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https://github.com/josepizarro3/nomad-parser-dmft

A compilation of NOMAD parsers for input/output files of DMFT codes.
https://github.com/josepizarro3/nomad-parser-dmft

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A compilation of NOMAD parsers for input/output files of DMFT codes.

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# nomad-parser-dmft



A compilation of NOMAD parsers for input/output files of DMFT codes.



This `nomad` plugin was generated with `Cookiecutter` along with `@nomad`'s [`cookiecutter-nomad-plugin`](https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin) template.



## Development



If you want to develop locally this plugin, clone the project and in the plugin folder, create a virtual environment (you can use Python 3.9, 3.10, or 3.11):

```sh

git clone https://github.com/JosePizarro3/nomad-parser-dmft.git

cd nomad-parser-dmft

python3.11 -m venv .pyenv

. .pyenv/bin/activate

```



Make sure to have `pip` upgraded:

```sh

pip install --upgrade pip

```



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

```sh

pip install uv

```



Install the `nomad-lab` package (the flag `-e` ensures that you can develop the package by installing it in editable mode):

```sh

uv pip install -e '.[dev]'

```



**Note!**

If you do not use `uv` and 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.

```sh

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:

```sh

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:

```sh

uv pip install pytest-cov

python -m pytest --cov=src tests

```



### Run linting and auto-formatting



We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally:

```sh

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`:

```json

{

  "configurations": [

      {

        "name": "",

        "type": "debugpy",

        "request": "launch",

        "cwd": "${workspaceFolder}",

        "program": "${workspaceFolder}/.pyenv/bin/pytest",

        "justMyCode": true,

        "env": {

            "_PYTEST_RAISE": "1"

        },

        "args": [

            "-sv",

            "--pdb",

            "",

        ]

    }

  ]

}

```



where `` 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:

```sh

uv pip install -r requirements_docs.txt

```



Run the documentation server:

```sh

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](#adding-this-plugin-in-your-nomad-oasis): any user with a NOMAD Oasis instance.

2. [Local NOMAD installation and the source code of NOMAD](#adding-this-plugin-in-your-local-nomad-installation-and-the-source-code-of-nomad): internal developers.



### Adding this plugin in your NOMAD Oasis



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 NOMAD instance.



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



Modify the text file under `/nomad/default_plugins.txt` and add:

```sh



nomad-parser-dmft==x.y.z

```

where `x.y.z` represents the released version of this plugin.



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

```sh

deactivate

cd /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, see [NOMAD Oasis - Install plugins](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html).



### Build the python package



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:



```sh

pip install build

python -m build --sdist

```



You can install the package with pip:



```sh

pip install dist/nomad-parser-dmft-0.1.0

```



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/).



### Template update



We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests.



To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project).



## Main contributors

| Name | E-mail     |

|------|------------|

| Jose Pizarro | [[email protected]](mailto:[email protected])