Update to Dodal with Pydantic2 support, remove deprecated Pydantic us…

…age (#625)

dev-requirements.txt

@@ -10,6 +10,7 @@ anyio==4.4.0
 appdirs==1.4.4
 asciitree==0.3.3
 asttokens==2.4.1
+async-timeout==4.0.3
 attrs==24.2.0
 babel==2.16.0
 beautifulsoup4==4.12.3
@@ -19,46 +20,51 @@ bluesky-kafka==0.10.0
 bluesky-live==0.0.8
 bluesky-stomp==0.1.0
 boltons==24.0.0
+bump-pydantic==0.8.0
 cachetools==5.5.0
 caproto==1.1.1
-certifi==2024.7.4
+certifi==2024.8.30
 cfgv==3.4.0
 charset-normalizer==3.3.2
 click==8.1.7
 cloudpickle==3.0.0
 colorama==0.4.6
 colorlog==6.8.2
 comm==0.2.2
-confluent-kafka==2.5.0
+compress-pickle==2.1.0
+confluent-kafka==2.5.3
 contourpy==1.3.0
 copier==9.3.1
 coverage==7.6.1
 cycler==0.12.1
-dask==2024.8.1
+dask==2024.8.2
 databroker==1.2.5
 dataclasses-json==0.6.7
 decorator==5.1.1
-deepmerge==1.1.1
+deepmerge==2.0
 distlib==0.3.8
 dls-bluesky-core==0.0.4
-dls-dodal==1.29.4
+dls-dodal==1.31.0
 dnspython==2.6.1
 docopt==0.6.2
 doct==1.1.0
 docutils==0.21.2
 dunamai==1.22.0
+email_validator==2.2.0
 entrypoints==0.4
 epicscorelibs==7.0.7.99.0.2
-event-model==1.20.0
-executing==2.0.1
-fastapi==0.112.2
+event-model==1.21.0
+exceptiongroup==1.2.2
+executing==2.1.0
+fastapi==0.113.0
+fastapi-cli==0.0.5
 fasteners==0.19
 filelock==3.15.4
 flexcache==0.3
 flexparser==0.3.1
 fonttools==4.53.1
 frozenlist==1.4.1
-fsspec==2024.6.1
+fsspec==2024.9.0
 funcy==2.0
 gitdb==4.0.11
 GitPython==3.1.43
@@ -68,6 +74,7 @@ h5py==3.11.0
 HeapDict==1.0.1
 historydict==1.2.6
 httpcore==1.0.5
+httptools==0.6.1
 httpx==0.27.2
 humanize==4.10.0
 identify==2.6.0
@@ -80,15 +87,19 @@ iniconfig==2.0.0
 intake==0.6.4
 ipython==8.18.0
 ipywidgets==8.1.5
+itsdangerous==2.2.0
 jedi==0.19.1
 Jinja2==3.1.4
 jinja2-ansible-filters==1.3.2
 jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 jupyterlab_widgets==3.0.13
-kiwisolver==1.4.5
+kiwisolver==1.4.7
 ldap3==2.9.1
+libcst==1.4.0
+livereload==2.7.0
 locket==1.0.0
+lz4==4.3.3
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
 marshmallow==3.22.0
@@ -113,7 +124,7 @@ numcodecs==0.13.0
 numpy==1.26.4
 opencv-python-headless==4.10.0.84
 ophyd==1.9.0
-ophyd-async==0.3.4
+ophyd-async==0.5.2
 orjson==3.10.7
 p4p==4.1.12
 packaging==24.1
@@ -143,9 +154,11 @@ pvxslibs==1.3.1
 py==1.11.0
 pyasn1==0.6.0
 pycryptodome==3.20.0
-pydantic==2.8.2
+pydantic==2.9.0
+pydantic-extra-types==2.9.0
 pydantic-settings==2.4.0
-pydantic_core==2.20.1
+pydantic_core==2.23.2
+pydantic_numpy==5.0.2
 pydata-sphinx-theme==0.15.4
 pyepics==3.5.7
 Pygments==2.18.0
@@ -157,26 +170,33 @@ pytest-asyncio==0.24.0
 pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
+python-multipart==0.0.9
 pytz==2024.1
 PyYAML==6.0.2
+pyyaml-include==2.1
 questionary==2.0.1
 redis==5.0.8
 redis-json-dict==0.2.0
 referencing==0.35.1
 requests==2.32.3
 responses==0.25.3
+rich==13.7.1
 rpds-py==0.20.0
-ruff==0.6.2
+ruamel.yaml==0.18.6
+ruamel.yaml.clib==0.2.8
+ruff==0.6.4
 scanspec==0.7.2
+semver==3.0.2
 setuptools-dso==2.11
+shellingham==1.5.4
 six==1.16.0
 slicerator==1.1.0
 smmap==5.0.1
 sniffio==1.3.1
 snowballstemmer==2.2.0
 soupsieve==2.6
 Sphinx==8.0.2
-sphinx-autobuild==2024.4.16
+sphinx-autobuild==2024.9.3
 sphinx-click==6.0.0
 sphinx-copybutton==0.5.2
 sphinx_design==0.6.1
@@ -190,28 +210,33 @@ sphinxcontrib-openapi==0.8.4
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
-starlette==0.38.2
+starlette==0.38.4
 stomp-py==8.1.2
 suitcase-mongo==0.6.0
 suitcase-msgpack==0.3.0
 suitcase-utils==0.5.4
 super-state-machine==2.0.2
-tifffile==2024.8.28
+tifffile==2024.8.30
+tomli==2.0.1
 toolz==0.12.1
+tornado==6.4.1
 tox==3.28.0
 tox-direct==0.4
 tqdm==4.66.5
 traitlets==5.14.3
+typer==0.12.4
 types-mock==5.1.0.20240425
 types-PyYAML==6.0.12.20240808
-types-requests==2.32.0.20240712
+types-requests==2.32.0.20240905
 types-urllib3==1.26.25.14
 typing-inspect==0.9.0
 typing_extensions==4.12.2
 tzdata==2024.1
 tzlocal==5.2
+ujson==5.10.0
 urllib3==2.2.2
 uvicorn==0.30.6
+uvloop==0.19.0
 virtualenv==20.26.3
 watchfiles==0.24.0
 wcwidth==0.2.13
@@ -220,8 +245,8 @@ websockets==13.0.1
 widgetsnbextension==4.0.13
 workflows==2.27
 xarray==2024.7.0
-yarl==1.9.4
-zarr==2.18.2
+yarl==1.9.11
+zarr==2.18.3
 zict==2.2.0
 zipp==3.20.1
 zocalo==1.1.0

docs/how-to/write-plans.md

@@ -36,7 +36,7 @@ For example, if a plan is written to drive a specific implementation of Movable,
 
 When added to the blueapi context, `PlanGenerator`\ s are formalised into their schema- `a Pydantic BaseModel <https://docs.pydantic.dev/1.10/usage/models/>`__ with the expected argument types and their defaults. 
 
-Therefore, `PlanGenerator`\ s must only take as arguments `those types which are valid Pydantic fields <https://docs.pydantic.dev/1.10/usage/types/>`__ or Device types which implement `BLUESKY_PROTOCOLS` defined in dodal, which are fetched from the context at runtime.
+Therefore, `PlanGenerator`\ s must only take as arguments `those types which are valid Pydantic fields <https://docs.pydantic.dev/dev/concepts/types/>`__ or Device types which implement `BLUESKY_PROTOCOLS` defined in dodal, which are fetched from the context at runtime.
 
  Allowed argument types for Pydantic BaseModels include the primitives, types that extend `BaseModel` and `dict`\ s, `list`\ s and other `sequence`\ s of supported types. Blueapi will deserialise these types from JSON, so `dict`\ s should use `str` keys.
 

pyproject.toml

@@ -27,11 +27,11 @@ dependencies = [
  "fastapi>=0.112.0",
  "uvicorn",
  "requests",
- "dls-bluesky-core", #requires ophyd-async
- "dls-dodal>=1.24.0",
- "super-state-machine", # See GH issue 553
+ "dls-bluesky-core",  #requires ophyd-async
+ "dls-dodal>=1.31.0",
+ "super-state-machine",  # See GH issue 553
  "GitPython",
- "bluesky-stomp>=0.1.0"
+ "bluesky-stomp>=0.1.0",
 ]
 dynamic = ["version"]
 license.file = "LICENSE"

src/blueapi/cli/cli.py

@@ -162,7 +162,7 @@ def on_event(
  event: WorkerEvent | ProgressEvent | DataEvent,
  context: MessageContext,
  ) -> None:
- converted = json.dumps(event.dict(), indent=2)
+ converted = json.dumps(event.model_dump(), indent=2)
  print(converted)
 
  print(
@@ -218,7 +218,7 @@ def on_event(event: AnyEvent) -> None:
  pprint("task could not run")
  return
 
- pprint(resp.dict())
+ pprint(resp.model_dump())
  if resp.task_status is not None and not resp.task_status.task_failed:
  print("Plan Succeeded")
 

src/blueapi/cli/format.py

@@ -57,11 +57,11 @@ def display_json(obj: Any, stream: Stream):
  print = partial(builtins.print, file=stream)
  match obj:
  case PlanResponse(plans=plans):
- print(json.dumps([p.dict() for p in plans], indent=2))
+ print(json.dumps([p.model_dump() for p in plans], indent=2))
  case DeviceResponse(devices=devices):
- print(json.dumps([d.dict() for d in devices], indent=2))
+ print(json.dumps([d.model_dump() for d in devices], indent=2))
  case BaseModel():
- print(json.dumps(obj.dict(), indent=2))
+ print(json.dumps(obj.model_dump(), indent=2))
  case _:
  print(json.dumps(obj))
 

src/blueapi/client/rest.py

@@ -2,7 +2,7 @@
 from typing import Any, Literal, TypeVar
 
 import requests
-from pydantic import parse_obj_as
+from pydantic import TypeAdapter
 
 from blueapi.config import RestConfig
 from blueapi.service.model import (
@@ -82,7 +82,7 @@ def create_task(self, task: Task) -> TaskResponse:
  "/tasks",
  TaskResponse,
  method="POST",
- data=task.dict(),
+ data=task.model_dump(),
  )
 
  def clear_task(self, task_id: str) -> TaskResponse:
@@ -95,7 +95,7 @@ def update_worker_task(self, task: WorkerTask) -> WorkerTask:
  "/worker/task",
  WorkerTask,
  method="PUT",
- data=task.dict(),
+ data=task.model_dump(),
  )
 
  def cancel_current_task(
@@ -134,7 +134,7 @@ def _request_and_deserialize(
  exception = get_exception(response)
  if exception is not None:
  raise exception
- deserialized = parse_obj_as(target_type, response.json())
+ deserialized = TypeAdapter(target_type).validate_python(response.json())
  return deserialized
 
  def _url(self, suffix: str) -> str:

src/blueapi/config.py

@@ -5,7 +5,7 @@
 from typing import Any, Generic, Literal, TypeVar
 
 import yaml
-from pydantic import BaseModel, Field, ValidationError, parse_obj_as, validator
+from pydantic import BaseModel, Field, TypeAdapter, ValidationError, field_validator
 
 from blueapi.utils import BlueapiBaseModel, InvalidConfigError
 
@@ -34,7 +34,8 @@ class BasicAuthentication(BaseModel):
  username: str = "guest"
  passcode: str = "guest"
 
- @validator("username", "passcode")
+ @field_validator("username", "passcode")
+ @classmethod
  def get_from_env(cls, v: str):
  if v.startswith("${") and v.endswith("}"):
  return os.environ[v.removeprefix("${").removesuffix("}").upper()]
@@ -129,12 +130,9 @@ class ConfigLoader(Generic[C]):
  of default values, dictionaries, YAML/JSON files etc.
  """
 
- _schema: type[C]
- _values: dict[str, Any]
-
  def __init__(self, schema: type[C]) -> None:
- self._schema = schema
- self._values = {}
+ self._adapter = TypeAdapter(schema)
+ self._values: dict[str, Any] = {}
 
  def use_values(self, values: Mapping[str, Any]) -> None:
  """
@@ -184,7 +182,7 @@ def load(self) -> C:
  """
 
  try:
- return parse_obj_as(self._schema, self._values)
+ return self._adapter.validate_python(self._values)
  except ValidationError as exc:
  raise InvalidConfigError(
  "Something is wrong with the configuration file: \n"

src/blueapi/core/context.py

@@ -4,7 +4,15 @@
 from importlib import import_module
 from inspect import Parameter, signature
 from types import ModuleType, UnionType
-from typing import Any, Generic, TypeVar, Union, get_args, get_origin, get_type_hints
+from typing import (
+ Any,
+ Generic,
+ TypeVar,
+ Union,
+ get_args,
+ get_origin,
+ get_type_hints,
+)
 
 from bluesky.run_engine import RunEngine
 from dodal.utils import make_all_devices
@@ -217,7 +225,7 @@ def __get_pydantic_json_schema__(
 
  def _type_spec_for_function(
  self, func: Callable[..., Any]
- ) -> dict[str, tuple[type, Any]]:
+ ) -> dict[str, tuple[type, FieldInfo]]:
  """
  Parse a function signature and build map of field types and default
  values that can be used to deserialise arguments from external sources.
@@ -234,7 +242,7 @@ def _type_spec_for_function(
  """
  args = signature(func).parameters
  types = get_type_hints(func)
- new_args = {}
+ new_args: dict[str, tuple[type, FieldInfo]] = {}
  for name, para in args.items():
  arg_type = types.get(name, Parameter.empty)
  if arg_type is Parameter.empty:

src/blueapi/utils/serialization.py

@@ -19,7 +19,7 @@ def serialize(obj: Any) -> Any:
  if isinstance(obj, BaseModel):
  # Serialize by alias so that our camelCase models leave the service
  # with camelCase field names
- return obj.dict(by_alias=True)
+ return obj.model_dump(by_alias=True)
  elif hasattr(obj, "__pydantic_model__"):
  return serialize(obj.__pydantic_model__)
  else: