diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 83136fcb7b9e..a17ee92c9b08 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -334,7 +334,6 @@ def regenerate_primary_file(self, dataset: DatasetProtocol) -> None:
         ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            f, e = os.path.splitext(fname)
             rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append("</ul></body></html>")
         with open(dataset.get_file_name(), "w") as f:
diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py
index c3728ef6b4ea..8e27fde546bf 100644
--- a/lib/galaxy/datatypes/spaln.py
+++ b/lib/galaxy/datatypes/spaln.py
@@ -91,7 +91,6 @@ def regenerate_primary_file(self, dataset: DatasetProtocol) -> None:
         ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            f, e = os.path.splitext(fname)
             rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append("</ul></body></html>")
         with open(dataset.get_file_name(), "w") as f:
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 37cfc753bfd8..1b1fcdde3007 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,3 +1,5 @@
+--extra-index-url https://wheels.galaxyproject.org/simple
+
 aiohttp==3.9.5 ; 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"
@@ -10,8 +12,8 @@ babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
-boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
+boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,8 +22,9 @@ charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
-contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
+contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9"
+contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
+coverage[toml]==7.5.4 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -33,7 +36,7 @@ deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
+filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
 fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -45,7 +48,7 @@ httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
 httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
 importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
 iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -61,7 +64,7 @@ jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
 keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
-lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
+lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -71,29 +74,29 @@ mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
+more-itertools==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
-pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
+pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
+pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
+playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.1.19 ; 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"
+psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -111,7 +114,7 @@ pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13"
 pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-postgresql==6.0.0 ; 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"
@@ -126,21 +129,22 @@ readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.25.2 ; python_version >= "3.8" and python_version < "3.13"
+responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; 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==34.4.2 ; python_version >= "3.9" and python_version < "3.13"
-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
+rucio-clients==34.5.0 ; python_version >= "3.9" and python_version < "3.13"
+s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; 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 < "3.13"
+scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
+scipy==1.14.0 ; 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==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.2.0 ; 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"
@@ -165,14 +169,15 @@ tomli==2.0.1 ; 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==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
-twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
+twill==3.2.5 ; 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==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
+urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
+urllib3[socks]==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
 watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
+websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
 werkzeug==3.0.3 ; 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"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 9cd22f68931b..3df072eefc30 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,7 @@
 attrs==23.2.0
-flake8==7.0.0
+flake8==7.1.0
 flake8-bugbear==24.4.26
 mccabe==0.7.0
-pycodestyle==2.11.1
+pycodestyle==2.12.0
 pyflakes==3.2.0
-ruff==0.4.8
+ruff==0.5.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index afe0a5f04880..a0b6b7e68228 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -1,14 +1,14 @@
 --extra-index-url https://wheels.galaxyproject.org/simple
 
-a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
+a2wsgi==1.10.6 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.13.1 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
-aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
+aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
 aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
 aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
+alembic==1.13.2 ; 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"
@@ -16,7 +16,7 @@ anyio==4.4.0 ; 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"
-argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
+argcomplete==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -33,8 +33,8 @@ bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
+bx-python==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -55,7 +55,6 @@ cryptography==42.0.8 ; 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==0.33 ; python_version >= "3.8" and python_version < "3.13"
 cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
-decorator==5.1.1 ; 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"
 dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -64,13 +63,13 @@ docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 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==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
+email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
 fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
+filelock==3.15.4 ; 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==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
+fsspec==2024.6.1 ; python_version >= "3.8" and python_version < "3.13"
 future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -79,7 +78,7 @@ graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"
 graphql-core==3.2.3 ; 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 >= "3.8" and 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")
+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"
 gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
 gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -87,9 +86,9 @@ h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
 importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
-isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
+isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13"
 isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -99,7 +98,7 @@ jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_versio
 jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13"
 lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
-lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
+lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13"
 mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
@@ -108,35 +107,35 @@ mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
+msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
+networkx==3.1 ; python_version >= "3.8" and python_version < "3.13"
 nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
-orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13"
+orjson==3.10.6 ; python_version >= "3.8" and python_version < "3.13"
 oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
 paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
-pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
+pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
-prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13"
+prompt-toolkit==3.0.47 ; python_version >= "3.8" and python_version < "3.13"
 prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
+psutil==6.0.0 ; 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==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic[email]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -171,17 +170,17 @@ routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; 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==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
+s3fs==2024.6.1 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; 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"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.31 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
@@ -189,7 +188,7 @@ starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette==0.37.2 ; 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==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
+tenacity==8.4.2 ; python_version >= "3.8" and python_version < "3.13"
 tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
@@ -201,7 +200,7 @@ typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; 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==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
+urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
 uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13"
 uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 4ea5a1375235..f37b1b56f55d 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,17 +1,19 @@
+--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]==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 cryptography==42.0.8 ; 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==1.34.120 ; python_version >= "3.8" and python_version < "3.13"
+mypy-boto3-s3==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
+mypy==1.10.1 ; 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==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13"
+types-awscrt==0.20.12 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
index 6bb140e8f078..c7eee2328ad7 100755
--- a/lib/galaxy/dependencies/update.sh
+++ b/lib/galaxy/dependencies/update.sh
@@ -89,6 +89,7 @@ split_requirement () {
 # supported by Galaxy, so Poetry resorts to an old version. Here we replace any
 # such requirement with multiple Python-version-specific requirements.
 # Packages which specify a maximum Python version pin:
+split_requirement contourpy
 split_requirement matplotlib
 split_requirement numpy
 split_requirement scipy
diff --git a/lib/galaxy/tool_util/verify/asserts/hdf5.py b/lib/galaxy/tool_util/verify/asserts/hdf5.py
index e94c61c3af04..ddbbcdd35cda 100644
--- a/lib/galaxy/tool_util/verify/asserts/hdf5.py
+++ b/lib/galaxy/tool_util/verify/asserts/hdf5.py
@@ -21,7 +21,7 @@ def assert_has_h5_attribute(output_bytes: bytes, key: str, value: str) -> None:
     local_attrs = h5py.File(output_temp, "r").attrs
     assert (
         key in local_attrs and str(local_attrs[key]) == value
-    ), f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})"
+    ), f"Not a HDF5 file or H5 attributes do not match:\n\t{[(key, str(value)) for key, value in local_attrs.items()]}\n\n\t({key} : {value})"
 
 
 # TODO the function actually queries groups. so the function and argument name are misleading
diff --git a/lib/galaxy/web_stack/message.py b/lib/galaxy/web_stack/message.py
index f7ef7f7d2ddf..15259b4cc50e 100644
--- a/lib/galaxy/web_stack/message.py
+++ b/lib/galaxy/web_stack/message.py
@@ -68,7 +68,9 @@ def _merge_class_tuples(self):
         names = set()
         for cls in reversed(self.__class__.mro()):
             names.update(
-                [x for x in dir(cls) if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple]
+                x
+                for x in dir(cls)
+                if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple  # noqa: E721
             )
         for name in names:
             setattr(self.__class__, name.lstrip("_"), property(lambda self, name=name: self._get_list_from_mro(name)))
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index a23240d0423a..c48c3d1825bc 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -45,7 +45,7 @@ install_requires =
     galaxy-sequence-utils
     h5grove>=1.2.1
     h5py
-    isa-rwval>=0.10.10
+    isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master
     isal
     MarkupSafe
     msal
diff --git a/pyproject.toml b/pyproject.toml
index 072f79f002e1..56147a86ef77 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,7 +70,7 @@ gxformat2 = "*"
 h5grove = ">=1.2.1"
 h5py = "*"
 importlib-resources = { version = "*", python = "<3.9" }  # for importlib.{abc.Traversable,resources.{files, Package}}
-isa-rwval = ">=0.10.10"
+isa-rwval = { git = "https://github.com/nsoranzo/isa-rwval.git", branch = "master" }  # https://github.com/ISA-tools/isa-rwval/pull/17
 jinja2 = "*"
 kombu = ">=5.3"  # for importlib-metadata fix
 isal = "*"
diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index a30410dd0207..80dd3789ef1b 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -1215,7 +1215,6 @@ def import_archive(archive_path, app, user, import_options=None):
     dest_dir = CompressedFile(archive_path).extract(dest_parent)
 
     import_options = import_options or store.ImportOptions()
-    new_history = None
     model_store = store.get_import_model_store_for_directory(
         dest_dir,
         app=app,
diff --git a/test/unit/tool_util/verify/test_asserts.py b/test/unit/tool_util/verify/test_asserts.py
index a7f419fa4a32..af357871ccad 100644
--- a/test/unit/tool_util/verify/test_asserts.py
+++ b/test/unit/tool_util/verify/test_asserts.py
@@ -1315,7 +1315,7 @@ def test_has_h5_attribute_failure():
         """test has_attribute .. negative"""
         a = run_assertions(H5_HAS_ATTRIBUTE_NEGATIVE, H5BYTES)
         assert (
-            "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', 1)]\n\n\t(myfileattr : wrong)"
+            "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', '1')]\n\n\t(myfileattr : wrong)"
             in a
         )
         assert len(a) == 1