Fix OligosynthesizeOligo serialization

[Alberto024]

Example given in documentation for protocol.oligosynthesize does not work because OligosynthesizeOligo objects do not get properly serialized by protocol.as_dict() method:

Python 3.11.4 | packaged by conda-forge | (main, Jun 10 2023, 18:10:28) [Clang 15.0.7 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from autoprotocol.protocol import Protocol
>>> import json
>>> p = Protocol()
>>> oligo_1 = p.ref("oligo_1", None, "micro-1.5", discard=True)
>>> 
>>> p.oligosynthesize([{"sequence": "CATGGTCCCCTGCACAGG",
...                     "destination": oligo_1.well(0),
...                     "scale": "25nm",
...                     "purification": "standard"}])
Instruction(oligosynthesize, {'oligos': [OligosynthesizeOligo(destination=Well(Container(oligo_1), 0, None), sequence='CATGGTCCCCTGCACAGG', scale='25nm', purification='standard')]}, [])
>>> print(json.dumps(p.as_dict(), indent=2))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/__init__.py", line 238, in dumps
    **kw).encode(obj)
          ^^^^^^^^^^^
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 202, in encode
    chunks = list(chunks)
             ^^^^^^^^^^^^
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 432, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 406, in _iterencode_dict
    yield from chunks
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 326, in _iterencode_list
    yield from chunks
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 406, in _iterencode_dict
    yield from chunks
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 326, in _iterencode_list
    yield from chunks
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 439, in _iterencode
    o = _default(o)
        ^^^^^^^^^^^
  File "/Users/albertonava/mambaforge/envs/dnada11/lib/python3.11/json/encoder.py", line 180, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type OligosynthesizeOligo is not JSON serializable
>>> print(p.as_dict())
{'instructions': [{'op': 'oligosynthesize', 'oligos': [OligosynthesizeOligo(destination=Well(Container(oligo_1), 0, None), sequence='CATGGTCCCCTGCACAGG', scale='25nm', purification='standard')]}], 'refs': {'oligo_1': {'new': 'micro-1.5', 'discard': True}}}

Python Version: 3.11.4
Autoprotocol-python Version: 10.3.0

This pull request fixes this bug. There are a few other additional line changes from black formatting.

[codecov-commenter]

Codecov Report

Merging #396 (e3545d9) into master (4795408) will decrease coverage by 0.02%.
The diff coverage is 60.00%.

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@@            Coverage Diff             @@
##           master     #396      +/-   ##
==========================================
- Coverage   84.57%   84.55%   -0.02%     
==========================================
  Files          24       24              
  Lines        4589     4591       +2     
==========================================
+ Hits         3881     3882       +1     
- Misses        708      709       +1     

Files Changed	Coverage Δ
autoprotocol/protocol.py	79.05% <60.00%> (-0.04%)	⬇️