Expand in-code documentation to ease potential contributions

[kallewesterling]

• [ ] Added some Black formatting to the files
• [ ] Added inline comments to the code explaining what it does in each step, to ease potential contributions
• [ ] Change name of extract_publications_text in the test files (from ept to full name extract_publications_text to make it easier to understand what's going on = see also #75)

Contributes to #72.

This was a step in the direction for me to wrap my head around what the code does and where. I want to see if I can take a stab at contributing something for #30 next.

[kallewesterling]

Don't know why black fails here since I'm formatting with black...?