nomad-utility-workflows plugin

Utilities for interfacing with NOMAD within workflows, e.g., via a workflow manager, including python API functions for uploading to NOMAD and querying the repository as well as automated generation of NOMAD custom workflow yaml file (NOMAD workflow data models).

This nomad plugin was generated with Cookiecutter along with @nomad's cookiecutter-nomad-plugin template.

Usage

For direct usage and integrating the utility module into other plugins or codes, nomad-utility-workflows is available as a PyPI package:

pip install nomad-utility-workflows>=0.2.0

If you are following the How-to guides in the docs, use the "vis" optional dependencies tag (includes dependencies for, e.g., Jupyter notebook and graph visualization):

pip install nomad-utility-workflows[vis]>=0.2.0

Caution

There were breaking changes made in the transition to nomad-utility-workflows version 0.2.0. This is particularly relevant for the functions called for building the workflow yaml. To use older versions, you should reference the corresponding docs pages by checking out an older branch and serving the mkdocs page locally (See README.md).

Caution

There were breaking changes made in the transition to nomad-utility-workflows version 0.1.0. This is particularly relevant for the structure of inputs of the workflow graph generation functions. To use older versions, you should reference the corresponding docs pages by checking out an older branch and serving the mkdocs page locally (See README.md).

Linking to your NOMAD account

Create an account on https://nomad-lab.eu/. Store your credentials in a .env file in your working directory, at the root plugin directory for developers, or in some directory that is added to your PYTHONPATH, with the following content

NOMAD_USERNAME="MyLogin"
NOMAD_PASSWORD="MyPassWord"

and insert your username and password.

Caution

Never push your .env file to a repository. This would expose your password.

Test Notebooks

To run the test notebooks, create a jupyter kernel using your venv:

python -m ipykernel install --user --name=nomad_utility_workflows

Development

If you want to develop this module locally, clone the project and in the plugin folder, create a virtual environment (you can use Python 3.10, or 3.11):

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

Make sure to have pip upgraded:

pip install --upgrade pip

We recommend installing uv for fast pip installation of the packages:

pip install uv

Install the nomad-lab package:

uv pip install '.[vis,dev]'

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

uv pip install -e '.[vis,dev]'

Run the tests

You can run locally the tests:

python -m pytest -sv tests

where the -s and -v options toggle the output verbosity.

Our CI/CD pipeline produces a more comprehensive test report using the pytest-cov package. You can generate a local coverage report:

uv pip install pytest-cov
python -m pytest --cov=src tests

Run linting and auto-formatting

We use Ruff for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally:

ruff check .
ruff format . --check

Debugging

For interactive debugging of the tests, use pytest with the --pdb flag. We recommend using an IDE for debugging, e.g., VSCode. If that is the case, add the following snippet to your .vscode/launch.json:

{
  "configurations": [
      {
        "name": "<descriptive tag>",
        "type": "debugpy",
        "request": "launch",
        "cwd": "${workspaceFolder}",
        "program": "${workspaceFolder}/.pyenv/bin/pytest",
        "justMyCode": true,
        "env": {
            "_PYTEST_RAISE": "1"
        },
        "args": [
            "-sv",
            "--pdb",
            "<path-to-plugin-tests>",
        ]
    }
  ]
}

where <path-to-plugin-tests> must be changed to the local path to the test module to be debugged.

The settings configuration file .vscode/settings.json automatically applies the linting and formatting upon saving the modified file.

Documentation on Github pages

To view the documentation locally, install the related packages using:

uv pip install -r requirements_docs.txt

Run the documentation server:

mkdocs serve

How to cite this work

Rudzinski, J.F., Albino, A., Bereau, T., Daelman, N., Ladines, A.N., Mohr, B., Pedersen, J., Walter, L.J., NOMAD Utility Workflows (all versions) [Computer software]. https://zenodo.org/doi/10.5281/zenodo.14895189

Main contributors

Name	E-mail
Joseph F. Rudzinski	[email protected]
Andrea Albino
Tristan Bereau
Nathan Daelman
Alvin N. Ladines
Bernadette Mohr
Jesper Pedersen
Luis J. Walter