Full Python dependencies update

using `make update-dependencies`.

Also:

- update pin on `pulsar-galaxy-lib` missed in commit
  461a7ce
- update pin on `social-auth-core` missed in commit
  44ad891

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -44,7 +44,7 @@ Mercurial = "*"
 nodeenv = "*"
 pycryptodome = "*"
 pyuwsgi = "*"
-pysam = "==0.15.2"
+pysam = "*"
 bdbag = "*"
 bleach = "*"
 cwltool = "==1.0.20191225192155"
@@ -74,15 +74,15 @@ bioblend = "*"
 boto = "*"
 kombu = "*"
 psutil = "*"
-pulsar-galaxy-lib = "==0.14.0.dev1"
+pulsar-galaxy-lib = "==0.14.0.dev3"
 sqlalchemy-migrate = "*"
 sqlparse = "*"
 svgwrite = "*"
 pyparsing = "*"
 "Fabric3" = "*"
 paramiko = "*"
 cloudbridge = "*"
-social_auth_core = {version = "==3.1.0+gx0", extras = ['openidconnect']}
+social_auth_core = {version = "==3.3.0", extras = ['openidconnect']}
 cloudauthz = "==0.6.0"
 gxformat2 = "*"
 

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -1,15 +1,16 @@
 -i https://wheels.galaxyproject.org/simple
 --extra-index-url https://pypi.python.org/simple
 alabaster==0.7.12
-atomicwrites==1.3.0
+atomicwrites==1.4.0
 attrs==19.3.0
 babel==2.8.0
 certifi==2020.4.5.1
 chardet==3.0.4
 commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-coverage==5.0.4
+cookies==2.2.1 ; python_version < '3.4'
+coverage==5.1
 deprecated==1.2.9
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
@@ -18,7 +19,7 @@ gunicorn==19.10.0
 idna==2.9
 imagesize==1.2.0
 importlib-metadata==1.6.0 ; python_version < '3.8'
-jinja2==2.11.1
+jinja2==2.11.2
 lxml==4.5.0
 markdown==3.1.1
 markupsafe==1.1.1
@@ -46,7 +47,7 @@ pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
 pytest==4.6.9
 python-irodsclient==0.8.2
-pytz==2019.3
+pytz==2020.1
 recommonmark==0.6.0
 requests==2.23.0
 responses==0.10.14
@@ -58,10 +59,10 @@ sphinx-markdown-tables==0.0.12
 sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
 sphinxcontrib-websupport==1.1.2
-testfixtures==6.14.0
+testfixtures==6.14.1
 twill==2.0
 typing==3.7.4.1 ; python_version < '3.5'
-urllib3==1.25.8
+urllib3==1.25.9
 watchdog==0.10.2
 wcwidth==0.1.9
 wrapt==1.12.1

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -23,7 +23,7 @@ bcrypt==3.1.7
 bdbag==1.5.6
 beaker==1.11.0
 bioblend==0.13.0
-bleach==3.1.4
+bleach==3.1.5
 boltons==20.1.0
 boto3==1.9.114
 boto==2.49.0
@@ -43,16 +43,16 @@ cmd2==0.8.9
 coloredlogs==14.0
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-cryptography==2.9
+cryptography==2.9.2
 cwltool==1.0.20191225192155
 debtcollector==1.22.0
 decorator==4.4.2
 deprecated==1.2.9
-deprecation==2.0.7
+deprecation==2.1.0
 dictobj==0.4
 docopt==0.6.2
 docutils==0.15.2
-dogpile.cache==0.9.0
+dogpile.cache==0.9.1
 ecdsa==0.15
 enum34==1.1.10 ; python_version < '3.4'
 fabric3==1.14.post1
@@ -63,11 +63,11 @@ futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
-google-auth==1.13.1
+google-auth==1.14.1
 gxformat2==0.11.1
 h5py==2.10.0
-httplib2==0.17.2
-humanfriendly==8.1
+httplib2==0.17.3
+humanfriendly==8.2
 idna==2.9
 importlib-metadata==1.6.0 ; python_version < '3.8'
 ipaddress==1.0.23 ; python_version < '3.3'
@@ -85,7 +85,7 @@ lxml==4.5.0
 mako==1.1.2
 markdown==3.1.1
 markupsafe==1.1.1
-mercurial==5.3.2
+mercurial==5.4
 mistune==0.8.4
 monotonic==1.5
 msgpack==1.0.0
@@ -136,7 +136,7 @@ pyopenssl==19.1.0
 pyparsing==2.4.7
 pyperclip==1.8.0
 pyrsistent==0.16.0
-pysam==0.15.2
+pysam==0.15.4
 pysftp==0.2.9
 python-cinderclient==4.0.0
 python-dateutil==2.8.1
@@ -147,7 +147,7 @@ python-neutronclient==6.9.0
 python-novaclient==11.0.0
 python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
-pytz==2019.3
+pytz==2020.1
 pyuwsgi==2.0.18.post0
 pyyaml==5.3.1
 rdflib-jsonld==0.4.0
@@ -173,7 +173,7 @@ six==1.11.0
 social-auth-core[openidconnect]==3.3.0
 sortedcontainers==2.1.0
 sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.36.3
+sqlalchemy-utils==0.36.4
 sqlalchemy==1.3.16
 sqlparse==0.3.1
 stevedore==1.32.0
@@ -185,8 +185,9 @@ typing-extensions==3.7.4.2
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
 unicodecsv==0.14.1 ; python_version < '3.0'
+unidecode==1.1.1 ; python_version < '3.0'
 uritemplate==3.0.1
-urllib3==1.25.8
+urllib3==1.25.9
 vine==1.3.0
 warlock==1.3.3
 wcwidth==0.1.9