Release v0.4.1

Release v0.4.1 - 05/10/2024

Added

• Dependabot now uses groups

Fixed

• Fixed CI for PyMOL 3 release
• Fixed CI for version releases
• Made defaults in WaterClustering consistent with HydrogenClustering.

Merge pull request #61 from JecaTosovic/release/v0.4.0

Release v0.4.0 - 04/09/2024

Added

• pre-commit support
• Theory section in the documentation has been added

Fixed

• Various improvements to documentation
• Fixed bug which prevent clustering on only oxygen data
• Fixed visualization bug for visualizing results of oxygen only clustering

Release v0.3.0

Release v0.3.0 - 10/20/2023

Breaking changes

• WaterClustering Class Update: Changed input parameters. All options, including method and clustering algorithm, are now set during the class creation.
• Unified Output Format: Output now streamlined into a single file. This file includes all clustering options and details of conserved waters, such as coordinates and types.
• New Run Method: Added Run method capable of executing all three methods: single clustering, MSRC, and quick MSRC.
• Restarting Methods Overhaul: Methods have been revamped to align with the new output structure.
• Results Reading Methods Update: Adjusted to be compatible with the new output format.

Added

• Added support for python 3.12
• CWS uses HDBSCAN from scikit-learn now
• New visualization options for pymol

Fixed

• Fixed visualization failing when no waters are found
• Smaller issues with docs in water clustering class
• Updated install docs
• Various other doc updates
• Fixed MSRC not looping properly over water types

v0.2.0

Release v0.2.0 - 9/5/2023

• Dropped support for python 3.8
• Switch to sklearn HDBSCAN implementation
• Changed requirements and added optional requirements - nglview and matplotlib are NOT installed by default
• add options to visualise_pymol to stop pymol startup and reinitialization
• Quick version of MSRC was added which does not reset the clustering parameter scan after a good cluster is found
• fixed MSRC missing the outermost loop over the water types

v0.1.2

Release v0.1.2 - 2/17/2023

• fixed a bug in pymol visualization when no output file was specified
• fixed wrong logic in pymol visualization when aligned reference is specified
• added a better warning when mac OS is used with pymol visualization
• if pymol visualization on mac OS is used without output file specified, we still save the session to a file instead of failing
• updates to docs for pymol visualization

v0.1.1

Release v0.1.1 - 2/11/2023

• conda-forge release
• updates to install docs
• updates to docs all around
• Minor bug fixes in visualisation
• python 3.11 suport
• remove python 3.7 support

Release beta version v0.1.0 - 29/12/2022

First beta version release v0.1.0

Updates and changes:

• Moved oxygen clustering and visualisation procedures to ConservedWaterSearch
• Updated documentation to include examples and detailed installation
• Changes to the API and variable names
• Added citation
• Remove support for python 3.6 and add support for python 3.11
• Added type hints
• Various bugfixes and documentation fixes

v0.0.1

First release