Merge branch 'master' into single_level

Author: LucasG0

.github/CODE_OF_CONDUCT.md

@@ -60,4 +60,3 @@ and the [Swift Code of Conduct][swift].
 [homepage]: https://www.contributor-covenant.org
 [version]: https://www.contributor-covenant.org/version/1/3/0/
 [swift]: https://swift.org/community/#code-of-conduct
-

.github/workflows/ci.yml

@@ -125,7 +125,7 @@ jobs:
     # This can be removed when the ipython directive fails when there are errors,
     # including the `tee sphinx.log` in te previous step (https://github.com/ipython/ipython/issues/11547)
     - name: Check ipython directive errors
-      run: "! grep -B1 \"^<<<-------------------------------------------------------------------------$\" sphinx.log"
+      run: "! grep -B10 \"^<<<-------------------------------------------------------------------------$\" sphinx.log"
 
     - name: Install ssh key
       run: |

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
     -   id: black
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+    rev: 3.8.4
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-comprehensions>=3.1.0]
@@ -43,3 +43,12 @@ repos:
         entry: python -m scripts.generate_pip_deps_from_conda
         files: ^(environment.yml|requirements-dev.txt)$
         pass_filenames: false
+-   repo: https://github.com/asottile/yesqa
+    rev: v1.2.2
+    hooks:
+    -   id: yesqa
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: end-of-file-fixer
+        exclude: '.html$|^LICENSES/|.csv$|.txt$|.svg$|.py$'

.travis.yml

@@ -41,10 +41,10 @@ matrix:
         - JOB="3.9-dev" PATTERN="(not slow and not network and not clipboard)"
 
     - env:
-        - JOB="3.8" ENV_FILE="ci/deps/travis-38.yaml" PATTERN="(not slow and not network and not clipboard)"
-
-    - env:
-        - JOB="3.7" ENV_FILE="ci/deps/travis-37.yaml" PATTERN="(not slow and not network and not clipboard)"
+      - JOB="3.8, slow" ENV_FILE="ci/deps/travis-38-slow.yaml" PATTERN="slow" SQL="1"
+      services:
+        - mysql
+        - postgresql
 
     - env:
         - JOB="3.7, locale" ENV_FILE="ci/deps/travis-37-locale.yaml" PATTERN="((not slow and not network and not clipboard) or (single and db))" LOCALE_OVERRIDE="zh_CN.UTF-8" SQL="1"

AUTHORS.md

@@ -54,4 +54,3 @@ pandas is distributed under a 3-clause ("Simplified" or "New") BSD
 license. Parts of NumPy, SciPy, numpydoc, bottleneck, which all have
 BSD-compatible licenses, are included. Their licenses follow the pandas
 license.
-

asv_bench/benchmarks/dtypes.py

@@ -1,5 +1,9 @@
+import string
+
 import numpy as np
 
+from pandas import DataFrame
+import pandas._testing as tm
 from pandas.api.types import pandas_dtype
 
 from .pandas_vb_common import (
@@ -62,4 +66,57 @@ def time_infer(self, dtype):
         lib.infer_dtype(self.data_dict[dtype], skipna=False)
 
 
+class SelectDtypes:
+
+    params = [
+        tm.ALL_INT_DTYPES
+        + tm.ALL_EA_INT_DTYPES
+        + tm.FLOAT_DTYPES
+        + tm.COMPLEX_DTYPES
+        + tm.DATETIME64_DTYPES
+        + tm.TIMEDELTA64_DTYPES
+        + tm.BOOL_DTYPES
+    ]
+    param_names = ["dtype"]
+
+    def setup(self, dtype):
+        N, K = 5000, 50
+        self.index = tm.makeStringIndex(N)
+        self.columns = tm.makeStringIndex(K)
+
+        def create_df(data):
+            return DataFrame(data, index=self.index, columns=self.columns)
+
+        self.df_int = create_df(np.random.randint(low=100, size=(N, K)))
+        self.df_float = create_df(np.random.randn(N, K))
+        self.df_bool = create_df(np.random.choice([True, False], size=(N, K)))
+        self.df_string = create_df(
+            np.random.choice(list(string.ascii_letters), size=(N, K))
+        )
+
+    def time_select_dtype_int_include(self, dtype):
+        self.df_int.select_dtypes(include=dtype)
+
+    def time_select_dtype_int_exclude(self, dtype):
+        self.df_int.select_dtypes(exclude=dtype)
+
+    def time_select_dtype_float_include(self, dtype):
+        self.df_float.select_dtypes(include=dtype)
+
+    def time_select_dtype_float_exclude(self, dtype):
+        self.df_float.select_dtypes(exclude=dtype)
+
+    def time_select_dtype_bool_include(self, dtype):
+        self.df_bool.select_dtypes(include=dtype)
+
+    def time_select_dtype_bool_exclude(self, dtype):
+        self.df_bool.select_dtypes(exclude=dtype)
+
+    def time_select_dtype_string_include(self, dtype):
+        self.df_string.select_dtypes(include=dtype)
+
+    def time_select_dtype_string_exclude(self, dtype):
+        self.df_string.select_dtypes(exclude=dtype)
+
+
 from .pandas_vb_common import setup  # noqa: F401 isort:skip

asv_bench/benchmarks/indexing.py

@@ -191,7 +191,7 @@ def setup(self, index):
         }
         index = indexes[index]
         self.s = Series(np.random.rand(N), index=index)
-        self.indexer = [True, False, True, True, False] * 20000
+        self.indexer = np.random.randint(0, N, size=N)
 
     def time_take(self, index):
         self.s.take(self.indexer)

asv_bench/benchmarks/pandas_vb_common.py

@@ -15,7 +15,7 @@
 
 # Compatibility import for the testing module
 try:
-    import pandas._testing as tm  # noqa
+    import pandas._testing as tm
 except ImportError:
     import pandas.util.testing as tm  # noqa
 

asv_bench/benchmarks/tslibs/offsets.py

@@ -9,7 +9,7 @@
 from pandas import offsets
 
 try:
-    import pandas.tseries.holiday  # noqa
+    import pandas.tseries.holiday
 except ImportError:
     pass
 

ci/azure/posix.yml

@@ -20,39 +20,35 @@ jobs:
           CONDA_PY: "37"
           PATTERN: "not slow and not network and not clipboard"
 
+        py37:
+          ENV_FILE: ci/deps/azure-37.yaml
+          CONDA_PY: "37"
+          PATTERN: "not slow and not network and not clipboard"
+
         py37_locale_slow:
           ENV_FILE: ci/deps/azure-37-locale_slow.yaml
           CONDA_PY: "37"
           PATTERN: "slow"
-          # pandas does not use the language (zh_CN), but should support different encodings (utf8)
-          # we should test with encodings different than utf8, but doesn't seem like Ubuntu supports any
-          LANG: "zh_CN.utf8"
-          LC_ALL: "zh_CN.utf8"
-          EXTRA_APT: "language-pack-zh-hans"
+          LANG: "it_IT.utf8"
+          LC_ALL: "it_IT.utf8"
+          EXTRA_APT: "language-pack-it xsel"
 
         py37_slow:
           ENV_FILE: ci/deps/azure-37-slow.yaml
           CONDA_PY: "37"
           PATTERN: "slow"
 
-        py37_locale:
-          ENV_FILE: ci/deps/azure-37-locale.yaml
-          CONDA_PY: "37"
-          PATTERN: "not slow and not network"
-          LANG: "it_IT.utf8"
-          LC_ALL: "it_IT.utf8"
-          EXTRA_APT: "language-pack-it xsel"
-
-#        py37_32bit:
-#          ENV_FILE: ci/deps/azure-37-32bit.yaml
-#          CONDA_PY: "37"
-#          PATTERN: "not slow and not network and not clipboard"
-#          BITS32: "yes"
+        py38:
+          ENV_FILE: ci/deps/azure-38.yaml
+          CONDA_PY: "38"
+          PATTERN: "not slow and not network and not clipboard"
 
         py38_locale:
           ENV_FILE: ci/deps/azure-38-locale.yaml
           CONDA_PY: "38"
           PATTERN: "not slow and not network"
+          # pandas does not use the language (zh_CN), but should support different encodings (utf8)
+          # we should test with encodings different than utf8, but doesn't seem like Ubuntu supports any
           LANG: "zh_CN.utf8"
           LC_ALL: "zh_CN.utf8"
           EXTRA_APT: "language-pack-zh-hans xsel"

ci/deps/azure-37-32bit.yaml

@@ -10,6 +10,7 @@ dependencies:
   - pytest>=5.0.1
   - pytest-xdist>=1.21
   - hypothesis>=3.58.0
+  - pytest-azurepipelines
 
   # pandas dependencies
   - beautifulsoup4

ci/deps/azure-37-slow.yaml

@@ -10,6 +10,7 @@ dependencies:
   - pytest>=5.0.1
   - pytest-xdist>=1.21
   - hypothesis>=3.58.0
+  - pytest-azurepipelines
 
   # pandas dependencies
   - botocore>=1.11

ci/deps/travis-37.yaml renamed to ci/deps/azure-37.yaml

@@ -10,11 +10,11 @@ dependencies:
   - pytest>=5.0.1
   - pytest-xdist>=1.21
   - hypothesis>=3.58.0
+  - pytest-azurepipelines
 
   # pandas dependencies
   - numpy
   - python-dateutil
   - nomkl
   - pytz
-  - pip
   - tabulate==0.8.3

ci/deps/travis-38.yaml renamed to ci/deps/azure-38.yaml

@@ -11,7 +11,12 @@ dependencies:
   - pytest-xdist>=1.21
   - hypothesis>=3.58.0
 
-  # pandas dependencies
+  # required
+  - numpy
+  - python-dateutil
+  - pytz
+
+  # optional
   - beautifulsoup4
   - blosc=1.15.0
   - python-blosc
@@ -20,22 +25,23 @@ dependencies:
   - ipython
   - jinja2
   - lxml=4.3.0
-  - matplotlib=3.0.*
+  - matplotlib
   - nomkl
   - numexpr
-  - numpy
   - openpyxl
   - pandas-gbq
   - google-cloud-bigquery>=1.27.2 # GH 36436
   - pyarrow>=0.17
-  - psycopg2=2.7
-  - pymysql=0.7.11
   - pytables>=3.5.1
-  - python-dateutil
-  - pytz
   - scipy
-  - sqlalchemy=1.3.0
   - xarray=0.12.0
   - xlrd
   - xlsxwriter
   - xlwt
+  - moto
+  - flask
+
+  # sql
+  - psycopg2=2.7
+  - pymysql=0.7.11
+  - sqlalchemy=1.3.0

ci/deps/travis-37-locale.yaml

@@ -3,35 +3,35 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - python=3.7.*
+  - python=3.8.*
 
   # tools
   - cython>=0.29.21
   - pytest>=5.0.1
   - pytest-xdist>=1.21
-  - pytest-asyncio
   - hypothesis>=3.58.0
-  - pytest-azurepipelines
 
   # pandas dependencies
   - beautifulsoup4
+  - fsspec>=0.7.4
   - html5lib
-  - ipython
-  - jinja2
   - lxml
-  - matplotlib>=3.3.0
-  - moto
-  - flask
-  - nomkl
+  - matplotlib
   - numexpr
-  - numpy=1.16.*
+  - numpy
   - openpyxl
+  - patsy
+  - psycopg2
+  - pymysql
   - pytables
   - python-dateutil
   - pytz
+  - s3fs>=0.4.0
+  - moto>=1.3.14
   - scipy
-  - xarray
+  - sqlalchemy
   - xlrd
   - xlsxwriter
   - xlwt
   - moto
+  - flask

ci/deps/azure-37-locale.yaml renamed to ci/deps/travis-38-slow.yaml

@@ -10,4 +10,3 @@ elif [[ -n ${!TRAVIS_IV_ENV} ]]; then
     export GBQ_PROJECT_ID='pandas-gbq-tests';
     echo 'Successfully decrypted gbq credentials'
 fi
-

ci/travis_process_gbq_encryption.sh

@@ -1,7 +1,7 @@
 codecov:
   branch: master
 
-comment: off
+comment: false
 
 coverage:
   status:
@@ -11,3 +11,6 @@ coverage:
     patch:
       default:
         target: '50'
+
+github_checks:
+    annotations: false

codecov.yml

@@ -148,4 +148,4 @@ SepalLength,SepalWidth,PetalLength,PetalWidth,Name
 6.3,2.5,5.0,1.9,Iris-virginica
 6.5,3.0,5.2,2.0,Iris-virginica
 6.2,3.4,5.4,2.3,Iris-virginica
-5.9,3.0,5.1,1.8,Iris-virginica
+5.9,3.0,5.1,1.8,Iris-virginica