.cargo/config.toml | 2 +- .github/workflows/reuse.yml | 4 - CITATION.cff | 53 ++-- Cargo.toml | 9 +- README.md | 1 + cellular_raza-benchmarks/Cargo.toml | 9 +- cellular_raza-benchmarks/benches/interactions.rs | 104 ++++++++ cellular_raza-benchmarks/src/cell_sorting.rs | 6 +- cellular_raza-building-blocks/Cargo.toml | 4 +- .../src/cell_building_blocks/bacterial_rods.rs | 71 ++++- .../src/cell_building_blocks/interaction.rs | 44 ++- .../src/cell_models/modular_cell.rs | 10 +- .../src/cell_models/pool_bacteria.rs | 4 +- .../src/domains/cartesian_cuboid_n_old.rs | 1 - cellular_raza-concepts-derive/src/cell_agent.rs | 161 +++++++---- cellular_raza-concepts-derive/src/domain.rs | 295 +++++++++++---------- cellular_raza-concepts-derive/src/lib.rs | 2 + cellular_raza-concepts-derive/src/subdomain.rs | 35 ++- cellular_raza-concepts/Cargo.toml | 4 +- cellular_raza-concepts/src/cell.rs | 224 ++++++++++++---- cellular_raza-concepts/src/domain.rs | 40 ++- cellular_raza-concepts/src/domain_old.rs | 10 +- cellular_raza-concepts/src/interaction.rs | 38 +-- cellular_raza-concepts/src/plotting.rs | 4 +- cellular_raza-concepts/tests/derive_cell_agent.rs | 19 +- cellular_raza-core-proc-macro/src/communicator.rs | 2 +- cellular_raza-core-proc-macro/src/run_sim.rs | 54 ++-- .../src/simulation_aspects.rs | 6 +- cellular_raza-core/Cargo.toml | 8 +- cellular_raza-core/build.rs | 7 +- .../src/backend/chili/aux_storage.rs | 63 ----- .../src/backend/chili/datastructures.rs | 13 +- cellular_raza-core/src/backend/chili/errors.rs | 29 +- cellular_raza-core/src/backend/chili/mod.rs | 108 +------- cellular_raza-core/src/backend/chili/proc_macro.rs | 3 + cellular_raza-core/src/backend/chili/setup.rs | 12 +- .../src/backend/chili/update_cycle.rs | 3 +- .../src/backend/chili/update_mechanics.rs | 115 +++++++- .../src/backend/cpu_os_threads/config.rs | 28 +- .../backend/cpu_os_threads/domain_decomposition.rs | 38 +-- .../src/backend/cpu_os_threads/supervisor.rs | 16 +- .../src/backend/cpu_os_threads/trait_bounds.rs | 4 +- cellular_raza-examples/README.md | 2 +- .../bacteria_population/src/bacteria_properties.rs | 4 +- .../bacteria_population/src/main.rs | 11 +- cellular_raza-examples/bacterial_rods/src/main.rs | 12 +- .../cell_sorting/src/main-brownian.rs | 2 + .../cell_sorting/src/main-langevin.rs | 16 +- cellular_raza-examples/cell_sorting/src/main.rs | 2 + cellular_raza-examples/cellular_raza-template | 2 +- cellular_raza-examples/cellular_raza-template-pyo3 | 2 +- .../src/building_blocks/switching.rs | 54 ++-- .../organoid_turing_growth/src/cell_properties.rs | 4 +- cellular_raza-examples/pool_model_pyo3/Cargo.toml | 2 +- .../pool_model_pyo3/src/bacteria_properties.rs | 4 +- cellular_raza-examples/puzzle/src/main.rs | 8 +- .../puzzle/src/puzzle_mechanics.rs | 10 + .../semi_vertex/src/cell_properties.rs | 8 +- .../sender-receiver/src/bacteria_properties.rs | 2 + .../sender-receiver/src/controller.rs | 4 +- .../ureter_signalling/src/cell_properties.rs | 4 +- cellular_raza/Cargo.toml | 18 +- cellular_raza/README.md | 6 +- cellular_raza/tests/domain_force_spring.rs | 16 +- .../tests/interaction_two_body_problem.rs | 20 +- update_version.sh | 4 +- 66 files changed, 1154 insertions(+), 726 deletions(-)