<p align="center"><img width="50.0%" src="pics/aton.png"></p>
# Welcome to ATON
The **A**dvanced **T**ext **O**perations for scie**N**tific python,
or [ATON](https://pablogila.github.io/aton/),
is a package that provides powerful and comprehensive text-edition tools
to edit and analyse simuation data.
In a nod to its [ancient Egyptian deity](https://en.wikipedia.org/wiki/Aten) counterpart,
this Python package aims to provide straightforward, comprehensive tools
for easily creating custom interfaces for any text-based software.
The heart and soul of ATON is the [txt](#general-text-edition) module,
which simplifies the automation of text edition tasks.
It also includes an [api](#interfaces-for-ab-initio-codes) module with interfaces for simulation and HPC codes,
such as [Slurm](https://slurm.schedmd.com/documentation.html),
[Quantum ESPRESSO](https://www.quantum-espresso.org/),
[Phonopy](https://phonopy.github.io/phonopy/) and
[CASTEP](https://castep-docs.github.io/castep-docs/).
The source code is available on [GitHub](https://github.com/pablogila/aton/).
Check the [full documentation online](https://pablogila.github.io/aton/).
---
# Installation
As always, it is recommended to install your packages in a virtual environment:
```bash
python3 -m venv .venv
source .venv/bin/activate
```
## With pip
Install or upgrade ATON with
```bash
pip install aton -U
```
## From source
Optionally, you can install ATON from the [GitHub repo](https://github.com/pablogila/aton/).
Clone the repository or download the [latest stable release](https://github.com/pablogila/aton/tags)
as a ZIP, unzip it, and run inside it:
```bash
pip install .
```
---
# Documentation
The full ATON documentation is available [online](https://pablogila.github.io/aton/).
An offline version is found at `docs/aton.html`.
Code examples are included in the [`examples/`](https://github.com/pablogila/aton/tree/main/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](#interfaces-for-ab-initio-codes) module.
### [aton.txt](https://pablogila.github.io/aton/aton/txt.html)
| | |
| --- | --- |
| [txt.find](https://pablogila.github.io/aton/aton/txt/find.html) | Search for specific content in text files |
| [txt.edit](https://pablogila.github.io/aton/aton/txt/edit.html) | Manipulate text files |
| [txt.extract](https://pablogila.github.io/aton/aton/txt/extract.html) | Extract data from raw text strings |
## Interfaces for *ab-initio* and HPC codes
The **api** module contains Python interfaces for several *ab-initio* codes and related.
These are powered by the [aton.txt](#general-text-edition) module and can be easily extended.
### [aton.api](https://pablogila.github.io/aton/aton/api.html)
| | |
| --- | --- |
| [api.pwx](https://pablogila.github.io/aton/aton/api/pwx.html) | Interface for [Quantum ESPRESSO](https://www.quantum-espresso.org/)'s [pw.x](https://www.quantum-espresso.org/Doc/INPUT_PW.html) module |
| [api.phonopy](https://pablogila.github.io/aton/aton/api/phonopy.html) | Interface for [Phonopy](https://phonopy.github.io/phonopy/) calculations |
| [api.castep](https://pablogila.github.io/aton/aton/api/castep.html) | Interface for [CASTEP](https://castep-docs.github.io/castep-docs/) calculations |
| [api.slurm](https://pablogila.github.io/aton/aton/api/slurm.html) | Batch jobs via [Slurm](https://slurm.schedmd.com/) |
## System tools
Additional utility tools are available for common system tasks:
| | |
| --- | --- |
| [aton.file](https://pablogila.github.io/aton/aton/file.html) | Easy file manipulation |
| [aton.alias](https://pablogila.github.io/aton/aton/alias.html) | Useful dictionaries for user input correction |
| [aton.call](https://pablogila.github.io/aton/aton/call.html) | Run bash scripts and related |
---
# Contributing
If you are interested in opening an issue or a pull request, please feel free to do so on [GitHub](https://github.com/pablogila/aton/).
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](#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/`](https://github.com/pablogila/aton/tree/main/tests) folder to check that everything works as intended.
To do so, first install PyTest in your environment,
```bash
pip install pytest
```
And then run PyTest inside the `ATON/` directory,
```bash
pytest -vv
```
## Compiling the documentation
The documentation can be compiled automatically to `docs/aton.html` with [Pdoc](https://pdoc.dev/) and ATON itself, by running:
```shell
python3 makedocs.py
```
This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the `css/` folder.
---
# Citation
ATON development started for the following paper, please cite if you use ATON in your work:
[*Cryst. Growth Des.* 2024, 24, 391−404](https://doi.org/10.1021/acs.cgd.3c01112)
# 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.
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"description": "<p align=\"center\"><img width=\"50.0%\" src=\"pics/aton.png\"></p>\n\n\n# Welcome to ATON\n\nThe **A**dvanced **T**ext **O**perations for scie**N**tific python,\nor [ATON](https://pablogila.github.io/aton/),\nis a package that provides powerful and comprehensive text-edition tools\nto edit and analyse simuation data.\n\nIn a nod to its [ancient Egyptian deity](https://en.wikipedia.org/wiki/Aten) counterpart,\nthis Python package aims to provide straightforward, comprehensive tools\nfor easily creating custom interfaces for any text-based software.\n\nThe heart and soul of ATON is the [txt](#general-text-edition) module,\nwhich simplifies the automation of text edition tasks.\nIt also includes an [api](#interfaces-for-ab-initio-codes) module with interfaces for simulation and HPC codes,\nsuch as [Slurm](https://slurm.schedmd.com/documentation.html),\n[Quantum ESPRESSO](https://www.quantum-espresso.org/),\n[Phonopy](https://phonopy.github.io/phonopy/) and\n[CASTEP](https://castep-docs.github.io/castep-docs/).\n\nThe source code is available on [GitHub](https://github.com/pablogila/aton/). \nCheck the [full documentation online](https://pablogila.github.io/aton/). \n\n\n---\n\n\n# Installation\n\nAs always, it is recommended to install your packages in a virtual environment: \n```bash\npython3 -m venv .venv\nsource .venv/bin/activate\n```\n\n\n## With pip\n\nInstall or upgrade ATON with \n```bash\npip install aton -U\n```\n\n\n## From source\n\nOptionally, you can install ATON from the [GitHub repo](https://github.com/pablogila/aton/).\nClone the repository or download the [latest stable release](https://github.com/pablogila/aton/tags)\nas a ZIP, unzip it, and run inside it: \n```bash\npip install .\n```\n\n\n---\n\n\n# Documentation\n\nThe full ATON documentation is available [online](https://pablogila.github.io/aton/). \nAn offline version is found at `docs/aton.html`. \nCode examples are included in the [`examples/`](https://github.com/pablogila/aton/tree/main/examples) folder. \n\n\n## General text edition\n\nThe **txt** module is used to automate the editing of text files.\nIt enables the creation of more powerful interfaces,\nsuch as those from the [aton.api](#interfaces-for-ab-initio-codes) module.\n\n### [aton.txt](https://pablogila.github.io/aton/aton/txt.html)\n\n| | | \n| --- | --- | \n| [txt.find](https://pablogila.github.io/aton/aton/txt/find.html) | Search for specific content in text files | \n| [txt.edit](https://pablogila.github.io/aton/aton/txt/edit.html) | Manipulate text files | \n| [txt.extract](https://pablogila.github.io/aton/aton/txt/extract.html) | Extract data from raw text strings | \n\n\n## Interfaces for *ab-initio* and HPC codes\n\nThe **api** module contains Python interfaces for several *ab-initio* codes and related.\nThese are powered by the [aton.txt](#general-text-edition) module and can be easily extended.\n\n### [aton.api](https://pablogila.github.io/aton/aton/api.html)\n\n| | | \n| --- | --- | \n| [api.pwx](https://pablogila.github.io/aton/aton/api/pwx.html) | Interface for [Quantum ESPRESSO](https://www.quantum-espresso.org/)'s [pw.x](https://www.quantum-espresso.org/Doc/INPUT_PW.html) module | \n| [api.phonopy](https://pablogila.github.io/aton/aton/api/phonopy.html) | Interface for [Phonopy](https://phonopy.github.io/phonopy/) calculations | \n| [api.castep](https://pablogila.github.io/aton/aton/api/castep.html) | Interface for [CASTEP](https://castep-docs.github.io/castep-docs/) calculations | \n| [api.slurm](https://pablogila.github.io/aton/aton/api/slurm.html) | Batch jobs via [Slurm](https://slurm.schedmd.com/) |\n\n\n## System tools\n\nAdditional utility tools are available for common system tasks:\n\n| | | \n| --- | --- | \n| [aton.file](https://pablogila.github.io/aton/aton/file.html) | Easy file manipulation | \n| [aton.alias](https://pablogila.github.io/aton/aton/alias.html) | Useful dictionaries for user input correction | \n| [aton.call](https://pablogila.github.io/aton/aton/call.html) | Run bash scripts and related | \n\n\n---\n\n\n# Contributing\n\nIf you are interested in opening an issue or a pull request, please feel free to do so on [GitHub](https://github.com/pablogila/aton/). \nFor major changes, please get in touch first to discuss the details. \n\n\n## Code style\n\nPlease try to follow some general guidelines: \n- Use a code style consistent with the rest of the project. \n- Include docstrings to document new additions. \n- Include automated tests for new features or modifications, see [automated testing](#automated-testing). \n- Arrange function arguments by order of relevance. Most implemented functions follow something similar to `function(file, key/s, value/s, optional)`. \n\n\n## Automated testing\n\nIf you are modifying the source code, you should run the automated tests of the [`tests/`](https://github.com/pablogila/aton/tree/main/tests) folder to check that everything works as intended.\nTo do so, first install PyTest in your environment,\n```bash\npip install pytest\n```\n\nAnd then run PyTest inside the `ATON/` directory,\n```bash\npytest -vv\n```\n\n\n## Compiling the documentation\n\nThe documentation can be compiled automatically to `docs/aton.html` with [Pdoc](https://pdoc.dev/) and ATON itself, by running:\n```shell\npython3 makedocs.py\n```\n\nThis runs Pdoc, updating links and pictures, and using the custom theme CSS template from the `css/` folder.\n\n\n---\n\n\n# Citation\n\nATON development started for the following paper, please cite if you use ATON in your work: \n[*Cryst. Growth Des.* 2024, 24, 391\u2212404](https://doi.org/10.1021/acs.cgd.3c01112) \n\n\n# License\n\nCopyright (C) 2025 Pablo Gila-Herranz \nThis program is free software: you can redistribute it and/or modify\nit under the terms of the **GNU Affero General Public License** as published\nby the Free Software Foundation, either version **3** of the License, or\n(at your option) any later version. \nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. \nSee the attached GNU Affero General Public License for more details. \n\n",
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