Update all dependencies

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

@@ -10,38 +10,37 @@
 alabaster==0.7.12
 attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 babel==2.9.0
-certifi==2020.11.8
+certifi==2020.12.5
 chardet==3.0.4
 commonmark==0.9.1
 coverage==5.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
 deprecated==1.2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-docutils==0.15.2
+docutils==0.16
 gunicorn==20.0.4
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 imagesize==1.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==2.0.0; python_version == '3.6' and python_version < '3.8'
+importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
 iniconfig==1.1.1
 jinja2==2.11.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-lxml==4.6.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.3.3
 markupsafe==1.1.1
 mirakuru==2.3.0; python_version >= '3.6'
 nose==1.3.7
 nosehtml==0.4.6
-packaging==20.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pathtools==0.1.2
+packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 port-for==0.4
 prettytable==0.7.2
 psutil==5.7.3
 py==1.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygithub==1.53
-pygments==2.7.2; python_version >= '3.5'
+pygithub==1.54
+pygments==2.7.3; python_version >= '3.5'
 pyjwt==1.7.1
 pyparsing==2.4.7
 pytest-cov==2.10.1
-pytest-html==3.0.0
-pytest-metadata==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+pytest-html==3.1.0
+pytest-metadata==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 pytest-mock==3.3.1
 pytest-postgresql==2.5.2
 pytest-pythonpath==0.7.3
@@ -64,12 +63,12 @@ sphinxcontrib-htmlhelp==1.0.3; python_version >= '3.5'
 sphinxcontrib-jsmath==1.0.1; python_version >= '3.5'
 sphinxcontrib-qthelp==1.0.3; python_version >= '3.5'
 sphinxcontrib-serializinghtml==1.1.4; python_version >= '3.5'
-testfixtures==6.15.0
+testfixtures==6.16.0
 toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 twill==2.0.1
-urllib3==1.25.11; python_version >= '3.4'
-watchdog==0.10.3
-wcwidth==0.2.5
+urllib3==1.26.2; python_version != '3.4'
+watchdog==1.0.0
+wcwidth==0.2.5; sys_platform != 'win32'
 wrapt==1.12.1
 xmlrunner==1.7.7
 zipp==3.4.0; python_version < '3.8'

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

@@ -10,22 +10,9 @@
 adal==1.2.5
 amqp==5.0.2; python_version >= '3.6'
 appdirs==1.4.4
-argcomplete==1.12.1
+argcomplete==1.12.2
 attmap==0.12.11
 attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-azure-common==1.1.14
-azure-cosmosdb-nspkg==2.0.2
-azure-cosmosdb-table==1.0.4
-azure-mgmt-compute==4.0.1
-azure-mgmt-devtestlabs==2.2.0
-azure-mgmt-network==2.1.0
-azure-mgmt-nspkg==3.0.2
-azure-mgmt-resource==2.0.0
-azure-mgmt-storage==2.0.0
-azure-nspkg==3.0.2
-azure-storage-blob==1.3.1
-azure-storage-common==1.4.2
-azure-storage-nspkg==3.1.0
 babel==2.9.0
 bagit==1.7.0
 bcrypt==3.2.0; python_version >= '3.6'
@@ -34,73 +21,70 @@ beaker==1.11.0
 bioblend==0.14.0
 bleach==3.2.1
 boltons==20.2.1
-boto3==1.9.114
+boto3==1.16.33
 boto==2.49.0
-botocore==1.12.253
+botocore==1.19.33
 bx-python==0.8.9
 cachecontrol==0.11.7
 cached-property==1.5.2; python_version < '3.8'
 cachetools==4.1.1; python_version ~= '3.5'
-certifi==2020.11.8
-cffi==1.14.3
+certifi==2020.12.5
+cffi==1.14.4
 chardet==3.0.4
 cheetah3==3.2.6
 click==7.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 cliff==3.5.0; python_version >= '3.6'
 cloudauthz==0.6.0
-cloudbridge==2.0.0
+cloudbridge==2.1.0
 cmd2==1.4.0; python_version >= '3.5'
 colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-coloredlogs==14.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-cryptography==3.2.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+coloredlogs==14.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+cryptography==3.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 cwltool==3.0.20201109103151
 dataclasses==0.8; python_version < '3.7'
 debtcollector==2.2.0; python_version >= '3.6'
 decorator==4.4.2
 defusedxml==0.6.0; python_version >= '3.0'
-deprecated==1.2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 deprecation==2.1.0
 dictobj==0.4
 docopt==0.6.2
-docutils==0.15.2
-dogpile.cache==1.1.0; python_version >= '3.6'
+docutils==0.16
+dogpile.cache==1.1.1; python_version >= '3.6'
 ecdsa==0.14.1; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 fabric3==1.14.post1
 fastapi-utils==0.2.1
 fastapi==0.62.0
 future==0.18.2
-futures==3.1.1
 galaxy-sequence-utils==1.1.5
-google-api-python-client==1.7.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+google-api-core==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+google-api-python-client==1.12.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 google-auth-httplib2==0.0.4
 google-auth==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+googleapis-common-protos==1.52.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 gxformat2==0.15.0
 h11==0.11.0
 h5py==3.1.0
 httplib2==0.18.1
-humanfriendly==8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==2.0.0; python_version == '3.6' and python_version < '3.8'
+importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
 importlib-resources==3.3.0; python_version < '3.7'
 isa-rwval==0.10.9
 iso8601==0.1.13
 isodate==0.6.0
 jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-jsonpatch==1.26; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+jsonpatch==1.28; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 jsonpointer==2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-jsonschema==3.2.0
-keystoneauth1==4.2.1; python_version >= '3.6'
+keystoneauth1==4.3.0; python_version >= '3.6'
 kombu==5.0.2
 lockfile==0.12.2
-lxml==4.6.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 mako==1.1.3
 markdown==3.3.3
 markupsafe==1.1.1
-mercurial==5.6
+mercurial==5.6.1
 mistune==0.8.4
 msgpack==1.0.0
-msrest==0.5.5
-msrestazure==0.5.0
 munch==2.5.0
 mypy-extensions==0.4.3
 netaddr==0.8.0
@@ -111,18 +95,18 @@ nose==1.3.7
 numpy==1.19.4
 oauth2client==4.1.3
 oauthlib==3.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-openstacksdk==0.17.0
+openstacksdk==0.52.0; python_version >= '3.6'
 os-client-config==2.1.0
 os-service-types==1.7.0
 osc-lib==2.3.0; python_version >= '3.6'
-oslo.config==8.3.2; python_version >= '3.6'
+oslo.config==8.4.0; python_version >= '3.6'
 oslo.context==3.1.1; python_version >= '3.6'
 oslo.i18n==5.0.1; python_version >= '3.6'
 oslo.log==4.4.0; python_version >= '3.6'
 oslo.serialization==4.0.1; python_version >= '3.6'
 oslo.utils==4.7.0; python_version >= '3.6'
 oyaml==1.0
-packaging==20.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 paramiko==2.7.2
 parsley==1.3
 paste==3.5.0
@@ -138,28 +122,23 @@ pyasn1-modules==0.2.8
 pyasn1==0.4.8
 pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycryptodome==3.9.9
-pydantic==1.7.2; python_version >= '3.6'
+pydantic==1.7.3; python_version >= '3.6'
 pydot==1.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyeventsystem==0.1.0
-pyfaidx==0.5.9.1
+pyfaidx==0.5.9.2
 pyinotify==0.9.6; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
 pyjwt==1.7.1
 pykwalify==1.7.0
 pynacl==1.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyopenssl==19.1.0
 pyparsing==2.4.7
 pyperclip==1.8.1
-pyrsistent==0.17.3; python_version >= '3.5'
 pysam==0.16.0.1
-pysftp==0.2.9
-python-cinderclient==4.0.0
-python-dateutil==2.8.1; python_version >= '2.7'
-python-glanceclient==2.12.0
+python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jose==3.2.0
-python-keystoneclient==3.17.0
-python-neutronclient==6.9.0
-python-novaclient==11.0.0
-python-swiftclient==3.6.0
+python-keystoneclient==4.1.1; python_version >= '3.6'
+python-neutronclient==7.2.1; python_version >= '3.6'
+python-novaclient==17.2.1; python_version >= '3.6'
+python-swiftclient==3.10.1
 python3-openid==3.2.0; python_version >= '3.0'
 pytz==2020.4
 pyuwsgi==2.0.19.1.post0
@@ -177,8 +156,8 @@ routes==2.5.1
 rsa==4.6; python_version >= '3.5'
 ruamel.yaml.clib==0.2.2; python_version < '3.8' and platform_python_implementation == 'CPython'
 ruamel.yaml==0.16.5
-s3transfer==0.2.1
-schema-salad==7.0.20200811075006; python_version >= '3.5'
+s3transfer==0.3.3
+schema-salad==7.0.20201119201711; python_version >= '3.6'
 setuptools-scm==4.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 shellescape==3.4.1
 simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
@@ -191,21 +170,20 @@ sqlalchemy==1.3.20
 sqlitedict==1.7.0
 sqlparse==0.4.1
 starlette==0.13.6; python_version >= '3.6'
-stevedore==3.2.2; python_version >= '3.6'
+stevedore==3.3.0; python_version >= '3.6'
 svgwrite==1.4
 tempita==0.5.2
-tenacity==4.12.0
-tqdm==4.52.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-typing-extensions==3.7.4.3
+tenacity==6.2.0
+tqdm==4.54.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+typing-extensions==3.7.4.3; python_version < '3.8'
 tzlocal==2.1
 ubiquerg==0.6.1
 unidecode==1.1.1; python_version >= '3.0'
 uritemplate==3.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 urllib3==1.26.2; python_version != '3.4'
 uvicorn==0.13.0
 vine==5.0.0; python_version >= '3.6'
-warlock==1.3.3
-wcwidth==0.2.5
+wcwidth==0.2.5; sys_platform != 'win32'
 webencodings==0.5.1
 webob==1.8.6
 whoosh==2.7.4

lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt

@@ -8,7 +8,7 @@
 -i https://pypi.python.org/simple
 flake8-import-order==0.18.1
 flake8==3.8.4
-importlib-metadata==2.0.0; python_version < '3.8'
+importlib-metadata==3.1.1; python_version < '3.8'
 mccabe==0.6.1
 pycodestyle==2.6.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyflakes==2.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'