Lint, guard Molecule import

[mattwthompson]

Fixes #56

Changes made in this Pull Request:

• Update pre-commit config
• Re-run linters
• Avoid Molecule import at high-level import time

>>> import sys
>>> from openff.nagl import __version__
>>> len([key for key in sys.modules if key.startswith("openff.toolkit.utils")])
# upstream/main -> HEAD
12 -> 11
>>> len([key for key in sys.modules if key.startswith("openff.toolkit.topology")])
4 -> 0

Questions

• Since some of the wrappers here import from various openff.toolkit.utils classes, I'm not sure if all toolkit imports can easily be guarded
• Import time on my machine is really slow - I haven't profiled this but I'm assuming it's heavy upstreams (PyTorch? DGL?)
• Open to adding the https://pre-commit.ci/ bot here? Mostly to keep the config up-to-date

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov-commenter]

Codecov Report

Merging #57 (07fef28) into main (707926f) will increase coverage by 0.00%.
The diff coverage is 86.02%.

Additional details and impacted files

[lilyminium]

Would it be possible to separate out the linting from the Molecule imports? It's a bit difficult to see what's meaningfully changed 😅

[lilyminium]

Since some of the wrappers here import from various openff.toolkit.utils classes, I'm not sure if all toolkit imports can easily be guarded

That's a good point. The toolkitwrappers are also somewhat separate from the rest of the code though and should mostly be used in featurising -- I suspect that the vast majority of the imports of openff.nagl.toolkits actually import capture_toolkit_warnings, a non-essential utility that we could potentially upstream (it fixes openforcefield/openff-toolkit#1655).

[lilyminium]

Import time on my machine is really slow - I haven't profiled this but I'm assuming it's heavy upstreams (PyTorch? DGL?)

Raised #58 to look at!

[lilyminium]

Open to adding the pre-commit.ci bot here? Mostly to keep the config up-to-date

Sure :)

[mattwthompson]

I think I'll probably two this in two (independent) steps

1. Lint, possibly with a few smaller PRs into a staging branch so that each can be accepted or declined more easily
2. Guard toolkit imports, including both Molecule and wrappers (possibly requiring Do not raise warning when allow_undefined_stereo=True openff-toolkit#1705?)