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Update Python dependencies
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@galaxybot
galaxybot authored Oct 7, 2023
1 parent 0bb93e5 commit fe200a3
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Showing 4 changed files with 38 additions and 27 deletions.
26 changes: 16 additions & 10 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12"
asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12"
axe-selenium-python==2.1.6 ; python_version >= "3.7" and python_version < "3.12"
babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12"
babel==2.13.0 ; python_version >= "3.7" and python_version < "3.12"
billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12"
black==23.3.0 ; python_version >= "3.7" and python_version < "3.12"
bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -18,7 +18,7 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12"
cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -40,6 +40,7 @@ fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
galaxy-release-util==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
greenlet==2.0.2 ; python_version >= "3.7" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12"
httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12"
Expand Down Expand Up @@ -77,19 +78,21 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.2 ; python_version >= "3.7" and python_version < "3.12"
pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.12"
pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"
platformdirs==3.10.0 ; python_version >= "3.7" and python_version < "3.12"
platformdirs==3.11.0 ; python_version >= "3.7" and python_version < "3.12"
playwright==1.35.0 ; python_version >= "3.7" and python_version < "3.12"
pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin"
py==1.11.0 ; python_version >= "3.7" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
pyee==9.0.4 ; python_version >= "3.7" and python_version < "3.12"
pygithub==2.1.1 ; python_version >= "3.7" and python_version < "3.12"
pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.12"
pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -98,19 +101,21 @@ pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-asyncio==0.21.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-base-url==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.12"
pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-playwright==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-playwright==0.3.3 ; python_version >= "3.7" and python_version < "3.12"
pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12"
python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
python-slugify==8.0.1 ; python_version >= "3.7" and python_version < "3.12"
pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32"
pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -120,8 +125,8 @@ requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
responses==0.23.3 ; python_version >= "3.7" and python_version < "3.12"
rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12"
ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
rich==13.6.0 ; python_version >= "3.7" and python_version < "3.12"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12"
scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
Expand All @@ -146,6 +151,7 @@ sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12
sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12"
testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.12"
text-unidecode==1.3 ; python_version >= "3.7" and python_version < "3.12"
tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6"
Expand All @@ -157,11 +163,11 @@ twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12"
typed-ast==1.5.5 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7"
types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.12"
typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
urllib3[socks]==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.12"
urllib3[socks]==1.26.17 ; python_version >= "3.7" and python_version < "3.12"
vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12"
watchdog==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12"
wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.12"
webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12"
werkzeug==2.2.3 ; python_version >= "3.7" and python_version < "3.12"
wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Expand Up @@ -5,6 +5,6 @@ importlib-metadata==4.2.0
mccabe==0.7.0
pycodestyle==2.9.1
pyflakes==2.5.0
ruff==0.0.291
ruff==0.0.292
typing_extensions==4.7.1
zipp==3.15.0
33 changes: 19 additions & 14 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12"
adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12"
aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12"
aiodataloader==0.4.0 ; python_version >= "3.7" and python_version < "3.12"
aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12"
aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.12"
amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
aniso8601==9.0.1 ; python_version >= "3.7" and python_version < "3.12"
anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -16,7 +18,7 @@ async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12"
asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12"
attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12"
babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12"
babel==2.13.0 ; python_version >= "3.7" and python_version < "3.12"
backports-zoneinfo==0.2.1 ; python_version >= "3.7" and python_version < "3.9"
bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -35,7 +37,7 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12"
cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12"
circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -51,7 +53,6 @@ cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
cython==3.0.2 ; python_version >= "3.7" and python_version < "3.12"
decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -74,6 +75,9 @@ future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
graphene-sqlalchemy==3.0.0b3 ; python_version >= "3.7" and python_version < "3.12"
graphene==3.3 ; python_version >= "3.7" and python_version < "3.12"
graphql-core==3.2.3 ; python_version >= "3.7" and python_version < "3.12"
graphql-relay==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12"
Expand Down Expand Up @@ -114,13 +118,14 @@ numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.12"
oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.2 ; python_version >= "3.7" and python_version < "3.12"
paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12"
parsley==1.3 ; python_version >= "3.7" and python_version < "3.12"
paste==3.5.3 ; python_version >= "3.7" and python_version < "3.12"
paste==3.6.0 ; python_version >= "3.7" and python_version < "3.12"
pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.12"
pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.12"
pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9"
promise==2.3 ; python_version >= "3.7" and python_version < "3.12"
prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -144,7 +149,7 @@ pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"
pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"
pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12"
pysam==0.21.0 ; python_version >= "3.7" and python_version < "3.12"
pysam==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -155,17 +160,17 @@ pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12"
rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12"
regex==2023.8.8 ; python_version >= "3.7" and python_version < "3.12"
regex==2023.10.3 ; python_version >= "3.7" and python_version < "3.12"
repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12"
requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12"
rich==13.6.0 ; python_version >= "3.7" and python_version < "3.12"
rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12"
routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
rsa==4.9 ; python_version >= "3.7" and python_version < "3.12"
ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -180,7 +185,7 @@ sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12"
sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12"
starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
starlette_graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
starlette-graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12"
supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -194,18 +199,18 @@ tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12"
typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
tzdata==2023.3 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
tzlocal==5.0.1 ; python_version >= "3.7" and python_version < "3.12"
tzlocal==5.1 ; python_version >= "3.7" and python_version < "3.12"
ubiquerg==0.6.3 ; python_version >= "3.7" and python_version < "3.12"
urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.12"
uvicorn==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.12"
vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12"
wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12"
wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.12"
webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12"
webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12"
whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12"
wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12"
yacman==0.9.1 ; python_version >= "3.7" and python_version < "3.12"
yacman==0.9.2 ; python_version >= "3.7" and python_version < "3.12"
yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12"
zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12"
zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,12 @@ pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
typed-ast==1.5.5 ; python_version >= "3.7" and python_version < "3.8"
types-bleach==6.0.0.4 ; python_version >= "3.7" and python_version < "3.12"
types-bleach==6.1.0.0 ; python_version >= "3.7" and python_version < "3.12"
types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.12"
types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.12"
types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.12"
types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.12"
types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.12"
types-markdown==3.5.0.0 ; python_version >= "3.7" and python_version < "3.12"
types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.12"
types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.12"
types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.12"
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