Support Pydantic v2 installation (#524)

* Support Pydantic v2 installation * No channel priority * Add shim file * Re-jigger test environment setup * Syntax? * Loadscope * Run tutorials sequentially * Typo * Fix import
openforcefield · Nov 17, 2023 · 4fe5b81 · 4fe5b81
1 parent 6575945
commit 4fe5b81
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Showing 12 changed files with 69 additions and 20 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -18,7 +18,7 @@ jobs:
 
   test:
 
-    name: 💻 ${{ matrix.os }}, 🐍 ${{ matrix.python-version }}, 👀 ${{ matrix.openeye }}, pymbar ${{ matrix.pymbar-version }}, OpenMM ${{ matrix.openmm-version }}
+    name: 💻 ${{ matrix.os }}, 🐍 ${{ matrix.python-version }}, 👀 ${{ matrix.openeye }}, pymbar ${{ matrix.pymbar-version }}, Pydantic ${{ matrix.pydantic-version }}, OpenMM ${{ matrix.openmm-version }}
     runs-on: ${{ matrix.os }}
 
     env:
@@ -35,6 +35,9 @@ jobs:
           - "3.10"
         pymbar-version:
           - "3.1"
+        pydantic-version:
+          - "1"
+          - "2"
         openmm-version:
           - "7"
           - "8"
@@ -55,9 +58,8 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pymbar=${{ matrix.pymbar-version }}
+            pydantic=${{ matrix.pydantic-version }}
             openmm=${{ matrix.openmm-version }}
-            jax>=0.3
-            jaxlib>=0.3
 
       - name: Install OpenEye
         if: matrix.openeye
@@ -69,6 +71,11 @@ jobs:
         env:
           SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
+      - name: Install Foyer
+        if: ${{ matrix.pydantic-version == 1 }}
+        shell: bash -l {0}
+        run: micromamba install foyer -c conda-forge
+
       - name: Install PASCAL Compiler (MacOS)
         if: startsWith(matrix.os, 'macOS')
         run: brew install fpc
@@ -88,20 +95,19 @@ jobs:
       - name: Install Package and test plugins
         run: python -m pip install . utilities/test_plugins/
 
-      - name: Conda Environment Information
-        run: conda info && conda list
-
       - name: Run tests
         run: python -m pytest -v --cov=openff openff/evaluator/_tests/ --cov-report=xml --color=yes
 
       - name: Run (non-GPU) tutorials
-        if: ${{ matrix.pymbar-version == 3 }}
+        if: ${{ matrix.pymbar-version == 3.1 }}
         run: |
           # ForceBalance requires pymbar 3, so don't run these tests if we are using pymbar 4,
           # even though we're not running the fitting tutorial
           # https://github.com/conda-forge/forcebalance-feedstock/blob/9793b0205489f8ec7826d301a3c82cfb96997c57/recipe/meta.yaml#L29
           micromamba install "forcebalance >=1.9.5" -c conda-forge -yq
-          python -m pytest --nbval-lax docs/tutorials/tutorial01.ipynb docs/tutorials/tutorial03.ipynb
+          python -m pytest --nbval-lax --dist loadscope -nauto -p no:randomly \
+            docs/tutorials/tutorial01.ipynb \
+            docs/tutorials/tutorial03.ipynb
 
       - name: Code coverage
         uses: codecov/codecov-action@v3

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -15,7 +15,8 @@ dependencies:
   - nbval
   - requests-mock # For testing http requests.
   # smirnoff-plugins =0.0.3
-  - foyer
+  # Add back when MoSDeF supports pydantic v2
+  # foyer
 
     # Shims
   - pint =0.20.1
@@ -32,7 +33,7 @@ dependencies:
   - pyyaml
   - requests
   - python-dateutil
-  - pydantic <2.0.0a0
+  - pydantic
   - paprika
   - taproom
   - dataclasses

diff --git a/openff/evaluator/_pydantic.py b/openff/evaluator/_pydantic.py
@@ -0,0 +1,32 @@
+try:
+    from pydantic.v1 import (
+        BaseModel,
+        Field,
+        HttpUrl,
+        PositiveFloat,
+        PositiveInt,
+        ValidationError,
+        confloat,
+        conint,
+        conlist,
+        constr,
+        root_validator,
+        validator,
+    )
+    from pydantic.v1.validators import dict_validator
+except ModuleNotFoundError:
+    from pydantic import (
+        BaseModel,
+        Field,
+        HttpUrl,
+        PositiveFloat,
+        PositiveInt,
+        ValidationError,
+        confloat,
+        conint,
+        conlist,
+        constr,
+        root_validator,
+        validator,
+    )
+    from pydantic.validators import dict_validator
diff --git a/openff/evaluator/_tests/test_datasets/test_curation/test_filtering.py b/openff/evaluator/_tests/test_datasets/test_curation/test_filtering.py
@@ -4,8 +4,8 @@
 import pandas
 import pytest
 from openff.units import unit
-from pydantic import ValidationError
 
+from openff.evaluator._pydantic import ValidationError
 from openff.evaluator.datasets import (
     MeasurementSource,
     PhysicalPropertyDataSet,

diff --git a/openff/evaluator/_tests/test_protocols/test_forcefield.py b/openff/evaluator/_tests/test_protocols/test_forcefield.py
@@ -8,6 +8,7 @@
 from openff.toolkit.topology import Molecule
 from openff.toolkit.utils.rdkit_wrapper import RDKitToolkitWrapper
 from openff.units import unit
+from openff.utilities import skip_if_missing
 
 from openff.evaluator._tests.utils import build_tip3p_smirnoff_force_field
 from openff.evaluator.backends import ComputeResources
@@ -168,6 +169,7 @@ def download_callback(_, context):
         assert path.isfile(assign_parameters.parameterized_system.system_path)
 
 
+@skip_if_missing("foyer")
 def test_build_foyer_oplsaa_system():
     force_field_source = FoyerForceFieldSource("oplsaa")
     substance = Substance.from_components("C", "CC", "c1ccccc1", "CC(=O)O")
@@ -202,6 +204,7 @@ def test_build_foyer_oplsaa_system():
         assert path.isfile(energy_minimisation.output_coordinate_file)
 
 
+@skip_if_missing("foyer")
 def test_build_foyer_xml_system():
     with tempfile.TemporaryDirectory() as directory:
         force_field_source_path = path.join(directory, "ff.json")

diff --git a/openff/evaluator/datasets/curation/components/components.py b/openff/evaluator/datasets/curation/components/components.py
@@ -3,8 +3,8 @@
 from typing import overload
 
 import pandas
-from pydantic import BaseModel
 
+from openff.evaluator._pydantic import BaseModel
 from openff.evaluator.datasets import PhysicalPropertyDataSet
 
 logger = logging.getLogger(__name__)

diff --git a/openff/evaluator/datasets/curation/components/conversion.py b/openff/evaluator/datasets/curation/components/conversion.py
@@ -5,9 +5,9 @@
 from typing import TYPE_CHECKING, Union
 
 import pandas
-from pydantic import Field
 from typing_extensions import Literal
 
+from openff.evaluator._pydantic import Field
 from openff.evaluator.datasets.curation.components import (
     CurationComponent,
     CurationComponentSchema,
@@ -19,7 +19,7 @@
     PositiveFloat = float
 
 else:
-    from pydantic import conint
+    from openff.evaluator._pydantic import conint
 
 logger = logging.getLogger(__name__)
 

diff --git a/openff/evaluator/datasets/curation/components/filtering.py b/openff/evaluator/datasets/curation/components/filtering.py
@@ -7,10 +7,10 @@
 import numpy
 import pandas
 from openff.units import unit
-from pydantic import Field, root_validator, validator
 from scipy.optimize import linear_sum_assignment
 from typing_extensions import Literal
 
+from openff.evaluator._pydantic import Field, root_validator, validator
 from openff.evaluator.datasets.curation.components import (
     CurationComponent,
     CurationComponentSchema,
@@ -31,7 +31,13 @@
     PositiveFloat = float
 
 else:
-    from pydantic import PositiveFloat, PositiveInt, confloat, conint, constr
+    from openff.evaluator._pydantic import (
+        PositiveFloat,
+        PositiveInt,
+        confloat,
+        conint,
+        constr,
+    )
 
 logger = logging.getLogger(__name__)
 

diff --git a/openff/evaluator/datasets/curation/components/selection.py b/openff/evaluator/datasets/curation/components/selection.py
@@ -5,9 +5,9 @@
 
 import numpy
 import pandas
-from pydantic import BaseModel, Field, conlist, validator
 from typing_extensions import Literal
 
+from openff.evaluator._pydantic import BaseModel, Field, conlist, validator
 from openff.evaluator.datasets.curation.components import (
     CurationComponent,
     CurationComponentSchema,
@@ -36,7 +36,7 @@
         OEFingerPrint = None
 
 else:
-    from pydantic import PositiveInt
+    from openff.evaluator._pydantic import PositiveInt
 
 
 class State(BaseModel):

diff --git a/openff/evaluator/datasets/curation/components/thermoml.py b/openff/evaluator/datasets/curation/components/thermoml.py
@@ -8,9 +8,9 @@
 
 import pandas
 import requests
-from pydantic import Field, HttpUrl
 from typing_extensions import Literal
 
+from openff.evaluator._pydantic import Field, HttpUrl
 from openff.evaluator.datasets.curation.components import (
     CurationComponent,
     CurationComponentSchema,

diff --git a/openff/evaluator/datasets/curation/workflow.py b/openff/evaluator/datasets/curation/workflow.py
@@ -3,8 +3,8 @@
 
 import numpy
 import pandas
-from pydantic import BaseModel, Field
 
+from openff.evaluator._pydantic import BaseModel, Field
 from openff.evaluator.datasets import PhysicalPropertyDataSet
 from openff.evaluator.datasets.curation.components import CurationComponent
 from openff.evaluator.datasets.curation.components.conversion import (

diff --git a/setup.cfg b/setup.cfg
@@ -13,6 +13,7 @@ ignore = E203, E266, E501, W503
 select = B,C,E,F,W,T4,B9
 per-file-ignores =
     openff/evaluator/__init__.py:F401
+    openff/evaluator/_pydantic.py:F401
 
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