mxlmodels 1.1.0__tar.gz → 1.3.0__tar.gz

mxlmodels-1.3.0/.editorconfig

@@ -0,0 +1,19 @@
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+# Matches multiple files with brace expansion notation
+# Set default charset
+[*.{js,py}]
+charset = utf-8
+
+# 4 space indentation
+[*.py]
+indent_style = space
+indent_size = 4
+
+[.toml]
+indent_style = space
+indent_size = 2

{mxlmodels-1.1.0 → mxlmodels-1.3.0}/.github/dependabot.yml

@@ -5,7 +5,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
-      day: "monday"
+      day: "saturday"
       time: "05:00"
     assignees:
       - "marvinvanaalst"

mxlmodels-1.3.0/.github/workflows/release.yml

@@ -0,0 +1,166 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+
+permissions:
+  contents: read
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.2.0
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v5
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+
+      - run: uv sync --all-extras --all-groups
+      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV
+      - run: uv run mike deploy --update-aliases --push ${{ env.VERSION }} latest
+      - run: uv run mike set-default --push latest
+
+  build-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.2.0
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Set Python version
+        run: uv venv --python 3.13
+
+      - name: Build release distribution
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v7
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - build-release
+      - build-documentation
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v8
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+
+  notify-slack:
+    runs-on: ubuntu-latest
+    needs:
+      - pypi-publish
+
+    # github.event.release.* not populated if run via
+    # workflow_dispatch
+    if: github.event_name == 'release'
+
+    steps:
+      - name: Send release notification to Slack
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
+          RELEASE_NAME: ${{ github.event.release.name }}
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+          RELEASE_BODY: ${{ github.event.release.body }}
+          RELEASE_URL: ${{ github.event.release.html_url }}
+          REPO: ${{ github.repository }}
+        run: |
+          payload=$(jq -n \
+            --arg text "*New Release Published* :tada:" \
+            --arg repo "$REPO" \
+            --arg name "$RELEASE_NAME" \
+            --arg tag "$RELEASE_TAG" \
+            --arg body "$RELEASE_BODY" \
+            --arg url "$RELEASE_URL" \
+            '{
+              text: $text,
+              blocks: [
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*New Release Published* :tada:"
+                  }
+                },
+                {
+                  type: "section",
+                  fields: [
+                    { type: "mrkdwn", text: "*Repository:*\n\($repo)" },
+                    { type: "mrkdwn", text: "*Tag:*\n\($tag)" }
+                  ]
+                },
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*Release:*\n\($name)"
+                  }
+                },
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*Notes:*\n\($body)"
+                  }
+                },
+                {
+                  type: "actions",
+                  elements: [
+                    {
+                      type: "button",
+                      text: {
+                        type: "plain_text",
+                        text: "View Release"
+                      },
+                      url: $url
+                    }
+                  ]
+                }
+              ]
+            }')
+
+          curl -X POST -H 'Content-type: application/json' \
+            --data "$payload" \
+            "$SLACK_WEBHOOK_URL"

{mxlmodels-1.1.0 → mxlmodels-1.3.0}/.github/workflows/tests.yml

@@ -12,10 +12,10 @@ jobs:
   default-tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v8.2.0
 
       - name: Set up Python
         run: uv python install 3.13

{mxlmodels-1.1.0 → mxlmodels-1.3.0}/.gitignore

@@ -1,3 +1,10 @@
+# temporary files and folders
+papers/
+*temp*
+tmp
+src/mxlbricks
+src/mxlweb
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -102,11 +109,6 @@ venv.bak/
 # mypy
 .mypy_cache/
 
-# temporary files and folders
-*temp*
-tmp
-src/mxlbricks
-src/mxlweb
 
 # pixi environments
 .pixi

{mxlmodels-1.1.0 → mxlmodels-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlmodels
-Version: 1.1.0
+Version: 1.3.0
 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>
@@ -55,6 +55,8 @@ Done. Simple as that.
 | Matuszyńska 2019     | Merges PETC (Ebenhöh 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000)   |
 | Saadat 2021          | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |
 | Ebeling 2026         | unpublishd                                                                  |
+| Hahn 1987            | Photosynthesis and Photorespiration                                         |
+| Lazar 1997           | Fluorescence induction                                                      |
 
 
 ## Tool family 🏠

{mxlmodels-1.1.0 → mxlmodels-1.3.0}/README.md

@@ -28,6 +28,8 @@ Done. Simple as that.
 | Matuszyńska 2019     | Merges PETC (Ebenhöh 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000)   |
 | Saadat 2021          | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |
 | Ebeling 2026         | unpublishd                                                                  |
+| Hahn 1987            | Photosynthesis and Photorespiration                                         |
+| Lazar 1997           | Fluorescence induction                                                      |
 
 
 ## Tool family 🏠

mxlmodels-1.3.0/docs/_dynamic_enterobactin.ipynb

@@ -0,0 +1,153 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "8616db3a",
+   "metadata": {},
+   "source": [
+    "# Race for iron: shaping tripartite community\n",
+    "\n",
+    "This model was being developed collaboratively within the SFB MibiNet community to study how the structure of a synthetic microbial community is shaped by different siderophores"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c6f8d298",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.lines as mlines\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from matplotlib import colormaps\n",
+    "from matplotlib import pyplot as plt\n",
+    "from mxlpy import Simulator, plot, scan\n",
+    "\n",
+    "from mxlmodels import get_dynamic_enterobactin"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "40b6a58d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "_ = (\n",
+    "    Simulator(get_dynamic_enterobactin())\n",
+    "    .simulate(20)\n",
+    "    .get_result()\n",
+    "    .unwrap_or_err()\n",
+    "    .variables.plot()\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "35201750",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "total_biomass = 0.11  # g/L\n",
+    "\n",
+    "res = scan.time_course(\n",
+    "    get_dynamic_enterobactin(),\n",
+    "    to_scan=pd.DataFrame(\n",
+    "        [\n",
+    "            (f * total_biomass, (1 - f) * total_biomass)\n",
+    "            for f in np.linspace(0.05, 0.95, 19)\n",
+    "        ],\n",
+    "        columns=[\"x1\", \"x2\"],\n",
+    "    ),\n",
+    "    time_points=np.linspace(0, 20, 101),\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "07954d38",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig, ax = plt.subplots(figsize=(6, 4))\n",
+    "res.variables[\"x1\"].unstack().T.plot(\n",
+    "    ax=ax, lw=\"0.8\", alpha=0.3, color=\"green\", legend=False\n",
+    ")\n",
+    "res.variables[\"x2\"].unstack().T.plot(\n",
+    "    ax=ax, lw=\"0.8\", alpha=0.5, color=\"red\", legend=False\n",
+    ")\n",
+    "res.variables[\"s1\"].unstack().T.plot(\n",
+    "    ax=ax, lw=\"0.8\", alpha=0.5, color=\"black\", legend=False\n",
+    ")\n",
+    "plot.add_grid(ax)\n",
+    "ax.legend(\n",
+    "    handles=[\n",
+    "        mlines.Line2D([], [], color=\"green\", label=\"x1\"),\n",
+    "        mlines.Line2D([], [], color=\"red\", label=\"x2\"),\n",
+    "        mlines.Line2D([], [], color=\"black\", label=\"s1\"),\n",
+    "    ]\n",
+    ")\n",
+    "ax.set(\n",
+    "    title=\"\",\n",
+    "    xlabel=\"time / h\",\n",
+    "    ylabel=\"conc / (g / L)\",\n",
+    ")\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d22b8f7e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cmap = colormaps[\"RdYlGn_r\"]\n",
+    "colors = cmap(res.to_scan[\"x2\"] / res.to_scan.sum(axis=1))\n",
+    "\n",
+    "fig, (ax1, ax2) = plt.subplots(2, 1)\n",
+    "\n",
+    "ax = res.fluxes[\"mu1\"].unstack().T.plot(ax=ax1, color=colors, legend=False)\n",
+    "ax.set(\n",
+    "    ylim=(0.0, 0.5),\n",
+    "    xlabel=\"time / h\",\n",
+    "    ylabel=\"growth rate e. coli / (1/h)\",\n",
+    ")\n",
+    "plot.add_grid(ax)\n",
+    "\n",
+    "ax = res.fluxes[\"mu2\"].unstack().T.plot(ax=ax2, color=colors, legend=False)\n",
+    "ax.set(\n",
+    "    ylim=(0.0, 0.5),\n",
+    "    xlabel=\"time / h\",\n",
+    "    ylabel=\"growth rate c. glut / (1/h)\",\n",
+    ")\n",
+    "plot.add_grid(ax)\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "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-1.3.0/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-1.3.0/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",