From 0f95335b204bff9144ad8cd1d6bb54392c131a80 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>
Date: Tue, 19 Sep 2023 22:30:16 +0200
Subject: [PATCH 1/3] Doc: Rename 'steadystate example'

New title + some minor updates

Closes #1990
---
 binder/overview.ipynb                         |  2 +-
 .../ExampleSteadystate.ipynb                  | 39 +++++++++----------
 2 files changed, 19 insertions(+), 22 deletions(-)

diff --git a/binder/overview.ipynb b/binder/overview.ipynb
index 6d98f0f9fb..0a7ce81084 100644
--- 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
index 502174fe15..e2197ae5c7 100644
--- 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,

From 8a66dc8bd13f36a92e243768309d7768673522c7 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>
Date: Wed, 20 Sep 2023 14:12:59 +0200
Subject: [PATCH 2/3] Always execute

---
 python/examples/example_steadystate/ExampleSteadystate.ipynb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/python/examples/example_steadystate/ExampleSteadystate.ipynb b/python/examples/example_steadystate/ExampleSteadystate.ipynb
index e2197ae5c7..a1b4314c6c 100644
--- a/python/examples/example_steadystate/ExampleSteadystate.ipynb
+++ b/python/examples/example_steadystate/ExampleSteadystate.ipynb
@@ -2020,7 +2020,10 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.7.7",
+   "nbsphinx": {
+    "execute": "always"
+   }
   },
   "toc": {
    "base_numbering": 1,

From efc752a11cee6bb3ef169962f9f3552bde9c542f Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>
Date: Wed, 20 Sep 2023 14:36:23 +0200
Subject: [PATCH 3/3] Always execute

---
 .../examples/example_steadystate/ExampleSteadystate.ipynb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/python/examples/example_steadystate/ExampleSteadystate.ipynb b/python/examples/example_steadystate/ExampleSteadystate.ipynb
index a1b4314c6c..09590a3b1a 100644
--- a/python/examples/example_steadystate/ExampleSteadystate.ipynb
+++ b/python/examples/example_steadystate/ExampleSteadystate.ipynb
@@ -2020,10 +2020,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7",
-   "nbsphinx": {
-    "execute": "always"
-   }
+   "version": "3.7.7"
   },
   "toc": {
    "base_numbering": 1,
@@ -2037,6 +2034,9 @@
    "toc_position": {},
    "toc_section_display": true,
    "toc_window_display": false
+  },
+  "nbsphinx": {
+   "execute": "always"
   }
  },
  "nbformat": 4,