hybrid notebook tests are non-deterministic

[wholtz]

The number of groups is sometimes 6 instead of the expected 4.

[bkieft-usa]

This also happens when export_msms_fragment_ions is set to True within analysis.parameters. This setting causes process.py to call write_msms_fragment_ions() within targeted_output.py, which prints out a csv file that contains all fragment ions from the MSMS instead of just fragment ions that match the reference. The file with the highest fragment ion intensity is not always in the same position in the list that is returned. This was discovered because if the file with the highest intensity is the index of 0, there was an if statement (basically, if index, which on 0 skipped the statement) that caused no fragment ions to be printed to the spectra_0.00pct_0cut.csv file.