spatial-model-editor/spatial-model-editor-latest.zip
spatial-model-editor-spatial-model-editor-413e436
.clang-format
4.2 kB
.cmake-format.yaml
8.3 kB
.github
CONTRIBUTING.md
2.2 kB
ISSUE_TEMPLATE
bug_report.md
323 Bytes
feature_request.md
365 Bytes
workflows
quality.yml
2.3 kB
release.yml
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wheels.yml
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.gitignore
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.gitmodules
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.pre-commit-config.yaml
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.readthedocs.yml
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CHANGELOG.md
13.8 kB
CMakeLists.txt
3.3 kB
LICENSE
1.1 kB
README.md
6.4 kB
benchmark
CMakeLists.txt
691 Bytes
README.md
312 Bytes
bench.cpp
506 Bytes
bench.hpp
3.1 kB
benchmark.cpp
5.6 kB
geometry.png
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mesh.png
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model.png
20.3 kB
pixel.cpp
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plot.py
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simulate.png
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update_benchmarks.sh
190 Bytes
ci
README.md
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asan.sh
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codecov.sh
3.9 kB
getlibs.sh
545 Bytes
linux-gui.sh
1.9 kB
linux-install.sh
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linux-wheels.sh
471 Bytes
macos-gui.sh
1.7 kB
macos-wheels.sh
997 Bytes
pre-commit.sh
350 Bytes
set-latest-version.sh
531 Bytes
sonar.sh
2.8 kB
tsan.sh
1.3 kB
ubsan.sh
1.5 kB
windows-gui.sh
1.8 kB
windows-wheels.sh
1.6 kB
cli
CMakeLists.txt
881 Bytes
spatial-cli.cpp
429 Bytes
src
CMakeLists.txt
158 Bytes
cli_params.cpp
2.9 kB
cli_params.hpp
468 Bytes
cli_params_t.cpp
685 Bytes
cli_simulate.cpp
2.1 kB
cli_simulate.hpp
129 Bytes
cli_simulate_t.cpp
2.2 kB
cmake
Findtbb.cmake
507 Bytes
checkSpatialSBML.cpp
262 Bytes
checkSymEngineLLVM.cpp
177 Bytes
codecov.yml
193 Bytes
docs
Doxyfile.in
116.4 kB
Makefile
223 Bytes
README.md
1.5 kB
_templates
autosummary
base.rst
106 Bytes
class.rst
557 Bytes
module.rst
1.1 kB
conf.py
2.7 kB
developer
common
inc.rst
254 Bytes
src.rst
8 Bytes
core.rst
1.2 kB
mesh
inc.rst
54 Bytes
src.rst
535 Bytes
model
inc.rst
1.0 kB
src.rst
8 Bytes
simulate
inc.rst
692 Bytes
src.rst
561 Bytes
tests
diffusion.rst
1.9 kB
tests.rst
209 Bytes
img
icon-docs.png
1.5 kB
icon-linux.png
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icon-osx.png
1.6 kB
icon-windows.png
1.1 kB
mesh.png
153.4 kB
index.rst
762 Bytes
peek.sh
349 Bytes
quickstart
get-started.rst
1.5 kB
img
concentration.apng
256.3 kB
geometry.apng
495.4 kB
mesh.apng
3.2 MB
model.apng
63.3 kB
simulation.apng
1.3 MB
simulation.png
48.5 kB
import-geometry.rst
921 Bytes
import-model.rst
380 Bytes
mesh.rst
815 Bytes
reactions.rst
1.5 kB
run-simulation.rst
965 Bytes
species.rst
571 Bytes
reference
CHANGELOG.md
18 Bytes
cli.rst
3.4 kB
dune.rst
3.0 kB
img
convergence.plot
846 Bytes
convergence.png
7.9 kB
dune_options.png
36.6 kB
embedded.plot
624 Bytes
embedded.png
8.5 kB
mesh_interiorpoint_1.apng
5.4 kB
mesh_interiorpoint_2.apng
2.8 kB
mesh_interiorpoint_3.apng
4.2 kB
mesh_original_image.png
9.4 kB
mesh_pixel_contours.png
12.4 kB
mesh_simplify_lines.png
25.1 kB
mesh_split_edge_contours.png
11.7 kB
mesh_triangulate_0.png
206.7 kB
mesh_triangulate_1.png
491.6 kB
mesh_triangulate_2.png
524.9 kB
mesh_triangulate_3.png
590.7 kB
pixel_options.png
44.5 kB
rk1
1.7 kB
rk2
1.7 kB
rk3
1.6 kB
rk4
1.2 kB
runtime.plot
822 Bytes
runtime.png
7.8 kB
license.rst
748 Bytes
maths.rst
2.0 kB
mesh.rst
6.9 kB
pixel.rst
8.9 kB
source-code.rst
447 Bytes
units.pdf
108.6 kB
units.rst
1.4 kB
units.tex
5.8 kB
requirements.txt
247 Bytes
sme
api.rst
115 Bytes
notebooks
getting_started.ipynb
7.0 kB
simulating.ipynb
6.0 kB
visualization.ipynb
5.2 kB
notebooks.rst
155 Bytes
sme.rst
847 Bytes
ext
CLI11
getdeps.sh
315 Bytes
pybind11
setup.py
4.7 kB
sme
CMakeLists.txt
731 Bytes
README.md
1.4 kB
requirements.txt
6 Bytes
sme.cpp
804 Bytes
src
CMakeLists.txt
334 Bytes
sme_common.cpp
925 Bytes
sme_common.hpp
2.5 kB
sme_compartment.cpp
3.6 kB
sme_compartment.hpp
767 Bytes
sme_exception.cpp
426 Bytes
sme_exception.hpp
493 Bytes
sme_membrane.cpp
1.8 kB
sme_membrane.hpp
666 Bytes
sme_model.cpp
17.9 kB
sme_model.hpp
1.7 kB
sme_module.cpp
3.1 kB
sme_module.hpp
292 Bytes
sme_parameter.cpp
2.0 kB
sme_parameter.hpp
625 Bytes
sme_reaction.cpp
1.8 kB
sme_reaction.hpp
632 Bytes
sme_reactionparameter.cpp
2.4 kB
sme_reactionparameter.hpp
773 Bytes
sme_simulationresult.cpp
7.0 kB
sme_simulationresult.hpp
546 Bytes
sme_species.cpp
2.0 kB
sme_species.hpp
635 Bytes
test
__init__.py
0 Bytes
concave-cell-nucleus-100x100.png
359 Bytes
modified-concave-cell-nucleus-100x100.png
348 Bytes
sme_doctest.py
87 Bytes
test_compartment.py
1.3 kB
test_membrane.py
1.4 kB
test_model.py
8.6 kB
test_module.py
205 Bytes
test_parameter.py
1.2 kB
test_reaction.py
2.0 kB
test_reactionparameter.py
1.3 kB
test_species.py
1.1 kB
sonar-project.properties
517 Bytes
src
CMakeLists.txt
893 Bytes
core
CMakeLists.txt
4.6 kB
cmake
smeConfig.cmake.in
663 Bytes
common
CMakeLists.txt
300 Bytes
inc
logger.hpp
97 Bytes
serialization.hpp
564 Bytes
symbolic.hpp
2.9 kB
tiff.hpp
1.1 kB
utils.hpp
10.3 kB
version.hpp
122 Bytes
src
CMakeLists.txt
489 Bytes
logger.cpp
22 Bytes
logger_t.cpp
180 Bytes
serialization.cpp
4.4 kB
serialization_t.cpp
6.9 kB
symbolic.cpp
12.6 kB
symbolic_t.cpp
17.7 kB
tiff.cpp
8.5 kB
tiff_t.cpp
1.1 kB
utils.cpp
4.7 kB
utils_t.cpp
6.9 kB
version.cpp.in
139 Bytes
mesh
CMakeLists.txt
304 Bytes
inc
mesh.hpp
7.2 kB
mesh_types.hpp
204 Bytes
src
CMakeLists.txt
991 Bytes
boundary.cpp
6.0 kB
boundary.hpp
2.2 kB
boundary_bench.cpp
702 Bytes
boundary_t.cpp
9.1 kB
contour_map.cpp
1.7 kB
contour_map.hpp
632 Bytes
contour_map_t.cpp
2.7 kB
interior_point.cpp
4.6 kB
interior_point.hpp
453 Bytes
interior_point_bench.cpp
344 Bytes
interior_point_t.cpp
564 Bytes
line_simplifier.cpp
10.7 kB
line_simplifier.hpp
2.5 kB
line_simplifier_bench.cpp
487 Bytes
line_simplifier_t.cpp
7.8 kB
mesh.cpp
12.3 kB
mesh_bench.cpp
871 Bytes
mesh_t.cpp
9.2 kB
mesh_utils.cpp
594 Bytes
mesh_utils.hpp
286 Bytes
mesh_utils_t.cpp
1.1 kB
pixel_corner_iterator.cpp
2.4 kB
pixel_corner_iterator.hpp
2.2 kB
pixel_corner_iterator_t.cpp
1.6 kB
triangulate.cpp
7.6 kB
triangulate.hpp
1.8 kB
triangulate_bench.cpp
548 Bytes
triangulate_common.cpp
3.8 kB
triangulate_common.hpp
1.0 kB
triangulate_t.cpp
4.8 kB
model
CMakeLists.txt
384 Bytes
inc
geometry.hpp
4.3 kB
model.hpp
4.5 kB
model_compartments.hpp
2.4 kB
model_events.hpp
1.6 kB
model_functions.hpp
1.3 kB
model_geometry.hpp
2.5 kB
model_math.hpp
961 Bytes
model_membranes.hpp
2.0 kB
model_parameters.hpp
1.8 kB
model_reactions.hpp
2.6 kB
model_settings.hpp
2.6 kB
model_species.hpp
3.7 kB
model_units.hpp
3.5 kB
xml_annotation.hpp
296 Bytes
src
CMakeLists.txt
1.4 kB
geometry.cpp
11.3 kB
geometry_analytic.cpp
6.1 kB
geometry_analytic.hpp
439 Bytes
geometry_analytic_t.cpp
1.5 kB
geometry_bench.cpp
2.0 kB
geometry_parametric.cpp
7.6 kB
geometry_parametric.hpp
1.5 kB
geometry_sampled_field.cpp
10.8 kB
geometry_sampled_field.hpp
738 Bytes
geometry_t.cpp
8.0 kB
id.cpp
1.7 kB
id.hpp
569 Bytes
id_t.cpp
2.4 kB
model.cpp
10.0 kB
model_bench.cpp
543 Bytes
model_compartments.cpp
16.0 kB
model_compartments_t.cpp
15.9 kB
model_events.cpp
11.9 kB
model_events_t.cpp
8.3 kB
model_functions.cpp
8.6 kB
model_functions_t.cpp
3.7 kB
model_geometry.cpp
17.3 kB
model_geometry_t.cpp
5.9 kB
model_math.cpp
2.2 kB
model_math_t.cpp
4.0 kB
model_membranes.cpp
9.7 kB
model_membranes_t.cpp
2.8 kB
model_membranes_util.cpp
3.8 kB
model_membranes_util.hpp
1.3 kB
model_membranes_util_bench.cpp
365 Bytes
model_membranes_util_t.cpp
4.5 kB
model_parameters.cpp
15.2 kB
model_parameters_t.cpp
6.5 kB
model_reactions.cpp
26.3 kB
model_reactions_t.cpp
9.9 kB
model_species.cpp
28.0 kB
model_species_t.cpp
18.7 kB
model_t.cpp
47.8 kB
model_units.cpp
10.5 kB
model_units_t.cpp
5.3 kB
sbml_math.cpp
7.3 kB
sbml_math.hpp
1.7 kB
sbml_utils.cpp
8.0 kB
sbml_utils.hpp
1.5 kB
validation.cpp
3.2 kB
validation.hpp
369 Bytes
xml_annotation.cpp
2.3 kB
xml_annotation_t.cpp
4.1 kB
xml_legacy_annotation.cpp
6.1 kB
xml_legacy_annotation.hpp
1.2 kB
xml_legacy_annotation_t.cpp
4.0 kB
resources
CMakeLists.txt
43 Bytes
concentration
gradient-100x100.png
6.7 kB
one-blob-100x100.png
823 Bytes
three-blobs-100x100.png
2.0 kB
two-blobs-100x100.png
1.3 kB
white-noise-100x100.png
13.8 kB
white-noise-blurred-100x100.png
7.2 kB
white-noise2-100x100.png
13.8 kB
geometry
circle-100x100.png
232 Bytes
concave-cell-nucleus-100x100.png
359 Bytes
concave-cell-nucleus-membranes-200x200.png
7.8 kB
filled-donut-100x100.png
382 Bytes
four-compartments-150x100.png
4.4 kB
liver-cells-200x100.png
1.2 kB
one-blob-100x100.png
209 Bytes
single-liver-cell-180x140.png
611 Bytes
single-pixels-3x1.png
75 Bytes
two-blobs-100x100.png
321 Bytes
icon
create_icon.sh
179 Bytes
icon.ico
97.9 kB
icon128.png
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icon.iconset
icon_128x128.png
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icon_128x128@2x.png
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icon_16x16.png
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icon_16x16@2x.png
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icon_256x256.png
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icon_256x256@2x.png
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icon_32x32.png
1.3 kB
icon_32x32@2x.png
2.2 kB
icon_512x512.png
16.0 kB
icon_512x512@2x.png
34.3 kB
models
ABtoC.xml
179.3 kB
NFkappaB.xml
146.6 kB
brusselator-model.xml
177.7 kB
circadian-clock.xml
304.1 kB
gray-scott
43.4 kB
gray-scott.xml
177.8 kB
liver-cells.xml
287.9 kB
liver-simplified-non-spatial.xml
81.9 kB
liver-simplified.xml
387.0 kB
single-compartment-diffusion.xml
160.8 kB
very-simple-model.xml
138.1 kB
resources.qrc
1.2 kB
simulate
CMakeLists.txt
259 Bytes
inc
duneconverter.hpp
1.4 kB
pde.hpp
2.8 kB
simulate.hpp
4.1 kB
simulate_data.hpp
1.1 kB
simulate_options.hpp
3.0 kB
src
CMakeLists.txt
902 Bytes
basesim.cpp
23 Bytes
basesim.hpp
650 Bytes
dune_headers.hpp
1.8 kB
duneconverter.cpp
17.4 kB
duneconverter_bench.cpp
371 Bytes
duneconverter_impl.cpp
3.2 kB
duneconverter_impl.hpp
672 Bytes
duneconverter_impl_t.cpp
3.7 kB
duneconverter_t.cpp
6.1 kB
dunefunction.cpp
28 Bytes
dunefunction.hpp
3.6 kB
dunefunction_t.cpp
6.9 kB
dunegrid.cpp
24 Bytes
dunegrid.hpp
4.5 kB
dunegrid_t.cpp
2.8 kB
duneini.cpp
1.8 kB
duneini.hpp
1.2 kB
duneini_t.cpp
1.1 kB
dunesim.cpp
12.3 kB
dunesim.hpp
2.2 kB
dunesim_impl.cpp
920 Bytes
dunesim_impl.hpp
1.3 kB
dunesim_impl_coupled.cpp
36 Bytes
dunesim_impl_coupled.hpp
2.8 kB
dunesim_impl_independent.cpp
40 Bytes
dunesim_impl_independent.hpp
3.5 kB
dunesim_t.cpp
3.6 kB
pde.cpp
8.1 kB
pde_t.cpp
6.0 kB
pixelsim.cpp
14.7 kB
pixelsim.hpp
2.4 kB
pixelsim_impl.cpp
19.4 kB
pixelsim_impl.hpp
6.3 kB
simulate.cpp
21.7 kB
simulate_bench.cpp
1.2 kB
simulate_data.cpp
685 Bytes
simulate_data_t.cpp
2.1 kB
simulate_options.cpp
1.2 kB
simulate_options_t.cpp
1.7 kB
simulate_t.cpp
77.2 kB
gui
CMakeLists.txt
808 Bytes
dialogs
CMakeLists.txt
904 Bytes
dialogabout.cpp
4.7 kB
dialogabout.hpp
267 Bytes
dialogabout.ui
5.4 kB
dialogabout_t.cpp
478 Bytes
dialoganalytic.cpp
7.5 kB
dialoganalytic.hpp
1.5 kB
dialoganalytic.ui
4.9 kB
dialoganalytic_t.cpp
3.9 kB
dialogconcentrationimage.cpp
12.5 kB
dialogconcentrationimage.hpp
1.6 kB
dialogconcentrationimage.ui
10.8 kB
dialogconcentrationimage_t.cpp
11.0 kB
dialogcoordinates.cpp
767 Bytes
dialogcoordinates.hpp
426 Bytes
dialogcoordinates.ui
2.2 kB
dialogcoordinates_t.cpp
572 Bytes
dialogdisplayoptions.cpp
6.3 kB
dialogdisplayoptions.hpp
1.2 kB
dialogdisplayoptions.ui
4.3 kB
dialogdisplayoptions_t.cpp
8.1 kB
dialogeditunit.cpp
3.0 kB
dialogeditunit.hpp
910 Bytes
dialogeditunit.ui
3.0 kB
dialogeditunit_t.cpp
2.2 kB
dialogexport.cpp
3.3 kB
dialogexport.hpp
830 Bytes
dialogexport.ui
3.3 kB
dialogexport_t.cpp
5.1 kB
dialoggeometryimage.cpp
10.4 kB
dialoggeometryimage.hpp
1.6 kB
dialoggeometryimage.ui
8.5 kB
dialoggeometryimage_t.cpp
9.0 kB
dialogimage.cpp
657 Bytes
dialogimage.hpp
399 Bytes
dialogimage.ui
1.9 kB
dialogimage_t.cpp
579 Bytes
dialogimageslice.cpp
5.2 kB
dialogimageslice.hpp
1.1 kB
dialogimageslice.ui
5.2 kB
dialogimageslice_t.cpp
3.7 kB
dialogsimulationoptions.cpp
9.6 kB
dialogsimulationoptions.hpp
1.4 kB
dialogsimulationoptions.ui
18.0 kB
dialogsimulationoptions_t.cpp
5.1 kB
dialogunits.cpp
5.0 kB
dialogunits.hpp
835 Bytes
dialogunits.ui
6.7 kB
dialogunits_t.cpp
2.9 kB
guiutils.cpp
4.5 kB
guiutils.hpp
696 Bytes
guiutils_t.cpp
722 Bytes
mainwindow.cpp
21.1 kB
mainwindow.hpp
2.4 kB
mainwindow.ui
18.7 kB
mainwindow_t.cpp
13.8 kB
tabs
CMakeLists.txt
511 Bytes
tabevents.cpp
8.3 kB
tabevents.hpp
961 Bytes
tabevents.ui
11.2 kB
tabevents_t.cpp
8.6 kB
tabfunctions.cpp
6.7 kB
tabfunctions.hpp
939 Bytes
tabfunctions.ui
11.2 kB
tabfunctions_t.cpp
9.6 kB
tabgeometry.cpp
19.9 kB
tabgeometry.hpp
1.8 kB
tabgeometry.ui
21.6 kB
tabgeometry_t.cpp
14.6 kB
tabparameters.cpp
4.7 kB
tabparameters.hpp
792 Bytes
tabparameters.ui
8.9 kB
tabparameters_t.cpp
5.2 kB
tabreactions.cpp
17.2 kB
tabreactions.hpp
1.7 kB
tabreactions.ui
15.3 kB
tabreactions_t.cpp
10.1 kB
tabsimulate.cpp
15.0 kB
tabsimulate.hpp
1.9 kB
tabsimulate.ui
4.3 kB
tabsimulate_t.cpp
5.9 kB
tabspecies.cpp
14.2 kB
tabspecies.hpp
1.4 kB
tabspecies.ui
20.0 kB
tabspecies_t.cpp
12.2 kB
widgets
CMakeLists.txt
372 Bytes
plotwrapper.cpp
6.4 kB
plotwrapper.hpp
1.1 kB
plotwrapper_t.cpp
3.5 kB
qlabelmousetracker.cpp
9.4 kB
qlabelmousetracker.hpp
2.6 kB
qlabelmousetracker_t.cpp
7.4 kB
qlabelslice.cpp
4.4 kB
qlabelslice.hpp
1.9 kB
qlabelslice_t.cpp
4.9 kB
qplaintextmathedit.cpp
16.2 kB
qplaintextmathedit.hpp
2.7 kB
qplaintextmathedit_t.cpp
10.6 kB
icon.rc
63 Bytes
icon.svg
5.5 kB
icon.xcf
5.5 kB
spatial-model-editor.cpp
1.1 kB
test
CMakeLists.txt
2.1 kB
README.md
1.4 kB
main.cpp
782 Bytes
resources
16bit_gray.tif
20.2 kB
8bit_gray_3x.tif
1.1 kB
geometry
cell.png
3.5 kB
gt1.png
662 Bytes
gt10.png
543 Bytes
gt11.png
640 Bytes
gt12.png
520 Bytes
gt13.png
522 Bytes
gt14.png
571 Bytes
gt15.png
738 Bytes
gt16.png
556 Bytes
gt17.png
597 Bytes
gt18.png
567 Bytes
gt19.png
536 Bytes
gt2.png
553 Bytes
gt20.png
572 Bytes
gt3.png
541 Bytes
gt4.png
560 Bytes
gt5.png
715 Bytes
gt6.png
697 Bytes
gt7.png
576 Bytes
gt8.png
2.9 kB
gt9.png
687 Bytes
potato_alpha_channel.png
2.1 kB
models
ABtoC-invalid-annotation.xml
178.6 kB
ABtoC-v1.0.9.xml
172.6 kB
analytic_2d.xml
11.1 kB
analytic_3d.xml
21.5 kB
example2D.xml
69.5 kB
fish_300x300.xml
40.2 kB
invalid-dune-names.xml
5.5 kB
membrane-reaction-circle.xml
628.1 kB
membrane-reaction-pixels.xml
9.7 kB
non-spatial-multi-compartment.xml
15.4 kB
single-pixel-meshing.xml
10.7 kB
small-single-compartment-diffusion.xml
9.4 kB
txy.xml
132.3 kB
very-simple-model-non-spatial.xml
7.8 kB
very-simple-model-uint8.xml
55.5 kB
weird-units.xml
2.0 kB
yeast-glycolysis.xml
40.5 kB
smefiles
brusselator-model-corrupted.sme
210.5 kB
brusselator-model-truncated.sme
213.3 kB
very-simple-model-v0.sme
1.0 MB
very-simple-model-v1.sme
1.1 MB
test_resources.qrc
2.1 kB
test_utils
CMakeLists.txt
185 Bytes
catch_wrapper.cpp
1.0 kB
catch_wrapper.hpp
988 Bytes
math_test_utils.cpp
2.5 kB
math_test_utils.hpp
292 Bytes
model_test_utils.cpp
2.1 kB
model_test_utils.hpp
832 Bytes
qt_test_utils.cpp
7.3 kB
qt_test_utils.hpp
3.5 kB