Control: clone -1 -2
Control: reassign -2 python3-vtk9
Control: retitle -2 python3-vtk9: segfault on Python 3.13
Control: tags -2 patch
On Sat, Jan 04, 2025 at 12:36:21PM +0100, Matthias Klose wrote:
> mayavi2 ftbfs with Python 3.13 as the default
>
> [...]
> debian/rules binary
> dh binary --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> pybuild --configure -i python{version} -p 3.13
> I: pybuild base:311: python3.13 setup.py config
> running config
> debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> find /<<PKGBUILDDIR>>/* -name '*.pyx' -exec cython3 '{}' ';'
> LD_PRELOAD=libgomp.so.1 xvfb-run --auto-servernum --server-args="-screen 0
> 1024x768x24" dh_auto_build
> pybuild --build -i python{version} -p 3.13
> I: pybuild base:311: /usr/bin/python3 setup.py build
> running build
> running build_py
> Segmentation fault (core dumped)
Most of this is due to vtk9. I've attached a patch cherry-picked from
upstream which fixes this.
There's one remaining problem after this, which I haven't been able to
figure out myself so far. Here's the test log:
dh_auto_test -O--buildsystem=pybuild
pybuild --test -i python{version} -p 3.13
I: pybuild base:311: cd
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build; cd
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build ;
LD_PRELOAD=libgomp.so.1 xvfb-run --auto-servernum --server-args="-screen 0
1024x768x24" python3.13 -m pytest -k 'not test_array2vtk'
============================= test session starts
==============================
platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
rootdir: /build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build
configfile: setup.cfg
plugins: typeguard-4.4.1
collected 444 items / 1 deselected / 443 selected
mayavi/tests/test_array_source.py ......... [
2%]
mayavi/tests/test_builtin_image.py ... [
2%]
mayavi/tests/test_builtin_surface.py ... [
3%]
mayavi/tests/test_composite_data.py .... [
4%]
mayavi/tests/test_contour.py .... [
5%]
mayavi/tests/test_core_common.py ........ [
6%]
mayavi/tests/test_core_utils.py ... [
7%]
mayavi/tests/test_csv_sniff.py ..................... [
12%]
mayavi/tests/test_customize.py . [
12%]
mayavi/tests/test_cut_plane.py .. [
13%]
mayavi/tests/test_dataset_manager.py ........ [
14%]
mayavi/tests/test_engine_manager.py ......... [
16%]
mayavi/tests/test_extract_grid_filter.py ss [
17%]
mayavi/tests/test_file_timestep.py ...... [
18%]
mayavi/tests/test_filters.py . [
18%]
mayavi/tests/test_garbage_collection.py ...... [
20%]
mayavi/tests/test_glyph.py ...... [
21%]
mayavi/tests/test_grid_plane.py ... [
22%]
mayavi/tests/test_image_data_probe.py ... [
23%]
mayavi/tests/test_image_data_reader.py ...... [
24%]
mayavi/tests/test_image_plane_widget.py .... [
25%]
mayavi/tests/test_ipw_multiple_scalars.py . [
25%]
mayavi/tests/test_mayavi_traits.py ....... [
27%]
mayavi/tests/test_mlab_integration.py ............................. [
33%]
mayavi/tests/test_mlab_null_engine.py .. [
34%]
mayavi/tests/test_mlab_scene_model.py . [
34%]
mayavi/tests/test_mlab_source.py ....................................... [
43%]
[
43%]
mayavi/tests/test_mlab_source_integration.py ....... [
44%]
mayavi/tests/test_mouse_pick_dispatcher.py . [
44%]
mayavi/tests/test_no_ui_toolkit.py . [
45%]
mayavi/tests/test_optional_collection.py ... [
45%]
mayavi/tests/test_pipeline_info.py .. [
46%]
mayavi/tests/test_plot3d_mb_reader.py ... [
46%]
mayavi/tests/test_poly_data_reader.py ........................... [
53%]
mayavi/tests/test_preferences_mirror.py .... [
53%]
mayavi/tests/test_pylab_luts.py s [
54%]
mayavi/tests/test_recorder.py ............. [
57%]
mayavi/tests/test_registry.py ..... [
58%]
mayavi/tests/test_script_recording.py . [
58%]
mayavi/tests/test_set_active_attribute.py ... [
59%]
mayavi/tests/test_sources.py . [
59%]
mayavi/tests/test_streamline.py .... [
60%]
mayavi/tests/test_text3d.py ... [
60%]
mayavi/tests/test_threshold_filter.py .... [
61%]
mayavi/tests/test_unstructured_data_reader.py ...s... [
63%]
mayavi/tests/test_user_defined.py ... [
64%]
mayavi/tests/test_volume.py . [
64%]
mayavi/tests/test_vtk_data_source.py ......... [
66%]
mayavi/tests/test_vtk_file_reader.py ...... [
67%]
mayavi/tests/test_vtk_object_source.py ..... [
68%]
mayavi/tests/test_vtk_xml_reader.py ... [
69%]
tvtk/tests/test_array_ext.py .. [
69%]
tvtk/tests/test_array_handler.py ......... [
72%]
tvtk/tests/test_browser.py ...... [
73%]
tvtk/tests/test_class_tree.py ...... [
74%]
tvtk/tests/test_ctf_util.py X. [
75%]
tvtk/tests/test_garbage_collection.py ...F [
76%]
tvtk/tests/test_indenter.py ......... [
78%]
tvtk/tests/test_messenger.py ..... [
79%]
tvtk/tests/test_misc.py ..... [
80%]
tvtk/tests/test_movie_maker.py .... [
81%]
tvtk/tests/test_pyface_utils.py .. [
81%]
tvtk/tests/test_tvtk.py .........s..............s..................... [
92%]
tvtk/tests/test_tvtk_base.py ............. [
95%]
tvtk/tests/test_tvtk_scene.py . [
95%]
tvtk/tests/test_visual.py .......... [
97%]
tvtk/tests/test_vtk_parser.py ........ [
99%]
tvtk/tests/test_wrapper_gen.py ...
[100%]
=================================== FAILURES
===================================
__________________ TestTVTKGarbageCollection.test_tvtk_scene
___________________
tvtk/tests/test_garbage_collection.py:50: in test_tvtk_scene
self.check_object_garbage_collected(create_fn, close_fn)
tvtk/tests/common.py:61: in check_object_garbage_collected
self.assertTrue(object_collected[0])
E IndexError: list index out of range
=============================== warnings summary
===============================
../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258
/usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258:
DeprecationWarning: module 'sre_parse' is deprecated
import sre_parse
../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259
/usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259:
DeprecationWarning: module 'sre_constants' is deprecated
import sre_constants
mayavi/tests/test_composite_data.py: 1 warning
mayavi/tests/test_contour.py: 34 warnings
mayavi/tests/test_image_data_probe.py: 16 warnings
mayavi/tests/test_mlab_integration.py: 4 warnings
mayavi/tests/test_mlab_null_engine.py: 1 warning
mayavi/tests/test_optional_collection.py: 6 warnings
mayavi/tests/test_script_recording.py: 2 warnings
mayavi/tests/test_set_active_attribute.py: 6 warnings
mayavi/tests/test_vtk_data_source.py: 31 warnings
mayavi/tests/test_vtk_xml_reader.py: 21 warnings
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/mayavi/components/contour.py:222:
DeprecationWarning: In the future, lists will no longer be accepted by the
Tuple trait type. Lists should be converted to tuples prior to validation.
self._current_range = rng
mayavi/tests/test_mlab_integration.py::TestMlabNullEngineMisc::test_user_defined_filter
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/tools/tvtk_doc.py:77:
DeprecationWarning: Call to deprecated class vtkOutputWindowCleanup.
(`vtkOutputWindowCleanup` is no longer necessary) -- Deprecated since version
9.3.0.
c = klass()
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
mayavi/tests/test_volume.py::TestVolumeWorksWithProbe::test_volume_works_with_probe
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/mayavi/modules/volume.py:469:
DeprecationWarning: In the future, lists will no longer be accepted by the
Tuple trait type. Lists should be converted to tuples prior to validation.
self.current_range = rng
tvtk/tests/test_array_handler.py::TestArrayHandler::test_arr2cell_array
tvtk/tests/test_array_handler.py::TestArrayHandler::test_arr2cell_array
/usr/lib/python3.13/unittest/case.py:606: DeprecationWarning: `alltrue` is
deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use
`all` instead.
if method() is not None:
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_instantiable
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_traits_can_be_obtained
tvtk/tests/test_tvtk.py::TestTVTKModule::test_no_trait_has_ptr_address_as_value
tvtk/tests/test_tvtk.py::TestTVTKModule::test_trait_with_range
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/tvtk_base.py:575:
DeprecationWarning: Call to deprecated method GetPreserveInputEntityGroups.
(PreserveInputEntityGroups is no longer needed.) -- Deprecated since version
9.3.0.
val = getattr(vtk_obj, getter)()
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_instantiable
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_traits_can_be_obtained
tvtk/tests/test_tvtk.py::TestTVTKModule::test_no_trait_has_ptr_address_as_value
tvtk/tests/test_tvtk.py::TestTVTKModule::test_trait_with_range
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/tvtk_base.py:575:
DeprecationWarning: Call to deprecated method GetOptimizeForRealInput.
(Function has been renamed GetReturnOnesided) -- Deprecated since version 9.3.0.
val = getattr(vtk_obj, getter)()
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_instantiable
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_traits_can_be_obtained
tvtk/tests/test_tvtk.py::TestTVTKModule::test_no_trait_has_ptr_address_as_value
tvtk/tests/test_tvtk.py::TestTVTKModule::test_trait_with_range
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/tvtk_base.py:575:
DeprecationWarning: Call to deprecated method GetNumberOfBlock. (Block
behavior is not controlled using BlockSize and BlockOverlap properties.) --
Deprecated since version 9.3.0.
val = getattr(vtk_obj, getter)()
tvtk/tests/test_vtk_parser.py::TestVTKParser::test_parse_all
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/vtk_parser.py:536:
DeprecationWarning: Call to deprecated method GetPreserveInputEntityGroups.
(PreserveInputEntityGroups is no longer needed.) -- Deprecated since version
9.3.0.
tm[key] = getattr(obj, 'Get%s'%key)()
tvtk/tests/test_vtk_parser.py::TestVTKParser::test_parse_all
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/vtk_parser.py:536:
DeprecationWarning: Call to deprecated method GetOptimizeForRealInput.
(Function has been renamed GetReturnOnesided) -- Deprecated since version 9.3.0.
tm[key] = getattr(obj, 'Get%s'%key)()
tvtk/tests/test_vtk_parser.py::TestVTKParser::test_parse_all
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build/tvtk/vtk_parser.py:713:
DeprecationWarning: Call to deprecated method GetNumberOfBlock. (Block
behavior is not controlled using BlockSize and BlockOverlap properties.) --
Deprecated since version 9.3.0.
default = getattr(obj, 'Get%s' % key)()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=================================== XPASSES
====================================
============================= slowest 20 durations
=============================
5.08s call tvtk/tests/test_tvtk.py::TestTVTKModule::test_trait_with_range
1.93s call tvtk/tests/test_vtk_parser.py::TestVTKParser::test_parse_all
1.39s call
tvtk/tests/test_tvtk.py::TestTVTK::test_contextdevice2d_matrix_api
0.54s call
tvtk/tests/test_tvtk.py::TestTVTKModule::test_import_tvtk_does_not_import_gui
0.31s call
mayavi/tests/test_core_common.py::test_core_common_pyface_import_honors_env_var
0.30s call
mayavi/tests/test_vtk_data_source.py::TestVTKDataSource::test_deepcopied
0.29s call
mayavi/tests/test_mlab_null_engine.py::TestRealMlabNullEngine::test_test_backend_clf
0.24s call
tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_traits_can_be_obtained
0.23s call
tvtk/tests/test_tvtk.py::TestTVTKModule::test_no_trait_has_ptr_address_as_value
0.23s call tvtk/tests/test_tvtk.py::TestTVTKModule::test_all_instantiable
0.22s call tvtk/tests/test_tvtk.py::TestTVTK::test_object_cache
0.21s call
mayavi/tests/test_image_plane_widget.py::TestImagePlaneWidget::test_save_and_restore
0.19s call
mayavi/tests/test_mlab_integration.py::TestMlabModules::test_volume
0.15s call
mayavi/tests/test_vtk_data_source.py::TestVTKDataSource::test_save_and_restore
0.15s call
mayavi/tests/test_contour.py::TestContour::test_save_and_restore
0.13s call
mayavi/tests/test_mlab_integration.py::TestMlabNullEngineMisc::test_user_defined_filter
0.13s call
tvtk/tests/test_garbage_collection.py::TestTVTKGarbageCollection::test_tvtk_scene
0.13s call
mayavi/tests/test_streamline.py::TestStreamline::test_save_and_restore
0.12s call
mayavi/tests/test_filters.py::TestFilters::test_cell_to_point_data
0.12s call mayavi/tests/test_contour.py::TestContour::test_deepcopied
=========================== short test summary info
============================
SKIPPED [1] mayavi/tests/test_extract_grid_filter.py:101: actor.bounds
returns incorrect values
SKIPPED [1] mayavi/tests/test_extract_grid_filter.py:137: actor.bounds
returns incorrect values
SKIPPED [1] mayavi/tests/test_pylab_luts.py:9: mayavi.core.lut_manager is
already loaded in another tests. Can't run this test.
SKIPPED [1] mayavi/tests/test_unstructured_data_reader.py:65: ExodusIIReader
support is disabled for now.
SKIPPED [1] tvtk/tests/test_tvtk.py:710: ContextDevice2D has a subclass. This
may cause the TVTK API to be different from if it had not
SKIPPED [1] tvtk/tests/test_tvtk.py:690: ObjectFactory has a subclass. This
may cause the TVTK API to be different from if it had not
XPASS tvtk/tests/test_ctf_util.py::TestCTFUtil::test_rescale_ctf - Failing on
osmesa / headless tests
FAILED
tvtk/tests/test_garbage_collection.py::TestTVTKGarbageCollection::test_tvtk_scene
= 1 failed, 435 passed, 6 skipped, 1 deselected, 1 xpassed, 148 warnings in
18.15s =
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/build/reproducible-path/mayavi2-4.8.2/.pybuild/cpython3_3.13/build; cd
{build_dir} ; LD_PRELOAD=libgomp.so.1 xvfb-run --auto-servernum
--server-args="-screen 0 1024x768x24" {interpreter} -m pytest -k 'not
test_array2vtk'
Any clues? It's possible that some other cherry-pick in VTK would help,
I suppose, but given the long build times I haven't tried this myself.
I didn't see anything immediately obvious in mayavi or VTK upstream git
repositories; however, this looks like the sort of integration test that
might be quite sensitive to subtle changes in various places.
Thanks,
--
Colin Watson (he/him) [cjwat...@debian.org]
diff -Nru vtk9-9.3.0+dfsg1/debian/changelog vtk9-9.3.0+dfsg1/debian/changelog
--- vtk9-9.3.0+dfsg1/debian/changelog 2024-11-22 10:49:45.000000000 +0000
+++ vtk9-9.3.0+dfsg1/debian/changelog 2025-01-07 13:22:11.000000000 +0000
@@ -1,3 +1,10 @@
+vtk9 (9.3.0+dfsg1-1.2) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Python 3.13 fix for missing dict segfault (closes: #1092083).
+
+ -- Colin Watson <cjwat...@debian.org> Tue, 07 Jan 2025 13:22:11 +0000
+
vtk9 (9.3.0+dfsg1-1.1) unstable; urgency=medium
* Non-maintainer upload.
diff -Nru vtk9-9.3.0+dfsg1/debian/patches/130_py313-missing-dict-segfault.patch
vtk9-9.3.0+dfsg1/debian/patches/130_py313-missing-dict-segfault.patch
--- vtk9-9.3.0+dfsg1/debian/patches/130_py313-missing-dict-segfault.patch
1970-01-01 01:00:00.000000000 +0100
+++ vtk9-9.3.0+dfsg1/debian/patches/130_py313-missing-dict-segfault.patch
2025-01-07 13:21:47.000000000 +0000
@@ -0,0 +1,52 @@
+From: David Gobbi <david.go...@gmail.com>
+Date: Tue, 7 Jan 2025 13:21:44 +0000
+Subject: Python 3.13 fix for missing dict segfault
+
+Python 3.13 removed a safety net from PyModule_Type's tp_init slot
+that created the module's md_dict member if it was NULL. This
+safety net was removed because, since Python 3.11, the md_dict is
+created by tp_new and is never expected to be NULL. So, in our
+own code, we must ensure that tp_new is called before tp_init.
+
+Origin: upstream,
https://gitlab.kitware.com/vtk/vtk/-/commit/675929762a09ad0b40cb2667918a7061c47a418c
+Bug-Debian: https://bugs.debian.org/1092083
+Last-Update: 2025-01-07
+---
+ Wrapping/PythonCore/PyVTKNamespace.cxx | 6 ++++--
+ Wrapping/PythonCore/PyVTKTemplate.cxx | 6 ++++--
+ 2 files changed, 8 insertions(+), 4 deletions(-)
+
+diff --git a/Wrapping/PythonCore/PyVTKNamespace.cxx
b/Wrapping/PythonCore/PyVTKNamespace.cxx
+index bed60dc..c182308 100644
+--- a/Wrapping/PythonCore/PyVTKNamespace.cxx
++++ b/Wrapping/PythonCore/PyVTKNamespace.cxx
+@@ -112,8 +112,10 @@ PyObject* PyVTKNamespace_New(const char* name)
+ {
+ // make sure python has readied the type object
+ PyType_Ready(&PyVTKNamespace_Type);
+- // call the allocator provided by python for this type
+- self = PyVTKNamespace_Type.tp_alloc(&PyVTKNamespace_Type, 0);
++ // call the superclass new function
++ PyObject* empty = PyTuple_New(0);
++ self = PyVTKNamespace_Type.tp_base->tp_new(&PyVTKNamespace_Type, empty,
nullptr);
++ Py_DECREF(empty);
+ // call the superclass init function
+ PyObject* pyname = PyUnicode_FromString(name);
+ PyObject* args = PyTuple_Pack(1, pyname);
+diff --git a/Wrapping/PythonCore/PyVTKTemplate.cxx
b/Wrapping/PythonCore/PyVTKTemplate.cxx
+index 26421f6..e7780bf 100644
+--- a/Wrapping/PythonCore/PyVTKTemplate.cxx
++++ b/Wrapping/PythonCore/PyVTKTemplate.cxx
+@@ -761,8 +761,10 @@ PyObject* PyVTKTemplate_New(const char* name, const char*
docstring)
+ {
+ // make sure python has readied the type object
+ PyType_Ready(&PyVTKTemplate_Type);
+- // call the allocator provided by python for this type
+- PyObject* self = PyVTKTemplate_Type.tp_alloc(&PyVTKTemplate_Type, 0);
++ // call the superclass new function
++ PyObject* empty = PyTuple_New(0);
++ PyObject* self = PyVTKTemplate_Type.tp_base->tp_new(&PyVTKTemplate_Type,
empty, nullptr);
++ Py_DECREF(empty);
+ // call the superclass init function
+ PyObject* pyname = PyUnicode_FromString(name);
+ PyObject* pydoc = PyUnicode_FromString(docstring);
diff -Nru vtk9-9.3.0+dfsg1/debian/patches/series
vtk9-9.3.0+dfsg1/debian/patches/series
--- vtk9-9.3.0+dfsg1/debian/patches/series 2024-06-06 06:04:23.000000000
+0100
+++ vtk9-9.3.0+dfsg1/debian/patches/series 2025-01-07 13:21:47.000000000
+0000
@@ -12,3 +12,4 @@
99_fix_ftbfs.patch
100_add_missing_gl_header.patch
121_add_support_for_loong64.patch
+130_py313-missing-dict-segfault.patch
