Pydantic2 and MBE procedure

[loriab]

Description

Changelog description

Status

• Code base linted
• Ready to go

[github-advanced-security]

CodeQL found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

[susilehtola]

fwiw this PR still crashes with pydantic v2 due to qcelemental

  File "/usr/lib/rpm/redhat/import_all_modules.py", line 106, in import_modules
    importlib.import_module(module)
    ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
  File "/usr/lib64/python3.14/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1398, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1371, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1342, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 938, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 762, in exec_module
  File "<frozen importlib._bootstrap>", line 491, in _call_with_frames_removed
  File "/builddir/build/BUILD/python-qcengine-0.30.0-build/BUILDROOT/usr/lib/python3.14/site-packages/qcengine/__init__.py", line 5, in <module>
    from . import config, exceptions
  File "/builddir/build/BUILD/python-qcengine-0.30.0-build/BUILDROOT/usr/lib/python3.14/site-packages/qcengine/exceptions.py", line 4, in <module>
    from qcelemental.models import AtomicInput
  File "/usr/lib/python3.14/site-packages/qcelemental/__init__.py", line 10, in <module>
    from . import covalent_radii, models, molparse, molutil, periodic_table, physical_constants, util, vanderwaals_radii
  File "/usr/lib/python3.14/site-packages/qcelemental/covalent_radii.py", line 9, in <module>
    from .datum import Datum, print_variables
  File "/usr/lib/python3.14/site-packages/qcelemental/datum.py", line 16, in <module>
    class Datum(BaseModel):
    ...<88 lines>...
                return factor * self.data
  File "/usr/lib/python3.14/site-packages/pydantic/v1/main.py", line 221, in __new__
    inferred = ModelField.infer(
        name=var_name,
    ...<3 lines>...
        config=config,
    )
  File "/usr/lib/python3.14/site-packages/pydantic/v1/fields.py", line 504, in infer
    return cls(
        name=name,
    ...<7 lines>...
        field_info=field_info,
    )
  File "/usr/lib/python3.14/site-packages/pydantic/v1/fields.py", line 434, in __init__
    self.prepare()
    ~~~~~~~~~~~~^^
  File "/usr/lib/python3.14/site-packages/pydantic/v1/fields.py", line 544, in prepare
    self._set_default_and_type()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3.14/site-packages/pydantic/v1/fields.py", line 576, in _set_default_and_type
    raise errors_.ConfigError(f'unable to infer type for attribute "{self.name}"')
pydantic.v1.errors.ConfigError: unable to infer type for attribute "doi"
Check import: qcengine.cli
Traceback (most recent call last):
  File "/usr/lib/rpm/redhat/import_all_modules.py", line 106, in import_modules
    importlib.import_module(module)
    ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
  File "/usr/lib64/python3.14/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1398, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1371, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1314, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 491, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1398, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1371, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1342, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 938, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 762, in exec_module
  File "<frozen importlib._bootstrap>", line 491, in _call_with_frames_removed
  File "/builddir/build/BUILD/python-qcengine-0.30.0-build/BUILDROOT/usr/lib/python3.14/site-packages/qcengine/__init__.py", line 5, in <module>
    from . import config, exceptions
  File "/builddir/build/BUILD/python-qcengine-0.30.0-build/BUILDROOT/usr/lib/python3.14/site-packages/qcengine/exceptions.py", line 4, in <module>
    from qcelemental.models import AtomicInput
  File "/usr/lib/python3.14/site-packages/qcelemental/__init__.py", line 10, in <module>
    from . import covalent_radii, models, molparse, molutil, periodic_table, physical_constants, util, vanderwaals_radii
  File "/usr/lib/python3.14/site-packages/qcelemental/covalent_radii.py", line 9, in <module>
    from .datum import Datum, print_variables
  File "/usr/lib/python3.14/site-packages/qcelemental/datum.py", line 16, in <module>
    class Datum(BaseModel):
    ...<88 lines>...
                return factor * self.data
  File "/usr/lib/python3.14/site-packages/qcelemental/datum.py", line 62, in Datum
    @validator("data")
     ~~~~~~~~~^^^^^^^^
  File "/usr/lib/python3.14/site-packages/pydantic/v1/class_validators.py", line 93, in dec
    f_cls = _prepare_validator(f, allow_reuse)
  File "/usr/lib/python3.14/site-packages/pydantic/v1/class_validators.py", line 156, in _prepare_validator
    raise ConfigError(f'duplicate validator function "{ref}"; if this is intended, set `allow_reuse=True`')
pydantic.v1.errors.ConfigError: duplicate validator function "qcelemental.datum.Datum.must_be_numerical"; if this is intended, set `allow_reuse=True`