aton 1.1.1

The Advanced Text Operations for scieNtific python (ATON) provides powerful and comprehensive text-edition tools to edit and analyse simuation data.

Welcome to ATON

The Atomic Text Operations for pythoN, or ATON, provides fast and comprehensive text analysis and edition tools.

In a nod to its ancient Egyptian deity counterpart, this Python package aims to provide straightforward, easy-to-implement tools for easily creating custom interfaces for any text-based software.

The heart and soul of ATON is the txt module, which simplifies the automation of text edition tasks. It also includes an api module with interfaces for simulation and HPC codes, such as Slurm, Quantum ESPRESSO, Phonopy and CASTEP.

The source code is available on GitHub.
Check the full documentation online.

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Installation

As always, it is recommended to install your packages in a virtual environment:

python3 -m venv .venv
source .venv/bin/activate

With pip

Install or upgrade ATON with

pip install aton -U

From source

Optionally, you can install ATON from the GitHub repo. Clone the repository or download the latest stable release as a ZIP, unzip it, and run inside it:

pip install .

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Documentation

The full ATON documentation is available online.
An offline version is found at docs/aton.html.
Code examples are included in the examples/ folder.

General text edition

The txt module is used to automate the editing of text files. It enables the creation of more powerful interfaces, such as those from the aton.api module.

aton.txt

txt.find	Search for specific content in text files
txt.edit	Manipulate text files
txt.extract	Extract data from raw text strings

Interfaces for atomic and HPC codes

The api module contains Python interfaces for several ab-initio codes and related. These are powered by the aton.txt module and can be easily extended.

aton.api

api.pwx	Interface for Quantum ESPRESSO's pw.x module
api.phonopy	Interface for Phonopy calculations
api.castep	Interface for CASTEP calculations
api.slurm	Batch jobs via Slurm

System tools

Additional utility tools are available for common system tasks:

aton.file	Easy file manipulation
aton.alias	Useful dictionaries for user input correction
aton.call	Run bash scripts and related

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Contributing

If you are interested in opening an issue or a pull request, please feel free to do so on GitHub.
For major changes, please get in touch first to discuss the details.

Code style

Please try to follow some general guidelines:

• Use a code style consistent with the rest of the project.
• Include docstrings to document new additions.
• Include automated tests for new features or modifications, see automated testing.
• Arrange function arguments by order of relevance. Most implemented functions follow something similar to function(file, key/s, value/s, optional).

Automated testing

If you are modifying the source code, you should run the automated tests of the tests/ folder to check that everything works as intended. To do so, first install PyTest in your environment,

pip install pytest

And then run PyTest inside the ATON/ directory,

pytest -vv

Compiling the documentation

The documentation can be compiled automatically to docs/aton.html with Pdoc and ATON itself, by running:

python3 makedocs.py

This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the css/ folder.

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Citation

ATON development started for the following paper, please cite if you use ATON in your work:
Cryst. Growth Des. 2024, 24, 391−404

License

Copyright (C) 2025 Pablo Gila-Herranz
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the attached GNU Affero General Public License for more details.