fix import, tests, etc

.github/workflows/CI.yaml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.7", "3.9", "3.11", "3.12"]
-        pydantic-version: ["1", "2"]
+        pydantic-version: ["2"]
         runs-on: [ubuntu-latest, windows-latest]
         exclude:
           - runs-on: windows-latest
@@ -35,15 +35,6 @@ jobs:
         uses: actions/checkout@v3
       - name: Install poetry
         run: pip install poetry
-      # Force pydantic 1.0 by modifying poetry dep "pydantic" string with in-place sed
-      # -i is zero-length extension which does effectively in-place sub.
-      # Can't do -i '' because Ubuntu sed is -i{suffix} whereas OSX sed is -i {suffix}... ugh
-      # ^ start of line, pydantic, optional spaces and > sign, capture the version, replace with ^{version}
-      # Should avoid also replacing the autodoc-pydantic spec later on.
-      - name: Sed replace pydantic on repo
-        if: matrix.pydantic-version == '1'
-        run: |
-          sed -i 's/^pydantic *= *">*= *\([0-9.]*\)"/pydantic = "^\1"/' pyproject.toml
       - name: Install repo with poetry (full deps)
         if: matrix.python-version != '3.9'
         run: poetry install --no-interaction --no-ansi --all-extras
@@ -76,10 +67,6 @@ jobs:
           python-version: "3.10"
       - name: Install poetry
         run: pip install poetry
-      # Force pydantic 1.0 by modifying poetry dep "pydantic" string with in-place sed (see above for details)
-      - name: Sed replace pydantic on repo
-        run: |
-          sed -i 's/^pydantic *= *">*= *\([0-9.]*\)"/pydantic = "^\1"/' pyproject.toml
       - name: Install repo
         run: poetry install --no-interaction --no-ansi
       - name: Build Documentation

docs/changelog.rst

@@ -26,13 +26,18 @@ Changelog
 Breaking Changes
 ++++++++++++++++
 * The very old model names `ResultInput`, `Result`, `ResultProperties`, `Optimization` deprecated in 2019 are now only available through `qcelelemental.models.v1`
+* ``models.v2`` do not support AutoDoc. The AutoDoc routines have been left at pydantic v1 syntax. Use autodoc-pydantic for Sphinx instead.
 
 New Features
 ++++++++++++
 * Downstream code should ``from qcelemental.models.v1 import Molecule, AtomicResult`` etc. to assure medium-term availability of existing models.
+* New pydantic v2 models available as ``from qcelemental.models.v2 import Molecule, AtomicResult`` etc.
 
 Enhancements
 ++++++++++++
+* The ``models.v2`` have had their `schema_version` bumped for ``BasisSet``, ``AtomicInput``, ``OptimizationInput`` (implicit for ``AtomicResult`` and ``OptimizationResult``), ``TorsionDriveInput`` , and ``TorsionDriveResult``.
+* The ``models.v2`` ``AtomicResultProperties`` has been given a ``schema_name`` and ``schema_version`` (2) for the first time.
+* Note that ``models.v2`` ``QCInputSpecification`` and ``OptimizationSpecification`` have *not* had schema_version bumped.
 
 Bug Fixes
 +++++++++

pyproject.toml

@@ -36,13 +36,13 @@ packaging = [
     { version = ">=24.1", python = ">=3.8" },
 ]
 # qcel is compatible with most any numpy, v1 or v2, but numpy v2 only works with pint >=0.24, which is only available for py >=3.10
-python = "^3.7"
+python = "^3.7.1"
 pint = [
     { version = ">=0.10", python = ">=3.7,<3.9" },
     { version = ">=0.23", python = ">=3.9,<3.10" },
     { version = ">=0.24", python = ">=3.10,<3.13" },
 ]
-pydantic = ">=1.8.2"
+pydantic = ">=2.0"
 nglview = { version = "^3.0.3", optional = true }
 ipykernel = { version = "<6.0.0", optional = true }
 importlib-metadata = { version = ">=4.8", python = "<3.8" }
@@ -73,7 +73,7 @@ docutils = "<0.19"
 sphinx = "<6.0.0"
 sphinxcontrib-napoleon = "^0.7"
 sphinx-rtd-theme = "^1.2.0"
-autodoc-pydantic = "^1.8.0"
+autodoc-pydantic = { version = "2.0.0", python = ">=3.7.1,<4.0" }
 sphinx-automodapi = "^0.15.0"
 sphinx-autodoc-typehints = "^1.22"
 

qcelemental/models/__init__.py

@@ -1 +1,10 @@
+try:
+    import pydantic
+except ImportError:  # pragma: no cover
+    raise ImportError(
+        "Python module pydantic not found. Solve by installing it: "
+        "`conda install pydantic -c conda-forge` or `pip install pydantic`"
+    )
+
+from . import v1, v2
 from .v1 import *

qcelemental/models/v1/__init__.py

@@ -1,11 +1,3 @@
-try:
-    import pydantic
-except ImportError:  # pragma: no cover
-    raise ImportError(
-        "Python module pydantic not found. Solve by installing it: "
-        "`conda install pydantic -c conda-forge` or `pip install pydantic`"
-    )
-
 from . import types
 from .align import AlignmentMill
 from .basemodels import AutodocBaseSettings  # remove when QCFractal merges `next`

qcelemental/models/v1/align.py

@@ -1,11 +1,7 @@
 from typing import Optional
 
 import numpy as np
-
-try:
-    from pydantic.v1 import Field, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field, validator
+from pydantic.v1 import Field, validator
 
 from ...util import blockwise_contract, blockwise_expand
 from .basemodels import ProtoModel

qcelemental/models/v1/basemodels.py

@@ -3,13 +3,8 @@
 from typing import Any, Dict, Optional, Set, Union
 
 import numpy as np
-
-try:
-    from pydantic.v1 import BaseSettings  # remove when QCFractal merges `next`
-    from pydantic.v1 import BaseModel
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import BaseSettings  # remove when QCFractal merges `next`
-    from pydantic import BaseModel
+from pydantic.v1 import BaseSettings  # remove when QCFractal merges `next`
+from pydantic.v1 import BaseModel
 
 from qcelemental.util import deserialize, serialize
 from qcelemental.util.autodocs import AutoPydanticDocGenerator  # remove when QCFractal merges `next`

qcelemental/models/v1/basis.py

@@ -1,10 +1,7 @@
 from enum import Enum
 from typing import Dict, List, Optional
 
-try:
-    from pydantic.v1 import ConstrainedInt, Field, constr, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import ConstrainedInt, Field, constr, validator
+from pydantic.v1 import ConstrainedInt, Field, constr, validator
 
 from ...exceptions import ValidationError
 from .basemodels import ProtoModel, qcschema_draft

qcelemental/models/v1/common_models.py

@@ -2,20 +2,13 @@
 from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 
 import numpy as np
-
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic.v1 import Field
 
 from .basemodels import ProtoModel, qcschema_draft
 from .basis import BasisSet
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.typing import ReprArgs
-    except ImportError:  # Will also trap ModuleNotFoundError
-        from pydantic.typing import ReprArgs
+    from pydantic.v1.typing import ReprArgs
 
 
 # Encoders, to be deprecated

qcelemental/models/v1/molecule.py

@@ -10,11 +10,7 @@
 from typing import TYPE_CHECKING, Any, Dict, Iterable, List, Optional, Tuple, Union, cast
 
 import numpy as np
-
-try:
-    from pydantic.v1 import ConstrainedFloat, ConstrainedInt, Field, constr, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import ConstrainedFloat, ConstrainedInt, Field, constr, validator
+from pydantic.v1 import ConstrainedFloat, ConstrainedInt, Field, constr, validator
 
 # molparse imports separated b/c https://github.com/python/mypy/issues/7203
 from ...molparse.from_arrays import from_arrays
@@ -31,10 +27,7 @@
 from .types import Array
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.typing import ReprArgs
-    except ImportError:  # Will also trap ModuleNotFoundError
-        from pydantic.typing import ReprArgs
+    from pydantic.v1.typing import ReprArgs
 
 # Rounding quantities for hashing
 GEOMETRY_NOISE = 8

qcelemental/models/v1/procedures.py

@@ -1,10 +1,7 @@
 from enum import Enum
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
 
-try:
-    from pydantic.v1 import Field, conlist, constr, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field, conlist, constr, validator
+from pydantic.v1 import Field, conlist, constr, validator
 
 from ...util import provenance_stamp
 from .basemodels import ProtoModel
@@ -23,10 +20,7 @@
 from .results import AtomicResult
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.typing import ReprArgs
-    except ImportError:  # Will also trap ModuleNotFoundError
-        from pydantic.typing import ReprArgs
+    from pydantic.v1.typing import ReprArgs
 
 
 class TrajectoryProtocolEnum(str, Enum):

qcelemental/models/v1/results.py

@@ -3,11 +3,7 @@
 from typing import TYPE_CHECKING, Any, Dict, Optional, Set, Union
 
 import numpy as np
-
-try:
-    from pydantic.v1 import Field, constr, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field, constr, validator
+from pydantic.v1 import Field, constr, validator
 
 from ...util import provenance_stamp
 from .basemodels import ProtoModel, qcschema_draft
@@ -17,10 +13,7 @@
 from .types import Array
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.typing import ReprArgs
-    except ImportError:  # Will also trap ModuleNotFoundError
-        from pydantic.typing import ReprArgs
+    from pydantic.v1.typing import ReprArgs
 
 
 class AtomicResultProperties(ProtoModel):

qcelemental/models/v2/__init__.py

@@ -0,0 +1,19 @@
+from . import types
+from .align import AlignmentMill
+from .basemodels import ProtoModel
+from .basis import BasisSet
+from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
+from .molecule import Molecule
+from .procedures import OptimizationInput, OptimizationResult
+from .results import AtomicInput, AtomicResult, AtomicResultProperties
+
+
+def qcschema_models():
+    return [
+        AtomicInput,
+        AtomicResult,
+        AtomicResultProperties,
+        BasisSet,
+        Molecule,
+        Provenance,
+    ]

qcelemental/models/v2/basemodels.py

@@ -5,10 +5,8 @@
 
 import numpy as np
 from pydantic import BaseModel, ConfigDict, model_serializer
-from pydantic_settings import BaseSettings  # remove when QCFractal merges `next`
 
 from qcelemental.util import deserialize, serialize
-from qcelemental.util.autodocs import AutoPydanticDocGenerator  # remove when QCFractal merges `next`
 
 
 def _repr(self) -> str:
@@ -279,10 +277,4 @@ def _merge_config_with(cls, *args, **kwargs):
         return ExtendedConfigDict(**output_dict)
 
 
-# remove when QCFractal merges `next`
-class AutodocBaseSettings(BaseSettings):
-    def __init_subclass__(cls) -> None:
-        cls.__doc__ = AutoPydanticDocGenerator(cls, always_apply=True)
-
-
 qcschema_draft = "http://json-schema.org/draft-04/schema#"

qcelemental/models/v2/basis.py

@@ -172,7 +172,7 @@ class BasisSet(ProtoModel):
         description=f"The QCSchema specification to which this model conforms. Explicitly fixed as qcschema_basis.",
     )
     schema_version: int = Field(  # type: ignore
-        1,
+        2,
         description="The version number of :attr:`~qcelemental.models.BasisSet.schema_name` "
         "to which this model conforms.",
     )

qcelemental/models/v2/procedures.py

@@ -70,7 +70,7 @@ class OptimizationInput(ProtoModel):
     schema_name: constr(  # type: ignore
         strip_whitespace=True, pattern=qcschema_optimization_input_default
     ) = qcschema_optimization_input_default
-    schema_version: int = 1
+    schema_version: int = 2
 
     keywords: Dict[str, Any] = Field({}, description="The optimization specific keywords to be used.")
     extras: Dict[str, Any] = Field({}, description="Extra fields that are not part of the schema.")
@@ -205,7 +205,7 @@ class TorsionDriveInput(ProtoModel):
     schema_name: constr(
         strip_whitespace=True, pattern=qcschema_torsion_drive_input_default
     ) = qcschema_torsion_drive_input_default  # type: ignore
-    schema_version: int = 1
+    schema_version: int = 2
 
     keywords: TDKeywords = Field(..., description="The torsion drive specific keywords to be used.")
     extras: Dict[str, Any] = Field({}, description="Extra fields that are not part of the schema.")
@@ -239,7 +239,7 @@ class TorsionDriveResult(TorsionDriveInput):
     schema_name: constr(
         strip_whitespace=True, pattern=qcschema_torsion_drive_output_default
     ) = qcschema_torsion_drive_output_default  # type: ignore
-    schema_version: int = 1
+    schema_version: int = 2
 
     final_energies: Dict[str, float] = Field(
         ..., description="The final energy at each angle of the TorsionDrive scan."
@@ -261,18 +261,3 @@ class TorsionDriveResult(TorsionDriveInput):
     )
     error: Optional[ComputeError] = Field(None, description=str(ComputeError.__doc__))
     provenance: Provenance = Field(..., description=str(Provenance.__doc__))
-
-
-def Optimization(*args, **kwargs):
-    """QC Optimization Results Schema.
-
-    .. deprecated:: 0.12
-       Use :py:func:`qcelemental.models.OptimizationResult` instead.
-
-    """
-    from warnings import warn
-
-    warn(
-        "Optimization has been renamed to OptimizationResult and will be removed as soon as v0.13.0", DeprecationWarning
-    )
-    return OptimizationResult(*args, **kwargs)