Merge pull request #787 from mattwthompson/pydantic-v2

Enable Pydantic v1/v2 dual-compatibility

docs/requirements.txt

@@ -1,8 +1,9 @@
 sphinx_design
 pydata_sphinx_theme
 sphinx
-autodoc-pydantic
 sphinx-copybutton
+autodoc-pydantic==1.9.0
+pydantic==1.10.11
 myst-nb
 nglview
 -e ../qcportal

qcarchivetesting/conda-envs/fulltest_qcportal.yaml

@@ -9,11 +9,11 @@ dependencies:
   - msgpack-python
   - requests
   - pyyaml
-  - pydantic<2.0
+  - pydantic
   - zstandard
   - qcelemental
   - tabulate
   - tqdm
   - pandas
   - pyjwt
-  - packaging
+  - packaging

qcarchivetesting/conda-envs/fulltest_server.yaml

@@ -13,7 +13,7 @@ dependencies:
   - msgpack-python
   - requests
   - pyyaml
-  - pydantic<2.0
+  - pydantic
   - zstandard
   - qcelemental
   - tabulate

qcarchivetesting/conda-envs/fulltest_snowflake.yaml

@@ -14,7 +14,7 @@ dependencies:
   - msgpack-python
   - requests
   - pyyaml
-  - pydantic<2.0
+  - pydantic
   - zstandard
   - qcelemental
   - tabulate
@@ -49,4 +49,4 @@ dependencies:
 
   - pip:
       - "geometric @ git+https://github.com/hjnpark/geomeTRIC"
-      - scipy # for geometric
+      - scipy # for geometric

qcarchivetesting/conda-envs/fulltest_worker.yaml

@@ -13,7 +13,7 @@ dependencies:
   - msgpack-python
   - requests
   - pyyaml
-  - pydantic<2.0
+  - pydantic
   - zstandard
   - qcelemental
   - tabulate

qcfractal/qcfractal/components/gridoptimization/record_socket.py

@@ -7,7 +7,10 @@
 
 import numpy as np
 import sqlalchemy.orm.attributes
-from pydantic import BaseModel, Extra, parse_obj_as
+try:
+    from pydantic.v1 import BaseModel, Extra, parse_obj_as
+except ImportError:
+    from pydantic import BaseModel, Extra, parse_obj_as
 from sqlalchemy import select, func
 from sqlalchemy.dialects.postgresql import insert
 from sqlalchemy.orm import lazyload, joinedload, undefer, defer

qcfractal/qcfractal/components/gridoptimization/testing_helpers.py

@@ -3,7 +3,10 @@
 import json
 from typing import TYPE_CHECKING, Tuple, Optional, Dict, Union, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, OptimizationResult
 from qcelemental.models.procedures import OptimizationProtocols
 

qcfractal/qcfractal/components/managers/test_manager_client.py

@@ -4,7 +4,10 @@
 from typing import TYPE_CHECKING
 
 import pytest
-from pydantic import ValidationError
+try:
+    from pydantic.v1 import ValidationError
+except ImportError:
+    from pydantic import ValidationError
 
 from qcfractal.components.singlepoint.testing_helpers import submit_test_data
 from qcportal import PortalRequestError

qcfractal/qcfractal/components/manybody/testing_helpers.py

@@ -2,7 +2,10 @@
 
 from typing import TYPE_CHECKING, Tuple, Optional, Dict, Union, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, AtomicResult
 
 from qcarchivetesting.helpers import read_record_data

qcfractal/qcfractal/components/neb/record_socket.py

@@ -8,7 +8,11 @@
 import numpy as np
 import sqlalchemy.orm.attributes
 import tabulate
-from pydantic import BaseModel, Extra
+try:
+    from pydantic.v1 import BaseModel, Extra
+except ImportError:
+    from pydantic import BaseModel, Extra
+
 from sqlalchemy import select, func
 from sqlalchemy.dialects.postgresql import insert, array_agg, aggregate_order_by, DOUBLE_PRECISION, TEXT
 from sqlalchemy.orm import lazyload, joinedload, defer, undefer

qcfractal/qcfractal/components/neb/testing_helpers.py

@@ -2,7 +2,10 @@
 
 from typing import TYPE_CHECKING, Tuple, Optional, Dict, List, Union, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, AtomicResult, OptimizationResult
 
 from qcarchivetesting.helpers import read_record_data

qcfractal/qcfractal/components/optimization/testing_helpers.py

@@ -3,7 +3,10 @@
 from datetime import datetime
 from typing import TYPE_CHECKING, Tuple, Optional, Union, Dict, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, OptimizationResult
 
 from qcarchivetesting.helpers import read_record_data

qcfractal/qcfractal/components/reaction/testing_helpers.py

@@ -2,7 +2,10 @@
 
 from typing import TYPE_CHECKING, Tuple, Optional, Dict, List, Union, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, AtomicResult, OptimizationResult
 
 from qcarchivetesting.helpers import read_record_data

qcfractal/qcfractal/components/singlepoint/testing_helpers.py

@@ -3,7 +3,10 @@
 from datetime import datetime
 from typing import TYPE_CHECKING, Tuple, Optional, Union, Dict, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, AtomicResult
 
 from qcarchivetesting.helpers import read_record_data

qcfractal/qcfractal/components/tasks/socket.py

@@ -5,7 +5,10 @@
 from datetime import datetime
 from typing import TYPE_CHECKING
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import FailedOperation
 from sqlalchemy import select, func
 from sqlalchemy.dialects.postgresql import array

qcfractal/qcfractal/components/torsiondrive/record_socket.py

@@ -9,7 +9,10 @@
 from typing import TYPE_CHECKING
 
 import sqlalchemy.orm.attributes
-from pydantic import BaseModel, Extra
+try:
+    from pydantic.v1 import BaseModel, Extra
+except ImportError:
+    from pydantic import BaseModel, Extra
 from sqlalchemy import select, func
 from sqlalchemy.dialects.postgresql import insert, array_agg, aggregate_order_by, DOUBLE_PRECISION, TEXT
 from sqlalchemy.orm import lazyload, joinedload, defer, undefer

qcfractal/qcfractal/components/torsiondrive/testing_helpers.py

@@ -3,7 +3,10 @@
 import json
 from typing import TYPE_CHECKING, Tuple, Optional, Dict, List, Union, Any
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from qcelemental.models import Molecule, FailedOperation, ComputeError, OptimizationResult
 from qcelemental.models.procedures import OptimizationProtocols
 

qcfractal/qcfractal/config.py

@@ -11,8 +11,12 @@
 
 import yaml
 from psycopg2.extensions import make_dsn, parse_dsn
-from pydantic import BaseSettings, Field, validator, root_validator, ValidationError
-from pydantic.env_settings import SettingsSourceCallable
+try:
+    from pydantic.v1 import BaseSettings, Field, validator, root_validator, ValidationError
+    from pydantic.v1.env_settings import SettingsSourceCallable
+except ImportError:
+    from pydantic import BaseSettings, Field, validator, root_validator, ValidationError
+    from pydantic.env_settings import SettingsSourceCallable
 from sqlalchemy.engine.url import URL, make_url
 
 from qcfractal.port_util import find_open_port

qcfractal/qcfractal/db_socket/base_orm.py

@@ -10,7 +10,10 @@
 
 if TYPE_CHECKING:
     from typing import Any, TypeVar, Type, Dict, Optional, Iterable, Union, List
-    from pydantic import BaseModel
+    try:
+        from pydantic.v1 import BaseModel
+    except ImportError:
+        from pydantic import BaseModel
 
     _T = TypeVar("_T")
 

qcfractal/qcfractal/flask_app/api_v1/helpers.py

@@ -1,7 +1,10 @@
 from functools import wraps
 from typing import Callable
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 from flask import request, Response
 from werkzeug.exceptions import BadRequest
 

qcfractal/qcfractal/old_config.py

@@ -9,7 +9,10 @@
 from typing import Optional
 
 import yaml
-from pydantic import Field, validator
+try:
+    from pydantic.v1 import Field, validator
+except ImportError:
+    from pydantic import Field, validator
 
 from .config import ConfigBase, ConfigCommon
 

qcfractalcompute/qcfractalcompute/apps/models.py

@@ -1,6 +1,9 @@
 from __future__ import annotations
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 
 from qcportal.compression import decompress, CompressionEnum
 

qcfractalcompute/qcfractalcompute/compute_manager.py

@@ -17,7 +17,10 @@
 from parsl.dataflow.dflow import DataFlowKernel
 from parsl.dataflow.futures import Future as ParslFuture
 from parsl.executors import HighThroughputExecutor, ThreadPoolExecutor
-from pydantic import BaseModel, Extra, Field
+try:
+    from pydantic.v1 import BaseModel, Extra, Field
+except ImportError:
+    from pydantic import BaseModel, Extra, Field
 from requests.exceptions import Timeout
 
 from qcfractalcompute.apps.app_manager import AppManager

qcfractalcompute/qcfractalcompute/config.py

@@ -3,7 +3,10 @@
 from typing import List, Optional, Union, Dict, Any
 
 import yaml
-from pydantic import BaseModel, Field, validator
+try:
+    from pydantic.v1 import BaseModel, Field, validator
+except ImportError:
+    from pydantic import BaseModel, Field, validator
 from typing_extensions import Literal
 
 from qcportal.utils import seconds_to_hms

qcportal/pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "msgpack",
     "requests",
     "pyyaml",
-    "pydantic<2.0",
+    "pydantic",
     "zstandard",
     "qcelemental",
     "tabulate",

qcportal/qcportal/auth/models.py

@@ -3,7 +3,10 @@
 from enum import Enum
 from typing import Optional, Union, List
 
-from pydantic import BaseModel, Field, validator, constr, Extra
+try:
+    from pydantic.v1 import BaseModel, Field, validator, constr, Extra
+except ImportError:
+    from pydantic import BaseModel, Field, validator, constr, Extra
 
 from ..exceptions import InvalidPasswordError, InvalidUsernameError, InvalidRolenameError, InvalidGroupnameError
 

qcportal/qcportal/base_models.py

@@ -2,7 +2,10 @@
 
 from typing import Optional, List, Iterator, Generic, TypeVar
 
-from pydantic import BaseModel, validator, Extra
+try:
+    from pydantic.v1 import BaseModel, validator, Extra
+except ImportError:
+    from pydantic import BaseModel, validator, Extra
 
 T = TypeVar("T")
 

qcportal/qcportal/client_base.py

@@ -14,7 +14,10 @@
 )
 
 import jwt
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 import requests
 import yaml
 from packaging.version import parse as parse_version

qcportal/qcportal/dataset_models.py

@@ -4,8 +4,12 @@
 from typing import Optional, Dict, Any, List, Iterable, Type, Tuple, Union, Callable, ClassVar, Sequence
 
 import pandas as pd
-import pydantic
-from pydantic import BaseModel, Extra, validator, PrivateAttr, Field
+try:
+    import pydantic.v1 as pydantic
+    from pydantic.v1 import BaseModel, Extra, validator, PrivateAttr, Field
+except ImportError:
+    import pydantic
+    from pydantic import BaseModel, Extra, validator, PrivateAttr, Field
 from qcelemental.models.types import Array
 from tabulate import tabulate
 from tqdm import tqdm

qcportal/qcportal/dataset_view.py

@@ -5,7 +5,10 @@
 from typing import Optional, Dict, Any, List, Iterable
 
 import zstandard
-from pydantic import BaseModel, validator, PrivateAttr, parse_obj_as, Extra
+try:
+    from pydantic.v1 import BaseModel, validator, PrivateAttr, parse_obj_as, Extra
+except ImportError:
+    from pydantic import BaseModel, validator, PrivateAttr, parse_obj_as, Extra
 
 from qcportal.serialization import deserialize
 

qcportal/qcportal/gridoptimization/dataset_models.py

@@ -1,6 +1,9 @@
 from typing import Dict, Any, Union, Optional, Iterable, Tuple
 
-from pydantic import BaseModel, Extra
+try:
+    from pydantic.v1 import BaseModel, Extra
+except ImportError:
+    from pydantic import BaseModel, Extra
 from typing_extensions import Literal
 
 from qcportal.dataset_models import BaseDataset

qcportal/qcportal/gridoptimization/record_models.py

@@ -2,7 +2,10 @@
 from enum import Enum
 from typing import List, Union, Optional, Dict, Iterable, Tuple, Sequence, Any
 
-from pydantic import BaseModel, Extra, Field, constr, validator
+try:
+    from pydantic.v1 import BaseModel, Extra, Field, constr, validator
+except ImportError:
+    from pydantic import BaseModel, Extra, Field, constr, validator
 from typing_extensions import Literal
 
 from qcportal.molecules import Molecule

qcportal/qcportal/internal_jobs/models.py

@@ -3,7 +3,10 @@
 from typing import Optional, Dict, Any, List, Union
 
 from dateutil.parser import parse as date_parser
-from pydantic import BaseModel, Extra, validator
+try:
+    from pydantic.v1 import BaseModel, Extra, validator
+except ImportError:
+    from pydantic import BaseModel, Extra, validator
 
 from qcportal.base_models import QueryProjModelBase
 from ..base_models import QueryIteratorBase