action will fail.

ruff check .

ruff format . --check

Alternatively, if you are using VSCode as your IDE, we added the settings configuration file, .vscode/settings.json, such that it performs ruff format whenever you save progress in a file.