Modernise build system

[lohedges]

This PR modernises the BioSimSpace build system by switching to pixi for environment creation/maintenance and rattler-build for building conda packages. This builds on top of the changes to the Sire build system introduced here. In addition, the PR also removes the outdated setup.py installation by introducing the a standard src/BioSimSpace layout using a pyproject.tom. I've also switched to using versioningit for package versioning for consistency with other downstream OpenBioSim packages.

Other unrelated changes are:

• Import Process base class through the sub-module __init__ to avoid lazy-loading issues.
• Sort imports to avoid Sandpit drift. The refactor to local imports script didn't have a sorting rule, so the imports in the Sandpit are randomised with respect to the core code, despite the rest of the code being identical. This makes it hard to diff the files.
• Add support for the recent namd3, which was released in late 2025.

This is the first time the CI will be run, so there might be minor issues to iron out.

Closes #358

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a test for any new functionality in this pull request: [y]
• I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[lohedges]

This is because rattler-build only copies the first entry in the source list to the test directory! For BioSimSpace, we had entries for the python code and test files, since we run black check on the source too. The second entry was silently ignored, hence pytest not being able to find the test files. It's a strange omission, since it's so simple to implement.

One other thing to note is that it looks like test files might be included in the final package, so this would be a good reason not to duplicate the source. I'll check this and consider moving to pre commit, or similar. The legacy black check was essentially a fail-safe.

[lohedges]

Finally fixed all the CI issues, what an absolute pain. Turns out the version of rattler-build that comes with their own action had a load of weird bugs. Changing everything to manually install via pixi works, although there are some differences in the way the test environment handles PYTHONPATH, etc. Will merge this tomorrow and move on to the other packages.