graphchem 2.3.4

Summary

API-stable modernization release. Public callables and behavioral contracts are unchanged.

Highlights

• src/graphchem/ layout; rdkit replaces rdkit-pypi; dependency ranges; Python 3.10+
• Contract suite, encoding oracles, coverage ≥90%, CI matrix + lint/docs jobs
• Sphinx + Furo docs; governance files; OIDC PyPI publish workflow

Deferred to 2.4.0

• JSON encoder serialization, CLI, pretrained weights, benchmark harness

See CHANGELOG.md for full notes.

Note: PyPI upload requires a GitHub Environment named pypi and a matching PyPI trusted publisher for graphchem.

Bug fix

Fixes import for rdkit Chem module

Update type hints

Add quotes to RDKit atom/bond object type hints, plays nicer with RDKit imports

Update version

Version bump: 2.2.0 -> 2.3.1

MoleculeGCN updates

• add option to omit MoleculeGCN readout layer(s)
• add option to specify MoleculeGCN activation function
• add comments throughout MoleculeGCN

Various improvements

• better handling of target variable tensors with varying shapes
• add .gitignore
• updates to docstrings, type hints
• add unit tests
• updates to example notebooks
• update dependency versions
• version bump: 2.1.4 -> 2.2.0

Update dependencies

• numpy==1.26.4

Update dependencies, add MANIFEST.in

• updates PyTorch to 2.4.0
• adds MANIFEST.in for including CSV datasets with GraphChem
• bump version to 2.1.3

Update install method, PyPI GitHub actions workflow, encoder saving/loading

• graphchem.preprocessing.MoleculeEncoder how has the save and load methods
• graphchem.preprocessing.load_encoder allows users to load pre-saved MoleculeEncoder objects
• Build/installation now relies on pyproject.toml instead of the deprecated setup.py
• Added a GitHub action workflow to publish GraphChem to PyPI whenever a new version is published

2.1.1

Use pre-built RDKit binaries
Added readthedocs API documentation
Preparing for Azure unit testing