Pydantic v1/v2 compatibility

.github/workflows/CI.yml

@@ -17,14 +17,19 @@ defaults:
 jobs:
   test:
 
-    name: ${{ matrix.cfg.os }}, 🐍=${{ matrix.python-version }}, program=${{ matrix.cfg.conda-env }}
+    name: ${{ matrix.cfg.os }}, 🐍=${{ matrix.python-version }}, program=${{ matrix.cfg.conda-env }}, pydantic=${{ matrix.pydantic-version }}
     runs-on: ${{ matrix.cfg.os }}
 
     strategy:
       fail-fast: false
       matrix:
         python-version:
           - "3.9"
+          - "3.10"
+          - "3.11"
+        pydantic-version:
+          - "1"
+          - "2"
         cfg:
           - os: ubuntu-latest
             conda-env: basic
@@ -46,7 +51,9 @@ jobs:
 
         with:
           environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
-          create-args: python=${{ matrix.python-version }}
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pydantic=${{ matrix.pydantic-version }}
 
       - name: License OpenEye
 

.github/workflows/Lint.yaml

@@ -17,20 +17,17 @@ jobs:
     steps:
 
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5.0.0
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.10'
       - name: Install the package
         run: python -m pip install .
 
       - name: Install isort / black
-        run: |
-          pip install isort black
+        run: pip install isort black
 
       - name: Run isort
-        run: |
-          isort --recursive --check-only openff
+        run: isort --check-only openff
 
       - name: Run black
-        run: |
-          black openff --check
+        run: black openff --check

devtools/conda-envs/basic.yaml

@@ -14,15 +14,16 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
+  - pytest-randomly
   - pytest-xdist
   - pytest-randomly
   - requests-mock
 
   - qcengine >=0.25
   - qcelemental >=0.25.1
-  - qcfractal>0.49
-  - qcarchivetesting>0.49
-  - qcportal>=0.49
+  - qcfractal >=0.52
+  - qcarchivetesting
+  - qcportal
 
   - postgresql
 
@@ -35,7 +36,7 @@ dependencies:
 
   - openff-toolkit >= 0.14.0
   - openff-units >=0.2.1
-  - pydantic =1
+  - pydantic
   - pyyaml
   - torsiondrive
   - basis_set_exchange

devtools/conda-envs/docs.yaml

@@ -27,9 +27,9 @@ dependencies:
 
   - openff-toolkit-base =0.14.0
   - rdkit
-  - pydantic =1
+  - pydantic
   - pyyaml
-  - qcportal >=0.15
+  - qcportal >=0.52
   - torsiondrive
   - basis_set_exchange
   - typing-extensions

devtools/conda-envs/psi4.yaml

@@ -14,14 +14,15 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
-  - codecov
+  - pytest-randomly
+  - pytest-xdist
   - requests-mock
 
   - qcengine >=0.25
   - qcelemental >=0.25.1
-  - qcfractal>0.49
-  - qcarchivetesting>0.49
-  - qcportal>=0.49
+  - qcfractal >=0.52
+  - qcarchivetesting
+  - qcportal
 
   - openeye-toolkits
 
@@ -32,7 +33,7 @@ dependencies:
   - openff-toolkit-base >= 0.14.0
   - openff-units >=0.2.1
   - rdkit
-  - pydantic =1
+  - pydantic
   - pyyaml
   - torsiondrive
   - basis_set_exchange

openff/qcsubmit/_pydantic.py

@@ -0,0 +1,21 @@
+"""Centralized shim for Pydantic v1/v2 compatible import."""
+try:
+    from pydantic.v1 import (
+        BaseModel,
+        Field,
+        PrivateAttr,
+        ValidationError,
+        constr,
+        root_validator,
+        validator,
+    )
+except ImportError:
+    from pydantic import (
+        BaseModel,
+        Field,
+        PrivateAttr,
+        ValidationError,
+        constr,
+        root_validator,
+        validator,
+    )

openff/qcsubmit/_tests/results/__init__.py

@@ -4,14 +4,14 @@
 import numpy
 from openff.toolkit.topology import Molecule
 from openff.units import unit
-from pydantic import BaseModel
 from qcelemental.models import DriverEnum
 from qcelemental.models.procedures import TDKeywords
 from qcportal.optimization import OptimizationRecord, OptimizationSpecification
 from qcportal.record_models import RecordStatusEnum
 from qcportal.singlepoint import QCSpecification, SinglepointRecord
 from qcportal.torsiondrive import TorsiondriveRecord, TorsiondriveSpecification
 
+from openff.qcsubmit._pydantic import BaseModel
 from openff.qcsubmit.results import (
     BasicResult,
     BasicResultCollection,

openff/qcsubmit/_tests/results/test_filters.py

@@ -5,10 +5,10 @@
 import pytest
 from openff.toolkit.topology import Molecule
 from openff.units import unit
-from pydantic import ValidationError
 from qcelemental.models import DriverEnum
 from qcportal.singlepoint import QCSpecification
 
+from openff.qcsubmit._pydantic import ValidationError
 from openff.qcsubmit._tests.results import mock_optimization_result_collection
 from openff.qcsubmit.results import (
     BasicResult,

openff/qcsubmit/_tests/results/test_results.py

@@ -7,14 +7,14 @@
 import pytest
 from openff.toolkit.topology import Molecule
 from openff.toolkit.typing.engines.smirnoff import ForceField
-from pydantic import ValidationError
 from qcelemental.models import DriverEnum
 from qcportal.torsiondrive import (
     TorsiondriveKeywords,
     TorsiondriveRecord,
     TorsiondriveSpecification,
 )
 
+from openff.qcsubmit._pydantic import ValidationError
 from openff.qcsubmit._tests import does_not_raise
 from openff.qcsubmit.common_structures import QCSpec
 from openff.qcsubmit.exceptions import RecordTypeError

openff/qcsubmit/_tests/test_datasets.py

@@ -9,9 +9,9 @@
 from openff.toolkit.topology import Molecule
 from openff.toolkit.typing.engines.smirnoff import ForceField
 from openff.units import unit
-from pydantic import ValidationError
 from qcelemental.models.procedures import OptimizationProtocols
 
+from openff.qcsubmit._pydantic import ValidationError
 from openff.qcsubmit.common_structures import MoleculeAttributes, QCSpec
 from openff.qcsubmit.constraints import Constraints, PositionConstraintSet
 from openff.qcsubmit.datasets import (

openff/qcsubmit/_tests/test_factories.py

@@ -4,9 +4,9 @@
 
 import pytest
 from openff.toolkit.topology import Molecule
-from pydantic import ValidationError
 
 from openff.qcsubmit import workflow_components
+from openff.qcsubmit._pydantic import ValidationError
 from openff.qcsubmit.datasets import BasicDataset, OptimizationDataset
 from openff.qcsubmit.exceptions import DriverError, InvalidWorkflowComponentError
 from openff.qcsubmit.factories import (

openff/qcsubmit/_tests/test_workflow_components.py

@@ -12,10 +12,10 @@
     RDKitToolkitWrapper,
     ToolkitRegistry,
 )
-from pydantic import ValidationError
 from typing_extensions import Literal
 
 from openff.qcsubmit import workflow_components
+from openff.qcsubmit._pydantic import ValidationError
 from openff.qcsubmit.common_structures import ComponentProperties
 from openff.qcsubmit.exceptions import (
     ComponentRegisterError,

openff/qcsubmit/common_structures.py

@@ -22,18 +22,6 @@
 
 import numpy as np
 from openff.toolkit.topology import Molecule
-from pydantic import (
-    BaseModel,
-    Field,
-    HttpUrl,
-    PositiveInt,
-    StrictBool,
-    StrictFloat,
-    StrictInt,
-    StrictStr,
-    constr,
-    validator,
-)
 from qcelemental import constants
 from qcelemental.models.common_models import Model
 from qcelemental.models.results import WavefunctionProtocolEnum
@@ -46,6 +34,33 @@
 )
 from openff.qcsubmit.utils.smirnoff import split_openff_molecule
 
+try:
+    from pydantic.v1 import (
+        BaseModel,
+        Field,
+        HttpUrl,
+        PositiveInt,
+        StrictBool,
+        StrictFloat,
+        StrictInt,
+        StrictStr,
+        constr,
+        validator,
+    )
+except ImportError:
+    from pydantic import (
+        BaseModel,
+        Field,
+        HttpUrl,
+        PositiveInt,
+        StrictBool,
+        StrictFloat,
+        StrictInt,
+        StrictStr,
+        constr,
+        validator,
+    )
+
 if TYPE_CHECKING:
     DictStrAny = Dict[str, Any]
     IntStr = Union[int, str]

openff/qcsubmit/constraints.py

@@ -3,9 +3,9 @@
 """
 from typing import List, Tuple, Union
 
-from pydantic import Field, ValidationError, validator
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import Field, ValidationError, validator
 from openff.qcsubmit.common_structures import ResultsConfig
 from openff.qcsubmit.exceptions import ConstraintError
 

openff/qcsubmit/datasets/datasets.py

@@ -18,7 +18,6 @@
 import qcelemental as qcel
 import qcportal as ptl
 from openff.toolkit import topology as off
-from pydantic import Field, constr, validator
 from qcelemental.models import AtomicInput, OptimizationInput
 from qcelemental.models.procedures import OptimizationProtocols, QCInputSpecification
 from qcportal import PortalClient, PortalRequestError
@@ -31,6 +30,7 @@
 from qcportal.torsiondrive import TorsiondriveDatasetNewEntry, TorsiondriveSpecification
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import Field, constr, validator
 from openff.qcsubmit.common_structures import CommonBase, Metadata, MoleculeAttributes
 from openff.qcsubmit.constraints import Constraints
 from openff.qcsubmit.datasets.entries import (

openff/qcsubmit/datasets/entries.py

@@ -10,9 +10,9 @@
 import qcelemental as qcel
 import qcelemental.models
 from openff.units import unit
-from pydantic import Field, validator
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import Field, validator
 from openff.qcsubmit.common_structures import (
     DatasetConfig,
     MoleculeAttributes,

openff/qcsubmit/factories.py

@@ -5,10 +5,10 @@
 import tqdm
 from openff.toolkit import topology as off
 from openff.toolkit.utils import GLOBAL_TOOLKIT_REGISTRY, ToolkitRegistry
-from pydantic import Field, validator
 from qcportal.singlepoint import SinglepointDriver
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import Field, validator
 from openff.qcsubmit.common_structures import CommonBase, Metadata
 from openff.qcsubmit.datasets import (
     BasicDataset,

openff/qcsubmit/procedures.py

@@ -4,10 +4,10 @@
 
 from typing import Any, Dict
 
-from pydantic import BaseModel, Field, validator
 from qcportal.optimization import OptimizationSpecification
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import BaseModel, Field, validator
 from openff.qcsubmit.validators import literal_lower, literal_upper
 
 

openff/qcsubmit/results/filters.py

@@ -15,13 +15,19 @@
 )
 from openff.units import unit
 from openff.utilities import requires_package
-from pydantic import BaseModel, Field, PrivateAttr, root_validator, validator
 from qcelemental.molutil import guess_connectivity
 from qcportal.optimization import OptimizationRecord
 from qcportal.record_models import BaseRecord, RecordStatusEnum
 from qcportal.singlepoint import SinglepointRecord
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import (
+    BaseModel,
+    Field,
+    PrivateAttr,
+    root_validator,
+    validator,
+)
 from openff.qcsubmit.results.results import (
     TorsionDriveResultCollection,
     _BaseResult,

openff/qcsubmit/results/results.py

@@ -25,7 +25,6 @@
 from openff.toolkit.topology import Molecule
 from openff.toolkit.typing.engines.smirnoff import ForceField
 from openff.units import unit
-from pydantic import BaseModel, Field, validator
 from qcportal import PortalClient
 from qcportal.dataset_models import BaseDataset as QCPDataset
 from qcportal.optimization import OptimizationDataset, OptimizationRecord
@@ -38,6 +37,7 @@
 from qcportal.torsiondrive import TorsiondriveDataset, TorsiondriveRecord
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import BaseModel, Field, validator
 from openff.qcsubmit.common_structures import Metadata, MoleculeAttributes, QCSpec
 from openff.qcsubmit.datasets import BasicDataset
 from openff.qcsubmit.exceptions import RecordTypeError

openff/qcsubmit/serializers.py

@@ -9,9 +9,9 @@
 from typing import IO, Dict, Optional, Tuple, Union
 
 import yaml
-from pydantic import BaseModel
 from typing_extensions import Literal
 
+from openff.qcsubmit._pydantic import BaseModel
 from openff.qcsubmit.exceptions import UnsupportedFiletypeError
 
 __all__ = [