Move `pymcubes` to an optional dependency.

[willGraham01]

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Description

What is this PR

• [ ] Bug fix
• [ ] Addition of a new feature
• [x] Other

Why is this PR needed?

PyMCubes is a dependency that is only required during atlas generation, and currently doesn't have an ARM package on conda-forge.

Forcing it to be a core dependency results in failed builds when installing via conda-forge, and since it's not needed for registration, we have decided to move it to an optional atlasgen dependency that users will not obtain by default.

After this, we'll need a new PyPI release and then to fix the corresponding conda-forge feedstock PR that will be created.

What does this PR do?

Moves PyMCubes (and other altas-generation only) dependencies to an optional atlasgen dependency group.

References

https://github.com/brainglobe/brainreg/issues/206

How has this PR been tested?

Local pip install -e ..

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

• [ ] The code has been tested locally
• [ ] Tests have been added to cover all new functionality (unit & integration)
• [ ] The documentation has been updated to reflect any changes
• [ ] The code has been formatted with pre-commit

[adamltyson]

Should we add other packages that aren't needed for the atlasAPI? Maybe ITK is one?

[willGraham01]

A quick search of this repo indicates that the following packages are only used in the atlas_generation/ submodule:

• loguru
• PyMCubes
• SimpleITK
• tqdm
• vedo
• xmltodict

Also, we seem to be fetching scikit-image but never actually importing it... so I guess it can just go?

Changes applied in https://github.com/brainglobe/brainglobe-atlasapi/pull/310/commits/663bb21e13f635bbda8976621dd3c1050dd12015

[willGraham01]

https://github.com/brainglobe/brainglobe.github.io/issues/203

Will also publish a new release once the tests pass on main.