Categorical in GroupBy with aggregations raise error under specific conditions

[ant1j]

ticks = pd.DataFrame.from_dict({
    'cid':   [1, 1, 2, 2, 3],
    'date':  ['2019-01-01' , '2020-01-02' , '2020-01-03' , '2019-01-04' , '2020-01-05'],
    'tid':   [1, 2, 3, 4, 5],
    'amount':[1, 1, 2, 2, 3],
})
ticks['date'] = pd.to_datetime(ticks['date'])
ticks['year'] = ticks['date'].dt.year
ticks['year'] = ticks['year'].astype('category')

ticks.groupby(['cid', 'year'], as_index=False, observed=False).agg({'amount': sum})

Outputs a: ValueError: Length of values (5) does not match length of index (6)

Full traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-15-502fa0f135e2> in <module>
      9 
     10 
---> 11         ticks.groupby(['cid', 'year'], as_index=False, observed=False).agg({'amount': sum})
     12 )

c:\users\a.jouanjean\htdocs\factbook-py\.venv\lib\site-packages\pandas\core\groupby\generic.py in aggregate(self, func, engine, engine_kwargs, *args, **kwargs)
    992 
    993         if not self.as_index:
--> 994             self._insert_inaxis_grouper_inplace(result)
    995             result.index = np.arange(len(result))
    996 

c:\users\a.jouanjean\htdocs\factbook-py\.venv\lib\site-packages\pandas\core\groupby\generic.py in _insert_inaxis_grouper_inplace(self, result)
   1716             # When using .apply(-), name will be in columns already
   1717             if in_axis and name not in columns:
-> 1718                 result.insert(0, name, lev)
   1719 
   1720     def _wrap_aggregated_output(

c:\users\a.jouanjean\htdocs\factbook-py\.venv\lib\site-packages\pandas\core\frame.py in insert(self, loc, column, value, allow_duplicates)
   3620         """
   3621         self._ensure_valid_index(value)
-> 3622         value = self._sanitize_column(column, value, broadcast=False)
   3623         self._mgr.insert(loc, column, value, allow_duplicates=allow_duplicates)
   3624 

c:\users\a.jouanjean\htdocs\factbook-py\.venv\lib\site-packages\pandas\core\frame.py in _sanitize_column(self, key, value, broadcast)
   3761 
   3762             # turn me into an ndarray
-> 3763             value = sanitize_index(value, self.index)
   3764             if not isinstance(value, (np.ndarray, Index)):
   3765                 if isinstance(value, list) and len(value) > 0:

c:\users\a.jouanjean\htdocs\factbook-py\.venv\lib\site-packages\pandas\core\internals\construction.py in sanitize_index(data, index)
    745     """
    746     if len(data) != len(index):
--> 747         raise ValueError(
    748             "Length of values "
    749             f"({len(data)}) "

ValueError: Length of values (5) does not match length of index (6)

Problem description

After quite some time trying to narrow down the origin of a ValueError: Length of values (N) does not match length of index (M), it seems to occur, only when these conditions are met:

• groupby() done using a categorical variables in the by list
• as_index=False, but as_index=True is OK
• observed=False, but observed=True is OK
• aggregate() is performed, while applying directly a sum() on the DataFrameGroupBy is OK

see the different combinations in details below.

Expected Output

Would it be possible to issue an early check and error/exception raise when such conditions are met?

It would definitely help user to understand clearly where the problem comes from and how to correct it.

I am aware that some parts of the issue are being addressed (see PR #35967), but this will not help the user to understand what is actually going on when all conditions are met.

Conditions under which Error is not raised

# with observed=True
ticks.groupby(['cid', 'year'], as_index=False, observed=True).agg({'amount': sum}),

# with as_index=True
ticks.groupby(['cid', 'year'], as_index=True, observed=False).agg({'amount': sum}),  

# without using aggregate() but sum() directly [will also sum tid, but still no error]
ticks.groupby(['cid', 'year'], as_index=False, observed=False).sum(),

Output of pd.show_versions()

INSTALLED VERSIONS

commit : 2a7d332
python : 3.8.3.final.0
python-bits : 64
OS : Windows
OS-release : 10
Version : 10.0.18362
machine : AMD64
processor : Intel64 Family 6 Model 142 Stepping 10, GenuineIntel
byteorder : little
LC_ALL : None
LANG : None
LOCALE : fr_FR.cp1252

pandas : 1.1.2
numpy : 1.19.2
pytz : 2020.1
dateutil : 2.8.1
pip : 20.2.3
setuptools : 41.2.0
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : None
IPython : 7.18.1
pandas_datareader: None
bs4 : None
bottleneck : None
fsspec : None
fastparquet : None
gcsfs : None
matplotlib : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : 1.0.1
pytables : None
pyxlsb : None
s3fs : None
scipy : None
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlwt : None
numba : None

[dsaxton]

It looks like the groups attribute is ignoring the "unobserved" groups (this is ultimately what causes it to raise I think), even though they show when you do operations on the groupby:

import pandas as pd

df = pd.DataFrame(
    {
        "x": pd.Categorical(["a", "b", "c", "a", "b"]),
        "y": [1, 1, 1, 2, 2],
        "z": [1, 1, 1, 1, 1],
    }
)
grouped = df.groupby(["x", "y"], observed=False)
print(grouped.size())
# x  y
# a  1    1
#    2    1
# b  1    1
#    2    1
# c  1    1
#    2    0
# dtype: int64
print(grouped.groups.keys()). # ("c", 2) group is missing
# dict_keys([('a', 1), ('a', 2), ('b', 1), ('b', 2), ('c', 1)])

More investigations / PR welcome.

[sacgov]

take

[buhtz]

I ran into the groupby()-with-Categorial-groupers problem and read a bit about it here on GitHub.
But I am a bit confused about the many Issues and PR's here.

What is the current state of this situation? What is the plan for the future?

In pandas 1.3.1 (installed on Debian10.10 via pip)
observed is by default False and causes (for newbies) "strange" behaviour.

[rhshadrach]

When we take the code path for dict-likes within agg, we split up the DataFrameGroupBy into SeriesGroupBy for each element of the dictionary. This returns the result for that particular entry, including the reindexing operation due to missing categories. However because SeriesGroupBy does not support as_index=False, the index is not properly set. We take care of this in agg afterwards, however the aforementioned reindexing causes this to fail due to the unexpected length.

One possible resolution would be to support as_index=False in SeriesGroupBy.

[jhalak27]

@rhshadrach Getting the same index error
Can you update on when this fix will be deployed? or if there is any workaround for this?

[rhshadrach]

Can you update on when this fix will be deployed?

As far as I know, no one is currently working on the fix. Further investigations and PRs to fix are welcome.

or if there is any workaround for this?

Use as_index=True and call .reset_index() after the op.