Format update

Author: pgleeson

.github/workflows/ci.yml

@@ -112,7 +112,7 @@ jobs:
         python contributors.py
         cd sphinx
         make clean
-        make html  
+        make html
 
     - name: Install and test with OMV
       if: ${{ matrix.runs-on != 'windows-latest' }}

docs/sphinx/source/api/Contributors.md

@@ -3,7 +3,7 @@
 # Modelspec contributors
 
 This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2024-04-12.
+This page is generated periodically, most recently on 2024-04-25.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

examples/neuroml2/neuroml2_spec.py

@@ -128,7 +128,6 @@ class neuroml(Base):
 
 
 if __name__ == "__main__":
-
     nml_doc = neuroml(id="TestNeuroML")
 
     izh = izhikevich2007Cell(

examples/sbml/sbml32spec.py

@@ -82,7 +82,6 @@ class SBase(Base):
 
 @modelspec.define
 class SBaseWithId(SBase):
-
     id: str = field(default=None, validator=optional([instance_of(str), valid_sid]))
 
 

examples/sbml/sbml_validators.py

@@ -168,7 +168,6 @@ def validate_sbml(doc, units_consistency: bool = False) -> None:
 
 
 if __name__ == "__main__":
-
     import libsbml
 
     sbml_file = sys.argv[1]

src/modelspec/base_types.py

@@ -147,7 +147,6 @@ def from_dict(cls, d: Dict[str, Any]) -> "Base":
         # If this object has an id attribute, it may have been serialized within a dict with the id as the key, even if
         # it is a single object.
         if "id" in [f.name for f in attr.fields(cls)] and "id" not in d.keys():
-
             keys = list(d.keys())
             if len(keys) == 0:
                 raise ValueError(
@@ -297,7 +296,6 @@ def to_yaml_file(
             filename = f"{self.id}.yaml"
 
         with open(filename, "w") as outfile:
-
             # We need to setup another
             yaml.dump(
                 yaml_converter.unstructure(self.to_dict()),
@@ -313,7 +311,6 @@ def to_xml_file(
         filename: Optional[str] = None,
         include_metadata: bool = True,
     ) -> str:
-
         if filename is None:
             filename = f"{self.id}.xml"
 
@@ -636,7 +633,6 @@ def _is_base_type(
         can_be_none=False,
         can_be_eval_expr=False,
     ):
-
         import numpy
 
         if verbose:
@@ -730,7 +726,6 @@ def _cls_generate_documentation(cls, format: str = MARKDOWN_FORMAT):
         rst_url_format = "`%s <%s>`__"
 
         def insert_links(text, format=MARKDOWN_FORMAT):
-
             code_ref = ":code:`"
             # print("    > Converting: %s" % text)
             text2 = text

src/modelspec/utils.py

@@ -192,14 +192,12 @@ def convert_xml_dict_values(value):
 
 
 def save_to_json_file(info_dict, filename, indent=4):
-
     strj = json.dumps(info_dict, indent=indent)
     with open(filename, "w") as fp:
         fp.write(strj)
 
 
 def save_to_yaml_file(info_dict, filename, indent=4):
-
     if sys.version_info[0] == 2:
         stry = yaml.dump(info_dict, indent=indent, default_flow_style=False)
     else:
@@ -251,7 +249,6 @@ def build_xml_element(data, parent=None):
 
     attrs = attr.fields(data.__class__)
     for aattr in attrs:
-
         print_("     == Looking at: {} ({})".format(aattr, type(aattr)), verbose)
         if isinstance(aattr.default, attr.Factory):
             children = data.__getattribute__(aattr.name)
@@ -280,7 +277,6 @@ def build_xml_element(data, parent=None):
                 ):
                     parent.set(attribute_name, str(attribute_value))
                 elif type(attribute_value) == dict:
-
                     """for k, v in attribute_value.items():
                     child_element = build_xml_element(v)"""
                 else:
@@ -309,7 +305,6 @@ def ascii_encode_dict(data):
 
 
 def _parse_element(dict_format, to_build):
-
     print_("Parse for element: [%s]" % dict_format, verbose)
     for k in dict_format.keys():
         print_(
@@ -323,7 +318,6 @@ def _parse_element(dict_format, to_build):
 
 
 def _parse_attributes(dict_format, to_build):
-
     for key in dict_format:
         value = dict_format[key]
         new_format = True
@@ -489,7 +483,6 @@ def evaluate(
                 else:
                     expr = int(expr)
             except:
-
                 try:
                     if array_format == FORMAT_TENSORFLOW:
                         expr = tf.constant(float(expr))
@@ -557,7 +550,6 @@ def evaluate(
             )
 
             if (type(v) is float or type(v) is str) and int(v) == v:
-
                 print_("   Returning int: %s" % int(v), verbose)
 
                 if array_format == FORMAT_TENSORFLOW:
@@ -576,7 +568,6 @@ def evaluate(
 
 
 def parse_list_like(list_str):
-
     if isinstance(list_str, int):
         return [list_str]
     elif isinstance(list_str, float):

tests/test_utils.py

@@ -12,7 +12,6 @@
 
 class TestUtils(unittest.TestCase):
     def test_evaluate(self):
-
         assert evaluate("33") == 33.0
         assert evaluate("33") == 33
         assert evaluate(33) == 33