nomad-analysis 0.1.3

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. The plugin provides schemas to create entries for analysis that can interact with other entries, using them as analysis inputs. Jupyter Analysis schemas generate analysis entries that are connected with an external programming interface, JupyterHub, which allows users to run custom code on the connected input entries.

To install the package as a dependency for your NOMAD Oasis, add it to your pyproject.toml as under project.dependencies table:

[project]
dependencies = [
    ...
    "nomad-analysis",
]

Or you can use pip to install the package in your Python environment:

pip install nomad-analysis

Development

The plugin is still under development. If you would like to contribute, follow these steps:

Install the dependencies

Clone the project and go into the cloned directory. Create and start a virtual environment (note this project uses Python 3.11):

git clone https://github.com/FAIRmat-NFDI/nomad-analysis.git
cd nomad-analysis
python3.11 -m venv .pyenv
source .pyenv/bin/activate

Install the nomad-analysis package in editable mode (with -e flag) along with development dependencies (with '.[dev]'):

pip install --upgrade pip
uv pip install -e '.[dev]'

Note: uv uses NOMAD's internal package registry via index-url defined under tool.uv.index-url in pyproject.toml. If you want to use pip directly without uv wrapper, use the following:

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

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

Set 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.