nomad-parser-magres
NOMAD’s parser for magres
This is a parser plugin for the magres file format developed in the CCP-NC for Nuclear Magnetic Resonance (NMR) data.
Getting started
Installation
To add this plugin to your Custom NOMAD Oasis image, you can follow the instructions in the dedicated repository
Adding this plugin to NOMAD custom image
Modify nomad.yaml to exclude the magres plugin provided by the electronicparser package:
plugins:
exclude:
- electronicparsers:magres_parser_entry_point
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.
Development
The plugin is still under development. If you would like to contribute, install the package in your development distro and follow the instructions to get started.
Adding this plugin to NOMAD development distro
As already mentioned in Installation section, modify nomad.yaml to exclude the magres plugin provided by the electronicparser package:
plugins:
exclude:
- electronicparsers:magres_parser_entry_point
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
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