Merge remote-tracking branch 'upstream/master' into io-parquet-multiindex

Author: hweecat

.pre-commit-config.yaml

@@ -46,6 +46,14 @@ repos:
         files: ^(environment.yml|requirements-dev.txt)$
         pass_filenames: false
         additional_dependencies: [pyyaml]
+    -   id: flake8-rst
+        name: flake8-rst
+        description: Run flake8 on code snippets in docstrings or RST files
+        language: python
+        entry: flake8-rst
+        types: [rst]
+        args: [--filename=*.rst]
+        additional_dependencies: [flake8-rst==0.7.0, flake8==3.7.9]
 -   repo: https://github.com/asottile/yesqa
     rev: v1.2.2
     hooks:

ci/code_checks.sh

@@ -73,13 +73,6 @@ if [[ -z "$CHECK" || "$CHECK" == "lint" ]]; then
     flake8 --format="$FLAKE8_FORMAT" pandas/_libs --append-config=flake8/cython-template.cfg
     RET=$(($RET + $?)) ; echo $MSG "DONE"
 
-    echo "flake8-rst --version"
-    flake8-rst --version
-
-    MSG='Linting code-blocks in .rst documentation' ; echo $MSG
-    flake8-rst doc/source --filename=*.rst --format="$FLAKE8_FORMAT"
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
-
     # Check that cython casting is of the form `<type>obj` as opposed to `<type> obj`;
     # it doesn't make a difference, but we want to be internally consistent.
     # Note: this grep pattern is (intended to be) equivalent to the python

ci/deps/travis-37-cov.yaml

@@ -32,15 +32,15 @@ dependencies:
   - google-cloud-bigquery>=1.27.2 # GH 36436
   - psycopg2
   - pyarrow>=0.15.0
-  - pymysql=0.7.11
+  - pymysql<0.10.0 # temporary pin, GH 36465
   - pytables
   - python-snappy
   - python-dateutil
   - pytz
   - s3fs>=0.4.0
   - scikit-learn
   - scipy
-  - sqlalchemy=1.3.0
+  - sqlalchemy
   - statsmodels
   - xarray
   - xlrd

doc/source/ecosystem.rst

@@ -435,6 +435,11 @@ found in NumPy or pandas, which work well with pandas' data containers.
 Cyberpandas provides an extension type for storing arrays of IP Addresses. These
 arrays can be stored inside pandas' Series and DataFrame.
 
+`Pandas-Genomics`_
+~~~~~~~~~~~~~~~~~~
+
+Pandas-Genomics provides extension types and extension arrays for working with genomics data
+
 `Pint-Pandas`_
 ~~~~~~~~~~~~~~
 
@@ -465,6 +470,7 @@ Library         Accessor   Classes                   Description
 .. _cyberpandas: https://cyberpandas.readthedocs.io/en/latest
 .. _pdvega: https://altair-viz.github.io/pdvega/
 .. _Altair: https://altair-viz.github.io/
+.. _pandas-genomics: https://pandas-genomics.readthedocs.io/en/latest/
 .. _pandas_path: https://github.com/drivendataorg/pandas-path/
 .. _pathlib.Path: https://docs.python.org/3/library/pathlib.html
 .. _pint-pandas: https://github.com/hgrecco/pint-pandas