General tidying of code and actions

.github/workflows/ci.yml

@@ -14,7 +14,9 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
-    - uses: pre-commit/[email protected]
+      with:
+        python-version: "3.10"
+    - uses: pre-commit/[email protected]
       with:
         extra_args: --hook-stage manual --all-files
 
@@ -52,6 +54,7 @@ jobs:
       run: |
         cd examples
         python document.py
+        git diff
 
         cd test
         python test.py

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 2024-02-07.
+This page is generated periodically, most recently on 2024-03-21.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

docs/sphinx/source/api/examples/document.py

@@ -3,6 +3,9 @@
 from modelspec.base_types import Base
 from typing import List
 import sys
+import json
+import yaml
+import bson
 
 # Example showing how to create a model of a document and use it to create/serialize instances
 
@@ -96,9 +99,6 @@ class Document(Base):
 print("\n  >> Generating specification in dict form...")
 doc_dict = doc.generate_documentation(format="dict")
 
-import json
-import yaml
-import bson
 
 with open("document.specification.json", "w") as d:
     d.write(json.dumps(doc_dict, indent=4))

examples/document.py

@@ -3,6 +3,9 @@
 from modelspec.base_types import Base
 from typing import List
 import sys
+import json
+import yaml
+import bson
 
 # Example showing how to create a model of a document and use it to create/serialize instances
 
@@ -96,9 +99,6 @@ class Document(Base):
 print("\n  >> Generating specification in dict form...")
 doc_dict = doc.generate_documentation(format="dict")
 
-import json
-import yaml
-import bson
 
 with open("document.specification.json", "w") as d:
     d.write(json.dumps(doc_dict, indent=4))

examples/test/test.py

@@ -1,10 +1,9 @@
 import modelspec
 from modelspec import field, instance_of, optional
 from modelspec.base_types import Base
-from modelspec.utils import load_json
-from typing import List
 from typing import Any
 import sys
+import yaml
 
 
 # Example testing multiple options...
@@ -104,7 +103,6 @@ class TopClass(Base):
 print("\nGenerating specification in dict form")
 doc_dict = tc.generate_documentation(format="dict")
 
-import yaml
 
 print("Generating specification in YAML")
 with open("test.specification.yaml", "w") as d:

src/modelspec/base_types.py

@@ -169,18 +169,13 @@ def from_yaml(cls, yaml_str: str) -> "Base":
     @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_str, Loader=yaml.SafeLoader))
+        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"""
         return cls.from_dict(json.loads(json_str))
 
-    @classmethod
-    def from_json_file(cls, json_file: str) -> "Base":
-        """Instantiate an modelspec object from a file containing JSON"""
-        return cls.from_dict(json.load(json_file))
-
     @classmethod
     def from_bson(cls, bson_str: str) -> "Base":
         """Instantiate an modelspec object from a BSON string"""
@@ -318,7 +313,6 @@ def to_xml_file(
         filename: Optional[str] = None,
         include_metadata: bool = True,
     ) -> str:
-        from modelspec.utils import build_xml_element
 
         if filename is None:
             filename = f"{self.id}.xml"

src/modelspec/utils.py

@@ -14,7 +14,7 @@
 from modelspec.base_types import EvaluableExpression
 
 from random import Random
-from typing import Union, Dict
+from typing import Union
 
 verbose = False
 
@@ -272,11 +272,11 @@ def build_xml_element(data, parent=None):
             )
             if attribute_value is not None:
                 if (
-                    type(attribute_value) == int
-                    or type(attribute_value) == float
-                    or type(attribute_value) == str
-                    or type(attribute_value) == bool
-                    or type(attribute_value) == list
+                    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
                 ):
                     parent.set(attribute_name, str(attribute_value))
                 elif type(attribute_value) == dict:
@@ -411,15 +411,15 @@ def _val_info(param_val):
         pp = "%s" % param_val
         pp = pp.replace("\n", "")
         # pp+=' (TF %s %s)'%(param_val.shape,param_val.dtype)
-    elif type(param_val) == tuple:
+    elif type(param_val) is tuple:
         # If param_val is a tuple, recursively print its elements
         # separated by commas and wrapped in parentheses
         pp = "(" + ", ".join([_val_info(el) for el in param_val]) + ")"
     else:
         pp = "%s" % param_val
         t = type(param_val)
-        if not (t == int or t == float):
-            pp += "(%s)" % (t if type(t) == str else t.__name__)
+        if not (t is int or t is float):
+            pp += "(%s)" % (t if type(t) is str else t.__name__)
     return pp
 
 
@@ -476,13 +476,13 @@ def evaluate(
         verbose,
     )
     try:
-        if type(expr) == str and expr in parameters:
+        if type(expr) is str and expr in parameters:
             expr = parameters[
                 expr
             ]  # replace with the value in parameters & check whether it's float/int...
             print_("   Using for that param: %s" % _val_info(expr), verbose)
 
-        if type(expr) == str:
+        if type(expr) is str:
             try:
                 if array_format == FORMAT_TENSORFLOW:
                     expr = tf.constant(int(expr))
@@ -498,14 +498,14 @@ def evaluate(
                 except:
                     pass
 
-        if type(expr) == list:
+        if type(expr) is list:
             print_("   Returning a list in format: %s" % array_format, verbose)
             if array_format == FORMAT_TENSORFLOW:
                 return tf.constant(expr, dtype=tf.float64)
             else:
                 return np.array(expr)
 
-        if type(expr) == np.ndarray:
+        if type(expr) is np.ndarray:
             print_("   Returning a numpy array in format: %s" % array_format, verbose)
             if array_format == FORMAT_TENSORFLOW:
                 return tf.convert_to_tensor(expr, dtype=tf.float64)
@@ -538,9 +538,9 @@ def evaluate(
                     "The expression [%s] contains a random() call, but a random number generator (rng) must be supplied to the evaluate() call when this expression string is to be evaluated"
                 )
 
-            if type(expr) == str and "math." in expr:
+            if type(expr) is str and "math." in expr:
                 parameters["math"] = math
-            if type(expr) == str and "numpy." in expr:
+            if type(expr) is str and "numpy." in expr:
                 parameters["numpy"] = np
 
             print_(
@@ -556,7 +556,7 @@ def evaluate(
                 verbose,
             )
 
-            if (type(v) == float or type(v) == str) and int(v) == v:
+            if (type(v) is float or type(v) is str) and int(v) == v:
 
                 print_("   Returning int: %s" % int(v), verbose)
 
@@ -583,7 +583,7 @@ def parse_list_like(list_str):
         return [list_str]
     elif isinstance(list_str, list):
         return list_str
-    elif type(list_str) == str:
+    elif type(list_str) is str:
         try:
             expr = int(list_str)
             return [expr]

test_all.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
 set -ex
 
-## Install
+## Install modelspec incl. dev dependencies
 
-pip install .
+pip install .[dev]
 
 
 ## Test main example

tests/test_base.py

@@ -192,8 +192,9 @@ def test_save_load_json(tmp_path):
     nety3 = NewNetwork.from_yaml_file(filenamey)
     str_nety3 = str(nety3)
 
-    # datax = load_xml(filenamex)
-    # print_v("Loaded network specification from %s" % filenamex)
+    datax = load_xml(filenamex)
+    assert len(datax) > 0
+    print_v("Loaded network specification from %s" % filenamex)
 
     # netx = NewNetwork.from_dict(datax)
     # str_netx = str(netx)