[DNM]: Conversion to version 0.0.3

[mattwthompson]

This PR is not to be merged, it's only to document the process I took.

• [x] Remove stereochemistry from SMIRKS patterns (fixes #38)
• [x] Use fractional_bondorder_method = "AM1-Wiberg" (fixes #37)
• [x] Port tests in parameter_deduplication notebook to pytest tests
• [x] Run test ALA-ALA test (1 passed in 16.47s)
• [x] Run T4 test (forgot how long, but on the order of hours)

[mattwthompson]

This is linked to from various place in releases, no need to keep open.