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https://github.com/kjappelbaum/structuregraph-helpers
Helpers for working with pymatgen structure graphs.
https://github.com/kjappelbaum/structuregraph-helpers
chemistry computational-materials-science graph materials-informatics materials-science pymatgen structure structure-graph
Last synced: about 1 month ago
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Helpers for working with pymatgen structure graphs.
- Host: GitHub
- URL: https://github.com/kjappelbaum/structuregraph-helpers
- Owner: kjappelbaum
- License: mit
- Created: 2022-07-28T06:32:25.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-23T22:44:37.000Z (3 months ago)
- Last Synced: 2024-09-27T06:10:44.222Z (3 months ago)
- Topics: chemistry, computational-materials-science, graph, materials-informatics, materials-science, pymatgen, structure, structure-graph
- Language: Python
- Homepage: https://structuregraph-helpers.readthedocs.io
- Size: 140 KB
- Stars: 9
- Watchers: 3
- Forks: 1
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
Awesome Lists containing this project
README
structuregraph_helpers
Utilities for working with `pymatgen` structure graphs.
## 💪 Getting Started
```python
import structuregraph_helpers as sgh
mols, graphs, indices, centers, coordinates = sgh.subgraphg.get_subgraphs_as_molecules(structuregraph)
graph_hash = sgh.hash.decorated_graph_hash(structuregraph)
scaffold_hash = sgh.hash.decorated_scaffold_hash(structuregraph)
```
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/structuregraph_helpers/) with:
```bash
$ pip install structuregraph_helpers
```
The most recent code and data can be installed directly from GitHub with:
```bash
$ pip install git+https://github.com/kjappelbaum/structuregraph-helpers.git
```
To install in development mode, use the following:
```bash
$ git clone git+https://github.com/kjappelbaum/structuregraph-helpers.git
$ cd structuregraph-helpers
$ pip install -e .
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.rst](https://github.com/kjappelbaum/structuregraph-helpers/blob/master/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](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/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:
```shell
$ tox
```
Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/kjappelbaum/structuregraph-helpers/actions?query=workflow%3ATests).
### 📦 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:
```shell
$ tox -e finish
```
This script does the following:
1. Uses BumpVersion to switch the version number in the `setup.cfg` and
`src/structuregraph_helpers/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.