ModECI · pgleeson · Apr 29, 2026 · Apr 29, 2026 · Apr 29, 2026 · Apr 29, 2026
diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml
@@ -31,6 +31,10 @@ jobs:
         brew install hdf5
 
     - name: Install & test package
+      shell: bash
+      env:
+        PYTHONUTF8: "1"
+        PYTHONIOENCODING: "utf-8"
       run: |
         python -m pip install --upgrade pip
         # pip install 'numpy<2.0.0' # due to lingering issues with other modules & numpy...

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
 #  - id: black
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v6.0.0
   hooks:
   - id: check-added-large-files
     args: ['--maxkb=800']
@@ -46,6 +46,6 @@ repos:
 #    files: src
 
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 24.10.0
   hooks:
   - id: black
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 2026-05-19.
+This page is generated periodically, most recently on 2026-06-24.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

diff --git a/examples/sbml/SBML.md b/examples/sbml/SBML.md
@@ -1670,95 +1670,6 @@ XHTML field of SBase
  </tr>
 
 
-</table>
-
-## SpeciesReference
-### Allowed parameters
-<table>
-  <tr>
-    <td><b>sid</b></td>
-    <td>str</td>
-    <td><i>    SId optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>name</b></td>
-    <td>str</td>
-    <td><i>   string optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>metaid</b></td>
-    <td>str</td>
-    <td><i> XML ID optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>sboTerm</b></td>
-    <td>str</td>
-    <td><i>SBOTerm optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>notes</b></td>
-    <td><a href="#notes">Notes</a></td>
-    <td><i>     XHTML 1.0 optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>annotation</b></td>
-    <td>str</td>
-    <td><i>XML content optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>species</b></td>
-    <td>str</td>
-    <td><i>SIdRef</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>stoichiometry</b></td>
-    <td>float</td>
-    <td><i>double optional</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>constant</b></td>
-    <td>bool</td>
-    <td><i>boolean</i></td>
- </tr>
-
-
-</table>
-
-## Notes
-XHTML field of SBase
-
-### Allowed parameters
-<table>
-  <tr>
-    <td><b>xmlns</b></td>
-    <td>str</td>
-    <td><i>str fixed "http://www.w3.org/1999/xhtml"</i></td>
- </tr>
-
-
-  <tr>
-    <td><b>content</b></td>
-    <td>str</td>
-    <td><i>str valid XHTML</i></td>
- </tr>
-
-
 </table>
 
 ## ModifierSpeciesReference

diff --git a/examples/sbml/SBML.rst b/examples/sbml/SBML.rst
@@ -650,39 +650,6 @@ Allowed field    Data Type    Description
 **content**      str          str valid XHTML
 ===============  ===========  ========================================
 
-================
-SpeciesReference
-================
-**Allowed parameters**
-
-=================  =======================================  ====================
-Allowed field      Data Type                                Description
-=================  =======================================  ====================
-**sid**            str                                      SId optional
-**name**           str                                      string optional
-**metaid**         str                                      XML ID optional
-**sboTerm**        str                                      SBOTerm optional
-**notes**          `<class 'sbml32spec.Notes'> <#notes>`__  XHTML 1.0 optional
-**annotation**     str                                      XML content optional
-**species**        str                                      SIdRef
-**stoichiometry**  float                                    double optional
-**constant**       bool                                     boolean
-=================  =======================================  ====================
-
-=====
-Notes
-=====
-XHTML field of SBase
-
-**Allowed parameters**
-
-===============  ===========  ========================================
-Allowed field    Data Type    Description
-===============  ===========  ========================================
-**xmlns**        str          str fixed "http://www.w3.org/1999/xhtml"
-**content**      str          str valid XHTML
-===============  ===========  ========================================
-
 ========================
 ModifierSpeciesReference
 ========================

diff --git a/examples/test/test.md b/examples/test/test.md
@@ -13,21 +13,21 @@ A model....
   <tr>
     <td><b>float_like_req</b></td>
     <td>float</td>
-    <td><i>name says it all...</i></td>
+    <td><i>Anything (float, str, int) which can be converted to a float with float(x)</i></td>
  </tr>
 
 
   <tr>
     <td><b>float_like_optional</b></td>
     <td>float</td>
-    <td><i>name also says it all...</i></td>
+    <td><i>Same as float<a href="#like">like</a>req, but optional</i></td>
  </tr>
 
 
   <tr>
     <td><b>int_like_optional</b></td>
     <td>int</td>
-    <td><i>name also says it all...</i></td>
+    <td><i>Same as float<a href="#like">like</a>req, but optional int</i></td>
  </tr>
 
 

diff --git a/examples/test/test.py b/examples/test/test.py
@@ -48,9 +48,9 @@ class TopClass(Base):
 
     Args:
         id: The unique id of the thing
-        float_like_req: name says it all...
-        float_like_optional: name also says it all...
-        int_like_optional: name also says it all...
+        float_like_req: Anything (float, str, int) which can be converted to a float with float(x)
+        float_like_optional: Same as float_like_req, but optional
+        int_like_optional: Same as float_like_req, but optional int
     """
 
     id: str = field(validator=instance_of(str))
@@ -74,7 +74,7 @@ class TopClass(Base):
 )  # a string which can be converted to a float...
 
 # tc.float_like_req = 2.01
-tc.float_like_optional = 44
+tc.float_like_optional = "42"
 # tc.float_like_optional2 = 66
 tc.mid = MidClassNoId(int_val=4, str_val="three")
 

diff --git a/examples/test/test.specification.yaml b/examples/test/test.specification.yaml
@@ -6,13 +6,14 @@ TopClass:
             description: The unique id of the thing
         float_like_req:
             type: float
-            description: name says it all...
+            description: Anything (float, str, int) which can be converted to a float
+                with float(x)
         float_like_optional:
             type: float
-            description: name also says it all...
+            description: Same as float_like_req, but optional
         int_like_optional:
             type: int
-            description: name also says it all...
+            description: Same as float_like_req, but optional int
         mid:
             type: MidClassNoId
             description: ''

diff --git a/examples/test/test_instance.json b/examples/test/test_instance.json
@@ -1,7 +1,7 @@
 {
     "MyTest": {
         "float_like_req": 4.0,
-        "float_like_optional": 44.0,
+        "float_like_optional": 42.0,
         "mid": {
             "int_val": 4,
             "str_val": "three"

diff --git a/examples/test/test_instance.xml b/examples/test/test_instance.xml
@@ -1,4 +1,4 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<TopClass id="MyTest" float_like_req="4.0" float_like_optional="44.0">
+<TopClass id="MyTest" float_like_req="4.0" float_like_optional="42.0">
     <mid int_val="4" str_val="three"/>
 </TopClass>
diff --git a/examples/test/test_instance.yaml b/examples/test/test_instance.yaml
@@ -1,6 +1,6 @@
 MyTest:
     float_like_req: 4.0
-    float_like_optional: 44.0
+    float_like_optional: 42.0
     mid:
         int_val: 4
         str_val: three
diff --git a/src/modelspec/__init__.py b/src/modelspec/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.3.9"
+__version__ = "0.4.0"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_