Duplicate Labels#
Index objects are not required to be unique; you can have duplicate row
or column labels. This may be a bit confusing at first. If you’re familiar with
SQL, you know that row labels are similar to a primary key on a table, and you
would never want duplicates in a SQL table. But one of pandas’ roles is to clean
messy, real-world data before it goes to some downstream system. And real-world
data has duplicates, even in fields that are supposed to be unique.
This section describes how duplicate labels change the behavior of certain operations, and how prevent duplicates from arising during operations, or to detect them if they do.
In [1]: import pandas as pd
In [2]: import numpy as np
Consequences of Duplicate Labels#
Some pandas methods (Series.reindex() for example) just don’t work with
duplicates present. The output can’t be determined, and so pandas raises.
In [3]: s1 = pd.Series([0, 1, 2], index=["a", "b", "b"])
In [4]: s1.reindex(["a", "b", "c"])
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[4], line 1
----> 1 s1.reindex(["a", "b", "c"])
File ~/work/pandas/pandas/pandas/core/series.py:5172, in Series.reindex(self, index, axis, method, copy, level, fill_value, limit, tolerance)
5155 @doc(
5156 NDFrame.reindex, # type: ignore[has-type]
5157 klass=_shared_doc_kwargs["klass"],
(...)
5170 tolerance=None,
5171 ) -> Series:
-> 5172 return super().reindex(
5173 index=index,
5174 method=method,
5175 copy=copy,
5176 level=level,
5177 fill_value=fill_value,
5178 limit=limit,
5179 tolerance=tolerance,
5180 )
File ~/work/pandas/pandas/pandas/core/generic.py:5632, in NDFrame.reindex(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)
5629 return self._reindex_multi(axes, copy, fill_value)
5631 # perform the reindex on the axes
-> 5632 return self._reindex_axes(
5633 axes, level, limit, tolerance, method, fill_value, copy
5634 ).__finalize__(self, method="reindex")
File ~/work/pandas/pandas/pandas/core/generic.py:5655, in NDFrame._reindex_axes(self, axes, level, limit, tolerance, method, fill_value, copy)
5652 continue
5654 ax = self._get_axis(a)
-> 5655 new_index, indexer = ax.reindex(
5656 labels, level=level, limit=limit, tolerance=tolerance, method=method
5657 )
5659 axis = self._get_axis_number(a)
5660 obj = obj._reindex_with_indexers(
5661 {axis: [new_index, indexer]},
5662 fill_value=fill_value,
5663 copy=copy,
5664 allow_dups=False,
5665 )
File ~/work/pandas/pandas/pandas/core/indexes/base.py:4436, in Index.reindex(self, target, method, level, limit, tolerance)
4433 raise ValueError("cannot handle a non-unique multi-index!")
4434 elif not self.is_unique:
4435 # GH#42568
-> 4436 raise ValueError("cannot reindex on an axis with duplicate labels")
4437 else:
4438 indexer, _ = self.get_indexer_non_unique(target)
ValueError: cannot reindex on an axis with duplicate labels
Other methods, like indexing, can give very surprising results. Typically
indexing with a scalar will reduce dimensionality. Slicing a DataFrame
with a scalar will return a Series. Slicing a Series with a scalar will
return a scalar. But with duplicates, this isn’t the case.
In [5]: df1 = pd.DataFrame([[0, 1, 2], [3, 4, 5]], columns=["A", "A", "B"])
In [6]: df1
Out[6]:
A A B
0 0 1 2
1 3 4 5
We have duplicates in the columns. If we slice 'B', we get back a Series
In [7]: df1["B"] # a series
Out[7]:
0 2
1 5
Name: B, dtype: int64
But slicing 'A' returns a DataFrame
In [8]: df1["A"] # a DataFrame
Out[8]:
A A
0 0 1
1 3 4
This applies to row labels as well
In [9]: df2 = pd.DataFrame({"A": [0, 1, 2]}, index=["a", "a", "b"])
In [10]: df2
Out[10]:
A
a 0
a 1
b 2
In [11]: df2.loc["b", "A"] # a scalar
Out[11]: 2
In [12]: df2.loc["a", "A"] # a Series
Out[12]:
a 0
a 1
Name: A, dtype: int64
Duplicate Label Detection#
You can check whether an Index (storing the row or column labels) is
unique with Index.is_unique:
In [13]: df2
Out[13]:
A
a 0
a 1
b 2
In [14]: df2.index.is_unique
Out[14]: False
In [15]: df2.columns.is_unique
Out[15]: True
Note
Checking whether an index is unique is somewhat expensive for large datasets. pandas does cache this result, so re-checking on the same index is very fast.
Index.duplicated() will return a boolean ndarray indicating whether a
label is repeated.
In [16]: df2.index.duplicated()
Out[16]: array([False, True, False])
Which can be used as a boolean filter to drop duplicate rows.
In [17]: df2.loc[~df2.index.duplicated(), :]
Out[17]:
A
a 0
b 2
If you need additional logic to handle duplicate labels, rather than just
dropping the repeats, using groupby() on the index is a common
trick. For example, we’ll resolve duplicates by taking the average of all rows
with the same label.
In [18]: df2.groupby(level=0).mean()
Out[18]:
A
a 0.5
b 2.0
Disallowing Duplicate Labels#
Added in version 1.2.0.
As noted above, handling duplicates is an important feature when reading in raw
data. That said, you may want to avoid introducing duplicates as part of a data
processing pipeline (from methods like pandas.concat(),
rename(), etc.). Both Series and DataFrame
disallow duplicate labels by calling .set_flags(allows_duplicate_labels=False).
(the default is to allow them). If there are duplicate labels, an exception
will be raised.
In [19]: pd.Series([0, 1, 2], index=["a", "b", "b"]).set_flags(allows_duplicate_labels=False)
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Cell In[19], line 1
----> 1 pd.Series([0, 1, 2], index=["a", "b", "b"]).set_flags(allows_duplicate_labels=False)
File ~/work/pandas/pandas/pandas/core/generic.py:511, in NDFrame.set_flags(self, copy, allows_duplicate_labels)
509 df = self.copy(deep=copy and not using_copy_on_write())
510 if allows_duplicate_labels is not None:
--> 511 df.flags["allows_duplicate_labels"] = allows_duplicate_labels
512 return df
File ~/work/pandas/pandas/pandas/core/flags.py:109, in Flags.__setitem__(self, key, value)
107 if key not in self._keys:
108 raise ValueError(f"Unknown flag {key}. Must be one of {self._keys}")
--> 109 setattr(self, key, value)
File ~/work/pandas/pandas/pandas/core/flags.py:96, in Flags.allows_duplicate_labels(self, value)
94 if not value:
95 for ax in obj.axes:
---> 96 ax._maybe_check_unique()
98 self._allows_duplicate_labels = value
File ~/work/pandas/pandas/pandas/core/indexes/base.py:716, in Index._maybe_check_unique(self)
713 duplicates = self._format_duplicate_message()
714 msg += f"\n{duplicates}"
--> 716 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
b [1, 2]
This applies to both row and column labels for a DataFrame
In [20]: pd.DataFrame([[0, 1, 2], [3, 4, 5]], columns=["A", "B", "C"],).set_flags(
....: allows_duplicate_labels=False
....: )
....:
Out[20]:
A B C
0 0 1 2
1 3 4 5
This attribute can be checked or set with allows_duplicate_labels,
which indicates whether that object can have duplicate labels.
In [21]: df = pd.DataFrame({"A": [0, 1, 2, 3]}, index=["x", "y", "X", "Y"]).set_flags(
....: allows_duplicate_labels=False
....: )
....:
In [22]: df
Out[22]:
A
x 0
y 1
X 2
Y 3
In [23]: df.flags.allows_duplicate_labels
Out[23]: False
DataFrame.set_flags() can be used to return a new DataFrame with attributes
like allows_duplicate_labels set to some value
In [24]: df2 = df.set_flags(allows_duplicate_labels=True)
In [25]: df2.flags.allows_duplicate_labels
Out[25]: True
The new DataFrame returned is a view on the same data as the old DataFrame.
Or the property can just be set directly on the same object
In [26]: df2.flags.allows_duplicate_labels = False
In [27]: df2.flags.allows_duplicate_labels
Out[27]: False
When processing raw, messy data you might initially read in the messy data (which potentially has duplicate labels), deduplicate, and then disallow duplicates going forward, to ensure that your data pipeline doesn’t introduce duplicates.
>>> raw = pd.read_csv("...")
>>> deduplicated = raw.groupby(level=0).first() # remove duplicates
>>> deduplicated.flags.allows_duplicate_labels = False # disallow going forward
Setting allows_duplicate_labels=False on a Series or DataFrame with duplicate
labels or performing an operation that introduces duplicate labels on a Series or
DataFrame that disallows duplicates will raise an
errors.DuplicateLabelError.
In [28]: df.rename(str.upper)
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Cell In[28], line 1
----> 1 df.rename(str.upper)
File ~/work/pandas/pandas/pandas/core/frame.py:5789, in DataFrame.rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
5658 def rename(
5659 self,
5660 mapper: Renamer | None = None,
(...)
5668 errors: IgnoreRaise = "ignore",
5669 ) -> DataFrame | None:
5670 """
5671 Rename columns or index labels.
5672
(...)
5787 4 3 6
5788 """
-> 5789 return super()._rename(
5790 mapper=mapper,
5791 index=index,
5792 columns=columns,
5793 axis=axis,
5794 copy=copy,
5795 inplace=inplace,
5796 level=level,
5797 errors=errors,
5798 )
File ~/work/pandas/pandas/pandas/core/generic.py:1143, in NDFrame._rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
1141 return None
1142 else:
-> 1143 return result.__finalize__(self, method="rename")
File ~/work/pandas/pandas/pandas/core/generic.py:6284, in NDFrame.__finalize__(self, other, method, **kwargs)
6277 if other.attrs:
6278 # We want attrs propagation to have minimal performance
6279 # impact if attrs are not used; i.e. attrs is an empty dict.
6280 # One could make the deepcopy unconditionally, but a deepcopy
6281 # of an empty dict is 50x more expensive than the empty check.
6282 self.attrs = deepcopy(other.attrs)
-> 6284 self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
6285 # For subclasses using _metadata.
6286 for name in set(self._metadata) & set(other._metadata):
File ~/work/pandas/pandas/pandas/core/flags.py:96, in Flags.allows_duplicate_labels(self, value)
94 if not value:
95 for ax in obj.axes:
---> 96 ax._maybe_check_unique()
98 self._allows_duplicate_labels = value
File ~/work/pandas/pandas/pandas/core/indexes/base.py:716, in Index._maybe_check_unique(self)
713 duplicates = self._format_duplicate_message()
714 msg += f"\n{duplicates}"
--> 716 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
X [0, 2]
Y [1, 3]
This error message contains the labels that are duplicated, and the numeric positions
of all the duplicates (including the “original”) in the Series or DataFrame
Duplicate Label Propagation#
In general, disallowing duplicates is “sticky”. It’s preserved through operations.
In [29]: s1 = pd.Series(0, index=["a", "b"]).set_flags(allows_duplicate_labels=False)
In [30]: s1
Out[30]:
a 0
b 0
dtype: int64
In [31]: s1.head().rename({"a": "b"})
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Cell In[31], line 1
----> 1 s1.head().rename({"a": "b"})
File ~/work/pandas/pandas/pandas/core/series.py:5109, in Series.rename(self, index, axis, copy, inplace, level, errors)
5102 axis = self._get_axis_number(axis)
5104 if callable(index) or is_dict_like(index):
5105 # error: Argument 1 to "_rename" of "NDFrame" has incompatible
5106 # type "Union[Union[Mapping[Any, Hashable], Callable[[Any],
5107 # Hashable]], Hashable, None]"; expected "Union[Mapping[Any,
5108 # Hashable], Callable[[Any], Hashable], None]"
-> 5109 return super()._rename(
5110 index, # type: ignore[arg-type]
5111 copy=copy,
5112 inplace=inplace,
5113 level=level,
5114 errors=errors,
5115 )
5116 else:
5117 return self._set_name(index, inplace=inplace, deep=copy)
File ~/work/pandas/pandas/pandas/core/generic.py:1143, in NDFrame._rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
1141 return None
1142 else:
-> 1143 return result.__finalize__(self, method="rename")
File ~/work/pandas/pandas/pandas/core/generic.py:6284, in NDFrame.__finalize__(self, other, method, **kwargs)
6277 if other.attrs:
6278 # We want attrs propagation to have minimal performance
6279 # impact if attrs are not used; i.e. attrs is an empty dict.
6280 # One could make the deepcopy unconditionally, but a deepcopy
6281 # of an empty dict is 50x more expensive than the empty check.
6282 self.attrs = deepcopy(other.attrs)
-> 6284 self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
6285 # For subclasses using _metadata.
6286 for name in set(self._metadata) & set(other._metadata):
File ~/work/pandas/pandas/pandas/core/flags.py:96, in Flags.allows_duplicate_labels(self, value)
94 if not value:
95 for ax in obj.axes:
---> 96 ax._maybe_check_unique()
98 self._allows_duplicate_labels = value
File ~/work/pandas/pandas/pandas/core/indexes/base.py:716, in Index._maybe_check_unique(self)
713 duplicates = self._format_duplicate_message()
714 msg += f"\n{duplicates}"
--> 716 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
b [0, 1]
Warning
This is an experimental feature. Currently, many methods fail to
propagate the allows_duplicate_labels value. In future versions
it is expected that every method taking or returning one or more
DataFrame or Series objects will propagate allows_duplicate_labels.