split skbio.util.exception into subpackage-specific exception modules

[jairideout]

@ebolyen, @gregcaporaso, and I discussed the following:

skbio.util.exception has many exceptions, most of which are specific to subpackages. For example, there are several exception classes specific to distance matrices, while others are specific to trees. Many of the names are not immediately obvious; for example, it isn't clear what skbio.util.exception.NoLengthError refers to (it happens to be a tree-related error, but could easily apply to a sequence or alignment). Likewise, it isn't obvious that skbio.util.exception.MissingIDError is related to distance matrices.

We propose that each subpackage has its own exception (and warning, if there are any) module with these custom types defined. These exceptions/warnings will be included in the subpackage documentation, just as functions and classes are documented.

This has the advantage of making the exception types clearer; in the above example, skbio.tree.exception.NoLengthError is more descriptive than skbio.util.exception.NoLengthError. This also prevents us from having a huge exception/warning file that contains all exceptions/warnings defined in scikit-bio.

If there are any truly general exceptions or warnings, these will live at a top-level skbio.exception/skbio.warning module.

Assigning to myself.

[wasade]

+1, that is awesome. A subpackage specific error module could be useful too

[gregcaporaso]

👍