atomea 0.0.0.post171
Extensible schema for atomistic data and calculations.
License: Apache-2.0
Requires Python: <4.0,>=3.10

<h1 align="center">atomea</h1>
<h4 align="center">Extensible schema for atomistic data and calculations.</h4>
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<h4 align="center"><a href="https://atomea.oasci.org">Documentation</a></h4>

## Overview

Atomea is a Python package designed to simplify and standardize the setup and data management for atomistic data and calculations.
It leverages the power of [Pydantic][pydantic] for schema definition and [Jinja2][jinja] templates for input file generation, making it easy to automate, document, and prepare input files for various computational chemistry and biology tools.

## Key features

-   **Extensible Schema Definition:** Easily define schemas for various computational packages using [Pydantic][pydantic].
-   **Automated Input File Preparation:** Generate input files with [Jinja2][jinja] templates to ensure consistency and reproducibility.
-   **Data Digestion:** Convert raw output files into optimized storage formats (e.g., [Zarr][zarr]) with a consistent interface.
-   **YAML Integration:** Save and load configurations and data in YAML format for easy sharing and reproducibility.

## Installation

Atomea requires Python 3.10 or later.
You can install it using pip, the Python package installer.
This will install atomea along with its core dependencies: loguru, pydantic, pyyaml, and numpy.

```bash
pip install atomea
```

Atomea has several optional dependency groups that you can install based on your needs.
You can include these when installing atomea or add them later.

-   `storage`: Allows saving digested outputs to several file types.
-   `sim`: Allows digesting simulations using MDAnalysis.

For example, we can install both of these optional dependencies.

```bash
pip install atomea[storage,sim]
```

## Deploying

We use [bump-my-version](https://github.com/callowayproject/bump-my-version) to release a new version.
This will create a git tag that is used by [poetry-dynamic-version](https://github.com/mtkennerly/poetry-dynamic-versioning) to generate version strings and update [`CHANGELOG.md`](https://gitlab.com/oasci/software/atomea/-/blob/main/CHANGELOG.md).

For example, to bump the `minor` version you would run the following command.

```bash
poetry run bump-my-version bump minor
```

After releasing a new version, you need to push and include all tags.

```bash
git push --follow-tags
```

## License

This project is released under the Apache-2.0 License as specified in [`LICENSE.md`](https://gitlab.com/oasci/software/atomea/-/blob/main/LICENSE.md).

<!-- REFERENCES -->

[pydantic]: https://docs.pydantic.dev/latest/
[jinja]: https://palletsprojects.com/p/jinja/
[zarr]: https://zarr.dev/