Switch to typed lists from biocutils

[jkanche]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 76.89243% with 58 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.20%. Comparing base (bb2f8aa) to head (423ea91).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/compressed_lists/split_generic.py	59.52%	10 Missing and 7 partials ⚠️
src/compressed_lists/biocframe_list.py	70.58%	9 Missing and 1 partial ⚠️
src/compressed_lists/numpy_list.py	68.75%	9 Missing and 1 partial ⚠️
src/compressed_lists/bool_list.py	70.83%	6 Missing and 1 partial ⚠️
src/compressed_lists/float_list.py	83.33%	2 Missing and 2 partials ⚠️
src/compressed_lists/integer_list.py	83.33%	3 Missing and 1 partial ⚠️
src/compressed_lists/string_list.py	84.61%	3 Missing and 1 partial ⚠️
src/compressed_lists/base.py	93.10%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master       #5      +/-   ##
==========================================
- Coverage   73.43%   72.20%   -1.24%     
==========================================
  Files           5       10       +5     
  Lines         320      500     +180     
  Branches       30       53      +23     
==========================================
+ Hits          235      361     +126     
- Misses         80      120      +40     
- Partials        5       19      +14     

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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