fixed merge conflicts

Author: jacobaustin123

asv_bench/benchmarks/arithmetic.py

@@ -67,7 +67,7 @@ def time_series_op_with_fill_value_no_nas(self):
         self.ser.add(self.ser, fill_value=4)
 
 
-class MixedFrameWithSeriesAxis0:
+class MixedFrameWithSeriesAxis:
     params = [
         [
             "eq",
@@ -78,7 +78,7 @@ class MixedFrameWithSeriesAxis0:
             "gt",
             "add",
             "sub",
-            "div",
+            "truediv",
             "floordiv",
             "mul",
             "pow",
@@ -87,15 +87,19 @@ class MixedFrameWithSeriesAxis0:
     param_names = ["opname"]
 
     def setup(self, opname):
-        arr = np.arange(10 ** 6).reshape(100, -1)
+        arr = np.arange(10 ** 6).reshape(1000, -1)
         df = DataFrame(arr)
         df["C"] = 1.0
         self.df = df
         self.ser = df[0]
+        self.row = df.iloc[0]
 
     def time_frame_op_with_series_axis0(self, opname):
         getattr(self.df, opname)(self.ser, axis=0)
 
+    def time_frame_op_with_series_axis1(self, opname):
+        getattr(operator, opname)(self.df, self.ser)
+
 
 class Ops:
 

asv_bench/benchmarks/frame_methods.py

@@ -564,7 +564,7 @@ def setup(self):
 
     def time_frame_get_dtype_counts(self):
         with warnings.catch_warnings(record=True):
-            self.df._data.get_dtype_counts()
+            self.df.dtypes.value_counts()
 
     def time_info(self):
         self.df.info()

asv_bench/benchmarks/groupby.py

@@ -626,4 +626,96 @@ def time_first(self):
         self.df_nans.groupby("key").transform("first")
 
 
+class TransformEngine:
+    def setup(self):
+        N = 10 ** 3
+        data = DataFrame(
+            {0: [str(i) for i in range(100)] * N, 1: list(range(100)) * N},
+            columns=[0, 1],
+        )
+        self.grouper = data.groupby(0)
+
+    def time_series_numba(self):
+        def function(values, index):
+            return values * 5
+
+        self.grouper[1].transform(function, engine="numba")
+
+    def time_series_cython(self):
+        def function(values):
+            return values * 5
+
+        self.grouper[1].transform(function, engine="cython")
+
+    def time_dataframe_numba(self):
+        def function(values, index):
+            return values * 5
+
+        self.grouper.transform(function, engine="numba")
+
+    def time_dataframe_cython(self):
+        def function(values):
+            return values * 5
+
+        self.grouper.transform(function, engine="cython")
+
+
+class AggEngine:
+    def setup(self):
+        N = 10 ** 3
+        data = DataFrame(
+            {0: [str(i) for i in range(100)] * N, 1: list(range(100)) * N},
+            columns=[0, 1],
+        )
+        self.grouper = data.groupby(0)
+
+    def time_series_numba(self):
+        def function(values, index):
+            total = 0
+            for i, value in enumerate(values):
+                if i % 2:
+                    total += value + 5
+                else:
+                    total += value * 2
+            return total
+
+        self.grouper[1].agg(function, engine="numba")
+
+    def time_series_cython(self):
+        def function(values):
+            total = 0
+            for i, value in enumerate(values):
+                if i % 2:
+                    total += value + 5
+                else:
+                    total += value * 2
+            return total
+
+        self.grouper[1].agg(function, engine="cython")
+
+    def time_dataframe_numba(self):
+        def function(values, index):
+            total = 0
+            for i, value in enumerate(values):
+                if i % 2:
+                    total += value + 5
+                else:
+                    total += value * 2
+            return total
+
+        self.grouper.agg(function, engine="numba")
+
+    def time_dataframe_cython(self):
+        def function(values):
+            total = 0
+            for i, value in enumerate(values):
+                if i % 2:
+                    total += value + 5
+                else:
+                    total += value * 2
+            return total
+
+        self.grouper.agg(function, engine="cython")
+
+
 from .pandas_vb_common import setup  # noqa: F401 isort:skip

asv_bench/benchmarks/stat_ops.py

@@ -11,8 +11,8 @@ class FrameOps:
     param_names = ["op", "dtype", "axis"]
 
     def setup(self, op, dtype, axis):
-        if op == "mad" and dtype == "Int64" and axis == 1:
-            # GH-33036
+        if op == "mad" and dtype == "Int64":
+            # GH-33036, GH#33600
             raise NotImplementedError
         values = np.random.randn(100000, 4)
         if dtype == "Int64":

ci/code_checks.sh

@@ -150,7 +150,13 @@ if [[ -z "$CHECK" || "$CHECK" == "patterns" ]]; then
     # Check for imports from pandas._testing instead of `import pandas._testing as tm`
     invgrep -R --include="*.py*" -E "from pandas._testing import" pandas/tests
     RET=$(($RET + $?)) ; echo $MSG "DONE"
-    invgrep -R --include="*.py*" -E "from pandas.util import testing as tm" pandas/tests
+    invgrep -R --include="*.py*" -E "from pandas import _testing as tm" pandas/tests
+    RET=$(($RET + $?)) ; echo $MSG "DONE"
+
+    # No direct imports from conftest
+    invgrep -R --include="*.py*" -E "conftest import" pandas/tests
+    RET=$(($RET + $?)) ; echo $MSG "DONE"
+    invgrep -R --include="*.py*" -E "import conftest" pandas/tests
     RET=$(($RET + $?)) ; echo $MSG "DONE"
 
     MSG='Check for use of exec' ; echo $MSG

ci/deps/azure-36-minimum_versions.yaml

@@ -21,7 +21,7 @@ dependencies:
   - numexpr=2.6.2
   - numpy=1.13.3
   - openpyxl=2.5.7
-  - pytables=3.4.2
+  - pytables=3.4.3
   - python-dateutil=2.7.3
   - pytz=2017.2
   - scipy=0.19.0

doc/source/getting_started/index.rst

@@ -398,7 +398,7 @@ data set, a sliding window of the data or grouped by categories. The latter is a
                 <div class="card-body">
 
 Change the structure of your data table in multiple ways. You can :func:`~pandas.melt` your data table from wide to long/tidy form or :func:`~pandas.pivot`
-from long to wide format. With aggregations built-in, a pivot table is created with a sinlge command.
+from long to wide format. With aggregations built-in, a pivot table is created with a single command.
 
 .. image:: ../_static/schemas/07_melt.svg
    :align: center

doc/source/getting_started/install.rst

@@ -262,7 +262,7 @@ BeautifulSoup4            4.6.0              HTML parser for read_html (see :ref
 Jinja2                                       Conditional formatting with DataFrame.style
 PyQt4                                        Clipboard I/O
 PyQt5                                        Clipboard I/O
-PyTables                  3.4.2              HDF5-based reading / writing
+PyTables                  3.4.3              HDF5-based reading / writing
 SQLAlchemy                1.1.4              SQL support for databases other than sqlite
 SciPy                     0.19.0             Miscellaneous statistical functions
 XLsxWriter                0.9.8              Excel writing
@@ -279,7 +279,7 @@ psycopg2                                     PostgreSQL engine for sqlalchemy
 pyarrow                   0.12.0             Parquet, ORC (requires 0.13.0), and feather reading / writing
 pymysql                   0.7.11             MySQL engine for sqlalchemy
 pyreadstat                                   SPSS files (.sav) reading
-pytables                  3.4.2              HDF5 reading / writing
+pytables                  3.4.3              HDF5 reading / writing
 pyxlsb                    1.0.6              Reading for xlsb files
 qtpy                                         Clipboard I/O
 s3fs                      0.3.0              Amazon S3 access

doc/source/getting_started/intro_tutorials/03_subset_data.rst

@@ -23,7 +23,7 @@
                     <div class="card-body">
                         <p class="card-text">
 
-This tutorial uses the titanic data set, stored as CSV. The data
+This tutorial uses the Titanic data set, stored as CSV. The data
 consists of the following data columns:
 
 -  PassengerId: Id of every passenger.
@@ -72,7 +72,7 @@ How do I select specific columns from a ``DataFrame``?
     <ul class="task-bullet">
         <li>
 
-I’m interested in the age of the titanic passengers.
+I’m interested in the age of the Titanic passengers.
 
 .. ipython:: python
 
@@ -111,7 +111,7 @@ the number of rows is returned.
     <ul class="task-bullet">
         <li>
 
-I’m interested in the age and sex of the titanic passengers.
+I’m interested in the age and sex of the Titanic passengers.
 
 .. ipython:: python
 
@@ -198,7 +198,7 @@ can be used to filter the ``DataFrame`` by putting it in between the
 selection brackets ``[]``. Only rows for which the value is ``True``
 will be selected.
 
-We now from before that the original titanic ``DataFrame`` consists of
+We know from before that the original Titanic ``DataFrame`` consists of
 891 rows. Let’s have a look at the amount of rows which satisfy the
 condition by checking the ``shape`` attribute of the resulting
 ``DataFrame`` ``above_35``:
@@ -212,7 +212,7 @@ condition by checking the ``shape`` attribute of the resulting
     <ul class="task-bullet">
         <li>
 
-I’m interested in the titanic passengers from cabin class 2 and 3.
+I’m interested in the Titanic passengers from cabin class 2 and 3.
 
 .. ipython:: python
 

doc/source/getting_started/intro_tutorials/10_text_data.rst

@@ -199,7 +199,7 @@ names in the ``Name`` column. By using pandas string methods, the
 
 Next, we need to get the corresponding location, preferably the index
 label, in the table for which the name length is the largest. The
-:meth:`~Series.idxmax`` method does exactly that. It is not a string method and is
+:meth:`~Series.idxmax` method does exactly that. It is not a string method and is
 applied to integers, so no ``str`` is used.
 
 .. ipython:: python

doc/source/user_guide/computation.rst

@@ -312,14 +312,36 @@ We provide a number of common statistical functions:
     :meth:`~Rolling.median`, Arithmetic median of values
     :meth:`~Rolling.min`, Minimum
     :meth:`~Rolling.max`, Maximum
-    :meth:`~Rolling.std`, Bessel-corrected sample standard deviation
-    :meth:`~Rolling.var`, Unbiased variance
+    :meth:`~Rolling.std`, Sample standard deviation
+    :meth:`~Rolling.var`, Sample variance
     :meth:`~Rolling.skew`, Sample skewness (3rd moment)
     :meth:`~Rolling.kurt`, Sample kurtosis (4th moment)
     :meth:`~Rolling.quantile`, Sample quantile (value at %)
     :meth:`~Rolling.apply`, Generic apply
-    :meth:`~Rolling.cov`, Unbiased covariance (binary)
-    :meth:`~Rolling.corr`, Correlation (binary)
+    :meth:`~Rolling.cov`, Sample covariance (binary)
+    :meth:`~Rolling.corr`, Sample correlation (binary)
+
+.. _computation.window_variance.caveats:
+
+.. note::
+
+   Please note that :meth:`~Rolling.std` and :meth:`~Rolling.var` use the sample
+   variance formula by default, i.e. the sum of squared differences is divided by
+   ``window_size - 1`` and not by ``window_size`` during averaging. In statistics,
+   we use sample when the dataset is drawn from a larger population that we
+   don't have access to. Using it implies that the data in our window is a
+   random sample from the population, and we are interested not in the variance
+   inside the specific window but in the variance of some general window that
+   our windows represent. In this situation, using the sample variance formula
+   results in an unbiased estimator and so is preferred.
+
+   Usually, we are instead interested in the variance of each window as we slide
+   it over the data, and in this case we should specify ``ddof=0`` when calling
+   these methods to use population variance instead of sample variance. Using
+   sample variance under the circumstances would result in a biased estimator
+   of the variable we are trying to determine.
+
+   The same caveats apply to using any supported statistical sample methods.
 
 .. _stats.rolling_apply:
 
@@ -360,8 +382,8 @@ and their default values are set to ``False``, ``True`` and ``False`` respective
 .. note::
 
    In terms of performance, **the first time a function is run using the Numba engine will be slow**
-   as Numba will have some function compilation overhead. However, ``rolling`` objects will cache
-   the function and subsequent calls will be fast. In general, the Numba engine is performant with
+   as Numba will have some function compilation overhead. However, the compiled functions are cached,
+   and subsequent calls will be fast. In general, the Numba engine is performant with
    a larger amount of data points (e.g. 1+ million).
 
 .. code-block:: ipython
@@ -848,14 +870,23 @@ Method summary
     :meth:`~Expanding.median`, Arithmetic median of values
     :meth:`~Expanding.min`, Minimum
     :meth:`~Expanding.max`, Maximum
-    :meth:`~Expanding.std`, Unbiased standard deviation
-    :meth:`~Expanding.var`, Unbiased variance
-    :meth:`~Expanding.skew`, Unbiased skewness (3rd moment)
-    :meth:`~Expanding.kurt`, Unbiased kurtosis (4th moment)
+    :meth:`~Expanding.std`, Sample standard deviation
+    :meth:`~Expanding.var`, Sample variance
+    :meth:`~Expanding.skew`, Sample skewness (3rd moment)
+    :meth:`~Expanding.kurt`, Sample kurtosis (4th moment)
     :meth:`~Expanding.quantile`, Sample quantile (value at %)
     :meth:`~Expanding.apply`, Generic apply
-    :meth:`~Expanding.cov`, Unbiased covariance (binary)
-    :meth:`~Expanding.corr`, Correlation (binary)
+    :meth:`~Expanding.cov`, Sample covariance (binary)
+    :meth:`~Expanding.corr`, Sample correlation (binary)
+
+.. note::
+
+   Using sample variance formulas for :meth:`~Expanding.std` and
+   :meth:`~Expanding.var` comes with the same caveats as using them with rolling
+   windows. See :ref:`this section <computation.window_variance.caveats>` for more
+   information.
+
+   The same caveats apply to using any supported statistical sample methods.
 
 .. currentmodule:: pandas
 

doc/source/user_guide/cookbook.rst

@@ -1333,33 +1333,6 @@ Values can be set to NaT using np.nan, similar to datetime
    y[1] = np.nan
    y
 
-Aliasing axis names
--------------------
-
-To globally provide aliases for axis names, one can define these 2 functions:
-
-.. ipython:: python
-
-   def set_axis_alias(cls, axis, alias):
-       if axis not in cls._AXIS_NUMBERS:
-           raise Exception("invalid axis [%s] for alias [%s]" % (axis, alias))
-       cls._AXIS_ALIASES[alias] = axis
-
-.. ipython:: python
-
-   def clear_axis_alias(cls, axis, alias):
-       if axis not in cls._AXIS_NUMBERS:
-           raise Exception("invalid axis [%s] for alias [%s]" % (axis, alias))
-       cls._AXIS_ALIASES.pop(alias, None)
-
-.. ipython:: python
-
-   set_axis_alias(pd.DataFrame, 'columns', 'myaxis2')
-   df2 = pd.DataFrame(np.random.randn(3, 2), columns=['c1', 'c2'],
-                      index=['i1', 'i2', 'i3'])
-   df2.sum(axis='myaxis2')
-   clear_axis_alias(pd.DataFrame, 'columns', 'myaxis2')
-
 Creating example data
 ---------------------