Merge branch 'master' into misc/remove-docs

Author: jameslamb

.pre-commit-config.yaml

@@ -47,11 +47,11 @@ repos:
         types: [text]
         args: [--append-config=flake8/cython-template.cfg]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.7.0
+    rev: 5.8.0
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.10.0
+    rev: v2.11.0
     hooks:
     -   id: pyupgrade
         args: [--py37-plus, --keep-runtime-typing]

asv_bench/benchmarks/io/style.py

@@ -3,7 +3,7 @@
 from pandas import DataFrame
 
 
-class RenderApply:
+class Render:
 
     params = [[12, 24, 36], [12, 120]]
     param_names = ["cols", "rows"]
@@ -14,15 +14,21 @@ def setup(self, cols, rows):
             columns=[f"float_{i+1}" for i in range(cols)],
             index=[f"row_{i+1}" for i in range(rows)],
         )
-        self._style_apply()
 
-    def time_render(self, cols, rows):
+    def time_apply_render(self, cols, rows):
+        self._style_apply()
         self.st.render()
 
-    def peakmem_apply(self, cols, rows):
+    def peakmem_apply_render(self, cols, rows):
         self._style_apply()
+        self.st.render()
 
-    def peakmem_render(self, cols, rows):
+    def time_classes_render(self, cols, rows):
+        self._style_classes()
+        self.st.render()
+
+    def peakmem_classes_render(self, cols, rows):
+        self._style_classes()
         self.st.render()
 
     def _style_apply(self):
@@ -32,3 +38,8 @@ def _apply_func(s):
             ]
 
         self.st = self.df.style.apply(_apply_func, axis=1)
+
+    def _style_classes(self):
+        classes = self.df.applymap(lambda v: ("cls-1" if v > 0 else ""))
+        classes.index, classes.columns = self.df.index, self.df.columns
+        self.st = self.df.style.set_td_classes(classes)

ci/code_checks.sh

@@ -118,7 +118,7 @@ import sys
 import pandas
 
 blocklist = {'bs4', 'gcsfs', 'html5lib', 'http', 'ipython', 'jinja2', 'hypothesis',
-             'lxml', 'matplotlib', 'numexpr', 'openpyxl', 'py', 'pytest', 's3fs', 'scipy',
+             'lxml', 'matplotlib', 'openpyxl', 'py', 'pytest', 's3fs', 'scipy',
              'tables', 'urllib.request', 'xlrd', 'xlsxwriter', 'xlwt'}
 
 # GH#28227 for some of these check for top-level modules, while others are

ci/run_tests.sh

@@ -29,3 +29,8 @@ fi
 
 echo $PYTEST_CMD
 sh -c "$PYTEST_CMD"
+
+PYTEST_AM_CMD="PANDAS_DATA_MANAGER=array pytest -m \"$PATTERN and arraymanager\" -n $PYTEST_WORKERS  --dist=loadfile -s --strict-markers --durations=30 --junitxml=test-data.xml $TEST_ARGS $COVERAGE pandas"
+
+echo $PYTEST_AM_CMD
+sh -c "$PYTEST_AM_CMD"

doc/make.py

@@ -54,7 +54,6 @@ def __init__(
 
         if single_doc:
             single_doc = self._process_single_doc(single_doc)
-            include_api = False
             os.environ["SPHINX_PATTERN"] = single_doc
         elif not include_api:
             os.environ["SPHINX_PATTERN"] = "-api"

doc/source/development/contributing.rst

@@ -325,7 +325,11 @@ Creating a Python environment (pip)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 If you aren't using conda for your development environment, follow these instructions.
-You'll need to have at least Python 3.6.1 installed on your system.
+You'll need to have at least Python 3.7.0 installed on your system. If your Python version
+is 3.8.0 (or later), you might need to update your ``setuptools`` to version 42.0.0 (or later)
+in your development environment before installing the build dependencies::
+
+      pip install --upgrade setuptools
 
 **Unix**/**macOS with virtualenv**
 

doc/source/user_guide/io.rst

@@ -5240,6 +5240,7 @@ Write to a feather file.
 Read from a feather file.
 
 .. ipython:: python
+   :okwarning:
 
    result = pd.read_feather("example.feather")
    result
@@ -5323,6 +5324,7 @@ Write to a parquet file.
 Read from a parquet file.
 
 .. ipython:: python
+   :okwarning:
 
    result = pd.read_parquet("example_fp.parquet", engine="fastparquet")
    result = pd.read_parquet("example_pa.parquet", engine="pyarrow")

doc/source/whatsnew/v1.2.4.rst

@@ -16,6 +16,9 @@ Fixed regressions
 ~~~~~~~~~~~~~~~~~
 
 - Fixed regression in :meth:`DataFrame.sum` when ``min_count`` greater than the :class:`DataFrame` shape was passed resulted in a ``ValueError`` (:issue:`39738`)
+- Fixed regression in :meth:`DataFrame.to_json` raising ``AttributeError`` when run on PyPy (:issue:`39837`)
+- Fixed regression in :meth:`DataFrame.where` not returning a copy in the case of an all True condition (:issue:`39595`)
+- Fixed regression in :meth:`DataFrame.replace` raising ``IndexError`` when ``regex`` was a multi-key dictionary (:issue:`39338`)
 -
 
 .. ---------------------------------------------------------------------------

doc/source/whatsnew/v1.3.0.rst

@@ -128,13 +128,15 @@ Other enhancements
 - :meth:`.Rolling.sum`, :meth:`.Expanding.sum`, :meth:`.Rolling.mean`, :meth:`.Expanding.mean`, :meth:`.Rolling.median`, :meth:`.Expanding.median`, :meth:`.Rolling.max`, :meth:`.Expanding.max`, :meth:`.Rolling.min`, and :meth:`.Expanding.min` now support ``Numba`` execution with the ``engine`` keyword (:issue:`38895`)
 - :meth:`DataFrame.apply` can now accept NumPy unary operators as strings, e.g. ``df.apply("sqrt")``, which was already the case for :meth:`Series.apply` (:issue:`39116`)
 - :meth:`DataFrame.apply` can now accept non-callable DataFrame properties as strings, e.g. ``df.apply("size")``, which was already the case for :meth:`Series.apply` (:issue:`39116`)
+- :meth:`DataFrame.applymap` can now accept kwargs to pass on to func (:issue:`39987`)
 - Disallow :class:`DataFrame` indexer for ``iloc`` for :meth:`Series.__getitem__` and :meth:`DataFrame.__getitem__`, (:issue:`39004`)
 - :meth:`Series.apply` can now accept list-like or dictionary-like arguments that aren't lists or dictionaries, e.g. ``ser.apply(np.array(["sum", "mean"]))``, which was already the case for :meth:`DataFrame.apply` (:issue:`39140`)
 - :meth:`DataFrame.plot.scatter` can now accept a categorical column as the argument to ``c`` (:issue:`12380`, :issue:`31357`)
 - :meth:`.Styler.set_tooltips` allows on hover tooltips to be added to styled HTML dataframes (:issue:`35643`, :issue:`21266`, :issue:`39317`, :issue:`39708`, :issue:`40284`)
 - :meth:`.Styler.set_table_styles` amended to optionally allow certain css-string input arguments (:issue:`39564`)
 - :meth:`.Styler.apply` now more consistently accepts ndarray function returns, i.e. in all cases for ``axis`` is ``0, 1 or None`` (:issue:`39359`)
 - :meth:`.Styler.apply` and :meth:`.Styler.applymap` now raise errors if wrong format CSS is passed on render (:issue:`39660`)
+- :meth:`.Styler.format` adds keyword argument ``escape`` for optional HTML escaping (:issue:`40437`)
 - Builtin highlighting methods in :class:`Styler` have a more consistent signature and css customisability (:issue:`40242`)
 - :meth:`Series.loc.__getitem__` and :meth:`Series.loc.__setitem__` with :class:`MultiIndex` now raising helpful error message when indexer has too many dimensions (:issue:`35349`)
 - :meth:`pandas.read_stata` and :class:`StataReader` support reading data from compressed files.
@@ -299,6 +301,24 @@ cast to ``dtype=object`` (:issue:`38709`)
    ser
    ser2
 
+
+.. _whatsnew_130.notable_bug_fixes.rolling_var_precision:
+
+Removed artificial truncation in rolling variance and standard deviation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+:meth:`core.window.Rolling.std` and :meth:`core.window.Rolling.var` will no longer
+artificially truncate results that are less than ``~1e-8`` and ``~1e-15`` respectively to
+zero (:issue:`37051`, :issue:`40448`, :issue:`39872`).
+
+However, floating point artifacts may now exist in the results when rolling over larger values.
+
+.. ipython:: python
+
+   s = pd.Series([7, 5, 5, 5])
+   s.rolling(3).var()
+
+
 .. _whatsnew_130.api_breaking.deps:
 
 Increased minimum versions for dependencies
@@ -617,6 +637,7 @@ Groupby/resample/rolling
 - Bug in :class:`core.window.ewm.ExponentialMovingWindow` when calling ``__getitem__`` would incorrectly raise a ``ValueError`` when providing ``times`` (:issue:`40164`)
 - Bug in :class:`core.window.ewm.ExponentialMovingWindow` when calling ``__getitem__`` would not retain ``com``, ``span``, ``alpha`` or ``halflife`` attributes  (:issue:`40164`)
 - :class:`core.window.ewm.ExponentialMovingWindow` now raises a ``NotImplementedError`` when specifying ``times`` with ``adjust=False`` due to an incorrect calculation (:issue:`40098`)
+- Bug in :meth:`Series.asfreq` and :meth:`DataFrame.asfreq` dropping rows when the index is not sorted (:issue:`39805`)
 
 Reshaping
 ^^^^^^^^^
@@ -635,6 +656,7 @@ Reshaping
 - Allow :class:`Index` to be passed to the :func:`numpy.all` function (:issue:`40180`)
 - Bug in :meth:`DataFrame.stack` not preserving ``CategoricalDtype`` in a ``MultiIndex`` (:issue:`36991`)
 - Bug in :func:`to_datetime` raising error when input sequence contains unhashable items (:issue:`39756`)
+- Bug in :meth:`Series.explode` preserving index when ``ignore_index`` was ``True`` and values were scalars (:issue:`40487`)
 
 Sparse
 ^^^^^^
@@ -666,6 +688,7 @@ Other
 - Bug in :class:`Styler` where rendered HTML was missing a column class identifier for certain header cells (:issue:`39716`)
 - Bug in :meth:`Styler.background_gradient` where text-color was not determined correctly (:issue:`39888`)
 - Bug in :class:`Styler` where multiple elements in CSS-selectors were not correctly added to ``table_styles`` (:issue:`39942`)
+- Bug in :class:`.Styler` where copying from Jupyter dropped top left cell and misaligned headers (:issue:`12147`)
 - Bug in :meth:`DataFrame.equals`, :meth:`Series.equals`, :meth:`Index.equals` with object-dtype containing ``np.datetime64("NaT")`` or ``np.timedelta64("NaT")`` (:issue:`39650`)
 - Bug in :func:`pandas.util.show_versions` where console JSON output was not proper JSON (:issue:`39701`)
 - Bug in :meth:`DataFrame.convert_dtypes` incorrectly raised ValueError when called on an empty DataFrame (:issue:`40393`)

pandas/_libs/algos.pxd

@@ -1,21 +1,4 @@
 from pandas._libs.util cimport numeric
 
 
-cdef inline Py_ssize_t swap(numeric *a, numeric *b) nogil:
-    cdef:
-        numeric t
-
-    # cython doesn't allow pointer dereference so use array syntax
-    t = a[0]
-    a[0] = b[0]
-    b[0] = t
-    return 0
-
-
-cdef enum TiebreakEnumType:
-    TIEBREAK_AVERAGE
-    TIEBREAK_MIN,
-    TIEBREAK_MAX
-    TIEBREAK_FIRST
-    TIEBREAK_FIRST_DESCENDING
-    TIEBREAK_DENSE
+cdef numeric kth_smallest_c(numeric* arr, Py_ssize_t k, Py_ssize_t n) nogil