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.
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).
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
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
Read the NOMAD plugin documentation for all details on how to deploy the plugin on your local NOMAD installation.
To deploy the plugin in your local NOMAD installation, follow the next steps:
Add the configurations related to NOMAD. This is already implemented through the plugin definition file src/nomad_analysis/nomad_plugin.yaml
:
plugin_type: schema
name: schemas/nomad_analysis
description: |
This plugin is used to analyze parsed raw data from the NOMAD standard schema.
and the nomad.yaml
configuration file:
plugins:
include:
- 'schemas/nomad_analysis'
options:
schemas/nomad_analysis:
python_package: nomad_analysis
nomad.yaml
file.Add to your local NOMAD installation environment the PYTHONPATH
to your plugin. This can be done either by running the following command every time you start a new terminal for running the appworker, or by adding it to your virtual environment in the <path-to-local-nomad-installation>/.pyenv/bin/activate
file:
export PYTHONPATH="$PYTHONPATH:<path-to-nomad-analysis-cloned-repo>/src"
If you are working in this repository, you just need to activate the environment to start working using the nomad-analysis
package locally in your own Python scripts.
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.