Merge pull request #74 from ModECI/development

pgleeson · web-flow · commit 21a644e22e88 · 2024-04-25T13:58:08.000+01:00
To v0.3.4, mainly code cleanup &amp; tests on mac14/py3.12
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,9 +12,11 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/action@v3.0.0
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - uses: pre-commit/action@v3.0.1
       with:
         extra_args: --hook-stage manual --all-files
 
@@ -24,16 +26,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.8", "3.9", "3.10", "3.11"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
+        exclude:
+          - runs-on: macos-latest
+            python-version: "3.8"
+          - runs-on: macos-latest
+            python-version: "3.9"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 
+    - name: Install HDF5 for pytables on macos-14
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
 
     - name: Install package
       run: |
@@ -52,12 +63,12 @@ jobs:
       run: |
         cd examples
         python document.py
+        git diff
 
         cd test
         python test.py
 
     - name: Test NeuroML examples
-      if: ${{ matrix.python-version != '3.7'}}
       run: |
 
         cd examples/neuroml2
@@ -66,7 +77,6 @@ jobs:
         # Note: NeuroML files will be validated with OMV below
 
     - name: Test SBML examples
-      if: ${{ matrix.python-version != '3.7'}}
       run: |
 
         cd examples/sbml
@@ -76,11 +86,11 @@ jobs:
       run: |
         pytest tests -v
 
-    - name: Install & test NeuroMLlite
+    - name: Test NeuroMLlite
       run: |
           git clone --branch development https://github.com/NeuroML/NeuroMLlite.git
           cd NeuroMLlite
-          #pip install . # Use versions of neuroml libs as set in setup.py
+          # pip install . # Use versions of neuroml libs as set in modelspec's setup.cfg -> dev -> NeuroMLlite
           cd examples
           python Example1.py
 
@@ -94,7 +104,6 @@ jobs:
           python arrays.py -run   # test one example
 
     - name: Build Documentation
-      if: ${{ matrix.python-version != '3.7'}}
       run: |
         # Note: contributors generation below fails on py 3.7 due to pandas version...
         pip install .[docs]
diff --git a/.gitignore b/.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
diff --git a/docs/contributors.py b/docs/contributors.py
@@ -1,6 +1,5 @@
 import requests
 import pandas as pd
-import json
 import textwrap
 from datetime import date
 
diff --git a/docs/sphinx/source/api/Contributors.md b/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 2023-12-13.
+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))
@@ -12,3 +12,4 @@ This page is generated periodically, most recently on 2023-12-13.
 - Parikshit Singh Rathore ([@parikshit14](https://github.com/parikshit14))
 - Ankur Sinha ([@sanjayankur31](https://github.com/sanjayankur31))
 - kmantel ([@kmantel](https://github.com/kmantel))
+- Robert Vickerstaff ([@robertvi](https://github.com/robertvi))
diff --git a/docs/sphinx/source/api/examples/document.py b/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))
diff --git a/examples/document.py b/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))
diff --git a/examples/neuroml2/neuroml2_spec.py b/examples/neuroml2/neuroml2_spec.py
@@ -128,7 +128,6 @@ class neuroml(Base):
 
 
 if __name__ == "__main__":
-
     nml_doc = neuroml(id="TestNeuroML")
 
     izh = izhikevich2007Cell(
diff --git a/examples/sbml/sbml32spec.py b/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]))
 
 
diff --git a/examples/sbml/sbml_validators.py b/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]
diff --git a/examples/sbml/test_sbml3.py b/examples/sbml/test_sbml3.py
@@ -7,7 +7,6 @@
 
 import json
 import yaml
-import os
 
 from sbml32spec import *
 
diff --git a/examples/test/test.py b/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:
diff --git a/src/modelspec/__init__.py b/src/modelspec/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.3.3"
+__version__ = "0.3.4"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 
diff --git a/src/modelspec/base_types.py b/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(
@@ -166,21 +165,11 @@ 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_str, 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"""
@@ -302,7 +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()),
@@ -318,8 +306,6 @@ 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"
 
@@ -642,7 +628,6 @@ def _is_base_type(
         can_be_none=False,
         can_be_eval_expr=False,
     ):
-
         import numpy
 
         if verbose:
@@ -736,7 +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
diff --git a/src/modelspec/utils.py b/src/modelspec/utils.py
diff --git a/test_all.sh b/test_all.sh
diff --git a/tests/test_base.py b/tests/test_base.py
diff --git a/tests/test_utils.py b/tests/test_utils.py
