Find and correct copy / paste errors and typos and minor code fixes

[cjgrady]

Describe the bug

There are some copy / paste errors and typos that were generated when new scripts were created that are very similar to others (ex. wrangle_species_list, wrangle_matrix, etc.). @zzeppozz has seen a few of these errors and there are others to be found. Carefully look through the code and fix as many of these as possible before releasing version 3.2.

There are a few of other things that can be improved found by lgtm (https://lgtm.com/projects/g/specifysystems/lmpy/?mode=list).

Clean things up as much as possible for version 3.2.

Note any problems encountered here.

To fix:

• Issues at https://lgtm.com/projects/g/specifysystems/lmpy/?mode=list
• lmpy.tools.wrangle_species_list -> program name is wrong (wrangle_matrix)
• Fix double file extension for generated temporary files
• Document using the data wrangler factory with module specifications

[cjgrady]

Double file extension and wrangle_species_list program were fixed in f4223d8

[zzeppozz]

Tons of untested code fixed