Pydanticv2again (#414)

* Use Pydantic v1 API even with v2

The correct version of #736. I had originally had branched from a point way in the past.

* alt qcngrecords

* no records for now

* faux upgrate

* better sed

* only certain lanes

* tweak

* records back

* master qcenginerecords

* forgive

* mamba

* where'd they go?

* still work?

* update node12 to 16. retract adcc

* now adcc?

* try again adcc

* my bad

* adcc again

* check sphinx

* appease sphinx black

* sphinx

* maybe finally ready

---------

Co-authored-by: Levi Naden <lnaden@vt.edu>

.github/workflows/CI.yml

@@ -72,7 +72,7 @@ jobs:
     runs-on: ${{ matrix.cfg.runs-on }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
@@ -83,6 +83,12 @@ jobs:
         environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
         python-version: ${{ matrix.cfg.python-version }}
         auto-activate-base: false
+        show-channel-urls: true
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        add-pip-as-python-dependency: true
+        # note: conda-forge chnl req'd for Mambaforge, but we'll spec in file, not here `channels: conda-forge,...`
+        # note: any activate/deactivate use the conda cmd. other cmds use mamba cmd.
 
     - name: Special Config - NWChem
       if: "(matrix.cfg.label == 'NWChem')"
@@ -94,15 +100,30 @@ jobs:
       run: |
         qcore --accept-license
 
+    # note: psi4 on c-f pins to a single qcel and qcng, so this may be handy for solve-and-replace
+    #- name: Special Config - QCElemental Dep
+    #  if: (matrix.cfg.label == 'ADCC')
+    #  run: |
+    #    conda remove qcelemental --force
+    #    python -m pip install qcelemental>=0.26.0 --no-deps
+
+      # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
+      #       alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75
     - name: Special Config - QCEngine Dep
       if: "(matrix.cfg.label == 'Psi4-nightly') || (matrix.cfg.label == 'ADCC') || (matrix.cfg.label == 'optimization-dispersion')"
       run: |
         conda remove qcengine --force
 
+      # QCEngine CI and Psi4 are circularly dependent, so a hack is in order
+    - name: Special Config - Faux Pydantic Upgrade
+      if: "(matrix.cfg.label == 'Psi4-nightly') || (matrix.cfg.label == 'optimization-dispersion')"
+      run: |
+        sed -i s/from\ pydantic\ /from\ pydantic.v1\ /g ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/*py
+
     - name: Environment Information
       run: |
-        conda info
-        conda list --show-channel-urls
+        mamba info
+        mamba list
 
     - name: Install QCEngine
       run: |
@@ -120,7 +141,7 @@ jobs:
         pytest -rws -v --cov=qcengine --color=yes --cov-report=xml qcengine/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
 
   release_sphinx:
     needs: [build]
@@ -140,7 +161,7 @@ jobs:
     runs-on: ${{ matrix.cfg.runs-on }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Create Environment
       uses: conda-incubator/setup-miniconda@v2
@@ -149,11 +170,15 @@ jobs:
         environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
         python-version: ${{ matrix.cfg.python-version }}
         auto-activate-base: false
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        add-pip-as-python-dependency: true
+        channels: conda-forge
 
     - name: Environment Information
       run: |
-        conda info
-        conda list --show-channel-urls
+        mamba info
+        mamba list --show-channel-urls
 
     - name: Build Documentation
       run: |

devtools/conda-envs/adcc.yaml

@@ -1,22 +1,19 @@
 name: test
 channels:
   #- adcc
-  - defaults
-  - psi4/label/dev
   - conda-forge
+  - nodefaults
 dependencies:
-  - conda-forge::adcc>=0.15.7
-  - psi4
-  - blas=*=mkl  # not needed but an example of disuading solver from openblas and old psi
-  - intel-openmp!=2019.5
+  - adcc>=0.15.7
+  - psi4>=1.8.1
+  - conda-forge/label/libint_dev::libint
 
   # Core
   - python
-  - pyyaml
   - py-cpuinfo
   - psutil
   - qcelemental >=0.24.0
-  - pydantic>=1.0.0
+  - pydantic=1
   - msgpack-python
 
     # Testing

devtools/conda-envs/docs-cf.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - python
   - networkx
-  - pydantic
+  - pydantic=1
   - numpy
   - pint
 

devtools/conda-envs/opt-disp.yaml

@@ -24,7 +24,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - qcelemental >=0.24.0
+  - qcelemental >=0.26.0
   - pydantic>=1.0.0
   - msgpack-python
 

devtools/conda-envs/psi-nightly.yaml

@@ -5,14 +5,13 @@ channels:
 dependencies:
   - psi4
   - blas=*=mkl  # not needed but an example of disuading solver from openblas and old psi
-  - intel-openmp!=2019.5
 
     # Core
   - python
   - pyyaml
   - py-cpuinfo
   - psutil
-  - qcelemental >=0.24.0
+  - qcelemental >=0.26.0
   - pydantic>=1.0.0
   - msgpack-python
 

devtools/conda-envs/psi.yaml

@@ -17,6 +17,7 @@ dependencies:
   - psutil
   - qcelemental=0.24.0
   - pydantic=1.8.2  # test minimun stated version.
+  - msgpack-python
 
     # Testing
   - pytest

docs/source/changelog.rst

@@ -1,7 +1,8 @@
 Changelog
 =========
 
-.. vX.Y.0 / 2022-MM-DD
+.. vX.Y.0 / 2023-MM-DD
+.. Unreleased
 .. --------------------
 ..
 .. Breaking Changes
@@ -17,6 +18,22 @@ Changelog
 .. +++++++++
 
 
+v0.27.0 / 2023-08-DD
+--------------------
+
+Bug Fixes
++++++++++
+- (:pr:`414`) Import `pydantic.v1` from pydantic v2 so that QCEngine can work with any >=1.8.2 pydantic
+  until QCEngine is updated for v2. If using v2, use QCElemental >=v0.26.0 that has a similar change.
+  QCEngineRecords received similar treatment. @Lnaden, @loriab
+- (:pr:`414`) Versioneer - update so works with Python 3.12.
+- (:pr:`414`) Maintenance
+   - Sphinx - fix build errors.
+   - Lint - pin black to 2022 format.
+   - GHA - switch to mamba solver. @loriab
+- (:pr:`394`) Entos/Qcore - updated model environments. @loriab
+
+
 v0.26.0 / 2022-11-30
 --------------------
 

docs/source/conf.py

@@ -90,7 +90,7 @@
 #
 # 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.
@@ -190,8 +190,8 @@
 # -- Extension configuration -------------------------------------------------
 
 extlinks = {
-    'issue': ('https://github.com/MolSSI/QCEngine/issues/%s', 'GH#'),
-    'pr': ('https://github.com/MolSSI/QCEngine/pull/%s', 'GH#')
+    'issue': ('https://github.com/MolSSI/QCEngine/issues/%s', 'GH#%s'),
+    'pr': ('https://github.com/MolSSI/QCEngine/pull/%s', 'GH#%s')
 }
 
 # -- Options for intersphinx extension ---------------------------------------

qcengine/compute.py

@@ -13,7 +13,10 @@
 from .util import compute_wrapper, environ_context, handle_output_metadata, model_wrapper
 
 if TYPE_CHECKING:
-    from pydantic.main import BaseModel
+    try:
+        from pydantic.v1.main import BaseModel
+    except ImportError:
+        from pydantic.main import BaseModel
     from qcelemental.models import AtomicResult
 
 

qcengine/config.py

@@ -9,7 +9,10 @@
 import socket
 from typing import Any, Dict, Optional, Union
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 
 from .extras import get_information
 

qcengine/procedures/model.py

@@ -1,7 +1,10 @@
 import abc
 from typing import Any, Dict, Union
 
-from pydantic import BaseModel
+try:
+    from pydantic.v1 import BaseModel
+except ImportError:
+    from pydantic import BaseModel
 
 from ..util import model_wrapper
 

qcengine/programs/model.py

@@ -2,7 +2,10 @@
 import logging
 from typing import Any, Dict, List, Optional, Tuple, Union
 
-from pydantic import BaseModel
+try:
+    from pydantic.v1 import BaseModel
+except ImportError:
+    from pydantic import BaseModel
 from qcelemental.models import AtomicInput, AtomicResult, FailedOperation
 
 from qcengine.exceptions import KnownErrorException

qcengine/programs/tests/test_qchem.py

@@ -16,6 +16,7 @@
     "root.provenance.routine",
     "root.provenance.creator",
     "root.extras",
+    "root.molecule.extras",
 ]
 
 

qcengine/testing.py

@@ -12,7 +12,7 @@
 
 import qcengine as qcng
 
-QCENGINE_RECORDS_COMMIT = "aa4a1b2"
+QCENGINE_RECORDS_COMMIT = "0e2fdb4"
 
 
 def _check_qcenginerecords(return_data=False):

qcengine/tests/test_config.py

@@ -4,7 +4,10 @@
 
 import copy
 
-import pydantic
+try:
+    import pydantic.v1 as pydantic
+except ImportError:
+    import pydantic
 import pytest
 
 import qcengine as qcng

qcengine/tests/test_harness_canonical.py

@@ -84,7 +84,7 @@ def test_compute_gradient(program, model, keywords):
         with pytest.raises(qcng.exceptions.InputError) as e:
             qcng.compute(inp, program, raise_error=True)
 
-        assert "Driver gradient not implemented" in str(e.value)
+        assert "gradient not implemented" in str(e.value)
 
     else:
         ret = qcng.compute(inp, program, raise_error=True)

qcengine/util.py

@@ -18,7 +18,10 @@
 from threading import Thread
 from typing import Any, BinaryIO, Dict, List, Optional, TextIO, Tuple, Union
 
-from pydantic import BaseModel, ValidationError
+try:
+    from pydantic.v1 import BaseModel, ValidationError
+except ImportError:
+    from pydantic import BaseModel, ValidationError
 from qcelemental.models import AtomicResult, FailedOperation, OptimizationResult
 
 from qcengine.config import TaskConfig

setup.py

@@ -28,7 +28,7 @@
         cmdclass=versioneer.get_cmdclass(),
         packages=setuptools.find_packages(),
         setup_requires=[] + pytest_runner,
-        install_requires=["pyyaml", "py-cpuinfo", "psutil", "qcelemental>=0.24.0,<0.26.0", "pydantic>=1.8.2"],
+        install_requires=["pyyaml", "py-cpuinfo", "psutil", "qcelemental>=0.24.0,<0.27.0", "pydantic>=1.8.2"],
         entry_points={"console_scripts": ["qcengine=qcengine.cli:main"]},
         extras_require={
             "docs": [
@@ -38,7 +38,7 @@
                 "numpydoc",
             ],
             "tests": ["pytest", "pytest-cov"],
-            "lint": ["black"],
+            "lint": ["black>=22.1.0,<23.0a0"],
         },
         tests_require=["pytest", "pytest-cov"],
         classifiers=[
@@ -50,6 +50,8 @@
             "Programming Language :: Python :: 3.7",
             "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
+            "Programming Language :: Python :: 3.10",
+            "Programming Language :: Python :: 3.11",
         ],
         zip_safe=False,
         long_description=long_description,

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):