mxlpy 0.9.0__py3-none-any.whl → 0.11.0__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

@@ -154,7 +154,7 @@ def _time_course_residual(
     par_names: list[str],
     data: pd.DataFrame,
     model: Model,
-    y0: dict[str, float],
+    y0: dict[str, float] | None,
     integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
 ) -> float:
     """Calculate residual error between model time course and experimental data.

mxlpy/identify.py

@@ -0,0 +1,68 @@
+"""Numerical parameter identification estimations."""
+
+from functools import partial
+
+import numpy as np
+import pandas as pd
+from tqdm import tqdm
+
+from mxlpy import fit
+from mxlpy.distributions import LogNormal, sample
+from mxlpy.model import Model
+from mxlpy.parallel import parallelise
+from mxlpy.types import Array
+
+__all__ = ["profile_likelihood"]
+
+
+def _mc_fit_time_course_worker(
+    p0: pd.Series,
+    model: Model,
+    data: pd.DataFrame,
+) -> float:
+    p_fit = fit.time_course(model=model, p0=p0.to_dict(), data=data)
+    return fit._time_course_residual(  # noqa: SLF001
+        par_values=list(p_fit.values()),
+        par_names=list(p_fit.keys()),
+        data=data,
+        model=model,
+        y0=None,
+        integrator=fit.DefaultIntegrator,
+    )
+
+
+def profile_likelihood(
+    model: Model,
+    data: pd.DataFrame,
+    parameter_name: str,
+    parameter_values: Array,
+    n_random: int = 10,
+) -> pd.Series:
+    """Estimate the profile likelihood of model parameters given data.
+
+    Args:
+        model: The model to be fitted.
+        data: The data to fit the model to.
+        parameter_name: The name of the parameter to profile.
+        parameter_values: The values of the parameter to profile.
+        n_random: Number of Monte Carlo samples.
+
+    """
+    parameter_distributions = sample(
+        {k: LogNormal(np.log(v), sigma=1) for k, v in model.parameters.items()},
+        n=n_random,
+    )
+
+    res = {}
+    for value in tqdm(parameter_values, desc=parameter_name):
+        model.update_parameter(parameter_name, value)
+        res[value] = parallelise(
+            partial(_mc_fit_time_course_worker, model=model, data=data),
+            inputs=list(
+                parameter_distributions.drop(columns=parameter_name).iterrows()
+            ),
+            disable_tqdm=True,
+        )
+    errors = pd.DataFrame(res, dtype=float).T.abs().mean(axis=1)
+    errors.index.name = "fitting error"
+    return errors

mxlpy/plot.py

@@ -18,12 +18,17 @@ Functions:
 
 from __future__ import annotations
 
+import contextlib
+
+from cycler import cycler
+
 __all__ = [
     "FigAx",
     "FigAxs",
     "Linestyle",
     "add_grid",
     "bars",
+    "context",
     "grid_layout",
     "heatmap",
     "heatmap_from_2d_idx",
@@ -66,6 +71,8 @@ from mpl_toolkits.mplot3d import Axes3D
 from mxlpy.label_map import LabelMapper
 
 if TYPE_CHECKING:
+    from collections.abc import Generator
+
     from matplotlib.collections import QuadMesh
 
     from mxlpy.linear_label_map import LinearLabelMapper
@@ -259,6 +266,12 @@ def rotate_xlabels(
 
 
 def show(fig: Figure | None = None) -> None:
+    """Show the given figure or the current figure.
+
+    Args:
+        fig: Figure to show.
+
+    """
     if fig is None:
         plt.show()
     else:
@@ -266,9 +279,39 @@ def show(fig: Figure | None = None) -> None:
 
 
 def reset_prop_cycle(ax: Axes) -> None:
+    """Reset the property cycle of the given axis.
+
+    Args:
+        ax: Axis to reset the property cycle of.
+
+    """
     ax.set_prop_cycle(plt.rcParams["axes.prop_cycle"])
 
 
+@contextlib.contextmanager
+def context(
+    colors: list[str] | None = None,
+    line_width: float | None = None,
+) -> Generator[None, None, None]:
+    """Context manager to set the defaults for plots.
+
+    Args:
+        colors: colors to use for the plot.
+        line_width: line width to use for the plot.
+
+    """
+    rc = {}
+
+    if colors is not None:
+        rc["axes.prop_cycle"] = cycler(color=colors)
+
+    if line_width is not None:
+        rc["lines.linewidth"] = line_width
+
+    with plt.rc_context(rc):
+        yield
+
+
 ##########################################################################
 # General plot layout
 ##########################################################################

mxlpy/report.py

@@ -0,0 +1,209 @@
+"""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 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-0.9.0.dist-info → mxlpy-0.11.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.9.0
+Version: 0.11.0
 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>
@@ -59,6 +59,8 @@ Provides-Extra: torch
 Requires-Dist: torch>=2.5.1; extra == 'torch'
 Description-Content-Type: text/markdown
 
+<img src="docs/assets/logo-diagram.png" style="display: block; max-height: 30rem; margin: auto; padding: 0" alt='mxlpy-logo'>
+
 # mxlpy
 
 [![pypi](https://img.shields.io/pypi/v/mxlpy.svg)](https://pypi.python.org/pypi/mxlpy)
@@ -84,6 +86,13 @@ pixi add python assimulo
 pixi add --pypi mxlpy[torch]
 ```
 
+## How to cite
+
+If you use this software in your scientific work, please cite [this article](...):
+
+- [doi](https://doi.org/)
+- [bibtex file](https://fillme.out)
+
 
 ## Development setup
 

{mxlpy-0.9.0.dist-info → mxlpy-0.11.0.dist-info}/RECORD

@@ -1,7 +1,8 @@
-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=M8F5s9RUoUPr2s-pCLFZD_ebP2uGvajNCn7XYh1w7Tc,8078
+mxlpy/fit.py,sha256=vJ0AWCvERxPkxgwuOmL9rsH4vXnlBSco4vG-5X98RK8,8085
 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
@@ -11,8 +12,9 @@ mxlpy/npe.py,sha256=oiRLA43-qf-AcS2KpQfJIOt7-Ev9Aj5sF6TMq9bJn84,8747
 mxlpy/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
 mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
-mxlpy/plot.py,sha256=1sI18HAQXeBNo_H6ctS9pwLdmp3MSkGgaGQK7IrTUBc,23498
+mxlpy/plot.py,sha256=z1JW7Si1JQyNMj_MMLkgbLkOkSjVcfAZJGjm_WqCgT4,24355
 mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mxlpy/report.py,sha256=TYG-cKo9u6izlnjB4vgu6I2hYrtS9e8wYc_A4MrHq-g,6982
 mxlpy/scan.py,sha256=3k4084d4eg-3Ok24cL8KWPF7P1L6fbEtiaOM9VC5Eko,19210
 mxlpy/simulator.py,sha256=T9t2jZ6U5NyK1ICF1UkST8M8v4EPV_H98kzZ4TvQK-w,20115
 mxlpy/types.py,sha256=ksdn76Sdw0XhQEpQepcETvuGqcJolfrmbIRBT0R_2Bg,13612
@@ -42,7 +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-0.9.0.dist-info/METADATA,sha256=LThtovqTN7iDo4vJSmmuhP6rZ9no5IlOrRkMjN4vJTU,4245
-mxlpy-0.9.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.9.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
-mxlpy-0.9.0.dist-info/RECORD,,
+mxlpy-0.11.0.dist-info/METADATA,sha256=N1-dMC1k0QUlSF2ZN_URFUyg119f9QUz7xcBS2Ia_PQ,4536
+mxlpy-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.11.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
+mxlpy-0.11.0.dist-info/RECORD,,