Installed precommit

- Installed precommit and ran against all files.
- Code black reformatted.
- Added flake8 as a dev dependency since it is used in ci script.

Author: davidt0x

LICENSE

@@ -198,4 +198,4 @@
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
-   limitations under the License.
+   limitations under the License.

examples/document.json

@@ -12,4 +12,4 @@
             "Chapter 1": {}
         }
     }
-}
+}

examples/document.md

@@ -40,4 +40,3 @@ A model of a paragraph
 
 
 </table>
-

examples/document.py

@@ -1,4 +1,3 @@
-
 import modelspec
 from modelspec import field, instance_of, optional
 from modelspec.base_types import Base
@@ -15,6 +14,7 @@ class Paragraph(Base):
     Args:
         contents: Paragraph contents, which make up the _Section_s.
     """
+
     contents: str = field(validator=instance_of(str))
 
 
@@ -27,6 +27,7 @@ class Section(Base):
         id: The id of the section
         paragraphs: The paragraphs
     """
+
     id: str = field(validator=instance_of(str))
     paragraphs: List[Paragraph] = field(factory=list)
 
@@ -42,6 +43,7 @@ class Document(Base):
         ISBN: International Standard Book Number
         sections: The sections of the document
     """
+
     id: str = field(validator=instance_of(str))
     title: str = field(default=None, validator=optional(instance_of(str)))
     ISBN: int = field(default=None, validator=optional(instance_of(int)))

examples/document.rst

@@ -54,4 +54,3 @@ Allowed field    Data Type    Description
 ===============  ===========  =================================================
 **contents**     str          *Paragraph contents, which make up the Sections.*
 ===============  ===========  =================================================
-

pyproject.toml

@@ -6,4 +6,4 @@ requires = [
     "setuptools_scm>=4.1.2"
 ]
 
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -116,4 +116,4 @@ ignore =
     CONTRIBUTING.md
     *.html
     src/modeci_mdf/version.py
-    tests/.pytest_cache/**
+    tests/.pytest_cache/**

setup.py

@@ -23,9 +23,9 @@
         "pytorch-sphinx-theme==0.0.19",
         "sphinxcontrib-versioning",
     ],
-    "dev": [],
+    "dev": ["flake8"],
 }
 extras["all"] = sum(extras.values(), [])
 extras["dev"] += extras["test"]
 
-setup(extras_require=extras)
+setup(extras_require=extras)

src/modelspec/__init__.py

@@ -1,24 +1,5 @@
 __version__ = "0.1.5"
 
-from .base_types import (
-    Base,
-    define,
-    has,
-    field,
-    fields,
-    optional,
-    instance_of,
-    in_
-)
-
-__all__ = [
-    "Base",
-    "define",
-    "has",
-    "field",
-    "fields",
-    "optional",
-    "instance_of",
-    "in_"
-]
+from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 
+__all__ = ["Base", "define", "has", "field", "fields", "optional", "instance_of", "in_"]

src/modelspec/base_types.py

@@ -51,6 +51,7 @@ class EvaluableExpression(str):
     EvaluableExpression is a string that can be evaluated to a value during MDF execution. This class inherits from
     str, so it can be used as a string.
     """
+
     def __init__(self, expr):
         self.expr = expr
 
@@ -68,7 +69,7 @@ def print_(text: str, print_it: bool = False):
     if not isinstance(text, str):
         text = ("%s" % text).decode("ascii")
     if print_it:
-        print("%s%s" % (prefix, text.replace("\n", "\n" + prefix)))
+        print("{}{}".format(prefix, text.replace("\n", "\n" + prefix)))
 
 
 def print_v(text: str):
@@ -372,7 +373,9 @@ def _is_child_field(cls, field_name: str) -> bool:
         try:
             f = attr.fields_dict(cls)[field_name]
         except KeyError:
-            raise ValueError(f"Field '{field_name}' not found in modelspec class '{cls.__name__}'")
+            raise ValueError(
+                f"Field '{field_name}' not found in modelspec class '{cls.__name__}'"
+            )
 
         # Check if the type of the field is a list or dict
         collection_arg = None
@@ -430,13 +433,13 @@ def _is_evaluable_expression(value: Any) -> bool:
 
     @classmethod
     def _is_base_type(
-            cls,
-            value,
-            can_be_list=False,
-            can_be_dict=False,
-            can_be_ndarray=False,
-            can_be_none=False,
-            can_be_eval_expr=False,
+        cls,
+        value,
+        can_be_list=False,
+        can_be_dict=False,
+        can_be_ndarray=False,
+        can_be_none=False,
+        can_be_eval_expr=False,
     ):
 
         import numpy
@@ -452,16 +455,16 @@ def _is_base_type(
             value = get_origin(value)
 
         return (
-                value == int
-                or value == str
-                or value == bool
-                or value == float
-                or (can_be_list and value == list)
-                or (can_be_dict and value == dict)
-                or (can_be_ndarray and value == numpy.ndarray)
-                or (can_be_none and value is type(None))
-                or (can_be_eval_expr and cls._is_evaluable_expression(value))
-                or value == Union
+            value == int
+            or value == str
+            or value == bool
+            or value == float
+            or (can_be_list and value == list)
+            or (can_be_dict and value == dict)
+            or (can_be_ndarray and value == numpy.ndarray)
+            or (can_be_none and value is type(None))
+            or (can_be_eval_expr and cls._is_evaluable_expression(value))
+            or value == Union
         )
 
     @staticmethod
@@ -488,7 +491,11 @@ def _type_to_str(type_: Any) -> str:
             elif get_origin(type_) == dict and len(get_args(type_)) > 0:
                 return Base._type_to_str(get_args(type_)[1])
             elif get_origin(type_) == Union and len(get_args(type_)) > 0:
-                return "Union[" + ", ".join([Base._type_to_str(arg) for arg in get_args(type_)]) + "]"
+                return (
+                    "Union["
+                    + ", ".join([Base._type_to_str(arg) for arg in get_args(type_)])
+                    + "]"
+                )
 
         # Fallback to returning just the string representation. Drop any occurrence of typing
         return str(type_).replace("typing.", "")
@@ -520,9 +527,9 @@ def _cls_generate_documentation(cls, format: str = MARKDOWN_FORMAT):
         allowed_fields = cls._parse_allowed_fields()
         allowed_children = cls._parse_allowed_children()
 
-        print(" - %s (%s)" % (cls.__name__, definition))
+        print(f" - {cls.__name__} ({definition})")
 
-        rst_url_format = '`%s <%s>`_'
+        rst_url_format = "`%s <%s>`_"
 
         def insert_links(text, format=MARKDOWN_FORMAT):
             if not "_" in text:
@@ -534,12 +541,15 @@ def insert_links(text, format=MARKDOWN_FORMAT):
             for i in range(int(len(split) / 2.0)):
                 pre = split[i * 2]
                 type = split[i * 2 + 1]
-                if format==MARKDOWN_FORMAT:
-                    text2 += '%s<a href="#%s">%s</a>' % (pre, type.lower(), type)
-                elif format==RST_FORMAT:
-                    #text2 += ('%s'+rst_url_format) % (pre, type, '#'+type.lower # problem with handling links ending with s e.g. _Graph_s
-
-                    text2 += ('%s%s') % (pre, type) # temp hack... problem with handling links ending with s e.g. _Graph_s
+                if format == MARKDOWN_FORMAT:
+                    text2 += f'{pre}<a href="#{type.lower()}">{type}</a>'
+                elif format == RST_FORMAT:
+                    # text2 += ('%s'+rst_url_format) % (pre, type, '#'+type.lower # problem with handling links ending with s e.g. _Graph_s
+
+                    text2 += ("%s%s") % (
+                        pre,
+                        type,
+                    )  # temp hack... problem with handling links ending with s e.g. _Graph_s
             if int(len(split) / 2.0) != len(split) / 2.0:
                 text2 += split[-1]
             return text2
@@ -551,7 +561,7 @@ def insert_links(text, format=MARKDOWN_FORMAT):
             if definition is not None:
                 doc_string += "%s\n\n" % insert_links(definition)
         elif format == RST_FORMAT:
-            doc_string += "%s\n%s\n%s\n" % ("="*len(name), name, "="*len(name))
+            doc_string += "{}\n{}\n{}\n".format("=" * len(name), name, "=" * len(name))
             if definition is not None:
                 doc_string += "%s\n\n" % insert_links(definition, format=RST_FORMAT)
         elif format == DICT_FORMAT:
@@ -576,19 +586,17 @@ def insert_links(text, format=MARKDOWN_FORMAT):
                 type_, can_be_eval_expr=True, can_be_dict=True
             )
             type_str = Base._type_to_str(type_)
-            print("    Allowed parameter: %s %s" % (f, (description, type_str)))
+            print("    Allowed parameter: {} {}".format(f, (description, type_str)))
 
             if format == DICT_FORMAT:
                 doc_dict[name]["allowed_parameters"][f] = {}
                 doc_dict[name]["allowed_parameters"][f]["type"] = type_str
-                doc_dict[name]["allowed_parameters"][f][
-                    "description"
-                ] = description
+                doc_dict[name]["allowed_parameters"][f]["description"] = description
 
             elif format == MARKDOWN_FORMAT:
-                doc_string += "<tr><td><b>%s</b></td><td>%s</td>" % (
+                doc_string += "<tr><td><b>{}</b></td><td>{}</td>".format(
                     f,
-                    '<a href="#%s">%s</a>' % (type_str.lower(), type_str)
+                    f'<a href="#{type_str.lower()}">{type_str}</a>'
                     if referencable
                     else type_str,
                 )
@@ -598,14 +606,12 @@ def insert_links(text, format=MARKDOWN_FORMAT):
 
             elif format == RST_FORMAT:
                 n = "**%s**" % f
-                t = "%s" % (
-                    rst_url_format % (type_, '#'+type_str.lower())
+                t = "{}".format(
+                    rst_url_format % (type_, "#" + type_str.lower())
                     if referencable
                     else type_str,
                 )
-                d = "*%s*" % (
-                    insert_links(description, format=RST_FORMAT)
-                )
+                d = "*%s*" % (insert_links(description, format=RST_FORMAT))
                 table_info.append([n, t, d])
 
             if referencable:
@@ -615,7 +621,13 @@ def insert_links(text, format=MARKDOWN_FORMAT):
             if format == MARKDOWN_FORMAT:
                 doc_string += "\n</table>\n\n"
             elif format == RST_FORMAT:
-                doc_string += "%s\n\n" % (tabulate(table_info, ['Allowed field', 'Data Type', 'Description'], tablefmt="rst"))
+                doc_string += "%s\n\n" % (
+                    tabulate(
+                        table_info,
+                        ["Allowed field", "Data Type", "Description"],
+                        tablefmt="rst",
+                    )
+                )
 
         if len(allowed_children) > 0:
             if format == MARKDOWN_FORMAT:
@@ -629,23 +641,21 @@ def insert_links(text, format=MARKDOWN_FORMAT):
 
         for c, (description, type_) in allowed_children.items():
             type_str = Base._type_to_str(type_)
-            print("    Allowed child: %s %s" % (c, (description, type_str)))
+            print("    Allowed child: {} {}".format(c, (description, type_str)))
 
-            referencable = not Base._is_base_type(
-                type_, can_be_dict=True
-            )
+            referencable = not Base._is_base_type(type_, can_be_dict=True)
 
             if format == DICT_FORMAT:
                 doc_dict[name]["allowed_children"][c] = {}
                 doc_dict[name]["allowed_children"][c]["type"] = type_str
-                doc_dict[name]["allowed_children"][c][
-                    "description"
-                ] = allowed_children[c][0]
+                doc_dict[name]["allowed_children"][c]["description"] = allowed_children[
+                    c
+                ][0]
 
             elif format == MARKDOWN_FORMAT:
-                doc_string += "<tr><td><b>%s</b></td><td>%s</td>" % (
+                doc_string += "<tr><td><b>{}</b></td><td>{}</td>".format(
                     c,
-                    '<a href="#%s">%s</a>' % (type_str.lower(), type_str)
+                    f'<a href="#{type_str.lower()}">{type_str}</a>'
                     if referencable
                     else type_str,
                 )
@@ -655,14 +665,12 @@ def insert_links(text, format=MARKDOWN_FORMAT):
 
             elif format == RST_FORMAT:
                 n = "**%s**" % c
-                t = "%s" % (
-                    rst_url_format % (type_str, '#'+type_str.lower())
+                t = "{}".format(
+                    rst_url_format % (type_str, "#" + type_str.lower())
                     if referencable
                     else type_str,
                 )
-                d = "*%s*" % (
-                    insert_links(description, format=RST_FORMAT)
-                )
+                d = "*%s*" % (insert_links(description, format=RST_FORMAT))
                 table_info.append([n, t, d])
 
             # Get the contained type
@@ -677,7 +685,13 @@ def insert_links(text, format=MARKDOWN_FORMAT):
             if format == MARKDOWN_FORMAT:
                 doc_string += "\n</table>\n\n"
             elif format == RST_FORMAT:
-                doc_string += "%s\n\n"%(tabulate(table_info, ['Allowed child','Data Type','Description'], tablefmt="rst"))
+                doc_string += "%s\n\n" % (
+                    tabulate(
+                        table_info,
+                        ["Allowed child", "Data Type", "Description"],
+                        tablefmt="rst",
+                    )
+                )
 
         for r in referenced:
             if format in (MARKDOWN_FORMAT, RST_FORMAT):