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Update Python dependencies #17201

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Dec 16, 2023
Merged

Update Python dependencies #17201

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22 changes: 11 additions & 11 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@ ase==3.22.1 ; python_version >= "3.8" and python_version < "3.12"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12"
axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.12"
babel==2.13.1 ; python_version >= "3.8" and python_version < "3.12"
babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12"
backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.12"
black==23.11.0 ; python_version >= "3.8" and python_version < "3.12"
black==23.12.0 ; python_version >= "3.8" and python_version < "3.12"
build==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -25,7 +25,7 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.12"
codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.12"
colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
coverage[toml]==7.3.2 ; python_version >= "3.8" and python_version < "3.12"
coverage[toml]==7.3.3 ; python_version >= "3.8" and python_version < "3.12"
cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12"
cwltest==2.4.20231031143732 ; python_version >= "3.8" and python_version < "3.12"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -37,7 +37,7 @@ exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
fonttools==4.46.0 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.12"
galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.12"
greenlet==3.0.1 ; python_version >= "3.8" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -49,7 +49,7 @@ importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12"
importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12"
isort==5.12.0 ; python_version >= "3.8" and python_version < "3.12"
isort==5.13.2 ; python_version >= "3.8" and python_version < "3.12"
jaraco-classes==3.3.0 ; python_version >= "3.8" and python_version < "3.12"
jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux"
jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -77,7 +77,7 @@ numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12"
packaging==23.2 ; python_version >= "3.8" and python_version < "3.12"
pathspec==0.11.2 ; python_version >= "3.8" and python_version < "3.12"
pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.12"
pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12"
pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -86,9 +86,9 @@ playwright==1.40.0 ; python_version >= "3.8" and python_version < "3.12"
pluggy==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.12"
prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.12"
psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" and sys_platform != "cygwin"
psycopg==3.1.14 ; python_version >= "3.8" and python_version < "3.12"
psycopg==3.1.15 ; python_version >= "3.8" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12"
pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.12"
pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -153,11 +153,11 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.12"
trio==0.23.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
trio==0.23.2 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
twill==3.2.1 ; python_version >= "3.8" and python_version < "3.12"
twine==4.0.2 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"
tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12"
urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.12"
urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.12"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==23.12.2
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.1.0
ruff==0.1.7
ruff==0.1.8
26 changes: 13 additions & 13 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12"
aiobotocore==2.8.0 ; python_version >= "3.8" and python_version < "3.12"
aiobotocore==2.9.0 ; python_version >= "3.8" and python_version < "3.12"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12"
aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12"
aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -13,24 +13,24 @@ anyio==4.1.0 ; python_version >= "3.8" and python_version < "3.12"
apispec==6.3.0 ; python_version >= "3.8" and python_version < "3.12"
appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.12"
arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.12"
argcomplete==3.1.6 ; python_version >= "3.8" and python_version < "3.12"
argcomplete==3.2.1 ; python_version >= "3.8" and python_version < "3.12"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.12"
attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12"
babel==2.13.1 ; python_version >= "3.8" and python_version < "3.12"
babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12"
backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.12"
bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.12"
bcrypt==4.1.1 ; python_version >= "3.8" and python_version < "3.12"
bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.12"
bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.12"
beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.12"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.12"
bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12"
boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12"
boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12"
botocore==1.33.1 ; python_version >= "3.8" and python_version < "3.12"
botocore==1.33.13 ; python_version >= "3.8" and python_version < "3.12"
bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -49,7 +49,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and platfo
coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.12"
conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.12"
cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12"
cwl-upgrader==1.2.10 ; python_version >= "3.8" and python_version < "3.12"
cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.12"
cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12"
cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12"
decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -67,9 +67,9 @@ exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
fastapi-utils==0.2.1 ; python_version >= "3.8" and python_version < "3.12"
fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.12"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12"
fsspec==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.12"
future==0.18.3 ; python_version >= "3.8" and python_version < "3.12"
galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12"
galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -125,7 +125,7 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12"
pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12"
pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
promise==2.3 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.12"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.12"
psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12"
pulsar-galaxy-lib==0.15.5 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -171,7 +171,7 @@ rpds-py==0.13.2 ; python_version >= "3.8" and python_version < "3.12"
rsa==4.9 ; python_version >= "3.8" and python_version < "3.12"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8"
ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12"
s3fs==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.12"
schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12"
setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -180,7 +180,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12"
sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12"
spython==0.3.11 ; python_version >= "3.8" and python_version < "3.12"
spython==0.3.13 ; python_version >= "3.8" and python_version < "3.12"
sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12"
sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -195,9 +195,9 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
tornado==6.4 ; python_version >= "3.8" and python_version < "3.12"
tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"
tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12"
tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.12"
ubiquerg==0.6.3 ; python_version >= "3.8" and python_version < "3.12"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,4 +18,4 @@ types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.12"
types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.12"
types-six==1.16.21.9 ; python_version >= "3.8" and python_version < "3.12"
types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"
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