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IKZ Plugin

This directory contains a plugin called nomad-ikz-plugin designed for the IKZ institute.

This a python package that contains several subpackages for each technique.

Check the README within each subfolder for more deatils on each technique.

Structure

The directory tree:

nomad-ikz-plugin/
├── src
│   └── nomad-ikz-plugin
│       ├── general
│       ├── characterization
│       ├── czochralski
│       ├── directional_solidification
│       ├── pld
│       ├── mbe
│       └── movpe
└── tests
    └── data
        ├── czochralski
        ├── directional_solidification
        ├── pld
        ├── mbe
        └── movpe
  • src/: contains the source code for the plugins.
  • tests/: contains tests for the plugins.

Installation

To use this plugin you need to install several dependent packages.

There are at least two ways of installing them, depending on your aim:

  • Deploy a custom NOMAD Oasis image. Refer to the IKZ NOMAD Oasis custom image to discover how the pyproject.toml is composed. If you are using some plugins in your Oasis deployment that are also dependencies of this plugin, make sure to have compatible version tags. To do this, you will need the following lines in your Oasis deployment's pyproject.toml:

    [project.optional-dependencies]
plugins = [
  "nomad-material-processing @ git+https://github.com/FAIRmat-NFDI/nomad-material-processing.git@<desired_commit_id>",
  "nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@<desired_commit_id>",
  "nomad-analysis @ git+https://github.com/FAIRmat-NFDI/nomad-analysis.git@<desired_commit_id>",
  "nomad-ikz-plugin",
  "uv_vis_nir_transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@<desired_commit_id>#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin",
  "lakeshore-nomad-plugin @ git+https://github.com/IKZ-Berlin/lakeshore-nomad-plugin.git@<desired_commit_id>",
  "laytec_epitt_plugin @ git+https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin.git@<desired_commit_id>",
  "statsmodels" 
  ]
  [tool.uv.sources]
  nomad-ikz-plugin = { git = "https://github.com/IKZ-Berlin/nomad-ikz-plugin.git", rev = "v0.1.2" }

Note

the toml above shows that the nomad-ikz-plugin is not bound to a commit, rather to a release

  • Develop the plugin in your development environment. Refer to the nomad-distro-dev repository to setup your environment. You will then need to add all the dependencies as submodules and also to use the uv command add to have them in your python env.

    git submodule add https://github.com/FAIRmat-NFDI/nomad-measurements packages/nomad-measurements
git submodule add https://github.com/FAIRmat-NFDI/nomad-material-processing packages/nomad-material-processing
git submodule add https://github.com/IKZ-Berlin/nomad-ikz-plugin packages/nomad-ikz-plugin
git submodule add https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin packages/laytec_epitt_nomad_plugin
git submodule add https://github.com/IKZ-Berlin/lakeshore-nomad-plugin packages/lakeshore-nomad-plugin
git submodule update --init --recursive
uv add packages/nomad-ikz-plugin
uv add packages/lakeshore-nomad-plugin
uv add packages/laytec_epitt_nomad_plugin
uv add packages/nomad-measurements
uv add packages/nomad-material-processing

For more details on what happens in this plugin under the hood, check the .toml file in the nomad-ikz-plugin folder:

  • all the installed subpackages are listed under the section [project.entry-points.'nomad.plugin'].
  • dependencies and [project.optional-dependencies] contain all the other packages installed along to this one.

Usage

You need to copy and fill the tabular files in tests/data folder, then drag and drop them into a new NOMAD upload.

Please refer to the README.md file in each subdirectory for more information about each plugin.

Development

Clone your fork

Follow the github instructions. The URL and directory depends on your user name or organization and the project name you choose. But, it should look somewhat like this:

git clone [email protected]:markus1978/my-nomad-schema.git
cd my-nomad-schema

Install the dependencies

You should create a virtual environment. You will need the nomad-lab package (and pytest). You need at least Python 3.9.

python3 -m venv .pyenv
source .pyenv/bin/activate
pip install -r requirements.txt --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple

to ensure installation of all the packages required, make sure in to install:

pip install nomad-lab[parsing, infrastructure]

Run the tests

Make sure the current directory is in your path:

export PYTHONPATH=.

You can run automated tests with pytest:

pytest -svx tests

You can parse an example archive that uses the schema with nomad command (installed via nomad-lab Python package):

nomad parse tests/data/test.archive.yaml --show-archive

Developing your schema

Refer to official NOMAD docs to learn how to develop schemas and parsers and plugins, how to add them to an Oasis, how to publish them: https://nomad-lab/prod/v1/staging/docs/plugins.html