Update node serialization/deserialization and other Pydantic issues

.gitignore

@@ -61,3 +61,6 @@ docker-bake.override.json
 
 # benchmark
 .benchmarks/
+
+# dev files
+.dev

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
 

environment.yml

@@ -25,7 +25,7 @@ dependencies:
 - pgsu~=0.3.0
 - psutil~=7.0
 - psycopg[binary]<4,>=3.0.2
-- pydantic~=2.6
+- pydantic~=2.12
 - pytz~=2021.1
 - pyyaml~=6.0
 - requests~=2.0

pyproject.toml

@@ -48,7 +48,7 @@ dependencies = [
   'pgsu~=0.3.0',
   'psutil~=7.0',
   'psycopg[binary]>=3.0.2,<4',
-  'pydantic~=2.6',
+  'pydantic~=2.12',
   'pytz~=2021.1',
   'pyyaml~=6.0',
   'requests~=2.0',

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: type[Code], **kwargs) -> None:
     """Create a new `Code` instance."""
     try:
-        instance = cls._from_model(cls.Model(**kwargs))
+        model = cls.CliModel(**kwargs)
+        instance = cls.from_model(model)
     except (TypeError, ValueError) as exception:
         echo.echo_critical(f'Failed to create instance `{cls}`: {exception}')
 
@@ -223,50 +229,27 @@ def code_duplicate(ctx, code, non_interactive, **kwargs):
 @verdi_code.command()
 @arguments.CODE()
 @with_dbenv()
-def show(code):
+def show(code: Code):
     """Display detailed information for a code."""
     from aiida.cmdline import is_verbose
-    from aiida.common.pydantic import get_metadata
 
     table = []
 
     # These are excluded from the CLI, so we add them manually
     table.append(['PK', code.pk])
     table.append(['UUID', code.uuid])
-    table.append(['Type', code.entry_point.name])
-
-    for field_name, field_info in code.Model.model_fields.items():
-        # Skip fields excluded from CLI
-        if get_metadata(
-            field_info,
-            key='exclude_from_cli',
-            default=False,
-        ):
-            continue
-
-        # Skip fields that are not stored in the attributes column
-        # NOTE: this also catches e.g., filepath_files for PortableCode, which is actually a "misuse"
-        # of the is_attribute metadata flag, as there it is flagging that the field is not stored at all!
-        # TODO (edan-bainglass) consider improving this by introducing a new metadata flag or reworking PortableCode
-        # TODO see also Dict and InstalledCode for other potential misuses of is_attribute
-        if not get_metadata(
-            field_info,
-            key='is_attribute',
-            default=True,
-        ):
-            continue
-
-        value = getattr(code, field_name)
+    table.append(['Type', code.entry_point.name if code.entry_point else None])
+    table.append(['Label', code.label])
+    table.append(['Description', code.description or ''])
 
-        # Special handling for computer field to show additional info
-        if field_name == 'computer':
-            value = f'{value.label} ({value.hostname}), pk: {value.pk}'
+    if code.computer is not None:
+        table.append(['Computer', f'{code.computer.label} ({code.computer.hostname}), pk: {code.computer.pk}'])
 
-        # Use the field's title as display name.
-        # This allows for custom titles (class-cased by default from Pydantic).
-        display_name = field_info.title
-
-        table.append([display_name, value])
+    for key, field in code.AttributesModel.model_fields.items():
+        if key == 'source':
+            continue
+        value = getattr(code, key)
+        table.append([field.title, value])
 
     if is_verbose():
         table.append(['Calculations', len(code.base.links.get_outgoing().all())])

src/aiida/cmdline/commands/cmd_computer.py

@@ -229,7 +229,7 @@ def _computer_use_login_shell_performance(transport, scheduler, authinfo, comput
 
     if not isclose(timing_true, timing_false, rel_tol=rel_tol, abs_tol=abs_tol):
         return True, (
-            f"\n\n{click.style('Warning:', fg='yellow', bold=True)} "
+            f'\n\n{click.style("Warning:", fg="yellow", bold=True)} '
             'The computer is configured to use a login shell, which is slower compared to a normal shell.\n'
             f'Command execution time of {timing_true:.3f} versus {timing_false:.3f} seconds, respectively).\n'
             'Unless this setting is really necessary, consider disabling it with:\n'
@@ -347,7 +347,7 @@ def computer_duplicate(ctx, computer, non_interactive, **kwargs):
     from aiida.orm.utils.builders.computer import ComputerBuilder
 
     if kwargs['label'] in get_computer_names():
-        echo.echo_critical(f"A computer called {kwargs['label']} already exists")
+        echo.echo_critical(f'A computer called {kwargs["label"]} already exists')
 
     kwargs['transport'] = kwargs['transport'].name
     kwargs['scheduler'] = kwargs['scheduler'].name
@@ -652,7 +652,7 @@ def computer_delete(computer, dry_run):
     # Sofar, we can only get this info with QueryBuilder
     builder = QueryBuilder()
     builder.append(Computer, filters={'label': label}, tag='computer')
-    builder.append(Node, with_computer='computer', project=Node.fields.pk)  # type: ignore[arg-type]
+    builder.append(Node, with_computer='computer', project='pk')
     associated_nodes_pk = builder.all(flat=True)
 
     echo.echo_report(f'This computer has {len(associated_nodes_pk)} associated nodes')
@@ -741,7 +741,7 @@ def computer_config_show(computer, user, defaults, as_option_string):
             if config.get(option.name) or config.get(option.name) is False:
                 if t_opt.get('switch'):
                     option_value = (
-                        option.opts[-1] if config.get(option.name) else f"--no-{option.name.replace('_', '-')}"  # type: ignore[union-attr]
+                        option.opts[-1] if config.get(option.name) else f'--no-{option.name.replace("_", "-")}'  # type: ignore[union-attr]
                     )
                 elif t_opt.get('is_flag'):
                     is_default = config.get(option.name) == transport_cli.transport_option_default(

src/aiida/cmdline/groups/dynamic.py

@@ -95,20 +95,22 @@ def call_command(self, ctx: click.Context, cls: t.Any, non_interactive: bool, **
         """Call the ``command`` after validating the provided inputs."""
         from pydantic import ValidationError
 
-        if hasattr(cls, 'Model'):
-            # The plugin defines a pydantic model: use it to validate the provided arguments
-            try:
-                cls.Model(**kwargs)
-            except ValidationError as exception:
-                param_hint = [
-                    f'--{loc.replace("_", "-")}'  # type: ignore[union-attr]
-                    for loc in exception.errors()[0]['loc']
-                ]
-                message = '\n'.join([str(e['msg']) for e in exception.errors()])
-                raise click.BadParameter(
-                    message,
-                    param_hint=param_hint or 'one or more parameters',  # type: ignore[arg-type]
-                ) from exception
+        CliModel = getattr(cls, 'CliModel', None)  # noqa: N806
+        if not CliModel:
+            return self._command(ctx, cls, **kwargs)
+
+        try:
+            CliModel(**kwargs)
+        except ValidationError as exception:
+            param_hint = [
+                f'--{loc.replace("_", "-")}'  # type: ignore[union-attr]
+                for loc in exception.errors()[0]['loc']
+            ]
+            message = '\n'.join([str(e['msg']) for e in exception.errors()])
+            raise click.BadParameter(
+                message,
+                param_hint=param_hint or 'one or more parameters',  # type: ignore[arg-type]
+            ) from exception
 
         return self._command(ctx, cls, **kwargs)
 
@@ -153,27 +155,22 @@ def list_options(self, entry_point: str) -> list[t.Callable[[FC], FC]]:
         """
         from pydantic_core import PydanticUndefined
 
-        from aiida.common.pydantic import get_metadata
-
         cls = self.factory(entry_point)
 
-        if not hasattr(cls, 'Model'):
+        CliModel = getattr(cls, 'CliModel', None)  # noqa: N806
+        if not CliModel:
             from aiida.common.warnings import warn_deprecation
 
             warn_deprecation(
-                'Relying on `_get_cli_options` is deprecated. The options should be defined through a '
-                '`pydantic.BaseModel` that should be assigned to the `Model` class attribute.',
+                'Relying on `_get_cli_options` is deprecated. The options should be defined through a `CliModel`.',
                 version=3,
             )
             options_spec = self.factory(entry_point).get_cli_options()  # type: ignore[union-attr]
             return [self.create_option(*item) for item in options_spec]
 
         options_spec = {}
 
-        for key, field_info in cls.Model.model_fields.items():
-            if get_metadata(field_info, 'exclude_from_cli'):
-                continue
-
+        for key, field_info in CliModel.model_fields.items():
             default = field_info.default_factory if field_info.default is PydanticUndefined else field_info.default
 
             # If the annotation has the ``__args__`` attribute it is an instance of a type from ``typing`` and the real

src/aiida/common/__init__.py

@@ -81,6 +81,7 @@
     'TransportTaskException',
     'UniquenessError',
     'UnstashTargetMode',
+    'UnsupportedSchemaError',
     'UnsupportedSpeciesError',
     'ValidationError',
     'create_callback',

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/exceptions.py

@@ -50,6 +50,7 @@
     'TestsNotAllowedError',
     'TransportTaskException',
     'UniquenessError',
+    'UnsupportedSchemaError',
     'UnsupportedSpeciesError',
     'ValidationError',
 )
@@ -294,3 +295,7 @@ class LockedProfileError(AiidaException):
 
 class LockingProfileError(AiidaException):
     """Raised if the profile can`t be locked"""
+
+
+class UnsupportedSchemaError(AiidaException):
+    """Raised when a schema (model) is not supported by the entity."""