Pandas concat dataframes with different columns: AttributeError: 'NoneType' object has no attribute 'is_extension'

Question

I am trying to concatenate two dataframes which have different column names along the 0 axis. I found a similar question here How to use join_axes in the column-wise axis concatenation using pandas DataFrame? however this solution does not work for me since the column-names of my two dataframes are not the same. Since my original data is too large to post here the following example should illustrates what I am trying to do:

df1 = pd.DataFrame(np.random.randint(0,100,size=(1, 4)), columns=list('ABCD'))
df2 = pd.DataFrame(np.random.randint(0,100,size=(1, 4)), columns=list('EFGH'))

#df1
    A   B   C   D
0   26  39  7   44

#df2
    E   F   G   H
0   12  44  26  64

pd.concat([df1,df2],axis=0).reset_index(drop=True)
# desired output looks like this
A   B   C   D   E   F   G   H
0   26.0    39.0    7.0 44.0    NaN NaN NaN NaN
1   NaN NaN NaN NaN 12.0    44.0    26.0    64.0

The above code works perfectly. However, once I input my own dataframes for df1 and df2, using the exact same syntax above, I get an error.

# my real dfs are called data1 & data2, I tried setting ignore_index=True and ignore_index=False
pd.concat([data1, data2],axis=0, ignore_index=True)

results in the following error:

Error:

 ---------------------------------------------------------------------------
    AttributeError                            Traceback (most recent call last)
    <ipython-input-194-dbee1fd0bdea> in <module>
    ----> 1 pd.concat([data1, data2],axis=0, ignore_index=True)

    ~\AppData\Local\Continuum\anaconda3\envs\tensorflow-gpu\lib\site-packages\pandas\core\reshape\concat.py in concat(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, sort, copy)
        224                        verify_integrity=verify_integrity,
        225                        copy=copy, sort=sort)
    --> 226     return op.get_result()
        227 
        228 

    ~\AppData\Local\Continuum\anaconda3\envs\tensorflow-gpu\lib\site-packages\pandas\core\reshape\concat.py in get_result(self)
        421             new_data = concatenate_block_managers(
        422                 mgrs_indexers, self.new_axes, concat_axis=self.axis,
    --> 423                 copy=self.copy)
        424             if not self.copy:
        425                 new_data._consolidate_inplace()

    ~\AppData\Local\Continuum\anaconda3\envs\tensorflow-gpu\lib\site-packages\pandas\core\internals.py in concatenate_block_managers(mgrs_indexers, axes, concat_axis, copy)
       5414                 values = values.view()
       5415             b = b.make_block_same_class(values, placement=placement)
    -> 5416         elif is_uniform_join_units(join_units):
       5417             b = join_units[0].block.concat_same_type(
       5418                 [ju.block for ju in join_units], placement=placement)

    ~\AppData\Local\Continuum\anaconda3\envs\tensorflow-gpu\lib\site-packages\pandas\core\internals.py in is_uniform_join_units(join_units)
       5438         # no blocks that would get missing values (can lead to type upcasts)
       5439         # unless we're an extension dtype.
    -> 5440         all(not ju.is_na or ju.block.is_extension for ju in join_units) and
       5441         # no blocks with indexers (as then the dimensions do not fit)
       5442         all(not ju.indexers for ju in join_units) and

    ~\AppData\Local\Continuum\anaconda3\envs\tensorflow-gpu\lib\site-packages\pandas\core\internals.py in <genexpr>(.0)
       5438         # no blocks that would get missing values (can lead to type upcasts)
       5439         # unless we're an extension dtype.
    -> 5440         all(not ju.is_na or ju.block.is_extension for ju in join_units) and
       5441         # no blocks with indexers (as then the dimensions do not fit)
       5442         all(not ju.indexers for ju in join_units) and

    AttributeError: 'NoneType' object has no attribute 'is_extension'

I do not quite understand what this error message is trying to tell me. I've been trying to use fillna on both dataframes such that there should be no 'NoneType' anymore:

data2 = data2.fillna(999)
data1 = data1.fillna(999)

However, I still get the same error message.

The two dataframes I am using are quite large, so I cant unfortunately post the entire example here. The content of my two dataframes are just integers, floats and strings so nothing fancy going on here that would strike a possible cause of error. Any idea on what might cause this error or what I could check to narrow down the problem?

Thank you very much!

Answer 1

Turns out the problem were just duplicate column names in one of my dataframes...Getting rid of those duplicates solved the problem. Above code now works flawless.