Pin pydantic to >=2.7.4

Pydantic <2.7.4 is broken on Python>=3.12.4 , see pydantic/pydantic#9609 . Fixed upstream in pydantic/pydantic#9639 . Fix the following traceback in startup test on Python 3.12: ``` Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/bin/galaxyctl", line 10, in <module> sys.exit(galaxyctl()) ^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1682, in invoke cmd_name, cmd, args = self.resolve_command(ctx, args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1729, in resolve_command cmd = self.get_command(ctx, cmd_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 59, in get_command return name_to_command(name) ^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 45, in name_to_command mod = __import__(mod_name, None, None, ["cli"]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/commands/cmd_stop.py", line 4, in <module> from gravity import process_manager File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/process_manager/__init__.py", line 14, in <module> from gravity.config_manager import ConfigManager File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/config_manager.py", line 18, in <module> from gravity.state import ConfigFile, service_for_service_type File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/state.py", line 42, in <module> class ConfigFile(BaseModel): File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 286, in __new__ cls.__try_update_forward_refs__() File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 807, in __try_update_forward_refs__ update_model_forward_refs(cls, cls.__fields__.values(), cls.__config__.json_encoders, localns, (NameError,)) File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 554, in update_model_forward_refs update_field_forward_refs(f, globalns=globalns, localns=localns) File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 520, in update_field_forward_refs field.type_ = evaluate_forwardref(field.type_, globalns, localns or None) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 66, in evaluate_forwardref return cast(Any, type_)._evaluate(globalns, localns, set()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: ForwardRef._evaluate() missing 1 required keyword-only argument: 'recursive_guard' ``` Example: https://github.com/galaxyproject/galaxy/actions/runs/9581802216/job/26419972297
nsoranzo · Jun 19, 2024 · f7e8469 · f7e8469
1 parent 08d42ea
commit f7e8469
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Showing 13 changed files with 17 additions and 17 deletions.
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -133,10 +133,10 @@ psutil==5.9.8 ; 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==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.1 ; 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"
 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"

diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -8,8 +8,8 @@ mypy-boto3-s3==1.34.105 ; 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"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
+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"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
 types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"

diff --git 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,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     pysam>=0.21
     PyJWT
     PyYAML

diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
@@ -53,7 +53,7 @@ install_requires =
     numpy
     parsley
     pycryptodome
-    pydantic[email]>=2,!=2.6.0,!=2.6.1
+    pydantic[email]>=2.7.4
     pylibmagic
     python-magic
     pysam>=0.21

diff --git 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[config_template]
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     PyYAML
 packages = find:
 python_requires = >=3.7

diff --git 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,!=2.6.0,!=2.6.1
+    pydantic[email]>=2.7.4
 packages = find:
 python_requires = >=3.8
 

diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg
@@ -50,7 +50,7 @@ install_requires =
     MarkupSafe
     mercurial
     Paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     Routes
     SQLAlchemy>=2.0,<2.1
     starlette

diff --git 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,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     PyYAML
     requests
     sortedcontainers

diff --git 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,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     PyYAML
 packages = find:
 python_requires = >=3.8

diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
@@ -55,7 +55,7 @@ template =
     future>=1.0.0
 config_template =
     Jinja2
-    pydantic
+    pydantic>=2.7.4
 
 [options.packages.find]
 exclude =

diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
@@ -50,7 +50,7 @@ install_requires =
     Mako
     MarkupSafe
     Paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     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
@@ -37,7 +37,7 @@ install_requires =
     babel
     MarkupSafe
     paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     requests
     Routes
     SQLAlchemy>=2.0,<2.1

diff --git a/pyproject.toml b/pyproject.toml
@@ -92,7 +92,7 @@ pillow = "*"
 psutil = "*"
 pulsar-galaxy-lib = ">=0.15.0.dev0"
 pycryptodome = "*"
-pydantic = {version = ">=2.7.0", extras = ["email"]}  # https://github.com/pydantic/pydantic/issues/8760
+pydantic = {version = ">=2.7.4", extras = ["email"]}  # https://github.com/pydantic/pydantic/pull/9639
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"
@@ -175,7 +175,7 @@ Werkzeug = "*"
 mypy = "*"
 boto3-stubs = {version = "*", extras = ["s3"]}
 lxml-stubs = "*"
-pydantic = ">=2, !=2.6.0, !=2.6.1"  # for pydantic.mypy plugin
+pydantic = ">=2.7.4"  # for pydantic.mypy plugin
 types-bleach = "*"
 types-boto = "*"
 types-contextvars = "*"