Merge branch 'experimental' into test_neuroml

.github/workflows/ci.yml

@@ -12,8 +12,8 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
     - uses: pre-commit/[email protected]
       with:
         extra_args: --hook-stage manual --all-files
@@ -24,16 +24,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     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 package
       run: |
         python -m pip install --upgrade pip
@@ -51,12 +52,12 @@ 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
@@ -65,21 +66,20 @@ jobs:
         # Note: NeuroML files will be validated with OMV below
 
     - name: Test SBML examples
-      if: ${{ matrix.python-version != '3.7'}}
       run: |
 
         cd examples/sbml
         ./regenerateAndTest.sh
 
     - name: Run pytest
       run: |
-        pytest tests
+        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
 
@@ -93,7 +93,6 @@ 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]

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 2023-09-19.
+This page is generated periodically, most recently on 2024-03-06.
 
 - 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 2023-09-19.
 - 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))

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

@@ -1,6 +1,7 @@
 {
     "MyBook": {
         "title": "My life in Python",
+        "ISBN": 123,
         "sections": {
             "Abstract": {
                 "paragraphs": [

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

@@ -52,7 +52,7 @@ class Document(Base):
     sections: List[Section] = field(factory=list)
 
 
-doc = Document(id="MyBook")
+doc = Document(id="MyBook", ISBN=123)
 doc.title = "My life in Python"
 
 a = Section(id="Abstract")

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

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Document id="MyBook" title="My life in Python">
+<Document id="MyBook" title="My life in Python" ISBN="123">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

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

@@ -1,5 +1,6 @@
 MyBook:
     title: My life in Python
+    ISBN: 123
     sections:
         Abstract:
             paragraphs:

examples/document.json

@@ -1,6 +1,7 @@
 {
     "MyBook": {
         "title": "My life in Python",
+        "ISBN": 123,
         "sections": {
             "Abstract": {
                 "paragraphs": [

examples/document.py

@@ -52,7 +52,7 @@ class Document(Base):
     sections: List[Section] = field(factory=list)
 
 
-doc = Document(id="MyBook")
+doc = Document(id="MyBook", ISBN=123)
 doc.title = "My life in Python"
 
 a = Section(id="Abstract")

examples/document.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Document id="MyBook" title="My life in Python">
+<Document id="MyBook" title="My life in Python" ISBN="123">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

examples/document.yaml

@@ -1,5 +1,6 @@
 MyBook:
     title: My life in Python
+    ISBN: 123
     sections:
         Abstract:
             paragraphs:

setup.cfg

@@ -22,10 +22,10 @@ classifiers =
     Programming Language :: Python
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Scientific/Engineering
     Topic :: Software Development
     Typing :: Typed
@@ -38,7 +38,7 @@ install_requires =
    numpy
    tabulate
    attrs
-   cattrs
+   cattrs>=23.2.3 # Issue with JSON serialisation in some versions, see https://github.com/ModECI/modelspec/issues/66
    docstring-parser
    typing_extensions;python_version<'3.8'
    typing_compat;python_version<'3.8'
@@ -68,6 +68,7 @@ test =
     typing_extensions; python_version<'3.8'
 
 docs =
+    pandas
     requests
     Sphinx
     recommonmark>=0.5.0

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_