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https://github.com/josepizarro3/nomad-networkx

Utility tool to map NetworkX graph representations into NOMAD workflow data models.
https://github.com/josepizarro3/nomad-networkx

Last synced: about 2 months ago
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Utility tool to map NetworkX graph representations into NOMAD workflow data models.

Host: GitHub
URL: https://github.com/josepizarro3/nomad-networkx
Owner: JosePizarro3
License: apache-2.0
Created: 2024-06-13T07:20:54.000Z (7 months ago)
Default Branch: develop
Last Pushed: 2024-06-13T09:26:46.000Z (7 months ago)
Last Synced: 2024-06-14T10:50:10.246Z (7 months ago)
Language: Python
Size: 13.7 KB
Stars: 1
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

# NOMAD-NetworkX
Utility tool to map [NetworkX graph representations](https://networkx.org/documentation/stable/index.html) into [NOMAD workflow data models](https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow).

## Getting started

### Install the dependencies

Clone the repository and enter in the directory:
```sh
git clone https://github.com/JosePizarro3/nomad-networkx.git
cd nomad-networkx
```

Create a new virtual environment with Python 3.10 in the root folder of the project:
```sh
python3.10 -m venv .pyenv
source .pyenv/bin/activate
```

Make sure to have pip upgraded to its latest version:
```sh
pip install --upgrade pip
```

We recommend using `uv` for pip installing all packages due to its improved performance and speed when installing Pypi packages:
```sh
pip install uv
```

Install the development packages as well as specify the URL of the `nomad-lab` package using the `--index-url` flag:
```sh
uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
```

In order to develop the code, add the editable (`e`) flag to the installation step:
```sh
uv pip install -e '.[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).

### Run the tests

You can run local tests using the `pytest` package:

```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 `coverage` and `coveralls` packages. We suggest you to generate your own coverage reports locally by doing:

```sh
uv pip install coverage coveralls
python -m pytest --cov=src tests
```

### Run linting and auto-formatting

We use [Ruff](https://docs.astral.sh/ruff/) for auto-formatting our Python modules. This package is included as part of the `[dev]` dependencies of the project, and can be run in the terminal:

```sh
ruff check .
ruff format . --check
```

Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, `ruff format . --check` runs in your local without any errors otherwise the workflow action will fail.

### Using VSCode for debugging

I recommend to use VSCode as your visual editor for debugging. The project comes with a `settings.json` file which already takes care of formatting everytime you save changes in a file (using [Ruff](https://docs.astral.sh/ruff/)).

You can also create your own personal debugger `launch.json`. As an example, this is my current debug file:
```json
{
"version": "0.2.0",
"configurations": [
{
"name": "nomad-networkx python",
"type": "debugpy",
"request": "launch",
"program": "${workspaceFolder}/debug.py",
"python": "${workspaceFolder}/.pyenv/bin/python",
"console": "integratedTerminal",
"justMyCode": true,
"env": {
"PYTHONDONTWRITEBYTECODE": "1"
}
},
{
"name": "nomad-networkx pytest",
"type": "debugpy",
"request": "launch",
"module": "pytest",
"args": [
"-sv",
"${workspaceFolder}/tests"
],
"python": "${workspaceFolder}/.pyenv/bin/python",
"console": "integratedTerminal",
"justMyCode": true,
"env": {
"PYTHONDONTWRITEBYTECODE": "1"
}
},
]
}
```

Feel free to modify the relative paths under `"program"` or `"args"` respectively.