fix docs after models refactor (#23)

* mdantic * tables * tabulate * restore lane * note in docs * fix docs
MolSSI · Apr 27, 2024 · b2ea3c6 · b2ea3c6
1 parent 7e8e1fd
commit b2ea3c6
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Showing 4 changed files with 24 additions and 55 deletions.
diff --git a/docs/qcschema.md b/docs/qcschema.md
@@ -2,27 +2,29 @@
 <!-- ====  Inputs  ================================================================= -->
 
 ::: qcmanybody.models.BsseEnum
+    options:
+        show_root_heading: true
 
 
 ::: qcmanybody.models.ManyBodyKeywords
     options:
         show_root_heading: true
 
-$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyKeywords
+$pydantic: qcmanybody.models.manybody_input_pydv1.ManyBodyKeywords
 
 
-::: qcmanybody.models.manybody_pydv1.ManyBodySpecification
+::: qcmanybody.models.ManyBodySpecification
     options:
         show_root_heading: true
 
-$pydantic: qcmanybody.models.manybody_pydv1.ManyBodySpecification
+$pydantic: qcmanybody.models.manybody_input_pydv1.ManyBodySpecification
 
 
 ::: qcmanybody.models.ManyBodyInput
     options:
         show_root_heading: true
 
-$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyInput
+$pydantic: qcmanybody.models.manybody_input_pydv1.ManyBodyInput
 
 
 <!-- ====  Protocols  ============================================================== -->
@@ -31,16 +33,27 @@ $pydantic: qcmanybody.models.manybody_pydv1.ManyBodyInput
 ::: qcmanybody.models.manybody_pydv1.ManyBodyProtocolEnum
 
 
-::: qcmanybody.models.manybody_pydv1.ManyBodyProtocols
+::: qcmanybody.models.manybody_input_pydv1.ManyBodyProtocols
     options:
         show_root_heading: true
 
-$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyProtocols
+$pydantic: qcmanybody.models.manybody_input_pydv1.ManyBodyProtocols
 -->
 
 
 <!-- ====  Properties/Outputs  ===================================================== -->
 
+!!! note
+
+    The properties model is generated dynamically based on a constant
+    ``MAX_NBODY``. To not overload the docs table, this is set to 5, which
+    covers full calculations on tetramers. To use a larger
+    ``ManyBodyKeywords.max_nbody``, reset this value.
+
+        import qcmanybody as qcmb
+        qcmb.models.MAX_NBODY = 8
+
+
 ::: qcmanybody.models.ManyBodyResultProperties
     options:
         show_root_heading: true
@@ -90,7 +103,3 @@ SuccessfulResultBase
           - copy
 -->
 
-::: qcmanybody.resize_gradient
-    options:
-        show_root_heading: true
-
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -61,6 +61,9 @@ plugins:
 
 markdown_extensions:
   - mdantic_v1
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
 
 nav:
   - Home: index.md

diff --git a/qcmanybody/models/__init__.py b/qcmanybody/models/__init__.py
@@ -4,6 +4,7 @@
     FragBasIndex,
     ManyBodyInput,
     ManyBodyKeywords,
+    ManyBodySpecification,
 )
 from .manybody_output_pydv1 import (
     ManyBodyResult,

diff --git a/qcmanybody/qcng_computer.py b/qcmanybody/qcng_computer.py
@@ -534,34 +534,7 @@ def get_results(self, external_results: Dict, client: Optional["qcportal.Fractal
         pp.pprint(qcvars)
 
         for qcv, val in qcvars.items():
-            if isinstance(val, dict):
-                if qcv in [
-#            #"energies",  # retired
-#            #"ptype",     # retired
-#            "intermediates",
-#            "intermediates_energy",  #"intermediates2",
-#            "intermediates_gradient",  #"intermediates_ptype",
-#            "intermediates_hessian",  #"intermediates_ptype",
-#            "energy_body_dict",
-#            "gradient_body_dict",  # ptype_body_dict
-#            "hessian_body_dict",  # ptype_body_dict
-#            "nbody",
-#            "cp_energy_body_dict",
-#            "nocp_energy_body_dict",
-#            "vmfc_energy_body_dict",
-#            "cp_gradient_body_dict",
-#            "nocp_gradient_body_dict",
-#            "vmfc_gradient_body_dict",
-#            "cp_hessian_body_dict",
-#            "nocp_hessian_body_dict",
-#            "vmfc_hessian_body_dict",
-                ]:
-                    for qcv2, val2 in val.items():
-#                        try:
-                            qcvars[str(qcv2)] = val2
-#                        except ValidationError:
-#                            obj.set_variable(f"{self.driver.name} {qcv2}", val2)
-            else:
+            if not isinstance(val, dict):
                 qcvars[qcv] = val
 
         # v2: component_results = self.model_dump()['task_list']  # TODO when/where include the indiv outputs
@@ -593,23 +566,6 @@ def get_results(self, external_results: Dict, client: Optional["qcportal.Fractal
         return nbody_model
 
 
-
-
-
-def lab_delabeler(item: str, return_obj: bool = False) -> Union[Tuple[str, str, str], Tuple[int, Tuple[int], Tuple[int]]]:
-    """Transform labels like string "1_((2,), (1, 2))" into string tuple ("1", "2", "1, 2") or
-    object tuple (1, (2,), (1, 2)).
-
-    """
-    mc, _, fragbas = item.partition("_")
-    frag, bas = literal_eval(fragbas)
-
-    if return_obj:
-        return int(mc), frag, bas
-    else:
-        return mc, ", ".join(map(str, frag)), ", ".join(map(str, bas))
-
-
 qcvars_to_manybodyproperties = {}
 # v2: for skprop in ManyBodyResultProperties.model_fields.keys():
 for skprop in ManyBodyResultProperties.__fields__.keys():