Merge pull request #24 from ModECI/development

To v0.2.7

Author: pgleeson

.github/workflows/ci.yml

@@ -51,27 +51,23 @@ jobs:
         cd examples
         python document.py
 
+        cd test
+        python test.py
+
     - name: Run pytest
       run: |
         pytest tests
 
     - name: Install & test NeuroMLlite
       run: |
-          git clone --branch experimental https://github.com/NeuroML/NeuroMLlite.git
+          git clone --branch development https://github.com/NeuroML/NeuroMLlite.git
           cd NeuroMLlite
-          pip install .
-          pip install pyneuroml>=0.5.18
+          #pip install . # Use versions of neuroml libs as set in setup.py
           cd examples
           python Example1.py
 
 
-    - name: Install GPy (py3.9)
-      if: ${{ matrix.python-version == '3.9' }}
-      run: python -m pip install git+https://github.com/SheffieldML/GPy.git@devel
-
-
     - name: Install MDF
-      if: ${{ matrix.python-version != '3.10' }}
       run: |
 
           git clone --branch development https://github.com/ModECI/MDF.git

examples/test/test.md

@@ -0,0 +1,27 @@
+## TopClass
+A model....
+
+### Allowed parameters
+<table>
+  <tr>
+    <td><b>id</b></td>
+    <td>str</td>
+    <td><i>The unique id of the thing</i></td>
+ </tr>
+
+
+  <tr>
+    <td><b>float_like_req</b></td>
+    <td>int</td>
+    <td><i>name says it all...</i></td>
+ </tr>
+
+
+  <tr>
+    <td><b>float_like_optional</b></td>
+    <td>int</td>
+    <td><i>name also says it all...</i></td>
+ </tr>
+
+
+</table>

examples/test/test.py

@@ -0,0 +1,65 @@
+import modelspec
+from modelspec import field, instance_of, optional
+from modelspec.base_types import Base
+from typing import List
+
+# Example testing multiple options...
+
+from typing import Any
+
+
+def convert2float(x: Any) -> float:
+    print("Converting {} ({})".format(x, type(x)))
+    """Convert to float if not None"""
+    if x is not None:
+        return float(x)
+    else:
+        return None
+
+
+@modelspec.define
+class TopClass(Base):
+    """
+    A model....
+
+    Args:
+        id: The unique id of the thing
+        float_like_req: name says it all...
+        float_like_optional: name also says it all...
+    """
+
+    id: str = field(validator=instance_of(str))
+    float_like_req: int = field(
+        default=None, validator=instance_of(float), converter=convert2float
+    )
+    float_like_optional: int = field(
+        default=None, validator=optional(instance_of(float)), converter=convert2float
+    )
+
+
+tc = TopClass(
+    id="MyTest", float_like_req="03"
+)  # a string which can be converted to a float...
+
+# tc.float_like_req = 2.01
+tc.float_like_optional = 43
+
+
+print(tc)
+
+tc.to_yaml_file("test_instance.yaml")
+
+doc_md = tc.generate_documentation(format="markdown")
+
+with open("test.md", "w") as d:
+    d.write(doc_md)
+
+
+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:
+    d.write(yaml.dump(doc_dict, indent=4, sort_keys=False))

examples/test/test.specification.yaml

@@ -0,0 +1,12 @@
+TopClass:
+    definition: A model....
+    allowed_parameters:
+        id:
+            type: str
+            description: The unique id of the thing
+        float_like_req:
+            type: int
+            description: name says it all...
+        float_like_optional:
+            type: int
+            description: name also says it all...

examples/test/test_instance.yaml

@@ -0,0 +1,3 @@
+MyTest:
+    float_like_req: 3.0
+    float_like_optional: 43.0

setup.py

@@ -23,7 +23,7 @@
         "pytorch-sphinx-theme==0.0.19",
         "sphinxcontrib-versioning",
     ],
-    "dev": ["flake8"],
+    "dev": ["flake8", "pyneuroml>=0.7.2", "NeuroMLlite>=0.5.3"],
 }
 extras["all"] = sum(extras.values(), [])
 extras["dev"] += extras["test"]

src/modelspec/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.6"
+__version__ = "0.2.7"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 

src/modelspec/base_types.py

@@ -33,6 +33,7 @@
 MARKDOWN_FORMAT = "markdown"
 RST_FORMAT = "rst"
 DICT_FORMAT = "dict"
+ALL_FORMATS = [MARKDOWN_FORMAT, RST_FORMAT, DICT_FORMAT]
 
 
 class EvaluableExpression(str):
@@ -572,8 +573,12 @@ def _cls_generate_documentation(cls, format: str = MARKDOWN_FORMAT):
 
         if format == MARKDOWN_FORMAT or format == RST_FORMAT:
             doc_string = ""
-        if format == DICT_FORMAT:
+        elif format == DICT_FORMAT:
             doc_dict = {}
+        else:
+            raise ValueError(
+                f"Unknown format: '{format}', recognised formats: '{ALL_FORMATS}''"
+            )
 
         definition = cls._parse_definition()
         allowed_fields = cls._parse_allowed_fields()

test_all.sh

@@ -6,8 +6,11 @@ pip install .
 cd examples
 python document.py
 
-cd ..
+cd test
+python test.py
 
-pytest tests
+cd ../..
+
+pytest tests -v
 
 pre-commit run --all-files