CytoTable breaks with new verison of duckdb #376
Description
See the original post made by John A. in the copairs repository: cytomining/copairs#100 (comment)
When discussing with @axiomcura, we discovered that the issues I was having with copairs was duckdb version 1.4.0 breaking existing software. See the error below for more details. I am adding this issue to CytoTable, as I know that this is a dependency, and I do not believe there is a cap added to the pyproject file.
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AttributeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 import copairs
3 copairs.__version__ # noqa: B018
File ~/.cache/pypoetry/virtualenvs/cosmicqc-vNopUmqk-py3.11/lib/python3.11/site-packages/copairs/__init__.py:3
1 """Package to create pairwise lists based on sameby and diffby criteria."""
----> 3 from .matching import Matcher, MatcherMultilabel
5 __all__ = ["Matcher", "MatcherMultilabel"]
File ~/.cache/pypoetry/virtualenvs/cosmicqc-vNopUmqk-py3.11/lib/python3.11/site-packages/copairs/matching.py:471
465 return set(x) not in pairs
467 return {None: list(filter(filter_fn, all_pairs))}
470 def find_pairs(
--> 471 dframe: Union[pd.DataFrame, duckdb.duckdb.DuckDBPyRelation],
472 sameby: Union[str, ColumnList],
473 diffby: Union[str, ColumnList],
474 rev: bool = False,
475 ) -> np.ndarray:
476 """Find the indices pairs sharing values in `sameby` columns but not on `diffby` columns.
477
478 If `rev` is True sameby and diffby are swapped.
479 """
480 sameby, diffby = _validate(sameby, diffby)
AttributeError: module 'duckdb' has no attribute 'duckdb'