Merge pull request #10660 from nsoranzo/update_dependencies

Full Python dependencies update

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -39,7 +39,7 @@ Markdown = "*"
 # Weasyprint = "==0.42"
 PyYAML = "*"
 SQLAlchemy = "*"
-SQLAlchemy-Utils = "*"
+SQLAlchemy-Utils = "!=0.36.8"  # https://github.com/kvesteri/sqlalchemy-utils/issues/462
 Mercurial = "*"
 nodeenv = "*"
 pycryptodome = "*"
@@ -63,7 +63,7 @@ Parsley = "*"
 sortedcontainers = "*"
 Whoosh = "*"
 galaxy_sequence_utils = "*"
-"h5py" = "!=2.7.0, !=2.7.1"
+h5py = "!=2.7.0, !=2.7.1"
 pykwalify = "*"
 "Cheetah3" = "*"
 requests = "*"
@@ -84,6 +84,7 @@ social_auth_core = {version = "==3.3.0", extras = ['openidconnect']}
 cloudauthz = "==0.6.0"
 gxformat2 = "*"
 refgenconf = ">=0.7.0"
+future = "*"
 
 [requires]
 python_version = "3.6"

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

@@ -1,68 +1,74 @@
+#
+# These requirements were autogenerated by pipenv
+# To regenerate from the project's Pipfile, run:
+#
+#    pipenv lock --requirements --dev-only
+#
+
 -i https://wheels.galaxyproject.org/simple
 --extra-index-url https://pypi.python.org/simple
 alabaster==0.7.12
-attrs==19.3.0
-babel==2.8.0
-certifi==2020.6.20
+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
 chardet==3.0.4
 commonmark==0.9.1
-coverage==5.1
-deprecated==1.2.10
+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
 gunicorn==20.0.4
-idna==2.9
-imagesize==1.2.0
-importlib-metadata==1.6.1 ; python_version < '3.8'
-jinja2==2.11.2
-lxml==4.5.1
-markdown==3.2.2
+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'
+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'
+markdown==3.3.3
 markupsafe==1.1.1
-mirakuru==2.0.2
-mock==3.0.5
-more-itertools==8.4.0
+mirakuru==2.3.0; python_version >= '3.6'
 nose==1.3.7
 nosehtml==0.4.6
-packaging==20.4
-pathlib2==2.3.5 ; python_version < '3.6'
+packaging==20.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pathtools==0.1.2
-pluggy==0.13.1
+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==5.7.0
-py==1.8.2
-pygithub==1.51
-pygments==2.6.1
+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'
 pyjwt==1.7.1
 pyparsing==2.4.7
-pytest-cov==2.10.0
-pytest-html==1.22.1
-pytest-metadata==1.8.0
-pytest-mock==3.1.1
-pytest-postgresql==2.3.0
+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-mock==3.3.1
+pytest-postgresql==2.5.2
 pytest-pythonpath==0.7.3
-pytest==5.4.3
-python-irodsclient==0.8.4
-pytz==2020.1
+pytest==6.1.2
+python-irodsclient==0.8.5
+pytz==2020.4
 recommonmark==0.6.0
-requests==2.24.0
-responses==0.10.15
+requests==2.25.0
+responses==0.12.1
 selenium==3.141.0
-six==1.15.0
+six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 snowballstemmer==2.0.0
 sphinx-markdown-tables==0.0.15
 sphinx-rtd-theme==0.5.0
-sphinx==3.1.1
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==1.0.3
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.4
-testfixtures==6.14.1
-twill==2.0
-urllib3==1.25.9
-watchdog==0.10.2
+sphinx==3.3.1
+sphinxcontrib-applehelp==1.0.2; python_version >= '3.5'
+sphinxcontrib-devhelp==1.0.2; python_version >= '3.5'
+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
+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
 wrapt==1.12.1
 xmlrunner==1.7.7
-zipp==1.2.0 ; python_version < '3.8'
+zipp==3.4.0; python_version < '3.8'