Update node serialization/deserialization and other Pydantic issues

docs/source/nitpick-exceptions

@@ -26,6 +26,7 @@ py:class json.encoder.JSONEncoder
 py:class EXPOSED_TYPE
 py:class EVENT_CALLBACK_TYPE
 py:class datetime
+py:class UUID
 py:class types.LambdaType
 py:meth tempfile.TemporaryDirectory
 
@@ -68,6 +69,8 @@ py:class aiida.orm.groups.SelfType
 py:class aiida.orm.implementation.entitites.EntityType
 py:class aiida.engine.processes.functions.FunctionType
 py:class aiida.engine.processes.workchains.workchain.MethodType
+py:class aiida.orm.entities.EntityInputModel
+py:class aiida.orm.entities.EntityModelType
 py:class aiida.orm.entities.EntityType
 py:class aiida.orm.entities.BackendEntityType
 py:class aiida.orm.entities.CollectionType

src/aiida/cmdline/commands/cmd_code.py

@@ -8,11 +8,13 @@
 ###########################################################################
 """`verdi code` command."""
 
+from __future__ import annotations
+
 import pathlib
 import warnings
 from collections import defaultdict
 from functools import partial
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 import click
 
@@ -26,16 +28,20 @@
 from aiida.cmdline.utils.decorators import with_dbenv
 from aiida.common import exceptions
 
+if TYPE_CHECKING:
+    from aiida.orm import Code
+
 
 @verdi.group('code')
 def verdi_code():
     """Setup and manage codes."""
 
 
-def create_code(ctx: click.Context, cls, **kwargs) -> None:
+def create_code(ctx: click.Context, cls: Code, **kwargs) -> None:
     """Create a new `Code` instance."""
     try:
-        instance = cls._from_model(cls.Model(**kwargs))
+        model = cls.InputModel(**kwargs)
+        instance = cls.from_model(model)  # type: ignore[arg-type]
     except (TypeError, ValueError) as exception:
         echo.echo_critical(f'Failed to create instance `{cls}`: {exception}')
 

src/aiida/cmdline/groups/dynamic.py

@@ -97,8 +97,9 @@ def call_command(self, ctx: click.Context, cls: t.Any, non_interactive: bool, **
 
         if hasattr(cls, 'Model'):
             # The plugin defines a pydantic model: use it to validate the provided arguments
+            Model = cls.InputModel if hasattr(cls, 'InputModel') else cls.Model  # noqa: N806
             try:
-                cls.Model(**kwargs)
+                Model(**kwargs)
             except ValidationError as exception:
                 param_hint = [
                     f'--{loc.replace("_", "-")}'  # type: ignore[union-attr]
@@ -168,9 +169,11 @@ def list_options(self, entry_point: str) -> list[t.Callable[[FC], FC]]:
             options_spec = self.factory(entry_point).get_cli_options()  # type: ignore[union-attr]
             return [self.create_option(*item) for item in options_spec]
 
+        Model = cls.InputModel if hasattr(cls, 'InputModel') else cls.Model  # noqa: N806
+
         options_spec = {}
 
-        for key, field_info in cls.Model.model_fields.items():
+        for key, field_info in Model.model_fields.items():
             if get_metadata(field_info, 'exclude_from_cli'):
                 continue
 

src/aiida/common/datastructures.py

@@ -167,8 +167,8 @@ class CalcInfo(DefaultFieldsAttributeDict):
         max_wallclock_seconds: None | int
         max_memory_kb: None | int
         rerunnable: bool
-        retrieve_list: None | list[str | tuple[str, str, str]]
-        retrieve_temporary_list: None | list[str | tuple[str, str, str]]
+        retrieve_list: None | list[str | tuple[str, str, int]]
+        retrieve_temporary_list: None | list[str | tuple[str, str, int]]
         local_copy_list: None | list[tuple[str, str, str]]
         remote_copy_list: None | list[tuple[str, str, str]]
         remote_symlink_list: None | list[tuple[str, str, str]]

src/aiida/common/pydantic.py

@@ -66,7 +66,7 @@ class Model(BaseModel):
     :param short_name: Optional short name to use for an option on a command line interface.
     :param option_cls: The :class:`click.Option` class to use to construct the option.
     :param orm_class: The class, or entry point name thereof, to which the field should be converted. If this field is
-        defined, the value of this field should acccept an integer which will automatically be converted to an instance
+        defined, the value of this field should accept an integer which will automatically be converted to an instance
         of said ORM class using ``orm_class.collection.get(id={field_value})``. This is useful, for example, where a
         field represents an instance of a different entity, such as an instance of ``User``. The serialized data would
         store the ``pk`` of the user, but the ORM entity instance would receive the actual ``User`` instance with that
@@ -75,10 +75,10 @@ class Model(BaseModel):
     :param model_to_orm: Optional callable to convert the value of a field from a model instance to an ORM instance.
     :param exclude_to_orm: When set to ``True``, this field value will not be passed to the ORM entity constructor
         through ``Entity.from_model``.
-    :param exclude_to_orm: When set to ``True``, this field value will not be exposed on the CLI command that is
+    :param exclude_from_cli: When set to ``True``, this field value will not be exposed on the CLI command that is
         dynamically generated to create a new instance.
-    :param is_attribute: Whether the field is stored as an attribute.
-    :param is_subscriptable: Whether the field can be indexed like a list or dictionary.
+    :param is_attribute: Whether the field is stored as an attribute. Used by `QbFields`.
+    :param is_subscriptable: Whether the field can be indexed like a list or dictionary. Used by `QbFields`.
     """
     field_info = Field(default, **kwargs)
 
@@ -97,4 +97,9 @@ class Model(BaseModel):
         if value is not None:
             field_info.metadata.append({key: value})
 
+    if exclude_to_orm:
+        extra = getattr(field_info, 'json_schema_extra', None) or {}
+        extra.update({'readOnly': True})
+        field_info.json_schema_extra = extra
+
     return field_info

src/aiida/common/typing.py

@@ -11,11 +11,12 @@
 from __future__ import annotations
 
 import pathlib
+import sys
 from typing import Union
 
-try:
+if sys.version_info >= (3, 11):
     from typing import Self
-except ImportError:
+else:
     from typing_extensions import Self
 
 __all__ = ('FilePath', 'Self')

src/aiida/orm/authinfos.py

@@ -10,7 +10,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Dict, Optional, Type
+from typing import TYPE_CHECKING, Any, Dict, Optional, Type, cast
 
 from aiida.common import exceptions
 from aiida.common.pydantic import MetadataField
@@ -55,13 +55,13 @@ class Model(entities.Entity.Model):
             description='The PK of the computer',
             is_attribute=False,
             orm_class=Computer,
-            orm_to_model=lambda auth_info, _: auth_info.computer.pk,  # type: ignore[attr-defined]
+            orm_to_model=lambda auth_info, _: cast('AuthInfo', auth_info).computer.pk,
         )
         user: int = MetadataField(
             description='The PK of the user',
             is_attribute=False,
             orm_class=User,
-            orm_to_model=lambda auth_info, _: auth_info.user.pk,  # type: ignore[attr-defined]
+            orm_to_model=lambda auth_info, _: cast('AuthInfo', auth_info).user.pk,
         )
         enabled: bool = MetadataField(
             True,

src/aiida/orm/comments.py

@@ -10,6 +10,7 @@
 
 from datetime import datetime
 from typing import TYPE_CHECKING, List, Optional, Type, cast
+from uuid import UUID
 
 from aiida.common.pydantic import MetadataField
 from aiida.manage import get_manager
@@ -68,14 +69,20 @@ class Comment(entities.Entity['BackendComment', CommentCollection]):
     _CLS_COLLECTION = CommentCollection
 
     class Model(entities.Entity.Model):
-        uuid: Optional[str] = MetadataField(
-            description='The UUID of the comment', is_attribute=False, exclude_to_orm=True
+        uuid: UUID = MetadataField(
+            description='The UUID of the comment',
+            is_attribute=False,
+            exclude_to_orm=True,
         )
-        ctime: Optional[datetime] = MetadataField(
-            description='Creation time of the comment', is_attribute=False, exclude_to_orm=True
+        ctime: datetime = MetadataField(
+            description='Creation time of the comment',
+            is_attribute=False,
+            exclude_to_orm=True,
         )
-        mtime: Optional[datetime] = MetadataField(
-            description='Modified time of the comment', is_attribute=False, exclude_to_orm=True
+        mtime: datetime = MetadataField(
+            description='Modified time of the comment',
+            is_attribute=False,
+            exclude_to_orm=True,
         )
         node: int = MetadataField(
             description='Node PK that the comment is attached to',
@@ -89,7 +96,10 @@ class Model(entities.Entity.Model):
             orm_class='core.user',
             orm_to_model=lambda comment, _: cast('Comment', comment).user.pk,
         )
-        content: str = MetadataField(description='Content of the comment', is_attribute=False)
+        content: str = MetadataField(
+            description='Content of the comment',
+            is_attribute=False,
+        )
 
     def __init__(
         self, node: 'Node', user: 'User', content: Optional[str] = None, backend: Optional['StorageBackend'] = None

src/aiida/orm/computers.py

@@ -8,9 +8,12 @@
 ###########################################################################
 """Module for Computer entities"""
 
+from __future__ import annotations
+
 import logging
 import os
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Type, Union
+from uuid import UUID
 
 from aiida.common import exceptions
 from aiida.common.pydantic import MetadataField
@@ -74,13 +77,37 @@ class Computer(entities.Entity['BackendComputer', ComputerCollection]):
     _CLS_COLLECTION = ComputerCollection
 
     class Model(entities.Entity.Model):
-        uuid: str = MetadataField(description='The UUID of the computer', is_attribute=False, exclude_to_orm=True)
-        label: str = MetadataField(description='Label for the computer', is_attribute=False)
-        description: str = MetadataField(description='Description of the computer', is_attribute=False)
-        hostname: str = MetadataField(description='Hostname of the computer', is_attribute=False)
-        transport_type: str = MetadataField(description='Transport type of the computer', is_attribute=False)
-        scheduler_type: str = MetadataField(description='Scheduler type of the computer', is_attribute=False)
-        metadata: Dict[str, Any] = MetadataField(description='Metadata of the computer', is_attribute=False)
+        uuid: UUID = MetadataField(
+            description='The UUID of the computer',
+            is_attribute=False,
+            exclude_to_orm=True,
+        )
+        label: str = MetadataField(
+            description='Label for the computer',
+            is_attribute=False,
+        )
+        description: str = MetadataField(
+            '',
+            description='Description of the computer',
+            is_attribute=False,
+        )
+        hostname: str = MetadataField(
+            description='Hostname of the computer',
+            is_attribute=False,
+        )
+        transport_type: str = MetadataField(
+            description='Transport type of the computer',
+            is_attribute=False,
+        )
+        scheduler_type: str = MetadataField(
+            description='Scheduler type of the computer',
+            is_attribute=False,
+        )
+        metadata: Dict[str, Any] = MetadataField(
+            default_factory=dict,
+            description='Metadata of the computer',
+            is_attribute=False,
+        )
 
     def __init__(
         self,