mxlmodels 1.1.0__tar.gz → 1.2.0__tar.gz

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlmodels
-Version: 1.1.0
+Version: 1.2.0
 Summary: MxlModels is a Python package of reference mechanistic models.
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>

mxlmodels-1.2.0/docs/_dynamic_enterobactin.ipynb

@@ -0,0 +1,49 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "323f3026",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_dynamic_enterobactin, plot\n",
+    "\n",
+    "res = Simulator(get_dynamic_enterobactin()).simulate(0.2).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2, ax3) = plot.grid_layout(3, n_cols=3)\n",
+    "_ = plot.lines(res.get_variables(include_derived_variables=False).iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(\n",
+    "    res.get_args(\n",
+    "        include_variables=False,\n",
+    "        include_derived_variables=True,\n",
+    "        include_reactions=False,\n",
+    "    ).iloc[:, :10],\n",
+    "    ax=ax2,\n",
+    ")\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax3)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "git-mxl-meta (3.13.12)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

mxlmodels-1.1.0/docs/pop_dyn.ipynb → mxlmodels-1.2.0/docs/_population_dynamics.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_population_dynamics\n",
+    "from mxlmodels import Simulator, get_population_dynamics, plot\n",
     "\n",
     "res = Simulator(get_population_dynamics()).simulate(1).get_result().unwrap_or_err()\n",
     "\n",

mxlmodels-1.1.0/docs/trip_dyn.ipynb → mxlmodels-1.2.0/docs/_tripartite_dynamics.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_tripartite_dynamics\n",
+    "from mxlmodels import Simulator, get_tripartite_dynamics, plot\n",
     "\n",
     "res = Simulator(get_tripartite_dynamics()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/ebeling2026.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_ebeling_2026\n",
+    "from mxlmodels import Simulator, get_ebeling_2026, plot\n",
     "\n",
     "res = Simulator(get_ebeling_2026()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/elowitz2000_repressilator.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_elowitz2000_repressilator\n",
+    "from mxlmodels import Simulator, get_elowitz2000_repressilator, plot\n",
     "\n",
     "res = (\n",
     "    Simulator(get_elowitz2000_repressilator()).simulate(10).get_result().unwrap_or_err()\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/lotka_volterra.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_lotka_volterra_v1\n",
+    "from mxlmodels import Simulator, get_lotka_volterra_v1, plot\n",
     "\n",
     "res = Simulator(get_lotka_volterra_v1()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/matuszynska2016_npq.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_matuszynska2016_npq\n",
+    "from mxlmodels import Simulator, get_matuszynska2016_npq, plot\n",
     "\n",
     "res = Simulator(get_matuszynska2016_npq()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/matuszynska2016_phd.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_matuszynska2016_phd\n",
+    "from mxlmodels import Simulator, get_matuszynska2016_phd, plot\n",
     "\n",
     "res = Simulator(get_matuszynska2016_phd()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/matuszynska2019.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_matuszynska2019\n",
+    "from mxlmodels import Simulator, get_matuszynska2019, plot\n",
     "\n",
     "res = Simulator(get_matuszynska2019()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

mxlmodels-1.2.0/docs/nguyen2026_tomato.ipynb

@@ -0,0 +1,69 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "db264b37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_nguyen2026_tomato, plot\n",
+    "\n",
+    "res = (\n",
+    "    Simulator(get_nguyen2026_tomato())\n",
+    "    .update_variables(\n",
+    "        {\n",
+    "            \"B0\": 1.9587919653281205,\n",
+    "            \"B1\": 5.308607566760226e-08,\n",
+    "            \"B2\": 0.5412079539026975,\n",
+    "            \"PQH2\": 14.753583247530687,\n",
+    "            \"ATP\": 23.681707158359565,\n",
+    "            \"H_lumen\": 0.004056077821448256,\n",
+    "            \"delta_psi\": 0.02512099319259713,\n",
+    "            \"Vx\": 0.9500845858289113,\n",
+    "            \"PsbS\": 0.6863197475682336,\n",
+    "            \"ATPactivity\": 1.0,\n",
+    "            \"K_lumen\": 400.0,\n",
+    "            \"K_stroma\": 3200.0,\n",
+    "        }\n",
+    "    )\n",
+    "    .simulate(10)\n",
+    "    .get_result()\n",
+    "    .unwrap_or_err()\n",
+    ")\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 4))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97322ab1",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "git-mxl-meta (3.13.12)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

mxlmodels-1.1.0/docs/pfennig2024-synechocystis.ipynb → mxlmodels-1.2.0/docs/pfennig2024_synechocystis.ipynb

@@ -7,22 +7,22 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
+    "from mxlmodels import Simulator, data, get_pfennig2024_synechocystis, plot\n",
     "\n",
-    "import mxlmodels\n",
-    "from mxlmodels import get_pfennig2024_synechocystis\n",
-    "\n",
-    "data = mxlmodels.data.pfennig2024.load()\n",
+    "dfs = data.pfennig2024.load()\n",
     "\n",
     "model = get_pfennig2024_synechocystis(\n",
-    "    light_spectrum=data.light_spectrum,\n",
-    "    light_spectrum_measure=data.light_spectrum_measure,\n",
-    "    ocp_absorption=data.ocp_absorption_per_wavelength,\n",
-    "    abs_coef=data.pigment_abs_coef_per_wavelength,\n",
-    "    molar_masses=data.molar_masses,\n",
-    "    ps_comp=data.ps_comp,\n",
-    "    pigment_content=data.pigment_content,\n",
-    ")"
+    "    light_spectrum=dfs.light_spectrum,\n",
+    "    light_spectrum_measure=dfs.light_spectrum_measure,\n",
+    "    ocp_absorption=dfs.ocp_absorption_per_wavelength,\n",
+    "    abs_coef=dfs.pigment_abs_coef_per_wavelength,\n",
+    "    molar_masses=dfs.molar_masses,\n",
+    "    ps_comp=dfs.ps_comp,\n",
+    "    pigment_content=dfs.pigment_content,\n",
+    ")\n",
+    "\n",
+    "res = Simulator(model).simulate(10).get_result().unwrap_or_err()\n",
+    "fig, ax = plot.lines(res.fluxes.loc[:, [\"vPS2\"]])"
    ]
   },
   {
@@ -31,10 +31,7 @@
    "id": "3e475022",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "res = Simulator(model).simulate(10).get_result().unwrap_or_err()\n",
-    "fig, ax = plot.lines(res.fluxes.loc[:, [\"vPS2\"]])"
-   ]
+   "source": []
   }
  ],
  "metadata": {

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/poolman2000.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_poolman2000\n",
+    "from mxlmodels import Simulator, get_poolman2000, plot\n",
     "\n",
     "res = Simulator(get_poolman2000()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/prigogine1968_brusselator.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_prigogine1968_brusselator\n",
+    "from mxlmodels import Simulator, get_prigogine1968_brusselator, plot\n",
     "\n",
     "res = (\n",
     "    Simulator(get_prigogine1968_brusselator()).simulate(10).get_result().unwrap_or_err()\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/saadat2021.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_saadat2021\n",
+    "from mxlmodels import Simulator, get_saadat2021, plot\n",
     "\n",
     "res = Simulator(get_saadat2021()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/selkov1968_oscillator.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_selkov1968_glycolysis_oscillator\n",
+    "from mxlmodels import Simulator, get_selkov1968_glycolysis_oscillator, plot\n",
     "\n",
     "res = (\n",
     "    Simulator(get_selkov1968_glycolysis_oscillator())\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/docs/yokota1985.ipynb

@@ -7,9 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxlpy import Simulator, plot\n",
-    "\n",
-    "from mxlmodels import get_yokota1985\n",
+    "from mxlmodels import Simulator, get_yokota1985, plot\n",
     "\n",
     "res = Simulator(get_yokota1985()).simulate(10).get_result().unwrap_or_err()\n",
     "\n",

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/pyproject.toml

@@ -45,7 +45,7 @@ maintainers = [
 name = "mxlmodels"
 readme = "README.md"
 requires-python = ">=3.13"
-version = "1.1.0"
+version = "1.2.0"
 
 [tool.hatchling]
 from    = "src"

mxlmodels-1.2.0/src/mxlmodels/__init__.py

@@ -0,0 +1,55 @@
+"""MxlModels is a Python package of reference mechanistic models.
+
+It contains the same models as in the [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) repo,
+but written as single, flat files to make inspection easier.
+
+"""
+
+# Re-export mxlpy modules for easy access
+from mxlpy import Simulator, fit, mc, mca, plot, scan
+
+from . import data
+from ._dynamic_enterobactin import get_dynamic_enterobactin
+from ._population_dynamics import get_population_dynamics
+from ._tripartite_dynamics import get_tripartite_dynamics
+from .ebeling2026 import get_ebeling_2026
+from .elowitz2000_repressilator import get_elowitz2000_repressilator
+from .lotka_volterra_v1 import get_lotka_volterra_v1
+from .lotka_volterra_v2 import get_lotka_volterra_v2
+from .matuszynska2016_npq import get_matuszynska2016_npq
+from .matuszynska2016_phd import get_matuszynska2016_phd
+from .matuszynska2019 import get_matuszynska2019
+from .nguyen2026_tomato import get_nguyen2026_tomato
+from .pfennig2024_synechocystis import get_pfennig2024_synechocystis
+from .poolman2000 import get_poolman2000
+from .prigogine1968_brusselator import get_prigogine1968_brusselator
+from .saadat2021 import get_saadat2021 as get_saadat2021
+from .selkov1968_oscillator import get_selkov1968_glycolysis_oscillator
+from .yokota1985 import get_yokota1985
+
+__all__ = [
+    "Simulator",
+    "data",
+    "fit",
+    "get_dynamic_enterobactin",
+    "get_ebeling_2026",
+    "get_elowitz2000_repressilator",
+    "get_lotka_volterra_v1",
+    "get_lotka_volterra_v2",
+    "get_matuszynska2016_npq",
+    "get_matuszynska2016_phd",
+    "get_matuszynska2019",
+    "get_nguyen2026_tomato",
+    "get_pfennig2024_synechocystis",
+    "get_poolman2000",
+    "get_population_dynamics",
+    "get_prigogine1968_brusselator",
+    "get_saadat2021",
+    "get_selkov1968_glycolysis_oscillator",
+    "get_tripartite_dynamics",
+    "get_yokota1985",
+    "mc",
+    "mca",
+    "plot",
+    "scan",
+]

mxlmodels-1.1.0/src/mxlmodels/dyn_entro.py → mxlmodels-1.2.0/src/mxlmodels/_dynamic_enterobactin.py

@@ -79,7 +79,7 @@ def _d_bdt(
     return -_cons_term_c * r_cons_c - _cons_term_e * r_cons_e + enterobactin * r_prod
 
 
-def create_model() -> Model:
+def get_dynamic_enterobactin() -> Model:
     """Build the dynamic enterobactin cross-feeding model (E. coli / C. glutamicum)."""
     return (
         Model()

mxlmodels-1.2.0/src/mxlmodels/_names.py

@@ -0,0 +1,235 @@
+from __future__ import annotations
+
+from typing import Literal
+
+EMPTY: Literal[""] = ""
+
+###############################################################################
+# Parameter fns
+###############################################################################
+
+
+def loc(name: str, compartment: str, tissue: str) -> str:
+    """Localise a component to a compartment and tissue."""
+    return f"{name}{compartment}{tissue}"
+
+
+def e0(enzyme: str) -> str:
+    return f"E0_{enzyme}"
+
+
+def e(enzyme: str) -> str:
+    return f"E_{enzyme}"
+
+
+def kcat(enzyme: str) -> str:
+    return f"kcat_{enzyme}"
+
+
+def vmax(enzyme: str) -> str:
+    return f"vmax_{enzyme}"
+
+
+def keq(enzyme: str) -> str:
+    return f"keq_{enzyme}"
+
+
+def kre(enzyme: str) -> str:
+    return f"kre_{enzyme}"
+
+
+def kf(enzyme: str) -> str:
+    return f"kf_{enzyme}"
+
+
+def kh(enzyme: str) -> str:
+    """Hill constant"""
+    return f"kh_{enzyme}"
+
+
+def ksat(enzyme: str) -> str:
+    return f"ksat_{enzyme}"
+
+
+def km(enzyme: str, substrate: str | None = None) -> str:
+    if substrate is None:
+        return f"km_{enzyme}"
+    return f"km_{enzyme}_{substrate}"
+
+
+def kms(enzyme: str) -> str:
+    return km(enzyme, "s")
+
+
+def kmp(enzyme: str) -> str:
+    return km(enzyme, "p")
+
+
+def ki(enzyme: str, substrate: str | None = None) -> str:
+    if substrate is None:
+        return f"ki_{enzyme}"
+    return f"ki_{enzyme}_{substrate}"
+
+
+def ka(enzyme: str, substrate: str | None = None) -> str:
+    if substrate is None:
+        return f"ki_{enzyme}"
+    return f"ki_{enzyme}_{substrate}"
+
+
+def k(n: str) -> str:
+    return f"k_{n}"
+
+
+# def ph(n: str) -> str:
+#     return f"ph_{n}"
+
+
+def proton_fn(n: str) -> str:
+    return f"h_{n}"
+
+
+def act_energy(n: str) -> str:
+    return f"activation_energy_{n}"
+
+
+def q10(n: str) -> str:
+    return f"q10_{n}"
+
+
+###############################################################################
+# Parameters / Variables
+###############################################################################
+
+
+def a0(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    """Photosystem II reaction center 0"""
+    return loc("A0", compartment, tissue)
+
+
+def p700_fa(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("P700FA", compartment, tissue)
+
+
+def p700_plus_fa_minus(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("P700+FA-", compartment, tissue)
+
+
+def p700_fa_minus(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("P700FA-", compartment, tissue)
+
+
+def p700_plus_fa(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("P700+FA", compartment, tissue)
+
+
+def a1(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    """Photosystem II reaction center 1"""
+    return loc("A1", compartment, tissue)
+
+
+def a2(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    """Photosystem II reaction center 2"""
+    return loc("A2", compartment, tissue)
+
+
+def b0(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("B0", compartment, tissue)
+
+
+def b1(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("B1", compartment, tissue)
+
+
+def b2(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("B2", compartment, tissue)
+
+
+def b3(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("B3", compartment, tissue)
+
+
+def fd_ox(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Ferredoxine (oxidised)", compartment, tissue)
+
+
+def fd_red(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Ferredoxine (reduced)", compartment, tissue)
+
+
+def pc_ox(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Plastocyanine (oxidised)", compartment, tissue)
+
+
+def pc_red(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Plastocyanine (reduced)", compartment, tissue)
+
+
+def pq_ox(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Plastoquinone (oxidised)", compartment, tissue)
+
+
+def pq_red(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("Plastoquinone (reduced)", compartment, tissue)
+
+
+def pfd(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    """Photosynthetic Photon Flux Density"""
+    return loc("PPFD", compartment, tissue)
+
+
+def h2o2(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("H2O2", compartment, tissue)
+
+
+def ps2cs(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("PSII_cross_section", compartment, tissue)
+
+
+def o2(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("O2 (dissolved)", compartment, tissue)
+
+
+def h(compartment: str = EMPTY, tissue: str = EMPTY) -> str:
+    return loc("H", compartment, tissue)
+
+
+atp = "ATP"
+adp = "ADP"
+pq = "PQ"
+pqh2 = "PQH2"
+proton = "H"
+
+quencher = "Quencher act."
+zx = "Zx"
+vx = "Vx"
+psbs = "PsbS"
+psbsp = "PsbSP"
+
+pc = "PC"  # oxidised plastocyan
+fd = "Fd"  # oxidised ferrodoxin
+nadph = "NADPH"  # stromal concentration of NADPH
+lhc = "LHC"
+
+atpact = "ATPactivity"
+
+fluo = "Fluorescence"
+light = "pfd"
+fr_light = "pfd_fr"
+
+temp_c = "temperature(deg.C)"
+temp_k = "T"  # modified for now
+
+k_lumen = "K_lumen"
+k_stroma = "K_stroma"
+
+h_lumen = "H_lumen"
+h_stroma = "H_stroma"
+
+ph_lumen = "pH_lumen"
+ph_stroma = "pH_stroma"
+
+pmf = "pmf(V)"
+delta_psi = "delta_psi"  # r'$\Delta \Psi$'
+delta_ph = "delta_pH"  # r'$\Delta pH$'
+delta_mu_proton = "delta_mu_proton"  # r'$\Delta \tilde{\mu}_{H^+}$'

mxlmodels-1.1.0/src/mxlmodels/pop_dyn.py → mxlmodels-1.2.0/src/mxlmodels/_population_dynamics.py

@@ -22,7 +22,7 @@ def _d_cdt(
     return a_c * c_gluta * mu_c - c_gluta**2.0 * theta
 
 
-def create_model() -> Model:
+def get_population_dynamics() -> Model:
     """Build the two-species population dynamics model (E. coli / C. glutamicum)."""
     return (
         Model()

mxlmodels-1.1.0/src/mxlmodels/trip_dyn.py → mxlmodels-1.2.0/src/mxlmodels/_tripartite_dynamics.py

@@ -42,7 +42,7 @@ def _d_mdt(
     return -private * public * beta + private * r_m - private**2.0 * gamma
 
 
-def create_model() -> Model:
+def get_tripartite_dynamics() -> Model:
     """Build the three-strain public-goods game model (Public / Cheater / Private)."""
     return (
         Model()

{mxlmodels-1.1.0 → mxlmodels-1.2.0}/src/mxlmodels/ebeling2026.py

@@ -1034,7 +1034,7 @@ def _div(
     return x / y
 
 
-def create_model() -> Model:
+def get_ebeling_2026() -> Model:
     """Ebeling 2026 extended chloroplast model with ion transport, ROS, and Calvin cycle.
 
     Reference: tbd