aiida-atoms

AiiDA Plugin for keeping track of structure manipulations of an ase.Atoms objects. Every operation acted through the AtomsTracker object will be recorded on the provenance graph.

Repository contents

• .github/: Github Actions configuration
  • ci.yml: runs tests, checks test coverage and builds documentation at every new commit
  • publish-on-pypi.yml: automatically deploy git tags to PyPI - just generate a PyPI API token for your PyPI account and add it to the pypi_token secret of your github repository
• aiida_atoms/: The main source code of the plugin package
• docs/: A documentation template ready for publication on Read the Docs
• examples/: An example of how to submit a calculation using this plugin
• tests/: Basic regression tests using the pytest framework (submitting a calculation, ...). Install pip install -e .[testing] and run pytest.
• .gitignore: Telling git which files to ignore
• .pre-commit-config.yaml: Configuration of pre-commit hooks that sanitize coding style and check for syntax errors. Enable via pip install -e .[pre-commit] && pre-commit install
• LICENSE: License for your plugin
• README.md: This file
• conftest.py: Configuration of fixtures for pytest
• pyproject.toml: Python package metadata for registration on PyPI and the AiiDA plugin registry (including entry points)

Features

• Automatic tracking of changes made to ase.Atoms object through its methods, and saving them to the provenance graph.
• Wrapped other common routines that records provenance for tracking.
• Provenance graph visualization.

Installation

pip install aiida-atoms

Usage

Development

git clone https://github.com/zhubonan/aiida-atoms .
cd aiida-atoms
pip install --upgrade pip
pip install -e .[pre-commit,testing]  # install extra dependencies
pre-commit install  # install pre-commit hooks
pytest -v  # discover and run all tests

License

MIT

Contact

zhubonan@outlook.com