Merge branch 'develop' into keep_tmpdir

AMICI-dev · Dec 3, 2023 · 2dca397 · 2dca397
2 parents d0f5433 + 52b1af6
commit 2dca397
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Showing 3 changed files with 180 additions and 107 deletions.
diff --git a/python/tests/valgrind-python.supp b/python/tests/valgrind-python.supp
@@ -76,17 +76,28 @@
    Memcheck:Leak
    fun:malloc
    ...
-   fun:__pyx_pw_5numpy_6random_13bit_generator_12BitGenerator_1__init__
+   fun:__pyx_pw_5numpy_*
 }
 
 {
    numpy
    Memcheck:Leak
-   match-leak-kinds: definite
+   match-leak-kinds: possible
    fun:malloc
-   obj:/usr/bin/python3.?
+   fun:PyUFunc_FromFuncAndDataAndSignatureAndIdentity
+   fun:initumath
+   fun:PyInit__multiarray_umath
+   ...
+}
+
+{
+   numpy
+   Memcheck:Leak
+   match-leak-kinds: possible
+   fun:malloc
+   fun:default_malloc
+   fun:PyDataMem_UserNEW
    ...
-   fun:gentype_generic_method
 }
 
 #
@@ -178,26 +189,26 @@
 {
    other
    Memcheck:Cond
-   obj:/usr/bin/python3.?
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
+   obj:/usr/bin/python3.*
    fun:_PyEval_EvalFrameDefault
    fun:_PyEval_EvalCodeWithName
    fun:_PyFunction_Vectorcall
    fun:_PyEval_EvalFrameDefault
    fun:_PyEval_EvalCodeWithName
    fun:_PyFunction_Vectorcall
    fun:_PyEval_EvalFrameDefault
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:_PyEval_EvalFrameDefault
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
 }
 
 {
    other
    Memcheck:Value8
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:__Pyx_PyObject_Call
    fun:__Pyx__PyObject_CallOneArg
 }
@@ -308,7 +319,7 @@
    ...
    fun:PyBytes_Repr
    fun:PyObject_Str
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
    fun:PyObject_Format
    ...
@@ -382,9 +393,9 @@
 {
    other
    Memcheck:Cond
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:__Pyx_PyObject_Call
    fun:__Pyx__PyObject_CallOneArg
    ...
@@ -410,9 +421,9 @@
    other
    Memcheck:Cond
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:_PyObject_CallMethodIdObjArgs
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
 }
 
@@ -437,9 +448,9 @@
    other
    Memcheck:Value8
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:_PyObject_CallMethodIdObjArgs
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
 }
 
@@ -455,74 +466,52 @@
    other
    Memcheck:Value8
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    fun:PyDict_SetItem
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
 }
 
 {
    other
    Memcheck:Cond
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
 }
 
 {
    other
    Memcheck:Cond
    fun:realloc
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
    fun:_PyFunction_Vectorcall
 }
 
 {
    other
    Memcheck:Value8
-   obj:/usr/bin/python3.?
+   obj:/usr/bin/python3.*
    ...
-   obj:/usr/bin/python3.?
-}
-
-{
-   other
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.?
-   fun:_PyObject_MakeTpCall
+   obj:/usr/bin/python3.*
 }
 
 {
    other
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.?
-   obj:/usr/bin/python3.?
+   Memcheck:Value8
+   obj:/usr/bin/python3.*
    fun:_PyObject_MakeTpCall
-}
-
-{
-   other
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.?
-   ...
-   fun:PyTuple_New
-   ...
-}
-
-{
-   other
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.?
-   fun:PyList_AsTuple
+   fun:_PyEval_EvalFrameDefault
+   obj:/usr/bin/python3.11
+   obj:/usr/bin/python3.11
+   obj:/usr/bin/python3.11
+   fun:PyIter_Next
+   obj:/usr/bin/python3.11
+   fun:PyBytes_FromObject
+   obj:/usr/bin/python3.11
+   obj:/usr/bin/python3.11
+   fun:PyObject_Vectorcall
 }
 
 {
@@ -544,7 +533,6 @@
 {
    Pandas
    Memcheck:Leak
-   match-leak-kinds: definite
    fun:malloc
    ...
    obj:*site-packages/pandas/_libs/*.cpython-3*-x86_64-linux-gnu.so
@@ -561,30 +549,6 @@
    ...
 }
 
-
-{
-   PyTuple_Pack
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.*
-   fun:PyTuple_Pack
-   obj:/usr/bin/python3.*
-   ...
-}
-
-{
-   PyAST_CompileObject
-   Memcheck:Leak
-   match-leak-kinds: definite
-   fun:malloc
-   obj:/usr/bin/python3.*
-   ...
-   fun:PyAST_CompileObject
-   obj:/usr/bin/python3.*
-   ...
-}
-
 {
    other
    Memcheck:Value8
@@ -775,3 +739,103 @@
    fun:os_stat
    ...
 }
+
+{
+   Python PyLong_FromUnicodeObject
+   Memcheck:Cond
+   fun:PyLong_FromString
+   fun:PyLong_FromUnicodeObject
+}
+
+{
+   Python PyLong_FromUnicodeObject
+   Memcheck:Value8
+   fun:PyLong_FromString
+   fun:PyLong_FromUnicodeObject
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: possible
+   fun:realloc
+   obj:/usr/bin/python3.*
+   fun:_PyEval_EvalFrameDefault
+   fun:_PyFunction_Vectorcall
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: possible
+   fun:calloc
+   fun:PyList_New
+   fun:_PyEval_EvalFrameDefault
+   fun:_PyFunction_Vectorcall
+   ...
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: possible
+   fun:malloc
+   fun:PyModule_ExecDef
+   obj:/usr/bin/python3.*
+   ...
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: possible
+   fun:malloc
+   obj:/usr/bin/python3.*
+   ...
+}
+
+{
+   Python
+   Memcheck:Addr32
+   fun:__wcsncpy_avx2
+   fun:_Py_wgetcwd
+   obj:/usr/bin/python3.*
+   fun:Py_RunMain
+   fun:Py_BytesMain
+   fun:(below main)
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:malloc
+   obj:/usr/bin/python3.*
+   ...
+}
+
+{
+   Python
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:*alloc
+   fun:_PyObject_GC_*
+   obj:/usr/bin/python3.*
+}
+
+
+{
+   Antimony with libsbml 5.20.1
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:_Znwm
+   fun:_ZN7libsbml12SBMLDocument14getAllElementsEPNS_13ElementFilterE
+   fun:_ZN7libsbml23CompFlatteningConverter21unsetExplicitlyListedEv
+   fun:_ZN7libsbml23CompFlatteningConverter17performConversionEv
+   fun:_ZN7libsbml23CompFlatteningConverter7convertEv
+   fun:_ZN7libsbml22CompSBMLDocumentPlugin16checkConsistencyEv
+   fun:_ZN7libsbml12SBMLDocument16checkConsistencyEv
+   ...
+   fun:loadAntimonyString
+   ...
+}
diff --git a/scripts/run-valgrind-py.sh b/scripts/run-valgrind-py.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
-# Test python model wrapping inside virtual environment
+# Without arguments: run Python test suite under valgrind
+# With arguments: run whatever was passed as arguments under valgrind
 
 script_path=$(dirname $BASH_SOURCE)
 amici_path=$(cd "$script_path"/.. && pwd)
@@ -9,23 +10,31 @@ set -e
 if [[ -z "${BNGPATH}" ]]; then
     export BNGPATH=${amici_path}/ThirdParty/BioNetGen-2.7.0
 fi
+suppressions="${amici_path}/python/tests/valgrind-python.supp"
+if [ $# -eq 0 ]
+  then
+    # No arguments supplied, run all tests
+    cd "${amici_path}"/python/tests
+    source "${amici_path}"/build/venv/bin/activate
+    pip install scipy h5py pytest pytest-rerunfailures
+    command=(python -m pytest -vv --ignore-glob=*petab* -W 'ignore:Signature ')
+    #                                                    ^ ignores the following warning that occurs only under valgrind,
+    # e.g. `valgrind python -c "import h5py"`:
+    # UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00'
+    # for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
+else
+    # Run whatever was passed as arguments
+    command=($@)
+fi
 
-cd "${amici_path}"/python/tests
-
-source "${amici_path}"/build/venv/bin/activate
-
-pip install scipy h5py pytest pytest-rerunfailures
 
+set -x
 PYTHONMALLOC=malloc valgrind \
-  --suppressions=valgrind-python.supp \
+  --suppressions="${suppressions}" \
   --show-leak-kinds=definite \
   --errors-for-leak-kinds=definite \
   --error-exitcode=1 \
   --leak-check=full \
   --gen-suppressions=all \
   -v \
-  python -m pytest -vv --ignore-glob=*petab* -W "ignore:Signature "
-#                                               ^ ignores the following warning that occurs only under valgrind,
-# e.g. `valgrind python -c "import h5py"`:
-# UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00'
-# for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
+  "${command[@]}"