DOC: Add scaling to large datasets section

doc/.gitignore

@@ -0,0 +1,4 @@
+data/
+timeseries.csv
+timeseries.parquet
+timeseries_wide.parquet

doc/source/index.rst.template

@@ -83,6 +83,7 @@ See the :ref:`overview` for more detail about what's in the library.
   * :doc:`user_guide/style`
   * :doc:`user_guide/options`
   * :doc:`user_guide/enhancingperf`
+  * :doc:`user_guide/scale`
   * :doc:`user_guide/sparse`
   * :doc:`user_guide/gotchas`
   * :doc:`user_guide/cookbook`

doc/source/user_guide/scale.rst

@@ -0,0 +1,343 @@
+.. _scale:
+
+*************************
+Scaling to large datasets
+*************************
+
+Pandas provide data structures for in-memory analytics. This makes using pandas
+to analyze larger than memory datasets somewhat tricky.
+
+This document provides a few recommendations for scaling to larger datasets.
+It's a complement to :ref:`enhancingperf`, which focuses on speeding up analysis
+for datasets that fit in memory.
+
+But first, it's worth considering *not using pandas*. Pandas isn't the right
+tool for all situations. If you're working with very large datasets and a tool
+like PostgreSQL fits your needs, then you should probably be using that.
+Assuming you want or need the expressivity and power of pandas, let's carry on.
+
+.. ipython:: python
+
+   import pandas as pd
+   import numpy as np
+   from pandas.util.testing import make_timeseries
+
+
+Use more efficient file formats
+-------------------------------
+
+Depending on your workload, data loading may be a bottleneck. In these case you
+might consider switching from a slow format like CSV to a faster format like
+Parquet. Loading from a file format like Parquet will also require less memory
+usage, letting you load larger datasets into pandas before running out of
+memory.
+
+.. ipython:: python
+
+   # Make a random in-memory dataset
+   ts = make_timeseries(freq="30S", seed=0)
+   ts
+
+
+We'll now write and read the file using CSV and parquet.
+
+
+.. ipython:: python
+
+   %time ts.to_csv("timeseries.csv")
+
+.. ipython:: python
+
+   %time ts2 = pd.read_csv("timeseries.csv", index_col="timestamp", parse_dates=["timestamp"])
+
+.. ipython:: python
+
+   %time ts.to_parquet("timeseries.parquet")
+
+.. ipython:: python
+
+   %time _ = pd.read_parquet("timeseries.parquet")
+
+Notice that parquet gives much higher performance for reading and writing, both
+in terms of speed and lower peak memory usage. See :ref:`io` for more.
+
+Load less data
+--------------
+
+Suppose our raw dataset on disk has many columns, but we need just a subset
+for our analysis. To get those columns, we can either
+
+1. Load the entire dataset then select those columns.
+2. Just load the columns we need.
+
+Loading just the columns you need can be much faster and requires less memory.
+
+.. ipython:: python
+
+   # make a similar dataset with many columns
+   timeseries = [
+       make_timeseries(freq="1T", seed=i).rename(columns=lambda x: f"{x}_{i}")
+       for i in range(10)
+   ]
+   ts_wide = pd.concat(timeseries, axis=1)
+   ts_wide.head()
+   ts_wide.to_parquet("timeseries_wide.parquet")
+
+
+Option 1 loads in all the data and then filters to what we need.
+
+.. ipython:: python
+
+   columns = ['id_0', 'name_0', 'x_0', 'y_0']
+
+   %time _ = pd.read_parquet("timeseries_wide.parquet")[columns]
+
+Option 2 only loads the columns we request. This is faster and has a lower peak
+memory usage, since the entire dataset isn't in memory at once.
+
+.. ipython:: python
+
+   %time _ = pd.read_parquet("timeseries_wide.parquet", columns=columns)
+
+
+With :func:`pandas.read_csv`, you can specify ``usecols`` to limit the columns
+read into memory.
+
+
+Use efficient datatypes
+-----------------------
+
+The default pandas data types are not the most memory efficient. This is
+especially true for high-cardinality text data (columns with relatively few
+unique values). By using more efficient data types you can store larger datasets
+in memory.
+
+.. ipython:: python
+
+   ts.dtypes
+
+.. ipython:: python
+
+   ts.memory_usage(deep=True)  # memory usage in bytes
+
+
+The ``name`` column is taking up much more memory than any other. It has just a
+few unique values, so it's a good candidate for converting to a
+:class:`Categorical`. With a Categorical, we store each unique name once and use
+space-efficient integers to know which specific name is used in each row.
+
+
+.. ipython:: python
+
+   ts2 = ts.copy()
+   ts2['name'] = ts2['name'].astype('category')
+   ts2.memory_usage(deep=True)
+
+We can go a bit further and downcast the numeric columns to their smallest types
+using :func:`pandas.to_numeric`.
+
+.. ipython:: python
+
+   ts2['id'] = pd.to_numeric(ts2['id'], downcast='unsigned')
+   ts2[['x', 'y']] = ts2[['x', 'y']].apply(pd.to_numeric, downcast='float')
+   ts2.dtypes
+
+.. ipython:: python
+
+   ts2.memory_usage(deep=True)
+
+.. ipython:: python
+
+   reduction = ts2.memory_usage(deep=True).sum() / ts.memory_usage(deep=True).sum()
+   print(f"{reduction:0.2f}")
+
+In all, we've reduced the in-memory footprint of this dataset to 1/5 of its
+original size.
+
+See :ref:`categorical` for more on ``Categorical`` and :ref:`basics.dtypes`
+for an overview of all of pandas' dtypes.
+
+Use Other libraries
+-------------------
+
+Pandas is just one library offering a DataFrame API. Because of its popularity,
+pandas' API has become something of a standard that other libraries implement.
+
+For example, `Dask`_, a parallel computing library, has `dask.dataframe`_, a
+pandas-like API for working with larger than memory datasets in parallel. Dask
+can use multiple threads or processes on a single machine, or a cluster of
+machines to process data in parallel.
+
+Let's make a larger dataset on disk (as parquet files) that's split into chunks,
+one per year.
+
+.. ipython:: python
+
+   import pathlib
+
+   N = 12
+   starts = [f'20{i:>02d}-01-01' for i in range(N)]
+   ends = [f'20{i:>02d}-12-13' for i in range(N)]
+
+   pathlib.Path("data/timeseries").mkdir(exist_ok=True)
+
+   for i, (start, end) in enumerate(zip(starts, ends)):
+       ts = make_timeseries(start=start, end=end, freq='1T', seed=i)
+       ts.to_parquet(f"data/timeseries/ts-{i}.parquet")
+
+We'll import ``dask.dataframe`` and notice that the API feels similar to pandas.
+We can use Dask's ``read_parquet`` function, but provide a globstring of files to read in.
+
+.. ipython:: python
+
+   import dask.dataframe as dd
+
+   ddf = dd.read_parquet("data/timeseries/ts*.parquet", engine="pyarrow")
+   ddf
+
+Inspecting the ``ddf`` object, we see a few things
+
+* There are familiar attributes like ``.columns`` and ``.dtypes``
+* There are familiar methods like ``.groupby``, ``.sum``, etc.
+* There are new attributes like ``.npartitions`` and ``.divisions``
+
+The partitions and divisions are how Dask parallizes computation. A **Dask**
+DataFrame is made up of many **Pandas** DataFrames. A single method call on a
+Dask DataFrame ends up making many pandas method calls, and Dask knows how to
+coordinate everything to get the result.
+
+.. ipython:: python
+
+   ddf.columns
+   ddf.dtypes
+   ddf.npartitions
+
+One major difference: the ``dask.dataframe`` API is *lazy*. If you look at the
+repr above, you'll notice that the values aren't actually printed out; just the
+column names and dtypes. That's because Dask hasn't actually read the data yet.
+Rather than executing immediately, doing operations build up a **task graph**.
+
+.. ipython:: python
+
+   ddf
+   ddf['name']
+   ddf['name'].value_counts()
+
+Each of these calls is instant because the result isn't being computed yet.
+We're just building up a list of computation to do when someone needs the
+result. Dask knows that the return type of a ``pandas.Series.value_counts``
+is a pandas Series with a certain dtype and a certain name. So the Dask version
+returns a Dask Series with the same dtype and the same name.
+
+To get the actual result you can call ``.compute()``.
+
+.. ipython:: python
+
+   %time ddf['name'].value_counts().compute()
+
+At that point, the full task graph (reading in data, selecting the columns,
+doing the ``value_counts``) is executed *in parallel*. You get back the same
+thing you'd get back from pandas, in this case a concrete pandas Series with the
+count of each ``name``.
+
+By default, ``dask.dataframe`` operations use a threadpool to do operations in
+parallel. We can also connect to a cluster to distribute the work on many
+machines. In this case we'll connect to a local "cluster" made up of several
+processes on this single machine.
+
+.. ipython:: python
+
+   from dask.distributed import Client, LocalCluster
+
+   cluster = LocalCluster()
+   client = Client(cluster)
+   client
+
+Once this ``client`` is created, all of Dask's computation will take place on
+the cluster (which is just processes in this case).
+
+Dask implements the most used parts of the pandas API. For example, we can do
+a familiar groupby aggregation.
+
+.. ipython:: python
+
+   %time ddf.groupby('name')[['x', 'y']].mean().compute().head()
+
+The grouping and aggregation is done out-of-core and in parallel.
+
+When Dask knows the ``divisions`` of a dataset, certain optimizations are
+possible. When reading parquet datasets written by dask, the divisions will be
+known automatically. In this case, since we created the parquet files manually,
+we need to supply the divisions manually.
+
+.. ipython:: python
+
+   divisions = tuple(pd.to_datetime(starts)) + (pd.Timestamp(ends[-1]),)
+   ddf.divisions = divisions
+   ddf
+
+Now we can do things like fast random access with ``.loc``.
+
+.. ipython:: python
+
+   ddf.loc['2002-01-01 12:01':'2002-01-01 12:05'].compute()
+
+Dask knows to just look in the 3rd partition for selecting values in `2002`. It
+doesn't need to look at any other data.
+
+Many workflows involve a large amount of data and processing it in a way that
+reduces the size to something that fits in memory. In this case, we'll resample
+to daily frequency and take the mean. Once we've taken the mean, we know the
+results will fit in memory, so we can safely call ``compute`` without running
+out of memory. At that point it's just a regular pandas object.
+
+.. ipython:: python
+
+   @savefig dask_resample.png
+   ddf[['x', 'y']].resample("1D").mean().cumsum().compute().plot()
+
+These Dask examples have all be done using multiple processes on a single
+machine. Dask can be `deployed on a cluster
+<https://docs.dask.org/en/latest/setup.html>`_ to scale up to even larger
+datasets.
+
+You see more dask examples at https://examples.dask.org.
+
+Use chunking
+------------
+
+If using another library like Dask is not an option, you can achieve similar
+results with a bit of work.
+
+For example, we can recreate the out-of-core ``value_counts`` we did earlier
+with Dask. The peak memory usage of this will be the size of the single largest
+DataFrame.
+
+.. ipython:: python
+
+   files = list(pathlib.Path("data/timeseries/").glob("ts*.parquet"))
+   files
+
+.. ipython:: python
+
+   %%time
+   counts = pd.Series(dtype=int)
+   for path in files:
+       df = pd.read_parquet(path)
+       counts = counts.add(df['name'].value_counts(), fill_value=0)
+   counts.astype(int)
+
+This matches the counts we saw above with Dask.
+
+Some readers, like :meth:`pandas.read_csv` offer parameters to control the
+``chunksize``. Manually chunking is an OK option for workflows that don't
+require too sophisticated of operations. Some operations, like ``groupby``, are
+much harder to do chunkwise. In these cases, you may be better switching to a
+library like Dask, which implements these chunked algorithms for you.
+
+.. ipython:: python
+
+   del client, cluster
+
+.. _Dask: https://dask.org
+.. _dask.dataframe: https://docs.dask.org/en/latest/dataframe.html

environment.yml

@@ -35,6 +35,8 @@ dependencies:
   - nbconvert>=5.4.1
   - nbsphinx
   - pandoc
+  - dask
+  - distributed
 
   # web (jinja2 is also needed, but it's also an optional pandas dependency)
   - markdown