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Pandas Extension Arrays

Extensibility was a major theme in pandas development over the last couple of releases. This post introduces the pandas extension array interface: the motivation behind it and how it might affect you as a pandas user. Finally, we look at how extension arrays may shape the future of pandas.

Extension Arrays are just one of the changes in pandas 0.24.0. See the whatsnew for a full changelog.

The Motivation

Pandas is built on top of NumPy. You could roughly define a Series as a wrapper around a NumPy array, and a DataFrame as a collection of Series with a shared index. That's not entirely correct for several reasons, but I want to focus on the "wrapper around a NumPy array" part. It'd be more correct to say "wrapper around an array-like object".

Pandas mostly uses NumPy's builtin data representation; we've restricted it in places and extended it in others. For example, pandas' early users cared greatly about timezone-aware datetimes, which NumPy doesn't support. So pandas internally defined a DatetimeTZ dtype (which mimics a NumPy dtype), and allowed you to use that dtype in Index, Series, and as a column in a DataFrame. That dtype carried around the tzinfo, but wasn't itself a valid NumPy dtype.

As another example, consider Categorical. This actually composes two arrays: one for the categories and one for the codes. But it can be stored in a DataFrame like any other column.

Each of these extension types pandas added is useful on its own, but carries a high maintenance cost. Large sections of the codebase need to be aware of how to handle a NumPy array or one of these other kinds of special arrays. This made adding new extension types to pandas very difficult.

Anaconda, Inc. had a client who regularly dealt with datasets with IP addresses. They wondered if it made sense to add an IPArray to pandas. In the end, we didn't think it passed the cost-benefit test for inclusion in pandas itself, but we were interested in defining an interface for third-party extensions to pandas. Any object implementing this interface would be allowed in pandas. I was able to write cyberpandas outside of pandas, but it feels like using any other dtype built into pandas.

The Current State

As of pandas 0.24.0, all of pandas' internal extension arrays (Categorical, Datetime with Timezone, Period, Interval, and Sparse) are now built on top of the ExtensionArray interface. Users shouldn't notice many changes. The main thing you'll notice is that things are cast to object dtype in fewer places, meaning your code will run faster and your types will be more stable. This includes storing Period and Interval data in Series (which were previously cast to object dtype).

Additionally, we'll be able to add new extension arrays with relative ease. For example, 0.24.0 (optionally) solved one of pandas longest-standing pain points: missing values casting integer-dtype values to float.

>>> int_ser = pd.Series([1, 2], index=[0, 2])
>>> int_ser
0    1
2    2
dtype: int64

>>> int_ser.reindex([0, 1, 2])
0    1.0
1    NaN
2    2.0
dtype: float64

With the new IntegerArray and nullable integer dtypes, we can natively represent integer data with missing values.

>>> int_ser = pd.Series([1, 2], index=[0, 2], dtype=pd.Int64Dtype())
>>> int_ser
0    1
2    2
dtype: Int64

>>> int_ser.reindex([0, 1, 2])
0      1
1    NaN
2      2
dtype: Int64

One thing it does slightly change how you should access the raw (unlabeled) arrays stored inside a Series or Index, which is occasionally useful. Perhaps the method you're calling only works with NumPy arrays, or perhaps you want to disable automatic alignment.

In the past, you'd hear things like "Use .values to extract the NumPy array from a Series or DataFrame." If it were a good resource, they'd tell you that's not entirely true, since there are some exceptions. I'd like to delve into those exceptions.

The fundamental problem with .values is that it serves two purposes:

  1. Extracting the array backing a Series, Index, or DataFrame
  2. Converting the Series, Index, or DataFrame to a NumPy array

As we saw above, the "array" backing a Series or Index might not be a NumPy array, it may instead be an extension array (from pandas or a third-party library). For example, consider Categorical,

>>> cat = pd.Categorical(['a', 'b', 'a'], categories=['a', 'b', 'c'])
>>> ser = pd.Series(cat)
>>> ser
0    a
1    b
2    a
dtype: category
Categories (3, object): [a, b, c]

>>> ser.values
[a, b, a]
Categories (3, object): [a, b, c]

In this case .values is a Categorical, not a NumPy array. For period-dtype data, .values returns a NumPy array of Period objects, which is expensive to create. For timezone-aware data, .values converts to UTC and drops the timezone info. These kind of surprises (different types, or expensive or lossy conversions) stem from trying to shoehorn these extension arrays into a NumPy array. But the entire point of an extension array is for representing data NumPy can't natively represent.

To solve the .values problem, we've split its roles into two dedicated methods:

  1. Use .array to get a zero-copy reference to the underlying data
  2. Use .to_numpy() to get a (potentially expensive, lossy) NumPy array of the data.

So with our Categorical example,

>>> ser.array
[a, b, a]
Categories (3, object): [a, b, c]

>>> ser.to_numpy()
array(['a', 'b', 'a'], dtype=object)

To summarize:

  • .array will always be a an ExtensionArray, and is always a zero-copy reference back to the data.
  • .to_numpy() is always a NumPy array, so you can reliably call ndarray-specific methods on it.

You shouldn't ever need .values anymore.

Possible Future Paths

Extension Arrays open up quite a few exciting opportunities. Currently, pandas represents string data using Python objects in a NumPy array, which is slow. Libraries like Apache Arrow provide native support for variable-length strings, and the Fletcher library provides pandas extension arrays for Arrow arrays. It will allow GeoPandas to store geometry data more efficiently. Pandas (or third-party libraries) will be able to support nested data, data with units, geo data, GPU arrays. Keep an eye on the pandas ecosystem page, which will keep track of third-party extension arrays. It's an exciting time for pandas development.

Other Thoughts

I'd like to emphasize that this is an interface, and not a concrete array implementation. We are not reimplementing NumPy here in pandas. Rather, this is a way to take any array-like data structure (one or more NumPy arrays, an Apache Arrow array, a CuPy array) and place it inside a DataFrame. I think getting pandas out of the array business, and instead thinking about higher-level tabular data things, is a healthy development for the project.

This works perfectly with NumPy's __array_ufunc__ protocol and NEP-18. You'll be able to use the familiar NumPy API on objects that aren't backed by NumPy memory.

Upgrade

These new goodies are all available in the recently released pandas 0.24.

conda:

conda install -c conda-forge pandas

pip:

pip install --upgrade pandas

As always, we're happy to hear feedback on the mailing list, @pandas-dev, or issue tracker.

Thanks to the many contributors, maintainers, and institutional partners involved in the pandas community.