From 35c12a4cd4047171fdc591b76cfab648602f541d Mon Sep 17 00:00:00 2001
From: "Lori A. Burns" <lori.burns@gmail.com>
Date: Thu, 22 Aug 2024 09:12:41 -0400
Subject: [PATCH 1/4] move models to models/v1

---
 qcelemental/models/{ => v1}/__init__.py      | 0
 qcelemental/models/{ => v1}/align.py         | 0
 qcelemental/models/{ => v1}/basemodels.py    | 0
 qcelemental/models/{ => v1}/basis.py         | 0
 qcelemental/models/{ => v1}/common_models.py | 0
 qcelemental/models/{ => v1}/molecule.py      | 0
 qcelemental/models/{ => v1}/procedures.py    | 0
 qcelemental/models/{ => v1}/results.py       | 0
 qcelemental/models/{ => v1}/types.py         | 0
 9 files changed, 0 insertions(+), 0 deletions(-)
 rename qcelemental/models/{ => v1}/__init__.py (100%)
 rename qcelemental/models/{ => v1}/align.py (100%)
 rename qcelemental/models/{ => v1}/basemodels.py (100%)
 rename qcelemental/models/{ => v1}/basis.py (100%)
 rename qcelemental/models/{ => v1}/common_models.py (100%)
 rename qcelemental/models/{ => v1}/molecule.py (100%)
 rename qcelemental/models/{ => v1}/procedures.py (100%)
 rename qcelemental/models/{ => v1}/results.py (100%)
 rename qcelemental/models/{ => v1}/types.py (100%)

diff --git a/qcelemental/models/__init__.py b/qcelemental/models/v1/__init__.py
similarity index 100%
rename from qcelemental/models/__init__.py
rename to qcelemental/models/v1/__init__.py
diff --git a/qcelemental/models/align.py b/qcelemental/models/v1/align.py
similarity index 100%
rename from qcelemental/models/align.py
rename to qcelemental/models/v1/align.py
diff --git a/qcelemental/models/basemodels.py b/qcelemental/models/v1/basemodels.py
similarity index 100%
rename from qcelemental/models/basemodels.py
rename to qcelemental/models/v1/basemodels.py
diff --git a/qcelemental/models/basis.py b/qcelemental/models/v1/basis.py
similarity index 100%
rename from qcelemental/models/basis.py
rename to qcelemental/models/v1/basis.py
diff --git a/qcelemental/models/common_models.py b/qcelemental/models/v1/common_models.py
similarity index 100%
rename from qcelemental/models/common_models.py
rename to qcelemental/models/v1/common_models.py
diff --git a/qcelemental/models/molecule.py b/qcelemental/models/v1/molecule.py
similarity index 100%
rename from qcelemental/models/molecule.py
rename to qcelemental/models/v1/molecule.py
diff --git a/qcelemental/models/procedures.py b/qcelemental/models/v1/procedures.py
similarity index 100%
rename from qcelemental/models/procedures.py
rename to qcelemental/models/v1/procedures.py
diff --git a/qcelemental/models/results.py b/qcelemental/models/v1/results.py
similarity index 100%
rename from qcelemental/models/results.py
rename to qcelemental/models/v1/results.py
diff --git a/qcelemental/models/types.py b/qcelemental/models/v1/types.py
similarity index 100%
rename from qcelemental/models/types.py
rename to qcelemental/models/v1/types.py

From 2d227ca96bf66727e1d3bbf07ff391de1e3633e6 Mon Sep 17 00:00:00 2001
From: "Lori A. Burns" <lori.burns@gmail.com>
Date: Mon, 26 Aug 2024 12:01:14 -0400
Subject: [PATCH 2/4] fix up imports. tests clean

---
 qcelemental/models/__init__.py          |  1 +
 qcelemental/models/v1/align.py          |  2 +-
 qcelemental/models/v1/basis.py          |  2 +-
 qcelemental/models/v1/molecule.py       | 24 ++++++++++++------------
 qcelemental/models/v1/procedures.py     |  2 +-
 qcelemental/models/v1/results.py        |  2 +-
 qcelemental/molutil/align.py            | 14 ++++++++++----
 qcelemental/testing.py                  |  5 +++--
 qcelemental/tests/test_model_results.py |  2 +-
 9 files changed, 31 insertions(+), 23 deletions(-)
 create mode 100644 qcelemental/models/__init__.py

diff --git a/qcelemental/models/__init__.py b/qcelemental/models/__init__.py
new file mode 100644
index 00000000..e7e2ac4b
--- /dev/null
+++ b/qcelemental/models/__init__.py
@@ -0,0 +1 @@
+from .v1 import *
diff --git a/qcelemental/models/v1/align.py b/qcelemental/models/v1/align.py
index a994ee72..ca09504f 100644
--- a/qcelemental/models/v1/align.py
+++ b/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
 
diff --git a/qcelemental/models/v1/basis.py b/qcelemental/models/v1/basis.py
index dfd20b93..2a4b2c88 100644
--- a/qcelemental/models/v1/basis.py
+++ b/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
 
 
diff --git a/qcelemental/models/v1/molecule.py b/qcelemental/models/v1/molecule.py
index ac278a02..d2261f63 100644
--- a/qcelemental/models/v1/molecule.py
+++ b/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
diff --git a/qcelemental/models/v1/procedures.py b/qcelemental/models/v1/procedures.py
index 5aa7807f..90f3c7cf 100644
--- a/qcelemental/models/v1/procedures.py
+++ b/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,
diff --git a/qcelemental/models/v1/results.py b/qcelemental/models/v1/results.py
index 301e1734..44140729 100644
--- a/qcelemental/models/v1/results.py
+++ b/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
diff --git a/qcelemental/molutil/align.py b/qcelemental/molutil/align.py
index 4b3d8295..8c925250 100644
--- a/qcelemental/molutil/align.py
+++ b/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)
diff --git a/qcelemental/testing.py b/qcelemental/testing.py
index 6cf2e38a..6db0ada6 100644
--- a/qcelemental/testing.py
+++ b/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)
 
diff --git a/qcelemental/tests/test_model_results.py b/qcelemental/tests/test_model_results.py
index 7ce94efe..b3bba757 100644
--- a/qcelemental/tests/test_model_results.py
+++ b/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
 

From f2da61faecd2e338d27ac3476b8311c57ae13ad9 Mon Sep 17 00:00:00 2001
From: "Lori A. Burns" <lori.burns@gmail.com>
Date: Mon, 26 Aug 2024 13:21:34 -0400
Subject: [PATCH 3/4] check pre-commit on full repo

---
 .pre-commit-config.yaml | 2 ++
 docs/model_molecule.rst | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 37a79b5c..2d04f661 100644
--- a/.pre-commit-config.yaml
+++ b/.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
diff --git a/docs/model_molecule.rst b/docs/model_molecule.rst
index 79f5224a..0b76e76a 100644
--- a/docs/model_molecule.rst
+++ b/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
 +++++++++++++++++

From 5ab11195bf5700af77df40502f22a6a4210303cc Mon Sep 17 00:00:00 2001
From: "Lori A. Burns" <lori.burns@gmail.com>
Date: Tue, 3 Sep 2024 10:10:52 -0400
Subject: [PATCH 4/4] dummy

---
 docs/changelog.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/changelog.rst b/docs/changelog.rst
index b574e7f9..4f5cec1d 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -20,6 +20,7 @@ Changelog
 .. +++++
 
 
+
 0.28.0 / 2024-06-21
 -------------------