v0.3.0

Summary

Support Python 3.12 only.

Background:

• Python 3.8 to 3.11 only receives security support anymore, the current latest version is 3.12: https://devguide.python.org/versions/
• Since this package is intended as a standalone tool to visualize dynophore data, we focus on the latest Python version 3.12.

Changed

• Update setup.py Python version from >=3.8 to >=3.12
• Update versioneer.py so that it is compatible with Python 3.12
• Update CI Python version to 3.12 (drop support for 3.8, 3.9, and 3.10)
• Migrate deprecated matplotlib seaborn style from seaborn to seaborn-v0_8, fixes #65
• Fix black and flake8 issues due to Python update
• Drop support for black-nb and flake8-nb to lower maintenance burden of this repo

v0.2.2

Summary

Updated dependencies, API changes in pandas, documentation, and CI setup.

Changed / fixed

Package / dependencies

• Pin ipywidgets < 8 to solve #59 by @dominiquesydow in #60
• Update package w.r.t. new black & pandas versions by @dominiquesydow in #64

Documentation

• Fix CLI usage in docs by @dominiquesydow in #43
• Improve documentation by @dominiquesydow in #46
• Update user guide in docs by @dominiquesydow in #42
• Add docs on how to save figures by @dominiquesydow in #53
• Update install details with conda-forge channel by @dominiquesydow in #55

Repository / CI

• Replace in GH URLs dominiquesydow with wolberlab by @dominiquesydow in #47
• Upgrade codecov-action to v2 by @dominiquesydow in #49
• Trigger CI by @dominiquesydow in #56
• Fix docs CI by @dominiquesydow in #57
• Update CI schedule to Mondays 3 am UTC by @dominiquesydow in #61
• Update GHA CI.yml file by @dominiquesydow in #63

Full Changelog: v0.2.1...v0.2.2

v0.2.1

Changes

• Update notebooks (docs dynophore and library template notebook)
  • Add introduction text (what are dynophores and how to work with them)
  • Add description to each section, especially comment on all options for 3D view
• Update 3D view method arguments (select_cloud_range to frame_range)

v0.2

New

• Uses new output structure from dynophore_0_31 installer
• Added Ligand class; added as attribute to Dynophore class
• Indicate in distance series plot, which frames show interaction events; show in distance histograms only frames with interaction events (#35)
• Add option to collapse envpartners with same residue/different atoms for one superfeature (#36)
• Add pocket residue side chains (#28)
• Add temporal resolution of dynophores clouds by using point frame index (#32)
• Add 2D ligand view with highlighted features as done in KinFragLib (#17)

Changes

• Optimizes interactive plots for large dynophores
• Use matplotlib.pyplot.eventplot for occurrence plots instead of simple dot plots (#23)

More details

See more details in #8

Initial release

First functional dynophores release containing:

• First round of 3D visualization of dynophores (nglview) and interactive plots on dynophores statistics (ipywidgets) including the dynophores API for easy data manipulation
• CI and documentation (https://dynophores.readthedocs.io/en/latest/)
• CLI to create/re-open dynophore notebook

I will cut this release so that users can give us feedback on this first version of this package.