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Merge pull request #17764 from galaxybot/dev_auto_update_dependencies
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Update Python dependencies
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@nsoranzo
nsoranzo authored Mar 18, 2024
2 parents 8bdf4b7 + a55e4e4 commit 3083b5e
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Showing 7 changed files with 42 additions and 40 deletions.
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/conditional-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ pbs_python
drmaa
statsd
azure-storage==0.32.0
python-irodsclient==1.1.3
python-irodsclient==2.0.0
python-ldap==3.4.0
ldap3==2.9.1
python-pam
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26 changes: 14 additions & 12 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
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 < "3.13"
black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
black==24.3.0 ; python_version >= "3.8" and python_version < "3.13"
build==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -25,28 +25,30 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.4.3 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
darker==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
darkgraylib==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.49.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.50.0 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.10"
importlib-resources==6.3.1 ; python_version >= "3.8" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -66,7 +68,7 @@ matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -108,7 +110,7 @@ pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -126,13 +128,13 @@ rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13"
secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
selenium==4.18.1 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -153,7 +155,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
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 < "3.13"
trio==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
trio==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -168,4 +170,4 @@ werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.13"
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.2.6
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.3.2
ruff==0.3.3
32 changes: 16 additions & 16 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 @@
--extra-index-url https://wheels.galaxyproject.org/simple

a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13"
a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.12.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -13,7 +13,7 @@ amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.5.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.0 ; python_version >= "3.8" and python_version < "3.13"
appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
argcomplete==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -26,7 +26,7 @@ backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version <
bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.13"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -35,7 +35,7 @@ boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13"
boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.51 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -88,9 +88,9 @@ h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.9"
importlib-resources==6.3.1 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.0 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -102,11 +102,11 @@ lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
mako==1.3.2 ; python_version >= "3.8" and python_version < "3.13"
markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
markdown==3.5.2 ; python_version >= "3.8" and python_version < "3.13"
markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.6.3 ; python_version >= "3.8" and python_version < "3.13"
mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.7 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
msal==1.27.0 ; python_version >= "3.8" and python_version < "3.13"
msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -122,7 +122,7 @@ oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
paste==3.7.1 ; python_version >= "3.8" and python_version < "3.13"
paste==3.8.0 ; python_version >= "3.8" and python_version < "3.13"
pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
pebble==5.0.6 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -158,24 +158,24 @@ pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.13"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.33.0 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13"
refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13"
repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; python_version >= "3.8" and python_version < "3.13"
shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -213,6 +213,6 @@ whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
14 changes: 7 additions & 7 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Expand Up @@ -8,18 +8,18 @@ pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platfo
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.13"
types-bleach==6.1.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240317 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/update.sh
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Expand Up @@ -36,7 +36,7 @@ fi

# Install the latest version of poetry into the user account
curl -sSL https://install.python-poetry.org | python3 -
poetry self add poetry-plugin-export
poetry self add 'poetry-plugin-export!=1.7.0' # https://github.com/python-poetry/poetry-plugin-export/issues/269

# Run poetry (this may update pyproject.toml and poetry.lock).
if [ -z "$add" ]; then
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ pillow = "*"
psutil = "*"
pulsar-galaxy-lib = ">=0.15.0.dev0"
pycryptodome = "*"
pydantic = {version = ">=2, !=2.6.0, !=2.6.1, !=2.6.2, !=2.6.3", extras = ["email"]} # https://github.com/pydantic/pydantic/issues/8760
pydantic = {version = ">=2, !=2.6.0, !=2.6.1, !=2.6.2, !=2.6.3, !=2.6.4", extras = ["email"]} # https://github.com/pydantic/pydantic/issues/8760
PyJWT = "*"
pykwalify = "*"
pylibmagic = "*"
Expand Down Expand Up @@ -118,7 +118,7 @@ svgwrite = "*"
tifffile = "*"
tuswsgi = "*"
typing-extensions = "*"
uvicorn = "*"
uvicorn = "!=0.28.0" # https://github.com/galaxyproject/galaxy/issues/17669
uvloop = "*"
WebOb = "*"
Whoosh = "*"
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