modelbase2 0.5.0__py3-none-any.whl → 0.7.0__py3-none-any.whl

modelbase2/npe.py

@@ -174,7 +174,8 @@ def train_torch_ss_estimator(
         n_hidden = max(2 * len(features.columns) * len(targets.columns), 10)
         n_outputs = len(targets.columns)
         approximator = MLP(
-            n_inputs=len(features.columns), layers=[n_hidden, n_hidden, n_outputs]
+            n_inputs=len(features.columns),
+            neurons_per_layer=[n_hidden, n_hidden, n_outputs],
         ).to(device)
 
     features_ = torch.Tensor(features.to_numpy(), device=device)

modelbase2/parameterise.py

@@ -17,8 +17,7 @@ def get_km_and_kcat_from_brenda(
     You can obtain the database from https://www.brenda-enzymes.org/download.php
     """
     brenda = Brenda()
-    if brenda_path is not None:
-        brenda.read_database(brenda_path)
+    brenda.read_database(brenda_path)
 
     kms, kcats = brenda.get_kms_and_kcats(
         ec=ec,

modelbase2/sbml/_export.py

@@ -1,16 +1,14 @@
 from __future__ import annotations
 
 import ast
-import inspect
 import re
-import textwrap
 from datetime import UTC, datetime
 from typing import TYPE_CHECKING, Any, cast
 
-import dill
 import libsbml
 import numpy as np
 
+from modelbase2.experimental.source_tools import get_fn_ast
 from modelbase2.sbml._data import AtomicUnit, Compartment
 from modelbase2.types import Derived
 
@@ -322,17 +320,7 @@ def _tree_to_sbml(
 
 
 def _sbmlify_fn(fn: Callable, user_args: list[str]) -> libsbml.ASTNode:
-    try:
-        source = inspect.getsource(fn)
-    except OSError:  # could not get source code
-        source = dill.source.getsource(fn)
-
-    tree = ast.parse(textwrap.dedent(source))
-    if not isinstance(fn_def := tree.body[0], ast.FunctionDef):
-        msg = "Not a function"
-        raise TypeError(msg)
-
-    return _tree_to_sbml(fn_def, args=user_args)
+    return _tree_to_sbml(get_fn_ast(fn), args=user_args)
 
 
 ##########################################################################

modelbase2/sbml/_import.py

@@ -492,6 +492,16 @@ def _codgen(name: str, sbml: Parser) -> Path:
         else:
             variables[k] = v.size
 
+    # Ensure non-zero value for initial assignments
+    # EXPLAIN: we need to do this for the first round of get_dependent to work
+    # otherwise we run into a ton of DivisionByZero errors.
+    # Since the values are overwritte afterwards, it doesn't really matter anyways
+    for k in sbml.initial_assignment:
+        if k in parameters and parameters[k] == 0:
+            parameters[k] = 1
+        if k in variables and variables[k] == 0:
+            variables[k] = 1
+
     derived_str = "\n    ".join(
         f"m.add_derived('{k}', fn={k}, args={v.args})" for k, v in sbml.derived.items()
     )
@@ -539,7 +549,7 @@ def get_model() -> Model:
     {variables_str}
     {derived_str}
     {rxn_str}
-    args = m.get_args()
+    args = m.get_dependent()
     {initial_assignment_source}
     return m
 """

modelbase2/scan.py

@@ -35,7 +35,7 @@ import pandas as pd
 
 from modelbase2.parallel import Cache, parallelise
 from modelbase2.simulator import Simulator
-from modelbase2.types import ProtocolByPars, SteadyStates, TimeCourseByPars
+from modelbase2.types import ProtocolByPars, SteadyStates, TimeCourseByPars, unwrap
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -325,10 +325,10 @@ def _steady_state_worker(
 
     """
     try:
-        c, v = (
+        c, v = unwrap(
             Simulator(model, y0=y0)
             .simulate_to_steady_state(rel_norm=rel_norm)
-            .get_full_concs_and_fluxes()
+            .get_result()
         )
     except ZeroDivisionError:
         c = None
@@ -353,10 +353,10 @@ def _time_course_worker(
 
     """
     try:
-        c, v = (
+        c, v = unwrap(
             Simulator(model, y0=y0)
             .simulate_time_course(time_points=time_points)
-            .get_full_concs_and_fluxes()
+            .get_result()
         )
     except ZeroDivisionError:
         c = None
@@ -382,13 +382,13 @@ def _protocol_worker(
         TimeCourse: Object containing protocol series concentrations and fluxes.
 
     """
-    c, v = (
+    c, v = unwrap(
         Simulator(model, y0=y0)
         .simulate_over_protocol(
             protocol=protocol,
             time_points_per_step=time_points_per_step,
         )
-        .get_full_concs_and_fluxes()
+        .get_result()
     )
     time_points = np.linspace(
         0,
@@ -467,7 +467,7 @@ def steady_state(
     )
     concs.index = idx
     fluxes.index = idx
-    return SteadyStates(concs, fluxes, parameters=parameters)
+    return SteadyStates(concs=concs, fluxes=fluxes, parameters=parameters)
 
 
 def time_course(