Add Dimensions.__contains__

[mruffalo]

This allows straightforward checking of whether dimension S is present, since the interface of this class previously made this a bit clumsy.

Link to Relevant Issue

This pull request resolves #68.

Description of Changes

Implement Dimensions.__contains__, with similar semantics as __getitem__: accept a str or Sequence[str] and return True if all dimensions are present.

The isort, autoflake, and black lint steps passed, but flake8 and mypy fail both on current main and with my changes.

[BrianWhitneyAI]

I dont think we need the error handling since the function is typed.
maybe something like

  def __contains__(self, key: Union[str, Sequence[str]]) -> bool:
      if isinstance(key, str):
          return key in self._dims_shape
      return all(k in self._dims_shape for k in key)

[mruffalo]

That's fine with me -- I mimicked the same input type handling in __getitem__, and in this case it would just be a difference in the friendliness of the TypeError message. Without that error checking, one would see something like TypeError: 'int' object is not iterable if checking whether 3 in img.dims.

Despite the type hint, I would probably just expect object_of_incompatible_type in img.dims to return False, but I don't have a big stake in this.

[SeanDuHare]

If it is possible to supply the wrong type then this seems fine with me - python specific function like this tend to be lenient

[BrianWhitneyAI]

looks like linting is failing for these changes, maybe some config differences between your local setup and the repo defined setup?

- hook id: mypy
- exit code: 1

bioio_base/dimensions.py:160: error: Function is missing a return type annotation  [no-untyped-def]
bioio_base/dimensions.py:164: error: "type[Sequence[Any]]" has no attribute "__iter__" (not iterable)  [attr-defined]
Found 2 errors in 1 file (checked 22 source files)

[mruffalo]

Thanks @BrianWhitneyAI; I missed a return type declaration and fixed an actual typo in my original commit. I have not yet made any changes in reply to #69 (comment).

[mruffalo]

Squashed that follow-up commit as a fixup to avoid having something obviously broken in the commit history.

[mruffalo]

@BrianWhitneyAI @SeanDuHare I was just about to say that I pushed another commit implementing the following behavior:

• if checking membership of a sequence (but not a str), return True if all elements are present
• otherwise return membership of the passed item

with no TypeErrors thrown.

While typing this, I saw the PR approval -- thanks!