MAINT: update deprecated code from dependencies and remove warnings filters

[rossbar]

The current pytest configuration is suppressing all deprecation warnings, which includes warnings from dependency libraries. This makes it much more likely for code to fall out-of-date, as can be seen in the recent failing CI jobs due to changes in the lastest version of numpy which was just releases (1.24).

This PR addresses the issue in two ways:

1. Updates code to take into account changes in the underlying libraries, and
2. Removes the global warnings filter in favor of fine-grained warnings filtering.

The second bullet involves adding explicit checks for warnings raised by deepcell-toolbox itself, to ensure that warnings are being raised correctly in the expected cases.

[msschwartz21]

LGTM! This seems like a particularly good change to the testing workflow because I know I've been guilty of ignoring those deprecation warnings for a long time...