CITATION.cff
LICENSE
MANIFEST.in
README.md
environment-fenicsx.yml
environment.yml
pyproject.toml
docs/api_stability.md
docs/architecture.md
docs/backend_verification_1_1.md
docs/benchmark_contracts.md
docs/constrained_mixture.md
docs/custom_tissue.md
docs/distributed_unstructured_mixtures.md
docs/fenicsx_verification_environment.md
docs/migration_0_9_to_1_0.md
docs/modeling_scope.md
docs/presets.md
docs/quickstart.md
docs/rc3_hardening_report.md
docs/rc4_release_engineering_report.md
docs/release_checklist.md
docs/release_notes_v1.0.md
docs/release_notes_v1.1.md
docs/roadmap.md
docs/scalable_spatial_mixtures.md
docs/scientific_audit_resolution_v1.0.md
docs/scientific_contracts.md
docs/spatial_constrained_mixtures.md
docs/stable_api_v1.md
docs/units_and_dimensions.md
docs/assets/backend_matched_reference.png
docs/assets/cohort_age_distribution.png
docs/assets/constituent_density_history.png
docs/assets/mixture_stress_history.png
docs/assets/multi_tissue_turnover.png
docs/assets/scalable_cohort_count_history.png
docs/assets/scalable_compression_error_history.png
docs/assets/spatial_mixture_density_history.png
docs/assets/spatial_mixture_final_cohort_count.png
docs/assets/spatial_mixture_final_collagen_density.png
docs/assets/spatial_mixture_final_sigma_xx.png
docs/assets/spatial_mixture_final_total_density.png
docs/assets/spatial_mixture_reaction_history.png
docs/assets/survival_laws.png
docs/assets/universal_constituent_architecture.png
docs/assets/unstructured_3d_density_history.png
docs/assets/unstructured_3d_partition_map.png
docs/assets/unstructured_3d_reference_mesh.png
docs/assets/unstructured_3d_stress_history.png
docs/assets/v1_custom_tissue_material_point_density.png
docs/assets/v1_custom_tissue_spatial_reactions.png
examples/constrained_mixture.py
examples/custom_tissue_definition.py
examples/spatial_constrained_mixture.py
examples/unstructured_3d_mixture.py
notebooks/00_START_HERE.ipynb
notebooks/06_constituent_turnover_and_constrained_mixture.ipynb
notebooks/07_spatial_constrained_mixtures.ipynb
notebooks/08_scalable_spatial_mixtures.ipynb
notebooks/09_distributed_unstructured_mixtures.ipynb
notebooks/10_build_your_own_tissue_model.ipynb
notebooks/11_matched_backend_verification.ipynb
scripts/compare_fenicsx_mpi_results.py
scripts/run_backend_verification.py
scripts/run_fenicsx_mpi_matrix.bat
scripts/run_fenicsx_mpi_matrix.sh
scripts/run_fenicsx_mpi_probe.py
scripts/setup_anaconda_macos_linux.sh
scripts/setup_anaconda_windows.bat
scripts/static_hygiene_audit.py
scripts/verify_environment.py
src/biomechpy/__init__.py
src/biomechpy/__main__.py
src/biomechpy/_metadata.py
src/biomechpy/_version.py
src/biomechpy/api.py
src/biomechpy/architecture.py
src/biomechpy/cli.py
src/biomechpy/compat.py
src/biomechpy/definition.py
src/biomechpy/kinematics.py
src/biomechpy/py.typed
src/biomechpy/state.py
src/biomechpy/typing.py
src/biomechpy/validation.py
src/biomechpy/verification.py
src/biomechpy.egg-info/PKG-INFO
src/biomechpy.egg-info/SOURCES.txt
src/biomechpy.egg-info/dependency_links.txt
src/biomechpy.egg-info/entry_points.txt
src/biomechpy.egg-info/requires.txt
src/biomechpy.egg-info/top_level.txt
src/biomechpy/backends/__init__.py
src/biomechpy/backends/contract.py
src/biomechpy/backends/fenicsx.py
src/biomechpy/backends/numpy_reference.py
src/biomechpy/backends/status.py
src/biomechpy/backends/verification.py
src/biomechpy/benchmarks/__init__.py
src/biomechpy/benchmarks/scalable.py
src/biomechpy/benchmarks/spatial.py
src/biomechpy/benchmarks/turnover.py
src/biomechpy/benchmarks/unstructured3d.py
src/biomechpy/constituents/__init__.py
src/biomechpy/constituents/base.py
src/biomechpy/constituents/cohorts.py
src/biomechpy/data/__init__.py
src/biomechpy/data/backend_verification_contract_v1.json
src/biomechpy/data/benchmark_contracts_v1.json
src/biomechpy/experiments/__init__.py
src/biomechpy/experiments/protocols.py
src/biomechpy/fem/__init__.py
src/biomechpy/fem/assembly.py
src/biomechpy/fem/mesh.py
src/biomechpy/fem/solver.py
src/biomechpy/fem/spatial_mixture.py
src/biomechpy/fem/state.py
src/biomechpy/growth/__init__.py
src/biomechpy/growth/kinematics.py
src/biomechpy/materials/__init__.py
src/biomechpy/materials/base.py
src/biomechpy/materials/fiber.py
src/biomechpy/materials/fiber_reinforced.py
src/biomechpy/materials/neo_hookean.py
src/biomechpy/mixture/__init__.py
src/biomechpy/mixture/model.py
src/biomechpy/mixture/simulation.py
src/biomechpy/mixture/spatial_state.py
src/biomechpy/mixture/spatial_turnover.py
src/biomechpy/mixture/state.py
src/biomechpy/mixture/turnover.py
src/biomechpy/presets/__init__.py
src/biomechpy/presets/tissues.py
src/biomechpy/remodeling/__init__.py
src/biomechpy/remodeling/laws.py
src/biomechpy/remodeling/stimuli.py
src/biomechpy/scalable/__init__.py
src/biomechpy/scalable/checkpoint.py
src/biomechpy/scalable/compression.py
src/biomechpy/scalable/distributed_checkpoint.py
src/biomechpy/scalable/fenicsx.py
src/biomechpy/scalable/packing.py
src/biomechpy/turnover/__init__.py
src/biomechpy/turnover/production.py
src/biomechpy/turnover/survival.py
src/biomechpy/unstructured/__init__.py
src/biomechpy/unstructured/mesh.py
src/biomechpy/unstructured/mixture.py
src/biomechpy/unstructured/partition.py
tests/test_backend_cli_v1_1.py
tests/test_backend_contract_metadata_v1_1.py
tests/test_backend_verification_v1_1.py
tests/test_benchmark_contracts_v1.py
tests/test_checkpoint_restart.py
tests/test_cli_v1.py
tests/test_cohort_compression.py
tests/test_compressed_simulation.py
tests/test_compression_safety_v1_1.py
tests/test_constituents.py
tests/test_core.py
tests/test_current_deformation_roundtrip_v1_1.py
tests/test_distributed_checkpoint.py
tests/test_fem.py
tests/test_fenicsx_source_contract_v1_1.py
tests/test_independent_audit_regressions_v1_1.py
tests/test_mixture_mechanics.py
tests/test_mixture_state.py
tests/test_parameter_validation_v1.py
tests/test_partitioning.py
tests/test_presets.py
tests/test_production.py
tests/test_public_api_v1.py
tests/test_rc3_checkpoint_partition_hardening.py
tests/test_rc3_geometry_hardening.py
tests/test_rc3_protocol_hardening.py
tests/test_scalable_benchmark.py
tests/test_scalable_fenicsx_bridge.py
tests/test_scalable_packing.py
tests/test_scientific_invariants_v1.py
tests/test_simulation.py
tests/test_spatial_benchmark.py
tests/test_spatial_mixture_coupling.py
tests/test_spatial_mixture_fem.py
tests/test_spatial_mixture_state.py
tests/test_spatial_turnover.py
tests/test_survival.py
tests/test_unstructured_3d_mixture.py
tests/test_unstructured_mesh.py