Merge pull request #86 from ModECI/development

To v0.3.7; support for py 3.13

Author: pgleeson

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
         exclude:
           - runs-on: macos-latest
@@ -49,7 +49,6 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        pip install 'numpy<2.0.0' # due to lingering issues with other modules & numpy...
         pip install .[dev]
 
     - name: Lint with flake8
@@ -61,6 +60,7 @@ jobs:
         pip list
 
     - name: Run simple examples
+      shell: bash
       run: |
         cd examples
         python document.py
@@ -70,6 +70,7 @@ jobs:
         python test.py
 
     - name: Test NeuroML examples
+      shell: bash
       run: |
 
         cd examples/neuroml2
@@ -78,6 +79,7 @@ jobs:
         # Note: NeuroML files will be validated with OMV below
 
     - name: Test SBML examples
+      shell: bash
       run: |
 
         cd examples/sbml
@@ -126,7 +128,6 @@ jobs:
         # Run OMV tests on all engines
         cd examples
         omv all -V
-
         omv list -V # list installed engines
 
     - name: Final version info

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 2025-02-05.
+This page is generated periodically, most recently on 2025-04-16.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

setup.cfg

@@ -26,6 +26,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering
     Topic :: Software Development
     Typing :: Typed
@@ -44,7 +45,7 @@ install_requires =
    typing_compat;python_version<'3.8'
 
 
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 package_dir =
     =src
@@ -83,8 +84,8 @@ docs =
 
 dev =
     flake8
-    pyneuroml>=0.7.2
-    NeuroMLlite>=0.5.3
+    pyneuroml>=1.3.15
+    NeuroMLlite>=0.6.1
     python-libsbml
     modelspec[test]
     pre-commit

src/modelspec/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.6"
+__version__ = "0.3.7"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 

src/modelspec/base_types.py

@@ -566,9 +566,9 @@ def _is_child_field(cls, field_name: str) -> bool:
 
         # Check if the type of the field is a list or dict
         collection_arg = None
-        if get_origin(f.type) == list and len(get_args(f.type)) > 0:
+        if get_origin(f.type) is list and len(get_args(f.type)) > 0:
             collection_arg = get_args(f.type)[0]
-        elif get_origin(f.type) == dict and len(get_args(f.type)) > 0:
+        elif get_origin(f.type) is dict and len(get_args(f.type)) > 0:
             collection_arg = get_args(f.type)[1]
 
         try:
@@ -641,16 +641,16 @@ 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)
+            value is int
+            or value is str
+            or value is bool
+            or value is float
+            or (can_be_list and value is list)
+            or (can_be_dict and value is dict)
+            or (can_be_ndarray and value is numpy.ndarray)
             or (can_be_none and value is None)
             or (can_be_eval_expr and cls._is_evaluable_expression(value))
-            or value == Union
+            or value is Union
         )
 
     @staticmethod
@@ -671,11 +671,11 @@ def _type_to_str(type_: Any) -> str:
 
         # If its a Generic type
         elif get_origin(type_) is not None:
-            if get_origin(type_) == list and len(get_args(type_)) > 0:
+            if get_origin(type_) is list and len(get_args(type_)) > 0:
                 return Base._type_to_str(get_args(type_)[0])
-            elif get_origin(type_) == dict and len(get_args(type_)) > 0:
+            elif get_origin(type_) is 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:
+            elif get_origin(type_) is Union and len(get_args(type_)) > 0:
                 return (
                     "Union["
                     + ", ".join([Base._type_to_str(arg) for arg in get_args(type_)])
@@ -916,9 +916,9 @@ def insert_links(text, format=MARKDOWN_FORMAT):
                 table_info.append([n, t, d])
 
             # Get the contained type
-            if get_origin(type_) == list and len(get_args(type_)) > 0:
+            if get_origin(type_) is list and len(get_args(type_)) > 0:
                 referenced.append(get_args(type_)[0])
-            elif get_origin(type_) == dict and len(get_args(type_)) > 1:
+            elif get_origin(type_) is dict and len(get_args(type_)) > 1:
                 referenced.append(get_args(type_)[1])
             else:
                 referenced.append(type_)
@@ -1080,7 +1080,7 @@ def _is_list_base(cl):
     Check if a class is a list of Base objects. These will be serialized as dicts if the underlying class has an id
     attribute.
     """
-    return get_origin(cl) == list and issubclass(get_args(cl)[0], Base)
+    return get_origin(cl) is list and issubclass(get_args(cl)[0], Base)
 
 
 converter.register_unstructure_hook_factory(_is_list_base, _unstructure_list_base)

src/modelspec/utils.py

@@ -486,13 +486,13 @@ def evaluate(
                     expr = tf.constant(int(expr))
                 else:
                     expr = int(expr)
-            except:
+            except Exception:
                 try:
                     if array_format == FORMAT_TENSORFLOW:
                         expr = tf.constant(float(expr))
                     else:
                         expr = float(expr)
-                except:
+                except Exception:
                     pass
 
         if type(expr) is list:
@@ -525,7 +525,7 @@ def evaluate(
         else:  # will have failed if not number
             print_("   Returning {}: {}".format(type(expr), expr), verbose)
             return expr
-    except:
+    except Exception:
         try:
             if rng:
                 expr = expr.replace("random()", "rng.random()")
@@ -582,12 +582,12 @@ def parse_list_like(list_str):
         try:
             expr = int(list_str)
             return [expr]
-        except:
+        except Exception:
             pass
         try:
             expr = float(list_str)
             return [expr]
-        except:
+        except Exception:
             pass
         if "[" in list_str:
             return eval(list_str)

tests/test_utils.py

@@ -19,15 +19,15 @@ def test_evaluate(self):
         assert evaluate("p+p", params, verbose=True) == 66
 
         print("======")
-        assert type(evaluate("33")) == int
-        assert type(evaluate("33", cast_to_int=True)) == int
-        assert type(evaluate("33.0")) == float
-        assert type(evaluate("33.0", cast_to_int=True)) == int
+        assert type(evaluate("33")) is int
+        assert type(evaluate("33", cast_to_int=True)) is int
+        assert type(evaluate("33.0")) is float
+        assert type(evaluate("33.0", cast_to_int=True)) is int
 
-        assert type(evaluate("33.1")) == float
-        assert type(evaluate("33.1a", verbose=True)) == str
+        assert type(evaluate("33.1")) is float
+        assert type(evaluate("33.1a", verbose=True)) is str
 
-        assert type(evaluate("a")) == str
+        assert type(evaluate("a")) is str
 
         import random