fix import, tests, etc

MolSSI · Sep 9, 2024 · cf87140 · cf87140
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commit cf87140
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Showing 30 changed files with 184 additions and 253 deletions.
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.9", "3.11", "3.12"]
-        pydantic-version: ["1", "2"]
+        python-version: ["3.12"]
+        pydantic-version: ["2"]
         runs-on: [ubuntu-latest, windows-latest]
         exclude:
           - runs-on: windows-latest
@@ -35,15 +35,6 @@ jobs:
         uses: actions/checkout@v3
       - name: Install poetry
         run: pip install poetry
-      # Force pydantic 1.0 by modifying poetry dep "pydantic" string with in-place sed
-      # -i is zero-length extension which does effectively in-place sub.
-      # Can't do -i '' because Ubuntu sed is -i{suffix} whereas OSX sed is -i {suffix}... ugh
-      # ^ start of line, pydantic, optional spaces and > sign, capture the version, replace with ^{version}
-      # Should avoid also replacing the autodoc-pydantic spec later on.
-      - name: Sed replace pydantic on repo
-        if: matrix.pydantic-version == '1'
-        run: |
-          sed -i 's/^pydantic *= *">*= *\([0-9.]*\)"/pydantic = "^\1"/' pyproject.toml
       - name: Install repo with poetry (full deps)
         if: matrix.python-version != '3.9'
         run: poetry install --no-interaction --no-ansi --all-extras
@@ -74,12 +65,10 @@ jobs:
         name: Set up Python
         with:
           python-version: "3.10"
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
       - name: Install poetry
         run: pip install poetry
-      # Force pydantic 1.0 by modifying poetry dep "pydantic" string with in-place sed (see above for details)
-      - name: Sed replace pydantic on repo
-        run: |
-          sed -i 's/^pydantic *= *">*= *\([0-9.]*\)"/pydantic = "^\1"/' pyproject.toml
       - name: Install repo
         run: poetry install --no-interaction --no-ansi
       - name: Build Documentation

diff --git a/docs/api.rst b/docs/api.rst
@@ -12,7 +12,6 @@ QCElemental API
 .. automodapi:: qcelemental.testing
    :skip:tnm
 
-.. automodapi:: qcelemental.models
-   :skip:Optimization
+.. automodapi:: qcelemental.models.v2
    :skip:qcschema_models
 
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -26,13 +26,18 @@ Changelog
 Breaking Changes
 ++++++++++++++++
 * The very old model names `ResultInput`, `Result`, `ResultProperties`, `Optimization` deprecated in 2019 are now only available through `qcelelemental.models.v1`
+* ``models.v2`` do not support AutoDoc. The AutoDoc routines have been left at pydantic v1 syntax. Use autodoc-pydantic for Sphinx instead.
 
 New Features
 ++++++++++++
 * Downstream code should ``from qcelemental.models.v1 import Molecule, AtomicResult`` etc. to assure medium-term availability of existing models.
+* New pydantic v2 models available as ``from qcelemental.models.v2 import Molecule, AtomicResult`` etc.
 
 Enhancements
 ++++++++++++
+* The ``models.v2`` have had their `schema_version` bumped for ``BasisSet``, ``AtomicInput``, ``OptimizationInput`` (implicit for ``AtomicResult`` and ``OptimizationResult``), ``TorsionDriveInput`` , and ``TorsionDriveResult``.
+* The ``models.v2`` ``AtomicResultProperties`` has been given a ``schema_name`` and ``schema_version`` (2) for the first time.
+* Note that ``models.v2`` ``QCInputSpecification`` and ``OptimizationSpecification`` have *not* had schema_version bumped.
 
 Bug Fixes
 +++++++++

diff --git a/docs/conf.py b/docs/conf.py
@@ -88,7 +88,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -115,7 +115,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = []  # "_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -187,8 +187,8 @@
 # -- Extension configuration -------------------------------------------------
 
 extlinks = {
-    "issue": ("https://github.com/MolSSI/QCElemental/issues/%s", "GH#"),
-    "pr": ("https://github.com/MolSSI/QCElemental/pull/%s", "GH#"),
+    "issue": ("https://github.com/MolSSI/QCElemental/issues/%s", "GH#%s"),
+    "pr": ("https://github.com/MolSSI/QCElemental/pull/%s", "GH#%s"),
 }
 
 
@@ -200,8 +200,9 @@
     "numpy": ("https://numpy.org/doc/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
-    "qcengine": ("http://docs.qcarchive.molssi.org/projects/QCEngine/en/latest/", None),
-    "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None),
+    "qcengine": ("https://molssi.github.io/QCEngine/", None),
+    "qcfractal": ("https://molssi.github.io/QCFractal/", None),
+    "nglview": ("https://nglviewer.org/nglview/release/v2.7.7", None),
 }
 
 # -- Options for todo extension ----------------------------------------------

diff --git a/docs/model_common.rst b/docs/model_common.rst
@@ -6,40 +6,40 @@ Common Models used throughout the QCArchive ecosystem.
 BasisSet
 --------
 
-.. autopydantic_model:: qcelemental.models.BasisSet
+.. autopydantic_model:: qcelemental.models.v2.BasisSet
    :noindex:
 
-.. autopydantic_model:: qcelemental.models.basis.BasisCenter
+.. autopydantic_model:: qcelemental.models.v2.basis.BasisCenter
    :noindex:
 
-.. autopydantic_model:: qcelemental.models.basis.ElectronShell
+.. autopydantic_model:: qcelemental.models.v2.basis.ElectronShell
    :noindex:
 
-.. autopydantic_model:: qcelemental.models.basis.ECPPotential
+.. autopydantic_model:: qcelemental.models.v2.basis.ECPPotential
    :noindex:
 
 ComputeError
 ------------
 
-.. autopydantic_model:: qcelemental.models.ComputeError
+.. autopydantic_model:: qcelemental.models.v2.ComputeError
    :noindex:
 
 FailedOperation
 ---------------
 
-.. autopydantic_model:: qcelemental.models.FailedOperation
+.. autopydantic_model:: qcelemental.models.v2.FailedOperation
    :noindex:
 
 Provenance
 ----------
 
-.. autopydantic_model:: qcelemental.models.Provenance
+.. autopydantic_model:: qcelemental.models.v2.Provenance
    :noindex:
 
 DriverEnum
 ----------
 
-.. autoclass:: qcelemental.models.DriverEnum
+.. autoclass:: qcelemental.models.v2.DriverEnum
    :noindex:
    :members:
    :undoc-members:

diff --git a/docs/model_molecule.rst b/docs/model_molecule.rst
@@ -127,6 +127,6 @@ Obtaining fragments with ghost atoms is also supported:
 API
 ---
 
-.. autopydantic_model:: qcelemental.models.Molecule
+.. autopydantic_model:: qcelemental.models.v2.Molecule
    :noindex:
 
diff --git a/docs/model_result.rst b/docs/model_result.rst
@@ -8,25 +8,25 @@ A Python implementation of the `MolSSI QCSchema
 AtomicInput
 -----------
 
-.. autopydantic_model:: qcelemental.models.AtomicInput
+.. autopydantic_model:: qcelemental.models.v2.AtomicInput
    :noindex:
 
 AtomicResult
 ------------
 
-.. autopydantic_model:: qcelemental.models.AtomicResult
+.. autopydantic_model:: qcelemental.models.v2.AtomicResult
    :noindex:
 
 
 API
 ---
 
-.. autopydantic_model:: qcelemental.models.results.AtomicResultProtocols
+.. autopydantic_model:: qcelemental.models.v2.results.AtomicResultProtocols
    :noindex:
 
-.. autopydantic_model:: qcelemental.models.results.AtomicResultProperties
+.. autopydantic_model:: qcelemental.models.v2.results.AtomicResultProperties
    :noindex:
 
-.. autopydantic_model:: qcelemental.models.results.WavefunctionProperties
+.. autopydantic_model:: qcelemental.models.v2.results.WavefunctionProperties
    :noindex:
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,6 +23,8 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Framework :: Pydantic",
+    "Framework :: Pydantic :: 2",
 ]
 
 [tool.poetry.dependencies]
@@ -36,13 +38,13 @@ packaging = [
     { version = ">=24.1", python = ">=3.8" },
 ]
 # qcel is compatible with most any numpy, v1 or v2, but numpy v2 only works with pint >=0.24, which is only available for py >=3.10
-python = "^3.7"
+python = "^3.7.1"
 pint = [
     { version = ">=0.10", python = ">=3.7,<3.9" },
     { version = ">=0.23", python = ">=3.9,<3.10" },
     { version = ">=0.24", python = ">=3.10,<3.13" },
 ]
-pydantic = ">=1.8.2"
+pydantic = ">=2.0"
 nglview = { version = "^3.0.3", optional = true }
 ipykernel = { version = "<6.0.0", optional = true }
 importlib-metadata = { version = ">=4.8", python = "<3.8" }
@@ -59,23 +61,24 @@ align = ["networkx", "scipy"]
 test = ["pytest"]
 
 [tool.poetry.group.dev.dependencies]
-black = ">=22.1.0,<23.0a0"
-mypy = "^1.1.1"
-isort = "5.11.5"
-flake8 = "<6.0.0"
-pre-commit = "<3.2.0"
-pytest-cov = "^4.0.0"
-autoflake = "^2.0.2"
-jsonschema = "^4.17.3"
-msgpack = "^1.0.5"
-numpydoc = "^1.5.0"
-docutils = "<0.19"
-sphinx = "<6.0.0"
+black = ">=22.1.0,<23.0a0"  # unk
+mypy = "^1.1.1"  # unk
+isort = "5.11.5"  # unk
+flake8 = { version = "6.0.0", python = ">=3.8.1,<4.0.0" }
+pre-commit = { version = "^3.8.0", python = ">=3.9,<4.0.0" }
+pytest-cov = "^4.0.0"  # unk
+autoflake = "^2.0.2"  # unk
+jsonschema = { version = "^4.23.0", python = ">=3.8,<4.0.0" }
+msgpack = { version = "^1.0.8", python = ">=3.8,<4.0.0" }
+numpydoc = { version = "^1.8.0", python = ">=3.9,<4.0.0" }
+docutils = "0.20.1"
+sphinx = { version = "^7.0.0", python = ">=3.9,<4.0.0" }
 sphinxcontrib-napoleon = "^0.7"
-sphinx-rtd-theme = "^1.2.0"
-autodoc-pydantic = "^1.8.0"
-sphinx-automodapi = "^0.15.0"
-sphinx-autodoc-typehints = "^1.22"
+sphinx-rtd-theme = "^2.0.0"
+autodoc-pydantic = { version = "^2.1.0", python = ">=3.8,<4.0" }
+sphinx-automodapi = { version = "^0.17.0", python = ">=3.8,<4.0.0" }
+sphinx-autodoc-typehints = { version = "^2.3", python = ">=3.10,<4.0.0" }
+graphviz = "^0.20.0"  # insufficient on pypi as also need `dot`. python-graphviz sufficient in conda.
 
 [tool.black]
 line-length = 120

diff --git a/qcelemental/info/cpu_info.py b/qcelemental/info/cpu_info.py
@@ -8,10 +8,7 @@
 from functools import lru_cache
 from typing import List, Optional
 
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic.v1 import Field
 
 from ..models import ProtoModel
 

diff --git a/qcelemental/info/dft_info.py b/qcelemental/info/dft_info.py
@@ -4,10 +4,7 @@
 
 from typing import Dict
 
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic.v1 import Field
 
 from ..models import ProtoModel
 

diff --git a/qcelemental/models/__init__.py b/qcelemental/models/__init__.py
@@ -1 +1,10 @@
+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 v1, v2
 from .v1 import *
diff --git a/qcelemental/models/v1/__init__.py b/qcelemental/models/v1/__init__.py
@@ -1,11 +1,3 @@
-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`

diff --git a/qcelemental/models/v1/align.py b/qcelemental/models/v1/align.py
@@ -1,11 +1,7 @@
 from typing import Optional
 
 import numpy as np
-
-try:
-    from pydantic.v1 import Field, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field, validator
+from pydantic.v1 import Field, validator
 
 from ...util import blockwise_contract, blockwise_expand
 from .basemodels import ProtoModel

diff --git a/qcelemental/models/v1/basemodels.py b/qcelemental/models/v1/basemodels.py
@@ -3,13 +3,8 @@
 from typing import Any, Dict, Optional, Set, Union
 
 import numpy as np
-
-try:
-    from pydantic.v1 import BaseSettings  # remove when QCFractal merges `next`
-    from pydantic.v1 import BaseModel
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import BaseSettings  # remove when QCFractal merges `next`
-    from pydantic import BaseModel
+from pydantic.v1 import BaseSettings  # remove when QCFractal merges `next`
+from pydantic.v1 import BaseModel
 
 from qcelemental.util import deserialize, serialize
 from qcelemental.util.autodocs import AutoPydanticDocGenerator  # remove when QCFractal merges `next`

diff --git a/qcelemental/models/v1/basis.py b/qcelemental/models/v1/basis.py
@@ -1,10 +1,7 @@
 from enum import Enum
 from typing import Dict, List, Optional
 
-try:
-    from pydantic.v1 import ConstrainedInt, Field, constr, validator
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import ConstrainedInt, Field, constr, validator
+from pydantic.v1 import ConstrainedInt, Field, constr, validator
 
 from ...exceptions import ValidationError
 from .basemodels import ProtoModel, qcschema_draft

diff --git a/qcelemental/models/v1/common_models.py b/qcelemental/models/v1/common_models.py
@@ -2,20 +2,13 @@
 from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 
 import numpy as np
-
-try:
-    from pydantic.v1 import Field
-except ImportError:  # Will also trap ModuleNotFoundError
-    from pydantic import Field
+from pydantic.v1 import Field
 
 from .basemodels import ProtoModel, qcschema_draft
 from .basis import BasisSet
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.typing import ReprArgs
-    except ImportError:  # Will also trap ModuleNotFoundError
-        from pydantic.typing import ReprArgs
+    from pydantic.v1.typing import ReprArgs
 
 
 # Encoders, to be deprecated