[c++/python] Fix domain getter memory leak on C++/Python layer by XanthosXanthopoulos · Pull Request #4066 · single-cell-data/TileDB-SOMA

XanthosXanthopoulos · 2025-05-19T18:06:22Z

Issue and/or context: SOMA-169

Changes:

Notes for Reviewer:

codecov · 2025-05-19T18:25:47Z

Codecov Report

Attention: Patch coverage is 0% with 25 lines in your changes missing coverage. Please review.

Project coverage is 66.01%. Comparing base (f29839d) to head (b38fc54).
Report is 7 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #4066       +/-   ##
===========================================
- Coverage   88.97%   66.01%   -22.96%     
===========================================
  Files          59      158       +99     
  Lines        7073    21049    +13976     
  Branches        0     1236     +1236     
===========================================
+ Hits         6293    13895     +7602     
- Misses        780     6742     +5962     
- Partials        0      412      +412

Flag	Coverage Δ
libtiledbsoma	`54.25% <0.00%> (?)`
python	`89.26% <ø> (+0.29%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	`89.26% <ø> (+0.29%)`	⬆️
libtiledbsoma	`44.66% <0.00%> (∅)`

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

bkmartinjr · 2025-05-19T18:52:59Z

I built this branch and ran under valgrind. Am still seeing quite a few leaks in this call chain (i.e., _get_core_domainish)

My test case:

valgrind --max-threads=4096 --leak-check=full pytest -s -x -v apis/python/tests/test_shape.py

Leaks:

==361621== 12 bytes in 4 blocks are definitely lost in loss record 1,151 of 7,631
==361621==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==361621==    by 0x4A0E58E: strdup (strdup.c:42)
==361621==    by 0x873DDB4D: tiledbsoma::ArrowAdapter::make_arrow_schema_parent(unsigned long, std::basic_string_view<char, std::char_traits<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8731B0C0: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x87009C08: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x86D05613: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x323D37: cfunction_call (methodobject.c:537)
==361621==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==361621==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==361621==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==361621==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)

==361621== 28 bytes in 4 blocks are definitely lost in loss record 1,941 of 7,631
==361621==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==361621==    by 0x4A0E58E: strdup (strdup.c:42)
==361621==    by 0x873DDB5C: tiledbsoma::ArrowAdapter::make_arrow_schema_parent(unsigned long, std::basic_string_view<char, std::char_traits<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8731B0C0: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x87009C08: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x86D05613: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x323D37: cfunction_call (methodobject.c:537)
==361621==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==361621==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==361621==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==361621==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)

==361621== 555 (48 direct, 507 indirect) bytes in 4 blocks are definitely lost in loss record 6,649 of 7,631
==361621==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==361621==    by 0x873DDB85: tiledbsoma::ArrowAdapter::make_arrow_schema_parent(unsigned long, std::basic_string_view<char, std::char_traits<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8731B0C0: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x87009C08: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x86D05613: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x323D37: cfunction_call (methodobject.c:537)
==361621==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==361621==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==361621==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==361621==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)
==361621==    by 0x3FF2FA: slot_tp_call (typeobject.c:8791)

==361621== 728 (48 direct, 680 indirect) bytes in 4 blocks are definitely lost in loss record 6,751 of 7,631
==361621==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==361621==    by 0x873DE03A: tiledbsoma::ArrowAdapter::make_arrow_array_parent(unsigned long) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8731B0CD: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==361621==    by 0x87009C08: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x86D05613: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==361621==    by 0x323D37: cfunction_call (methodobject.c:537)
==361621==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==361621==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==361621==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==361621==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)
==361621==    by 0x3FF2FA: slot_tp_call (typeobject.c:8791)

bkmartinjr

Couple of items:

is this still WIP? (PR title)
I built the branch and ran valgrind - still see multiple leaks in this call chain. Left details in a comment

If you were intending to do a PR for each specific leak, LMK and I can re-review. No concerns with the actual changes in this PR.

johnkerl · 2025-05-19T20:45:55Z

@XanthosXanthopoulos #4067 may help?

bkmartinjr · 2025-05-20T14:41:37Z

Update after latest commit. Ran:

valgrind --max-threads=4096 --leak-check=full pytest -s -x -v apis/python/tests/test_shape.py -k test_canned_experiments[False]

And leaked:

==2066522== 4 bytes in 2 blocks are definitely lost in loss record 241 of 7,551
==2066522==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==2066522==    by 0x4A0E58E: strdup (strdup.c:42)
==2066522==    by 0x873E0309: tiledbsoma::ArrowAdapter::arrow_schema_from_tiledb_attribute(tiledb::Attribute const&, tiledb::Context const&, tiledb::Array const&) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x873579A2: tiledbsoma::SOMAAttribute::arrow_schema_slot(tiledbsoma::SOMAContext const&, tiledb::Array&) const (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x86FB7348: libtiledbsomacpp::load_soma_array(pybind11::module_&)::{lambda(tiledbsoma::SOMAArray&)#7}::operator()(tiledbsoma::SOMAArray&) const [clone .constprop.0] (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x86FB8452: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_array(pybind11::module_&)::{lambda(tiledbsoma::SOMAArray&)#7} const&, pybind11::object, tiledbsoma::SOMAArray&>(libtiledbsomacpp::load_soma_array(pybind11::module_&)::{lambda(tiledbsoma::SOMAArray&)#7} const&, pybind11::object (*)(tiledbsoma::SOMAArray&))::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x86D055C3: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x323D37: cfunction_call (methodobject.c:537)
==2066522==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==2066522==    by 0x330577: UnknownInlinedFun (pycore_call.h:90)
==2066522==    by 0x330577: UnknownInlinedFun (pycore_call.h:77)
==2066522==    by 0x330577: PyObject_CallOneArg (call.c:401)
==2066522==    by 0x322A55: _PyObject_GenericGetAttrWithDict (object.c:1447)
==2066522==    by 0x309720: UnknownInlinedFun (object.c:1538)


==2066522== 9 bytes in 3 blocks are definitely lost in loss record 742 of 7,551
==2066522==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==2066522==    by 0x4A0E58E: strdup (strdup.c:42)
==2066522==    by 0x873DDB4D: tiledbsoma::ArrowAdapter::make_arrow_schema_parent(unsigned long, std::basic_string_view<char, std::char_traits<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x8731B0C0: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x87009678: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x86D055C3: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x323D37: cfunction_call (methodobject.c:537)
==2066522==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==2066522==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==2066522==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==2066522==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)

==2066522== 21 bytes in 3 blocks are definitely lost in loss record 1,380 of 7,551
==2066522==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==2066522==    by 0x4A0E58E: strdup (strdup.c:42)
==2066522==    by 0x873DDB5C: tiledbsoma::ArrowAdapter::make_arrow_schema_parent(unsigned long, std::basic_string_view<char, std::char_traits<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x8731B0C0: tiledbsoma::SOMAArray::_get_core_domainish(Domainish) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x8732A218: tiledbsoma::SOMAArray::_set_soma_joinid_shape_helper(long, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (in /home/bruce/projects/TileDB-SOMA/dist/lib/libtiledbsoma.so)
==2066522==    by 0x87009678: pybind11::cpp_function::initialize<libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}, void, tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(libtiledbsomacpp::load_soma_dataframe(pybind11::module_&)::{lambda(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)#6}&&, void (*)(tiledbsoma::SOMADataFrame&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call&) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x86D055C3: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (in /home/bruce/projects/TileDB-SOMA/apis/python/src/tiledbsoma/pytiledbsoma.cpython-312-x86_64-linux-gnu.so)
==2066522==    by 0x323D37: cfunction_call (methodobject.c:537)
==2066522==    by 0x30726B: _PyObject_MakeTpCall (call.c:240)
==2066522==    by 0x21AB4E: _PyEval_EvalFrameDefault.cold (bytecodes.c:2715)
==2066522==    by 0x309CF1: _PyObject_FastCallDictTstate (call.c:144)
==2066522==    by 0x3327A8: _PyObject_Call_Prepend (call.c:508)

johnkerl · 2025-05-20T16:01:13Z

And leaked:

This is because of
https://github.com/single-cell-data/TileDB-SOMA/blob/xanthosxanthopoulos/soma-169-c-memory-leak-in-somaarray_get_core_domainish/libtiledbsoma/src/utils/arrow_adapter.cc#L539-L546

dict->format is strdup'ed outside the if
then again inside the if

johnkerl · 2025-05-20T16:10:05Z

With this mod compiled in my sandbox I re-ran

valgrind --error-limit=no --trace-children=yes -s --leak-check=full $(which python) ~/130.py

as detailed on #4065 and #4067, and I no longer see the strdup leak appearing in the output from valgrind

Co-authored-by: John Kerl <[email protected]>

bkmartinjr · 2025-05-21T15:19:40Z

I ran a couple of quick unit tests for validation, and for those I tested, things are clean.

bkmartinjr

am doing final testing in parallel, but LGTM

* Fix memory * Release exported arrays * fix double strdup which was leaking 2 bytes per enumerated column * More missing arrow releases * Use scoped executor for arrow cleanup * Release schema in `_set_soma_joinid_shape_helper` * Apply suggestions from code review Co-authored-by: John Kerl <[email protected]> * Release memory for outline transformer * lint fixes * Update changelog * Disable mdformat - CI failures not reproducing locally --------- Co-authored-by: John Kerl <[email protected]>

#4078) * Fix memory * Release exported arrays * fix double strdup which was leaking 2 bytes per enumerated column * More missing arrow releases * Use scoped executor for arrow cleanup * Release schema in `_set_soma_joinid_shape_helper` * Apply suggestions from code review * Release memory for outline transformer * lint fixes * Update changelog * Disable mdformat - CI failures not reproducing locally --------- Co-authored-by: XanthosXanthopoulos <[email protected]> Co-authored-by: John Kerl <[email protected]>

Fix memory

98e77dc

XanthosXanthopoulos requested a review from bkmartinjr May 19, 2025 18:23

bkmartinjr requested changes May 19, 2025

View reviewed changes

johnkerl changed the title ~~[c++/python] Fix domain getter memory leak on C++/Python layer [WIP]~~ [c++/python] Fix domain getter memory leak on C++/Python layer May 19, 2025

johnkerl changed the title ~~[c++/python] Fix domain getter memory leak on C++/Python layer~~ [c++/python] Fix domain getter memory leak on C++/Python layer [WIP] May 19, 2025

XanthosXanthopoulos marked this pull request as draft May 20, 2025 10:04

Release exported arrays

ab89219

jp-dark added the backport release-1.17 label May 20, 2025

fix double strdup which was leaking 2 bytes per enumerated column

b5babe9

This was referenced May 20, 2025

[python] Address memory leak in get_enumeration_values #4065

Closed

[python] Address memory leak in domain accessor #4067

Closed

XanthosXanthopoulos added 3 commits May 20, 2025 22:18

More missing arrow releases

64d8ac5

Use scoped executor for arrow cleanup

461929b

Release schema in _set_soma_joinid_shape_helper

8cb622a

johnkerl reviewed May 21, 2025

View reviewed changes

Comment thread apis/python/src/tiledbsoma/soma_array.cc Outdated

Comment thread apis/python/src/tiledbsoma/soma_array.cc Outdated

XanthosXanthopoulos changed the title ~~[c++/python] Fix domain getter memory leak on C++/Python layer [WIP]~~ [c++/python] Fix domain getter memory leak on C++/Python layer May 21, 2025

Apply suggestions from code review

4933ecb

Co-authored-by: John Kerl <[email protected]>

XanthosXanthopoulos requested a review from bkmartinjr May 21, 2025 14:59

XanthosXanthopoulos marked this pull request as ready for review May 21, 2025 14:59

XanthosXanthopoulos added 2 commits May 21, 2025 18:40

Release memory for outline transformer

8e00a72

lint fixes

94e74f2

bkmartinjr approved these changes May 21, 2025

View reviewed changes

Update changelog

80c3d6f

Disable mdformat - CI failures not reproducing locally

b38fc54

jp-dark merged commit f1b0ac5 into main May 21, 2025
25 of 26 checks passed

jp-dark deleted the xanthosxanthopoulos/soma-169-c-memory-leak-in-somaarray_get_core_domainish branch May 21, 2025 18:58

github-actions Bot mentioned this pull request May 21, 2025

[Backport release-1.17] [c++/python] Fix domain getter memory leak on C++/Python layer #4078

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[c++/python] Fix domain getter memory leak on C++/Python layer#4066

[c++/python] Fix domain getter memory leak on C++/Python layer#4066
jp-dark merged 11 commits intomainfrom
xanthosxanthopoulos/soma-169-c-memory-leak-in-somaarray_get_core_domainish

XanthosXanthopoulos commented May 19, 2025

Uh oh!

codecov Bot commented May 19, 2025 •

edited

Loading

Uh oh!

bkmartinjr commented May 19, 2025

Uh oh!

bkmartinjr left a comment

Uh oh!

johnkerl commented May 19, 2025

Uh oh!

bkmartinjr commented May 20, 2025

Uh oh!

johnkerl commented May 20, 2025

Uh oh!

johnkerl commented May 20, 2025 •

edited

Loading

Uh oh!

Uh oh!

Uh oh!

bkmartinjr commented May 21, 2025

Uh oh!

bkmartinjr left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

XanthosXanthopoulos commented May 19, 2025

Uh oh!

codecov Bot commented May 19, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

bkmartinjr commented May 19, 2025

Uh oh!

bkmartinjr left a comment

Choose a reason for hiding this comment

Uh oh!

johnkerl commented May 19, 2025

Uh oh!

bkmartinjr commented May 20, 2025

Uh oh!

johnkerl commented May 20, 2025

Uh oh!

johnkerl commented May 20, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Uh oh!

bkmartinjr commented May 21, 2025

Uh oh!

bkmartinjr left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

codecov Bot commented May 19, 2025 •

edited

Loading

johnkerl commented May 20, 2025 •

edited

Loading