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| [](https://nomad-lab.eu/prod/v1/staging/gui/) | ||
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| # NOMAD's parser for YAMBO | ||
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| This is a parser plugin for the [YAMBO](https://www.yambo-code.eu/) input/output files. | ||
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| ## Getting started | ||
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| ### Install the dependencies | ||
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| Clone the project and, in the workspace folder, create a virtual environment (note this project uses Python 3.9): | ||
| ```sh | ||
| git clone https://github.com/nomad-coe/nomad-parser-yambo.git | ||
| cd nomad-parser-yambo | ||
| python3.9 -m venv .pyenv | ||
| source .pyenv/bin/activate | ||
| ``` | ||
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| Install the `nomad-lab` package: | ||
| ```sh | ||
| pip install --upgrade pip | ||
| pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple | ||
| ``` | ||
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| > **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). | ||
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| ### Run the tests | ||
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| You can run the unit testing using the `pytest` package: | ||
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| ```sh | ||
| python -m pytest -sv | ||
| ``` | ||
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| We recommend to install the `coverage` and `coveralls` packages for a more comprehensive output of the testing: | ||
| ```sh | ||
| pip install coverage coveralls | ||
| python -m coverage run -m pytest -sv | ||
| ``` | ||
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| ## Development | ||
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| 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: | ||
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| ```sh | ||
| pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple | ||
| ``` | ||
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| ### Setting up the plugin on your local installation | ||
| Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your local NOMAD installation. | ||
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| To deploy the plugin in your local NOMAD installation, follow the next steps: | ||
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| 1. Add the configurations related to NOMAD. This is already implemented through the plugin definition file ```src/nomad_parser_yambo/nomad_plugin.yaml```: | ||
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| ```yaml | ||
| plugin_type: parser | ||
| name: parsers/yambo | ||
| description: | | ||
| This plugin is used to parsed YAMBO files into the NOMAD schema. | ||
| ``` | ||
| and the ```nomad.yaml``` configuration file: | ||
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| ```yaml | ||
| plugins: | ||
| include: | ||
| - 'parsers/yambo' | ||
| - 'runschema' | ||
| - 'simulationworkflowschema' | ||
| - 'nomad_simulations' | ||
| options: | ||
| parsers/yambo: | ||
| python_package: nomad_parser_yambo | ||
| runschema: | ||
| python_package: runschema | ||
| nomad_simulations: | ||
| python_package: nomad_simulations | ||
| ``` | ||
| 3. Add to your local NOMAD installation the same lines of your plugin ```nomad.yaml``` file. | ||
| 4. 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: | ||
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| ```sh | ||
| export PYTHONPATH="$PYTHONPATH:<path-to-nomad-parser-yambo-cloned-repo>/src" | ||
| ``` | ||
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| If you are working in this repository, you just need to activate the environment to start working using the ```nomad-parser-yambo``` package locally in your own Python scripts. | ||
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| ### Run linting and auto-formatting | ||
| 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. | ||
| ```sh | ||
| ruff check . | ||
| ``` | ||
| ```sh | ||
| ruff format . --check | ||
| ``` | ||
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| 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. | ||
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| <!-- | ||
| ## Build the python package | ||
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| The `pyproject.toml` file contains everything that is necessary to turn the project into a pip installable python package. Run the python build tool to create a package distribution: | ||
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| ``` | ||
| pip install build | ||
| python -m build --sdist | ||
| ``` | ||
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| You can install the package with pip: | ||
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| ``` | ||
| pip install dist/nomad-schema-plugin-example-1.0.tar.gz | ||
| ``` | ||
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| Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/). | ||
| --> | ||
| The new parser (2024) for YAMBO input/output files can be found in [FAIRmat-NFDI/nomad-parser-yambo](https://github.com/FAIRmat-NFDI/nomad-parser-yambo). |