kjappelbaum/element-coder

Encode chemical elements numerically and decode numerical representations of elements.

element_coder

Encode chemical elements numerically and decode numerical representations of elements.

💪 Getting Started

from element_coder import encode, decode

decode(encode('Si', 'mod_pettifor'), 'mod_pettifor')
>'Si'

Command Line Interface

The element_coder.encode and element_coder.decode command line tools are automatically installed. They can be used from the shell with the --help flag to show help:

$ element_coder.encode H
102

$ element_coder.decode 102
H

also works for vector-valued encodings

$ element_coder.decode 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 --property cgcnn
H

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install element_coder

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/kjappelbaum/element-coder.git

To install in development mode, use the following:

$ git clone git+https://github.com/kjappelbaum/element-coder.git
$ cd element-coder
$ pip install -e .

Background

For some applications (of ML in chemistry) elements must be numerically encoded. There are many libraries that do that. For most applications, even pymatgen can get the job done:

from pymatgen.core import Element
def encode_element(element: Element, property: str):
    return getattr(element, property)

However, this code has some issues, wherefore there are many other libraries that attempt to solve this issue including mendeleev, elementy, EIMD. However,

• none of these libraries supported all the properties I was interested in
• none of these libraries supported decoding of descriptors into Elements.

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instrutions

The final section of the README is for if you want to get involved by making a code contribution.

❓ Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses BumpVersion to switch the version number in the setup.cfg and src/element_coder/version.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.