Csse pyd2 506e (#456)

* program harnesses to v2

* mostly fixed up

* fix nwc

* qcer

* more fix

* fix qcel to fix qchem

* docs

* docs2

* docs3

* docs4

* docs again

* why the error

* release a few pins

* next rnd

* docs

* suppress some warnings

* rest of test lanes

.github/workflows/CI.yml

@@ -158,7 +158,7 @@ jobs:
       #if: false
       run: |
         conda remove qcelemental --force
-        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_pyd2_converterclasses' --no-deps
+        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_pyd2_warnings' --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
@@ -236,6 +236,12 @@ jobs:
         add-pip-as-python-dependency: true
         channels: conda-forge
 
+    - name: Special Config - QCElemental Dep
+      #if: false
+      run: |
+        conda remove qcelemental --force
+        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_pyd2_warnings' --no-deps
+
     - name: Environment Information
       run: |
         conda info
@@ -244,6 +250,8 @@ jobs:
     - name: Build Documentation
       run: |
         python -m pip install . --no-deps
+        python -c "import qcelemental as q;print(q.__file__, q.__version__)"
+        python -c "import qcengine as q;print(q.__file__, q.__version__)"
         cd docs
         make html
 

devtools/conda-envs/docs-cf.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - python
   - networkx
-  - pydantic=2
+  - pydantic=2.5
   - pydantic-settings
   - numpy
   - pint

docs/source/changelog.rst

@@ -29,7 +29,7 @@ Changelog
 
 
 vX.Y.0 / 2024-MM-DD (Unreleased)
---------------------
+--------------------------------
 
 Breaking Changes
 ++++++++++++++++

docs/source/conf.py

@@ -117,7 +117,7 @@
 # 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.

docs/source/single_compute.rst

@@ -52,6 +52,11 @@ By default the job is given resources relating to the compute environment it is
 
     >>> ret = qcng.compute(inp, "psi4", local_options={"memory": 2, "ncores": 3})
 
+By default, the job returns a QCSchema Result of the same ``schema_version`` as the Input (v1 if Input version can't be determined). To request a specific version back, use the ``return_version`` keyword:
+
+.. code:: python
+
+    >>> ret = qcng.compute(inp, "psi4", return_version=2)
 
 
 Results

qcengine/cli.py

@@ -77,7 +77,8 @@ def parse_args():
     run_procedure = subparsers.add_parser(
         "run-procedure",
         parents=[parent_parser],
-        help="Run a procedure on a given task. Output is printed as a JSON blob.",
+        help="Run a procedure on a given task. Output is printed as a JSON blob. "
+        "Since v0.50.0, favor 'run', even for procedures.",
     )
     run_procedure.add_argument("procedure", type=str, help="The procedure to run.")
     run_procedure.add_argument(

qcengine/compute.py

@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 
 import qcelemental
-from qcelemental.models import AtomicInput, AtomicResult, FailedOperation, OptimizationResult  # TODO
 
 from .config import get_config
 from .exceptions import InputError, RandomError
@@ -15,14 +14,13 @@
 
 if TYPE_CHECKING:
     from pydantic.main import BaseModel
-    from qcelemental.models import AtomicResult
 
 
 __all__ = ["compute", "compute_procedure"]
 
 
 def _process_failure_and_return(model, return_dict, raise_error):
-    if isinstance(model, FailedOperation):
+    if isinstance(model, (qcelemental.models.v1.FailedOperation, qcelemental.models.v2.FailedOperation)):
         if raise_error:
             raise InputError(model.error.error_message)
         elif return_dict:
@@ -71,6 +69,12 @@ def compute(
     result
         AtomicResult, OptimizationResult, FailedOperation, etc., or Dict representation of any object type
         A QCSchema representation of the requested output, type depends on return_dict key.
+
+    .. versionadded:: 0.50.0
+       input_data can newly be QCSchema v2 as well as longstanding v1.
+       The compute_procedure is newly incorporated into compute.
+       The *return_version* parameter was added.
+
     """
 
     try:
@@ -123,11 +127,11 @@ def compute(
 
 
 def compute_procedure(*args, **kwargs):
-    vchanges = qcelemental.models.common_models._qcsk_v2_default_v1_importpathschange
+    from qcelemental.models.common_models import _qcsk_v2_default_v1_importpathschange
 
     warnings.warn(
-        f"Using the `compute_procedure` function is deprecated in favor of using `compute`, "
-        "and as soon as version {vchanges} it will stop working.",
+        "Using the `compute_procedure` function is deprecated in favor of using `compute`, "
+        f"and as soon as version {_qcsk_v2_default_v1_importpathschange} it will stop working.",
         category=FutureWarning,
         stacklevel=2,
     )

qcengine/config.py

@@ -93,15 +93,16 @@ class NodeDescriptor(BaseModel):
     # Cluster options
     is_batch_node: bool = Field(
         False,
-        description="""Whether the node running QCEngine is a batch node
-    
+        description=r"""Whether the node running QCEngine is a batch node
+
     Some clusters are configured such that tasks are launched from a special "batch" or "MOM" onto the compute nodes.
     The compute nodes on such clusters often have a different CPU architecture than the batch nodes and 
     often are unable to launch MPI tasks, which has two implications:
-        1) QCEngine must make *all* calls to an executable via ``mpirun`` because the executables might not
-        be able to run on the batch node. 
-        2) QCEngine must run on the batch node to be able to launch tasks on the more than one compute nodes  
-    
+
+    1. QCEngine must make *all* calls to an executable via ``mpirun`` because the executables might not
+       be able to run on the batch node. 
+    2. QCEngine must run on the batch node to be able to launch tasks on the more than one compute nodes
+
     ``is_batch_node`` is used when creating the task configuration as a means of determining whether
     ``mpiexec_command`` must always be used even for serial jobs (e.g., getting the version number)
     """,

qcengine/exceptions.py

@@ -1,8 +1,6 @@
 import traceback
 from typing import Any, Dict, Optional
 
-from qcelemental.models import AtomicInput
-
 
 class QCEngineException(Exception):
     """
@@ -106,7 +104,7 @@ def detect_error(cls, outputs: Dict[str, str]):
         """
         raise NotImplementedError()
 
-    def create_keyword_update(self, input_data: AtomicInput) -> Dict[str, Any]:
+    def create_keyword_update(self, input_data: "AtomicInput") -> Dict[str, Any]:
         """Create an keyword used to the update the dictionary given observed error
 
         Parameters

qcengine/procedures/berny.py

@@ -5,7 +5,7 @@
 from typing import Any, ClassVar, Dict, Union
 
 import numpy as np
-from qcelemental.models import FailedOperation, OptimizationInput, OptimizationResult
+from qcelemental.models.v2 import FailedOperation, OptimizationInput, OptimizationResult
 from qcelemental.util import which_import
 
 import qcengine

qcengine/procedures/geometric.py

@@ -1,6 +1,6 @@
 from typing import Any, ClassVar, Dict, Union
 
-from qcelemental.models import OptimizationInput, OptimizationResult
+from qcelemental.models.v2 import OptimizationInput, OptimizationResult
 from qcelemental.util import safe_version, which_import
 
 from .model import ProcedureHarness

qcengine/procedures/model.py

@@ -73,13 +73,13 @@ def _build_model(
 
             # for now, the two dictionaries look the same, so cast to the one we want
             # note that this prevents correctly identifying the user schema version when dict passed in, so either as_v1/None or as_v2 will fail
-            mdl = model_wrapper(data, v1_model)  # TODO v2
+            mdl = model_wrapper(data, v1_model)
 
         input_schema_version = mdl.schema_version
         if return_input_schema_version:
-            return mdl.convert_v(1), input_schema_version  # non-psi4 return_dict=False fail w/o this
+            return mdl.convert_v(2), input_schema_version
         else:
-            return mdl.convert_v(1)
+            return mdl.convert_v(2)
 
     def get_version(self) -> str:
         """Finds procedure, extracts version, returns normalized version string.

qcengine/procedures/nwchem_opt/__init__.py

@@ -1,6 +1,6 @@
 from typing import Any, ClassVar, Dict, Union
 
-from qcelemental.models import AtomicInput, OptimizationInput, OptimizationResult, Provenance
+from qcelemental.models.v2 import AtomicInput, OptimizationInput, OptimizationResult, Provenance
 
 from qcengine.config import TaskConfig
 from qcengine.exceptions import InputError, UnknownError

qcengine/procedures/nwchem_opt/harvester.py

@@ -2,7 +2,7 @@
 from decimal import Decimal
 from typing import List, Tuple
 
-from qcelemental.models import AtomicResult, Molecule, OptimizationInput, Provenance
+from qcelemental.models.v2 import AtomicResult, Molecule, OptimizationInput, Provenance
 from qcelemental.util import unnp
 
 from qcengine.programs.nwchem.harvester import harvest_outfile_pass

qcengine/procedures/optking.py

@@ -1,6 +1,6 @@
 from typing import Any, ClassVar, Dict, Union
 
-from qcelemental.models import OptimizationInput, OptimizationResult
+from qcelemental.models.v2 import OptimizationInput, OptimizationResult
 from qcelemental.util import safe_version, which_import
 
 from .model import ProcedureHarness
@@ -40,6 +40,7 @@ def compute(self, input_model: "OptimizationInput", config: "TaskConfig") -> "Op
         if self.found(raise_error=True):
             import optking
 
+        input_data = input_model.convert_v(1)
         input_data = input_model.dict()
 
         # Set retries to two if zero while respecting local_config

qcengine/procedures/torsiondrive.py

@@ -4,8 +4,13 @@
 from typing import TYPE_CHECKING, Any, ClassVar, Dict, List, Tuple, Union
 
 import numpy as np
-from qcelemental.models import FailedOperation, Molecule
-from qcelemental.models.procedures import OptimizationInput, OptimizationResult, TorsionDriveInput, TorsionDriveResult
+from qcelemental.models.v2 import FailedOperation, Molecule
+from qcelemental.models.v2.procedures import (
+    OptimizationInput,
+    OptimizationResult,
+    TorsionDriveInput,
+    TorsionDriveResult,
+)
 from qcelemental.util import which_import
 
 from .model import ProcedureHarness
@@ -173,7 +178,7 @@ def _spawn_optimization(
             object.
         """
 
-        from qcengine import compute_procedure
+        from qcengine import compute
 
         input_molecule = input_model.initial_molecule[0].copy(deep=True).dict()
         input_molecule["geometry"] = np.array(job).reshape(len(input_molecule["symbols"]), 3)
@@ -204,9 +209,7 @@ def _spawn_optimization(
             initial_molecule=input_molecule,
         )
 
-        return compute_procedure(
-            input_data, procedure=input_model.optimization_spec.procedure, task_config=config.dict()
-        )
+        return compute(input_data, program=input_model.optimization_spec.procedure, task_config=config.dict())
 
     @staticmethod
     def _find_final_results(

qcengine/programs/adcc.py

@@ -3,22 +3,24 @@
 """
 from typing import TYPE_CHECKING, Any, ClassVar, Dict
 
-from qcelemental.models import AtomicResult, BasisSet, Provenance
+from qcelemental.models.v2 import AtomicResult, BasisSet, Provenance
 from qcelemental.util import safe_version, which_import
 
 from ..exceptions import InputError, UnknownError
 from .model import ProgramHarness
 from .qcvar_identities_resources import build_atomicproperties
 
 if TYPE_CHECKING:
-    from qcelemental.models import AtomicInput
+    from qcelemental.models.v2 import AtomicInput
 
     from ..config import TaskConfig
 
 #
 
 
 class AdccHarness(ProgramHarness):
+    """Interface for adcc project."""
+
     _defaults: ClassVar[Dict[str, Any]] = {
         "name": "adcc",
         "scratch": False,
@@ -113,7 +115,7 @@ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicRe
         except Exception as e:
             raise UnknownError(str(e))
 
-        input_data = input_model.dict(encoding="json")
+        input_data = input_model.model_dump(encoding="json")
         output_data = input_data.copy()
         output_data["success"] = compute_success
 

qcengine/programs/aimnet2.py

@@ -1,13 +1,13 @@
 from typing import TYPE_CHECKING, Any, ClassVar, Dict
 
-from qcelemental.models import AtomicResult, Provenance
+from qcelemental.models.v2 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 qcelemental.models.v2 import AtomicInput
 
     from qcengine.config import TaskConfig
 

qcengine/programs/cfour/harvester.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 import qcelemental as qcel
-from qcelemental.models import Molecule
+from qcelemental.models.v2 import Molecule
 from qcelemental.molparse import regex
 
 from ..util import PreservingDict, load_hessian

qcengine/programs/cfour/runner.py

@@ -7,7 +7,7 @@
 from typing import Any, ClassVar, Dict, Optional, Tuple
 
 import numpy as np
-from qcelemental.models import AtomicInput, AtomicResult, BasisSet, Provenance
+from qcelemental.models.v2 import AtomicInput, AtomicResult, BasisSet, Provenance
 from qcelemental.util import safe_version, which
 
 from ...exceptions import InputError, UnknownError
@@ -23,7 +23,7 @@
 
 
 class CFOURHarness(ProgramHarness):
-    """
+    """Interface for CFOUR project.
 
     Notes
     -----

qcengine/programs/dftd3.py

@@ -11,7 +11,7 @@
 
 import numpy as np
 import qcelemental as qcel
-from qcelemental.models import AtomicResult, FailedOperation, Provenance
+from qcelemental.models.v2 import AtomicResult, FailedOperation, Provenance
 from qcelemental.util import safe_version, which
 
 from ..exceptions import InputError, ResourceError, UnknownError
@@ -20,7 +20,7 @@
 from .model import ProgramHarness
 
 if TYPE_CHECKING:
-    from qcelemental.models import AtomicInput
+    from qcelemental.models.v2 import AtomicInput
 
     from ..config import TaskConfig
 
@@ -29,6 +29,7 @@
 
 
 class DFTD3Harness(ProgramHarness):
+    """Interface for DFTD3 executable project."""
 
     _defaults: ClassVar[Dict[str, Any]] = {
         "name": "DFTD3",