From f9384bb0df2032c8127b071d027dfc0f70a83dc8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 12 Feb 2024 10:30:15 +0000
Subject: [PATCH 1/5] Disallow pydantic 2.6.0 and 2.6.1

xref: https://github.com/pydantic/pydantic/issues/8760

Fix the following error when testing with mypy:

```
$ tox -e mypy
Deferral trace:
    cwltool.utils:62
    cwltool.utils:-1
    ...
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
lib/galaxy/model/__init__.py: error: INTERNAL ERROR: maximum semantic analysis
iteration count reached
Found 1 error in 1 file (errors prevented further checking)
```
---
 packages/app/setup.cfg           | 2 +-
 packages/data/setup.cfg          | 2 +-
 packages/objectstore/setup.cfg   | 2 +-
 packages/schema/setup.cfg        | 2 +-
 packages/tool_util/setup.cfg     | 2 +-
 packages/tours/setup.cfg         | 2 +-
 packages/web_apps/setup.cfg      | 2 +-
 packages/web_framework/setup.cfg | 2 +-
 pyproject.toml                   | 4 ++--
 9 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index d5e9717649ef..4360d7181811 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -61,7 +61,7 @@ install_requires =
     paramiko!=2.9.0,!=2.9.1
     pebble
     pulsar-galaxy-lib>=0.15.0.dev0
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     pysam>=0.21
     PyJWT
     PyYAML
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index b7f5afea24c9..5e97372d47ec 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -51,7 +51,7 @@ install_requires =
     numpy
     parsley
     pycryptodome
-    pydantic[email]>=2
+    pydantic[email]>=2,!=2.6.0,!=2.6.1
     pylibmagic
     python-magic
     pysam>=0.21
diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
index 2257e1f6efd5..496b60c2ce75 100644
--- a/packages/objectstore/setup.cfg
+++ b/packages/objectstore/setup.cfg
@@ -34,7 +34,7 @@ version = 23.2.dev0
 include_package_data = True
 install_requires =
     galaxy-util
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     PyYAML
 packages = find:
 python_requires = >=3.7
diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
index e374603fc2d0..dce6efc479ef 100644
--- a/packages/schema/setup.cfg
+++ b/packages/schema/setup.cfg
@@ -33,7 +33,7 @@ version = 23.2.dev0
 include_package_data = True
 install_requires =
     galaxy-util
-    pydantic[email]>=2
+    pydantic[email]>=2,!=2.6.0,!=2.6.1
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index e338e4989d36..e0753f1af3f0 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -38,7 +38,7 @@ install_requires =
     lxml!=4.2.2
     MarkupSafe
     packaging
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     PyYAML
     requests
     sortedcontainers
diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg
index 8ec2300750ff..1e14d2215a75 100644
--- a/packages/tours/setup.cfg
+++ b/packages/tours/setup.cfg
@@ -33,7 +33,7 @@ version = 23.2.dev0
 include_package_data = True
 install_requires =
     galaxy-navigation
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     PyYAML
 packages = find:
 python_requires = >=3.8
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 79a0bddbd172..77b1bed42159 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -51,7 +51,7 @@ install_requires =
     MarkupSafe
     mercurial
     Paste
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     PyJWT
     python-dateutil
     python-multipart  # required to support form parsing in FastAPI/Starlette
diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg
index 78b9b55b5439..e04d3f101f32 100644
--- a/packages/web_framework/setup.cfg
+++ b/packages/web_framework/setup.cfg
@@ -37,7 +37,7 @@ install_requires =
     babel
     MarkupSafe
     paste
-    pydantic>=2
+    pydantic>=2,!=2.6.0,!=2.6.1
     requests
     Routes
     SQLAlchemy>=1.4.25,<2
diff --git a/pyproject.toml b/pyproject.toml
index 6e4dafeafe8a..6dfa11dbc3cb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -88,7 +88,7 @@ pebble = "*"
 psutil = "*"
 pulsar-galaxy-lib = ">=0.15.0.dev0"
 pycryptodome = "*"
-pydantic = {version = ">=2", extras = ["email"]}
+pydantic = {version = ">=2, !=2.6.0, !=2.6.1", extras = ["email"]}  # https://github.com/pydantic/pydantic/issues/8760
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"
@@ -168,7 +168,7 @@ Werkzeug = "*"
 [tool.poetry.group.typecheck.dependencies]
 mypy = "*"
 lxml-stubs = "*"
-pydantic = ">=2"  # for pydantic.mypy plugin
+pydantic = ">=2, !=2.6.0, !=2.6.1"  # for pydantic.mypy plugin
 types-bleach = "*"
 types-boto = "*"
 types-contextvars = "*"

From 1efa675241d03fc68be107324244c3dbb73684ef Mon Sep 17 00:00:00 2001
From: galaxybot <galaxybot@users.noreply.github.com>
Date: Sat, 10 Feb 2024 03:10:14 +0000
Subject: [PATCH 2/5] Update Python dependencies

---
 lib/galaxy/dependencies/dev-requirements.txt  | 60 +++++++++----------
 .../dependencies/pinned-lint-requirements.txt |  4 +-
 .../dependencies/pinned-requirements.txt      | 52 ++++++++--------
 .../pinned-typecheck-requirements.txt         | 12 ++--
 4 files changed, 64 insertions(+), 64 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 3c1bb12a5eb7..a6a92842ef80 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,4 +1,4 @@
-aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.9.3 ; 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"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -11,11 +11,11 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
+black==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
 build==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -26,8 +26,8 @@ codespell==2.2.6 ; 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]==7.4.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -36,7 +36,7 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.47.2 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.48.1 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -50,7 +50,7 @@ importlib-resources==6.1.1 ; 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"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-classes==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-classes==3.3.1 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
@@ -60,7 +60,7 @@ kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; 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==2.1.4 ; python_version >= "3.8" and python_version < "3.13"
+markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9"
 matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -69,70 +69,70 @@ mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
 more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.0.4 ; 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==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13"
+numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.41.1 ; python_version >= "3.8" and python_version < "3.13"
+platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; 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==3.1.17 ; python_version >= "3.8" and python_version < "3.13"
+psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13"
 pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13"
-pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
+pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
 pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.13"
-pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-asyncio==0.23.5 ; python_version >= "3.8" and python_version < "3.13"
+pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-httpserver==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
+pytest-httpserver==1.0.9 ; 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==3.0.0 ; 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==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.4.3 ; python_version >= "3.8" and python_version < "3.13"
-pytest-postgresql==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
+pytest-postgresql==5.1.0 ; 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"
 python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
-python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.13"
-python-slugify==8.0.2 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.9"
+python-irodsclient==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
+pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
 pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==42.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.24.1 ; python_version >= "3.8" and python_version < "3.13"
+responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.0 ; 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13"
+ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.17.2 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -155,14 +155,14 @@ 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==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
-twine==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
+twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
+twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2023.4 ; python_version >= "3.8" and python_version < "3.13"
+tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 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"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
-watchdog==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
+watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
 werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; 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 021b153d7ad0..6133df8e071f 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-bugbear==24.1.17
+flake8-bugbear==24.2.6
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.1.14
+ruff==0.2.1
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 6e91ef9b5338..a2f72da952c3 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -1,9 +1,9 @@
 a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.11.1 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.11.2 ; 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"
-aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.9.3 ; 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"
@@ -31,11 +31,11 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.27 ; python_version >= "3.8" and python_version < "3.13"
-bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.34 ; python_version >= "3.8" and python_version < "3.13"
+bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
@@ -49,7 +49,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
 conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.2 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13"
 cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13"
@@ -65,7 +65,7 @@ ecdsa==0.18.0 ; 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==2.1.0.post1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
-fastapi==0.109.0 ; python_version >= "3.8" and python_version < "3.13"
+fastapi==0.109.2 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.13.1 ; 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"
@@ -77,12 +77,12 @@ graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.
 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==1.0.5 ; 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 (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 < "3.13"
 gunicorn==21.2.0 ; 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"
-h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
+h5grove==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
@@ -99,24 +99,24 @@ jsonschema==4.21.1 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.5 ; 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"
-mako==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
+mako==1.3.2 ; 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==3.5.2 ; python_version >= "3.8" and python_version < "3.13"
-markupsafe==2.1.4 ; python_version >= "3.8" and python_version < "3.13"
+markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.6.2 ; python_version >= "3.8" and python_version < "3.13"
+mercurial==6.6.3 ; python_version >= "3.8" and python_version < "3.13"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 msal==1.26.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.0.4 ; 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"
 nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13"
+numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
-orjson==3.9.12 ; python_version >= "3.8" and python_version < "3.13"
+orjson==3.9.13 ; python_version >= "3.8" and python_version < "3.13"
 oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -152,13 +152,13 @@ pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
 python-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
 python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
-python-multipart==0.0.7 ; python_version >= "3.8" and python_version < "3.13"
+python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
 python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.13"
+pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.32.1 ; python_version >= "3.8" and python_version < "3.13"
+referencing==0.33.0 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
 regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -172,11 +172,11 @@ routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.17.1 ; python_version >= "3.8" and python_version < "3.13"
 rsa==4.9 ; 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13"
+ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==69.1.0 ; 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==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -188,7 +188,7 @@ sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
 starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-starlette==0.35.1 ; python_version >= "3.8" and python_version < "3.13"
+starlette==0.36.3 ; 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==8.2.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -196,15 +196,15 @@ 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"
 tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
-tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.13"
+tqdm==4.66.2 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2023.4 ; 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==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
+ubiquerg==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-uvicorn==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
+uvicorn==0.27.1 ; 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"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
@@ -212,7 +212,7 @@ webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13"
 whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.13"
+yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
 zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13"
 zipstream-new==1.1.8 ; 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 9ae55e92df48..27e7dfdccf1a 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,6 +1,6 @@
 annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.1 ; 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -9,12 +9,12 @@ pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
 types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-types-boto==2.49.18.9 ; 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"
 types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.20.0.20240126 ; python_version >= "3.8" and python_version < "3.13"
-types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.13"
-types-paramiko==3.4.0.20240120 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.20.0.20240201 ; python_version >= "3.8" and python_version < "3.13"
+types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
+types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13"

From 167282f623f7324f668e516ba69cb6c3fc9fc373 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 14 Feb 2024 00:46:15 +0000
Subject: [PATCH 3/5] Update ruff settings for 0.2.0 deprecations

---
 pyproject.toml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6dfa11dbc3cb..34faa14f63e6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -183,10 +183,15 @@ types-requests = "*"
 types-six = "*"
 
 [tool.ruff]
+target-version = "py38"
+exclude = [
+  "lib/tool_shed/test/test_data/repos"
+]
+
+[tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
 # flake8-logging-format (G) and pyupgrade (UP)
 select = ["E", "F", "B", "G", "UP"]
-target-version = "py38"
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings
@@ -194,17 +199,14 @@ target-version = "py38"
 # E501 is line length (delegated to black)
 # G* are TODOs
 ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"]
-exclude = [
-  "lib/tool_shed/test/test_data/repos"
-]
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 # We are not selecting "I" rules in ruff yet because support for all the isort
 # options we need is not complete, but these are the one currently implemented.
 combine-as-imports = true
 relative-imports-order = "closest-to-furthest"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # Don't check pyupgrade rules on tool scripts, which may use different Python versions
 "test/functional/tools/*" = ["UP"]
 "tools/*" = ["UP"]

From 6250c9797cc142eb9e5b62ed16e9e900afb2fa8f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 12 Feb 2024 10:34:17 +0000
Subject: [PATCH 4/5] Allow manual dispatch of "Update dependencies" GH
 workflow

---
 .github/workflows/dependencies.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml
index 31405cc13498..12f2a0919a89 100644
--- a/.github/workflows/dependencies.yaml
+++ b/.github/workflows/dependencies.yaml
@@ -2,6 +2,7 @@ name: Update dependencies
 on:
   schedule:
     - cron: '0 3 * * 6'  # Run every saturday at 3 am.
+  workflow_dispatch:
 jobs:
   update_dependencies:
     name: Update dependencies

From ca1cf0a3ae96e7980e825f0c0e5707ba96b51d57 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 14 Feb 2024 12:32:44 +0000
Subject: [PATCH 5/5] Update ``test_api_meta`` integration test for h5grove
 2.0.0

---
 test/integration/test_structured_dataset.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_structured_dataset.py b/test/integration/test_structured_dataset.py
index 0f9a8196dd7d..ba81c3365cef 100644
--- a/test/integration/test_structured_dataset.py
+++ b/test/integration/test_structured_dataset.py
@@ -39,7 +39,7 @@ def test_api_meta(self):
         response = self._get(f"datasets/{dataset_id}/content/meta")
         self._assert_status_code_is(response, 200)
         hvals = response.json()
-        self._assert_has_keys(hvals, "attributes", "name", "type")
+        self._assert_has_keys(hvals, "attributes", "name", "kind")
 
     def test_api_attr(self):
         dataset = self.dataset_populator.new_dataset(