mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #21787 from galaxybot/dev_auto_update_dependencies
Update Python dependencies
This commit is contained in:
Nicola Soranzo
@@ -10,15 +10,15 @@ async-generator==1.10
|
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async-timeout==5.0.1 ; python_full_version < '3.11'
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attrs==25.4.0
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axe-selenium-python==2.1.6
|
||||
babel==2.17.0
|
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babel==2.18.0
|
||||
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
|
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backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
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black==26.1.0
|
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boto3==1.42.30
|
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botocore==1.42.30
|
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boto3==1.42.42
|
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botocore==1.42.42
|
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build==1.4.0
|
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cachecontrol==0.14.4
|
||||
cachetools==6.2.6
|
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cachetools==7.0.0
|
||||
cattrs==25.3.0
|
||||
certifi==2026.1.4
|
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cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
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@@ -29,7 +29,7 @@ colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
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colorlog==6.10.1
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contourpy==1.3.2 ; python_full_version < '3.11'
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contourpy==1.3.3 ; python_full_version >= '3.11'
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coverage==7.13.2
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coverage==7.13.3
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cryptography==46.0.4
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cwltest==2.6.20251216093331
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cycler==0.12.1
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@@ -46,27 +46,27 @@ filelock==3.20.3
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fluent-logger==0.11.1
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fonttools==4.61.1
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frozenlist==1.8.0
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fsspec==2026.1.0
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fsspec==2026.2.0
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galaxy-release-util==0.3.2
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gcsfs==2026.1.0
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gcsfs==2026.2.0
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google-api-core==2.29.0
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google-auth==2.48.0
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google-auth-oauthlib==1.2.4
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google-cloud-core==2.5.0
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google-cloud-storage==3.8.0
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google-cloud-storage==3.9.0
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google-cloud-storage-control==1.9.0
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google-crc32c==1.8.0
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google-resumable-media==2.8.0
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googleapis-common-protos==1.72.0
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greenlet==3.3.1
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grpc-google-iam-v1==0.14.3
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grpcio==1.76.0
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grpcio-status==1.76.0
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grpcio==1.78.0
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grpcio-status==1.78.0
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h11==0.16.0
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html5rdf==1.2.1
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httpcore==1.0.9
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httpx==0.28.1
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id==1.5.0
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id==1.6.1
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idna==3.11
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imagesize==1.4.1
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importlib-metadata==8.7.1
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@@ -107,7 +107,7 @@ 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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nh3==0.3.2
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numpy==2.2.6 ; python_full_version < '3.11'
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numpy==2.4.1 ; python_full_version >= '3.11'
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numpy==2.4.2 ; python_full_version >= '3.11'
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oauthlib==3.3.1
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onedatafilerestclient==21.2.5.2
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outcome==1.3.0.post0
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@@ -124,7 +124,7 @@ port-for==1.0.0
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prettytable==3.17.0
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prompt-toolkit==3.0.52
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propcache==0.4.1
|
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proto-plus==1.27.0
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proto-plus==1.27.1
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protobuf==6.33.5
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psutil==7.2.2 ; sys_platform != 'cygwin'
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psycopg==3.3.2
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@@ -162,20 +162,20 @@ rdflib==7.5.0
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readme-renderer==44.0
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referencing==0.36.2
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requests==2.32.5
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requests-cache==1.2.1
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requests-cache==1.3.0
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requests-oauthlib==2.0.0
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requests-toolbelt==1.0.0
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responses==0.25.8
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rfc3986==2.0.0
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rich==13.9.4
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rich-click==1.9.6
|
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rich-click==1.9.7
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roc-validator==0.8.0
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roman-numerals==4.1.0 ; python_full_version >= '3.11'
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rpds-py==0.30.0
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rsa==4.9.1
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ruamel-yaml==0.18.17
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ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
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rucio-clients==39.1.0
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rucio-clients==39.2.0
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s3transfer==0.16.0
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schema-salad==8.9.20251102115403
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scipy==1.15.3 ; python_full_version < '3.11'
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@@ -219,12 +219,12 @@ types-certifi==2021.10.8.3
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types-requests==2.32.4.20260107
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types-urllib3==1.26.25.14
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typing-extensions==4.15.0
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typos==1.42.3
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typos==1.43.3
|
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tzdata==2025.3 ; sys_platform == 'win32'
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url-normalize==2.2.1
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urllib3==2.6.3
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watchdog==6.0.0
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||||
wcwidth==0.5.2
|
||||
wcwidth==0.6.0
|
||||
websocket-client==1.9.0
|
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werkzeug==3.1.5
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wsproto==1.3.2
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@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
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mccabe==0.7.0
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pycodestyle==2.14.0
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pyflakes==3.4.0
|
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ruff==0.14.14
|
||||
ruff==0.15.0
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@@ -3,7 +3,7 @@
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a2wsgi==1.10.10
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adal==1.2.7
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||||
ag-ui-protocol==0.1.10
|
||||
aiobotocore==3.1.1
|
||||
aiobotocore==3.1.2
|
||||
aiofiles==25.1.0
|
||||
aiohappyeyeballs==2.6.1
|
||||
aiohttp==3.13.3
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||||
@@ -13,7 +13,7 @@ alembic==1.18.3
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amqp==5.3.1
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||||
annotated-doc==0.0.4
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||||
annotated-types==0.7.0
|
||||
anthropic==0.77.0
|
||||
anthropic==0.78.0
|
||||
anyio==4.12.1
|
||||
apispec==6.9.0
|
||||
appdirs==1.4.4
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||||
@@ -22,8 +22,8 @@ argcomplete==3.6.3
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async-timeout==5.0.1 ; python_full_version < '3.11.3'
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attmap==0.13.2
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||||
attrs==25.4.0
|
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authlib==1.6.6
|
||||
babel==2.17.0
|
||||
authlib==1.6.7
|
||||
babel==2.18.0
|
||||
backports-tarfile==1.2.0 ; python_full_version < '3.12'
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||||
bagit==1.9.0
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bagit-profile==1.3.1
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||||
@@ -36,11 +36,11 @@ bioblend==1.7.0
|
||||
bleach==6.3.0
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boltons==25.0.0
|
||||
boto==2.49.0
|
||||
boto3==1.42.30
|
||||
botocore==1.42.30
|
||||
boto3==1.42.42
|
||||
botocore==1.42.42
|
||||
bx-python==0.14.0
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||||
cachecontrol==0.14.4
|
||||
cachetools==6.2.6
|
||||
cachetools==7.0.0
|
||||
celery==5.6.2
|
||||
certifi==2026.1.4
|
||||
cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
|
||||
@@ -53,10 +53,11 @@ click-repl==0.3.0
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||||
cloudauthz==0.6.0
|
||||
cloudbridge==3.2.0
|
||||
cloudpickle==3.1.2
|
||||
cohere==5.20.2 ; sys_platform != 'emscripten'
|
||||
cohere==5.20.4 ; sys_platform != 'emscripten'
|
||||
colorama==0.4.6
|
||||
coloredlogs==15.0.1
|
||||
conda-package-streaming==0.12.0
|
||||
croniter==6.0.0
|
||||
cryptography==46.0.4
|
||||
ct3==3.4.0.post5
|
||||
cwl-upgrader==1.2.14
|
||||
@@ -82,28 +83,28 @@ eval-type-backport==0.3.1
|
||||
exceptiongroup==1.3.1
|
||||
executing==2.2.1
|
||||
fakeredis==2.33.0
|
||||
fastapi==0.128.0
|
||||
fastapi==0.128.3
|
||||
fastavro==1.12.1 ; sys_platform != 'emscripten'
|
||||
fastmcp==2.14.4
|
||||
fastmcp==2.14.5
|
||||
filelock==3.20.3
|
||||
fissix==24.4.24
|
||||
frozenlist==1.8.0
|
||||
fs==2.4.16
|
||||
fsspec==2026.1.0
|
||||
fsspec==2026.2.0
|
||||
future==1.0.0
|
||||
genai-prices==0.0.52
|
||||
google-api-core==2.29.0
|
||||
google-auth==2.48.0
|
||||
google-cloud-batch==0.20.0
|
||||
google-genai==1.61.0
|
||||
google-genai==1.62.0
|
||||
googleapis-common-protos==1.72.0
|
||||
gravity==1.2.0
|
||||
greenlet==3.3.1 ; 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'
|
||||
griffe==1.15.0
|
||||
groq==1.0.0
|
||||
grpcio==1.76.0
|
||||
grpcio-status==1.76.0
|
||||
gunicorn==24.1.1
|
||||
grpcio==1.78.0
|
||||
grpcio-status==1.78.0
|
||||
gunicorn==25.0.2
|
||||
gxformat2==0.21.0
|
||||
h11==0.16.0
|
||||
h5grove==2.3.0
|
||||
@@ -112,7 +113,7 @@ hf-xet==1.2.0 ; platform_machine == 'aarch64' or platform_machine == 'amd64' or
|
||||
httpcore==1.0.9
|
||||
httpx==0.28.1
|
||||
httpx-sse==0.4.3
|
||||
huggingface-hub==0.36.0
|
||||
huggingface-hub==0.36.2
|
||||
humanfriendly==10.0
|
||||
idna==3.11
|
||||
ijson==3.4.0.post0
|
||||
@@ -127,7 +128,7 @@ jaraco-context==6.1.0
|
||||
jaraco-functools==4.4.0
|
||||
jeepney==0.9.0 ; sys_platform == 'linux'
|
||||
jinja2==3.1.6
|
||||
jiter==0.12.0
|
||||
jiter==0.13.0
|
||||
jmespath==1.1.0
|
||||
jsonref==1.1.0
|
||||
jsonschema==4.26.0
|
||||
@@ -137,9 +138,9 @@ keyring==25.7.0
|
||||
kombu==5.6.2
|
||||
lagom==2.7.7
|
||||
legacy-cgi==2.6.4 ; python_full_version >= '3.13'
|
||||
limits==5.6.0
|
||||
logfire==4.21.0
|
||||
logfire-api==4.21.0
|
||||
limits==5.8.0
|
||||
logfire==4.22.0
|
||||
logfire-api==4.22.0
|
||||
lupa==2.6
|
||||
lxml==6.0.2
|
||||
mako==1.3.10
|
||||
@@ -164,22 +165,21 @@ nexus-rpc==1.2.0
|
||||
nodejs-wheel==22.20.0
|
||||
nodejs-wheel-binaries==22.20.0
|
||||
numpy==2.2.6 ; python_full_version < '3.11'
|
||||
numpy==2.4.1 ; python_full_version >= '3.11'
|
||||
numpy==2.4.2 ; python_full_version >= '3.11'
|
||||
oauthlib==3.3.1
|
||||
openai==2.16.0
|
||||
openai==2.17.0
|
||||
openapi-pydantic==0.5.1
|
||||
openpyxl==3.1.5
|
||||
opentelemetry-api==1.39.1
|
||||
opentelemetry-exporter-otlp-proto-common==1.39.1
|
||||
opentelemetry-exporter-otlp-proto-http==1.39.1
|
||||
opentelemetry-exporter-prometheus==0.60b1
|
||||
opentelemetry-instrumentation==0.60b1
|
||||
opentelemetry-instrumentation-httpx==0.60b1
|
||||
opentelemetry-proto==1.39.1
|
||||
opentelemetry-sdk==1.39.1
|
||||
opentelemetry-semantic-conventions==0.60b1
|
||||
opentelemetry-util-http==0.60b1
|
||||
orjson==3.11.6
|
||||
orjson==3.11.7
|
||||
oyaml==1.0
|
||||
packaging==26.0
|
||||
paramiko==4.0.0
|
||||
@@ -194,7 +194,7 @@ platformdirs==4.5.1
|
||||
prometheus-client==0.24.1
|
||||
prompt-toolkit==3.0.52
|
||||
propcache==0.4.1
|
||||
proto-plus==1.27.0
|
||||
proto-plus==1.27.1
|
||||
protobuf==6.33.5
|
||||
prov==1.5.1
|
||||
psutil==7.2.2
|
||||
@@ -214,7 +214,7 @@ pydantic-graph==1.44.0
|
||||
pydantic-settings==2.12.0
|
||||
pydantic-tes==0.2.0
|
||||
pydicom==3.0.1
|
||||
pydocket==0.16.6
|
||||
pydocket==0.17.5
|
||||
pydot==4.0.1
|
||||
pyeventsystem==0.1.0
|
||||
pyfaidx==0.9.0.3
|
||||
@@ -259,11 +259,11 @@ rpds-py==0.30.0
|
||||
rsa==4.9.1
|
||||
ruamel-yaml==0.18.17
|
||||
ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
|
||||
s3fs==2026.1.0
|
||||
s3fs==2026.2.0
|
||||
s3transfer==0.16.0
|
||||
schema-salad==8.9.20251102115403
|
||||
secretstorage==3.5.0 ; sys_platform == 'linux'
|
||||
setuptools==80.10.2
|
||||
setuptools==81.0.0
|
||||
shellingham==1.5.4
|
||||
six==1.17.0
|
||||
slowapi==0.1.9
|
||||
@@ -274,12 +274,13 @@ spython==0.3.14
|
||||
sqlalchemy==2.0.46
|
||||
sqlparse==0.5.5
|
||||
sse-starlette==3.2.0
|
||||
starlette==0.50.0
|
||||
starlette==0.52.1
|
||||
starlette-context==0.4.0
|
||||
supervisor==4.3.0
|
||||
svgwrite==1.4.3
|
||||
taskgroup==0.2.2 ; python_full_version < '3.11'
|
||||
temporalio==1.20.0
|
||||
tenacity==9.1.2
|
||||
tenacity==9.1.3
|
||||
text-unidecode==1.3
|
||||
tifffile==2025.5.10 ; python_full_version < '3.11'
|
||||
tifffile==2026.1.28 ; python_full_version >= '3.11'
|
||||
@@ -288,7 +289,7 @@ tinydb==4.8.2
|
||||
tokenizers==0.22.2 ; sys_platform != 'emscripten'
|
||||
tomli==2.4.0 ; python_full_version < '3.11'
|
||||
tornado==6.5.4
|
||||
tqdm==4.67.2
|
||||
tqdm==4.67.3
|
||||
tuspy==1.1.0
|
||||
tuspyserver==4.2.3
|
||||
typer==0.21.1
|
||||
@@ -303,7 +304,7 @@ urllib3==2.6.3
|
||||
uvicorn==0.40.0
|
||||
uvloop==0.22.1
|
||||
vine==5.1.0
|
||||
wcwidth==0.5.2
|
||||
wcwidth==0.6.0
|
||||
webencodings==0.5.1
|
||||
webob==1.8.9
|
||||
websockets==15.0.1
|
||||
|
||||
@@ -10,10 +10,10 @@ async-timeout==5.0.1 ; python_full_version < '3.11'
|
||||
attrs==25.4.0
|
||||
axe-selenium-python==2.1.6
|
||||
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
|
||||
boto3==1.42.30
|
||||
botocore==1.42.30
|
||||
boto3==1.42.42
|
||||
botocore==1.42.42
|
||||
cachecontrol==0.14.4
|
||||
cachetools==6.2.6
|
||||
cachetools==7.0.0
|
||||
cattrs==25.3.0
|
||||
certifi==2026.1.4
|
||||
cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
|
||||
@@ -23,7 +23,7 @@ colorama==0.4.6 ; sys_platform == 'win32'
|
||||
colorlog==6.10.1
|
||||
contourpy==1.3.2 ; python_full_version < '3.11'
|
||||
contourpy==1.3.3 ; python_full_version >= '3.11'
|
||||
coverage==7.13.2
|
||||
coverage==7.13.3
|
||||
cryptography==46.0.4
|
||||
cwltest==2.6.20251216093331
|
||||
cycler==0.12.1
|
||||
@@ -36,21 +36,21 @@ filelock==3.20.3
|
||||
fluent-logger==0.11.1
|
||||
fonttools==4.61.1
|
||||
frozenlist==1.8.0
|
||||
fsspec==2026.1.0
|
||||
gcsfs==2026.1.0
|
||||
fsspec==2026.2.0
|
||||
gcsfs==2026.2.0
|
||||
google-api-core==2.29.0
|
||||
google-auth==2.48.0
|
||||
google-auth-oauthlib==1.2.4
|
||||
google-cloud-core==2.5.0
|
||||
google-cloud-storage==3.8.0
|
||||
google-cloud-storage==3.9.0
|
||||
google-cloud-storage-control==1.9.0
|
||||
google-crc32c==1.8.0
|
||||
google-resumable-media==2.8.0
|
||||
googleapis-common-protos==1.72.0
|
||||
greenlet==3.3.1
|
||||
grpc-google-iam-v1==0.14.3
|
||||
grpcio==1.76.0
|
||||
grpcio-status==1.76.0
|
||||
grpcio==1.78.0
|
||||
grpcio-status==1.78.0
|
||||
h11==0.16.0
|
||||
html5rdf==1.2.1
|
||||
httpcore==1.0.9
|
||||
@@ -82,7 +82,7 @@ multidict==6.7.1
|
||||
mypy==1.19.1
|
||||
mypy-extensions==1.1.0
|
||||
numpy==2.2.6 ; python_full_version < '3.11'
|
||||
numpy==2.4.1 ; python_full_version >= '3.11'
|
||||
numpy==2.4.2 ; python_full_version >= '3.11'
|
||||
oauthlib==3.3.1
|
||||
onedatafilerestclient==21.2.5.2
|
||||
outcome==1.3.0.post0
|
||||
@@ -99,7 +99,7 @@ port-for==1.0.0
|
||||
prettytable==3.17.0
|
||||
prompt-toolkit==3.0.52
|
||||
propcache==0.4.1
|
||||
proto-plus==1.27.0
|
||||
proto-plus==1.27.1
|
||||
protobuf==6.33.5
|
||||
psutil==7.2.2 ; sys_platform != 'cygwin'
|
||||
psycopg==3.3.2
|
||||
@@ -130,17 +130,17 @@ pyyaml==6.0.3
|
||||
rdflib==7.5.0
|
||||
referencing==0.36.2
|
||||
requests==2.32.5
|
||||
requests-cache==1.2.1
|
||||
requests-cache==1.3.0
|
||||
requests-oauthlib==2.0.0
|
||||
responses==0.25.8
|
||||
rich==13.9.4
|
||||
rich-click==1.9.6
|
||||
rich-click==1.9.7
|
||||
roc-validator==0.8.0
|
||||
rpds-py==0.30.0
|
||||
rsa==4.9.1
|
||||
ruamel-yaml==0.18.17
|
||||
ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
|
||||
rucio-clients==39.1.0
|
||||
rucio-clients==39.2.0
|
||||
s3transfer==0.16.0
|
||||
schema-salad==8.9.20251102115403
|
||||
scipy==1.15.3 ; python_full_version < '3.11'
|
||||
@@ -170,12 +170,12 @@ types-certifi==2021.10.8.3
|
||||
types-requests==2.32.4.20260107
|
||||
types-urllib3==1.26.25.14
|
||||
typing-extensions==4.15.0
|
||||
typos==1.42.3
|
||||
typos==1.43.3
|
||||
tzdata==2025.3 ; sys_platform == 'win32'
|
||||
url-normalize==2.2.1
|
||||
urllib3==2.6.3
|
||||
watchdog==6.0.0
|
||||
wcwidth==0.5.2
|
||||
wcwidth==0.6.0
|
||||
websocket-client==1.9.0
|
||||
werkzeug==3.1.5
|
||||
wsproto==1.3.2
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
# 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==1.42.39
|
||||
botocore-stubs==1.42.39
|
||||
boto3-stubs==1.42.44
|
||||
botocore-stubs==1.42.41
|
||||
cffi==2.0.0 ; platform_python_implementation != 'PyPy'
|
||||
cryptography==46.0.4
|
||||
librt==0.7.8 ; platform_python_implementation != 'PyPy'
|
||||
|
||||
Reference in New Issue
Block a user