Peptacular

Added:
- speed_test.py to examples and more examples!
- more term functions! pop_c_term & pop_n_term & _get_c_term_index & _get_n_term_index
- split_sequence function to sequence.py, which splits a sequence into a list of modified single residues
- pop_modifications function to sequence.py, since it's useful!

Changed
- fragment.fragment now returns a list rather than a generator
- identify_cleavage_sites no longer returns cleavage sites at the beginning or end of the sequence (x)PEPTIDE(x)
- removed the x's appended onto sequence when calculating sites
- fixed bug with non-specific digestion
- made term functions more robust, using _get_c_term_index & _get_n_term_index when possible
- split term.py into term.modification and term.residue (it just got too large)

Added:
- term.py - a module for handling terminal modifications
- readthedocs 'sphynx-style' documentation
- examples folder

Changed:
- split up sequence module into sequence and digest
- split mass module into fragment and mass
- updated term modification notation to use square brackets
- renamed most functions... again
- updated documentation to be compatible with sphynx

Added:
- score.py - a module for scoring peptide matches

Changes:
- made Fragment dataclass frozen

Removed:
- removed indexing code from mass.py

Added:
- Fragmenter.py - an easier to use peptide fragmenter (returns dataclasses)
- Internal fragment ion support

Changes:
- fixed bug with C-Term PTMs

Added:
- spans.py to handle generating peptide spans from cleavage site info
- masses.py to handle generating peptide masses from sequences

Removed:
- refseq module - was a dumb idea

Added:
- fragment ion
- peptide mass and mz functions

Changes
- converted peptide.py to sequence.py (makes more sense since proteins are also sequences of amino acids)