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Update Python dependencies #13836

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merged 3 commits into from
May 17, 2022
Merged

Update Python dependencies #13836

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d60a149
Update Python dependencies
galaxybot May 14, 2022
02da77a
Use ``${{ github.workflow }}`` in concurrency group name
nsoranzo May 17, 2022
1ccfdbb
Don't fail-fast in API GitHub workflow
nsoranzo May 17, 2022
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54 changes: 27 additions & 27 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,24 +6,24 @@ aiofiles==0.8.0; python_version >= "3.6" and python_version < "4.0"
alabaster==0.7.12; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
alembic==1.7.7; python_version >= "3.6"
amqp==5.1.1; python_version >= "3.7"
anyio==3.5.0; python_version >= "3.7" and python_full_version >= "3.6.2"
apispec==5.1.1; python_version >= "3.6"
anyio==3.6.1; python_version >= "3.7" and python_full_version >= "3.6.2"
apispec==5.2.2; python_version >= "3.7"
appdirs==1.4.4
argcomplete==2.0.0; python_version >= "3.6" and python_version < "4"
ase==3.22.1; python_version >= "3.6"
asgiref==3.5.0; python_version >= "3.7"
asgiref==3.5.1; python_version >= "3.7"
async-generator==1.10; python_version >= "3.7" and python_version < "4.0"
atomicwrites==1.4.0; python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.4.0"
attmap==0.13.2
attrs==21.4.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4.0" or python_full_version >= "3.5.0" and python_version >= "3.7" and python_version < "4.0"
babel==2.10.1; python_version >= "3.6"
bagit-profile==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
bagit==1.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6"
bcrypt==3.2.0; python_version >= "3.6"
bcrypt==3.2.2; python_version >= "3.6"
bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4")
beaker==1.11.0
billiard==3.6.4.0; python_version >= "3.7"
bioblend==0.16.0; python_version >= "3.6"
bioblend==0.17.0; python_version >= "3.7"
black==22.3.0; python_full_version >= "3.6.2"
bleach==5.0.0; python_version >= "3.7"
boltons==21.0.0
Expand All @@ -40,14 +40,14 @@ circus==0.17.1
click-didyoumean==0.3.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.7"
click-plugins==1.1.1; python_version >= "3.7"
click-repl==0.2.0; python_version >= "3.7"
click==8.1.2; python_version >= "3.7" and python_full_version >= "3.6.2" and python_full_version < "4.0.0"
click==8.1.3; python_version >= "3.7" and python_full_version >= "3.6.2" and python_full_version < "4.0.0"
cloudauthz==0.6.0
cloudbridge==3.0.0
colorama==0.4.4; sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.6.2" and platform_system == "Windows" and (python_version >= "2.7" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and platform_system == "Windows") and (python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.5.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.5.0")
coloredlogs==15.0.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
commonmark==0.9.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0"
coverage==6.3.2; python_version >= "3.7"
cryptography==36.0.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
coverage==6.3.3; python_version >= "3.7"
cryptography==37.0.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
cwltest==2.2.20210901154959; python_version >= "3.6" and python_version < "4"
cwltool==3.1.20211107152837; python_version >= "3.6" and python_version < "4"
cycler==0.11.0; python_version >= "3.7"
Expand All @@ -63,10 +63,10 @@ ecdsa==0.17.0; python_version >= "2.6" and python_full_version < "3.0.0" or pyth
edam-ontology==1.25.2
fabric3==1.14.post1
fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
fastapi==0.75.2; python_full_version >= "3.6.1"
fastapi==0.77.1; python_full_version >= "3.6.1"
fluent-logger==0.10.0; python_version >= "3.5"
fonttools==4.33.2; python_version >= "3.7"
fs==2.4.15
fonttools==4.33.3; python_version >= "3.7"
fs==2.4.16
funcsigs==1.0.2
future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
galaxy-sequence-utils==1.1.5
Expand All @@ -87,9 +87,9 @@ iniconfig==1.1.1; python_version >= "3.7"
isa-rwval==0.10.10
isodate==0.6.1; python_version >= "3.7" and python_version < "4"
isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0"
jinja2==3.1.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7"
jinja2==3.1.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7"
jsonref==0.2; python_version >= "3.6"
jsonschema==4.4.0; python_version >= "3.7"
jsonschema==4.5.1; python_version >= "3.7"
junit-xml==1.9; python_version >= "3.6" and python_version < "4"
kiwisolver==1.4.2; python_version >= "3.7"
kombu==5.2.4; python_version >= "3.7"
Expand All @@ -98,10 +98,10 @@ lockfile==0.12.2; python_version >= "3.7" and python_version < "4"
lxml==4.8.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
mako==1.2.0; python_version >= "3.7"
markdown-it-reporter==0.0.2
markdown==3.3.6; python_version >= "3.6"
markdown==3.3.7; python_version >= "3.6"
markupsafe==2.1.1; python_version >= "3.7"
matplotlib==3.5.1; python_version >= "3.7"
mercurial==6.1.1
matplotlib==3.5.2; python_version >= "3.7"
mercurial==6.1.2
mirakuru==2.4.2; python_version >= "3.7"
mistune==0.8.4; python_version >= "3.7" and python_version < "4"
mrcfile==1.3.0
Expand All @@ -116,17 +116,17 @@ oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or py
outcome==1.1.0; python_version >= "3.7" and python_version < "4.0"
oyaml==1.0
packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7"
paramiko==2.10.3
paramiko==2.10.4
parsley==1.3
paste==3.5.0
pastedeploy==2.1.1
pathspec==0.9.0; python_full_version >= "3.6.2" and python_version >= "3.7"
pbr==5.8.1; python_version >= "2.6"
pbr==5.9.0; python_version >= "2.6"
pillow==9.1.0; python_version >= "3.7"
platformdirs==2.5.2; python_version >= "3.7" and python_full_version >= "3.6.2"
pluggy==1.0.0; python_version >= "3.7"
port-for==0.6.2; python_version >= "3.7"
prettytable==3.2.0; python_version >= "3.7"
prettytable==3.3.0; python_version >= "3.7"
prompt-toolkit==3.0.29; python_full_version >= "3.6.2" and python_version >= "3.7"
prov==1.5.1; python_version >= "3.6" and python_version < "4"
psutil==5.9.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
Expand All @@ -141,12 +141,12 @@ pyeventsystem==0.1.0
pyfaidx==0.6.4
pygithub==1.55; python_version >= "3.6"
pygments==2.12.0; python_full_version >= "3.6.3" and python_full_version < "4.0.0" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
pyjwt==2.3.0; python_version >= "3.6"
pyjwt==2.4.0; python_version >= "3.6"
pykwalify==1.8.0
pylibmagic==0.2.0; python_version >= "3.7"
pynacl==1.5.0; python_version >= "3.6"
pyopenssl==22.0.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
pyparsing==3.0.8; python_full_version >= "3.6.8"
pyparsing==3.0.9; python_full_version >= "3.6.8"
pyreadline3==3.4.1; sys_platform == "win32" and python_version >= "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0")
pyreadline==2.1; sys_platform == "win32" and python_version < "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0")
pyrsistent==0.18.1; python_version >= "3.7"
Expand Down Expand Up @@ -176,18 +176,18 @@ recommonmark==0.7.1
refgenconf==0.12.2
repoze.lru==0.7
requests-oauthlib==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
requests-toolbelt==0.9.1; python_version >= "3.6"
requests-toolbelt==0.9.1; python_version >= "3.7"
requests==2.27.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
responses==0.20.0; python_version >= "3.7"
rfc3986==1.5.0; python_version >= "3.6"
rich==12.2.0; python_full_version >= "3.6.3" and python_full_version < "4.0.0"
rich==12.4.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0"
routes==2.5.1
rsa==4.8; python_version >= "3.6" and python_version < "4"
ruamel.yaml.clib==0.2.6; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.6"
ruamel.yaml==0.17.17; python_version >= "3.7" and python_version < "4"
schema-salad==8.2.20220204150214; python_version >= "3.7" and python_version < "4"
scipy==1.7.3; python_version >= "3.7" and python_version < "3.11"
selenium==4.1.3; python_version >= "3.7" and python_version < "4.0"
selenium==4.1.5; python_version >= "3.7" and python_version < "4.0"
setuptools-scm==5.0.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7"
shellescape==3.8.1; python_version >= "3.6" and python_version < "4"
six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4"
Expand All @@ -205,11 +205,11 @@ sphinxcontrib-jsmath==1.0.1; python_version >= "3.6" and python_full_version < "
sphinxcontrib-qthelp==1.0.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
sphinxcontrib-serializinghtml==1.1.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
sqlalchemy-migrate==0.13.0
sqlalchemy==1.4.35; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
sqlalchemy==1.4.36; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
sqlitedict==2.0.0
sqlparse==0.4.2; python_version >= "3.5"
starlette-context==0.3.3; python_version >= "3.7"
starlette==0.17.1; python_version >= "3.6"
starlette==0.19.1; python_version >= "3.6"
statsd==3.3.0
supervisor==4.2.4; python_version >= "3.6"
svgwrite==1.4.2; python_version >= "3.6"
Expand Down Expand Up @@ -240,7 +240,7 @@ wcwidth==0.2.5; python_full_version >= "3.6.2" and python_version >= "3.7"
webencodings==0.5.1; python_version >= "3.7"
webob==1.8.7; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
whoosh==2.7.4
wrapt==1.14.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
wrapt==1.14.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
wsproto==1.1.0; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.7.0"
yacman==0.8.4
zipp==3.8.0; python_version < "3.8" and python_version >= "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7")
Expand Down
14 changes: 7 additions & 7 deletions lib/galaxy/dependencies/pinned-lint-requirements.txt
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -10,18 +10,18 @@ pyflakes==2.4.0
tomli==2.0.1
typed-ast==1.5.3
types-bleach==5.0.2
types-boto==2.49.14
types-boto==2.49.15
types-contextvars==2.4.5
types-cryptography==3.3.20
types-cryptography==3.3.21
types-dataclasses==0.6.5
types-docutils==0.18.3
types-Markdown==3.3.13
types-paramiko==2.8.19
types-Markdown==3.3.16
types-paramiko==2.10.0
types-pkg-resources==0.1.3
types-python-dateutil==2.8.12
types-python-dateutil==2.8.15
types-PyYAML==6.0.7
types-requests==2.27.20
types-requests==2.27.26
types-six==1.16.15
types-urllib3==1.26.13
types-urllib3==1.26.14
typing_extensions==4.2.0
zipp==3.8.0
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