modelbase2 0.3.0__tar.gz → 0.4.0__tar.gz

{modelbase2-0.3.0 → modelbase2-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modelbase2
-Version: 0.3.0
+Version: 0.4.0
 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>
@@ -33,6 +33,7 @@ Requires-Dist: pebble>=5.0.7
 Requires-Dist: python-libsbml>=5.20.4
 Requires-Dist: scipy>=1.14.1
 Requires-Dist: seaborn>=0.13.2
+Requires-Dist: symbtools>=0.4.0
 Requires-Dist: sympy>=1.13.1
 Requires-Dist: tabulate>=0.9.0
 Requires-Dist: tqdm>=4.66.6

{modelbase2-0.3.0 → modelbase2-0.4.0}/docs/basics.ipynb

@@ -1004,7 +1004,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "default",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -1018,7 +1018,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.2"
   }
  },
  "nbformat": 4,

{modelbase2-0.3.0 → modelbase2-0.4.0}/docs/experimental.ipynb

@@ -121,18 +121,72 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "source": [
+    "## Symbolic models & identifiability analysis"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "import sympy\n",
+    "\n",
+    "from modelbase2.experimental import strikepy\n",
+    "from modelbase2.experimental.symbolic import SymbolicModel, to_symbolic_model\n",
+    "from modelbase2.model import Model\n",
+    "\n",
+    "\n",
+    "def check_identifiability(\n",
+    "    sym_model: SymbolicModel, outputs: list[sympy.Symbol]\n",
+    ") -> strikepy.Result:\n",
+    "    strike_model = strikepy.Model(\n",
+    "        states=list(sym_model.variables.values()),\n",
+    "        pars=list(sym_model.parameters.values()),\n",
+    "        eqs=sym_model.eqs,\n",
+    "        outputs=outputs,\n",
+    "    )\n",
+    "    return strikepy.strike_goldd(strike_model)\n",
+    "\n",
+    "\n",
+    "def infect(s: float, i: float, n: float, beta: float) -> float:\n",
+    "    return beta / n * i * s\n",
+    "\n",
+    "\n",
+    "def recover(i: float, gamma: float) -> float:\n",
+    "    return gamma * i\n",
+    "\n",
+    "\n",
+    "def total_population(s: float, i: float, r: float) -> float:\n",
+    "    return s + i + r\n",
+    "\n",
+    "\n",
+    "def sir() -> Model:\n",
+    "    return (\n",
+    "        Model()\n",
+    "        .add_parameters({\"beta\": 1.0, \"gamma\": 0.1})\n",
+    "        .add_variables({\"s\": 99, \"i\": 1, \"r\": 0})\n",
+    "        .add_derived(\"n\", total_population, args=[\"s\", \"i\", \"r\"])\n",
+    "        .add_reaction(\n",
+    "            \"infect\",\n",
+    "            infect,\n",
+    "            args=[\"s\", \"i\", \"n\", \"beta\"],\n",
+    "            stoichiometry={\"s\": -1, \"i\": 1},\n",
+    "        )\n",
+    "        .add_reaction(\n",
+    "            \"recover\", recover, args=[\"i\", \"gamma\"], stoichiometry={\"i\": -1, \"r\": 1}\n",
+    "        )\n",
+    "    )\n",
+    "\n",
+    "\n",
+    "model = sir()\n",
+    "sym_model = to_symbolic_model(model)\n",
+    "res = check_identifiability(sym_model, [sympy.Symbol(\"i\"), sympy.Symbol(\"r\")])\n",
+    "print(res.summary())"
+   ]
   }
  ],
  "metadata": {
@@ -151,7 +205,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.1"
+   "version": "3.13.2"
   }
  },
  "nbformat": 4,

modelbase2-0.4.0/docs/tips.ipynb

@@ -0,0 +1,79 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "781154dc",
+   "metadata": {},
+   "source": [
+    "# Tips and tricks"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b4f4a61",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "from example_models import get_linear_chain_2v\n",
+    "from modelbase2 import Simulator, plot\n",
+    "from modelbase2.types import unwrap"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bbc332a4",
+   "metadata": {},
+   "source": [
+    "## Renaming plots arguments\n",
+    "\n",
+    "The easiest way to rename plot arguments, e.g. for `LaTeX` display, is to work on the `pandas.DataFrame` directly.  \n",
+    "This conveniently offers a `rename` method, to which you can supply a dictionary of desired names. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b8699e6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "concs = unwrap(Simulator(get_linear_chain_2v()).simulate(5).get_concs())\n",
+    "\n",
+    "fig, ax = plot.lines(\n",
+    "    concs.rename(\n",
+    "        columns={\n",
+    "            \"x\": r\"$x_{1}$\",\n",
+    "            \"y\": r\"$x_{2}$\",\n",
+    "        }\n",
+    "    )\n",
+    ")\n",
+    "ax.set(xlabel=\"time / a.u.\", ylabel=\"concentration / a.u.\")\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "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": "3.13.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{modelbase2-0.3.0 → modelbase2-0.4.0}/mkdocs.yml

@@ -14,6 +14,7 @@ nav:
   - Label models: label-models.ipynb
   - Model parameterisation: parameterise.ipynb
   - Experimental: experimental.ipynb
+  - Tips: tips.ipynb
 
 theme:
   name: material

{modelbase2-0.3.0 → modelbase2-0.4.0}/pixi.lock

@@ -4787,8 +4787,8 @@ packages:
   requires_python: '>=3.9,<3.13'
 - pypi: .
   name: modelbase2
-  version: 0.2.0
-  sha256: 9ca76a5244abc5e2b11dedee63b5560821beb8fb02c57e4fa189e3a8e0284ccc
+  version: 0.3.0
+  sha256: 91ca378219c5a463a834e92ad254af614059f6f96a44af9e1e16fd6f2e871a15
   requires_dist:
   - dill>=0.3.9
   - latexify-py>=0.4.4

{modelbase2-0.3.0 → modelbase2-0.4.0}/pyproject.toml

@@ -29,7 +29,7 @@ maintainers = [
 ]
 name = "modelbase2"
 readme = "README.md"
-version = "0.3.0"
+version = "0.4.0"
 dependencies = [
   "dill>=0.3.9",
   "latexify-py>=0.4.4",
@@ -42,6 +42,7 @@ dependencies = [
   "python-libsbml>=5.20.4",
   "scipy>=1.14.1",
   "seaborn>=0.13.2",
+  "symbtools>=0.4.0",
   "sympy>=1.13.1",
   "tabulate>=0.9.0",
   "tqdm>=4.66.6",

modelbase2-0.4.0/src/example_models/test_nested.py

@@ -0,0 +1,17 @@
+from modelbase2 import Model
+from modelbase2.fns import constant
+from modelbase2.types import Float
+
+__all__ = ["get_model", "wrapper"]
+
+
+def wrapper(x: Float) -> Float:
+    return constant(x)
+
+
+def get_model() -> Model:
+    return (
+        Model()
+        .add_variables({"x": 0})
+        .add_reaction("v1", wrapper, args=["x"], stoichiometry={"x": -1})
+    )

{modelbase2-0.3.0 → modelbase2-0.4.0}/src/modelbase2/distributions.py

@@ -146,8 +146,11 @@ class LogUniform:
         """
         if rng is None:
             rng = RNG
-        return stats.loguniform.rvs(
-            self.lower_bound, self.upper_bound, size=num, random_state=rng
+        return cast(
+            Array,
+            stats.loguniform.rvs(
+                self.lower_bound, self.upper_bound, size=num, random_state=rng
+            ),
         )
 
 

{modelbase2-0.3.0 → modelbase2-0.4.0}/src/modelbase2/experimental/__init__.py

@@ -7,11 +7,13 @@ from __future__ import annotations
 
 from .codegen import generate_model_code_py, generate_modelbase_code
 from .diff import model_diff
+from .symbolic import model_fn_to_sympy
 from .tex import to_tex
 
 __all__ = [
     "generate_model_code_py",
     "generate_modelbase_code",
     "model_diff",
+    "model_fn_to_sympy",
     "to_tex",
 ]