BUG: Merge error when merge col is int64 and Int64

[tritemio]

Pandas version checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

import pandas as pd

# First DF
df1 = pd.DataFrame({'col1': [1,1,2,2,3,pd.NA]})
df1['col1'] = df1['col1'].astype('Int64')

# Second DF
df2 = pd.DataFrame({'col1': [1,2,3], 'col2': list('abc')}).set_index('col1')

print(df1.dtypes)
print(df2.dtypes)
print(df1.merge(df2, left_on='col1', right_index=True))

Issue Description

Merging two DataFrames on a column (col1) that is Int64 in the first and int64 in the second DF, causes the following confusing error message:

Traceback (most recent call last):
  File "/Users/anto/xxx/src/bugs/pandas_join.py", line 30, in <module>
    print(df1.merge(df2, on='col1', how='left'))
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/frame.py", line 9339, in merge
    return merge(
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 122, in merge
    return op.get_result()
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 716, in get_result
    join_index, left_indexer, right_indexer = self._get_join_info()
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 967, in _get_join_info
    (left_indexer, right_indexer) = self._get_join_indexers()
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 941, in _get_join_indexers
    return get_join_indexers(
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 1484, in get_join_indexers
    zipped = zip(*mapped)
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 1481, in <genexpr>
    _factorize_keys(left_keys[n], right_keys[n], sort=sort, how=how)
  File "/Users/anto/miniconda3/conda-envs/py310/lib/python3.10/site-packages/pandas/core/reshape/merge.py", line 2164, in _factorize_keys
    lk = ensure_int64(np.asarray(lk))
  File "pandas/_libs/algos_common_helper.pxi", line 81, in pandas._libs.algos.ensure_int64
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NAType'

Expected Behavior

If the types of the "merge columns" are compatible, the merge should complete with no errors. Or, alternatively, the error message should warn the user of a type mismatch and of the need of casting one of the columns.

For example, casting the col1 in df2 from int64 to Int64 will result in the correct merge:

import pandas as pd

# First DF
df1 = pd.DataFrame({'col1': [1,1,2,2,3,pd.NA]})
df1['col1'] = df1['col1'].astype('Int64')

# Second DF
df2 = pd.DataFrame({'col1': [1,2,3], 'col2': list('abc')}).set_index('col1')

# These two lines are required for the merge to work
df2 = df2.reset_index()
df2['col1'] = df2['col1'].astype('Int64')


print(df1.dtypes)
print(df2.dtypes)
print(df1.merge(df2, on='col1', how='left'))

However, this workaround looks a bit too convoluted for me.

Installed Versions

1.4.1

[NickCrews]

I duplicate reported this bug in #46799, with a couple other notes there. I confirmed that this is present on main. Also, a slightly more precise description of the conditions that create this bug are:

• col1 is a nullable integer type (eg pd.Int64Dtype())
• col1 contains nulls
• col2 is an integer type (either nullable eg pd.Int64Dtype() or non-nullable eg np.int64)
• col1.dtype != col2.dtype

[phofl]

This was solved recently through mask support in merge operations

[Flowhill]

This was solved recently through mask support in merge operations

Can you tell me how this was solved? I still have the same error. Trying to merge two dataframes on a column that is read as an Int64 and contains missing values. int() check fails on the NAType in the column.

[NickCrews]

Bummer! Thanks for the report. What is pandas.__version__?

If both columns are Int64, then this might be a different (but related) bug (see my condition above where dtypes must be different).

Give us a reproducible example if you want us to investigate.

[GRcharles]

Hey! I'm running into this too.
In my case, I get the error merging a float field with an int64dtype field

>>> import pandas as pd
>>> pd.__version__
'2.0.2'
>>> pd.merge(pd.DataFrame([1.0]), pd.DataFrame([1.0]).astype(pd.Int64Dtype()))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "REDACTED\venv\lib\site-packages\pandas\core\reshape\merge.py", line 148, in merge
    op = _MergeOperation(
  File "REDACTED\venv\lib\site-packages\pandas\core\reshape\merge.py", line 741, in __init__
    self._maybe_coerce_merge_keys()
  File "REDACTED\venv\lib\site-packages\pandas\core\reshape\merge.py", line 1333, in _maybe_coerce_merge_keys
    casted = lk.astype(rk.dtype)  # type: ignore[arg-type]
TypeError: Cannot interpret 'Int64Dtype()' as a data type

[phofl]

Can you provide a reproducer?

[Flowhill]

I had a similar problem with Int32DType. Solved it by casting the column in question to int. Met vriendelijke groet / Kind regards René Flohil (hij/hem)

…

On Fri, 23 Jun 2023, 16:26 Charles Fauman, ***@***.***> wrote: Hey! I'm running into this too. In my case, I get the error merging a float field with an int64dtype field >>> import pandas as pd >>> pd.__version__ '2.0.2' >>> pd.merge(pd.DataFrame([1.0]), pd.DataFrame([1.0]).astype(pd.Int64Dtype())) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "E:\workspace\CottonEye\venv\lib\site-packages\pandas\core\reshape\merge.py", line 148, in merge op = _MergeOperation( File "E:\workspace\CottonEye\venv\lib\site-packages\pandas\core\reshape\merge.py", line 741, in __init__ self._maybe_coerce_merge_keys() File "E:\workspace\CottonEye\venv\lib\site-packages\pandas\core\reshape\merge.py", line 1333, in _maybe_coerce_merge_keys casted = lk.astype(rk.dtype) # type: ignore[arg-type] TypeError: Cannot interpret 'Int64Dtype()' as a data type — Reply to this email directly, view it on GitHub <#46178 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB7QAL75GRW3TWNCEJS2BNLXMWRSFANCNFSM5PQTZTAA> . You are receiving this because you commented.Message ID: ***@***.***>