begin new_alignment.SequenceCollection

[GavinHuttley]

Waiting on #1866

• Create a SequenceCollection class
• SequenceCollection(seq_data=, moltype=..)
• type hints the constructor
• Assigns seq_data to a _seq_data attribute
• Assigns self._seq_data.seq_maker = self.moltype.make_seq
• Implements a seqs property which returns the _seq_data
• Ports relevant tests from test_alignment.py into test_new_alignment.py, converting them into pytest style (sorry!)
• Implements a named_seqs property, which just returns .seqs . Deprecate this method and point to just using .seqs (give this 12 months).

[KatherineCaley]

@GavinHuttley will the new class be inheriting from _SequenceCollectionBase?

[GavinHuttley]

No. _SequenceCollectionBase is an artefact of needing core methods on both SequenceCollection (from which Alignment directly inherits) and ArrayAlignment (which inherits directly from _SequenceCollectionBase).

In new_alignment.py, define a SequenceCollection class without any reference to alignment.py classes. All it has to begin with is a constructor and .seqs attribute.