Fixing deprecations

[sethaxen]

There are quite a few deprecation warnings being emitted after CI on Python 3.10 that we should fix to avoid future breakage (e.g. this would have caught #62 before it became a problem for users). For example, see https://github.com/keiserlab/e3fp/runs/6722979838?check_suite_focus=true#step:6:105

The following is a not-necessarily-complete list:

• SafeConfigParser -> ConfigParser
• scipy.sqrt -> np.lib.scimath.sqrt
• np.matrix -> np.ndarray
• scipy.corrcoef -> np.corrcoef
• np.bool -> bool
• np.float -> float
• np.long -> int
• np.int -> int

For the latter 3, we need to examine each usage to ensure that the chosen type does not introduce an OS/architecture dependency regarding which fingerprint is returned.