Doc: hints for fixing simulation failures (#1946)

Notebook demonstrating common simulation failures and show how to analyze / fix them.

Co-authored-by: Fabian Fröhlich <[email protected]>

Author: dweindl

binder/overview.ipynb

@@ -22,10 +22,14 @@
     "* [Experimental conditions](../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
     "\n",
     "  How to represent different experimental conditions in AMICI and how to use preequilibration.\n",
-    "  \n",
+    "\n",
     "* [Steadystate (sensitivities)](../python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb)\n",
     "\n",
-    "  Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities."
+    "  Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities.\n",
+    "\n",
+    "* [Simulation errors](../python/examples/example_errors.ipynb)\n",
+    "\n",
+    "  Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.\n"
    ]
   }
  ],

binder/postBuild

@@ -1,6 +1,7 @@
 #!/bin/bash
 set -eou pipefail
 
+pip install -e "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab"
 pip install -e python/sdist[petab,pysb]
 
 scripts/buildBNGL.sh

documentation/example_errors.ipynb

@@ -0,0 +1 @@
+../python/examples/example_errors.ipynb

documentation/python_interface.rst

@@ -148,6 +148,7 @@ Examples
    petab.ipynb
    ExampleExperimentalConditions.ipynb
    ExampleEquilibrationLogic.ipynb
+   example_errors.ipynb
 
 Environment variables affecting model import
 ============================================

documentation/rtd_requirements.txt

@@ -21,4 +21,6 @@ sphinxcontrib-napoleon>=0.7
 pygments==2.13.0
 Jinja2==3.1.2
 git+https://github.com/readthedocs/readthedocs-sphinx-ext
+ipykernel
+-e git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab
 -e python/sdist/