Pydantic v2 Overhaul [DNM yet]

.github/workflows/CI.yaml

@@ -13,7 +13,6 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ["3.7", "3.9", "3.11"]
-        pydantic-version: ["1", "2"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -24,15 +23,6 @@ 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
-        run: |
-          sed -i 's/^pydantic *= *">*= *\([0-9.]*\)"/pydantic = "^\1"/' pyproject.toml
-        if: matrix.pydantic-version == '1'
       - name: Install repo with poetry (full deps)
         if: matrix.python-version != '3.9'
         run: poetry install --no-interaction --no-ansi --all-extras
@@ -65,10 +55,6 @@ jobs:
           python-version: "3.7"
       - 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

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "qcelemental"
-version = "0.26.0"
+version = "0.27.0"
 description = "Core data structures for Quantum Chemistry."
 authors = ["The QCArchive Development Team <[email protected]>"]
 license = "BSD-3-Clause"
@@ -29,9 +29,10 @@ numpy = [
     { version = ">=1.12.0", python = "3.8" },
     { version = ">=1.24.1", python = ">=3.9" },
 ]
-python = "^3.7"
+python = "^3.7.1"
 pint = ">=0.10.0"
-pydantic = ">=1.8.2"
+pydantic = "^2.1.0"
+pydantic-settings = "*"  # Maybe remove when Fractal merges next?
 nglview = { version = "^3.0.3", optional = true }
 ipykernel = { version = "<6.0.0", optional = true }
 importlib-metadata = { version = ">=4.8", python = "<3.8" }
@@ -62,7 +63,7 @@ docutils = "<0.19"
 sphinx = "<6.0.0"
 sphinxcontrib-napoleon = "^0.7"
 sphinx-rtd-theme = "^1.2.0"
-autodoc-pydantic = "^1.8.0"
+autodoc-pydantic = "^2.0.0"
 sphinx-automodapi = "^0.15.0"
 sphinx-autodoc-typehints = "^1.22"
 

qcelemental/datum.py

@@ -3,14 +3,46 @@
 """
 
 from decimal import Decimal
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Union
 
 import numpy as np
+from pydantic import BaseModel, ConfigDict, SerializerFunctionWrapHandler, WrapSerializer, field_validator
+from typing_extensions import Annotated
 
-try:
-    from pydantic.v1 import BaseModel, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import BaseModel, validator
+
+def cast_ndarray(v: Any, nxt: SerializerFunctionWrapHandler) -> str:
+    """Special helper to list NumPy arrays before serializing"""
+    if isinstance(v, np.ndarray):
+        return f"{nxt(v.flatten().tolist())}"
+    return f"{nxt(v)}"
+
+
+def cast_complex(v: Any, nxt: SerializerFunctionWrapHandler) -> str:
+    """Special helper to serialize NumPy arrays before serializing"""
+    if isinstance(v, complex):
+        return f"{nxt((v.real, v.imag))}"
+    return nxt(v)
+
+
+def preserve_decimal(v: Any, nxt: SerializerFunctionWrapHandler) -> Union[str, Decimal]:
+    """
+    Ensure Decimal types are preserved on the way out
+
+    This arose because Decimal was serialized to string and "dump" is equal to "serialize" in v2 pydantic
+    https://docs.pydantic.dev/latest/migration/#changes-to-json-schema-generation
+    """
+    if isinstance(v, Decimal):
+        return v
+    return nxt(v)
+
+
+# Serializers are pop'd out of the list in FILO (right to left)
+AnyArrayComplex = Annotated[
+    Any,
+    WrapSerializer(cast_ndarray, when_used="json"),
+    WrapSerializer(cast_complex, when_used="json"),
+    WrapSerializer(preserve_decimal),
+]
 
 
 class Datum(BaseModel):
@@ -38,15 +70,15 @@ class Datum(BaseModel):
     numeric: bool
     label: str
     units: str
-    data: Any
+    data: AnyArrayComplex
     comment: str = ""
     doi: Optional[str] = None
     glossary: str = ""
 
-    class Config:
-        extra = "forbid"
-        allow_mutation = False
-        json_encoders = {np.ndarray: lambda v: v.flatten().tolist(), complex: lambda v: (v.real, v.imag)}
+    model_config = ConfigDict(
+        extra="forbid",
+        frozen=True,
+    )
 
     def __init__(self, label, units, data, *, comment=None, doi=None, glossary=None, numeric=True):
         kwargs = {"label": label, "units": units, "data": data, "numeric": numeric}
@@ -59,20 +91,21 @@ def __init__(self, label, units, data, *, comment=None, doi=None, glossary=None,
 
         super().__init__(**kwargs)
 
-    @validator("data")
-    def must_be_numerical(cls, v, values, **kwargs):
+    @field_validator("data")
+    @classmethod
+    def must_be_numerical(cls, v, info):
         try:
             1.0 * v
         except TypeError:
             try:
                 Decimal("1.0") * v
             except TypeError:
-                if values["numeric"]:
+                if info.data["numeric"]:
                     raise ValueError(f"Datum data should be float, Decimal, or np.ndarray, not {type(v)}.")
             else:
-                values["numeric"] = True
+                info.data["numeric"] = True
         else:
-            values["numeric"] = True
+            info.data["numeric"] = True
 
         return v
 
@@ -91,7 +124,7 @@ def __str__(self, label=""):
         return "\n".join(text)
 
     def dict(self, *args, **kwargs):
-        return super().dict(*args, **{**kwargs, **{"exclude_unset": True}})
+        return super().model_dump(*args, **{**kwargs, **{"exclude_unset": True}})
 
     def to_units(self, units=None):
         from .physical_constants import constants

qcelemental/info/cpu_info.py

@@ -8,10 +8,8 @@
 from functools import lru_cache
 from typing import List, Optional
 
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic import BeforeValidator, Field
+from typing_extensions import Annotated
 
 from ..models import ProtoModel
 
@@ -25,6 +23,13 @@ class VendorEnum(str, Enum):
     arm = "arm"
 
 
+def stringify(v) -> str:
+    return str(v)
+
+
+Stringify = Annotated[str, BeforeValidator(stringify)]
+
+
 class InstructionSetEnum(int, Enum):
     """Allowed instruction sets for CPUs in an ordinal enum."""
 
@@ -40,13 +45,13 @@ class ProcessorInfo(ProtoModel):
     ncores: int = Field(..., description="The number of physical cores on the chip.")
     nthreads: Optional[int] = Field(..., description="The maximum number of concurrent threads.")
     base_clock: float = Field(..., description="The base clock frequency (GHz).")
-    boost_clock: Optional[float] = Field(..., description="The boost clock frequency (GHz).")
-    model: str = Field(..., description="The model number of the chip.")
+    boost_clock: Optional[float] = Field(None, description="The boost clock frequency (GHz).")
+    model: Stringify = Field(..., description="The model number of the chip.")
     family: str = Field(..., description="The family of the chip.")
-    launch_date: Optional[int] = Field(..., description="The launch year of the chip.")
+    launch_date: Optional[int] = Field(None, description="The launch year of the chip.")
     target_use: str = Field(..., description="Target use case (Desktop, Server, etc).")
     vendor: VendorEnum = Field(..., description="The vendor the chip is produced by.")
-    microarchitecture: Optional[str] = Field(..., description="The microarchitecture the chip follows.")
+    microarchitecture: Optional[str] = Field(None, description="The microarchitecture the chip follows.")
     instructions: InstructionSetEnum = Field(..., description="The maximum vectorized instruction set available.")
     type: str = Field(..., description="The type of chip (cpu, gpu, etc).")
 

qcelemental/info/dft_info.py

@@ -4,10 +4,7 @@
 
 from typing import Dict
 
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic import Field
 
 from ..models import ProtoModel
 
@@ -71,4 +68,4 @@ def get(name: str) -> DFTFunctionalInfo:
             name = name.replace(x, "")
             break
 
-    return dftfunctionalinfo.functionals[name].copy()
+    return dftfunctionalinfo.functionals[name].model_copy()

qcelemental/models/align.py

@@ -1,14 +1,10 @@
 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 import Field, field_validator
 
 from ..util import blockwise_contract, blockwise_expand
-from .basemodels import ProtoModel
+from .basemodels import ExtendedConfigDict, ProtoModel
 from .types import Array
 
 __all__ = ["AlignmentMill"]
@@ -30,19 +26,20 @@ class AlignmentMill(ProtoModel):
     atommap: Optional[Array[int]] = Field(None, description="Atom exchange map (nat,) for coordinates.")  # type: ignore
     mirror: bool = Field(False, description="Do mirror invert coordinates?")
 
-    class Config:
-        force_skip_defaults = True
+    model_config = ExtendedConfigDict(force_skip_defaults=True)
 
-    @validator("shift")
-    def _must_be_3(cls, v, values, **kwargs):
+    @field_validator("shift")
+    @classmethod
+    def _must_be_3(cls, v):
         try:
             v = v.reshape(3)
         except (ValueError, AttributeError):
             raise ValueError("Shift must be castable to shape (3,)!")
         return v
 
-    @validator("rotation")
-    def _must_be_33(cls, v, values, **kwargs):
+    @field_validator("rotation")
+    @classmethod
+    def _must_be_33(cls, v):
         try:
             v = v.reshape(3, 3)
         except (ValueError, AttributeError):