4.2

[BradyAJohnston]

This PR changes Molecular Nodes to be compatible with the Blender 4.2 extensions system, and brings a number a number of other major upgrades.

Extensions Platform

Changed architecture of add-on to be compatible with new extensions platform in Blender 4.2 (here). Bundles the add-on with the required python packages, so installation is as simple as clicking 'install' from inside of Blender's extension system. No need to manually download or install anything additional. Updates for the add-on can also be delivered and installed this way.

Nodes

Color Tag

Utilising the new color_tag attribute for custom node groups, all provided node groups are now colored appropriately.

Selection Nodes

Selection nodes have been split into individual node groups and given And and Or inputs to more easily construct selection chains with common boolean operations.

Topology Nodes

Topology nodes have been partially overhauled, with some nodes moved to utility nodes and extras included such as the DSSP and Phi / Psi nodes. Phi / Psi nodes do not require pre-computation of any values and can be used just like any other field.

Color Nodes

Res Name and Element nodes now go higher, utilising the Index Switch node underneath and panels to ensure the UI remains usable.

Trajectories

The underlying method for importing and managing MDAnalysis trajectory / Universes has been overhauled. They are now imported as a Trajectory object. Trajectories along with all other molecular data that is imported is now kept around inside of a MNSession, which is stored under bpy.context.scene.MNSession. This session is pickled and save next to the .blend file on save, so that all of the data can persist between Blender sessions on load.

Selections

Because the connection to the universe is maintained, we now have live and updateable selections.

Calculations

Initial support for functions can be added to the Trajectories. These functions will be executed with the universe as an input, and the output is stored on the resulting mesh. This gives access to custom calculations to be executed in python and the results to be used inside of Geometry Nodes.

Implement changes for compatibility with Blender 4.2

Current build is approved and hosted on the extensions website - need to finish final changes before 4.2 release (https://extensions.blender.org/add-ons/molecularnodes/)

• Change to distribution via the Blender Extensions platform (Support Extensions Platform #500)
• Add support for 4x4 matrix data format (Support 4x4 matrix data type #499)
• Change node groups to using colors and add descriptions (Update nodes with colors and split attributes into single nodes #522)
• Test cleanout of superfluous .whl files (like numpy, which is included with Blender)
• Refactor MD selections to be 'live' rather than only on import (Adds 'Live' MDAnalysis Selections #466)
• All relevant documentation is updated
• Update default materials and include some more (Defaul Materials #465)
• Cleanup the add node menu (cleanup and reorganise node add menu #537 )
• Update tests to run by building and installing the add-on
• Change panel to use new panel code
• Support adding selections from existing AtomGroups (Selection from atomgroup #538)
• Rename MNUniverse to Trajectory (Rename MNUniverse to Trajectory #541 )

Some feedback from extensions approval:

• Cleanup commented out lines of the blender_manifest.toml
• .DS_store and some other files can be cleaned up (potentially download .whl files then use Blender to build package)
• remove requirements.txt file as no longer needed for package management

[codecov]

Codecov Report

Attention: Patch coverage is 65.53899% with 601 lines in your changes missing coverage. Please review.

Project coverage is 71.11%. Comparing base (9c1f566) to head (7dfd9ea).
Report is 29 commits behind head on main.

Files	Patch %	Lines
molecularnodes/io/molecule/ui.py	43.06%	115 Missing ⚠️
molecularnodes/ui/panel.py	9.87%	73 Missing ⚠️
molecularnodes/ui/ops.py	45.76%	64 Missing ⚠️
molecularnodes/blender/nodes.py	62.72%	63 Missing ⚠️
molecularnodes/io/trajectory/selections.py	51.88%	51 Missing ⚠️
molecularnodes/io/trajectory/trajectory.py	83.33%	49 Missing ⚠️
molecularnodes/session.py	72.72%	36 Missing ⚠️
molecularnodes/io/ensemble/star.py	83.44%	25 Missing ⚠️
molecularnodes/io/ensemble/ui.py	62.00%	19 Missing ⚠️
molecularnodes/__init__.py	60.46%	17 Missing ⚠️
... and 12 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #501      +/-   ##
==========================================
- Coverage   76.06%   71.11%   -4.96%     
==========================================
  Files          42       48       +6     
  Lines        3786     4106     +320     
==========================================
+ Hits         2880     2920      +40     
- Misses        906     1186     +280     

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