rename computer (#27)

* edits

* rename and deprint

docs/api.md

@@ -1,9 +1,9 @@
 ::: qcmanybody.ManyBodyCalculator
 
-::: qcmanybody.qcng_computer.ManyBodyComputerQCNG
+::: qcmanybody.qcng_computer.ManyBodyComputer
     options:
         show_root_heading: true
         inherited_members: true
         members: true
 
-$pydantic: qcmanybody.qcng_computer.ManyBodyComputerQCNG
+$pydantic: qcmanybody.qcng_computer.ManyBodyComputer

docs/changelog.md

@@ -19,6 +19,14 @@
 -->
 
 
+## v0.2.1 / 2024-05-14
+
+#### Enhancements
+
+* [\#27](https://github.com/MolSSI/QCManyBody/pull/27) Intf -- move high-level interface from
+  `qcmb.qcng_computer.ManyBodyComputerQCNG` to `qcmb.computer.ManyBodyComputer`. Suppressed remaining printing. @loriab
+
+
 ## v0.2.0 / 2024-05-13
 
 #### New Features

docs/extensions/mdantic_v1/mdantic.py

@@ -6,7 +6,10 @@
 from typing import List, Dict, Optional
 
 import tabulate
-from pydantic.v1 import BaseModel
+try:
+    from pydantic.v1 import BaseModel
+except ModuleNotFoundError:
+    from pydantic import BaseModel
 from markdown import Markdown
 from markdown.extensions import Extension
 from markdown.preprocessors import Preprocessor

mkdocs.yml

@@ -34,6 +34,7 @@ extra_css:
 
 plugins:
 - search
+- autorefs
 - mkdocstrings:
     default_handler: python
     enable_inventory: true

qcmanybody/qcng_computer.py → qcmanybody/computer.py

@@ -51,7 +51,7 @@ class Config:
         allow_mutation = True
 
 
-class AtomicComputerQCNG(BaseComputerQCNG):
+class AtomicComputer(BaseComputerQCNG):
     """Computer for analytic single-geometry computations."""
 
     molecule: Molecule = Field(..., description="The molecule to use in the computation.")
@@ -130,7 +130,7 @@ def get_results(self, client: Optional["qcportal.FractalClient"] = None) -> Atom
             return self.result
 
 
-class ManyBodyComputerQCNG(BaseComputerQCNG):
+class ManyBodyComputer(BaseComputerQCNG):
 
     input_data: ManyBodyInput = Field(
         ...,
@@ -221,21 +221,21 @@ def set_bsse_type(cls, v: Any) -> List[BsseEnum]:
     @classmethod
     # v2: def set_embedding_charges(cls, v: Any, info: FieldValidationInfo) -> Dict[int, List[float]]:
     def set_embedding_charges(cls, v, values): # -> Dict[int, List[float]]:
-        print(f"hit embedding_charges validator with {v}", end="")
+        # print(f"hit embedding_charges validator with {v}", end="")
         nfr = len(values["molecule"].fragments)
         # v2: if len(v) != info.data["nfragments"]:
         if v and len(v) != nfr:
             raise ValueError(f"embedding_charges dict should have entries for each 1-indexed fragment ({nfr})")
 
-        print(f" ... setting embedding_charges={v}")
+        # print(f" ... setting embedding_charges={v}")
         return v
 
     # v2: @field_validator("return_total_data")
     @validator("return_total_data", always=True)
     @classmethod
     # v2: def set_return_total_data(cls, v: Optional[bool], info: FieldValidationInfo) -> bool:
     def set_return_total_data(cls, v: Optional[bool], values) -> bool:
-        print(f"hit return_total_data validator with {v}", end="")
+        # print(f"hit return_total_data validator with {v}", end="")
         if v is not None:
             rtd = v
         # v2: elif info.data["driver"] in ["gradient", "hessian"]:
@@ -248,15 +248,15 @@ def set_return_total_data(cls, v: Optional[bool], values) -> bool:
         if values.get("embedding_charges", False) and rtd is False:
             raise ValueError("Cannot return interaction data when using embedding scheme.")
 
-        print(f" ... setting rtd={rtd}")
+        # print(f" ... setting rtd={rtd}")
         return rtd
 
     # v2: @field_validator("levels")
     @validator("levels", always=True)
     @classmethod
     # v2: def set_levels(cls, v: Any, info: FieldValidationInfo) -> Dict[Union[int, Literal["supersystem"]], str]:
     def set_levels(cls, v: Any, values) -> Dict[Union[int, Literal["supersystem"]], str]:
-        print(f"hit levels validator with {v}", end="")
+        # print(f"hit levels validator with {v}", end="")
 
         if v is None:
             pass
@@ -269,7 +269,7 @@ def set_levels(cls, v: Any, values) -> Dict[Union[int, Literal["supersystem"]],
             # rearrange bodies in order with supersystem last lest body count fail in organization loop below
             v = dict(sorted(v.items(), key=lambda item: 1000 if item[0] == "supersystem" else item[0]))
 
-        print(f" ... setting levels={v}")
+        # print(f" ... setting levels={v}")
         return v
 
     # TODO @computed_field(
@@ -285,7 +285,7 @@ def set_levels(cls, v: Any, values) -> Dict[Union[int, Literal["supersystem"]],
         #},
     @property
     def nbodies_per_mc_level(self) -> List[List[Union[int, Literal["supersystem"]]]]:
-        print(f"hit nbodies_per_mc_level", end="")
+        # print(f"hit nbodies_per_mc_level", end="")
 
         # Organize nbody calculations into modelchem levels
         # * expand keys of `levels` into full lists of nbodies covered. save to plan, resetting max_nbody accordingly
@@ -304,20 +304,20 @@ def nbodies_per_mc_level(self) -> List[List[Union[int, Literal["supersystem"]]]]
             nbodies_per_mc_level.append(nbodies)
             prev_body = nb  # formerly buggy `+= 1`
 
-        print(f" ... setting nbodies_per_mc_level={nbodies_per_mc_level}")
+        # print(f" ... setting nbodies_per_mc_level={nbodies_per_mc_level}")
         return nbodies_per_mc_level
 
     # v2: @field_validator("max_nbody")
     @validator("max_nbody", always=True)
     @classmethod
     # v2: def set_max_nbody(cls, v: Any, info: FieldValidationInfo) -> int:
     def set_max_nbody(cls, v: Any, values) -> int:
-        print(f"hit max_nbody validator with {v}", end="")
+        # print(f"hit max_nbody validator with {v}", end="")
         # v2: levels_max_nbody = max(nb for nb in info.data["levels"] if nb != "supersystem")
         # v2: nfr = len(info.data["molecule"].fragments)
         levels_max_nbody = max(nb for nb in values["levels"] if nb != "supersystem")
         nfr = len(values["molecule"].fragments)
-        print(f" {levels_max_nbody=} {nfr=}", end="")
+        # print(f" {levels_max_nbody=} {nfr=}", end="")
 
         #ALT if v == -1:
         if v is None:
@@ -333,7 +333,7 @@ def set_max_nbody(cls, v: Any, values) -> int:
             pass
             # TODO once was           return min(v, nfragments)
 
-        print(f" ... setting max_nbody={v}")
+        # print(f" ... setting max_nbody={v}")
         return v
 
 #       levels          max_nbody           F-levels        F-max_nbody     result
@@ -350,7 +350,7 @@ def set_max_nbody(cls, v: Any, values) -> int:
     @classmethod
     # v2: def set_supersystem_ie_only(cls, v: Optional[bool], info: FieldValidationInfo) -> bool:
     def set_supersystem_ie_only(cls, v: Optional[bool], values) -> bool:
-        print(f"hit supersystem_ie_only validator with {v}", end="")
+        # print(f"hit supersystem_ie_only validator with {v}", end="")
         sio = v
         # v2: _nfr = len(info.data["molecule"].fragments)
         _nfr = len(values["molecule"].fragments)
@@ -364,7 +364,7 @@ def set_supersystem_ie_only(cls, v: Optional[bool], values) -> bool:
         if (sio is True) and ("vmfc" in values["bsse_type"]):
             raise ValueError(f"Cannot skip intermediate n-body jobs when VMFC in bsse_type={values['bsse_type']}. Use CP instead.")
 
-        print(f" ... setting {sio=}")
+        # print(f" ... setting {sio=}")
         return sio
 
     @classmethod
@@ -432,7 +432,7 @@ def from_manybodyinput(cls, input_model: ManyBodyInput, build_tasks: bool = True
             component_results[label] = result
 
             if not result.success:
-                print(result.error.error_message)
+                # print(result.error.error_message)
                 raise RuntimeError("Calculation did not succeed! Error:\n" + result.error.error_message)
 
             # pull out stuff

qcmanybody/models/manybody_input_pydv1.py

@@ -171,14 +171,14 @@ class ManyBodyKeywords(ProtoModel):
         # definitive description
         description="Target the supersystem total/interaction energy (IE) data over the many-body expansion (MBE) "
             "analysis, thereby omitting intermediate-body calculations. When False (default), compute each n-body level "
-            "in the MBE up through ``max_nbody``. When True (only allowed for ``max_nbody = nfragments``), only compute "
+            "in the MBE up through ``max_nbody``. When True (only allowed for ``max_nbody = nfragments`` ), only compute "
             "enough for the overall interaction/total energy: max_nbody-body and 1-body. When True, properties "
-            "``INTERACTION {driver} THROUGH {max_nbody}-BODY`` will always be available; ``TOTAL {driver} THROUGH "
-            "{max_nbody}-BODY`` will be available depending on ``return_total_data``; and ``{max_nbody}-BODY "
-            "CONTRIBUTION TO {driver}`` won't be available (except for dimers). This keyword produces no savings for a "
-            "two-fragment molecule. But for the interaction energy of a three-fragment molecule, for example, 2-body "
-            "subsystems can be skipped with ``supersystem_ie_only=True`` Do not use with ``vmfc`` in ``bsse_type``"
-            "as it cannot produce savings."
+            "``INTERACTION {driver} THROUGH {max_nbody}-BODY`` will always be available; "
+            "``TOTAL {driver} THROUGH {max_nbody}-BODY`` will be available depending on ``return_total_data`` ; and "
+            "``{max_nbody}-BODY CONTRIBUTION TO {driver}`` won't be available (except for dimers). This keyword produces "
+            "no savings for a two-fragment molecule. But for the interaction energy of a three-fragment molecule, for "
+            "example, 2-body subsystems can be skipped with ``supersystem_ie_only=True``. Do not use with ``vmfc`` in "
+            "``bsse_type`` as it cannot produce savings.",
     )
 
     # v2: @field_validator("bsse_type", mode="before")
@@ -201,7 +201,7 @@ class ManyBodySpecification(ProtoModel):
     schema_name: Literal["qcschema_manybodyspecification"] = "qcschema_manybodyspecification"
     #provenance: Provenance = Field(Provenance(**provenance_stamp(__name__)), description=Provenance.__doc__)
     keywords: ManyBodyKeywords = Field(..., description=ManyBodyKeywords.__doc__)
-    #program: str = Field(..., description="The program for which the Specification is intended.")
+    #program: str = Field(..., description="The program for which the Specification is intended.")  # TODO is qcmanybody
     protocols: ManyBodyProtocols = Field(ManyBodyProtocols(), description=str(ManyBodyProtocols.__doc__))
     driver: DriverEnum = Field(
         ...,

qcmanybody/tests/test_mbe_he4_multilevel.py

@@ -10,9 +10,8 @@
 from qcelemental.testing import compare_values, compare_recursive
 
 from qcmanybody.models import AtomicSpecification, ManyBodyKeywords, ManyBodyInput
-from qcmanybody.qcng_computer import ManyBodyComputerQCNG, qcvars_to_manybodyproperties
+from qcmanybody.computer import ManyBodyComputer, qcvars_to_manybodyproperties
 
-import qcengine as qcng
 from .addons import using
 from .test_mbe_he4_singlelevel import sumdict as sumdict_single
 
@@ -726,7 +725,7 @@ def test_nbody_he4_multi(levels, mbe_keywords, anskey, bodykeys, outstrs, calcin
     mbe_model = ManyBodyInput(**mbe_data_multilevel_631g)
 
     # qcng: ret = qcng.compute_procedure(mbe_model, "manybody", raise_error=True)
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model)
     print(f"MMMMMMM {request.node.name}")
     pprint.pprint(ret.dict(), width=200)
 
@@ -819,7 +818,7 @@ def test_nbody_he4_supersys(levels, mbe_keywords, anskey, bodykeys, outstrs, cal
     mbe_model = ManyBodyInput(**mbe_data_multilevel_631g)
 
     # qcng: ret = qcng.compute_procedure(mbe_model, "manybody", raise_error=True)
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model)
     print(f"MMMMMMM {request.node.name}")
     pprint.pprint(ret.dict(), width=200)
 
@@ -896,7 +895,7 @@ def test_count_he4_multi(mbe_keywords, ref_count, he_tetramer, request):
     atomic_spec = AtomicSpecification(model={"method": "mp2", "basis": "mybas"}, program="myqc", driver="energy")
     mbe_model = ManyBodyInput(specification={"specification": atomic_spec, "keywords": mbe_keywords, "driver": "energy"}, molecule=he_tetramer)
 
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model, build_tasks=False)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model, build_tasks=False)
     ret = ret.qcmb_calculator
 
     text, dcount = ret.format_calc_plan()

qcmanybody/tests/test_mbe_he4_singlelevel.py

@@ -9,9 +9,8 @@
 from qcelemental.testing import compare_values, compare_recursive
 
 from qcmanybody.models import AtomicSpecification, ManyBodyKeywords, ManyBodyInput
-from qcmanybody.qcng_computer import ManyBodyComputerQCNG, qcvars_to_manybodyproperties
+from qcmanybody.computer import ManyBodyComputer, qcvars_to_manybodyproperties
 
-import qcengine as qcng
 from .addons import using
 
 def skprop(qcvar):
@@ -625,7 +624,7 @@ def test_nbody_he4_single(program, basis, keywords, mbe_keywords, anskey, bodyke
     mbe_model = ManyBodyInput(specification={"specification": atomic_spec, "keywords": mbe_keywords, "driver": "energy", "protocols": {"component_results": "all"}}, molecule=he_tetramer)
 
     # qcng: ret = qcng.compute_procedure(mbe_model, "manybody", raise_error=True)
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model)
     print(f"SSSSSSS {request.node.name}")
     # v2: pprint.pprint(ret.model_dump(), width=200)
     pprint.pprint(ret.dict(), width=200)
@@ -712,7 +711,7 @@ def test_count_he4_single(mbe_keywords, ref_count, he_tetramer):
     atomic_spec = AtomicSpecification(model={"method": "mp2", "basis": "mybas"}, program="myqc", driver="energy")
     mbe_model = ManyBodyInput(specification={"specification": atomic_spec, "keywords": mbe_keywords, "driver": "energy"}, molecule=he_tetramer)
 
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model, build_tasks=False)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model, build_tasks=False)
     ret = ret.qcmb_calculator
 
     text, dcount = ret.format_calc_plan()

qcmanybody/tests/test_mbe_het4_grad.py

@@ -8,7 +8,7 @@
 from qcelemental.testing import compare_values
 
 from qcmanybody.models import ManyBodyKeywords, ManyBodyInput
-from qcmanybody.qcng_computer import ManyBodyComputerQCNG, qcvars_to_manybodyproperties
+from qcmanybody.computer import ManyBodyComputer, qcvars_to_manybodyproperties
 
 from .addons import uusing
 
@@ -258,7 +258,7 @@ def test_nbody_het4_grad(mbe_keywords, anskeyE, anskeyG, bodykeys, outstrs, calc
     mbe_model = ManyBodyInput(**mbe_data_grad_dtz)
 
     # qcng: ret = qcng.compute_procedure(mbe_model, "manybody", raise_error=True)
-    ret = ManyBodyComputerQCNG.from_manybodyinput(mbe_model)
+    ret = ManyBodyComputer.from_manybodyinput(mbe_model)
     print(f"MMMMMMM {request.node.name}")
     pprint.pprint(ret.dict(), width=200)
 

qcmanybody/tests/test_mbe_keywords.py

@@ -12,10 +12,8 @@
 from qcelemental.models import DriverEnum, Molecule
 from qcmanybody.models import BsseEnum, ManyBodyInput
 
-import qcengine as qcng
-
-# qcng: from qcengine.procedures.manybody import ManyBodyComputerQCNG
-from qcmanybody.qcng_computer import ManyBodyComputerQCNG
+# qcng: from qcengine.procedures.manybody import ManyBodyComputer
+from qcmanybody.computer import ManyBodyComputer
 from qcmanybody import ManyBodyCalculator
 
 
@@ -103,7 +101,7 @@ def test_mbe_rtd(mbe_data, driver, kws, ans):
     mbe_data["specification"]["keywords"] = kws
 
     input_model = ManyBodyInput(**mbe_data)
-    comp_model = ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+    comp_model = ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert comp_model.driver == driver
     assert comp_model.return_total_data == ans
@@ -150,7 +148,7 @@ def test_mbe_level_bodies(mbe_data, kws, ans):
     mbe_data["specification"]["keywords"] = kws
 
     input_model = ManyBodyInput(**mbe_data)
-    comp_model = ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+    comp_model = ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert comp_model.nfragments == 3
     assert comp_model.max_nbody == ans[0]
@@ -178,7 +176,7 @@ def test_mbe_level_5mer(mbe_data, kws, ans):
     mbe_data["specification"]["keywords"] = kws
 
     input_model = ManyBodyInput(**mbe_data)
-    comp_model = ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+    comp_model = ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert comp_model.nfragments == 5
     assert comp_model.max_nbody == ans[0]
@@ -200,7 +198,7 @@ def test_mbe_level_fails(mbe_data, kws, errmsg):
     # v2: with pytest.raises(Exception):
     with pytest.raises(ValidationError) as e:
         input_model = ManyBodyInput(**mbe_data)
-        ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+        ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert errmsg in str(e.value), e.value
 
@@ -230,7 +228,7 @@ def test_mbe_bsse_type(mbe_data, kws, ans):
         return
 
     input_model = ManyBodyInput(**mbe_data)
-    comp_model = ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+    comp_model = ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert comp_model.bsse_type == ans, f"{comp_model=} != {ans}"
 
@@ -252,13 +250,13 @@ def test_mbe_sie(mbe_data, kws, ans):
     if isinstance(ans, str):
         input_model = ManyBodyInput(**mbe_data)
         with pytest.raises(ValidationError) as e:
-            ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+            ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
         assert ans in str(e.value)
         return
 
     input_model = ManyBodyInput(**mbe_data)
-    comp_model = ManyBodyComputerQCNG.from_manybodyinput(input_model, build_tasks=False)
+    comp_model = ManyBodyComputer.from_manybodyinput(input_model, build_tasks=False)
 
     assert comp_model.supersystem_ie_only == ans