Upgrade to Blender 4.1

[BradyAJohnston]

Upgrading to 4.1 includes some changes. Branches for 4.1 will be merged into this branch, which will then be merged into main when ready to release.

• Change python environment to python==3.11
• upgrade biotite to 0.40.0
  • update tests for bond edges
  • change main import method to .bcif
• Change main nodes over to using menus
• Update documentation with new looking nodes
• Fix problems with testing suite
• Fix assembly creation via API
• Stops downloading so much and uses the tests/data as the cache directory and includes all testable structures in the repo

Issues with bpy 4.1:

• segfaulting the docs build (segfault when loading a .blend file) on ubuntu-latest GHA
• Unable to install on MacOS ARM
• Getting strange error with testing on windows / linux. All tests pass but there is an error / segfault on teardown so tests fail on GHA

The only reliable way to install an run tests seems to be running through actual Blender

Has been an absolute nightmare to to get the testing suite running again. As bpy is not installable on windows and segfaults on other platforms, I have switched it over to download full Blender and then run the test through Blender.

This does have the advantage of testing density import on each platform not just linux. Testing in 'full' Blender could be more robust. Doesn't test for installing in python, but as it's broken it just isn't testable currently

EDIT: Not going to update the look / menu of the nodes. Going to create a release from this and then deal with updated nodes later.