diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 0b87fe9c6a7..9e988283019 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -19,7 +19,7 @@ build==1.3.0
 cachecontrol==0.14.3
 cattrs==25.2.0
 certifi==2025.8.3
-cffi==1.17.1
+cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.3
 click==8.1.8 ; python_full_version < '3.10'
 click==8.2.1 ; python_full_version >= '3.10'
@@ -38,7 +38,7 @@ darkgraylib==2.4.0
 decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2
-dogpile-cache==1.4.0
+dogpile-cache==1.4.1
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.19.1
@@ -70,12 +70,12 @@ jmespath==1.0.1
 jsonpatch==1.33
 jsonpointer==3.0.0
 jsonschema==4.25.1
-jsonschema-specifications==2025.4.1
+jsonschema-specifications==2025.9.1
 junit-xml==1.9
 keyring==25.6.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.9 ; python_full_version >= '3.10'
-lxml==5.4.0
+lxml==6.0.1
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
 markupsafe==3.0.2
@@ -95,7 +95,7 @@ myst-parser==4.0.1 ; python_full_version >= '3.10'
 nh3==0.3.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.2 ; python_full_version >= '3.11'
+numpy==2.3.3 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
@@ -114,13 +114,13 @@ prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
 psutil==7.0.0 ; sys_platform != 'cygwin'
-psycopg==3.2.9
-pycparser==2.22
+psycopg==3.2.10
+pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
 pyee==13.0.0
 pygithub==2.8.1
 pygments==2.19.2
 pyjwt==2.10.1
-pynacl==1.5.0
+pynacl==1.6.0
 pyparsing==3.2.3
 pyproject-hooks==1.2.0
 pyshacl==0.26.0 ; python_full_version < '3.10'
@@ -129,13 +129,13 @@ pysocks==1.7.1
 pytest==7.4.4
 pytest-asyncio==0.23.8
 pytest-base-url==2.1.0
-pytest-cov==6.2.1
+pytest-cov==7.0.0
 pytest-html==4.1.1
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.15.0
-pytest-playwright==0.7.0
+pytest-playwright==0.7.1
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
@@ -165,9 +165,11 @@ s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.1 ; python_full_version >= '3.11'
-secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-selenium==4.32.0
+scipy==1.16.2 ; python_full_version >= '3.11'
+secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
+secretstorage==3.4.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
+selenium==4.32.0 ; python_full_version < '3.10'
+selenium==4.35.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -196,9 +198,9 @@ tomli==2.2.1 ; python_full_version <= '3.11'
 trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
-twill==3.3
+twill==3.3.1
 twine==6.2.0
-typing-extensions==4.15.0
+typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; python_full_version < '3.10'
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index f39f4467407..e04f311a57f 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.12.12
+ruff==0.13.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 253065586f2..5b1b7b6ea55 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -12,7 +12,7 @@ alembic==1.16.5
 amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.10.0
-apispec==6.8.2
+apispec==6.8.3
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.6.2
@@ -36,7 +36,7 @@ cachecontrol==0.14.3
 cachetools==5.5.2
 celery==5.5.3
 certifi==2025.8.3
-cffi==1.17.1
+cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.3
 circus==0.19.0
 click==8.1.8 ; python_full_version < '3.10'
@@ -52,13 +52,14 @@ conda-package-streaming==0.12.0
 cryptography==45.0.7
 ct3==3.4.0
 cwl-upgrader==1.2.12
-cwl-utils==0.39
+cwl-utils==0.40
 cwltool==3.1.20250715140722
 defusedxml==0.7.1
 deprecated==1.2.18
 deprecation==2.1.0
 dictobj==0.4
-dnspython==2.7.0
+dnspython==2.7.0 ; python_full_version < '3.10'
+dnspython==2.8.0 ; python_full_version >= '3.10'
 docopt==0.6.2
 docutils==0.21.2
 dparse==0.6.4
@@ -94,25 +95,25 @@ importlib-metadata==8.7.0 ; python_full_version < '3.10'
 importlib-resources==6.5.2 ; python_full_version < '3.12'
 invoke==2.2.0
 isa-rwval==0.10.11
-isal==1.7.2
+isal==1.8.0
 isodate==0.7.2 ; python_full_version < '3.11'
 jinja2==3.1.6
 jmespath==1.0.1
 jsonref==1.1.0
 jsonschema==4.25.1
-jsonschema-specifications==2025.4.1
+jsonschema-specifications==2025.9.1
 kombu==5.5.4
 lagom==2.7.7
 legacy-cgi==2.6.3 ; python_full_version >= '3.13'
 limits==4.2 ; python_full_version < '3.10'
 limits==5.5.0 ; python_full_version >= '3.10'
-lxml==5.4.0
+lxml==6.0.1
 mako==1.3.10
 markdown==3.9
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 mdurl==0.1.2
-mercurial==7.1
+mercurial==7.1.1
 mistune==3.0.2
 mrcfile==1.5.4
 msal==1.33.0
@@ -125,7 +126,7 @@ networkx==3.5 ; python_full_version >= '3.11'
 nodeenv==1.9.1
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.2 ; python_full_version >= '3.11'
+numpy==2.3.3 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 openpyxl==3.1.5
 orjson==3.11.3
@@ -141,15 +142,15 @@ pillow==11.3.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
 proto-plus==1.26.1
-protobuf==6.32.0
+protobuf==6.32.1
 prov==1.5.1
 psutil==7.0.0
 pulsar-galaxy-lib==0.15.10
 pyasn1==0.6.1
 pyasn1-modules==0.4.2
-pycparser==2.22
+pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
-pydantic==2.11.7
+pydantic==2.11.8
 pydantic-core==2.33.2
 pydantic-tes==0.2.0
 pydot==4.0.1
@@ -159,7 +160,7 @@ pygments==2.19.2
 pyjwt==2.10.1
 pykwalify==1.8.0
 pylibmagic==0.5.0
-pynacl==1.5.0
+pynacl==1.6.0
 pyparsing==3.2.3
 pypng==0.20220715.0
 pyreadline3==3.5.4 ; sys_platform == 'win32'
@@ -171,7 +172,7 @@ python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2025.2
 pyyaml==6.0.2
-pyzmq==27.0.2
+pyzmq==27.1.0
 rdflib==7.1.4
 referencing==0.36.2
 refgenconf==0.12.2
@@ -209,14 +210,14 @@ tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2024.8.30 ; python_full_version < '3.10'
 tifffile==2025.5.10 ; python_full_version == '3.10.*'
-tifffile==2025.8.28 ; python_full_version >= '3.11'
+tifffile==2025.9.9 ; python_full_version >= '3.11'
 tinydb==4.8.2
 tomli==2.2.1 ; python_full_version < '3.11'
 tornado==6.5.2
 tqdm==4.67.1
 tuspy==1.1.0
 tuswsgi==0.5.5
-typing-extensions==4.15.0
+typing-extensions==4.14.1
 typing-inspection==0.4.1
 tzdata==2025.2
 tzlocal==5.3.1
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index 913a2c8742b..840f9b92865 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -13,7 +13,7 @@ botocore==1.40.18
 cachecontrol==0.14.3
 cattrs==25.2.0
 certifi==2025.8.3
-cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
+cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt'
 charset-normalizer==3.4.3
 click==8.1.8 ; python_full_version < '3.10'
 click==8.2.1 ; python_full_version >= '3.10'
@@ -27,7 +27,7 @@ cwltest==2.6.20250818005349
 cycler==0.12.1
 decorator==5.2.1
 defusedxml==0.7.1
-dogpile-cache==1.4.0
+dogpile-cache==1.4.1
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.19.1
@@ -51,11 +51,11 @@ jmespath==1.0.1
 jsonpatch==1.33
 jsonpointer==3.0.0
 jsonschema==4.25.1
-jsonschema-specifications==2025.4.1
+jsonschema-specifications==2025.9.1
 junit-xml==1.9
 kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.9 ; python_full_version >= '3.10'
-lxml==5.4.0
+lxml==6.0.1
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 matplotlib==3.9.4 ; python_full_version < '3.10'
@@ -68,7 +68,7 @@ multidict==6.6.4
 mypy-extensions==1.1.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.2 ; python_full_version >= '3.11'
+numpy==2.3.3 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
@@ -86,8 +86,8 @@ prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
 psutil==7.0.0 ; sys_platform != 'cygwin'
-psycopg==3.2.9
-pycparser==2.22 ; implementation_name != 'pypy' and os_name == 'nt'
+psycopg==3.2.10
+pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt'
 pyee==13.0.0
 pygments==2.19.2
 pyparsing==3.2.3
@@ -97,13 +97,13 @@ pysocks==1.7.1
 pytest==7.4.4
 pytest-asyncio==0.23.8
 pytest-base-url==2.1.0
-pytest-cov==6.2.1
+pytest-cov==7.0.0
 pytest-html==4.1.1
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.15.0
-pytest-playwright==0.7.0
+pytest-playwright==0.7.1
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
@@ -128,8 +128,9 @@ s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.1 ; python_full_version >= '3.11'
-selenium==4.32.0
+scipy==1.16.2 ; python_full_version >= '3.11'
+selenium==4.32.0 ; python_full_version < '3.10'
+selenium==4.35.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -146,8 +147,8 @@ tomli==2.2.1 ; python_full_version <= '3.11'
 trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
-twill==3.3
-typing-extensions==4.15.0
+twill==3.3.1
+typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; python_full_version < '3.10'
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 84b9e7d0368..fbf9c9c809d 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,17 +1,17 @@
 # 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==1.40.25
-botocore-stubs==1.40.25
-cffi==1.17.1 ; platform_python_implementation != 'PyPy'
+boto3-stubs==1.40.30
+botocore-stubs==1.40.30
+cffi==2.0.0 ; platform_python_implementation != 'PyPy'
 cryptography==45.0.7
 lxml-stubs==0.5.1
-mypy==1.17.1
-mypy-boto3-s3==1.40.0
+mypy==1.18.1
+mypy-boto3-s3==1.40.26
 mypy-extensions==1.1.0
 pathspec==0.12.1
-pycparser==2.22 ; platform_python_implementation != 'PyPy'
-pydantic==2.11.7
+pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
+pydantic==2.11.8
 pydantic-core==2.33.2
 tomli==2.2.1 ; python_full_version < '3.11'
 types-awscrt==0.27.6
@@ -27,11 +27,11 @@ types-python-dateutil==2.9.0.20250822
 types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20250822
 types-requests==2.31.0.6 ; python_full_version < '3.10'
-types-requests==2.32.4.20250809 ; python_full_version >= '3.10'
+types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
 types-s3transfer==0.13.1
 types-setuptools==80.9.0.20250822
 types-six==1.17.0.20250515
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
-typing-extensions==4.15.0
+typing-extensions==4.14.1
 typing-inspection==0.4.1
 urllib3==2.5.0 ; python_full_version >= '3.10'