Merge pull request #73 from ModECI/experimental

Fixes for macos-latest

Author: pgleeson

.github/workflows/ci.yml

@@ -29,9 +29,9 @@ jobs:
         python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
         exclude:
-          - runs-on: macos-14
+          - runs-on: macos-latest
             python-version: "3.8"
-          - runs-on: macos-14
+          - runs-on: macos-latest
             python-version: "3.9"
 
     steps:
@@ -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' }}

.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
 

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

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

examples/sbml/test_sbml3.py

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

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(
@@ -166,11 +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"""
@@ -297,7 +291,6 @@ 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 +306,6 @@ def to_xml_file(
         filename: Optional[str] = None,
         include_metadata: bool = True,
     ) -> str:
-
         if filename is None:
             filename = f"{self.id}.xml"
 
@@ -636,7 +628,6 @@ def _is_base_type(
         can_be_none=False,
         can_be_eval_expr=False,
     ):
-
         import numpy
 
         if verbose:
@@ -730,7 +721,6 @@ 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)
@@ -272,15 +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:
@@ -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
@@ -333,7 +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:
@@ -345,11 +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)
@@ -370,11 +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:
@@ -403,7 +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})"
@@ -489,7 +487,6 @@ def evaluate(
                 else:
                     expr = int(expr)
             except:
-
                 try:
                     if array_format == FORMAT_TENSORFLOW:
                         expr = tf.constant(float(expr))
@@ -557,7 +554,6 @@ 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 +572,6 @@ def evaluate(
 
 
 def parse_list_like(list_str):
-
     if isinstance(list_str, int):
         return [list_str]
     elif isinstance(list_str, float):