mirror of
https://github.com/galaxyproject/galaxy.git
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Merge pull request #22517 from galaxybot/dev_auto_update_dependencies
Update Python dependencies
This commit is contained in:
Marius van den Beek
@@ -15518,32 +15518,7 @@ export interface components {
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type: "in_range";
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};
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/** IncomingToolOutputCollection */
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"IncomingToolOutputCollection-Input": {
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/**
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* hidden
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* @description If true, the output will not be shown in the history.
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*/
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hidden?: boolean | null;
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/**
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* label
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* @description Output label. Will be used as dataset name in history.
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*/
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label?: string | null;
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/**
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* name
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* @description Parameter name. Used when referencing parameter in workflows.
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*/
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name?: string | null;
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/** structure */
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structure: components["schemas"]["ToolOutputCollectionStructure"];
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/**
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* @description discriminator enum property added by openapi-typescript
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* @enum {string}
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*/
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type: "collection";
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};
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/** IncomingToolOutputCollection */
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"IncomingToolOutputCollection-Output": {
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IncomingToolOutputCollection: {
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/**
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* hidden
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* @description If true, the output will not be shown in the history.
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@@ -24795,7 +24770,7 @@ export interface components {
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*/
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outputs: (
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| components["schemas"]["IncomingToolOutputDataset"]
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| components["schemas"]["IncomingToolOutputCollection-Input"]
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| components["schemas"]["IncomingToolOutputCollection"]
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| components["schemas"]["ToolOutputText"]
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| components["schemas"]["ToolOutputInteger"]
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| components["schemas"]["ToolOutputFloat"]
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@@ -24894,7 +24869,7 @@ export interface components {
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*/
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outputs: (
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| components["schemas"]["IncomingToolOutputDataset"]
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| components["schemas"]["IncomingToolOutputCollection-Output"]
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| components["schemas"]["IncomingToolOutputCollection"]
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| components["schemas"]["ToolOutputText"]
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| components["schemas"]["ToolOutputInteger"]
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| components["schemas"]["ToolOutputFloat"]
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@@ -26591,7 +26566,7 @@ export interface components {
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*/
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outputs: (
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| components["schemas"]["IncomingToolOutputDataset"]
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| components["schemas"]["IncomingToolOutputCollection-Input"]
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| components["schemas"]["IncomingToolOutputCollection"]
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| components["schemas"]["ToolOutputText"]
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| components["schemas"]["ToolOutputInteger"]
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| components["schemas"]["ToolOutputFloat"]
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@@ -5,6 +5,7 @@ aiohappyeyeballs==2.6.1
|
||||
aiohttp==3.13.5
|
||||
aiosignal==1.4.0
|
||||
alabaster==1.0.0
|
||||
annotated-types==0.7.0
|
||||
ase==3.28.0
|
||||
async-timeout==5.0.1 ; python_full_version < '3.11'
|
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attrs==26.1.0
|
||||
@@ -41,7 +42,7 @@ docutils==0.22.4 ; python_full_version >= '3.11'
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dogpile-cache==1.5.0
|
||||
enum-tools==0.12.0
|
||||
exceptiongroup==1.3.1 ; python_full_version < '3.11'
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||||
filelock==3.25.2
|
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filelock==3.28.0
|
||||
fluent-logger==0.11.1
|
||||
fonttools==4.62.1
|
||||
frozenlist==1.8.0
|
||||
@@ -86,7 +87,7 @@ junit-xml==1.9
|
||||
keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
kiwisolver==1.5.0
|
||||
librt==0.9.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.0.3
|
||||
lxml==6.0.4
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
|
||||
markdown-it-reporter==0.0.2
|
||||
@@ -99,7 +100,7 @@ mistune==3.2.0
|
||||
more-itertools==11.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
|
||||
msgpack==1.1.2
|
||||
multidict==6.7.1
|
||||
mypy==1.20.0
|
||||
mypy==1.20.1
|
||||
mypy-extensions==1.1.0
|
||||
myst-parser==4.0.1 ; python_full_version < '3.11'
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myst-parser==5.0.0 ; python_full_version >= '3.11'
|
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@@ -129,8 +130,10 @@ psycopg==3.3.3
|
||||
pyasn1==0.6.3
|
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pyasn1-modules==0.4.2
|
||||
pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
|
||||
pydantic==2.13.2
|
||||
pydantic-core==2.46.2
|
||||
pyee==13.0.1
|
||||
pygithub==2.9.0
|
||||
pygithub==2.9.1
|
||||
pygments==2.20.0
|
||||
pyjwt==2.12.1
|
||||
pynacl==1.6.2
|
||||
@@ -174,7 +177,7 @@ rpds-py==0.30.0
|
||||
ruamel-yaml==0.19.1
|
||||
rucio-clients==39.4.1
|
||||
s3transfer==0.16.0
|
||||
schema-salad==8.9.20260327095315
|
||||
schema-salad==8.9.20260417192335
|
||||
scipy==1.15.3 ; python_full_version < '3.11'
|
||||
scipy==1.17.1 ; python_full_version >= '3.11'
|
||||
secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
|
||||
@@ -212,7 +215,8 @@ twine==6.2.0
|
||||
types-cachetools==6.2.0.20260408
|
||||
types-requests==2.33.0.20260408
|
||||
typing-extensions==4.15.0
|
||||
typos==1.45.0
|
||||
typing-inspection==0.4.2
|
||||
typos==1.45.1
|
||||
tzdata==2026.1 ; sys_platform == 'win32'
|
||||
url-normalize==2.2.1
|
||||
urllib3==2.6.3
|
||||
@@ -222,4 +226,4 @@ websocket-client==1.9.0
|
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werkzeug==3.1.8
|
||||
wsproto==1.3.2
|
||||
yarl==1.23.0
|
||||
zipp==3.23.0 ; python_full_version < '3.12'
|
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zipp==3.23.1 ; python_full_version < '3.12'
|
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|
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@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
|
||||
mccabe==0.7.0
|
||||
pycodestyle==2.14.0
|
||||
pyflakes==3.4.0
|
||||
ruff==0.15.10
|
||||
ruff==0.15.11
|
||||
|
||||
@@ -2,7 +2,7 @@
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# uv export --frozen --no-annotate --no-hashes --no-dev
|
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a2wsgi==1.10.10
|
||||
adal==1.2.7
|
||||
ag-ui-protocol==0.1.15
|
||||
ag-ui-protocol==0.1.16
|
||||
aiobotocore==3.4.0
|
||||
aiofile==3.9.0
|
||||
aiofiles==25.1.0
|
||||
@@ -14,7 +14,7 @@ alembic==1.18.4
|
||||
amqp==5.3.1
|
||||
annotated-doc==0.0.4
|
||||
annotated-types==0.7.0
|
||||
anthropic==0.94.0
|
||||
anthropic==0.96.0
|
||||
anyio==4.13.0
|
||||
apispec==6.10.0
|
||||
appdirs==1.4.4
|
||||
@@ -32,7 +32,7 @@ bdbag==1.8.0
|
||||
beaker==1.13.0
|
||||
beartype==0.22.9
|
||||
billiard==4.2.4
|
||||
bioblend==1.8.0
|
||||
bioblend==1.9.0
|
||||
bleach==6.3.0
|
||||
boltons==25.0.0
|
||||
boto==2.49.0
|
||||
@@ -53,7 +53,7 @@ click-plugins==1.1.1.2
|
||||
click-repl==0.3.0
|
||||
cloudauthz==0.6.0
|
||||
cloudbridge==3.2.0
|
||||
cohere==6.1.0 ; sys_platform != 'emscripten'
|
||||
cohere==5.21.1 ; sys_platform != 'emscripten'
|
||||
colorama==0.4.6 ; sys_platform == 'win32'
|
||||
coloredlogs==15.0.1
|
||||
conda-package-streaming==0.12.0
|
||||
@@ -61,7 +61,7 @@ cryptography==46.0.7
|
||||
ct3==3.4.0.post5
|
||||
cwl-upgrader==1.2.15
|
||||
cwl-utils==0.41
|
||||
cwltool==3.1.20260315121657
|
||||
cwltool==3.2.20260413085819
|
||||
cyclopts==4.10.2
|
||||
defusedxml==0.7.1
|
||||
deprecated==1.3.1
|
||||
@@ -70,7 +70,7 @@ dictobj==0.4
|
||||
distro==1.9.0
|
||||
dnspython==2.8.0
|
||||
docopt==0.6.2
|
||||
docstring-parser==0.17.0
|
||||
docstring-parser==0.18.0
|
||||
docutils==0.21.2 ; python_full_version < '3.11'
|
||||
docutils==0.22.4 ; python_full_version >= '3.11'
|
||||
dparse==0.6.4
|
||||
@@ -80,10 +80,10 @@ et-xmlfile==2.0.0
|
||||
eval-type-backport==0.3.1
|
||||
exceptiongroup==1.3.1
|
||||
executing==2.2.1
|
||||
fastapi==0.135.3
|
||||
fastapi==0.136.0
|
||||
fastavro==1.12.1 ; sys_platform != 'emscripten'
|
||||
fastmcp==3.2.3
|
||||
filelock==3.25.2
|
||||
fastmcp==3.2.4
|
||||
filelock==3.28.0
|
||||
fissix==24.4.24
|
||||
frozenlist==1.8.0
|
||||
fs==2.4.16
|
||||
@@ -93,7 +93,7 @@ genai-prices==0.0.56
|
||||
google-api-core==2.30.3
|
||||
google-auth==2.49.2
|
||||
google-cloud-batch==0.21.0
|
||||
google-genai==1.72.0
|
||||
google-genai==1.73.1
|
||||
googleapis-common-protos==1.74.0
|
||||
gravity==1.2.1
|
||||
greenlet==3.4.0 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
|
||||
@@ -104,18 +104,18 @@ grpcio-status==1.80.0
|
||||
gunicorn==25.3.0
|
||||
gxformat2==0.24.0
|
||||
h11==0.16.0
|
||||
h5grove==3.0.0
|
||||
h5grove==4.0.0
|
||||
h5py==3.16.0
|
||||
hf-xet==1.4.3 ; platform_machine == 'AMD64' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'
|
||||
httpcore==1.0.9
|
||||
httpx==0.28.1
|
||||
httpx-sse==0.4.3
|
||||
huggingface-hub==1.10.1
|
||||
huggingface-hub==1.11.0
|
||||
humanfriendly==10.0
|
||||
idna==3.11
|
||||
ijson==3.5.0
|
||||
importlib-metadata==8.7.1
|
||||
importlib-resources==6.5.2 ; python_full_version < '3.12'
|
||||
importlib-resources==7.1.0 ; python_full_version < '3.12'
|
||||
invoke==3.0.3
|
||||
isa-rwval==0.10.11
|
||||
isal==1.8.0
|
||||
@@ -137,9 +137,9 @@ kombu==5.6.2
|
||||
lagom==2.7.7
|
||||
legacy-cgi==2.6.4 ; python_full_version >= '3.13'
|
||||
limits==5.8.0
|
||||
logfire==4.32.0
|
||||
logfire-api==4.32.0
|
||||
lxml==6.0.3
|
||||
logfire==4.32.1
|
||||
logfire-api==4.32.1
|
||||
lxml==6.0.4
|
||||
mako==1.3.11
|
||||
markdown==3.10.2
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
@@ -148,7 +148,7 @@ markupsafe==3.0.3
|
||||
mcp==1.27.0
|
||||
mdurl==0.1.2
|
||||
mercurial==7.2.1
|
||||
mistralai==2.3.2
|
||||
mistralai==2.4.0
|
||||
mistune==3.2.0
|
||||
more-itertools==11.0.2
|
||||
mrcfile==1.5.4
|
||||
@@ -164,7 +164,7 @@ nodejs-wheel-binaries==22.20.0
|
||||
numpy==2.2.6 ; python_full_version < '3.11'
|
||||
numpy==2.4.4 ; python_full_version >= '3.11'
|
||||
oauthlib==3.3.1
|
||||
openai==2.31.0
|
||||
openai==2.32.0
|
||||
openapi-pydantic==0.5.1
|
||||
openpyxl==3.1.5
|
||||
opentelemetry-api==1.39.1
|
||||
@@ -198,12 +198,12 @@ pyasn1==0.6.3
|
||||
pyasn1-modules==0.4.2
|
||||
pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
|
||||
pycryptodome==3.23.0
|
||||
pydantic==2.12.5
|
||||
pydantic-ai==1.80.0
|
||||
pydantic-ai-slim==1.80.0
|
||||
pydantic-core==2.41.5
|
||||
pydantic-evals==1.80.0
|
||||
pydantic-graph==1.80.0
|
||||
pydantic==2.13.2
|
||||
pydantic-ai==1.84.1
|
||||
pydantic-ai-slim==1.84.1
|
||||
pydantic-core==2.46.2
|
||||
pydantic-evals==1.84.1
|
||||
pydantic-graph==1.84.1
|
||||
pydantic-handlebars==0.1.0
|
||||
pydantic-settings==2.13.1
|
||||
pydantic-tes==0.4.0
|
||||
@@ -250,7 +250,7 @@ rpds-py==0.30.0
|
||||
ruamel-yaml==0.19.1
|
||||
s3fs==2026.3.0
|
||||
s3transfer==0.16.0
|
||||
schema-salad==8.9.20260327095315
|
||||
schema-salad==8.9.20260417192335
|
||||
secretstorage==3.5.0 ; sys_platform == 'linux'
|
||||
setuptools==81.0.0
|
||||
shellingham==1.5.4
|
||||
@@ -267,11 +267,12 @@ starlette==1.0.0
|
||||
starlette-context==0.5.1
|
||||
supervisor==4.3.0
|
||||
svgwrite==1.4.3
|
||||
temporalio==1.25.0
|
||||
temporalio==1.26.0
|
||||
tenacity==9.1.4
|
||||
text-unidecode==1.3
|
||||
tifffile==2025.5.10 ; python_full_version < '3.11'
|
||||
tifffile==2026.3.3 ; python_full_version >= '3.11'
|
||||
tifffile==2026.3.3 ; python_full_version == '3.11.*'
|
||||
tifffile==2026.4.11 ; python_full_version >= '3.12'
|
||||
tiktoken==0.12.0
|
||||
tinydb==4.8.2
|
||||
tokenizers==0.22.2 ; sys_platform != 'emscripten'
|
||||
@@ -303,6 +304,6 @@ wrapt==1.17.3
|
||||
xai-sdk==1.11.0
|
||||
yacman==1.0.0
|
||||
yarl==1.23.0
|
||||
zipp==3.23.0
|
||||
zipp==3.23.1
|
||||
zipstream-new==1.1.8
|
||||
zstandard==0.25.0
|
||||
|
||||
@@ -4,6 +4,7 @@ aiocop==1.1.4
|
||||
aiohappyeyeballs==2.6.1
|
||||
aiohttp==3.13.5
|
||||
aiosignal==1.4.0
|
||||
annotated-types==0.7.0
|
||||
ase==3.28.0
|
||||
async-timeout==5.0.1 ; python_full_version < '3.11'
|
||||
attrs==26.1.0
|
||||
@@ -31,7 +32,7 @@ defusedxml==0.7.1
|
||||
dogpile-cache==1.5.0
|
||||
enum-tools==0.12.0
|
||||
exceptiongroup==1.3.1 ; python_full_version < '3.11'
|
||||
filelock==3.25.2
|
||||
filelock==3.28.0
|
||||
fluent-logger==0.11.1
|
||||
fonttools==4.62.1
|
||||
frozenlist==1.8.0
|
||||
@@ -67,7 +68,7 @@ jsonschema-specifications==2025.9.1
|
||||
junit-xml==1.9
|
||||
kiwisolver==1.5.0
|
||||
librt==0.9.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml==6.0.3
|
||||
lxml==6.0.4
|
||||
markdown-it-py==3.0.0 ; python_full_version < '3.11'
|
||||
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
|
||||
markupsafe==3.0.3
|
||||
@@ -77,7 +78,7 @@ mirakuru==3.0.2
|
||||
mistune==3.2.0
|
||||
msgpack==1.1.2
|
||||
multidict==6.7.1
|
||||
mypy==1.20.0
|
||||
mypy==1.20.1
|
||||
mypy-extensions==1.1.0
|
||||
numpy==2.2.6 ; python_full_version < '3.11'
|
||||
numpy==2.4.4 ; python_full_version >= '3.11'
|
||||
@@ -104,6 +105,8 @@ psycopg==3.3.3
|
||||
pyasn1==0.6.3
|
||||
pyasn1-modules==0.4.2
|
||||
pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
|
||||
pydantic==2.13.2
|
||||
pydantic-core==2.46.2
|
||||
pyee==13.0.1
|
||||
pygments==2.20.0
|
||||
pyparsing==3.3.2
|
||||
@@ -139,7 +142,7 @@ rpds-py==0.30.0
|
||||
ruamel-yaml==0.19.1
|
||||
rucio-clients==39.4.1
|
||||
s3transfer==0.16.0
|
||||
schema-salad==8.9.20260327095315
|
||||
schema-salad==8.9.20260417192335
|
||||
scipy==1.15.3 ; python_full_version < '3.11'
|
||||
scipy==1.17.1 ; python_full_version >= '3.11'
|
||||
selenium==4.43.0
|
||||
@@ -163,7 +166,8 @@ tuspy==1.1.0
|
||||
types-cachetools==6.2.0.20260408
|
||||
types-requests==2.33.0.20260408
|
||||
typing-extensions==4.15.0
|
||||
typos==1.45.0
|
||||
typing-inspection==0.4.2
|
||||
typos==1.45.1
|
||||
tzdata==2026.1 ; sys_platform == 'win32'
|
||||
url-normalize==2.2.1
|
||||
urllib3==2.6.3
|
||||
@@ -173,4 +177,4 @@ websocket-client==1.9.0
|
||||
werkzeug==3.1.8
|
||||
wsproto==1.3.2
|
||||
yarl==1.23.0
|
||||
zipp==3.23.0 ; python_full_version < '3.12'
|
||||
zipp==3.23.1 ; python_full_version < '3.12'
|
||||
|
||||
@@ -1,19 +1,19 @@
|
||||
# This file was autogenerated by uv via the following command:
|
||||
# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
|
||||
annotated-types==0.7.0
|
||||
boto3-stubs==1.42.88
|
||||
boto3-stubs==1.42.91
|
||||
botocore-stubs==1.42.41
|
||||
cffi==2.0.0 ; platform_python_implementation != 'PyPy'
|
||||
cryptography==46.0.7
|
||||
librt==0.9.0 ; platform_python_implementation != 'PyPy'
|
||||
lxml-stubs==0.5.1
|
||||
mypy==1.20.0
|
||||
mypy==1.20.1
|
||||
mypy-boto3-s3==1.42.85
|
||||
mypy-extensions==1.1.0
|
||||
pathspec==1.0.4
|
||||
pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
|
||||
pydantic==2.12.5
|
||||
pydantic-core==2.41.5
|
||||
pydantic==2.13.2
|
||||
pydantic-core==2.46.2
|
||||
tomli==2.4.1 ; python_full_version < '3.11'
|
||||
types-awscrt==0.31.3
|
||||
types-bleach==6.3.0.20260408
|
||||
|
||||
Reference in New Issue
Block a user