mofdscribe: A Python repository from hspark1212

Featurizing metal-organic frameworks (MOFs) made simple! This package builds on the power of matminer to make featurization of MOFs as easy as possible. Now, you can use features that are mostly used for porous materials in the same way as all other matminer featurizers. mofdscribe additionally includes routines that help with model validation.

💪 Getting Started

from mofdscribe.featurizers.chemistry import RACS
from pymatgen.core import Structure

structure = Structure.from_file(<my_cif.cif>)
featurizer = RACS()
racs_features = featurizer.featurize(structure)

🚀 Installation

While we are in the process of trying to make mofdscribe work on all operating system (we're waiting for conda recipies getting merged), it is currently not easy on Windows (and there might be potential issues on ARM-based Macs). For this reason, we recommend installing mofdscribe on a UNIX machine.

To install in development mode, use the following:

git clone git+https://github.com/kjappelbaum/mofdscribe.git
cd mofdscribe
pip install -e .

if you want to use all utilities, you can use the all extra: pip install -e ".[all]"

We depend on many other external tools. Currently, you need to manually install these dependencies (due to pending merges for conda-recipies):

# RASPA and Zeo++ (if you want to use energy grid/Henry coefficient and pore descriptors)
conda install -c conda-forge raspa2 zeopp-lsmo

# cgal dependency for moltda (if you want to use persistent-homology based features)
# on some systems, you might need to replace this with sudo apt-get install libcgal-dev or brew install cgal 
conda install -c conda-forge cgal dionysus

# openbabel dependency for moffragmentor (if you want to use SBU-centered features)
conda install -c conda-forge openbabel

👐 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.

📖 Citation

See the ChemRxiv preprint.

@article{Jablonka_2022,
	doi = {10.26434/chemrxiv-2022-4g7rx},
	url = {https://doi.org/10.26434%2Fchemrxiv-2022-4g7rx},
	year = 2022,
	month = {sep},
	publisher = {American Chemical Society ({ACS})},
	author = {Kevin Maik Jablonka and Andrew S. Rosen and Aditi S. Krishnapriyan and Berend Smit},
	title = {An ecosystem for digital reticular chemistry}
}

💰 Funding

The research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 666983, MaGic), by the NCCR-MARVEL, funded by the Swiss National Science Foundation, and by the Swiss National Science Foundation (SNSF) under Grant 200021_172759.

🍪 Cookiecutter

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

🛠️ For Developers

See developer instructions

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:

Uses BumpVersion to switch the version number in the setup.cfg and src/mofdscribe/version.py to not have the -dev suffix
Packages the code in both a tar archive and a wheel
Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
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.

hspark1212/mofdscribe