From 0e3567f090f141d4a70ec7cf62f9dcaec42d3ae1 Mon Sep 17 00:00:00 2001
From: Colton Hicks <github@coltonhicks.com>
Date: Wed, 30 Aug 2023 19:15:53 -0700
Subject: [PATCH] Updated pydantic v1 -> v2.

---
 CHANGELOG.md                |   4 +
 poetry.lock                 | 242 +++++++++++++++++++++++-------------
 pyproject.toml              |   4 +-
 qcio/helper_types.py        |  14 ++-
 qcio/models/base_models.py  | 115 +++++++----------
 qcio/models/inputs_base.py  |   7 +-
 qcio/models/molecule.py     |  19 ++-
 qcio/models/outputs.py      |  15 +--
 qcio/qcel.py                |   7 +-
 tests/test_base_io.py       |   6 +-
 tests/test_molecule.py      |  11 +-
 tests/test_serialization.py |  15 +--
 tests/test_single_point.py  |  11 +-
 13 files changed, 264 insertions(+), 206 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dc47e8f..0376771 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Changed
+
+- 🚨 BREAKING CHANGE 🚨 Updated `pydantic` from `v1` -> `v2`.
+
 ## [0.4.2]
 
 ### Added
diff --git a/poetry.lock b/poetry.lock
index ce2798f..c7b1a0d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,23 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+
+[[package]]
+name = "annotated-types"
+version = "0.5.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
+    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "black"
 version = "23.7.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -51,7 +64,6 @@ uvloop = ["uvloop (>=0.15.2)"]
 name = "cfgv"
 version = "3.3.1"
 description = "Validate configuration and produce human readable error messages."
-category = "dev"
 optional = false
 python-versions = ">=3.6.1"
 files = [
@@ -63,7 +75,6 @@ files = [
 name = "click"
 version = "8.1.5"
 description = "Composable command line interface toolkit"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -78,7 +89,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -90,7 +100,6 @@ files = [
 name = "coverage"
 version = "7.2.7"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -166,7 +175,6 @@ toml = ["tomli"]
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -178,7 +186,6 @@ files = [
 name = "exceptiongroup"
 version = "1.1.2"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -193,7 +200,6 @@ test = ["pytest (>=6)"]
 name = "filelock"
 version = "3.12.2"
 description = "A platform independent file lock."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -209,7 +215,6 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "p
 name = "identify"
 version = "2.5.24"
 description = "File identification library for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -224,7 +229,6 @@ license = ["ukkonen"]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -236,7 +240,6 @@ files = [
 name = "isort"
 version = "5.12.0"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -254,7 +257,6 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"]
 name = "mypy"
 version = "1.4.1"
 description = "Optional static typing for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -301,7 +303,6 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -313,7 +314,6 @@ files = [
 name = "nodeenv"
 version = "1.8.0"
 description = "Node.js virtual environment builder"
-category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
 files = [
@@ -328,7 +328,6 @@ setuptools = "*"
 name = "numpy"
 version = "1.24.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -366,7 +365,6 @@ files = [
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -378,7 +376,6 @@ files = [
 name = "pathspec"
 version = "0.11.1"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -390,7 +387,6 @@ files = [
 name = "pint"
 version = "0.21.1"
 description = "Physical quantities module"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -412,7 +408,6 @@ xarray = ["xarray"]
 name = "platformdirs"
 version = "3.9.1"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -428,7 +423,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-
 name = "pluggy"
 version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -444,7 +438,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pre-commit"
 version = "3.3.3"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -461,62 +454,145 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "pydantic"
-version = "1.10.11"
-description = "Data validation and settings management using python type hints"
-category = "main"
+version = "2.3.0"
+description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
-typing-extensions = ">=4.2.0"
+annotated-types = ">=0.4.0"
+pydantic-core = "2.6.3"
+typing-extensions = ">=4.6.1"
 
 [package.extras]
-dotenv = ["python-dotenv (>=0.10.4)"]
-email = ["email-validator (>=1.0.3)"]
+email = ["email-validator (>=2.0.0)"]
+
+[[package]]
+name = "pydantic-core"
+version = "2.6.3"
+description = ""
+optional = false
+python-versions = ">=3.7"
+files = [
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 [[package]]
 name = "pytest"
 version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
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@@ -539,7 +615,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-cov"
 version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -558,7 +633,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "pyyaml"
 version = "6.0"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -606,33 +680,32 @@ files = [
 
 [[package]]
 name = "qcelemental"
-version = "0.25.1"
-description = "Essentials for Quantum Chemistry."
-category = "dev"
+version = "0.26.0"
+description = "Core data structures for Quantum Chemistry."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7,<4.0"
 files = [
-    {file = "qcelemental-0.25.1-py3-none-any.whl", hash = "sha256:c923616ba29b50b9a99ea4fa1b6a1ad26d0f6070fc2b891e6e91f3df1de6d2ae"},
-    {file = "qcelemental-0.25.1.tar.gz", hash = "sha256:e3e0e53fe047d14756718441040a5d737135f0bdb33efb1d63a1935b95821a74"},
+    {file = "qcelemental-0.26.0-py3-none-any.whl", hash = "sha256:0b2e77e93dc8e14c78e54c2aafa6198661ffb49abae73a1352e5f384609dd5ff"},
+    {file = "qcelemental-0.26.0.tar.gz", hash = "sha256:a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd"},
 ]
 
 [package.dependencies]
-numpy = ">=1.12.0"
+numpy = [
+    {version = ">=1.12.0", markers = "python_version == \"3.8\""},
+    {version = ">=1.24.1", markers = "python_version >= \"3.9\""},
+]
 pint = ">=0.10.0"
 pydantic = ">=1.8.2"
 
 [package.extras]
-align = ["networkx (>=2.4.0)"]
-docs = ["autodoc-pydantic", "numpydoc", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-napoleon"]
-lint = ["autoflake", "black", "isort"]
-tests = ["pytest (>=4.0.0)", "pytest-cov"]
-viz = ["nglview"]
+align = ["networkx (<3.0)", "scipy (>=1.6.0)", "scipy (>=1.9.0)"]
+test = ["pytest (>=7.2.2,<8.0.0)"]
+viz = ["ipykernel (<6.0.0)", "nglview (>=3.0.3,<4.0.0)"]
 
 [[package]]
 name = "ruff"
 version = "0.0.260"
 description = "An extremely fast Python linter, written in Rust."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -659,7 +732,6 @@ files = [
 name = "setuptools"
 version = "68.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -676,7 +748,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -688,7 +759,6 @@ files = [
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -700,7 +770,6 @@ files = [
 name = "types-pyyaml"
 version = "6.0.12.10"
 description = "Typing stubs for PyYAML"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -712,7 +781,6 @@ files = [
 name = "types-toml"
 version = "0.10.8.6"
 description = "Typing stubs for toml"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -724,7 +792,6 @@ files = [
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -736,7 +803,6 @@ files = [
 name = "virtualenv"
 version = "20.24.0"
 description = "Virtual Python Environment builder"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -756,4 +822,4 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "d9f35f316a2ee4d1f285c7eaab13b1951762444bb94d5321260f80c7fd083d32"
+content-hash = "92fc36d95a6e694898268e1be3be3e6a89ece3020bacc8e513f3277c3c3eade6"
diff --git a/pyproject.toml b/pyproject.toml
index 0880ddc..c6cccaf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.8"
-pydantic = ">=1.7.4,!=1.8,!=1.8.1,<2.0.0"
+pydantic = ">=2.0.0"
 numpy = ">=1.20"
 toml = "^0.10.2"
 pyyaml = "^6.0"
@@ -26,7 +26,7 @@ pre-commit = "^3.2.1"
 pytest-cov = "^4.0.0"
 ruff = "^0.0.260"
 isort = "^5.12.0"
-qcelemental = "^0.25.1"
+qcelemental = ">=0.26.0"
 types-toml = "^0.10.8.6"
 types-pyyaml = "^6.0.12.10"
 
diff --git a/qcio/helper_types.py b/qcio/helper_types.py
index 0c14c80..7fd95aa 100644
--- a/qcio/helper_types.py
+++ b/qcio/helper_types.py
@@ -2,14 +2,22 @@
 from typing import List, Union
 
 import numpy as np
+from pydantic import PlainSerializer
+from typing_extensions import Annotated
 
-StrOrPath = Union[str, Path]
+StrOrPath = Annotated[Union[str, Path], PlainSerializer(lambda x: str(x))]
 
 # May be energy (float), gradient or hessian (List[List[float]])
 SPReturnResult = Union[float, List[List[float]]]
 
 # Type for any values that can be coerced to 2D numpy array
-ArrayLike2D = Union[List[List[float]], List[float], np.ndarray]
+ArrayLike2D = Annotated[
+    Union[List[List[float]], List[float], np.ndarray],
+    PlainSerializer(lambda x: np.array(x).tolist()),
+]
 
 # Type for any values that can be coerced to 3D numpy array
-ArrayLike3D = Union[List[List[List[float]]], List[List[float]], np.ndarray]
+ArrayLike3D = Annotated[
+    Union[List[List[List[float]]], List[List[float]], np.ndarray],
+    PlainSerializer(lambda x: np.array(x).tolist()),
+]
diff --git a/qcio/models/base_models.py b/qcio/models/base_models.py
index 565c5b9..91d3cbc 100644
--- a/qcio/models/base_models.py
+++ b/qcio/models/base_models.py
@@ -2,14 +2,13 @@
 import json
 from abc import ABC
 from base64 import b64decode, b64encode
-from enum import Enum
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
 
 import numpy as np
 import toml
 import yaml
-from pydantic import BaseModel, Extra, validator
+from pydantic import BaseModel, field_serializer, field_validator
 from typing_extensions import Self
 
 from ..helper_types import StrOrPath
@@ -35,49 +34,17 @@ class QCIOModelBase(BaseModel, ABC):
     # version: ClassVar[Literal["v1"]] = "v1"
     extras: Dict[str, Any] = {}
 
-    class Config:
+    model_config = {
         # Raises an error if extra fields are passed to model.
-        extra = Extra.forbid
+        "extra": "forbid",
         # Allow numpy types in models. Pydantic will no longer raise an exception for
         # types it doesn't recognize.
         # https://docs.pydantic.dev/latest/usage/types/#arbitrary-types-allowed
-        arbitrary_types_allowed = True
+        "arbitrary_types_allowed": True,
         # Don't allow mutation of objects
-        # https://docs.pydantic.dev/latest/usage/models/#faux-immutability
-        allow_mutation = False
-        # convert ndarray to list for JSON serialization
-        # https://docs.pydantic.dev/latest/usage/exporting_models/#json_encodershttps://docs.pydantic.dev/latest/usage/exporting_models/#json_encoders  # noqa: E501
-        json_encoders = {np.ndarray: lambda v: v.tolist()}
-        # exclude fields with value None from serialization
-        exclude_none = True
-
-    def dict(self, **kwargs):
-        """Convert the object to a dictionary.
-
-        Properly serialize numpy arrays. Serialization is performed in .dict() so that
-        multiple string serializers can used it without duplicating logic
-        (e.g. json, yaml, toml).
-        """
-        model_dict = super().dict(**kwargs)
-        to_pop = []
-        for key, value in model_dict.items():
-            # Custom serialization for numpy arrays, enums, and pathlib Paths
-            if isinstance(value, np.ndarray):
-                model_dict[key] = value.tolist()
-            elif issubclass(type(value), Enum):
-                model_dict[key] = value.value
-            elif isinstance(value, Path):
-                model_dict[key] = str(value)
-
-            # Exclude empty lists, dictionaries, and objects with all None values from
-            # serialization
-            elif value in [None, [], {}]:
-                to_pop.append(key)
-
-        for key in to_pop:
-            model_dict.pop(key)
-
-        return model_dict
+        # https://docs.pydantic.dev/2.3/api/config/#pydantic.config.ConfigDict.frozen
+        "frozen": True,
+    }
 
     @classmethod
     def open(cls, filepath: Union[Path, str]) -> Self:
@@ -95,37 +62,42 @@ def open(cls, filepath: Union[Path, str]) -> Self:
         data = filepath.read_text()
 
         if filepath.suffix in [".yaml", ".yml"]:
-            return cls.parse_obj(yaml.safe_load(data))
+            return cls.model_validate(yaml.safe_load(data))
         elif filepath.suffix == ".toml":
-            return cls.parse_obj(toml.loads(data))
+            return cls.model_validate(toml.loads(data))
 
         # Assume json for all other file extensions
-        return cls.parse_raw(data)
-        # pydantic v2
-        # return cls.model_validate_json(filepath.read_text())
+        return cls.model_validate_json(data)
 
-    def save(self, filepath: Union[Path, str], **kwargs) -> None:
-        """Write an object to disk as json.
+    def save(
+        self,
+        filepath: Union[Path, str],
+        exclude_none=True,
+        **kwargs,
+    ) -> None:
+        """Write an object to disk as json, yaml, or toml.
 
         Args:
-            filepath: The path to write the object to.I
+            filepath: The path to write the object to.
+            exclude_none: If True, attributes with a value of None will not be written.
+                Changing default behavior from pydantic.model_dump() to True.
         """
         filepath = Path(filepath)
         filepath.parent.mkdir(exist_ok=True, parents=True)
 
+        model_dict = self.model_dump(mode="json", exclude_none=exclude_none, **kwargs)
+
         if filepath.suffix in [".yaml", ".yml"]:
-            data = yaml.dump(self.dict(**kwargs))
+            data = yaml.dump(model_dict)
 
         elif filepath.suffix == ".toml":
-            data = toml.dumps(self.dict(**kwargs))
+            data = toml.dumps(model_dict)
 
         else:
             # Write data to json regardless of file extension
-            data = self.json(**kwargs)
+            data = json.dumps(model_dict)
 
         filepath.write_text(data)
-        # pydantic v2
-        # filepath.write(self.model_dump())
 
     def __repr_args__(self) -> "ReprArgs":
         """Only show non empty fields in repr."""
@@ -139,6 +111,15 @@ def exists(value):
             (name, value) for name, value in self.__dict__.items() if exists(value)
         ]
 
+    def __eq__(self, other: Any) -> bool:
+        """Check equality of two objects.
+
+        Necessary because BaseModel.__eq__ does not compare numpy arrays.
+        """
+        if isinstance(other, self.__class__):
+            return self.model_dump() == other.model_dump()
+        return False
+
 
 class Files(QCIOModelBase):
     """File model for handling string and binary data.
@@ -151,7 +132,7 @@ class Files(QCIOModelBase):
 
     files: Dict[str, Union[str, bytes]] = {}
 
-    @validator("files", pre=True)
+    @field_validator("files")
     def convert_base64_to_bytes(cls, value):
         """Convert base64 encoded data to bytes."""
         for filename, data in value.items():
@@ -159,21 +140,15 @@ def convert_base64_to_bytes(cls, value):
                 value[filename] = b64decode(data[7:])
         return value
 
-    def dict(self, *args, **kwargs):
-        """Return a dict representation of the object encoding bytes as b64 strings."""
-        dict = super().dict(*args, **kwargs)
-        if self.files:  # clause so that empty files dict is not included in dict
-            files = {}
-            for filename, data in self.files.items():
-                if isinstance(data, bytes):
-                    data = f"base64:{b64encode(data).decode('utf-8')}"
-                files[filename] = data
-            dict["files"] = files
-        return dict
-
-    def json(self, *args, **kwargs):
-        """Return a JSON representation of the object."""
-        return json.dumps(self.dict(*args, **kwargs))
+    @field_serializer("files")
+    def serialize_files(self, files, _info) -> Dict[str, str]:
+        """Serialize files to a dict of filename to base64 encoded string."""
+        return {
+            filename: f"base64:{b64encode(data).decode('utf-8')}"
+            if isinstance(data, bytes)
+            else data
+            for filename, data in files.items()
+        }
 
     def add_file(
         self, filepath: Union[Path, str], relative_dir: Optional[Path] = None
@@ -270,7 +245,7 @@ class Provenance(QCIOModelBase):
 
     program: str
     program_version: Optional[str] = None
-    scratch_dir: Optional[Path] = None
+    scratch_dir: Optional[StrOrPath] = None
     wall_time: Optional[float] = None
     hostname: Optional[str] = None
     hostcpus: Optional[int] = None
diff --git a/qcio/models/inputs_base.py b/qcio/models/inputs_base.py
index 4d4f1f9..a0ce9b5 100644
--- a/qcio/models/inputs_base.py
+++ b/qcio/models/inputs_base.py
@@ -4,7 +4,7 @@
 from enum import Enum
 from typing import Any, Dict, Optional
 
-from pydantic import BaseModel
+from pydantic import BaseModel, field_serializer
 
 from .base_models import Files
 from .molecule import Molecule
@@ -103,3 +103,8 @@ class StructuredInputBase(ProgramArgs):
 
     calctype: CalcType
     molecule: Molecule
+
+    @field_serializer("calctype")
+    def serialize_calctype(self, calctype: CalcType, _info) -> str:
+        """Serialize CalcType to string"""
+        return calctype.value
diff --git a/qcio/models/molecule.py b/qcio/models/molecule.py
index ee21c97..29bc53c 100644
--- a/qcio/models/molecule.py
+++ b/qcio/models/molecule.py
@@ -3,7 +3,7 @@
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
 
 import numpy as np
-from pydantic import validator
+from pydantic import field_serializer, field_validator
 from typing_extensions import Self
 
 from qcio.constants import BOHR_TO_ANGSTROM
@@ -102,12 +102,21 @@ def __repr_args__(self) -> "ReprArgs":
             ("formula", self.formula),
         ]
 
-    @validator("geometry")
+    @field_validator("geometry")
     def shape_n_by_3(cls, v, values, **kwargs):
         """Ensure there is an x, y, and z coordinate for each atom."""
-        n_atoms = len(values["symbols"])
+        n_atoms = len(values.data["symbols"])
         return np.array(v).reshape(n_atoms, 3)
 
+    @field_serializer("connectivity")
+    def serialize_connectivity(self, connectivity, _info) -> List[List[float]]:
+        """Serialize connectivity to a list of tuples.
+
+        Cannot have homogeneous data types in .toml files so must cast all values to
+        floats.
+        """
+        return [[float(val) for val in bond] for bond in connectivity]
+
     @property
     def formula(self) -> str:
         """Return the molecular formula of the molecule using the Hill System.
@@ -132,9 +141,9 @@ def formula(self) -> str:
             for element, count in sorted_elements
         )
 
-    def dict(self, **kwargs) -> Dict[str, Any]:
+    def model_dump(self, **kwargs) -> Dict[str, Any]:
         """Handle tuple in connectivity"""
-        as_dict = super().dict(**kwargs)
+        as_dict = super().model_dump(**kwargs)
         # Connectivity may be empty and super().dict() will remove empty values
         if (connectivity := as_dict.get("connectivity")) is not None:
             # Must cast all values to floats as toml cannot handle mixed types
diff --git a/qcio/models/outputs.py b/qcio/models/outputs.py
index 2cbfa7a..a776cd5 100644
--- a/qcio/models/outputs.py
+++ b/qcio/models/outputs.py
@@ -2,7 +2,7 @@
 from typing import List, Literal, Optional, Union
 
 import numpy as np
-from pydantic import validator
+from pydantic import field_validator
 
 from qcio.helper_types import ArrayLike2D, ArrayLike3D
 
@@ -55,13 +55,14 @@ class Wavefunction(QCIOModelBase):
     scf_occupations_a: Optional[ArrayLike2D] = None
     scf_occupations_b: Optional[ArrayLike2D] = None
 
-    _to_numpy = validator(
+    @field_validator(
         "scf_eigenvalues_a",
         "scf_eigenvalues_b",
         "scf_occupations_a",
         "scf_occupations_b",
-        allow_reuse=True,
-    )(lambda x: np.asarray(x) if x is not None else None)
+    )
+    def to_numpy(cls, val, _info) -> Optional[np.ndarray]:
+        return np.asarray(val) if val is not None else None
 
 
 class SinglePointResults(ResultsBase):
@@ -112,20 +113,20 @@ class SinglePointResults(ResultsBase):
     normal_modes_cartesian: Optional[ArrayLike3D] = None
     gibbs_free_energy: Optional[float] = None
 
-    @validator("normal_modes_cartesian")
+    @field_validator("normal_modes_cartesian")
     def validate_normal_modes_cartesian_shape(cls, v: ArrayLike3D):
         if v is not None:
             # Assume array has length of the number of normal modes
             n_normal_modes = len(v)
             return np.asarray(v).reshape(n_normal_modes, -1, 3)
 
-    @validator("gradient")
+    @field_validator("gradient")
     def validate_gradient_shape(cls, v: ArrayLike2D):
         """Validate gradient is n x 3"""
         if v is not None:
             return np.asarray(v).reshape(-1, 3)
 
-    @validator("hessian")
+    @field_validator("hessian")
     def validate_hessian_shape(cls, v: ArrayLike2D):
         """Validate hessian is square"""
         if v is not None:
diff --git a/qcio/qcel.py b/qcio/qcel.py
index 83d42a4..5d86ab6 100644
--- a/qcio/qcel.py
+++ b/qcio/qcel.py
@@ -30,12 +30,13 @@ def to_qcel_input(prog_input: ProgramInput) -> Dict[str, Any]:
             "connectivity": prog_input.molecule.connectivity or None,
             "identifiers": {
                 key: value
-                for key, value in prog_input.molecule.identifiers.dict().items()
-                if key not in ["name_IUPAC", "name_common"]  # not on qcel model
+                for key, value in prog_input.molecule.identifiers.model_dump().items()
+                if key
+                not in ["name_IUPAC", "name_common", "extras"]  # not on qcel model
             },
         },
         "driver": prog_input.calctype,
-        "model": prog_input.model.dict(),
+        "model": prog_input.model.model_dump(),
         "keywords": prog_input.keywords,
         "extras": prog_input.extras,
     }
diff --git a/tests/test_base_io.py b/tests/test_base_io.py
index 345e97f..d80f093 100644
--- a/tests/test_base_io.py
+++ b/tests/test_base_io.py
@@ -28,12 +28,10 @@ def test_file_b64(test_data_dir):
     mixin = Files()
     mixin.add_file(input_filepath)
     assert isinstance(mixin.files[input_filepath.name], bytes)
-    json_str = mixin.json()
+    json_str = mixin.model_dump_json()
     json_dict = json.loads(json_str)
     assert json_dict["files"][input_filepath.name].startswith("base64:")
-    mixin_new = mixin.parse_raw(json_str)
-    # v2
-    # file = File.model_validate_json(json_dict["data"])
+    mixin_new = mixin.model_validate_json(json_str)
     # Round trip of file is lossless
     assert mixin_new.files["c0"] == input_filepath.read_bytes()
 
diff --git a/tests/test_molecule.py b/tests/test_molecule.py
index 3717ead..72fe8b2 100644
--- a/tests/test_molecule.py
+++ b/tests/test_molecule.py
@@ -43,16 +43,11 @@ def test_to_from_file_json(test_data_dir, tmp_path):
     assert caffeine_copy.charge == caffeine.charge
 
 
-def test_molecule_dict_connectivity(water):
+def test_molecule_model_dump_connectivity(water):
     # Test that connectivity is a list of lists of floats
-    dict = water.dict()
+    # Must cast all to the same type as toml cannot handle mixed types
+    dict = water.model_dump()
     for bond in dict["connectivity"]:
         assert isinstance(bond, list)
         for val in bond:
             assert isinstance(val, float)
-
-    # Ensure the dict still works if connectivity not included
-    dict.pop("connectivity")
-    water = Molecule(**dict)
-    new_dict = water.dict()
-    assert "connectivity" not in new_dict
diff --git a/tests/test_serialization.py b/tests/test_serialization.py
index 11de90f..bd06310 100644
--- a/tests/test_serialization.py
+++ b/tests/test_serialization.py
@@ -18,16 +18,11 @@ def test_serialization_to_disk_json(sp_output, tmp_path):
 
 def test_serialization_to_disk_yaml(sp_output, tmp_path):
     """Test serialization to disk yaml"""
-
-    filename = tmp_path / "sp_output.yaml"
-    sp_output.save(filename)
-    reopened = SinglePointOutput.open(filename)
-    assert sp_output == reopened
-
-    filename = tmp_path / "sp_output.yml"
-    sp_output.save(filename)
-    reopened = SinglePointOutput.open(filename)
-    assert sp_output == reopened
+    for ext in [".yaml", ".yml"]:
+        filename = tmp_path / f"sp_output{ext}"
+        sp_output.save(filename)
+        reopened = SinglePointOutput.open(filename)
+        assert sp_output == reopened
 
 
 def test_serialization_to_disk_toml(sp_output, tmp_path):
diff --git a/tests/test_single_point.py b/tests/test_single_point.py
index 5b30271..c329abd 100644
--- a/tests/test_single_point.py
+++ b/tests/test_single_point.py
@@ -122,13 +122,15 @@ def test_return_result(sp_input):
     assert output.return_result == output.results.energy
 
     sp_inp_grad = sp_input("gradient")
-    output = SinglePointOutput(**{**output.dict(), **{"input_data": sp_inp_grad}})
+    output = SinglePointOutput(**{**output.model_dump(), **{"input_data": sp_inp_grad}})
 
     assert np.array_equal(output.return_result, gradient)
     assert np.array_equal(output.return_result, output.results.gradient)
 
     sp_inp_hessian = sp_input("hessian")
-    output = SinglePointOutput(**{**output.dict(), **{"input_data": sp_inp_hessian}})
+    output = SinglePointOutput(
+        **{**output.model_dump(), **{"input_data": sp_inp_hessian}}
+    )
 
     assert np.array_equal(output.return_result, hessian)
     assert np.array_equal(output.return_result, output.results.hessian)
@@ -136,9 +138,8 @@ def test_return_result(sp_input):
 
 def test_successful_output_serialization(sp_output):
     """Test that successful result serializes and deserializes"""
-    serialized = sp_output.json()
-    # model_validate_json in pydantic v2
-    deserialized = SinglePointOutput.parse_raw(serialized)
+    serialized = sp_output.model_dump_json()
+    deserialized = SinglePointOutput.model_validate_json(serialized)
     assert deserialized == sp_output
     assert deserialized.results == sp_output.results
     assert deserialized.input_data == sp_output.input_data