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Update Python dependencies #19031

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merged 3 commits into from
Oct 22, 2024
Merged

Update Python dependencies #19031

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3f9cdb4
Disallow SQLAlchemy 2.0.36
nsoranzo Oct 21, 2024
82e7fd9
Update Python dependencies
galaxybot Oct 19, 2024
9f78065
Fixes for mypy 1.12.0
nsoranzo Oct 21, 2024
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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 @@ -4,7 +4,7 @@ aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.10 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.2 ; python_version >= "3.8" and python_version < "3.13"
ase==3.23.0 ; python_version >= "3.8" and python_version < "3.13"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -26,7 +26,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_p
contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9"
contourpy==1.3.0 ; python_version >= "3.9" and python_version < "3.13"
coverage[toml]==7.6.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240906231108 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -98,7 +98,7 @@ pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psutil==6.1.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psycopg==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -122,7 +122,7 @@ pytest-postgresql==6.1.1 ; 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"
python-irodsclient==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
python-irodsclient==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.2 ; python_version >= "3.8" and python_version < "3.9"
pywin32-ctypes==0.2.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
Expand All @@ -138,16 +138,16 @@ rich==13.9.2 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.20.0 ; python_version >= "3.9" 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"
rucio-clients==35.4.0 ; python_version >= "3.9" and python_version < "3.13"
rucio-clients==35.4.1 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20241010092723 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
scipy==1.14.1 ; python_version >= "3.10" and python_version < "3.13"
secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
selenium==4.25.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.2.0 ; 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 @@ -166,13 +166,13 @@ stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13"
tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.2 ; python_version >= "3.8" and python_version < "3.13"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.2 ; 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==0.26.2 ; python_version >= "3.8" and python_version < "3.13"
trio==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
twill==3.3 ; python_version >= "3.8" and python_version < "3.13"
twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
Expand All @@ -184,5 +184,5 @@ websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.4 ; 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==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.15.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; 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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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.8.19
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.6.9
ruff==0.7.0
29 changes: 14 additions & 15 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,8 @@ aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.3 ; python_version >= "3.8" and python_version < "3.13"
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==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.2 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.1 ; 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"
Expand Down Expand Up @@ -52,9 +51,9 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
conda-package-streaming==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
cwl-utils==0.34 ; python_version >= "3.8" and python_version < "3.13"
cwl-utils==0.35 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20241007082533 ; python_version >= "3.8" and python_version < "3.13"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -66,16 +65,16 @@ dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
fastapi-slim==0.115.0 ; python_version >= "3.8" and python_version < "3.13"
fastapi-slim==0.115.2 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
fsspec==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13"
graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"
graphql-core==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
graphene==3.4 ; python_version >= "3.8" and python_version < "3.13"
graphql-core==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
greenlet==3.0.3 ; python_version < "3.13" 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 >= "3.8"
Expand Down Expand Up @@ -132,7 +131,7 @@ promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.48 ; python_version >= "3.8" and python_version < "3.13"
propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.21.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -175,9 +174,9 @@ rpds-py==0.20.0 ; 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==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20241010092723 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.2.0 ; 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"
social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -188,12 +187,12 @@ sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
starlette==0.38.6 ; python_version >= "3.8" and python_version < "3.13"
starlette==0.40.0 ; python_version >= "3.8" and python_version < "3.13"
supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13"
svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
tenacity==9.0.0 ; python_version >= "3.8" and python_version < "3.13"
tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -204,16 +203,16 @@ tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13"
tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.31.1 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.20.0 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.32.0 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.21.0 ; python_version >= "3.8" and python_version < "3.13"
vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
webob==1.8.8 ; python_version >= "3.8" and python_version < "3.13"
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==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.15.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13"
16 changes: 7 additions & 9 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,14 +1,12 @@
--extra-index-url https://wheels.galaxyproject.org/simple

annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.39 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.39 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.44 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.44 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
mypy-boto3-s3==1.35.32 ; python_version >= "3.8" and python_version < "3.13"
mypy-boto3-s3==1.35.42 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.11.2 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.12.0 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -19,14 +17,14 @@ types-boto==2.49.18.20240806 ; python_version >= "3.8" and python_version < "3.1
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==0.21.0.20241005 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20241018 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240917 ; 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-s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
types-setuptools==75.1.0.20240917 ; python_version >= "3.8" and python_version < "3.13"
types-setuptools==75.2.0.20241019 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20241009 ; 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==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
18 changes: 8 additions & 10 deletions lib/galaxy/managers/notification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -414,16 +414,14 @@ def update_broadcasted_notification(self, notification_id: int, request: Notific

def get_user_notification_preferences(self, user: User) -> UserNotificationPreferences:
"""Gets the user's current notification preferences or the default ones if no preferences are set."""
current_notification_preferences = (
user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]
if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences
else None
)
try:
return UserNotificationPreferences.model_validate_json(current_notification_preferences)
except ValidationError:
# Gracefully return default preferences is they don't exist or get corrupted
return UserNotificationPreferences.default()
current_notification_preferences = user.preferences.get(NOTIFICATION_PREFERENCES_SECTION_NAME)
if current_notification_preferences:
try:
return UserNotificationPreferences.model_validate_json(current_notification_preferences)
except ValidationError:
pass
# Gracefully return default preferences is they don't exist or get corrupted
return UserNotificationPreferences.default()

def update_user_notification_preferences(
self, user: User, request: UpdateUserNotificationPreferencesRequest
Expand Down
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