mxlpy 0.10.0__py3-none-any.whl → 0.12.0__py3-none-any.whl

mxlpy/__init__.py

@@ -49,6 +49,7 @@ from . import (
     mc,
     mca,
     plot,
+    report,
     sbml,
     surrogates,
 )
@@ -95,6 +96,7 @@ __all__ = [
     "mc",
     "mca",
     "plot",
+    "report",
     "sbml",
     "steady_state",
     "surrogates",

mxlpy/fit.py

@@ -22,7 +22,7 @@ from mxlpy.types import (
     Array,
     ArrayLike,
     Callable,
-    IntegratorProtocol,
+    IntegratorType,
     cast,
 )
 
@@ -57,7 +57,7 @@ class SteadyStateResidualFn(Protocol):
         data: pd.Series,
         model: Model,
         y0: dict[str, float],
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
     ) -> float:
         """Calculate residual error between model steady state and experimental data."""
         ...
@@ -74,7 +74,7 @@ class TimeSeriesResidualFn(Protocol):
         data: pd.DataFrame,
         model: Model,
         y0: dict[str, float],
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
     ) -> float:
         """Calculate residual error between model time course and experimental data."""
         ...
@@ -108,7 +108,7 @@ def _steady_state_residual(
     data: pd.Series,
     model: Model,
     y0: dict[str, float] | None,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> float:
     """Calculate residual error between model steady state and experimental data.
 
@@ -155,7 +155,7 @@ def _time_course_residual(
     data: pd.DataFrame,
     model: Model,
     y0: dict[str, float] | None,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> float:
     """Calculate residual error between model time course and experimental data.
 
@@ -194,7 +194,7 @@ def steady_state(
     y0: dict[str, float] | None = None,
     minimize_fn: MinimizeFn = _default_minimize_fn,
     residual_fn: SteadyStateResidualFn = _steady_state_residual,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> dict[str, float]:
     """Fit model parameters to steady-state experimental data.
 
@@ -248,7 +248,7 @@ def time_course(
     y0: dict[str, float] | None = None,
     minimize_fn: MinimizeFn = _default_minimize_fn,
     residual_fn: TimeSeriesResidualFn = _time_course_residual,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> dict[str, float]:
     """Fit model parameters to time course of experimental data.
 

mxlpy/integrators/int_assimulo.py

@@ -45,6 +45,7 @@ class Assimulo:
 
     rhs: Callable
     y0: ArrayLike
+    jacobian: Callable | None = None
     atol: float = 1e-8
     rtol: float = 1e-8
     maxnef: int = 4  # max error failures
@@ -61,7 +62,11 @@ class Assimulo:
         number of convergence failures (`self.maxncf`), and verbosity level (`self.verbosity`).
 
         """
-        self.integrator = CVode(Explicit_Problem(self.rhs, self.y0))
+        problem = Explicit_Problem(self.rhs, self.y0)
+        if self.jacobian is not None:
+            problem.jac = self.jacobian
+
+        self.integrator = CVode(problem)
         self.integrator.atol = self.atol
         self.integrator.rtol = self.rtol
         self.integrator.maxnef = self.maxnef

mxlpy/integrators/int_scipy.py

@@ -42,6 +42,7 @@ class Scipy:
 
     rhs: Callable
     y0: ArrayLike
+    jacobian: Callable | None = None
     atol: float = 1e-8
     rtol: float = 1e-8
     t0: float = 0.0
@@ -82,7 +83,7 @@ class Scipy:
         steps = 100 if steps is None else steps + 1
 
         return self.integrate_time_course(
-            time_points=np.linspace(self.t0, t_end, steps)
+            time_points=np.linspace(self.t0, t_end, steps, dtype=float)
         )
 
     def integrate_time_course(
@@ -97,17 +98,21 @@ class Scipy:
             tuple[ArrayLike, ArrayLike]: Tuple containing the time points and the integrated values.
 
         """
-        y = spi.odeint(
-            func=self.rhs,
+        res = spi.solve_ivp(
+            fun=self.rhs,
             y0=self.y0,
-            t=time_points,
-            tfirst=True,
+            t_span=(time_points[0], time_points[-1]),
+            t_eval=time_points,
+            jac=self.jacobian,
             atol=self.atol,
             rtol=self.rtol,
+            method="LSODA",
         )
-        self.t0 = time_points[-1]
-        self.y0 = y[-1, :]
-        return np.array(time_points, dtype=float), y
+        if res.success:
+            self.t0 = time_points[-1]
+            self.y0 = res.y[:, -1]
+            return np.array(time_points, dtype=float), res.y.T
+        return None, None
 
     def integrate_to_steady_state(
         self,
@@ -131,7 +136,7 @@ class Scipy:
 
         """
         self.reset()
-        integ = spi.ode(self.rhs)
+        integ = spi.ode(self.rhs, jac=self.jacobian)
         integ.set_integrator(name="lsoda")
         integ.set_initial_value(self.y0)
         t = self.t0 + step_size

mxlpy/mc.py

@@ -34,8 +34,7 @@ from mxlpy.scan import (
     _update_parameters_and,
 )
 from mxlpy.types import (
-    ArrayLike,
-    IntegratorProtocol,
+    IntegratorType,
     McSteadyStates,
     ProtocolByPars,
     ResponseCoefficientsByPars,
@@ -55,8 +54,6 @@ __all__ = [
 ]
 
 if TYPE_CHECKING:
-    from collections.abc import Callable
-
     from mxlpy.model import Model
     from mxlpy.types import Array
 
@@ -81,7 +78,7 @@ class ParameterScanWorker(Protocol):
         *,
         parameters: pd.DataFrame,
         rel_norm: bool,
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
     ) -> SteadyStates:
         """Call the worker function."""
         ...
@@ -93,7 +90,7 @@ def _parameter_scan_worker(
     *,
     parameters: pd.DataFrame,
     rel_norm: bool,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> SteadyStates:
     """Worker function for parallel steady state scanning across parameter sets.
 
@@ -137,7 +134,7 @@ def steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: SteadyStateWorker = _steady_state_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> SteadyStates:
     """Monte-carlo scan of steady states.
 
@@ -188,7 +185,7 @@ def time_course(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: TimeCourseWorker = _time_course_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> TimeCourseByPars:
     """MC time course.
 
@@ -241,7 +238,7 @@ def time_course_over_protocol(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> ProtocolByPars:
     """MC time course.
 
@@ -299,7 +296,7 @@ def scan_steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: ParameterScanWorker = _parameter_scan_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> McSteadyStates:
     """Parameter scan of mc distributed steady states.
 
@@ -501,7 +498,7 @@ def response_coefficients(
     disable_tqdm: bool = False,
     max_workers: int | None = None,
     rel_norm: bool = False,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> ResponseCoefficientsByPars:
     """Calculate response coefficients using Monte Carlo analysis.
 

mxlpy/mca.py

@@ -25,7 +25,7 @@ import pandas as pd
 from mxlpy.integrators import DefaultIntegrator
 from mxlpy.parallel import parallelise
 from mxlpy.scan import _steady_state_worker
-from mxlpy.types import ArrayLike, ResponseCoefficients
+from mxlpy.types import ResponseCoefficients
 
 __all__ = [
     "parameter_elasticities",
@@ -34,10 +34,8 @@ __all__ = [
 ]
 
 if TYPE_CHECKING:
-    from collections.abc import Callable
-
-    from mxlpy import IntegratorProtocol
     from mxlpy.model import Model
+    from mxlpy.types import IntegratorType
 
 
 ###############################################################################
@@ -169,7 +167,7 @@ def _response_coefficient_worker(
     normalized: bool,
     rel_norm: bool,
     displacement: float = 1e-4,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> tuple[pd.Series, pd.Series]:
     """Calculate response coefficients for a single parameter.
 
@@ -240,7 +238,7 @@ def response_coefficients(
     parallel: bool = True,
     max_workers: int | None = None,
     rel_norm: bool = False,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> ResponseCoefficients:
     """Calculate response coefficients.
 

mxlpy/report.py

@@ -0,0 +1,217 @@
+"""Generate a report comparing two models."""
+
+from collections.abc import Callable
+from datetime import UTC, datetime
+from pathlib import Path
+from typing import cast
+
+import sympy
+
+from mxlpy.meta.source_tools import fn_to_sympy
+from mxlpy.model import Model
+
+__all__ = ["AnalysisFn", "markdown"]
+
+type AnalysisFn = Callable[[Model, Model, Path], tuple[str, Path]]
+
+
+def _list_of_symbols(args: list[str]) -> list[sympy.Symbol | sympy.Expr]:
+    return [sympy.Symbol(arg) for arg in args]
+
+
+def _new_removed_changed[T](
+    d1: dict[str, T], d2: dict[str, T]
+) -> tuple[dict[str, T], list[str], dict[str, tuple[T, T]]]:
+    s1 = set(d1)
+    s2 = set(d2)
+
+    removed = sorted(s1 - s2)
+    new = {k: d2[k] for k in s2 - s1}
+    changed = {k: (v1, v2) for k in s1 - set(removed) if (v1 := d1[k]) != (v2 := d2[k])}
+    return new, removed, changed
+
+
+def _table_row(items: list[str]) -> str:
+    return f"| {' | '.join(items)} |"
+
+
+def _table_header(items: list[str]) -> str:
+    return f"{_table_row(items)}\n{_table_row(['---'] * len(items))}"
+
+
+def markdown(
+    m1: Model,
+    m2: Model,
+    analyses: list[AnalysisFn] | None = None,
+    rel_change: float = 1e-2,
+    img_path: Path = Path(),
+) -> str:
+    """Generate a markdown report comparing two models.
+
+    Args:
+        m1: The first model to compare.
+        m2: The second model to compare.
+        analyses: A list of functions that take a Path and return a tuple of a string and a Path. Defaults to None.
+        rel_change: The relative change threshold for numerical differences. Defaults to 1e-2.
+        img_path: The path to save images. Defaults to Path().
+
+    """
+    content: list[str] = [
+        f"# Report:  {datetime.now(UTC).strftime('%Y-%m-%d')}",
+    ]
+
+    # Variables
+    new_variables, removed_variables, changed_variables = _new_removed_changed(
+        m1.variables, m2.variables
+    )
+    variables = []
+    variables.extend(
+        f"| <span style='color:green'>{k}<span> | - | {v} |"
+        for k, v in new_variables.items()
+    )
+    variables.extend(
+        f"| <span style='color: orange'>{k}</span> | {v1} | {v2} |"
+        for k, (v1, v2) in changed_variables.items()
+    )
+    variables.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_variables
+    )
+    if len(variables) >= 1:
+        content.extend(
+            (
+                "## Variables\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(variables))
+
+    # Parameters
+    new_parameters, removed_parameters, changed_parameters = _new_removed_changed(
+        m1.parameters, m2.parameters
+    )
+    pars = []
+    pars.extend(
+        f"| <span style='color:green'>{k}<span> | - | {v} |"
+        for k, v in new_parameters.items()
+    )
+    pars.extend(
+        f"| <span style='color: orange'>{k}</span> | {v1} | {v2} |"
+        for k, (v1, v2) in changed_parameters.items()
+    )
+    pars.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_parameters
+    )
+    if len(pars) >= 1:
+        content.extend(
+            (
+                "## Parameters\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(pars))
+
+    # Derived
+    new_derived, removed_derived, changed_derived = _new_removed_changed(
+        m1.derived, m2.derived
+    )
+    derived = []
+    for k, v in new_derived.items():
+        expr = sympy.latex(fn_to_sympy(v.fn, _list_of_symbols(v.args)))
+        derived.append(f"| <span style='color:green'>{k}<span> | - | ${expr}$ |")
+    for k, (v1, v2) in changed_derived.items():
+        expr1 = sympy.latex(fn_to_sympy(v1.fn, _list_of_symbols(v1.args)))
+        expr2 = sympy.latex(fn_to_sympy(v2.fn, _list_of_symbols(v2.args)))
+        derived.append(
+            f"| <span style='color: orange'>{k}</span> | ${expr1}$ | ${expr2}$ |"
+        )
+    derived.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_derived
+    )
+    if len(derived) >= 1:
+        content.extend(
+            (
+                "## Derived\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(derived))
+
+    # Reactions
+    new_reactions, removed_reactions, changed_reactions = _new_removed_changed(
+        m1.reactions, m2.reactions
+    )
+    reactions = []
+    for k, v in new_reactions.items():
+        expr = sympy.latex(fn_to_sympy(v.fn, _list_of_symbols(v.args)))
+        reactions.append(f"| <span style='color:green'>{k}<span> | - | ${expr}$ |")
+    for k, (v1, v2) in changed_reactions.items():
+        expr1 = sympy.latex(fn_to_sympy(v1.fn, _list_of_symbols(v1.args)))
+        expr2 = sympy.latex(fn_to_sympy(v2.fn, _list_of_symbols(v2.args)))
+        reactions.append(
+            f"| <span style='color: orange'>{k}</span> | ${expr1}$ | ${expr2}$ |"
+        )
+    reactions.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_reactions
+    )
+
+    if len(reactions) >= 1:
+        content.extend(
+            (
+                "## Reactions\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(reactions))
+
+    # Now check for any numerical differences
+    dependent = []
+    d1 = m1.get_dependent()
+    d2 = m2.get_dependent()
+    rel_diff = ((d1 - d2) / d1).dropna()
+    for k, v in rel_diff.loc[rel_diff.abs() >= rel_change].items():
+        k = cast(str, k)
+        dependent.append(
+            f"| <span style='color:orange'>{k}</span> | {d1[k]:.2f} | {d2[k]:.2f} |  {v:.1%} |"
+        )
+    if len(dependent) >= 1:
+        content.extend(
+            (
+                "## Numerical differences of dependent values\n",
+                "| Name | Old Value | New Value | Relative Change | ",
+                "| ---- | --------- | --------- | --------------- | ",
+            )
+        )
+        content.append("\n".join(dependent))
+
+    rhs = []
+    r1 = m1.get_right_hand_side()
+    r2 = m2.get_right_hand_side()
+    rel_diff = ((r1 - r2) / r1).dropna()
+    for k, v in rel_diff.loc[rel_diff.abs() >= rel_change].items():
+        k = cast(str, k)
+        rhs.append(
+            f"| <span style='color:orange'>{k}</span> | {r1[k]:.2f} | {r2[k]:.2f} |  {v:.1%} |"
+        )
+    if len(rhs) >= 1:
+        content.extend(
+            (
+                "## Numerical differences of right hand side values\n",
+                "| Name | Old Value | New Value | Relative Change | ",
+                "| ---- | --------- | --------- | --------------- | ",
+            )
+        )
+        content.append("\n".join(rhs))
+
+    # Comparison functions
+    if analyses is not None:
+        for f in analyses:
+            name, img_path = f(m1, m2, img_path)
+            content.append(name)
+            # content.append(f"![{name}]({img_path})")
+            content.append(f"<img src='{img_path}' alt='{name}' width='500'/>")
+
+    return "\n".join(content)

mxlpy/scan.py

@@ -38,8 +38,7 @@ import pandas as pd
 from mxlpy.parallel import Cache, parallelise
 from mxlpy.simulator import Result, Simulator
 from mxlpy.types import (
-    ArrayLike,
-    IntegratorProtocol,
+    IntegratorType,
     ProtocolByPars,
     SteadyStates,
     TimeCourseByPars,
@@ -286,7 +285,7 @@ class SteadyStateWorker(Protocol):
         y0: dict[str, float] | None,
         *,
         rel_norm: bool,
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
     ) -> TimePoint:
         """Call the worker function."""
         ...
@@ -301,7 +300,7 @@ class TimeCourseWorker(Protocol):
         y0: dict[str, float] | None,
         time_points: Array,
         *,
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
     ) -> TimeCourse:
         """Call the worker function."""
         ...
@@ -316,7 +315,7 @@ class ProtocolWorker(Protocol):
         y0: dict[str, float] | None,
         protocol: pd.DataFrame,
         *,
-        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+        integrator: IntegratorType,
         time_points_per_step: int = 10,
     ) -> TimeCourse:
         """Call the worker function."""
@@ -328,7 +327,7 @@ def _steady_state_worker(
     y0: dict[str, float] | None,
     *,
     rel_norm: bool,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> TimePoint:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -357,7 +356,7 @@ def _time_course_worker(
     model: Model,
     y0: dict[str, float] | None,
     time_points: Array,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
+    integrator: IntegratorType,
 ) -> TimeCourse:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -391,7 +390,7 @@ def _protocol_worker(
     y0: dict[str, float] | None,
     protocol: pd.DataFrame,
     *,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
     time_points_per_step: int = 10,
 ) -> TimeCourse:
     """Simulate the model over a protocol and return concentrations and fluxes.
@@ -440,7 +439,7 @@ def steady_state(
     rel_norm: bool = False,
     cache: Cache | None = None,
     worker: SteadyStateWorker = _steady_state_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> SteadyStates:
     """Get steady-state results over supplied parameters.
 
@@ -515,7 +514,7 @@ def time_course(
     parallel: bool = True,
     cache: Cache | None = None,
     worker: TimeCourseWorker = _time_course_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> TimeCourseByPars:
     """Get time course for each supplied parameter.
 
@@ -601,7 +600,7 @@ def time_course_over_protocol(
     parallel: bool = True,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
-    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
+    integrator: IntegratorType = DefaultIntegrator,
 ) -> ProtocolByPars:
     """Get protocol series for each supplied parameter.
 

mxlpy/simulator.py

@@ -21,10 +21,10 @@ from mxlpy.integrators import DefaultIntegrator
 __all__ = ["Result", "Simulator"]
 
 if TYPE_CHECKING:
-    from collections.abc import Callable, Iterator
+    from collections.abc import Iterator
 
     from mxlpy.model import Model
-    from mxlpy.types import Array, ArrayLike, IntegratorProtocol
+    from mxlpy.types import Array, ArrayLike, IntegratorProtocol, IntegratorType
 
 
 def _normalise_split_results(
@@ -321,16 +321,14 @@ class Simulator:
     simulation_parameters: list[dict[str, float]] | None
 
     # For resets (e.g. update variable)
-    _integrator_type: Callable[[Callable, ArrayLike], IntegratorProtocol]
+    _integrator_type: IntegratorType
     _time_shift: float | None
 
     def __init__(
         self,
         model: Model,
         y0: dict[str, float] | None = None,
-        integrator: Callable[
-            [Callable, ArrayLike], IntegratorProtocol
-        ] = DefaultIntegrator,
+        integrator: IntegratorType = DefaultIntegrator,
         *,
         test_run: bool = True,
     ) -> None:
@@ -358,10 +356,26 @@ class Simulator:
         self._initialise_integrator()
 
     def _initialise_integrator(self) -> None:
+        from sympy import lambdify
+
+        from mxlpy.symbolic import to_symbolic_model
+
+        try:
+            jac = to_symbolic_model(self.model).jacobian()
+
+            _jacobian = lambda t, y: lambdify(  # noqa: E731
+                ("time", self.model.get_variable_names()),
+                jac.subs(self.model._parameters),  # noqa: SLF001
+            )(t, y)
+
+        except:  # noqa: E722
+            _jacobian = None  # type: ignore
+
         y0 = self.y0
         self.integrator = self._integrator_type(
             self.model,
             [y0[k] for k in self.model.get_variable_names()],
+            _jacobian,
         )
 
     def clear_results(self) -> None:

mxlpy/types.py

@@ -28,6 +28,7 @@ __all__ = [
     "Derived",
     "Float",
     "IntegratorProtocol",
+    "IntegratorType",
     "McSteadyStates",
     "MockSurrogate",
     "Param",
@@ -114,6 +115,7 @@ class IntegratorProtocol(Protocol):
         self,
         rhs: Callable,
         y0: ArrayLike,
+        jacobian: Callable | None = None,
     ) -> None:
         """Initialise the integrator."""
         ...
@@ -147,6 +149,11 @@ class IntegratorProtocol(Protocol):
         ...
 
 
+type IntegratorType = Callable[
+    [Callable, ArrayLike, Callable | None], IntegratorProtocol
+]
+
+
 @dataclass(kw_only=True, slots=True)
 class Derived:
     """Container for a derived value."""

{mxlpy-0.10.0.dist-info → mxlpy-0.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.10.0
+Version: 0.12.0
 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>
@@ -32,6 +32,7 @@ Requires-Dist: pandas>=2.2.3
 Requires-Dist: parameteriser>=0.1.0
 Requires-Dist: pebble>=5.0.7
 Requires-Dist: python-libsbml>=5.20.4
+Requires-Dist: salib>=1.5.1
 Requires-Dist: scipy>=1.14.1
 Requires-Dist: seaborn>=0.13.2
 Requires-Dist: symbtools>=0.4.0

{mxlpy-0.10.0.dist-info → mxlpy-0.12.0.dist-info}/RECORD

@@ -1,12 +1,12 @@
-mxlpy/__init__.py,sha256=HwV_l1PqCqWsn1TFwUMslbfuPjX6cUGzytyWPaUz4FM,4168
+mxlpy/__init__.py,sha256=XZYNFyDC5rWcKi6139mq04cROI7LwJvxB2_3ApKwcvY,4194
 mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
-mxlpy/fit.py,sha256=vJ0AWCvERxPkxgwuOmL9rsH4vXnlBSco4vG-5X98RK8,8085
+mxlpy/fit.py,sha256=LwSoLfNVrqSlTtuUApwH36LjzGU0HLs4C_2qqTTjXFE,7859
 mxlpy/fns.py,sha256=ct_RFj9koW8vXHyr27GnbZUHUS_zfs4rDysybuFiOaU,4599
 mxlpy/identify.py,sha256=af52SCG4nlY9sSw22goaIheuvXR09QYK4ksCT24QHWI,1946
 mxlpy/label_map.py,sha256=urv-QTb0MUEKjwWvKtJSB8H2kvhLn1EKfRIH7awQQ8Y,17769
 mxlpy/linear_label_map.py,sha256=2lgERcUVDLXruRI08HBYJo_wK654y46voLUeBTzBy3k,10312
-mxlpy/mc.py,sha256=GIuJJ-9QRqGsd2xl1LmjmMc-bOdihVShbFmXvu4o5p4,17305
-mxlpy/mca.py,sha256=MjhH0CcHmXGTR4PCHTTeCbZWGBUa5TyXWtWzcg7M4Vs,9453
+mxlpy/mc.py,sha256=HWuJq4fV_wfTDERbLJRSF3fjCCYMxzLdqAyO53Z_uF8,16985
+mxlpy/mca.py,sha256=H0dfV45Kz5nMIW8s2V61op7x6LmI21wWgRf94i6iIY4,9328
 mxlpy/model.py,sha256=-BmS4bGCq_fMUnRLZG5uwl86ip_SiaWxsbgLPeV0nHQ,57656
 mxlpy/npe.py,sha256=oiRLA43-qf-AcS2KpQfJIOt7-Ev9Aj5sF6TMq9bJn84,8747
 mxlpy/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
@@ -14,14 +14,15 @@ mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
 mxlpy/plot.py,sha256=z1JW7Si1JQyNMj_MMLkgbLkOkSjVcfAZJGjm_WqCgT4,24355
 mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mxlpy/scan.py,sha256=3k4084d4eg-3Ok24cL8KWPF7P1L6fbEtiaOM9VC5Eko,19210
-mxlpy/simulator.py,sha256=T9t2jZ6U5NyK1ICF1UkST8M8v4EPV_H98kzZ4TvQK-w,20115
-mxlpy/types.py,sha256=ksdn76Sdw0XhQEpQepcETvuGqcJolfrmbIRBT0R_2Bg,13612
+mxlpy/report.py,sha256=h7dhcBzPFydLPxdsEXokzDf7Ce4PirXMsvLqlDZLSWM,7181
+mxlpy/scan.py,sha256=-1SLyXJOX3U3CxeP1dEC4ytAoBMCH0Ql89wGvsG3LbI,18858
+mxlpy/simulator.py,sha256=CeMmm5SdgJphQWWBygnv0rxiXjBUJPWHV8-bh6miJNM,20494
+mxlpy/types.py,sha256=aWDtWOTZo4UQJ3rYGq1m6aV4hGxIjvycfJGc8CIDQLE,13775
 mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
 mxlpy/experimental/diff.py,sha256=4bztagJzFMsQJM7dlun_kv-WrWssM8CIw7gcL63hFf8,8952
 mxlpy/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
-mxlpy/integrators/int_assimulo.py,sha256=Y9jvpJWXkmueUyjDnu_6SqDntyMdG_DU370EtuRyMqA,4605
-mxlpy/integrators/int_scipy.py,sha256=Z9LSwqBKgYfwmrNiMxJ3-vRad5n_yQo1Ime4WDAAZEI,4343
+mxlpy/integrators/int_assimulo.py,sha256=d-4HHOj4vmGpg8ig2IXMO5CPiIrq89_quEKvCxIKrhw,4747
+mxlpy/integrators/int_scipy.py,sha256=dFHlYTeb2zX97f3VuNdMJdI7WEYshF4JAIgprKKk2z4,4581
 mxlpy/meta/__init__.py,sha256=Jyy4063fZy6iT4LSwjPyEAVr4N_3xxcLc8wDBoDPyKc,278
 mxlpy/meta/codegen_latex.py,sha256=1z0waYPmohY9GTJ_5DBuwXOXGTCHCH8E14tg6MYsf2A,13460
 mxlpy/meta/codegen_modebase.py,sha256=qQ8p6_KqMYCw7SRmf2HHRGvl25sYPKVI_zWKhzFhFLw,3138
@@ -43,7 +44,7 @@ mxlpy/surrogates/_torch.py,sha256=E_1eDUlPSVFwROkdMDCqYwwHE-61pjNMJWotnhjzge0,58
 mxlpy/symbolic/__init__.py,sha256=3hQjCMw8-6iOxeUdfnCg8449fF_BRF2u6lCM1GPpkRY,222
 mxlpy/symbolic/strikepy.py,sha256=r6nRtckV1nxKq3i1bYYWZOkzwZ5XeKQuZM5ck44vUo0,20010
 mxlpy/symbolic/symbolic_model.py,sha256=YL9noEeP3_0DoKXwMPELtfmPuP6mgNcLIJgDRCkyB7A,2434
-mxlpy-0.10.0.dist-info/METADATA,sha256=wwkTfCscHZzrydDqVdVhVNI7isEc2YcwN4ZC5OAWA8M,4536
-mxlpy-0.10.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.10.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
-mxlpy-0.10.0.dist-info/RECORD,,
+mxlpy-0.12.0.dist-info/METADATA,sha256=Ul9QrtiIlIBZSsRGrTF2J-D_ssjpQtpsw_4IA3LR_lg,4564
+mxlpy-0.12.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.12.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
+mxlpy-0.12.0.dist-info/RECORD,,