More flake highlighted code tweaks

Author: pgleeson

.gitignore

@@ -164,3 +164,4 @@ cython_debug/
 /examples/document.specification.bson
 /examples/neuroml2/hello_world.v.dat
 /examples/sbml/example_sbml_test.xml
+/updatelibs.sh

docs/contributors.py

@@ -1,6 +1,5 @@
 import requests
 import pandas as pd
-import json
 import textwrap
 from datetime import date
 

examples/sbml/sbml_validators.py

@@ -19,7 +19,7 @@
 
 
 def valid_kind(instance, attribute, value):
-    if not value in sbml_si_units:
+    if value not in sbml_si_units:
         raise ValueError(
             f"kind {value} must be one of the standard SI units: {sbml_si_units}"
         )

examples/sbml/test_sbml3.py

@@ -7,7 +7,6 @@
 
 import json
 import yaml
-import os
 
 from sbml32spec import *
 

src/modelspec/base_types.py

@@ -165,11 +165,6 @@ def from_yaml(cls, yaml_str: str) -> "Base":
         """Instantiate an modelspec object from a YAML string"""
         return cls.from_dict(yaml.load(yaml_str, Loader=yaml.SafeLoader))
 
-    @classmethod
-    def from_yaml_file(cls, yaml_file: str) -> "Base":
-        """Instantiate an modelspec object from a file containing YAML"""
-        return cls.from_dict(yaml.load(yaml_file, Loader=yaml.SafeLoader))
-
     @classmethod
     def from_json(cls, json_str: str) -> "Base":
         """Instantiate an modelspec object from a JSON string"""

src/modelspec/utils.py

@@ -269,14 +269,14 @@ def build_xml_element(data, parent=None):
             )
             if attribute_value is not None:
                 if (
-                    type(attribute_value) is int
-                    or type(attribute_value) is float
-                    or type(attribute_value) is str
-                    or type(attribute_value) is bool
-                    or type(attribute_value) is list
+                    isinstance(attribute_value, int)
+                    or isinstance(attribute_value, float)
+                    or isinstance(attribute_value, str)
+                    or isinstance(attribute_value, bool)
+                    or isinstance(attribute_value, list)
                 ):
                     parent.set(attribute_name, str(attribute_value))
-                elif type(attribute_value) == dict:
+                elif isinstance(attribute_value, dict):
                     """for k, v in attribute_value.items():
                     child_element = build_xml_element(v)"""
                 else:
@@ -327,7 +327,7 @@ def _parse_attributes(dict_format, to_build):
         )
 
         if new_format:
-            if type(to_build) == dict:
+            if isinstance(to_build, dict):
                 to_build[key] = value
 
             elif key in to_build.allowed_children:
@@ -339,11 +339,11 @@ def _parse_attributes(dict_format, to_build):
                     exec("to_build.%s.append(ff)" % key)
             else:
                 if (
-                    type(value) == str
-                    or type(value) == int
-                    or type(value) == float
-                    or type(value) == bool
-                    or type(value) == list
+                    isinstance(value, str)
+                    or isinstance(value, int)
+                    or isinstance(value, float)
+                    or isinstance(value, bool)
+                    or isinstance(value, list)
                     or value is None
                 ):
                     to_build.__setattr__(key, value)
@@ -364,11 +364,15 @@ def _parse_attributes(dict_format, to_build):
                         exec("to_build.%s = ff" % key)
 
         else:
-            if type(to_build) == dict:
+            if isinstance(to_build, dict):
                 to_build[key] = value
-            elif type(value) == str or type(value) == int or type(value) == float:
+            elif (
+                isinstance(value, str)
+                or isinstance(value, int)
+                or isinstance(value, float)
+            ):
                 to_build.__setattr__(key, value)
-            elif type(value) == list:
+            elif isinstance(value, list):
                 type_to_use = to_build.allowed_children[key][1]
 
                 for vl in value:
@@ -397,7 +401,7 @@ def locate_file(f, base_dir):
 
 
 def _val_info(param_val):
-    if type(param_val) == np.ndarray:
+    if isinstance(param_val, np.ndarray):
         pp = "%s" % (np.array2string(param_val, threshold=4, edgeitems=1))
         pp = pp.replace("\n", "")
         pp += f" (NP {param_val.shape} {param_val.dtype})"