From 69ddf5e09695f5d4f8b2ed6d5bd08b8100706672 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-munich.de>
Date: Wed, 8 May 2024 08:23:53 +0200
Subject: [PATCH] Update valgrind suppressions

for Python 3.11
---
 .../ExampleExperimentalConditions.ipynb       | 16 ++--
 python/tests/valgrind-python.supp             | 87 +++++++++++++++++++
 2 files changed, 97 insertions(+), 6 deletions(-)

diff --git a/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb b/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb
index 83f23273af..63fbc7a4ff 100644
--- a/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb
+++ b/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb
@@ -21,12 +21,16 @@
     "# Directory to which the generated model code is written\n",
     "model_output_dir = model_name\n",
     "\n",
-    "from pprint import pprint\n",
-    "\n",
     "import libsbml\n",
+    "import amici\n",
+    "import amici.plotting\n",
+    "import os\n",
+    "import sys\n",
+    "import importlib\n",
     "import numpy as np\n",
-    "\n",
-    "import amici.plotting"
+    "import pandas as pd\n",
+    "import matplotlib.pyplot as plt\n",
+    "from pprint import pprint"
    ]
   },
   {
@@ -139,7 +143,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For this example we want to specify the initial drug and kinase concentrations as experimental conditions. Accordingly, we specify them as `fixedParameters`. The meaning of `fixedParameters` is defined in the [Glossary](https://amici.readthedocs.io/en/latest/glossary.html#term-fixed-parameters), which we display here for convenience."
+    "For this example we want specify the initial drug and kinase concentrations as experimental conditions. Accordingly we specify them as `fixedParameters`. The meaning of `fixedParameters` is defined in the [Glossary](https://amici.readthedocs.io/en/latest/glossary.html#term-fixed-parameters), which we display here for convenience."
    ]
   },
   {
@@ -365,7 +369,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The resulting trajectory is definitely not what one may expect. The problem is that the `DRUG_0` and `KIN_0` set initial conditions for species in the model. By default, these initial conditions are only applied at the very beginning of the simulation, i.e., before the preequilibration. Accordingly, the `fixedParameters` that we specified do not have any effect. To fix this, we need to set the `reinitializeFixedParameterInitialStates` attribute to `True`, to specify that AMICI reinitializes all states that have `fixedParameter`-dependent initial states."
+    "The resulting trajectory is definitely not what one may expect. The problem is that the `DRUG_0` and `KIN_0` set initial conditions for species in the model. By default these initial conditions are only applied at the very beginning of the simulation, i.e., before the preequilibration. Accordingly, the `fixedParameters` that we specified do not have any effect. To fix this, we need to set the `reinitializeFixedParameterInitialStates` attribue to `True`, to spefify that AMICI reinitializes all states that have `fixedParameter`-dependent initial states."
    ]
   },
   {
diff --git a/python/tests/valgrind-python.supp b/python/tests/valgrind-python.supp
index 01bc776aec..dab3c06dc4 100644
--- a/python/tests/valgrind-python.supp
+++ b/python/tests/valgrind-python.supp
@@ -878,3 +878,90 @@
    fun:loadAntimonyString
    ...
 }
+
+{
+   Python
+   Memcheck:Cond
+   fun:maybe_small_long
+   ...
+}
+
+{
+   Python
+   Memcheck:Value8
+   fun:medium_value
+   ...
+}
+
+{
+   Python
+   Memcheck:Value8
+   fun:Py_INCREF
+   ...
+}
+{
+   Python
+   Memcheck:Value8
+   fun:Py_DECREF
+   ...
+}
+{
+   Python
+   Memcheck:Value8
+   fun:Py_SIZE
+   ...
+}
+{
+   Python
+   Memcheck:Value8
+   fun:Py_TYPE
+   ...
+}
+{
+   Python
+   Memcheck:Value8
+   fun:type_call
+   ...
+}
+
+{
+   Python
+   Memcheck:Value8
+   fun:_PyEval_EvalFrameDefault
+   ...
+}
+
+
+{
+   Python
+   Memcheck:Value8
+   fun:PyType_HasFeature
+   ...
+}
+
+{
+   Python
+   Memcheck:Value8
+   fun:unpack_indices
+   ...
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:malloc
+   fun:PyFloat_FromDouble
+   fun:fill_time
+   ...
+}
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:malloc
+   fun:gc_alloc
+   ...
+   fun:Py_CompileStringObject
+   ...
+}