diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index e6a381a64da3..0c94373a5f98 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -517,7 +517,7 @@ def resolve(key):
         for key in self.schema.paths_to_resolve:
             value = getattr(self, key)
             # Check if value is a list or should be listified; if so, listify and resolve each item separately.
-            if type(value) is list or (self.listify_options and key in self.listify_options):
+            if isinstance(value, list) or (self.listify_options and key in self.listify_options):
                 saved_values = listify(getattr(self, key), do_strip=True)  # listify and save original value
                 setattr(self, key, "_")  # replace value with temporary placeholder
                 resolve(key)  # resolve temporary value (`_` becomes `parent-path/_`)
@@ -546,7 +546,7 @@ def get_path(current_path, initial_path):
             return current_path
 
         current_value = getattr(self, key)  # resolved path or list of resolved paths
-        if type(current_value) is list:
+        if isinstance(current_value, list):
             initial_paths = listify(self._raw_config[key], do_strip=True)  # initial unresolved paths
             updated_paths = []
             # check and, if needed, update each path in the list
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 1d5dd3f2073c..2ef5e06b919b 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -12,7 +12,7 @@ babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12"
 billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12"
 black==23.3.0 ; python_version >= "3.7" and python_version < "3.12"
 bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12"
-build==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
+build==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12"
 cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
@@ -22,24 +22,24 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.7 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
-cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
+cwltest==2.3.20230825125225 ; python_version >= "3.7" and python_version < "3.12"
 cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
-exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.12"
+exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.12"
 filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
 fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
-galaxy-release-util==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
+galaxy-release-util==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
 httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12"
 httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -55,14 +55,15 @@ jeepney==0.8.0 ; python_version >= "3.7" and python_version < "3.12" and sys_pla
 jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
 junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12"
 keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.12"
-kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
+kiwisolver==1.4.5 ; python_version >= "3.7" and python_version < "3.12"
 kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
 lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8"
-matplotlib==3.7.2 ; python_version >= "3.8" and python_version < "3.12"
+matplotlib==3.7.3 ; python_version >= "3.8" and python_version < "3.9"
+matplotlib==3.8.0 ; python_version >= "3.9" and python_version < "3.12"
 mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 mirakuru==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -74,7 +75,7 @@ mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12"
+numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -106,10 +107,10 @@ pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
-pytest==7.4.0 ; python_version >= "3.7" and python_version < "3.12"
+pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12"
 python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
 python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
-pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
+pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
 pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32"
 pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -118,13 +119,13 @@ requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
 responses==0.23.3 ; python_version >= "3.7" and python_version < "3.12"
 rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
-rich==13.5.2 ; python_version >= "3.7" and python_version < "3.12"
+rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12"
 ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
 ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
 schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12"
 scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.11.1 ; python_version >= "3.9" and python_version < "3.12"
+scipy==1.11.2 ; python_version >= "3.9" and python_version < "3.12"
 secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
 selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.12"
 seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -133,7 +134,7 @@ six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
 sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12"
-sphinx-rtd-theme==1.2.2 ; python_version >= "3.7" and python_version < "3.12"
+sphinx-rtd-theme==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12"
 sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
 sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -143,11 +144,11 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.12
 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12"
-testfixtures==7.1.0 ; python_version >= "3.7" and python_version < "3.12"
+testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.12"
 tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
 toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12"
-tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
-trio-websocket==0.10.3 ; python_version >= "3.7" and python_version < "3.12"
+tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6"
+trio-websocket==0.10.4 ; python_version >= "3.7" and python_version < "3.12"
 trio==0.22.2 ; python_version >= "3.7" and python_version < "3.12"
 tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
 twill==3.1 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index cc18b68332c8..e60af3721d60 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.284
+ruff==0.0.290
 typing_extensions==4.7.1
 zipp==3.15.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 7d05a3f82cb2..af8f7fb5a32f 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -1,5 +1,3 @@
---extra-index-url https://wheels.galaxyproject.org/simple
-
 a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12"
 adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12"
 aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -7,13 +5,13 @@ aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12"
 aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
 aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
-alembic==1.11.2 ; python_version >= "3.7" and python_version < "3.12"
+alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
 anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
 apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
 appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
 arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
-argcomplete==3.1.1 ; python_version >= "3.7" and python_version < "3.12"
+argcomplete==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
 async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12"
 asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
 attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -43,17 +41,17 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.7 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
-cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+cloudbridge==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
 conda-package-streaming==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
 cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
 cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
 cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
-cython==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
+cython==3.0.2 ; python_version >= "3.7" and python_version < "3.12"
 decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -65,7 +63,7 @@ dparse==0.6.3 ; python_version >= "3.7" and python_version < "3.12"
 ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12"
-exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.11"
+exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
 fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.12"
 filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -76,7 +74,7 @@ future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
 gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
-greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64") and python_version < "3.12"
+greenlet==2.0.2 ; python_version >= "3.7" 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 < "3.12"
 gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12"
 gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -100,10 +98,10 @@ markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown==3.4.4 ; python_version >= "3.7" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
-mercurial==6.5.1 ; python_version >= "3.7" and python_version < "3.12"
+mercurial==6.5.2 ; python_version >= "3.7" and python_version < "3.12"
 mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12"
 mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
-msal==1.23.0 ; python_version >= "3.7" and python_version < "3.12"
+msal==1.24.0 ; python_version >= "3.7" and python_version < "3.12"
 msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12"
 multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12"
 mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -111,9 +109,9 @@ networkx==2.5 ; python_version >= "3.7" and python_version < "3.12"
 nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12"
+numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
-orjson==3.9.4 ; python_version >= "3.7" and python_version < "3.12"
+orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -125,10 +123,10 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
 prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
 prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12"
-pulsar-galaxy-lib==0.15.3 ; python_version >= "3.7" and python_version < "3.12"
+pulsar-galaxy-lib==0.15.5 ; python_version >= "3.7" and python_version < "3.12"
 pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
-pycryptodome==3.18.0 ; python_version >= "3.7" and python_version < "3.12"
+pycryptodome==3.19.0 ; python_version >= "3.7" and python_version < "3.12"
 pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
 pydantic==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
 pydantic[email]==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
@@ -151,7 +149,7 @@ python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
 python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12"
 python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12"
 python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
-pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
+pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
 pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
 pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -162,7 +160,7 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
-rich==13.5.2 ; python_version >= "3.7" and python_version < "3.12"
+rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12"
 rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12"
 routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
 rsa==4.9 ; python_version >= "3.7" and python_version < "3.12"
@@ -184,9 +182,10 @@ starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
 starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12"
 supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
-tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12"
+tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.12"
 tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12"
 tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
+tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
 tornado==6.2 ; python_version >= "3.7" and python_version < "3.12"
 tqdm==4.66.1 ; python_version >= "3.7" and python_version < "3.12"
 tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index ea39387ec32a..5237b18bd7dd 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,22 +1,22 @@
-cffi==1.15.1
-cryptography==41.0.3
-mypy==1.4.1
-mypy-extensions==1.0.0
-pycparser==2.21
-pydantic==1.10.12
-tomli==2.0.1
-typed-ast==1.5.5
-types-bleach==6.0.0.4
-types-boto==2.49.18.9
-types-contextvars==2.4.7.3
-types-dataclasses==0.6.6
-types-docutils==0.20.0.1
-types-Markdown==3.4.2.10
-types-paramiko==3.3.0.0
-types-pkg-resources==0.1.3
-types-python-dateutil==2.8.19.14
-types-PyYAML==6.0.12.11
-types-requests==2.31.0.2
-types-six==1.16.21.9
-types-urllib3==1.26.25.14
-typing_extensions==4.7.1
+cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
+mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
+mypy==1.4.1 ; python_version >= "3.7" and python_version < "3.12"
+pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
+pydantic==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
+tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
+typed-ast==1.5.5 ; python_version >= "3.7" and python_version < "3.8"
+types-bleach==6.0.0.4 ; python_version >= "3.7" and python_version < "3.12"
+types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.12"
+types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.12"
+types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.12"
+types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.12"
+types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.12"
+types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.12"
+types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.12"
+types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.12"
+types-pyyaml==6.0.12.11 ; python_version >= "3.7" and python_version < "3.12"
+types-requests==2.31.0.2 ; python_version >= "3.7" and python_version < "3.12"
+types-six==1.16.21.9 ; python_version >= "3.7" and python_version < "3.12"
+types-urllib3==1.26.25.14 ; python_version >= "3.7" and python_version < "3.12"
+typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 59d6d74fd603..aebe134af744 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -903,24 +903,24 @@ def get_job_runner_plugins(self, handler_id):
         return rval
 
     def is_id(self, collection):
-        """Given a collection of handlers or destinations, indicate whether the collection represents a tag or a real ID
+        """Given a collection of handlers or destinations, indicate whether the collection represents a real ID
 
         :param collection: A representation of a destination or handler
         :type collection: tuple or list
 
         :returns: bool
         """
-        return type(collection) == tuple
+        return isinstance(collection, tuple)
 
     def is_tag(self, collection):
-        """Given a collection of handlers or destinations, indicate whether the collection represents a tag or a real ID
+        """Given a collection of handlers or destinations, indicate whether the collection represents a tag
 
         :param collection: A representation of a destination or handler
         :type collection: tuple or list
 
         :returns: bool
         """
-        return type(collection) == list
+        return isinstance(collection, list)
 
     def convert_legacy_destinations(self, job_runners):
         """Converts legacy (from a URL) destinations to contain the appropriate runner params defined in the URL.
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 71764955fa4d..398e53abaabc 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -2028,7 +2028,7 @@ def assert_success_message(self, contains=None):
 
     def assert_message(self, element, contains=None):
         if contains is not None:
-            if type(element) == list:
+            if isinstance(element, list):
                 assert any(
                     contains in el.text for el in element
                 ), f"{contains} was not found in {[el.text for el in element]}"
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index 14e4861a9ad8..391b9b4a5ee1 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -55,7 +55,7 @@ def persist_uploads(params, trans):
                 local_filename = util.mkstemp_ln(f.file.name, "upload_file_data_")
                 f.file.close()
                 upload_dataset["file_data"] = dict(filename=f.filename, local_filename=local_filename)
-            elif type(f) == dict and "local_filename" not in f:
+            elif isinstance(f, dict) and "local_filename" not in f:
                 raise Exception("Uploaded file was encoded in a way not understood by Galaxy.")
             if (
                 "url_paste" in upload_dataset
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 6e16f7fc597c..a4cc61d5f66c 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -659,7 +659,7 @@ def from_json(self, value, trans=None, other_values=None):
         if isinstance(value, FilesPayload):
             # multi-part upload handled and persisted in service layer
             return value.dict()
-        if type(value) == dict:
+        elif isinstance(value, dict):
             if "session_id" in value:
                 # handle api upload
                 session_id = value["session_id"]
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index dc3713100660..f3f94d81fda9 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -150,7 +150,7 @@ def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd):
         workflow_ids = payload.get("workflow_ids")
         if workflow_ids is None:
             workflow_ids = []
-        elif type(workflow_ids) != list:
+        elif not isinstance(workflow_ids, list):
             workflow_ids = [workflow_ids]
         workflow_ids_decoded = []
         # Decode the encoded workflow ids
diff --git a/lib/galaxy/workflow/resources/__init__.py b/lib/galaxy/workflow/resources/__init__.py
index 29df790a05b3..d81e85d6e6c4 100644
--- a/lib/galaxy/workflow/resources/__init__.py
+++ b/lib/galaxy/workflow/resources/__init__.py
@@ -70,7 +70,7 @@ def _resource_parameters_by_group(trans, **kwds):
         for group_name, group_def in by_group.get("groups", {}).items():
             if group_name == default_group or group_name in user_groups:
                 for tag in group_def:
-                    if type(tag) is dict:
+                    if isinstance(tag, dict):
                         if tag.get("name") not in user_permissions:
                             user_permissions[tag.get("name")] = {}
                         for option in tag.get("options"):
@@ -131,7 +131,7 @@ def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_par
             )
         for group in by_group["groups"]:
             for attrib in by_group["groups"][group]:
-                if type(attrib) is dict:
+                if isinstance(attrib, dict):
                     if "name" not in attrib:
                         raise Exception(
                             "'workflow_resource_params_mapper' YAML file is malformed, "
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 21c0249e4d5b..c5d3806e2b02 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -1041,7 +1041,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
             local_filename = util.mkstemp_ln(file_data.file.name, "upload_file_data_")
             file_data.file.close()
             file_data = dict(filename=file_data.filename, local_filename=local_filename)
-        elif type(file_data) == dict and "local_filename" not in file_data:
+        elif isinstance(file_data, dict) and "local_filename" not in file_data:
             raise Exception("Uploaded file was encoded in a way not understood.")
 
         commit_message = kwd.get("commit_message", "Uploaded")
diff --git a/pyproject.toml b/pyproject.toml
index 9829bd1497fa..3a74fe4a38ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -68,7 +68,7 @@ h5grove = ">=1.2.1"
 h5py = "*"
 importlib-metadata = "<5"  # Work around https://github.com/celery/kombu/issues/1600
 importlib-resources = "*"
-isa-rwval = "*"
+isa-rwval = ">=0.10.10"
 kombu = "*"
 lagom = "*"
 Mako = "*"
@@ -152,7 +152,7 @@ responses = "*"
 selenium = "*"
 seletools = "*"
 Sphinx = ">=4.0"  # support docutils 0.17
-sphinx_rtd_theme = ">=1.0.0"
+sphinx-rtd-theme = ">=1.0.0,<2"  # https://github.com/python-poetry/poetry/issues/8194
 statsd = "*"
 testfixtures = "*"
 tuspy = "*"
diff --git a/scripts/api/common.py b/scripts/api/common.py
index 1b5a09e44070..9dca44f367fb 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -81,7 +81,7 @@ def display(api_key, url, return_formatted=True):
         sys.exit(1)
     if not return_formatted:
         return r
-    elif type(r) == list:
+    elif isinstance(r, list):
         # Response is a collection as defined in the REST style.
         print("Collection Members")
         print("------------------")
@@ -103,7 +103,7 @@ def display(api_key, url, return_formatted=True):
                         print(item)
         print("")
         print("%d element(s) in collection" % len(r))
-    elif type(r) == dict:
+    elif isinstance(r, dict):
         # Response is an element as defined in the REST style.
         print("Member Information")
         print("------------------")
@@ -133,11 +133,11 @@ def submit(api_key, url, data, return_formatted=True):
         return r
     print("Response")
     print("--------")
-    if type(r) == list:
+    if isinstance(r, list):
         # Currently the only implemented responses are lists of dicts, because
         # submission creates some number of collection elements.
         for i in r:
-            if type(i) == dict:
+            if isinstance(i, dict):
                 if "url" in i:
                     print(i.pop("url"))
                 else:
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 97b493dc5b06..704db36b7ca7 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -283,7 +283,7 @@ def __read_paramfile(path):
     with open(path) as fh:
         obj = load(fh)
     # If there's a single dataset in an old-style paramfile it'll still parse, but it'll be a dict
-    assert type(obj) == list
+    assert isinstance(obj, list)
     return obj
 
 
diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py
index 868b5d49cb20..3c164d6f1a7d 100755
--- a/tools/stats/gsummary.py
+++ b/tools/stats/gsummary.py
@@ -176,7 +176,7 @@ def main():
             stop_err("Computation resulted in the following error: %s" % str(s))
         summary = summary.as_py(BASIC_CONVERSION)
         outfile.write("#%s\n" % headings_str)
-        if type(summary) is dict:
+        if isinstance(summary, dict):
             # using rpy
             outfile.write("%s\n" % "\t".join("%g" % summary[k] for k in headings))
         else: