Remove nrrd IO

[adamltyson]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
pynrrd seems to be causing a few issues with newer versions of Python (t doesn't seem to have been updated for 2 years). Mostly because it uses nptyping, which itself needs updating.

However, I don't think we need nrrd IO functionality in brainglobe, because we only deal with tiffs and nii. We may use this functionality in the atlas generation code, but I think if we do, it should be a specific requirement for that script (and not for the whole of brainglobe as it is at the moment).

Keen to know if this is going to break anything, but I don't think it should.

What does this PR do?
Removes all nrrd IO code. It also removes (what I think is) some outdated error/warning handling.

References

N/A

How has this PR been tested?

Removed nrrd tests, and ran other tests as normal.

Is this a breaking change?

I don't think so.

Does this PR require an update to the documentation?

Yes, the reference to nrrd IO needs to be removed from the website docs.

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.43%. Comparing base (6185777) to head (38c21ac).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #82      +/-   ##
==========================================
- Coverage   90.53%   90.43%   -0.11%     
==========================================
  Files          35       35              
  Lines        1427     1411      -16     
==========================================
- Hits         1292     1276      -16     
  Misses        135      135              

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[alessandrofelder]

I am happy to approve this - the changes look reasonable. A double-check of our org suggests that it wouldn't break anything (apart from maybe some atlas generation parts, as implied in the PR summary.