Switch to typed lists from biocutils

[jkanche]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 60.16260% with 49 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.07%. Comparing base (bb2f8aa) to head (8d32fee).

Files with missing lines	Patch %	Lines
src/compressed_lists/split_generic.py	0.00%	35 Missing ⚠️
src/compressed_lists/bool_list.py	78.57%	2 Missing and 1 partial ⚠️
src/compressed_lists/float_list.py	78.57%	2 Missing and 1 partial ⚠️
src/compressed_lists/string_list.py	81.25%	2 Missing and 1 partial ⚠️
src/compressed_lists/integer_list.py	85.71%	2 Missing ⚠️
src/compressed_lists/numpy_list.py	83.33%	2 Missing ⚠️
src/compressed_lists/base.py	91.66%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (bb2f8aa) and HEAD (8d32fee). Click for more details.

HEAD has 20 uploads less than BASE

Flag	BASE (bb2f8aa)	HEAD (8d32fee)
	30	10

Additional details and impacted files

@@            Coverage Diff             @@
##           master       #5      +/-   ##
==========================================
- Coverage   73.43%   67.07%   -6.36%     
==========================================
  Files           5        9       +4     
  Lines         320      404      +84     
  Branches       30       43      +13     
==========================================
+ Hits          235      271      +36     
- Misses         80      125      +45     
- Partials        5        8       +3     

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[LTLA]

Random thoughts:

Also worth having a CompressedNumpyList so that NumPy columns of a CompressedDataFrameList can be easily extracted while preserving its type.

Make sure that the CompressedList base class is non-abstract so that any underlying concatenated store without its own CompressedList subclass won't just crash when you try to make a CompressedList out of it.

Also make a splitAsCompressedList() generic so that third parties can easily extend it with their own classes. For example, CompressedDataFrameList should call splitAsCompressedList() when extracting a column, which ensures that it will dispatch to the appropriate method.

[jkanche]

awesome, I already have the compressed numpy list. it'll probably need some work as I work on the other two suggestions.

[jkanche]

Couple of things

• from_list needs to be implemented in individual classes
• implement split generic
• biocframe compressed list

[jkanche]

running into limitations of python's singledispatch. It can only dispatch on a single type, not on complex types like Union or parameterized generics like List[List[int]]. Need to rethink how this can be implemented