Equality in Pandas DataFrames - Column Order Matters?

Question

As part of a unit test, I need to test two DataFrames for equality. The order of the columns in the DataFrames is not important to me. However, it seems to matter to Pandas:

import pandas
df1 = pandas.DataFrame(index = [1,2,3,4])
df2 = pandas.DataFrame(index = [1,2,3,4])
df1['A'] = [1,2,3,4]
df1['B'] = [2,3,4,5]
df2['B'] = [2,3,4,5]
df2['A'] = [1,2,3,4]
df1 == df2

Results in:

Exception: Can only compare identically-labeled DataFrame objects

I believe the expression df1 == df2 should evaluate to a DataFrame containing all True values. Obviously it's debatable what the correct functionality of == should be in this context. My question is: Is there a Pandas method that does what I want? That is, is there a way to do equality comparison that ignores column order?

Answer 1

The most common intent is handled like this:

def assertFrameEqual(df1, df2, **kwds ):
    """ Assert that two dataframes are equal, ignoring ordering of columns"""
    from pandas.util.testing import assert_frame_equal
    return assert_frame_equal(df1.sort_index(axis=1), df2.sort_index(axis=1), check_names=True, **kwds )

Of course see pandas.util.testing.assert_frame_equal for other parameters you can pass

Answer 2

def equal( df1, df2 ):
    """ Check if two DataFrames are equal, ignoring nans """
    return df1.fillna(1).sort_index(axis=1).eq(df2.fillna(1).sort_index(axis=1)).all().all()

Answer 3

Usually you're going to want speedy tests and the sorting method can be brutally inefficient for larger indices (like if you were using rows instead of columns for this problem). The sort method is also susceptible to false negatives on non-unique indices.

Fortunately, pandas.util.testing.assert_frame_equal has since been updated with a check_like option. Set this to true and the ordering will not be considered in the test.

With non-unique indices, you'll get the cryptic ValueError: cannot reindex from a duplicate axis. This is raised by the under-the-hood reindex_like operation that rearranges one of the DataFrames to match the other's order. Reindexing is much faster than sorting as evidenced below.

import pandas as pd
from pandas.util.testing import assert_frame_equal

df  = pd.DataFrame(np.arange(1e6))
df1 = df.sample(frac=1, random_state=42)
df2 = df.sample(frac=1, random_state=43)

%timeit -n 1 -r 5 assert_frame_equal(df1.sort_index(), df2.sort_index())
## 5.73 s ± 329 ms per loop (mean ± std. dev. of 5 runs, 1 loop each)

%timeit -n 1 -r 5 assert_frame_equal(df1, df2, check_like=True)
## 1.04 s ± 237 ms per loop (mean ± std. dev. of 5 runs, 1 loop each)

For those who enjoy a good performance comparison plot:

Reindexing vs sorting on int and str indices (str even more drastic)

Answer 4

Sorting column only works if the row and column labels match across the frames. Say, you have 2 dataframes with identical values in cells but with different labels,then the sort solution will not work. I ran into this scenario when implementing k-modes clustering using pandas.

I got around it with a simple equals function to check cell equality(code below)

def frames_equal(df1,df2) :
    if not isinstance(df1,DataFrame) or not isinstance(df2,DataFrame) :
        raise Exception(
            "dataframes should be an instance of pandas.DataFrame")

    if df1.shape != df2.shape:
        return False

    num_rows,num_cols = df1.shape
    for i in range(num_rows):
       match = sum(df1.iloc[i] == df2.iloc[i])
       if match != num_cols :
          return False
   return True

Answer 5

assert_frame_equal from pandas.testing is a function which checks frames equality. as mentioned in assert_frame_equal documentation, if set check_like parameter to True, it will ignore order of index and columns.

Answer 6

have you tried using df1.equals(df2)? i think it's more reliable that df1==df2, though i'm not sure if it will resolve your issues with column order.

http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.equals.html

Answer 7

Probably you may need function to compare DataFrames ignoring both row and column order? Only requirement is to have some unique column to use it as index.

f1 = pd.DataFrame([
    {"id": 1, "foo": "1", "bar": None},
    {"id": 2, "foo": "2", "bar": 2},
    {"id": 3, "foo": "3", "bar": 3},
    {"id": 4, "foo": "4", "bar": 4}
])
f2 = pd.DataFrame([
    {"id": 3, "foo": "3", "bar": 3},
    {"id": 1, "bar": None, "foo": "1",},
    {"id": 2, "foo": "2", "bar": 2},
    {"id": 4, "foo": "4", "bar": 4}
])

def comparable(df, index_col='id'):
    return df.fillna(value=0).set_index(index_col).to_dict('index')

comparable(f1) == comparable (f2)  # returns True

Answer 8

When working with dataframes containing python objects such as tuples and lists df.eq(df2) and df == df2 will not suffice. Even if a the same cells in each dataframes contain the same object, such as (0, 0), the equality comparison will result to False. To get around this, convert all columns to strings before comparison:

df.apply(lambda x: x.astype(str)).eq(df2.apply(lambda x: x.astype(str)))