upgrade shapely

Fixes: https://openedx.atlassian.net/browse/INCR-16

requirements/edx/base.in

@@ -138,7 +138,7 @@ redis==2.10.6                       # celery task broker
 requests-oauthlib                   # Simplifies use of OAuth via the requests library, used for CCX and LTI
 rules                               # Django extension for rules-based authorization checks
 sailthru-client==2.2.3              # For Sailthru integration
-Shapely==1.2.16                     # Geometry library, used for image click regions in capa
+Shapely                             # Geometry library, used for image click regions in capa
 six                                 # Utilities for supporting Python 2 & 3 in the same codebase
 sorl-thumbnail==12.3                # Image thumbnail management
 sortedcontainers                    # Provides SortedKeyList, used for lists of XBlock assets

requirements/edx/base.txt

@@ -205,7 +205,7 @@ python-swiftclient==3.7.0
 python3-saml==1.5.0
 pytz==2018.9
 pyuca==1.1
-pyyaml==3.13
+pyyaml==5.1
 redis==2.10.6
 reportlab==3.5.13
 requests-oauthlib==1.1.0
@@ -217,7 +217,7 @@ s3transfer==0.1.13        # via boto3
 sailthru-client==2.2.3
 scipy==0.14.0
 semantic-version==2.6.0   # via edx-drf-extensions
-shapely==1.2.16
+shapely==1.6.4.post2
 shortuuid==0.5.0          # via edx-django-oauth2-provider
 simplejson==3.16.0        # via django-rest-swagger, mailsnake, sailthru-client, zendesk
 singledispatch==3.4.0.3

requirements/edx/development.txt

@@ -227,7 +227,7 @@ numpy==1.6.2
 oauth2==1.9.0.post1
 oauthlib==2.1.0
 openapi-codec==1.3.2
-pa11ycrawler==1.7.2
+pa11ycrawler==1.7.3
 packaging==19.0
 parsel==1.5.1
 path.py==8.2.1
@@ -289,7 +289,7 @@ python-swiftclient==3.7.0
 python3-saml==1.5.0
 pytz==2018.9
 pyuca==1.1
-pyyaml==3.13
+pyyaml==5.1
 queuelib==1.5.0
 radon==3.0.1
 redis==2.10.6
@@ -307,7 +307,7 @@ scrapy==1.6.0
 selenium==3.141.0
 semantic-version==2.6.0
 service-identity==18.1.0
-shapely==1.2.16
+shapely==1.6.4.post2
 shortuuid==0.5.0
 simplejson==3.16.0
 singledispatch==3.4.0.3

requirements/edx/paver.txt

@@ -20,7 +20,7 @@ pbr==5.1.3                # via stevedore
 psutil==1.2.1
 pymongo==2.9.1
 python-memcached==1.48
-pyyaml==3.13              # via watchdog
+pyyaml==5.1               # via watchdog
 requests==2.21.0
 six==1.11.0
 stevedore==1.30.1

requirements/edx/testing.txt

@@ -220,7 +220,7 @@ numpy==1.6.2
 oauth2==1.9.0.post1
 oauthlib==2.1.0
 openapi-codec==1.3.2
-pa11ycrawler==1.7.2
+pa11ycrawler==1.7.3
 packaging==19.0           # via caniusepython3
 parsel==1.5.1             # via scrapy
 path.py==8.2.1
@@ -280,7 +280,7 @@ python-swiftclient==3.7.0
 python3-saml==1.5.0
 pytz==2018.9
 pyuca==1.1
-pyyaml==3.13
+pyyaml==5.1
 queuelib==1.5.0           # via scrapy
 radon==3.0.1
 redis==2.10.6
@@ -298,7 +298,7 @@ scrapy==1.6.0             # via pa11ycrawler
 selenium==3.141.0
 semantic-version==2.6.0
 service-identity==18.1.0  # via scrapy
-shapely==1.2.16
+shapely==1.6.4.post2
 shortuuid==0.5.0
 simplejson==3.16.0
 singledispatch==3.4.0.3