nomad-simulations

This is a plugin for NOMAD which contains the base sections definitions for materials science simulations. This schema can be used at any prefered level by the user, it can be modified and extended, and we welcome external collaborators.

Getting started

nomad-simulations can be installed as a PyPI package using pip. We require features from the nomad-lab package which are not publicly available in PyPI, so an extra flag --index-url needs to be specified when pip installing this package:

pip install nomad-simulations --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple

Development

If you want to develop locally this package, clone the project and in the workspace folder, create a virtual environment (note this project uses Python 3.9):

git clone https://github.com/nomad-coe/nomad-simulations.git
cd nomad-simulations
python3.9 -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 '.[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 plugins functionality make sure to include NOMAD's internal package registry (via --index-url in the above command).

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

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

You can also run the script to generate a local file coverage.txt with the same information:

./scripts/generate_coverage_txt.sh

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

Adding this plugin to NOMAD

Currently, NOMAD has two distinct flavors that are relevant depending on your role as an user:

1. A NOMAD Oasis: any user with a NOMAD Oasis instance.
2. Local NOMAD installation and the source code of NOMAD: internal developers.

Adding this plugin in your NOMAD Oasis

Read the NOMAD plugin documentation for all details on how to deploy the plugin on your NOMAD instance.

Adding this plugin in your local NOMAD installation and the source code of NOMAD

Modify the script under /nomad/scripts/install_default_plugins.sh and add the path to this repository pointing to the @develop branch:

<other-content-in-install_default_plugins.sh...>
pip install git+https://github.com/nomad-coe/nomad-simulations.git@develop

Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:

deactivate
cd <route-to-NOMAD-folder>/nomad
source .pyenv/bin/activate
./scripts/setup_dev_env.sh

Alternatively and only valid for your local NOMAD installation, you can modify nomad.yaml to include this plugin:

plugins:
  entry_points:
    include:
      - ["nomad_simulations.schema_packages:nomad_simulations_plugin"]

Note! Once you modify your nomad.yaml file adding include, all the default plugins will be disconnected, so you will need to include them as well.

Main contributors