mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Update Python dependencies
by running `make update-dependencies`. Downgrade gxformat2 to 0.24.0 to fix workflow API tests
This commit is contained in:
galaxybot
@@ -4,6 +4,7 @@ aiohappyeyeballs==2.6.1
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aiohttp==3.13.5
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aiosignal==1.4.0
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alabaster==1.0.0
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annotated-types==0.7.0
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ase==3.28.0
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async-timeout==5.0.1 ; python_full_version < '3.11'
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attrs==26.1.0
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@@ -40,7 +41,7 @@ docutils==0.22.4 ; python_full_version >= '3.11'
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dogpile-cache==1.5.0
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enum-tools==0.12.0
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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
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fluent-logger==0.11.1
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fonttools==4.62.1
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frozenlist==1.8.0
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@@ -85,7 +86,7 @@ junit-xml==1.9
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keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
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kiwisolver==1.5.0
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librt==0.9.0 ; platform_python_implementation != 'PyPy'
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lxml==6.0.3
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lxml==6.0.4
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markdown-it-py==3.0.0 ; python_full_version < '3.11'
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markdown-it-py==4.0.0 ; python_full_version >= '3.11'
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markdown-it-reporter==0.0.2
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@@ -98,7 +99,7 @@ mistune==3.2.0
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more-itertools==11.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
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msgpack==1.1.2
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multidict==6.7.1
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mypy==1.20.0
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mypy==1.20.1
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mypy-extensions==1.1.0
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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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@@ -128,8 +129,10 @@ psycopg==3.3.3
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pyasn1==0.6.3
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pyasn1-modules==0.4.2
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pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
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pydantic==2.13.2
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pydantic-core==2.46.2
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pyee==13.0.1
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pygithub==2.9.0
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pygithub==2.9.1
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pygments==2.20.0
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pyjwt==2.12.1
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pynacl==1.6.2
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@@ -173,7 +176,7 @@ rpds-py==0.30.0
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ruamel-yaml==0.19.1
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rucio-clients==39.4.1
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s3transfer==0.16.0
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schema-salad==8.9.20260327095315
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schema-salad==8.9.20260417192335
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scipy==1.15.3 ; python_full_version < '3.11'
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scipy==1.17.1 ; python_full_version >= '3.11'
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secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
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@@ -211,7 +214,8 @@ twine==6.2.0
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types-cachetools==6.2.0.20260408
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types-requests==2.33.0.20260408
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typing-extensions==4.15.0
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typos==1.45.0
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typing-inspection==0.4.2
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typos==1.45.1
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tzdata==2026.1 ; sys_platform == 'win32'
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url-normalize==2.2.1
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urllib3==2.6.3
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@@ -221,4 +225,4 @@ websocket-client==1.9.0
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werkzeug==3.1.8
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wsproto==1.3.2
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yarl==1.23.0
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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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@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
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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==0.15.10
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ruff==0.15.11
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@@ -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
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adal==1.2.7
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ag-ui-protocol==0.1.15
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ag-ui-protocol==0.1.16
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aiobotocore==3.4.0
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aiofile==3.9.0
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aiofiles==25.1.0
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@@ -14,7 +14,7 @@ alembic==1.18.4
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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
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anthropic==0.94.0
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anthropic==0.96.0
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anyio==4.13.0
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apispec==6.10.0
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appdirs==1.4.4
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@@ -32,7 +32,7 @@ bdbag==1.8.0
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beaker==1.13.0
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beartype==0.22.9
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billiard==4.2.4
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bioblend==1.8.0
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bioblend==1.9.0
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bleach==6.3.0
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boltons==25.0.0
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boto==2.49.0
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@@ -53,7 +53,7 @@ click-plugins==1.1.1.2
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click-repl==0.3.0
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cloudauthz==0.6.0
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cloudbridge==3.2.0
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cohere==6.1.0 ; sys_platform != 'emscripten'
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cohere==5.21.1 ; sys_platform != 'emscripten'
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colorama==0.4.6 ; sys_platform == 'win32'
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coloredlogs==15.0.1
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conda-package-streaming==0.12.0
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@@ -61,7 +61,7 @@ cryptography==46.0.7
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ct3==3.4.0.post5
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cwl-upgrader==1.2.15
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cwl-utils==0.41
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cwltool==3.1.20260315121657
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cwltool==3.2.20260413085819
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cyclopts==4.10.2
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defusedxml==0.7.1
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deprecated==1.3.1
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@@ -70,7 +70,7 @@ dictobj==0.4
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distro==1.9.0
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dnspython==2.8.0
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docopt==0.6.2
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docstring-parser==0.17.0
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docstring-parser==0.18.0
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docutils==0.21.2 ; python_full_version < '3.11'
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docutils==0.22.4 ; python_full_version >= '3.11'
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dparse==0.6.4
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@@ -80,10 +80,10 @@ et-xmlfile==2.0.0
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eval-type-backport==0.3.1
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exceptiongroup==1.3.1
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executing==2.2.1
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fastapi==0.135.3
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fastapi==0.136.0
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fastavro==1.12.1 ; sys_platform != 'emscripten'
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fastmcp==3.2.3
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filelock==3.25.2
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fastmcp==3.2.4
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filelock==3.28.0
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fissix==24.4.24
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frozenlist==1.8.0
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fs==2.4.16
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@@ -93,7 +93,7 @@ genai-prices==0.0.56
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google-api-core==2.30.3
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google-auth==2.49.2
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google-cloud-batch==0.21.0
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google-genai==1.72.0
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google-genai==1.73.1
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googleapis-common-protos==1.74.0
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gravity==1.2.1
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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'
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@@ -104,18 +104,18 @@ grpcio-status==1.80.0
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gunicorn==25.3.0
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gxformat2==0.24.0
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h11==0.16.0
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h5grove==3.0.0
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h5grove==4.0.0
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h5py==3.16.0
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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'
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httpcore==1.0.9
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httpx==0.28.1
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httpx-sse==0.4.3
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huggingface-hub==1.10.1
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huggingface-hub==1.11.0
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humanfriendly==10.0
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idna==3.11
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ijson==3.5.0
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importlib-metadata==8.7.1
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importlib-resources==6.5.2 ; python_full_version < '3.12'
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importlib-resources==7.1.0 ; python_full_version < '3.12'
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invoke==3.0.3
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isa-rwval==0.10.11
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isal==1.8.0
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@@ -137,9 +137,9 @@ kombu==5.6.2
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lagom==2.7.7
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legacy-cgi==2.6.4 ; python_full_version >= '3.13'
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limits==5.8.0
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logfire==4.32.0
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logfire-api==4.32.0
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lxml==6.0.3
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logfire==4.32.1
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logfire-api==4.32.1
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lxml==6.0.4
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mako==1.3.11
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markdown==3.10.2
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markdown-it-py==3.0.0 ; python_full_version < '3.11'
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@@ -148,7 +148,7 @@ markupsafe==3.0.3
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mcp==1.27.0
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mdurl==0.1.2
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mercurial==7.2.1
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mistralai==2.3.2
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mistralai==2.4.0
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mistune==3.2.0
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more-itertools==11.0.2
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mrcfile==1.5.4
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@@ -164,7 +164,7 @@ nodejs-wheel-binaries==22.20.0
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numpy==2.2.6 ; python_full_version < '3.11'
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numpy==2.4.4 ; python_full_version >= '3.11'
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oauthlib==3.3.1
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openai==2.31.0
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openai==2.32.0
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openapi-pydantic==0.5.1
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openpyxl==3.1.5
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opentelemetry-api==1.39.1
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@@ -198,12 +198,12 @@ pyasn1==0.6.3
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pyasn1-modules==0.4.2
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pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
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pycryptodome==3.23.0
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pydantic==2.12.5
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pydantic-ai==1.80.0
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pydantic-ai-slim==1.80.0
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pydantic-core==2.41.5
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pydantic-evals==1.80.0
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pydantic-graph==1.80.0
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pydantic==2.13.2
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pydantic-ai==1.84.1
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pydantic-ai-slim==1.84.1
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pydantic-core==2.46.2
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pydantic-evals==1.84.1
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pydantic-graph==1.84.1
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pydantic-handlebars==0.1.0
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pydantic-settings==2.13.1
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pydantic-tes==0.4.0
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@@ -250,7 +250,7 @@ rpds-py==0.30.0
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ruamel-yaml==0.19.1
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s3fs==2026.3.0
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s3transfer==0.16.0
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schema-salad==8.9.20260327095315
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schema-salad==8.9.20260417192335
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secretstorage==3.5.0 ; sys_platform == 'linux'
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setuptools==81.0.0
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shellingham==1.5.4
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@@ -267,11 +267,12 @@ starlette==1.0.0
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starlette-context==0.5.1
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supervisor==4.3.0
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svgwrite==1.4.3
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temporalio==1.25.0
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temporalio==1.26.0
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tenacity==9.1.4
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text-unidecode==1.3
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tifffile==2025.5.10 ; python_full_version < '3.11'
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tifffile==2026.3.3 ; python_full_version >= '3.11'
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tifffile==2026.3.3 ; python_full_version == '3.11.*'
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tifffile==2026.4.11 ; python_full_version >= '3.12'
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tiktoken==0.12.0
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tinydb==4.8.2
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tokenizers==0.22.2 ; sys_platform != 'emscripten'
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@@ -303,6 +304,6 @@ wrapt==1.17.3
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xai-sdk==1.11.0
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yacman==1.0.0
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yarl==1.23.0
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zipp==3.23.0
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zipp==3.23.1
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zipstream-new==1.1.8
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zstandard==0.25.0
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@@ -3,6 +3,7 @@
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aiohappyeyeballs==2.6.1
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aiohttp==3.13.5
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aiosignal==1.4.0
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annotated-types==0.7.0
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ase==3.28.0
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async-timeout==5.0.1 ; python_full_version < '3.11'
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attrs==26.1.0
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@@ -30,7 +31,7 @@ defusedxml==0.7.1
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dogpile-cache==1.5.0
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enum-tools==0.12.0
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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
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fluent-logger==0.11.1
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fonttools==4.62.1
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frozenlist==1.8.0
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@@ -66,7 +67,7 @@ jsonschema-specifications==2025.9.1
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junit-xml==1.9
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kiwisolver==1.5.0
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librt==0.9.0 ; platform_python_implementation != 'PyPy'
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lxml==6.0.3
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lxml==6.0.4
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markdown-it-py==3.0.0 ; python_full_version < '3.11'
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markdown-it-py==4.0.0 ; python_full_version >= '3.11'
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markupsafe==3.0.3
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@@ -76,7 +77,7 @@ mirakuru==3.0.2
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mistune==3.2.0
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msgpack==1.1.2
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multidict==6.7.1
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mypy==1.20.0
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mypy==1.20.1
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mypy-extensions==1.1.0
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numpy==2.2.6 ; python_full_version < '3.11'
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numpy==2.4.4 ; python_full_version >= '3.11'
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@@ -103,6 +104,8 @@ psycopg==3.3.3
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pyasn1==0.6.3
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pyasn1-modules==0.4.2
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pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
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pydantic==2.13.2
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pydantic-core==2.46.2
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pyee==13.0.1
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pygments==2.20.0
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pyparsing==3.3.2
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@@ -138,7 +141,7 @@ rpds-py==0.30.0
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ruamel-yaml==0.19.1
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rucio-clients==39.4.1
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s3transfer==0.16.0
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schema-salad==8.9.20260327095315
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schema-salad==8.9.20260417192335
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scipy==1.15.3 ; python_full_version < '3.11'
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scipy==1.17.1 ; python_full_version >= '3.11'
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selenium==4.43.0
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@@ -162,7 +165,8 @@ tuspy==1.1.0
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types-cachetools==6.2.0.20260408
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types-requests==2.33.0.20260408
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typing-extensions==4.15.0
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typos==1.45.0
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typing-inspection==0.4.2
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typos==1.45.1
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tzdata==2026.1 ; sys_platform == 'win32'
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url-normalize==2.2.1
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urllib3==2.6.3
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@@ -172,4 +176,4 @@ websocket-client==1.9.0
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werkzeug==3.1.8
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wsproto==1.3.2
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yarl==1.23.0
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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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@@ -1,19 +1,19 @@
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# This file was autogenerated by uv via the following command:
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# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
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annotated-types==0.7.0
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boto3-stubs==1.42.88
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boto3-stubs==1.42.91
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botocore-stubs==1.42.41
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cffi==2.0.0 ; platform_python_implementation != 'PyPy'
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cryptography==46.0.7
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librt==0.9.0 ; platform_python_implementation != 'PyPy'
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lxml-stubs==0.5.1
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mypy==1.20.0
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mypy==1.20.1
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mypy-boto3-s3==1.42.85
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mypy-extensions==1.1.0
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pathspec==1.0.4
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pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
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pydantic==2.12.5
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||||
pydantic-core==2.41.5
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pydantic==2.13.2
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||||
pydantic-core==2.46.2
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tomli==2.4.1 ; python_full_version < '3.11'
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types-awscrt==0.31.3
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||||
types-bleach==6.3.0.20260408
|
||||
|
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