Csse pyd2 pull altered qcel and run pre-commit (#452)

* pull altered qcel

* check nwchem

* revise nwchem version for version processing change in qcel

* set up pre-commit, run on project

* Update runner.py

.github/workflows/CI.yml

@@ -145,10 +145,10 @@ jobs:
         qcore --accept-license
 
     - name: Special Config - QCElemental Dep
-      if: false
+      #if: false
       run: |
         conda remove qcelemental --force
-        python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@loriab-patch-2' --no-deps
+        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_pyd2_shimclasses' --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

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    - id: check-yaml
+    - id: check-added-large-files
+      args: ["--maxkb=250"]
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+      - id: detect-secrets
+        stages: [commit]
+        exclude: "versioneer.py"
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black
+        language_version: python3.12
+        args: [--line-length=120]
+        exclude: 'test_|versioneer.py|examples/.*|docs/.*|devtools/.*'
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+        files: \.py$
+        args: ["--profile", "black", --line-length=120]

examples/terachem_pbs.py

@@ -1,7 +1,9 @@
 import os
-import qcengine as qcng
+
 import qcelemental as qcel
 
+import qcengine as qcng
+
 os.environ["TERACHEM_PBS_HOST"] = "127.0.0.1"
 os.environ["TERACHEM_PBS_PORT"] = "11111"
 

qcengine/procedures/base.py

@@ -7,10 +7,10 @@
 from ..exceptions import InputError, ResourceError
 from .berny import BernyProcedure
 from .geometric import GeometricProcedure
+from .model import ProcedureHarness
 from .nwchem_opt import NWChemDriverProcedure
 from .optking import OptKingProcedure
 from .torsiondrive import TorsionDriveProcedure
-from .model import ProcedureHarness
 
 __all__ = ["register_procedure", "get_procedure", "list_all_procedures", "list_available_procedures"]
 

qcengine/procedures/berny.py

@@ -1,15 +1,15 @@
 import logging
-from qcengine.exceptions import UnknownError
 import sys
 import traceback
 from io import StringIO
 from typing import Any, Dict, Union
 
 import numpy as np
-from qcelemental.models import OptimizationInput, OptimizationResult, FailedOperation
+from qcelemental.models import FailedOperation, OptimizationInput, OptimizationResult
 from qcelemental.util import which_import
 
 import qcengine
+from qcengine.exceptions import UnknownError
 
 from ..config import TaskConfig
 from .model import ProcedureHarness

qcengine/procedures/nwchem_opt/__init__.py

@@ -1,12 +1,12 @@
-from typing import Union, Dict, Any
+from typing import Any, Dict, Union
 
-from qcelemental.models import OptimizationInput, AtomicInput, OptimizationResult, Provenance
+from qcelemental.models import AtomicInput, OptimizationInput, OptimizationResult, Provenance
 
 from qcengine.config import TaskConfig
-from qcengine.exceptions import UnknownError, InputError
+from qcengine.exceptions import InputError, UnknownError
+from qcengine.procedures.model import ProcedureHarness
 from qcengine.procedures.nwchem_opt.harvester import harvest_as_atomic_result
 from qcengine.programs.nwchem.runner import NWChemHarness
-from qcengine.procedures.model import ProcedureHarness
 
 
 class NWChemDriverProcedure(ProcedureHarness):

qcengine/programs/aimnet2.py

@@ -1,11 +1,14 @@
 from typing import TYPE_CHECKING, Dict
-from qcengine.programs.model import ProgramHarness
-from qcelemental.util import safe_version, which_import
+
 from qcelemental.models import AtomicResult, Provenance
+from qcelemental.util import safe_version, which_import
+
 from qcengine.exceptions import InputError
+from qcengine.programs.model import ProgramHarness
 
 if TYPE_CHECKING:
     from qcelemental.models import AtomicInput
+
     from qcengine.config import TaskConfig
 
 
@@ -59,6 +62,7 @@ def load_model(self, name: str):
     def compute(self, input_data: "AtomicInput", config: "TaskConfig"):
         self.found(raise_error=True)
         import torch
+
         from qcengine.units import ureg
 
         # check we can run on the set of elements

qcengine/programs/base.py

@@ -5,13 +5,15 @@
 from typing import Set
 
 from ..exceptions import InputError, ResourceError
-from .model import ProgramHarness
 from .adcc import AdccHarness
+from .aimnet2 import AIMNET2Harness
 from .cfour import CFOURHarness
 from .dftd3 import DFTD3Harness
 from .dftd_ng import DFTD4Harness, SDFTD3Harness
 from .gamess import GAMESSHarness
 from .gcp import GCPHarness, MCTCGCPHarness
+from .mace import MACEHarness
+from .model import ProgramHarness
 from .molpro import MolproHarness
 from .mopac import MopacHarness
 from .mp2d import MP2DHarness
@@ -28,8 +30,6 @@
 from .torchani import TorchANIHarness
 from .turbomole import TurbomoleHarness
 from .xtb import XTBHarness
-from .mace import MACEHarness
-from .aimnet2 import AIMNET2Harness
 
 __all__ = ["register_program", "get_program", "list_all_programs", "list_available_programs"]
 

qcengine/programs/empirical_dispersion_resources.py

@@ -4,9 +4,10 @@
 import copy
 from typing import Dict, List, Optional, Union
 
-from ..exceptions import InputError
 from qcelemental.util import parse_version
 
+from ..exceptions import InputError
+
 ## ==> Dispersion Aliases and Parameters <== ##
 
 # The dashcoeff dict below defines the -D parameters for most of the DFT methods. Some 'd2' are

qcengine/programs/mace.py

@@ -1,12 +1,15 @@
 from typing import TYPE_CHECKING, Dict, Union
-from qcelemental.models import AtomicResult, Provenance, FailedOperation
+
+from qcelemental.models import AtomicResult, FailedOperation, Provenance
 from qcelemental.util import safe_version, which_import
+
 from qcengine.exceptions import InputError
 from qcengine.programs.model import ProgramHarness
 from qcengine.units import ureg
 
 if TYPE_CHECKING:
     from qcelemental.models import AtomicInput, FailedOperation
+
     from qcengine.config import TaskConfig
 
 

qcengine/programs/model.py

@@ -6,10 +6,11 @@
     from pydantic.v1 import BaseModel
 except ImportError:
     from pydantic import BaseModel
+
 from qcelemental.models import AtomicInput, AtomicResult, FailedOperation
 
-from qcengine.exceptions import KnownErrorException
 from qcengine.config import TaskConfig
+from qcengine.exceptions import KnownErrorException
 
 logger = logging.getLogger(__name__)
 

qcengine/programs/tests/standard_suite_runner.py

@@ -11,8 +11,8 @@
 import qcengine as qcng
 from qcengine.programs.util import mill_qcvars
 
-from .standard_suite_ref import answer_hash, std_suite
 from .standard_suite_contracts import *
+from .standard_suite_ref import answer_hash, std_suite
 
 pp = pprint.PrettyPrinter(width=120)
 

qcengine/programs/tests/test_ghost.py

@@ -1,8 +1,8 @@
 import pprint
 import re
 
-import pytest
 import numpy as np
+import pytest
 import qcelemental as qcel
 from qcelemental.testing import compare, compare_values
 

qcengine/programs/turbomole/harvester.py

@@ -1,6 +1,6 @@
-from math import sqrt
 import re
 from decimal import Decimal
+from math import sqrt
 
 import numpy as np
 

qcengine/programs/util/__init__.py

@@ -1,10 +1,10 @@
-from .hessparse import load_hessian
-from .pdict import PreservingDict
 from .ao_reordering import (
-    reorder_column_ao_indices,
-    reorder_row_and_column_ao_indices,
     cca_ao_order_spherical,
     error_stamp,
     get_ao_conversion,
     mill_qcvars,
+    reorder_column_ao_indices,
+    reorder_row_and_column_ao_indices,
 )
+from .hessparse import load_hessian
+from .pdict import PreservingDict

qcengine/tests/test_procedures.py

@@ -3,7 +3,7 @@
 """
 
 import pytest
-from qcelemental.models import DriverEnum, OptimizationInput, FailedOperation
+from qcelemental.models import DriverEnum, FailedOperation, OptimizationInput
 from qcelemental.models.common_models import Model
 from qcelemental.models.procedures import OptimizationSpecification, QCInputSpecification, TDKeywords, TorsionDriveInput
 
@@ -256,7 +256,7 @@ def test_geometric_generic(input_data, program, model, bench):
     input_data["initial_molecule"] = qcng.get_molecule("water")
     input_data["input_specification"]["model"] = model
     input_data["keywords"]["program"] = program
-    input_data["input_specification"]["extras"] = {"_secret_tags": {"mysecret_tag": "data1"}}
+    input_data["input_specification"]["extras"] = {"_secret_tags": {"mysecret_tag": "data1"}}  # pragma: allowlist secret
 
     ret = qcng.compute_procedure(input_data, "geometric", raise_error=True)
     assert ret.success is True

setup.py

@@ -1,5 +1,7 @@
 import sys
+
 import setuptools
+
 import versioneer
 
 short_description = (

versioneer.py

@@ -277,10 +277,12 @@
 """
 
 from __future__ import print_function
+
 try:
     import configparser
 except ImportError:
     import ConfigParser as configparser
+
 import errno
 import json
 import os
@@ -1561,6 +1563,7 @@ def run(self):
 
     if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
         from cx_Freeze.dist import build_exe as _build_exe
+
         # nczeczulin reports that py2exe won't like the pep440-style string
         # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
         # setup(console=[{