modelbase2 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

modelbase2/experimental/codegen.py

@@ -211,7 +211,7 @@ def generate_model_code_py(model: Model) -> str:
     stoich_source = []
     for variable, stoich in stoichiometries.items():
         stoich_source.append(
-            f"    d{variable}dt = {conditional_join(stoich, lambda x: x.startswith("-"), " ", " + ")}"
+            f"    d{variable}dt = {conditional_join(stoich, lambda x: x.startswith('-'), ' ', ' + ')}"
         )
 
     # Surrogates

modelbase2/experimental/tex.py

@@ -508,14 +508,10 @@ def get_model_tex_diff(
     gls = default_init(gls)
     section_label = "sec:model-diff"
 
-    return f"""{' start autogenerated ':%^60}
+    return f"""{" start autogenerated ":%^60}
 {_clearpage()}
-{_subsubsection('Model changes')}{_label(section_label)}
-{(
-    (_to_tex_export(m1) - _to_tex_export(m2))
-    .rename_with_glossary(gls)
-    .export_all()
-)}
+{_subsubsection("Model changes")}{_label(section_label)}
+{((_to_tex_export(m1) - _to_tex_export(m2)).rename_with_glossary(gls).export_all())}
 {_clearpage()}
-{' end autogenerated ':%^60}
+{" end autogenerated ":%^60}
 """

modelbase2/model.py

@@ -25,7 +25,13 @@ from modelbase2.types import (
     Readout,
 )
 
-__all__ = ["ArityMismatchError", "Model", "ModelCache", "SortError"]
+__all__ = [
+    "ArityMismatchError",
+    "CircularDependencyError",
+    "MissingDependenciesError",
+    "Model",
+    "ModelCache",
+]
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Mapping
@@ -34,19 +40,38 @@ if TYPE_CHECKING:
     from modelbase2.types import AbstractSurrogate, Callable, Param, RateFn, RetType
 
 
-class SortError(Exception):
+class MissingDependenciesError(Exception):
     """Raised when dependencies cannot be sorted topologically.
 
     This typically indicates circular dependencies in model components.
     """
 
-    def __init__(self, unsorted: list[str], order: list[str]) -> None:
+    def __init__(self, not_solvable: dict[str, list[str]]) -> None:
         """Initialise exception."""
+        missing_by_module = "\n".join(f"\t{k}: {v}" for k, v in not_solvable.items())
         msg = (
-            f"Exceeded max iterations on sorting derived. "
-            "Check if there are circular references.\n"
-            f"Unsorted: {unsorted}\n"
-            f"Order: {order}"
+            f"Dependencies cannot be solved. Missing dependencies:\n{missing_by_module}"
+        )
+        super().__init__(msg)
+
+
+class CircularDependencyError(Exception):
+    """Raised when dependencies cannot be sorted topologically.
+
+    This typically indicates circular dependencies in model components.
+    """
+
+    def __init__(
+        self,
+        missing: dict[str, set[str]],
+    ) -> None:
+        """Initialise exception."""
+        missing_by_module = "\n".join(f"\t{k}: {v}" for k, v in missing.items())
+        msg = (
+            f"Exceeded max iterations on sorting dependencies.\n"
+            "Check if there are circular references. "
+            "Missing dependencies:\n"
+            f"{missing_by_module}"
         )
         super().__init__(msg)
 
@@ -119,6 +144,24 @@ def _invalidate_cache(method: Callable[Param, RetType]) -> Callable[Param, RetTy
     return wrapper  # type: ignore
 
 
+def _check_if_is_sortable(
+    available: set[str],
+    elements: list[tuple[str, set[str]]],
+) -> None:
+    all_available = available.copy()
+    for name, _ in elements:
+        all_available.add(name)
+
+    # Check if it can be sorted in the first place
+    not_solvable = {}
+    for name, args in elements:
+        if not args.issubset(all_available):
+            not_solvable[name] = sorted(args.difference(all_available))
+
+    if not_solvable:
+        raise MissingDependenciesError(not_solvable=not_solvable)
+
+
 def _sort_dependencies(
     available: set[str], elements: list[tuple[str, set[str]]]
 ) -> list[str]:
@@ -137,6 +180,8 @@ def _sort_dependencies(
     """
     from queue import Empty, SimpleQueue
 
+    _check_if_is_sortable(available, elements)
+
     order = []
     # FIXME: what is the worst case here?
     max_iterations = len(elements) ** 2
@@ -170,7 +215,10 @@ def _sort_dependencies(
                     unsorted.append(queue.get_nowait()[0])
                 except Empty:
                     break
-            raise SortError(unsorted=unsorted, order=order)
+
+            mod_to_args: dict[str, set[str]] = dict(elements)
+            missing = {k: mod_to_args[k].difference(available) for k in unsorted}
+            raise CircularDependencyError(missing=missing)
     return order
 
 

modelbase2/plot.py

@@ -818,7 +818,7 @@ def relative_label_distribution(
                 isos = mapper.get_isotopomers_of_at_position(name, i)
                 labels = cast(pd.DataFrame, concs.loc[:, isos])
                 total = concs.loc[:, f"{name}__total"]
-                ax.plot(labels.index, (labels.sum(axis=1) / total), label=f"C{i+1}")
+                ax.plot(labels.index, (labels.sum(axis=1) / total), label=f"C{i + 1}")
             ax.set_title(name)
             ax.legend()
     else:
@@ -827,6 +827,6 @@ def relative_label_distribution(
         ):
             ax.plot(concs.index, concs.loc[:, isos])
             ax.set_title(name)
-            ax.legend([f"C{i+1}" for i in range(len(isos))])
+            ax.legend([f"C{i + 1}" for i in range(len(isos))])
 
     return fig, axs

modelbase2/sbml/_import.py

@@ -507,7 +507,11 @@ def _codgen(name: str, sbml: Parser) -> Path:
 
     # Initial assignments
     initial_assignment_order = _sort_dependencies(
-        available=set(sbml.initial_assignment) ^ set(parameters) ^ set(variables),
+        available=set(sbml.initial_assignment)
+        ^ set(parameters)
+        ^ set(variables)
+        ^ set(sbml.derived)
+        | {"time"},
         elements=[(k, set(v.args)) for k, v in sbml.initial_assignment.items()],
     )
 

{modelbase2-0.4.0.dist-info → modelbase2-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modelbase2
-Version: 0.4.0
+Version: 0.5.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>

{modelbase2-0.4.0.dist-info → modelbase2-0.5.0.dist-info}/RECORD

@@ -6,13 +6,13 @@ modelbase2/label_map.py,sha256=LUwcOHQWiGfBGV5XUmPM_SOwM9IyDVcQVJ11DPfVpAo,17774
 modelbase2/linear_label_map.py,sha256=gA8CHxcehgtI6ovwZ9qNUPDvxfqbO1J1kBC_mltD4TY,10225
 modelbase2/mc.py,sha256=zlDL7e_udpIMRhSjfFJo5AwkigD0B_3H2rQxyelBuzI,16285
 modelbase2/mca.py,sha256=nMS2VnzR2VEujCFUaj9WL82CNd-oxTb3jCHP8IlJvxA,8845
-modelbase2/model.py,sha256=mrc2Wz1IkINX1TQvuLZFdxSINqOaZGkn8FOd40qn5BY,53842
+modelbase2/model.py,sha256=d-iAu64oxVgH9QgNYhNnJnrISic_U1Z5hX6ij6eDqh0,55260
 modelbase2/nnarchitectures.py,sha256=OA1X4UHrn7gsLuuqxK6Dhv5aiKnQflhHezYCUV-NuO8,4012
 modelbase2/npe.py,sha256=o876zHjyfJelGijSmCL0vUBfWbIhcbQyyPkwp8hZ4NA,8743
 modelbase2/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
 modelbase2/parameterise.py,sha256=7VrYxrQv0visraqUthWSnWfx-cxh2evlXbszIY5031U,690
 modelbase2/paths.py,sha256=uatKXDa79uniUB2Z3dr8eBJVuUPXDI-o_bf-DqPKq1Y,1039
-modelbase2/plot.py,sha256=txKF6Xnyh2JPJ06Wu803Wn7_VijMMJ1Kbq4WQB-xKE8,22720
+modelbase2/plot.py,sha256=72Oivv-jsCF9J9U7Uli15p5SnuEHSnHRXCaRP8uUaJo,22724
 modelbase2/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 modelbase2/scan.py,sha256=PvWZA4EgNS0JVMvm87bF72hSmhvo6O2KGg4vRzxve_8,18104
 modelbase2/scope.py,sha256=4twnEh8LrTmlLE-uRvubVkE3SSWejlLvtBzTCPqG3Aw,3710
@@ -21,26 +21,26 @@ modelbase2/surrogates.py,sha256=Dk-YEXb-ot22W3r5Bl3rxApbCyvNdBnNCvRi_1f_NnA,9276
 modelbase2/types.py,sha256=N74pWUZDcGlSMfDkjqqwHn5dkozlqgS6Wqg-58YKdvg,9904
 modelbase2/experimental/__init__.py,sha256=IzgcQ7MtMII7n6cg1PMp-oZm06CNVR19ax2exvb9Ny0,444
 modelbase2/experimental/_backup.py,sha256=As-L75tMQjWfkheRPk8xcroQPKDsSSejBJ2dXqPXmVo,46644
-modelbase2/experimental/codegen.py,sha256=J_0iCtojwjmDXAfC8EqiXP0gmWaSH8MPkWvdLsZWsXU,6962
+modelbase2/experimental/codegen.py,sha256=i0soAT64oMBILGsWonoSSVkYMWOcCTY4RJ4TZoYlTos,6962
 modelbase2/experimental/diff.py,sha256=e7fjD9kqxkRUNxSevbAznd5cOlEdWJ6pj0y7Kd5KKrw,8973
 modelbase2/experimental/notes.md,sha256=YlM2biTzub6jSlx-aDZaBYsvQcGwb7NHyVAbbl2acGE,238
 modelbase2/experimental/strikepy.py,sha256=cKBs9InXR9mEPgx70Ynv0qkmAGfloksqinbpppTiC6U,19464
 modelbase2/experimental/symbolic.py,sha256=QT82TSW42RSVsvXK2WTQW1XluXnflWzrHbx6RFr_YmY,9953
-modelbase2/experimental/tex.py,sha256=M-Pdq3eQw1Huo-z1gv8EhWVO5ecJyFS8MMy9yoX81VI,13634
+modelbase2/experimental/tex.py,sha256=q9k9NfQucUhYzNjAKkroU9XnBcfdegPK6h3DHhkfGOg,13618
 modelbase2/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
 modelbase2/integrators/int_assimulo.py,sha256=VEQIZFZcEovLPy8i_jR8H8XcxBRQoRVmNzzCYzInPc0,4611
 modelbase2/integrators/int_scipy.py,sha256=-_9MS55eTc9jI7tk-3X49p-c7zrydoXaCCvDTn7Tybw,4334
 modelbase2/sbml/__init__.py,sha256=FBaQsVvrVc7QbCBXuG9tZOdSzHcqmmsaRbFx80rxrac,231
 modelbase2/sbml/_data.py,sha256=XwT1sSxn6KLTXYMbk4ORbEAEgZhQDBfoyrjMBDAoY_s,1135
 modelbase2/sbml/_export.py,sha256=9BLD3Qz86vlfDTZXwOnNOSVWq8mHrJoQjQmKJRZL_Wo,20285
-modelbase2/sbml/_import.py,sha256=uT5JpFvCKjQNBFmGPba61xYShHmjzjczqnaYflilSMI,21523
+modelbase2/sbml/_import.py,sha256=1hP3xSktmbNic5asyk-b7L-FYQccEYvGAPchuLT4gqE,21586
 modelbase2/sbml/_mathml.py,sha256=bNk9RQ_NQFDhY1R354p-gwqqHaIiyAwZ1xLPHHhiguQ,24436
 modelbase2/sbml/_name_conversion.py,sha256=XK9DEyzhrD0GBBwwjK9RA0yORrDX5c-Uvx0VtKMR5rA,1325
 modelbase2/sbml/_unit_conversion.py,sha256=dW_I6_Ou09ccwnp6LIdrPriIQnQUK5lJcjzM2Fawm6U,1927
 modelbase2/surrogates/__init__.py,sha256=N_iXERECKvmrHiihwnyQEKOSBsmlGEuQhEotn-mWKdk,924
 modelbase2/surrogates/_poly.py,sha256=zjlNL4iYR9G51gjvZPHe3CAYF-tgACGdIBe4QUYXLQk,3110
 modelbase2/surrogates/_torch.py,sha256=CBS_3JzSgI2-xQrbq9CIXY0fJQsxbhBnWkG2TQyj7Zs,5885
-modelbase2-0.4.0.dist-info/METADATA,sha256=esuEQXsT-gP3-f_UJe65bcmXTVO5J6D-MiegzUtmxak,3344
-modelbase2-0.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-modelbase2-0.4.0.dist-info/licenses/LICENSE,sha256=qvG2VolmSkrcocL34V1ieOx-Rn-fpVcUbb25gHzVgZw,35079
-modelbase2-0.4.0.dist-info/RECORD,,
+modelbase2-0.5.0.dist-info/METADATA,sha256=plD8PQFIOOvu2jENW3PLVROFUOuSrXElAj6knn0YDeo,3344
+modelbase2-0.5.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+modelbase2-0.5.0.dist-info/licenses/LICENSE,sha256=qvG2VolmSkrcocL34V1ieOx-Rn-fpVcUbb25gHzVgZw,35079
+modelbase2-0.5.0.dist-info/RECORD,,