Merge branch 'master' into parquet-categorical

* master: (22 commits)
  DOC: fix PR09,PR08 errors for pandas.Timestamp (pandas-dev#28739)
  WEB: Add diversity note to team.md (pandas-dev#28630)
  DOC: Minor fixes in pandas/testing.py docstring. (pandas-dev#28752)
  TST: port maybe_promote tests from pandas-dev#23982 (pandas-dev#28764)
  Bugfix/groupby datetime issue (pandas-dev#28569)
  reenable codecov (pandas-dev#28750)
  CLN: Centralised _check_percentile (pandas-dev#27584)
  DEPR: Deprecate Index.set_value (pandas-dev#28621)
  CLN: Fix typo in contributing.rst (pandas-dev#28761)
  Fixed docstring errors in pandas.period range and pandas.PeriodIndex (pandas-dev#28756)
  BUG: Fix TypeError raised in libreduction (pandas-dev#28643)
  DOC: Pandas.Series.drop docstring PR02 (pandas-dev#27976) (pandas-dev#28742)
  DOC: Fixed doctring errors PR08, PR09 in pandas.io (pandas-dev#28748)
  TST: Fix broken test cases where Timedelta/Timestamp raise (pandas-dev#28729)
  REF: Consolidate alignment calls in DataFrame ops (pandas-dev#28638)
  BUG: Fix dep generation (pandas-dev#28734)
  Added doctstring to fixture (pandas-dev#28727)
  DOC: Fixed PR06 docstrings errors in pandas.timedelta_range (pandas-dev#28719)
  replaced safe_import with a corresponding test decorator (pandas-dev#28731)
  BUG: Fix RangeIndex.get_indexer for decreasing RangeIndex (pandas-dev#28680)
  ...

Author: galuhsahid

ci/run_tests.sh

@@ -43,10 +43,9 @@ do
     # if no tests are found (the case of "single and slow"), pytest exits with code 5, and would make the script fail, if not for the below code
     sh -c "$PYTEST_CMD; ret=\$?; [ \$ret = 5 ] && exit 0 || exit \$ret"
 
-    # 2019-08-21 disabling because this is hitting HTTP 400 errors GH#27602
-    # if [[ "$COVERAGE" && $? == 0 && "$TRAVIS_BRANCH" == "master" ]]; then
-    #    echo "uploading coverage for $TYPE tests"
-    #    echo "bash <(curl -s https://codecov.io/bash) -Z -c -F $TYPE -f $COVERAGE_FNAME"
-    #          bash <(curl -s https://codecov.io/bash) -Z -c -F $TYPE -f $COVERAGE_FNAME
-    # fi
+    if [[ "$COVERAGE" && $? == 0 && "$TRAVIS_BRANCH" == "master" ]]; then
+        echo "uploading coverage for $TYPE tests"
+        echo "bash <(curl -s https://codecov.io/bash) -Z -c -F $TYPE -f $COVERAGE_FNAME"
+              bash <(curl -s https://codecov.io/bash) -Z -c -F $TYPE -f $COVERAGE_FNAME
+    fi
 done

doc/source/development/contributing.rst

@@ -952,7 +952,7 @@ the expected correct result::
 Transitioning to ``pytest``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-*pandas* existing test structure is *mostly* classed based, meaning that you will typically find tests wrapped in a class.
+*pandas* existing test structure is *mostly* class-based, meaning that you will typically find tests wrapped in a class.
 
 .. code-block:: python
 

doc/source/reference/indexing.rst

@@ -166,7 +166,6 @@ Selecting
    Index.get_slice_bound
    Index.get_value
    Index.get_values
-   Index.set_value
    Index.isin
    Index.slice_indexer
    Index.slice_locs

doc/source/whatsnew/v0.25.2.rst

@@ -50,6 +50,7 @@ Indexing
 ^^^^^^^^
 
 - Fix regression in :meth:`DataFrame.reindex` not following ``limit`` argument (:issue:`28631`).
+- Fix regression in :meth:`RangeIndex.get_indexer` for decreasing :class:`RangeIndex` where target values may be improperly identified as missing/present (:issue:`28678`)
 -
 -
 

doc/source/whatsnew/v1.0.0.rst

@@ -123,7 +123,9 @@ Documentation Improvements
 Deprecations
 ~~~~~~~~~~~~
 
--
+- ``Index.set_value`` has been deprecated. For a given index ``idx``, array ``arr``,
+  value in ``idx`` of ``idx_val`` and a new value of ``val``, ``idx.set_value(arr, idx_val, val)``
+  is equivalent to ``arr[idx.get_loc(idx_val)] = val``, which should be used instead (:issue:`28621`).
 -
 
 .. _whatsnew_1000.prior_deprecations:
@@ -190,7 +192,7 @@ Datetimelike
 - Bug in :class:`Series` and :class:`DataFrame` with integer dtype failing to raise ``TypeError`` when adding or subtracting a ``np.datetime64`` object (:issue:`28080`)
 - Bug in :class:`Week` with ``weekday`` incorrectly raising ``AttributeError`` instead of ``TypeError`` when adding or subtracting an invalid type (:issue:`28530`)
 - Bug in :class:`DataFrame` arithmetic operations when operating with a :class:`Series` with dtype `'timedelta64[ns]'` (:issue:`28049`)
--
+- Bug in :func:`pandas.core.groupby.generic.SeriesGroupBy.apply` raising ``ValueError`` when a column in the original DataFrame is a datetime and the column labels are not standard integers (:issue:`28247`)
 
 Timedelta
 ^^^^^^^^^

pandas/_libs/reduction.pyx

@@ -15,15 +15,15 @@ from numpy cimport (ndarray,
 cnp.import_array()
 
 cimport pandas._libs.util as util
-from pandas._libs.lib import maybe_convert_objects, values_from_object
+from pandas._libs.lib import maybe_convert_objects
 
 
 cdef _get_result_array(object obj, Py_ssize_t size, Py_ssize_t cnt):
 
     if (util.is_array(obj) or
             (isinstance(obj, list) and len(obj) == cnt) or
             getattr(obj, 'shape', None) == (cnt,)):
-        raise ValueError('function does not reduce')
+        raise ValueError('Function does not reduce')
 
     return np.empty(size, dtype='O')
 
@@ -103,7 +103,7 @@ cdef class Reducer:
             ndarray arr, result, chunk
             Py_ssize_t i, incr
             flatiter it
-            bint has_labels
+            bint has_labels, has_ndarray_labels
             object res, name, labels, index
             object cached_typ=None
 
@@ -113,14 +113,18 @@ cdef class Reducer:
         chunk.data = arr.data
         labels = self.labels
         has_labels = labels is not None
+        has_ndarray_labels = util.is_array(labels)
         has_index = self.index is not None
         incr = self.increment
 
         try:
             for i in range(self.nresults):
 
-                if has_labels:
+                if has_ndarray_labels:
                     name = util.get_value_at(labels, i)
+                elif has_labels:
+                    # labels is an ExtensionArray
+                    name = labels[i]
                 else:
                     name = None
 
@@ -362,7 +366,8 @@ cdef class SeriesGrouper:
 
     def get_result(self):
         cdef:
-            ndarray arr, result
+            # Define result to avoid UnboundLocalError
+            ndarray arr, result = None
             ndarray[int64_t] labels, counts
             Py_ssize_t i, n, group_size, lab
             object res
@@ -428,6 +433,9 @@ cdef class SeriesGrouper:
             islider.reset()
             vslider.reset()
 
+        if result is None:
+            raise ValueError("No result.")
+
         if result.dtype == np.object_:
             result = maybe_convert_objects(result)
 
@@ -639,11 +647,11 @@ def compute_reduction(arr, f, axis=0, dummy=None, labels=None):
     """
 
     if labels is not None:
-        if labels._has_complex_internals:
-            raise Exception('Cannot use shortcut')
+        # Caller is responsible for ensuring we don't have MultiIndex
+        assert not labels._has_complex_internals
 
-        # pass as an ndarray
-        labels = values_from_object(labels)
+        # pass as an ndarray/ExtensionArray
+        labels = labels._values
 
     reducer = Reducer(arr, f, axis=axis, dummy=dummy, labels=labels)
     return reducer.get_result()