mdantic (#16)

* mdantic

* path

* tables

* tabulate

* restore lane

* qcsk doc

.github/workflows/ci.yml

@@ -157,6 +157,7 @@ jobs:
             - mkdocs
             - mkdocs-material
             - mkdocstrings-python
+            - tabulate
           EOF
           cat export.yaml
 
@@ -179,7 +180,7 @@ jobs:
     - name: Build Documentation
       run: |
         python -m pip install . --no-deps
-        mkdocs build
+        PYTHONPATH=docs/extensions mkdocs build
         cd docs
 
     - name: GitHub Pages Deploy

codecov.yml

@@ -2,6 +2,7 @@ coverage:
   ignore:
     - qcmanybody/tests/component_data
     - qcmanybody/tests/ref_data
+    - qcmanybody/tests/generate_component_data.py
   status:
     project:
       default:

docs/extensions/mdantic_v1/__init__.py

@@ -0,0 +1,14 @@
+from .mdantic import (
+    Mdantic,
+    analyze,
+    Field,
+    get_related_enum,
+    get_enum_values,
+    get_related_enum_helper,
+    mk_struct,
+    fmt_tab,
+    MdanticPreprocessor,
+    makeExtension,
+)
+
+#from .samples import SampleModel

docs/extensions/mdantic_v1/mdantic.py

@@ -0,0 +1,174 @@
+import re
+import inspect
+import importlib
+from enum import Enum
+from collections import namedtuple
+from typing import List, Dict, Optional
+
+import tabulate
+from pydantic.v1 import BaseModel
+from markdown import Markdown
+from markdown.extensions import Extension
+from markdown.preprocessors import Preprocessor
+
+
+class Mdantic(Extension):
+    def __init__(self, configs=None):
+        if configs is None:
+            configs = {}
+        self.config = {
+            "init_code": ["", "python code to run when initializing"],
+            "columns": [
+                ["key", "type", "required", "description", "default"],
+                "Columns to use in table, comma separated list",
+            ],
+        }
+        for key, value in configs.items():
+            self.setConfig(key, value)
+        super().__init__()
+
+    def extendMarkdown(self, md: Markdown) -> None:
+        md.preprocessors.register(MdanticPreprocessor(md, self.getConfigs()), "mdantic", 100)
+
+
+Field = namedtuple("Field", "key type required description default")
+
+
+def analyze(cls_name: str) -> Optional[Dict[str, List[Field]]]:
+    paths = cls_name.rsplit(".", 1)
+    if len(paths) != 2:
+        return None
+
+    module = paths[0]
+    attr = paths[1]
+    try:
+        mod = importlib.import_module(module)
+    except ModuleNotFoundError:
+        return None
+    if not hasattr(mod, attr):
+        return None
+
+    cls = getattr(mod, attr)
+
+    if not issubclass(cls, BaseModel):
+        return None
+
+    structs = {}
+    mk_struct(cls, structs)
+    return structs
+
+
+def get_related_enum(ty: type):
+    visited = set()
+    result = []
+
+    get_related_enum_helper(ty, visited, result)
+
+    return result
+
+
+def get_enum_values(e):
+    return [x.value for x in list(e)]
+
+
+def get_related_enum_helper(ty, visited, result):
+    visited.add(ty)
+    if inspect.isclass(ty) and issubclass(ty, Enum) and ty not in result:
+        result.append(ty)
+
+    if hasattr(ty, "__args__"):
+        for sub_ty in getattr(ty, "__args__"):
+            if sub_ty not in visited:
+                get_related_enum_helper(sub_ty, visited, result)
+
+
+# v1:
+def mk_struct(cls: type[BaseModel], structs: Dict[str, List[Field]]) -> None:
+    this_struct: List[Field] = []
+    structs[cls.__name__] = this_struct
+    # v2: for field_name, f in cls.model_fields.items():
+    for field_name, f in cls.__fields__.items():
+        title = f.field_info.title or field_name
+        annotation = str(f.type_)
+        description = "" if f.field_info.description is None else f.field_info.description
+
+        if annotation is None:
+            return None
+
+        related_enums = get_related_enum(annotation)
+        if related_enums:
+            for e in related_enums:
+                description += f"</br>{e.__name__}: {get_enum_values(e)}"
+
+        default = f.get_default()
+        default = None if str(default) == "PydanticUndefined" else str(default)
+
+        if hasattr(annotation, "__origin__"):
+            ty = str(annotation)
+        elif hasattr(annotation, "__name__"):
+            ty = annotation.__name__
+        else:
+            ty = str(annotation)
+
+        this_struct.append(
+            Field(
+                title,
+                ty,
+                # v2: str(f.is_required()),
+                str(f.required),
+                description,
+                default,
+            )
+        )
+        if hasattr(annotation, "__mro__"):
+            if BaseModel in annotation.__mro__:
+                mk_struct(annotation, structs)
+
+
+def fmt_tab(structs: Dict[str, List[Field]], columns: List[str]) -> Dict[str, str]:
+    tabs = {}
+    for cls, struct in structs.items():
+        tab = []
+        for f in struct:
+            tab.append([getattr(f, name) for name in columns])
+        tabs[cls] = tabulate.tabulate(tab, headers=columns, tablefmt="github")
+    return tabs
+
+
+class MdanticPreprocessor(Preprocessor):
+    """
+    This provides an "include" function for Markdown, similar to that found in
+    LaTeX (also the C pre-processor and Fortran). The syntax is {!filename!},
+    which will be replaced by the contents of filename. Any such statements in
+    filename will also be replaced. This replacement is done prior to any other
+    Markdown processing. All file-names are evaluated relative to the location
+    from which Markdown is being called.
+    """
+
+    def __init__(self, md: Markdown, config):
+        super(MdanticPreprocessor, self).__init__(md)
+        self.init_code = config["init_code"]
+        if self.init_code:
+            exec(self.init_code)
+        self.columns = config["columns"]
+
+    def run(self, lines: List[str]):
+        for i, l in enumerate(lines):
+            g = re.match(r"^\$pydantic: (.*)$", l)
+            if g:
+                cls_name = g.group(1)
+                structs = analyze(cls_name)
+                if structs is None:
+                    print(f"warning: mdantic pattern detected but failed to process or import: {cls_name}")
+                    continue
+                tabs = fmt_tab(structs, self.columns)
+                table_str = ""
+                for cls, tab in tabs.items():
+                    table_str += "\n" + f"**{cls}**" + "\n\n" + str(tab) + "\n"
+                lines = lines[:i] + [table_str] + lines[i + 1 :]
+
+        return lines
+
+
+def makeExtension(*_, **kwargs):
+    return Mdantic(kwargs)

docs/qcschema.md

@@ -0,0 +1,96 @@
+
+<!-- ====  Inputs  ================================================================= -->
+
+::: qcmanybody.models.BsseEnum
+
+
+::: qcmanybody.models.ManyBodyKeywords
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyKeywords
+
+
+::: qcmanybody.models.manybody_pydv1.ManyBodySpecification
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.manybody_pydv1.ManyBodySpecification
+
+
+::: qcmanybody.models.ManyBodyInput
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyInput
+
+
+<!-- ====  Protocols  ============================================================== -->
+
+<!--
+::: qcmanybody.models.manybody_pydv1.ManyBodyProtocolEnum
+
+
+::: qcmanybody.models.manybody_pydv1.ManyBodyProtocols
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.manybody_pydv1.ManyBodyProtocols
+-->
+
+
+<!-- ====  Properties/Outputs  ===================================================== -->
+
+::: qcmanybody.models.ManyBodyResultProperties
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.ManyBodyResultProperties
+
+
+::: qcmanybody.models.ManyBodyResult
+    options:
+        show_root_heading: true
+
+$pydantic: qcmanybody.models.ManyBodyResult
+
+
+<!-- ====  Misc.  ================================================================== -->
+
+<!-- $pydantic: qcmanybody.models.manybody_pydv1.AtomicSpecification -->
+<!--
+AtomicSpecification
+ResultsBase
+SuccessfulResultBase
+-->
+
+<!--
+    options:
+        merge_init_into_class: false
+        group_by_category: false
+        # explicit members list so we can set order and include `__init__` easily
+        members:
+          - __init__
+          - molecule
+          - model_config
+          - model_computed_fields
+          - model_extra
+          - model_fields
+          - model_fields_set
+          - model_construct
+          - model_copy
+          - model_dump
+          - model_dump_json
+          - model_json_schema
+          - model_parametrized_name
+          - model_post_init
+          - model_rebuild
+          - model_validate
+          - model_validate_json
+          - copy
+-->
+
+::: qcmanybody.resize_gradient
+    options:
+        show_root_heading: true
+

mkdocs.yml

@@ -42,19 +42,31 @@ plugins:
         options:
           docstring_style: numpy
           allow_inspection: true
+          members_order: source
+          separate_signature: true
+          filters: ["!^_"]
+          docstring_options:
+            ignore_init_summary: true
+          merge_init_into_class: true
+          show_signature_annotations: true
+          signature_crossrefs: true
         import:
-        - https://docs.python.org/3.12/objects.inv
-        - https://numpy.org/doc/stable/objects.inv
-        - https://docs.scipy.org/doc/scipy/objects.inv
-        - https://matplotlib.org/stable/objects.inv
-        - https://molssi.github.io/QCElemental/objects.inv
-        - https://molssi.github.io/QCEngine/objects.inv
-        - https://molssi.github.io/QCFractal/objects.inv
+          - https://docs.python.org/3/objects.inv
+          - https://numpy.org/doc/stable/objects.inv
+          - https://docs.scipy.org/doc/scipy/objects.inv
+          - https://matplotlib.org/stable/objects.inv
+          - https://molssi.github.io/QCElemental/objects.inv
+          - https://molssi.github.io/QCEngine/objects.inv
+          - https://molssi.github.io/QCFractal/objects.inv
+
+markdown_extensions:
+  - mdantic_v1
 
 nav:
   - Home: index.md
   - high-level-interface.md
   - core-interface.md
+  - QCSchema: qcschema.md
   - How-To Guides: how-to-guides.md
   - API Documentation: api.md