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)
<ipython-input-4-18a38f6978fe> in <module>
----> 1 s1.reindex(["a", "b", "c"])

~/work/pandas/pandas/pandas/core/series.py in reindex(self, index, **kwargs)
   4392     )
   4393     def reindex(self, index=None, **kwargs):
-> 4394         return super().reindex(index=index, **kwargs)
   4395 
   4396     def drop(

~/work/pandas/pandas/pandas/core/generic.py in reindex(self, *args, **kwargs)
   4744 
   4745         # perform the reindex on the axes
-> 4746         return self._reindex_axes(
   4747             axes, level, limit, tolerance, method, fill_value, copy
   4748         ).__finalize__(self, method="reindex")

~/work/pandas/pandas/pandas/core/generic.py in _reindex_axes(self, axes, level, limit, tolerance, method, fill_value, copy)
   4764 
   4765             axis = self._get_axis_number(a)
-> 4766             obj = obj._reindex_with_indexers(
   4767                 {axis: [new_index, indexer]},
   4768                 fill_value=fill_value,

~/work/pandas/pandas/pandas/core/generic.py in _reindex_with_indexers(self, reindexers, fill_value, copy, allow_dups)
   4807 
   4808             # TODO: speed up on homogeneous DataFrame objects
-> 4809             new_data = new_data.reindex_indexer(
   4810                 index,
   4811                 indexer,

~/work/pandas/pandas/pandas/core/internals/managers.py in reindex_indexer(self, new_axis, indexer, axis, fill_value, allow_dups, copy, consolidate)
   1264         # some axes don't allow reindexing with dups
   1265         if not allow_dups:
-> 1266             self.axes[axis]._can_reindex(indexer)
   1267 
   1268         if axis >= self.ndim:

~/work/pandas/pandas/pandas/core/indexes/base.py in _can_reindex(self, indexer)
   3331         # trying to reindex on an axis with duplicates
   3332         if not self._index_as_unique and len(indexer):
-> 3333             raise ValueError("cannot reindex from a duplicate axis")
   3334 
   3335     def reindex(self, target, method=None, level=None, limit=None, tolerance=None):

ValueError: cannot reindex from a duplicate axis

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

New 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)
<ipython-input-19-11af4ee9738e> in <module>
----> 1 pd.Series([0, 1, 2], index=["a", "b", "b"]).set_flags(allows_duplicate_labels=False)

~/work/pandas/pandas/pandas/core/generic.py in set_flags(self, copy, allows_duplicate_labels)
    358         df = self.copy(deep=copy)
    359         if allows_duplicate_labels is not None:
--> 360             df.flags["allows_duplicate_labels"] = allows_duplicate_labels
    361         return df
    362 

~/work/pandas/pandas/pandas/core/flags.py in __setitem__(self, key, value)
    103         if key not in self._keys:
    104             raise ValueError(f"Unknown flag {key}. Must be one of {self._keys}")
--> 105         setattr(self, key, value)
    106 
    107     def __repr__(self):

~/work/pandas/pandas/pandas/core/flags.py in allows_duplicate_labels(self, value)
     90         if not value:
     91             for ax in obj.axes:
---> 92                 ax._maybe_check_unique()
     93 
     94         self._allows_duplicate_labels = value

~/work/pandas/pandas/pandas/core/indexes/base.py in _maybe_check_unique(self)
    462             msg += f"\n{duplicates}"
    463 
--> 464             raise DuplicateLabelError(msg)
    465 
    466     def _format_duplicate_message(self):

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=True 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)
<ipython-input-28-17c8fb0b7c7f> in <module>
----> 1 df.rename(str.upper)

~/work/pandas/pandas/pandas/util/_decorators.py in wrapper(*args, **kwargs)
    310         @wraps(func)
    311         def wrapper(*args, **kwargs) -> Callable[..., Any]:
--> 312             return func(*args, **kwargs)
    313 
    314         kind = inspect.Parameter.POSITIONAL_OR_KEYWORD

~/work/pandas/pandas/pandas/core/frame.py in rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
   4358         4  3  6
   4359         """
-> 4360         return super().rename(
   4361             mapper=mapper,
   4362             index=index,

~/work/pandas/pandas/pandas/core/generic.py in rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
   1070             return None
   1071         else:
-> 1072             return result.__finalize__(self, method="rename")
   1073 
   1074     @rewrite_axis_style_signature("mapper", [("copy", True), ("inplace", False)])

~/work/pandas/pandas/pandas/core/generic.py in __finalize__(self, other, method, **kwargs)
   5360                 self.attrs[name] = other.attrs[name]
   5361 
-> 5362             self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
   5363             # For subclasses using _metadata.
   5364             for name in set(self._metadata) & set(other._metadata):

~/work/pandas/pandas/pandas/core/flags.py in allows_duplicate_labels(self, value)
     90         if not value:
     91             for ax in obj.axes:
---> 92                 ax._maybe_check_unique()
     93 
     94         self._allows_duplicate_labels = value

~/work/pandas/pandas/pandas/core/indexes/base.py in _maybe_check_unique(self)
    462             msg += f"\n{duplicates}"
    463 
--> 464             raise DuplicateLabelError(msg)
    465 
    466     def _format_duplicate_message(self):

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)
<ipython-input-31-8f09bda3af1a> in <module>
----> 1 s1.head().rename({"a": "b"})

~/work/pandas/pandas/pandas/core/series.py in rename(self, index, axis, copy, inplace, level, errors)
   4350         """
   4351         if callable(index) or is_dict_like(index):
-> 4352             return super().rename(
   4353                 index, copy=copy, inplace=inplace, level=level, errors=errors
   4354             )

~/work/pandas/pandas/pandas/core/generic.py in rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
   1070             return None
   1071         else:
-> 1072             return result.__finalize__(self, method="rename")
   1073 
   1074     @rewrite_axis_style_signature("mapper", [("copy", True), ("inplace", False)])

~/work/pandas/pandas/pandas/core/generic.py in __finalize__(self, other, method, **kwargs)
   5360                 self.attrs[name] = other.attrs[name]
   5361 
-> 5362             self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
   5363             # For subclasses using _metadata.
   5364             for name in set(self._metadata) & set(other._metadata):

~/work/pandas/pandas/pandas/core/flags.py in allows_duplicate_labels(self, value)
     90         if not value:
     91             for ax in obj.axes:
---> 92                 ax._maybe_check_unique()
     93 
     94         self._allows_duplicate_labels = value

~/work/pandas/pandas/pandas/core/indexes/base.py in _maybe_check_unique(self)
    462             msg += f"\n{duplicates}"
    463 
--> 464             raise DuplicateLabelError(msg)
    465 
    466     def _format_duplicate_message(self):

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.