Merge remote-tracking branch 'upstream/master' into GH_37544

pandas-dev · Nov 4, 2020 · 54c0465 · 54c0465
2 parents eb6905c + a057135
commit 54c0465
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -119,6 +119,36 @@ repos:
         entry: python scripts/validate_unwanted_patterns.py --validation-type="private_function_across_module"
         types: [python]
         exclude: ^(asv_bench|pandas/tests|doc)/
+    -   id: FrameOrSeriesUnion
+        name: Check for use of Union[Series, DataFrame] instead of FrameOrSeriesUnion alias
+        entry: Union\[.*(Series.*DataFrame|DataFrame.*Series).*\]
+        language: pygrep
+        types: [python]
+        exclude: ^pandas/_typing\.py$
+    -   id: type-not-class
+        name: Check for use of foo.__class__ instead of type(foo)
+        entry: \.__class__
+        language: pygrep
+        files: \.(py|pyx)$
+    -   id: unwanted-typing
+        name: Check for use of comment-based annotation syntax and missing error codes
+        entry: |
+            (?x)
+            \#\ type:\ (?!ignore)|
+            \#\ type:\s?ignore(?!\[)
+        language: pygrep
+        types: [python]
+    -   id: no-os-remove
+        name: Check code for instances of os.remove
+        entry: os\.remove
+        language: pygrep
+        types: [python]
+        files: ^pandas/tests/
+        exclude: |
+            (?x)^
+            pandas/tests/io/excel/test_writers\.py|
+            pandas/tests/io/pytables/common\.py|
+            pandas/tests/io/pytables/test_store\.py$
 -   repo: https://github.com/asottile/yesqa
     rev: v1.2.2
     hooks:

diff --git a/ci/code_checks.sh b/ci/code_checks.sh
@@ -122,29 +122,6 @@ if [[ -z "$CHECK" || "$CHECK" == "patterns" ]]; then
     RET=$(($RET + $?)) ; echo $MSG "DONE"
 
     # -------------------------------------------------------------------------
-    # Type annotations
-
-    MSG='Check for use of comment-based annotation syntax' ; echo $MSG
-    invgrep -R --include="*.py" -P '# type: (?!ignore)' pandas
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
-    MSG='Check for missing error codes with # type: ignore' ; echo $MSG
-    invgrep -R --include="*.py" -P '# type:\s?ignore(?!\[)' pandas
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
-    MSG='Check for use of Union[Series, DataFrame] instead of FrameOrSeriesUnion alias' ; echo $MSG
-    invgrep -R --include="*.py" --exclude=_typing.py -E 'Union\[.*(Series.*DataFrame|DataFrame.*Series).*\]' pandas
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
-    # -------------------------------------------------------------------------
-    MSG='Check for use of foo.__class__ instead of type(foo)' ; echo $MSG
-    invgrep -R --include=*.{py,pyx} '\.__class__' pandas
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
-    MSG='Check code for instances of os.remove' ; echo $MSG
-    invgrep -R --include="*.py*" --exclude "common.py" --exclude "test_writers.py" --exclude "test_store.py" -E "os\.remove" pandas/tests/
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
     MSG='Check for inconsistent use of pandas namespace in tests' ; echo $MSG
     for class in "Series" "DataFrame" "Index" "MultiIndex" "Timestamp" "Timedelta" "TimedeltaIndex" "DatetimeIndex" "Categorical"; do
         check_namespace ${class}

diff --git a/doc/source/whatsnew/v1.1.5.rst b/doc/source/whatsnew/v1.1.5.rst
@@ -23,7 +23,7 @@ Fixed regressions
 
 Bug fixes
 ~~~~~~~~~
--
+- Bug in metadata propagation for ``groupby`` iterator (:issue:`37343`)
 -
 
 .. ---------------------------------------------------------------------------

diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
@@ -217,6 +217,7 @@ Other enhancements
 - ``Styler`` now allows direct CSS class name addition to individual data cells (:issue:`36159`)
 - :meth:`Rolling.mean()` and :meth:`Rolling.sum()` use Kahan summation to calculate the mean to avoid numerical problems (:issue:`10319`, :issue:`11645`, :issue:`13254`, :issue:`32761`, :issue:`36031`)
 - :meth:`DatetimeIndex.searchsorted`, :meth:`TimedeltaIndex.searchsorted`, :meth:`PeriodIndex.searchsorted`, and :meth:`Series.searchsorted` with datetimelike dtypes will now try to cast string arguments (listlike and scalar) to the matching datetimelike type (:issue:`36346`)
+-
 - Added methods :meth:`IntegerArray.prod`, :meth:`IntegerArray.min`, and :meth:`IntegerArray.max` (:issue:`33790`)
 - Where possible :meth:`RangeIndex.difference` and :meth:`RangeIndex.symmetric_difference` will return :class:`RangeIndex` instead of :class:`Int64Index` (:issue:`36564`)
 - Added :meth:`Rolling.sem()` and :meth:`Expanding.sem()` to compute the standard error of mean (:issue:`26476`).
@@ -341,6 +342,8 @@ Deprecations
 - Deprecate use of strings denoting units with 'M', 'Y' or 'y' in :func:`~pandas.to_timedelta` (:issue:`36666`)
 - :class:`Index` methods ``&``, ``|``, and ``^`` behaving as the set operations :meth:`Index.intersection`, :meth:`Index.union`, and :meth:`Index.symmetric_difference`, respectively, are deprecated and in the future will behave as pointwise boolean operations matching :class:`Series` behavior.  Use the named set methods instead (:issue:`36758`)
 - :meth:`Categorical.is_dtype_equal` and :meth:`CategoricalIndex.is_dtype_equal` are deprecated, will be removed in a future version (:issue:`37545`)
+- :meth:`Series.slice_shift` and :meth:`DataFrame.slice_shift` are deprecated, use :meth:`Series.shift` or :meth:`DataFrame.shift` instead (:issue:`37601`)
+
 
 .. ---------------------------------------------------------------------------
 
@@ -391,14 +394,18 @@ Datetimelike
 - Bug in :class:`DatetimeIndex.shift` incorrectly raising when shifting empty indexes (:issue:`14811`)
 - :class:`Timestamp` and :class:`DatetimeIndex` comparisons between timezone-aware and timezone-naive objects now follow the standard library ``datetime`` behavior, returning ``True``/``False`` for ``!=``/``==`` and raising for inequality comparisons (:issue:`28507`)
 - Bug in :meth:`DatetimeIndex.equals` and :meth:`TimedeltaIndex.equals` incorrectly considering ``int64`` indexes as equal (:issue:`36744`)
+- :meth:`to_json` and :meth:`read_json` now implements timezones parsing when orient structure is 'table'.
+- :meth:`astype` now attempts to convert to 'datetime64[ns, tz]' directly from 'object' with inferred timezone from string (:issue:`35973`).
 - Bug in :meth:`TimedeltaIndex.sum` and :meth:`Series.sum` with ``timedelta64`` dtype on an empty index or series returning ``NaT`` instead of ``Timedelta(0)`` (:issue:`31751`)
 - Bug in :meth:`DatetimeArray.shift` incorrectly allowing ``fill_value`` with a mismatched timezone (:issue:`37299`)
 - Bug in adding a :class:`BusinessDay` with nonzero ``offset`` to a non-scalar other (:issue:`37457`)
+- Bug in :func:`to_datetime` with a read-only array incorrectly raising (:issue:`34857`)
 
 Timedelta
 ^^^^^^^^^
 - Bug in :class:`TimedeltaIndex`, :class:`Series`, and :class:`DataFrame` floor-division with ``timedelta64`` dtypes and ``NaT`` in the denominator (:issue:`35529`)
 - Bug in parsing of ISO 8601 durations in :class:`Timedelta`, :meth:`pd.to_datetime` (:issue:`37159`, fixes :issue:`29773` and :issue:`36204`)
+- Bug in :func:`to_timedelta` with a read-only array incorrectly raising (:issue:`34857`)
 
 Timezones
 ^^^^^^^^^
@@ -469,6 +476,7 @@ MultiIndex
 
 - Bug in :meth:`DataFrame.xs` when used with :class:`IndexSlice` raises ``TypeError`` with message ``"Expected label or tuple of labels"`` (:issue:`35301`)
 - Bug in :meth:`DataFrame.reset_index` with ``NaT`` values in index raises ``ValueError`` with message ``"cannot convert float NaN to integer"`` (:issue:`36541`)
+- Bug in :meth:`DataFrame.combine_first` when used with :class:`MultiIndex` containing string and ``NaN`` values raises ``TypeError`` (:issue:`36562`)
 
 I/O
 ^^^
@@ -492,6 +500,8 @@ I/O
 - Bug in output rendering of complex numbers showing too many trailing zeros (:issue:`36799`)
 - Bug in :class:`HDFStore` threw a ``TypeError`` when exporting an empty :class:`DataFrame` with ``datetime64[ns, tz]`` dtypes with a fixed HDF5 store (:issue:`20594`)
 - Bug in :class:`HDFStore` was dropping timezone information when exporting :class:`Series` with ``datetime64[ns, tz]`` dtypes with a fixed HDF5 store (:issue:`20594`)
+- :func:`read_csv` was closing user-provided binary file handles when ``engine="c"`` and an ``encoding`` was requested (:issue:`36980`)
+- Bug in :meth:`DataFrame.to_hdf` was not dropping missing rows with ``dropna=True`` (:issue:`35719`)
 
 Plotting
 ^^^^^^^^
@@ -523,6 +533,7 @@ Groupby/resample/rolling
 - Using :meth:`Rolling.var()` instead of :meth:`Rolling.std()` avoids numerical issues for :meth:`Rolling.corr()` when :meth:`Rolling.var()` is still within floating point precision while :meth:`Rolling.std()` is not (:issue:`31286`)
 - Bug in :meth:`df.groupby(..).quantile() <pandas.core.groupby.DataFrameGroupBy.quantile>` and :meth:`df.resample(..).quantile() <pandas.core.resample.Resampler.quantile>` raised ``TypeError`` when values were of type ``Timedelta`` (:issue:`29485`)
 - Bug in :meth:`Rolling.median` and :meth:`Rolling.quantile` returned wrong values for :class:`BaseIndexer` subclasses with non-monotonic starting or ending points for windows (:issue:`37153`)
+- Bug in :meth:`DataFrame.groupby` dropped ``nan`` groups from result with ``dropna=False`` when grouping over a single column (:issue:`35646`, :issue:`35542`)
 
 Reshaping
 ^^^^^^^^^

diff --git a/pandas/_libs/join.pyx b/pandas/_libs/join.pyx
@@ -268,7 +268,7 @@ ctypedef fused join_t:
 
 @cython.wraparound(False)
 @cython.boundscheck(False)
-def left_join_indexer_unique(join_t[:] left, join_t[:] right):
+def left_join_indexer_unique(ndarray[join_t] left, ndarray[join_t] right):
     cdef:
         Py_ssize_t i, j, nleft, nright
         ndarray[int64_t] indexer

diff --git a/pandas/_libs/lib.pyx b/pandas/_libs/lib.pyx
@@ -896,21 +896,28 @@ def indices_fast(ndarray index, const int64_t[:] labels, list keys,
 
         if lab != cur:
             if lab != -1:
-                tup = PyTuple_New(k)
-                for j in range(k):
-                    val = keys[j][sorted_labels[j][i - 1]]
-                    PyTuple_SET_ITEM(tup, j, val)
-                    Py_INCREF(val)
-
+                if k == 1:
+                    # When k = 1 we do not want to return a tuple as key
+                    tup = keys[0][sorted_labels[0][i - 1]]
+                else:
+                    tup = PyTuple_New(k)
+                    for j in range(k):
+                        val = keys[j][sorted_labels[j][i - 1]]
+                        PyTuple_SET_ITEM(tup, j, val)
+                        Py_INCREF(val)
                 result[tup] = index[start:i]
             start = i
         cur = lab
 
-    tup = PyTuple_New(k)
-    for j in range(k):
-        val = keys[j][sorted_labels[j][n - 1]]
-        PyTuple_SET_ITEM(tup, j, val)
-        Py_INCREF(val)
+    if k == 1:
+        # When k = 1 we do not want to return a tuple as key
+        tup = keys[0][sorted_labels[0][n - 1]]
+    else:
+        tup = PyTuple_New(k)
+        for j in range(k):
+            val = keys[j][sorted_labels[j][n - 1]]
+            PyTuple_SET_ITEM(tup, j, val)
+            Py_INCREF(val)
     result[tup] = index[start:]
 
     return result