bool category not properly parsed #27
Description
Assume I have a metadata category like infection with values TRUE or FALSE. If I load these data as in your example metadata = pd.read_table("data/metadata.tsv", sep="\t", index_col=0) they are of type object and proper boolean values, i.e. True and False. If I would add a dtype=str, the values are still of type object but strings, namely 'TRUE' and 'FALSE'.
Only the dtype=str way works for me. Otherwise evident throws the error:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
3628 try:
-> 3629 return self._engine.get_loc(casted_key)
3630 except KeyError as err:
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 'infection'
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
/tmp/ipykernel_1855806/1849832882.py in <module>
1 for cat in ["birth_timestamp","cage","genotype","infection"]:
----> 2 print(adh.calculate_effect_size(column=cat))
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/evident/data_handler.py in calculate_effect_size(self, column, difference)
112 :rtype: evident.results.EffectSizeResult
113 """
--> 114 if self.metadata[column].dtype != np.dtype("object"):
115 raise exc.NonCategoricalColumnError(self.metadata[column])
116
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pandas/core/frame.py in __getitem__(self, key)
3503 if self.columns.nlevels > 1:
3504 return self._getitem_multilevel(key)
-> 3505 indexer = self.columns.get_loc(key)
3506 if is_integer(indexer):
3507 indexer = [indexer]
~/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
3629 return self._engine.get_loc(casted_key)
3630 except KeyError as err:
-> 3631 raise KeyError(key) from err
3632 except TypeError:
3633 # If we have a listlike key, _check_indexing_error will raise
KeyError: 'infection'
You might want to return a more explicit error message in those cases.