├── .coveragerc ├── .full_test.sh ├── .github └── workflows │ ├── python-package-conda.yml │ └── sdist.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── .travis.yml ├── CMakeLists.txt ├── CONTRIBUTING.md ├── INSTALL.md ├── LICENSE ├── Makefile ├── README.md ├── ROADMAP.md ├── changelog.md ├── cmake ├── FindNumPy.cmake ├── FindPythonLibsNew.cmake └── FindSciPy.cmake ├── doc ├── API.rst ├── Makefile ├── _config.yml ├── _toc.yml ├── bibliography │ └── tyssue.bib ├── conf.py ├── examples │ ├── before_apoptosis.hf5 │ ├── small_ellipsoid.hf5 │ └── small_hexagonal.hf5 ├── illus │ ├── 3D_STORM_format.png │ ├── Figure1.png │ ├── Figure1.svg │ ├── Figure1_v0.svg │ ├── Figure2.png │ ├── Figure2.svg │ ├── IH_transition.png │ ├── IH_transition.svg │ ├── banner.png │ ├── banner.svg │ ├── before.png │ ├── before_apoptosis.png │ ├── class_diagram.png │ ├── class_diagram.svg │ ├── class_diagram_continuous.svg │ ├── class_diagram_poly.svg │ ├── class_diagramm_poly.png │ ├── deformation_rate.svg │ ├── ellipsis.png │ ├── ellipsoid.png │ ├── energies.png │ ├── face_subdivision.png │ ├── face_subdivision.svg │ ├── figure1.jpg │ ├── fold_11.png │ ├── fold_12.png │ ├── geometrie_master.svg │ ├── geometry.png │ ├── in_out_decomposition.svg │ ├── logo.png │ ├── logo.svg │ ├── maille_elementaire.png │ ├── maille_elementaire.svg │ ├── minimal_eptm_2D.png │ ├── minimal_eptm_2D.svg │ ├── monolayer.png │ ├── monolayer_t1_transition.png │ ├── multi-layers.png │ ├── objects_architecture.png │ ├── objects_architecture.svg │ ├── oldroyd.svg │ ├── post_forces.png │ ├── prev_forces.png │ ├── retinal_neuroepithlium.png │ ├── rheology_model.png │ ├── self-crossing.svg │ ├── single_apopto_000.png │ ├── single_apopto_001.png │ ├── single_apopto_002.png │ ├── single_apopto_003.png │ ├── single_apopto_004.png │ ├── single_apopto_005.png │ ├── single_apopto_006.png │ ├── single_apopto_007.png │ ├── single_apopto_008.png │ ├── single_apopto_009.png │ ├── single_apopto_010.png │ ├── single_apopto_011.png │ ├── single_apopto_012.png │ ├── single_apopto_013.png │ ├── single_apopto_014.png │ ├── single_apopto_015.png │ ├── single_apopto_016.png │ ├── single_apopto_017.png │ ├── single_apopto_018.png │ ├── single_apopto_019.png │ ├── single_apopto_020.png │ ├── single_apopto_021.png │ ├── single_apopto_022.png │ ├── single_apopto_023.png │ ├── slice.png │ ├── sorted_edges.png │ ├── sorted_edges.svg │ ├── t1_transition.png │ ├── t1_transition.svg │ ├── test_apopto_102.545.png │ ├── test_apopto_122.182.png │ ├── test_apopto_141.818.png │ ├── test_apopto_161.455.png │ ├── test_apopto_181.091.png │ ├── test_apopto_200.727.png │ ├── test_apopto_220.364.png │ ├── test_apopto_24.000.png │ ├── test_apopto_240.000.png │ ├── test_apopto_43.636.png │ ├── test_apopto_63.273.png │ ├── test_apopto_82.909.png │ ├── test_pola.blend │ ├── test_pola.obj │ ├── test_pola.png │ ├── tissue_3d.png │ ├── two_models.png │ ├── two_models.svg │ ├── tyssue_data_management.png │ ├── tyssue_data_management.svg │ ├── tyssue_storm.png │ ├── vertex_rheology.png │ └── vertex_split.png ├── index.md ├── requirements.txt └── source │ ├── modules.rst │ ├── setup.rst │ ├── tests.rst │ ├── tyssue.behaviors.monolayer.rst │ ├── tyssue.behaviors.rst │ ├── tyssue.behaviors.sheet.rst │ ├── tyssue.collisions.cpp.rst │ ├── tyssue.collisions.rst │ ├── tyssue.config.core.rst │ ├── tyssue.config.draw.rst │ ├── tyssue.config.dynamics.rst │ ├── tyssue.config.geometry.rst │ ├── tyssue.config.rst │ ├── tyssue.config.solvers.rst │ ├── tyssue.config.stores.rst │ ├── tyssue.config.subdiv.rst │ ├── tyssue.core.rst │ ├── tyssue.draw.rst │ ├── tyssue.dynamics.rst │ ├── tyssue.generation.cpp.rst │ ├── tyssue.generation.rst │ ├── tyssue.geometry.rst │ ├── tyssue.io.rst │ ├── tyssue.particles.rst │ ├── tyssue.rst │ ├── tyssue.solvers.rst │ ├── tyssue.stores.rst │ ├── tyssue.topology.rst │ └── tyssue.utils.rst ├── docs_environment.yml ├── environment.yml ├── notebooks └── basic_usage_quick.ipynb ├── paper.bib ├── paper.md ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── src ├── main.cpp ├── tyssue │ ├── __init__.py │ ├── behaviors │ │ ├── __init__.py │ │ ├── event_manager.py │ │ ├── monolayer │ │ │ ├── __init__.py │ │ │ ├── actions.py │ │ │ ├── apoptosis_events.py │ │ │ ├── basic_events.py │ │ │ └── delamination_events.py │ │ └── sheet │ │ │ ├── __init__.py │ │ │ ├── actions.py │ │ │ ├── apoptosis_events.py │ │ │ ├── basic_events.py │ │ │ └── delamination_events.py │ ├── collisions │ │ ├── __init__.py │ │ ├── cpp │ │ │ └── __init__.py │ │ ├── intersection.py │ │ └── solvers.py │ ├── config │ │ ├── __init__.py │ │ ├── core │ │ │ ├── __init__.py │ │ │ └── core.json │ │ ├── draw │ │ │ ├── __init__.py │ │ │ └── sheet.json │ │ ├── dynamics │ │ │ ├── __init__.py │ │ │ ├── bulk_qs.json │ │ │ ├── ccmesh.json │ │ │ ├── plane_qs.json │ │ │ ├── sheet_qs.json │ │ │ └── sheet_qs_anchor.json │ │ ├── geometry │ │ │ ├── __init__.py │ │ │ ├── bulk.json │ │ │ ├── cylindrical_sheet.json │ │ │ ├── flat_sheet.json │ │ │ ├── planar.json │ │ │ ├── rod_sheet.json │ │ │ ├── sheet.json │ │ │ └── spherical_sheet.json │ │ ├── json_parser.py │ │ ├── solvers │ │ │ ├── __init__.py │ │ │ ├── minimize.json │ │ │ └── sheet.json │ │ ├── stores │ │ │ ├── __init__.py │ │ │ └── planar_periodic8x8.json │ │ └── subdiv │ │ │ ├── __init__.py │ │ │ └── bulk.json │ ├── core │ │ ├── __init__.py │ │ ├── history.py │ │ ├── lateralsheet.py │ │ ├── monolayer.py │ │ ├── multisheet.py │ │ ├── objects.py │ │ └── sheet.py │ ├── draw │ │ ├── __init__.py │ │ ├── ipv_draw.py │ │ ├── plt_draw.py │ │ ├── tyssue-logo.svg │ │ └── vispy_draw.py │ ├── dynamics │ │ ├── __init__.py │ │ ├── apoptosis_model.py │ │ ├── base_gradients.py │ │ ├── bulk_gradients.py │ │ ├── bulk_model.py │ │ ├── effectors.py │ │ ├── factory.py │ │ ├── planar_gradients.py │ │ ├── planar_vertex_model.py │ │ ├── sheet_gradients.py │ │ ├── sheet_vertex_model.py │ │ └── units.py │ ├── generation │ │ ├── __init__.py │ │ ├── cpp │ │ │ └── __init__.py │ │ ├── from_voronoi.py │ │ ├── hexagonal_grids.py │ │ ├── modifiers.py │ │ ├── shapes.py │ │ └── utils.py │ ├── geometry │ │ ├── __init__.py │ │ ├── base_geometry.py │ │ ├── bulk_geometry.py │ │ ├── multisheetgeometry.py │ │ ├── planar_geometry.py │ │ ├── sheet_geometry.py │ │ └── utils.py │ ├── io │ │ ├── __init__.py │ │ ├── csv.py │ │ ├── hdf5.py │ │ ├── meshes.py │ │ ├── obj.py │ │ ├── utils.py │ │ └── zarr.py │ ├── particles │ │ ├── __init__.py │ │ └── point_cloud.py │ ├── solvers │ │ ├── __init__.py │ │ ├── base.py │ │ ├── isotropic_solver.py │ │ ├── quasistatic.py │ │ ├── sheet_vertex_solver.py │ │ └── viscous.py │ ├── stores │ │ ├── 15_cells_patch.hf5 │ │ ├── __init__.py │ │ ├── before_apoptosis.hf5 │ │ ├── planar_periodic8x8.hf5 │ │ ├── rod_sheet.hf5 │ │ ├── sheet6x5.hf5 │ │ ├── small_ellipsoid.hf5 │ │ ├── small_hexagonal.hf5 │ │ ├── small_hexagonal_snaped.hf5 │ │ ├── with_4sided_cell.hf5 │ │ └── with_pinch.hf5 │ ├── topology │ │ ├── __init__.py │ │ ├── base_topology.py │ │ ├── bulk_topology.py │ │ ├── monolayer_topology.py │ │ └── sheet_topology.py │ └── utils │ │ ├── __init__.py │ │ ├── connectivity.py │ │ ├── decorators.py │ │ ├── testing.py │ │ ├── utils.py │ │ └── widgets.py └── tyssue_cpp │ ├── __init__.py │ ├── c_collisions.cpp │ └── mesh_generation.cpp └── tests ├── behaviors ├── test_monolayer_events.py └── test_sheet_events.py ├── collisions └── test_sheet_collision.py ├── config ├── test_config.json └── test_json_parser.py ├── core ├── test_history.py ├── test_lateralsheet.py ├── test_monolayer.py ├── test_multisheet.py └── test_objects.py ├── draw ├── test_plt.py ├── test_vispy.py └── test_volume.py ├── dynamics ├── test_apoptosis_model.py ├── test_bulk_model.py ├── test_effectors.py ├── test_factory.py ├── test_gradients.py └── test_sheet_model.py ├── generation ├── test_generation.py ├── test_hexgrid.py └── test_shapes.py ├── geometry ├── test_bulkgeometry.py ├── test_geometry.py ├── 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