Merge branch 'master' into fix-melt

Author: jbradt

ci/requirements-2.7.pip

@@ -1,4 +1,3 @@
-statsmodels
 blosc
 httplib2
 google-api-python-client==1.2

ci/requirements-2.7_COMPAT.run

@@ -4,7 +4,6 @@ pytz=2013b
 scipy=0.11.0
 xlwt=0.7.5
 xlrd=0.9.2
-statsmodels=0.4.3
 bottleneck=0.8.0
 numexpr=2.2.2
 pytables=3.0.0

ci/requirements-2.7_LOCALE.run

@@ -13,5 +13,4 @@ html5lib=1.0b2
 lxml=3.2.1
 scipy=0.11.0
 beautiful-soup=4.2.1
-statsmodels=0.4.3
 bigquery=2.0.17

ci/requirements-2.7_SLOW.run

@@ -4,7 +4,6 @@ numpy=1.8.2
 matplotlib=1.3.1
 scipy
 patsy
-statsmodels
 xlwt
 openpyxl
 xlsxwriter

ci/requirements-3.4_SLOW.run

@@ -17,5 +17,4 @@ sqlalchemy
 bottleneck
 pymysql
 psycopg2
-statsmodels
 jinja2=2.8

doc/source/install.rst

@@ -250,9 +250,9 @@ Optional Dependencies
 * `Feather Format <https://github.com/wesm/feather>`__: necessary for feather-based storage, version 0.3.1 or higher.
 * `SQLAlchemy <http://www.sqlalchemy.org>`__: for SQL database support. Version 0.8.1 or higher recommended. Besides SQLAlchemy, you also need a database specific driver. You can find an overview of supported drivers for each SQL dialect in the `SQLAlchemy docs <http://docs.sqlalchemy.org/en/latest/dialects/index.html>`__. Some common drivers are:
 
-    - `psycopg2 <http://initd.org/psycopg/>`__: for PostgreSQL
-    - `pymysql <https://github.com/PyMySQL/PyMySQL>`__: for MySQL.
-    - `SQLite <https://docs.python.org/3.5/library/sqlite3.html>`__: for SQLite, this is included in Python's standard library by default.
+  * `psycopg2 <http://initd.org/psycopg/>`__: for PostgreSQL
+  * `pymysql <https://github.com/PyMySQL/PyMySQL>`__: for MySQL.
+  * `SQLite <https://docs.python.org/3.5/library/sqlite3.html>`__: for SQLite, this is included in Python's standard library by default.
 
 * `matplotlib <http://matplotlib.org/>`__: for plotting
 * For Excel I/O:
@@ -272,11 +272,8 @@ Optional Dependencies
   <http://www.vergenet.net/~conrad/software/xsel/>`__, or `xclip
   <https://github.com/astrand/xclip/>`__: necessary to use
   :func:`~pandas.read_clipboard`. Most package managers on Linux distributions will have ``xclip`` and/or ``xsel`` immediately available for installation.
-* Google's `python-gflags <<https://github.com/google/python-gflags/>`__ ,
-  `oauth2client <https://github.com/google/oauth2client>`__ ,
-  `httplib2 <http://pypi.python.org/pypi/httplib2>`__
-  and `google-api-python-client <http://github.com/google/google-api-python-client>`__
-  : Needed for :mod:`~pandas.io.gbq`
+* For Google BigQuery I/O - see :ref:`here <io.bigquery_deps>`.
+
 * `Backports.lzma <https://pypi.python.org/pypi/backports.lzma/>`__: Only for Python 2, for writing to and/or reading from an xz compressed DataFrame in CSV; Python 3 support is built into the standard library.
 * One of the following combinations of libraries is needed to use the
   top-level :func:`~pandas.read_html` function:

doc/source/io.rst

@@ -39,7 +39,7 @@ object.
     * :ref:`read_json<io.json_reader>`
     * :ref:`read_msgpack<io.msgpack>`
     * :ref:`read_html<io.read_html>`
-    * :ref:`read_gbq<io.bigquery_reader>`
+    * :ref:`read_gbq<io.bigquery>`
     * :ref:`read_stata<io.stata_reader>`
     * :ref:`read_sas<io.sas_reader>`
     * :ref:`read_clipboard<io.clipboard>`
@@ -55,7 +55,7 @@ The corresponding ``writer`` functions are object methods that are accessed like
     * :ref:`to_json<io.json_writer>`
     * :ref:`to_msgpack<io.msgpack>`
     * :ref:`to_html<io.html>`
-    * :ref:`to_gbq<io.bigquery_writer>`
+    * :ref:`to_gbq<io.bigquery>`
     * :ref:`to_stata<io.stata_writer>`
     * :ref:`to_clipboard<io.clipboard>`
     * :ref:`to_pickle<io.pickle>`
@@ -4648,16 +4648,11 @@ DataFrame with a shape and data types derived from the source table.
 Additionally, DataFrames can be inserted into new BigQuery tables or appended
 to existing tables.
 
-You will need to install some additional dependencies:
-
-- Google's `python-gflags <https://github.com/google/python-gflags/>`__
-- `httplib2 <http://pypi.python.org/pypi/httplib2>`__
-- `google-api-python-client <http://github.com/google/google-api-python-client>`__
-
 .. warning::
 
    To use this module, you will need a valid BigQuery account. Refer to the
-   `BigQuery Documentation <https://cloud.google.com/bigquery/what-is-bigquery>`__ for details on the service itself.
+   `BigQuery Documentation <https://cloud.google.com/bigquery/what-is-bigquery>`__
+   for details on the service itself.
 
 The key functions are:
 
@@ -4671,7 +4666,44 @@ The key functions are:
 
 .. currentmodule:: pandas
 
-.. _io.bigquery_reader:
+
+Supported Data Types
+++++++++++++++++++++
+
+Pandas supports all these `BigQuery data types <https://cloud.google.com/bigquery/data-types>`__:
+``STRING``, ``INTEGER`` (64bit), ``FLOAT`` (64 bit), ``BOOLEAN`` and
+``TIMESTAMP`` (microsecond precision). Data types ``BYTES`` and ``RECORD``
+are not supported.
+
+Integer and boolean ``NA`` handling
++++++++++++++++++++++++++++++++++++
+
+.. versionadded:: 0.20
+
+Since all columns in BigQuery queries are nullable, and NumPy lacks of ``NA``
+support for integer and boolean types, this module will store ``INTEGER`` or
+``BOOLEAN`` columns with at least one ``NULL`` value as ``dtype=object``.
+Otherwise those columns will be stored as ``dtype=int64`` or ``dtype=bool``
+respectively.
+
+This is opposite to default pandas behaviour which will promote integer
+type to float in order to store NAs. See the :ref:`gotchas<gotchas.intna>`
+for detailed explaination.
+
+While this trade-off works well for most cases, it breaks down for storing
+values greater than 2**53. Such values in BigQuery can represent identifiers
+and unnoticed precision lost for identifier is what we want to avoid.
+
+.. _io.bigquery_deps:
+
+Dependencies
+++++++++++++
+
+This module requires following additional dependencies:
+
+- `httplib2 <https://github.com/httplib2/httplib2>`__: HTTP client
+- `google-api-python-client <http://github.com/google/google-api-python-client>`__: Google's API client
+- `oauth2client <https://github.com/google/oauth2client>`__: authentication and authorization for Google's API
 
 .. _io.bigquery_authentication:
 
@@ -4686,7 +4718,7 @@ Is possible to authenticate with either user account credentials or service acco
 Authenticating with user account credentials is as simple as following the prompts in a browser window
 which will be automatically opened for you. You will be authenticated to the specified
 ``BigQuery`` account using the product name ``pandas GBQ``. It is only possible on local host.
-The remote authentication using user account credentials is not currently supported in Pandas.
+The remote authentication using user account credentials is not currently supported in pandas.
 Additional information on the authentication mechanism can be found
 `here <https://developers.google.com/identity/protocols/OAuth2#clientside/>`__.
 
@@ -4695,8 +4727,6 @@ is particularly useful when working on remote servers (eg. jupyter iPython noteb
 Additional information on service accounts can be found
 `here <https://developers.google.com/identity/protocols/OAuth2#serviceaccount>`__.
 
-You will need to install an additional dependency: `oauth2client <https://github.com/google/oauth2client>`__.
-
 Authentication via ``application default credentials`` is also possible. This is only valid
 if the parameter ``private_key`` is not provided. This method also requires that
 the credentials can be fetched from the environment the code is running in.
@@ -4716,6 +4746,7 @@ Additional information on
    A private key can be obtained from the Google developers console by clicking
    `here <https://console.developers.google.com/permissions/serviceaccounts>`__. Use JSON key type.
 
+.. _io.bigquery_reader:
 
 Querying
 ''''''''
@@ -4775,7 +4806,6 @@ For more information about query configuration parameters see
 
 .. _io.bigquery_writer:
 
-
 Writing DataFrames
 ''''''''''''''''''
 
@@ -4865,6 +4895,8 @@ For example:
    often as the service seems to be changing and evolving. BiqQuery is best for analyzing large
    sets of data quickly, but it is not a direct replacement for a transactional database.
 
+.. _io.bigquery_create_tables:
+
 Creating BigQuery Tables
 ''''''''''''''''''''''''
 
@@ -4894,6 +4926,7 @@ produce the dictionary representation schema of the specified pandas DataFrame.
    the new table with a different name. Refer to
    `Google BigQuery issue 191 <https://code.google.com/p/google-bigquery/issues/detail?id=191>`__.
 
+
 .. _io.stata:
 
 Stata Format

doc/source/whatsnew/v0.20.0.txt

@@ -369,7 +369,9 @@ Other API Changes
 - ``pd.read_csv()`` will now raise a ``ValueError`` for the C engine if the quote character is larger than than one byte (:issue:`11592`)
 - ``inplace`` arguments now require a boolean value, else a ``ValueError`` is thrown (:issue:`14189`)
 - ``pandas.api.types.is_datetime64_ns_dtype`` will now report ``True`` on a tz-aware dtype, similar to ``pandas.api.types.is_datetime64_any_dtype``
- - ``DataFrame.asof()`` will return a null filled ``Series`` instead the scalar ``NaN`` if a match is not found (:issue:`15118`)
+- ``DataFrame.asof()`` will return a null filled ``Series`` instead the scalar ``NaN`` if a match is not found (:issue:`15118`)
+- The :func:`pd.read_gbq` method now stores ``INTEGER`` columns as ``dtype=object`` if they contain ``NULL`` values. Otherwise they are stored as ``int64``. This prevents precision lost for integers greather than 2**53. Furthermore ``FLOAT`` columns with values above 10**4 are no more casted to ``int64`` which also caused precision lost (:issue: `14064`, :issue:`14305`).
+
 .. _whatsnew_0200.deprecations:
 
 Deprecations
@@ -396,7 +398,7 @@ Removal of prior version deprecations/changes
 - The ``pandas.io.ga`` module with a ``google-analytics`` interface is removed (:issue:`11308`).
   Similar functionality can be found in the `Google2Pandas <https://github.com/panalysis/Google2Pandas>`__ package.
 - ``pd.to_datetime`` and ``pd.to_timedelta`` have dropped the ``coerce`` parameter in favor of ``errors`` (:issue:`13602`)
-
+- ``pandas.stats.fama_macbeth``, ``pandas.stats.ols``, ``pandas.stats.plm`` and ``pandas.stats.var``, as well as the top-level ``pandas.fama_macbeth`` and ``pandas.ols`` routines are removed. Similar functionaility can be found in the `statsmodels <shttp://www.statsmodels.org/dev/>`__ package. (:issue:`11898`)
 
 
 
@@ -439,6 +441,7 @@ Bug Fixes
 
 - Bug in ``DataFrame.loc`` with indexing a ``MultiIndex`` with a ``Series`` indexer (:issue:`14730`)
 
+
 - Bug in ``pd.read_msgpack()`` in which ``Series`` categoricals were being improperly processed (:issue:`14901`)
 - Bug in ``Series.ffill()`` with mixed dtypes containing tz-aware datetimes. (:issue:`14956`)
 
@@ -518,3 +521,4 @@ Bug Fixes
 - Bug in ``DataFrame.boxplot`` where ``fontsize`` was not applied to the tick labels on both axes (:issue:`15108`)
 - Bug in ``Series.replace`` and ``DataFrame.replace`` which failed on empty replacement dicts (:issue:`15289`)
 - Bug in ``pd.melt`` where passing a tuple value for ``value_vars`` caused a ``TypeError`` (:issue:`15348`)
+- Bug in ``.eval()`` which caused multiline evals to fail with local variables not on the first line (:issue:`15342`)

pandas/api/tests/test_api.py

@@ -42,7 +42,7 @@ class TestPDApi(Base, tm.TestCase):
                      'json', 'lib', 'index', 'parser']
 
     # these are already deprecated; awaiting removal
-    deprecated_modules = ['ols', 'stats', 'datetools']
+    deprecated_modules = ['stats', 'datetools']
 
     # misc
     misc = ['IndexSlice', 'NaT']
@@ -109,7 +109,7 @@ class TestPDApi(Base, tm.TestCase):
                         'expanding_max', 'expanding_mean', 'expanding_median',
                         'expanding_min', 'expanding_quantile',
                         'expanding_skew', 'expanding_std', 'expanding_sum',
-                        'expanding_var', 'fama_macbeth', 'rolling_apply',
+                        'expanding_var', 'rolling_apply',
                         'rolling_corr', 'rolling_count', 'rolling_cov',
                         'rolling_kurt', 'rolling_max', 'rolling_mean',
                         'rolling_median', 'rolling_min', 'rolling_quantile',

pandas/computation/eval.py

@@ -236,7 +236,7 @@ def eval(expr, parser='pandas', engine=None, truediv=True,
     first_expr = True
     if isinstance(expr, string_types):
         _check_expression(expr)
-        exprs = [e for e in expr.splitlines() if e != '']
+        exprs = [e.strip() for e in expr.splitlines() if e.strip() != '']
     else:
         exprs = [expr]
     multi_line = len(exprs) > 1
@@ -254,8 +254,7 @@ def eval(expr, parser='pandas', engine=None, truediv=True,
         _check_for_locals(expr, level, parser)
 
         # get our (possibly passed-in) scope
-        level += 1
-        env = _ensure_scope(level, global_dict=global_dict,
+        env = _ensure_scope(level + 1, global_dict=global_dict,
                             local_dict=local_dict, resolvers=resolvers,
                             target=target)
 

pandas/computation/tests/test_eval.py

@@ -1274,7 +1274,6 @@ def test_assignment_fails(self):
                           local_dict={'df': df, 'df2': df2})
 
     def test_assignment_column(self):
-        tm.skip_if_no_ne('numexpr')
         df = DataFrame(np.random.randn(5, 2), columns=list('ab'))
         orig_df = df.copy()
 
@@ -1346,7 +1345,6 @@ def test_column_in(self):
 
     def assignment_not_inplace(self):
         # GH 9297
-        tm.skip_if_no_ne('numexpr')
         df = DataFrame(np.random.randn(5, 2), columns=list('ab'))
 
         actual = df.eval('c = a + b', inplace=False)
@@ -1365,7 +1363,6 @@ def assignment_not_inplace(self):
 
     def test_multi_line_expression(self):
         # GH 11149
-        tm.skip_if_no_ne('numexpr')
         df = pd.DataFrame({'a': [1, 2, 3], 'b': [4, 5, 6]})
         expected = df.copy()
 
@@ -1393,7 +1390,6 @@ def test_multi_line_expression(self):
 
     def test_multi_line_expression_not_inplace(self):
         # GH 11149
-        tm.skip_if_no_ne('numexpr')
         df = pd.DataFrame({'a': [1, 2, 3], 'b': [4, 5, 6]})
         expected = df.copy()
 
@@ -1411,6 +1407,21 @@ def test_multi_line_expression_not_inplace(self):
         e = a + 2""", inplace=False)
         assert_frame_equal(expected, df)
 
+    def test_multi_line_expression_local_variable(self):
+        # GH 15342
+        df = pd.DataFrame({'a': [1, 2, 3], 'b': [4, 5, 6]})
+        expected = df.copy()
+
+        local_var = 7
+        expected['c'] = expected['a'] * local_var
+        expected['d'] = expected['c'] + local_var
+        ans = df.eval("""
+        c = a * @local_var
+        d = c + @local_var
+        """, inplace=True)
+        assert_frame_equal(expected, df)
+        self.assertIsNone(ans)
+
     def test_assignment_in_query(self):
         # GH 8664
         df = pd.DataFrame({'a': [1, 2, 3], 'b': [4, 5, 6]})

pandas/io/gbq.py

@@ -603,18 +603,14 @@ def _parse_data(schema, rows):
     # see:
     # http://pandas.pydata.org/pandas-docs/dev/missing_data.html
     # #missing-data-casting-rules-and-indexing
-    dtype_map = {'INTEGER': np.dtype(float),
-                 'FLOAT': np.dtype(float),
-                 # This seems to be buggy without nanosecond indicator
+    dtype_map = {'FLOAT': np.dtype(float),
                  'TIMESTAMP': 'M8[ns]'}
 
     fields = schema['fields']
     col_types = [field['type'] for field in fields]
     col_names = [str(field['name']) for field in fields]
     col_dtypes = [dtype_map.get(field['type'], object) for field in fields]
-    page_array = np.zeros((len(rows),),
-                          dtype=lzip(col_names, col_dtypes))
-
+    page_array = np.zeros((len(rows),), dtype=lzip(col_names, col_dtypes))
     for row_num, raw_row in enumerate(rows):
         entries = raw_row.get('f', [])
         for col_num, field_type in enumerate(col_types):
@@ -628,7 +624,9 @@ def _parse_data(schema, rows):
 def _parse_entry(field_value, field_type):
     if field_value is None or field_value == 'null':
         return None
-    if field_type == 'INTEGER' or field_type == 'FLOAT':
+    if field_type == 'INTEGER':
+        return int(field_value)
+    elif field_type == 'FLOAT':
         return float(field_value)
     elif field_type == 'TIMESTAMP':
         timestamp = datetime.utcfromtimestamp(float(field_value))
@@ -757,10 +755,14 @@ def read_gbq(query, project_id=None, index_col=None, col_order=None,
                 'Column order does not match this DataFrame.'
             )
 
-    # Downcast floats to integers and objects to booleans
-    # if there are no NaN's. This is presently due to a
-    # limitation of numpy in handling missing data.
-    final_df._data = final_df._data.downcast(dtypes='infer')
+    # cast BOOLEAN and INTEGER columns from object to bool/int
+    # if they dont have any nulls
+    type_map = {'BOOLEAN': bool, 'INTEGER': int}
+    for field in schema['fields']:
+        if field['type'] in type_map and \
+                final_df[field['name']].notnull().all():
+            final_df[field['name']] = \
+                final_df[field['name']].astype(type_map[field['type']])
 
     connector.print_elapsed_seconds(
         'Total time taken',