mxlmodels 1.0.0__tar.gz → 1.2.0__tar.gz

mxlmodels-1.2.0/.gitignore

@@ -0,0 +1,118 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+coverage.json
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+.ruff_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# temporary files and folders
+*temp*
+tmp
+src/mxlbricks
+src/mxlweb
+
+# pixi environments
+.pixi
+*.egg-info
+
+# AI config files
+.github/copilot-instructions.md
+.claude
+CLAUDE.md

mxlmodels-1.2.0/.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+  # Lint & format
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
+
+  - repo: https://github.com/aio-libs/sort-all
+    rev: v1.3.0
+    hooks:
+      - id: sort-all
+
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        files: \.ipynb$
+        stages: [ pre-commit ]
+        language: system
+        entry: uvx jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace

{mxlmodels-1.0.0 → mxlmodels-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlmodels
-Version: 1.0.0
+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-1.2.0/docs/_population_dynamics.ipynb

@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "323f3026",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_population_dynamics, plot\n",
+    "\n",
+    "res = Simulator(get_population_dynamics()).simulate(1).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "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-1.2.0/docs/_tripartite_dynamics.ipynb

@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "86589195",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_tripartite_dynamics, plot\n",
+    "\n",
+    "res = Simulator(get_tripartite_dynamics()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "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-1.2.0/docs/ebeling2026.ipynb

@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c496798a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_ebeling_2026, plot\n",
+    "\n",
+    "res = Simulator(get_ebeling_2026()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "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-1.2.0/docs/elowitz2000_repressilator.ipynb

@@ -0,0 +1,43 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a5b6e12b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_elowitz2000_repressilator, plot\n",
+    "\n",
+    "res = (\n",
+    "    Simulator(get_elowitz2000_repressilator()).simulate(10).get_result().unwrap_or_err()\n",
+    ")\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "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-1.2.0/docs/lotka_volterra.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "023f3645",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "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",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "git-mxl-meta (3.13.12)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

mxlmodels-1.2.0/docs/matuszynska2016_npq.ipynb

@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f006da9a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_matuszynska2016_npq, plot\n",
+    "\n",
+    "res = Simulator(get_matuszynska2016_npq()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "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-1.2.0/docs/matuszynska2016_phd.ipynb

@@ -0,0 +1,27 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5f7d0e15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_matuszynska2016_phd, plot\n",
+    "\n",
+    "res = Simulator(get_matuszynska2016_phd()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

mxlmodels-1.2.0/docs/matuszynska2019.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f5cc7bbf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_matuszynska2019, plot\n",
+    "\n",
+    "res = Simulator(get_matuszynska2019()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "git-mxl-meta (3.13.12)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

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-1.2.0/docs/pfennig2024_synechocystis.ipynb

@@ -0,0 +1,58 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6b8b849e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, data, get_pfennig2024_synechocystis, plot\n",
+    "\n",
+    "dfs = data.pfennig2024.load()\n",
+    "\n",
+    "model = get_pfennig2024_synechocystis(\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\"]])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e475022",
+   "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-1.2.0/docs/poolman2000.ipynb

@@ -0,0 +1,27 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5eb68a6a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mxlmodels import Simulator, get_poolman2000, plot\n",
+    "\n",
+    "res = Simulator(get_poolman2000()).simulate(10).get_result().unwrap_or_err()\n",
+    "\n",
+    "fig, (ax1, ax2) = plot.two_axes(figsize=(12, 6))\n",
+    "_ = plot.lines(res.variables.iloc[:, :10], ax=ax1)\n",
+    "_ = plot.lines(res.fluxes.iloc[:, :10], ax=ax2)"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}