CLN/DEPR: remove deprecated pandas.rpy module (GH9602)

Author: jorisvandenbossche

ci/lint.sh

@@ -8,10 +8,9 @@ RET=0
 
 if [ "$LINT" ]; then
 
-    # pandas/rpy is deprecated and will be removed.
     # pandas/src is C code, so no need to search there.
     echo "Linting  *.py"
-    flake8 pandas --filename=*.py --exclude pandas/rpy,pandas/src
+    flake8 pandas --filename=*.py --exclude pandas/src
     if [ $? -ne "0" ]; then
         RET=1
     fi

doc/source/r_interface.rst

@@ -1,5 +1,3 @@
-.. currentmodule:: pandas.rpy
-
 .. _rpy:
 
 .. ipython:: python
@@ -15,157 +13,63 @@ rpy2 / R interface
 
 .. warning::
 
-   In v0.16.0, the ``pandas.rpy`` interface has been **deprecated and will be
-   removed in a future version**. Similar functionality can be accessed
-   through the `rpy2 <https://rpy2.readthedocs.io/>`__ project.
-   See the :ref:`updating <rpy.updating>` section for a guide to port your
-   code from the ``pandas.rpy`` to ``rpy2`` functions.
-
-
-.. _rpy.updating:
-
-Updating your code to use rpy2 functions
-----------------------------------------
-
-In v0.16.0, the ``pandas.rpy`` module has been **deprecated** and users are
-pointed to the similar functionality in ``rpy2`` itself (rpy2 >= 2.4).
+    Up to pandas 0.19, a ``pandas.rpy`` module existed with functionality to
+    convert between pandas and ``rpy2`` objects. This functionality now lives in
+    the `rpy2 <https://rpy2.readthedocs.io/>`__ project itself.
+    See the `updating section <http://pandas.pydata.org/pandas-docs/version/0.19.0/r_interface.html#updating-your-code-to-use-rpy2-functions>`__
+    of the previous documentation for a guide to port your code from the
+    removed ``pandas.rpy`` to ``rpy2`` functions.
 
-Instead of importing ``import pandas.rpy.common as com``, the following imports
-should be done to activate the pandas conversion support in rpy2::
-
-    from rpy2.robjects import pandas2ri
-    pandas2ri.activate()
 
+`rpy2 <http://rpy2.bitbucket.org/>`__ is an interface to R running embedded in a Python process, and also includes functionality to deal with pandas DataFrames.
 Converting data frames back and forth between rpy2 and pandas should be largely
 automated (no need to convert explicitly, it will be done on the fly in most
 rpy2 functions).
-
 To convert explicitly, the functions are ``pandas2ri.py2ri()`` and
-``pandas2ri.ri2py()``. So these functions can be used to replace the existing
-functions in pandas:
-
-- ``com.convert_to_r_dataframe(df)`` should be replaced with ``pandas2ri.py2ri(df)``
-- ``com.convert_robj(rdf)`` should be replaced with ``pandas2ri.ri2py(rdf)``
-
-Note: these functions are for the latest version (rpy2 2.5.x) and were called
-``pandas2ri.pandas2ri()`` and ``pandas2ri.ri2pandas()`` previously.
-
-Some of the other functionality in `pandas.rpy` can be replaced easily as well.
-For example to load R data as done with the ``load_data`` function, the
-current method::
-
-    df_iris = com.load_data('iris')
-
-can be replaced with::
-
-    from rpy2.robjects import r
-    r.data('iris')
-    df_iris = pandas2ri.ri2py(r[name])
-
-The ``convert_to_r_matrix`` function can be replaced by the normal
-``pandas2ri.py2ri`` to convert dataframes, with a subsequent call to R
-``as.matrix`` function.
-
-.. warning::
-
-    Not all conversion functions in rpy2 are working exactly the same as the
-    current methods in pandas. If you experience problems or limitations in
-    comparison to the ones in pandas, please report this at the
-    `issue tracker <https://github.com/pandas-dev/pandas/issues>`_.
-
-See also the documentation of the `rpy2 <http://rpy2.bitbucket.org/>`__ project.
-
+``pandas2ri.ri2py()``.
 
-R interface with rpy2
----------------------
 
-If your computer has R and rpy2 (> 2.2) installed (which will be left to the
-reader), you will be able to leverage the below functionality. On Windows,
-doing this is quite an ordeal at the moment, but users on Unix-like systems
-should find it quite easy. rpy2 evolves in time, and is currently reaching
-its release 2.3, while the current interface is
-designed for the 2.2.x series. We recommend to use 2.2.x over other series
-unless you are prepared to fix parts of the code, yet the rpy2-2.3.0
-introduces improvements such as a better R-Python bridge memory management
-layer so it might be a good idea to bite the bullet and submit patches for
-the few minor differences that need to be fixed.
+See also the documentation of the `rpy2 <http://rpy2.bitbucket.org/>`__ project: https://rpy2.readthedocs.io.
 
+In the remainder of this page, a few examples of explicit conversion is given. The pandas conversion of rpy2 needs first to be activated:
 
-::
-
-    # if installing for the first time
-    hg clone http://bitbucket.org/lgautier/rpy2
-
-    cd rpy2
-    hg pull
-    hg update version_2.2.x
-    sudo python setup.py install
-
-.. note::
-
-    To use R packages with this interface, you will need to install
-    them inside R yourself. At the moment it cannot install them for
-    you.
+.. ipython:: python
 
-Once you have done installed R and rpy2, you should be able to import
-``pandas.rpy.common`` without a hitch.
+   from rpy2.robjects import r, pandas2ri
+   pandas2ri.activate()
 
 Transferring R data sets into Python
 ------------------------------------
 
-The **load_data** function retrieves an R data set and converts it to the
+The ``pandas2ri.ri2py`` function retrieves an R data set and converts it to the
 appropriate pandas object (most likely a DataFrame):
 
-
 .. ipython:: python
-   :okwarning:
-
-   import pandas.rpy.common as com
-   infert = com.load_data('infert')
 
-   infert.head()
+    r.data('iris')
+    df_iris = pandas2ri.ri2py(r['iris'])
+    df_iris.head()
 
 
 Converting DataFrames into R objects
 ------------------------------------
 
-.. versionadded:: 0.8
-
-Starting from pandas 0.8, there is **experimental** support to convert
+The ``pandas2ri.py2ri`` function support the reverse operation to convert
 DataFrames into the equivalent R object (that is, **data.frame**):
 
 .. ipython:: python
 
-   import pandas.rpy.common as com
    df = pd.DataFrame({'A': [1, 2, 3], 'B': [4, 5, 6], 'C':[7,8,9]},
                      index=["one", "two", "three"])
-   r_dataframe = com.convert_to_r_dataframe(df)
-
+   r_dataframe = pandas2ri.py2ri(df)
    print(type(r_dataframe))
    print(r_dataframe)
 
 
 The DataFrame's index is stored as the ``rownames`` attribute of the
 data.frame instance.
 
-You can also use **convert_to_r_matrix** to obtain a ``Matrix`` instance, but
-bear in mind that it will only work with homogeneously-typed DataFrames (as
-R matrices bear no information on the data type):
 
-
-.. ipython:: python
-
-   import pandas.rpy.common as com
-   r_matrix = com.convert_to_r_matrix(df)
-
-   print(type(r_matrix))
-   print(r_matrix)
-
-
-Calling R functions with pandas objects
----------------------------------------
-
-
-
-High-level interface to R estimators
-------------------------------------
+..
+   Calling R functions with pandas objects
+   High-level interface to R estimators

doc/source/whatsnew/v0.20.0.txt

@@ -343,6 +343,9 @@ Deprecations
 Removal of prior version deprecations/changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+- The ``pandas.rpy`` module is removed. Similar functionality can be accessed
+  through the `rpy2 <https://rpy2.readthedocs.io/>`__ project.
+  See the :ref:`R interfacing docs <rpy>` for more details.
 - ``pd.to_datetime`` and ``pd.to_timedelta`` have dropped the ``coerce`` parameter in favor of ``errors`` (:issue:`13602`)
 
 

pandas/api/tests/test_api.py

@@ -30,7 +30,7 @@ class TestPDApi(Base, tm.TestCase):
 
     # these are optionally imported based on testing
     # & need to be ignored
-    ignored = ['tests', 'rpy', 'locale']
+    ignored = ['tests', 'locale']
 
     # top-level sub-packages
     lib = ['api', 'compat', 'computation', 'core',