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Merged
pgleeson merged 1 commit into from
Jun 24, 2026
+44 −139
Merged

More internal fixes/tidying #101

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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/Contributors.md
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Expand Up @@ -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 2026-06-10.
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))
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89 changes: 0 additions & 89 deletions examples/sbml/SBML.md
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Expand Up @@ -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
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33 changes: 0 additions & 33 deletions examples/sbml/SBML.rst
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Expand Up @@ -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
========================
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2 changes: 1 addition & 1 deletion src/modelspec/__init__.py
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@@ -1,4 +1,4 @@
__version__ = "0.3.10"
__version__ = "0.4.0"

from .base_types import Base, define, has, field, fields, optional, instance_of, in_

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41 changes: 31 additions & 10 deletions src/modelspec/base_types.py
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Expand Up @@ -44,8 +44,10 @@ class EvaluableExpression(str):
str, so it can be used as a string.
"""

def __init__(self, expr):
self.expr = expr
@property
def expr(self):
"""The expression string. Always reflects the underlying str value."""
return str(self)


# Union of types that are allowed as value expressions for parameters.
Expand All @@ -62,7 +64,7 @@ def print_(text: str, print_it: bool = False):

prefix = "modelspec >>> "
if not isinstance(text, str):
text = ("%s" % text).decode("ascii")
text = "%s" % text
print("{}{}".format(prefix, text.replace("\n", "\n" + prefix)))


Expand Down Expand Up @@ -111,9 +113,9 @@ def to_json(self) -> str:
"""
return json.dumps(self.to_dict(), indent=4)

def to_bson(self) -> str:
def to_bson(self) -> bytes:
"""
Convert the Base object to a BSON string representation.
Convert the Base object to a BSON (bytes) representation.
"""
return bson.encode(self.to_dict())

Expand Down Expand Up @@ -238,7 +240,9 @@ def to_json_file(

return filename

def to_bson_file(self, filename: str, include_metadata: bool = True) -> str:
def to_bson_file(
self, filename: Optional[str] = None, include_metadata: bool = True
) -> str:
"""Convert modelspec format to bson format
Args:
Expand Down Expand Up @@ -321,7 +325,8 @@ def to_xml_file(
def from_file(cls, filename: str) -> "Base":
"""
Create a :class:`.Base` from its representation stored in a file. Auto-detect the correct deserialization code
based on file extension. Currently supported formats are; JSON(.json) and YAML (.yaml or .yml)
based on file extension. Currently supported formats are: JSON (.json), YAML (.yaml or .yml),
BSON (.bson) and XML (.xml).
Args:
filename: The name of the file to load.
Expand All @@ -340,7 +345,7 @@ def from_file(cls, filename: str) -> "Base":
else:
raise ValueError(
f"Cannot auto-detect modelspec serialization format from filename ({filename}). The filename "
f"must have one of the following extensions: .json, .yml, or .yaml."
f"must have one of the following extensions: .json, .yaml, .yml, .bson, or .xml."
)

@classmethod
Expand Down Expand Up @@ -945,10 +950,19 @@ def insert_links(text, format=MARKDOWN_FORMAT):
)
)

# De-duplicate while preserving order, so a type referenced by more than
# one field/child doesn't get its documentation section emitted twice.
seen = set()
unique_referenced = []
for r in referenced:
if r not in seen:
seen.add(r)
unique_referenced.append(r)

for r in unique_referenced:
if format in (MARKDOWN_FORMAT, RST_FORMAT):
doc_string += r._cls_generate_documentation(format=format)
if format in (DICT_FORMAT):
if format == DICT_FORMAT:
doc_dict.update(r._cls_generate_documentation(format=format))

if format in (MARKDOWN_FORMAT, RST_FORMAT):
Expand Down Expand Up @@ -1090,7 +1104,14 @@ def _is_list_base(cl):
Check if a class is a list of Base objects. These will be serialized as dicts if the underlying class has an id
attribute.
"""
return get_origin(cl) is list and issubclass(get_args(cl)[0], Base)
if get_origin(cl) is not list:
return False

args = get_args(cl)
# Guard against a bare ``list`` annotation (no args) and against element
# types that aren't classes (e.g. List[Union[A, B]]), which would make
# issubclass() raise TypeError.
return len(args) > 0 and isinstance(args[0], type) and issubclass(args[0], Base)


converter.register_unstructure_hook_factory(_is_list_base, _unstructure_list_base)
Expand Down
16 changes: 11 additions & 5 deletions src/modelspec/utils.py
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Expand Up @@ -336,7 +336,7 @@ def _parse_attributes(dict_format, to_build):
ff = type_to_use()
print_(f" Type for {key}: {type_to_use} ({ff})", verbose)
ff = _parse_element({v: value[v]}, ff)
exec("to_build.%s.append(ff)" % key)
getattr(to_build, key).append(ff)
else:
if (
isinstance(value, str)
Expand All @@ -361,7 +361,7 @@ def _parse_attributes(dict_format, to_build):
else:
ff = type_to_use()
ff = _parse_attributes(value, ff)
exec("to_build.%s = ff" % key)
setattr(to_build, key, ff)

else:
if isinstance(to_build, dict):
Expand All @@ -378,12 +378,12 @@ def _parse_attributes(dict_format, to_build):
for vl in value:
ff = type_to_use()
ff = _parse_element(vl, ff)
exec("to_build.%s.append(ff)" % key)
getattr(to_build, key).append(ff)
else:
type_to_use = to_build.allowed_fields[key][1]
ff = type_to_use()
ff = _parse_attributes(value, ff)
exec("to_build.%s = ff" % key)
setattr(to_build, key, ff)

return to_build

Expand Down Expand Up @@ -445,7 +445,7 @@ def _params_info(parameters, multiline=False):

def evaluate(
expr: Union[int, float, str, list, dict],
parameters: dict = {},
parameters: dict = None,
rng: Random = None,
array_format: str = FORMAT_NUMPY,
verbose: bool = False,
Expand All @@ -465,6 +465,10 @@ def evaluate(
cast_to_int: return an int for float/string values if castable
"""

# Work on a private copy so we never mutate the caller's dict (or a shared
# default) when injecting rng/math/numpy below or when eval() adds __builtins__.
parameters = dict(parameters) if parameters is not None else {}

if array_format == FORMAT_TENSORFLOW:
import tensorflow as tf

Expand Down Expand Up @@ -591,3 +595,5 @@ def parse_list_like(list_str):
pass
if "[" in list_str:
return eval(list_str)

raise ValueError(f"Cannot parse {list_str!r} ({type(list_str)}) as a list")
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