8000 Pin pydantic to >=2.7.4 · nsoranzo/galaxy@88d3849 · GitHub
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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
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‎lib/galaxy/dependencies/pinned-requirements.txt

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@@ -133,10 +133,10 @@ psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
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pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
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pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
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pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
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pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
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pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
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pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
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pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
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pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
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pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
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pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
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pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
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pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
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pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"

‎lib/galaxy/dependencies/pinned-typecheck-requirements.txt

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@@ -8,8 +8,8 @@ mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13"
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mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
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mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
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pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
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pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
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pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
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pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
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pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
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tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
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types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
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types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"

‎packages/app/setup.cfg

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@@ -61,7 +61,7 @@ install_requires =
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paramiko!=2.9.0,!=2.9.1
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pebble
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pulsar-galaxy-lib>=0.15.0.dev0
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pydantic>=2,!=2.6.0,!=2.6.1
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pydantic>=2.7.4
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pysam>=0.21
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PyJWT
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PyYAML

‎packages/data/setup.cfg

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@@ -53,7 +53,7 @@ install_requires =
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numpy
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parsley
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pycryptodome
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pydantic[email]>=2,!=2.6.0,!=2.6.1
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pydantic[email]>=2.7.4
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pylibmagic
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python-magic
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pysam>=0.21

‎packages/schema/setup.cfg

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@@ -33,7 +33,7 @@ version = 23.2.dev0
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include_package_data = True
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install_requires =
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galaxy-util
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pydantic[email]>=2,!=2.6.0,!=2.6.1
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pydantic[email]>=2.7.4
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packages = find:
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python_requires = >=3.8
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‎packages/tool_shed/setup.cfg

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@@ -50,7 +50,7 @@ install_requires =
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MarkupSafe
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mercurial
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Paste
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pydantic>=2,!=2.6.0,!=2.6.1
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pydantic>=2.7.4
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Routes
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SQLAlchemy>=2.0,<2.1
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starlette

‎packages/tours/setup.cfg

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@@ -33,7 +33,7 @@ version = 23.2.dev0
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include_package_data = True
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install_requires =
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galaxy-navigation
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pydantic>=2,!=2.6.0,!=2.6.1
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pydantic>=2.7.4
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PyYAML
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packages = find:
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python_requires = >=3.8

‎packages/web_apps/setup.cfg

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@@ -50,7 +50,7 @@ install_requires =
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Mako
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MarkupSafe
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Paste
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pydantic>=2,!=2.6.0,!=2.6.1
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pydantic>=2.7.4
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PyJWT
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python-dateutil
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python-multipart # required to support form parsing in FastAPI/Starlette

‎packages/web_framework/setup.cfg

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@@ -37,7 +37,7 @@ install_requires =
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babel
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MarkupSafe
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paste
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pydantic>=2,!=2.6.0,!=2.6.1
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pydantic>=2.7.4
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requests
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Routes
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SQLAlchemy>=2.0,<2.1

‎pyproject.toml

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

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