Csse pyd2 502

.pre-commit-config.yaml

@@ -2,6 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
+    # will fail with git < 1.8.5
     rev: v4.4.0
     hooks:
       - id: check-yaml
@@ -12,6 +13,7 @@ repos:
     hooks:
       - id: detect-secrets
         stages: [commit]
+        exclude: "raw_data/nist_data/"
   # TODO: Update to 5.12.x once we drop Python3.7 support
   # https://levelup.gitconnected.com/fix-runtimeerror-poetry-isort-5db7c67b60ff
   - repo: https://github.com/PyCQA/isort

docs/changelog.rst

@@ -20,6 +20,7 @@ Changelog
 .. +++++
 
 
+
 0.28.0 / 2024-06-21
 -------------------
 

docs/model_molecule.rst

@@ -62,7 +62,7 @@ database.
 
     >>> mol = qcel.models.Molecule(**{"symbols": ["He", "He"], "geometry": [0, 0, -3, 0, 0, 3]})
     >>> mol.get_hash()
-    '84872f975d19aafa62b188b40fbadaf26a3b1f84'
+    '84872f975d19aafa62b188b40fbadaf26a3b1f84'  # pragma: allowlist secret
 
 Molecular Formula
 +++++++++++++++++

qcelemental/models/__init__.py

@@ -1,32 +1 @@
-try:
-    import pydantic
-except ImportError:  # pragma: no cover
-    raise ImportError(
-        "Python module pydantic not found. Solve by installing it: "
-        "`conda install pydantic -c conda-forge` or `pip install pydantic`"
-    )
-
-from . import types
-from .align import AlignmentMill
-from .basemodels import AutodocBaseSettings  # remove when QCFractal merges `next`
-from .basemodels import ProtoModel
-from .basis import BasisSet
-from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
-from .molecule import Molecule
-from .procedures import Optimization  # scheduled for removal
-from .procedures import OptimizationInput, OptimizationResult
-from .results import Result  # scheduled for removal
-from .results import ResultInput  # scheduled for removal
-from .results import ResultProperties  # scheduled for removal
-from .results import AtomicInput, AtomicResult, AtomicResultProperties
-
-
-def qcschema_models():
-    return [
-        AtomicInput,
-        AtomicResult,
-        AtomicResultProperties,
-        BasisSet,
-        Molecule,
-        Provenance,
-    ]
+from .v1 import *

qcelemental/models/v1/__init__.py

@@ -0,0 +1,32 @@
+try:
+    import pydantic
+except ImportError:  # pragma: no cover
+    raise ImportError(
+        "Python module pydantic not found. Solve by installing it: "
+        "`conda install pydantic -c conda-forge` or `pip install pydantic`"
+    )
+
+from . import types
+from .align import AlignmentMill
+from .basemodels import AutodocBaseSettings  # remove when QCFractal merges `next`
+from .basemodels import ProtoModel
+from .basis import BasisSet
+from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
+from .molecule import Molecule
+from .procedures import Optimization  # scheduled for removal
+from .procedures import OptimizationInput, OptimizationResult
+from .results import Result  # scheduled for removal
+from .results import ResultInput  # scheduled for removal
+from .results import ResultProperties  # scheduled for removal
+from .results import AtomicInput, AtomicResult, AtomicResultProperties
+
+
+def qcschema_models():
+    return [
+        AtomicInput,
+        AtomicResult,
+        AtomicResultProperties,
+        BasisSet,
+        Molecule,
+        Provenance,
+    ]

qcelemental/models/align.py → qcelemental/models/v1/align.py

@@ -7,7 +7,7 @@
 except ImportError:  # Will also trap ModuleNotFoundError
     from pydantic import Field, validator
 
-from ..util import blockwise_contract, blockwise_expand
+from ...util import blockwise_contract, blockwise_expand
 from .basemodels import ProtoModel
 from .types import Array
 

qcelemental/models/basis.py → qcelemental/models/v1/basis.py

@@ -6,7 +6,7 @@
 except ImportError:  # Will also trap ModuleNotFoundError
     from pydantic import ConstrainedInt, Field, constr, validator
 
-from ..exceptions import ValidationError
+from ...exceptions import ValidationError
 from .basemodels import ProtoModel, qcschema_draft
 
 

qcelemental/models/molecule.py → qcelemental/models/v1/molecule.py

@@ -17,15 +17,15 @@
     from pydantic import ConstrainedFloat, ConstrainedInt, Field, constr, validator
 
 # molparse imports separated b/c https://github.com/python/mypy/issues/7203
-from ..molparse.from_arrays import from_arrays
-from ..molparse.from_schema import from_schema
-from ..molparse.from_string import from_string
-from ..molparse.to_schema import to_schema
-from ..molparse.to_string import to_string
-from ..periodic_table import periodictable
-from ..physical_constants import constants
-from ..testing import compare, compare_values
-from ..util import deserialize, measure_coordinates, msgpackext_loads, provenance_stamp, which_import
+from ...molparse.from_arrays import from_arrays
+from ...molparse.from_schema import from_schema
+from ...molparse.from_string import from_string
+from ...molparse.to_schema import to_schema
+from ...molparse.to_string import to_string
+from ...periodic_table import periodictable
+from ...physical_constants import constants
+from ...testing import compare, compare_values
+from ...util import deserialize, measure_coordinates, msgpackext_loads, provenance_stamp, which_import
 from .basemodels import ProtoModel, qcschema_draft
 from .common_models import Provenance, qcschema_molecule_default
 from .types import Array
@@ -831,7 +831,7 @@ def get_molecular_formula(self, order: str = "alphabetical") -> str:
 
         """
 
-        from ..molutil import molecular_formula_from_symbols
+        from ...molutil import molecular_formula_from_symbols
 
         return molecular_formula_from_symbols(symbols=self.symbols, order=order)
 
@@ -1209,7 +1209,7 @@ def align(
             from `concern_mol` and the optimally aligned geometry.
 
         """
-        from ..molutil.align import B787
+        from ...molutil.align import B787
 
         rgeom = np.array(ref_mol.geometry)
         runiq = np.asarray(
@@ -1358,7 +1358,7 @@ def scramble(
             transformations.
 
         """
-        from ..molutil.align import compute_scramble
+        from ...molutil.align import compute_scramble
 
         ref_mol = self
         rgeom = ref_mol.geometry

qcelemental/models/procedures.py → qcelemental/models/v1/procedures.py

@@ -6,7 +6,7 @@
 except ImportError:  # Will also trap ModuleNotFoundError
     from pydantic import Field, conlist, constr, validator
 
-from ..util import provenance_stamp
+from ...util import provenance_stamp
 from .basemodels import ProtoModel
 from .common_models import (
     ComputeError,

qcelemental/models/results.py → qcelemental/models/v1/results.py

@@ -9,7 +9,7 @@
 except ImportError:  # Will also trap ModuleNotFoundError
     from pydantic import Field, constr, validator
 
-from ..util import provenance_stamp
+from ...util import provenance_stamp
 from .basemodels import ProtoModel, qcschema_draft
 from .basis import BasisSet
 from .common_models import ComputeError, DriverEnum, Model, Provenance, qcschema_input_default, qcschema_output_default

qcelemental/molutil/align.py

@@ -1,16 +1,18 @@
 import collections
 import itertools
 import time
-from typing import List, Optional, Union
+from typing import TYPE_CHECKING, List, Optional, Union
 
 import numpy as np
 
 from ..exceptions import ValidationError
-from ..models import AlignmentMill
 from ..physical_constants import constants
 from ..testing import compare_values
 from ..util import distance_matrix, linear_sum_assignment, random_rotation_matrix, uno, which_import
 
+if TYPE_CHECKING:
+    from qcelemental.models import AlignmentMill  # TODO: recheck if .v1 needed
+
 
 def _nre(Z, geom):
     """Nuclear repulsion energy"""
@@ -100,11 +102,13 @@ def B787(
     float, AlignmentMill
         First item is RMSD [A] between `rgeom` and the optimally aligned
         geometry computed.
-        Second item is a AlignmentMill with fields
+        Second item is an AlignmentMill with fields
         (shift, rotation, atommap, mirror) that prescribe the transformation
         from `cgeom` and the optimally aligned geometry.
 
     """
+    from qcelemental.models import AlignmentMill
+
     # validation
     if rgeom.shape != cgeom.shape or rgeom.shape[1] != 3:
         raise ValidationError("""natom doesn't match: {} != {}""".format(rgeom.shape, cgeom.shape))
@@ -564,7 +568,7 @@ def compute_scramble(
     do_rotate: Union[bool, List, np.ndarray] = True,
     deflection: float = 1.0,
     do_mirror: bool = False,
-) -> AlignmentMill:
+) -> "AlignmentMill":
     r"""Generate a random or directed translation, rotation, and atom shuffling.
 
     Parameters
@@ -595,6 +599,8 @@ def compute_scramble(
         as requested: identity, random, or specified.
 
     """
+    from qcelemental.models import AlignmentMill
+
     rand_elord = np.arange(nat)
     if do_resort is True:
         np.random.shuffle(rand_elord)

qcelemental/testing.py

@@ -2,7 +2,7 @@
 import logging
 import pprint
 import sys
-from typing import Callable, Dict, List, Tuple, Union
+from typing import TYPE_CHECKING, Callable, Dict, List, Tuple, Union
 
 import numpy as np
 
@@ -11,7 +11,8 @@
 except ImportError:  # Will also trap ModuleNotFoundError
     from pydantic import BaseModel
 
-from qcelemental.models.basemodels import ProtoModel
+if TYPE_CHECKING:
+    from qcelemental.models import ProtoModel  # TODO: recheck if .v1 needed
 
 pp = pprint.PrettyPrinter(width=120)
 

qcelemental/tests/test_model_results.py

@@ -2,7 +2,7 @@
 import pytest
 
 import qcelemental as qcel
-from qcelemental.models import basis
+from qcelemental.models.v1 import basis  # TODO: generalize at parameterize v1/v2 stage
 
 from .addons import drop_qcsk