Doc: Rename 'steadystate example' (#2174)

New title + some minor updates Closes #1990 Mark notebook to always execute it under nbsphinx
AMICI-dev · Sep 20, 2023 · 5e5ec61 · 5e5ec61
1 parent 847a596
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Showing 2 changed files with 22 additions and 22 deletions.
diff --git a/binder/overview.ipynb b/binder/overview.ipynb
@@ -12,7 +12,7 @@
     "\n",
     "  Brief intro to AMICI for first-time users.\n",
     "\n",
-    "* [Example \"steadystate\"](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
+    "* [SBML import, observation model, sensitivity analysis, data export and visualization](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
     "\n",
     "  A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
     "\n",

diff --git a/python/examples/example_steadystate/ExampleSteadystate.ipynb b/python/examples/example_steadystate/ExampleSteadystate.ipynb
@@ -4,9 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# AMICI Python example \"steadystate\"\n",
+    "# SBML import, observation model, sensitivity analysis, data export and visualization\n",
     "\n",
-    "This is an example using the [model_steadystate_scaled.sbml] model to demonstrate and test SBML import and AMICI Python interface."
+    "This is an example using the [model_steadystate_scaled.sbml] model to demonstrate:\n",
+    "\n",
+    "* SBML import\n",
+    "* specifying the observation model\n",
+    "* performing sensitivity analysis\n",
+    "* exporting and visualizing simulation results"
    ]
   },
   {
@@ -23,10 +28,7 @@
     "model_output_dir = model_name\n",
     "\n",
     "import libsbml\n",
-    "import importlib\n",
     "import amici\n",
-    "import os\n",
-    "import sys\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt"
    ]
@@ -145,7 +147,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "constantParameters = [\"k0\"]"
+    "constant_parameters = [\"k0\"]"
    ]
   },
   {
@@ -341,7 +343,7 @@
     "    model_output_dir,\n",
     "    verbose=logging.INFO,\n",
     "    observables=observables,\n",
-    "    constant_parameters=constantParameters,\n",
+    "    constant_parameters=constant_parameters,\n",
     "    sigmas=sigmas,\n",
     ")"
    ]
@@ -361,8 +363,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sys.path.insert(0, os.path.abspath(model_output_dir))\n",
-    "model_module = importlib.import_module(model_name)"
+    "model_module = amici.import_model_module(model_name, model_output_dir)"
    ]
   },
   {
@@ -447,7 +448,7 @@
     "print(\n",
     "    \"Simulation was run using model default parameters as specified in the SBML model:\"\n",
     ")\n",
-    "print(model.getParameters())"
+    "print(dict(zip(model.getParameterIds(), model.getParameters())))"
    ]
   },
   {
@@ -862,18 +863,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "(1.0, 0.5, 0.4, 2.0, 0.1, 2.0, 3.0, 0.2)\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "outputs": [],
    "source": [
-    "print(model.getParameters())"
+    "# In particular for interactive use, ReturnDataView.by_id() and amici.evaluate provides a more convenient way to access slices of the result:\n",
+    "# Time trajectory of observable observable_x1\n",
+    "print(f\"{rdata.by_id('observable_x1')=}\")\n",
+    "# Time trajectory of state variable x2\n",
+    "print(f\"{rdata.by_id('x2')=}\")"
    ],
    "metadata": {
     "collapsed": false,
@@ -2037,6 +2034,9 @@
    "toc_position": {},
    "toc_section_display": true,
    "toc_window_display": false
+  },
+  "nbsphinx": {
+   "execute": "always"
   }
  },
  "nbformat": 4,