Conservedwatersearch

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Added
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- Dependabot now uses groups

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

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

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

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

Fixed
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- 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

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- 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

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- 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

=================

- 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

v.0.1.0