.cargo/config.toml | 6 + .github/workflows/generate_tests.py | 5 +- .github/workflows/reuse.yml | 6 +- ...ta_ubuntu-latest.yml => test_beta_macos-14.yml} | 6 +- .github/workflows/test_beta_ubuntu-22.04.yml | 10 + .github/workflows/test_beta_ubuntu-24.04.yml | 10 + ...ubuntu-latest.yml => test_nightly_macos-14.yml} | 6 +- .github/workflows/test_nightly_ubuntu-22.04.yml | 10 + .github/workflows/test_nightly_ubuntu-24.04.yml | 10 + ..._ubuntu-latest.yml => test_stable_macos-14.yml} | 6 +- .github/workflows/test_stable_ubuntu-22.04.yml | 10 + .github/workflows/test_stable_ubuntu-24.04.yml | 10 + CITATION.cff | 4 +- Cargo.toml | 17 +- README.md | 5 +- cellular_raza-benchmarks/Cargo.toml | 4 +- cellular_raza-benchmarks/plotting/cell_sorting.py | 282 +++++--- cellular_raza-benchmarks/src/cell_sorting.rs | 10 +- cellular_raza-building-blocks/Cargo.toml | 14 +- .../src/cell_building_blocks/bacterial_rods.rs | 217 +++--- .../src/cell_building_blocks/interaction.rs | 11 +- .../src/cell_building_blocks/mechanics.rs | 18 +- .../src/cell_models/pool_bacteria.rs | 6 +- .../src/domains/cartesian_2d_diffusion.rs | 200 +++--- .../src/domains/cartesian_cuboid_2_vertex_old.rs | 590 ---------------- .../src/domains/cartesian_cuboid_n.rs | 746 ++------------------- cellular_raza-building-blocks/src/domains/mod.rs | 9 +- cellular_raza-concepts/Cargo.toml | 5 +- cellular_raza-concepts/src/cycle.rs | 2 +- cellular_raza-concepts/src/errors.rs | 2 + cellular_raza-concepts/src/lib.rs | 5 + cellular_raza-core-proc-macro/src/run_sim.rs | 36 +- cellular_raza-core/Cargo.toml | 15 +- cellular_raza-core/src/backend/cara/cara.cu | 41 +- cellular_raza-core/src/backend/cara/mod.rs | 75 ++- cellular_raza-core/src/backend/chili/mod.rs | 8 +- cellular_raza-core/src/backend/chili/proc_macro.rs | 6 +- cellular_raza-core/src/backend/elli/mod.rs | 165 ++++- cellular_raza-core/src/backend/elli/saxpy.cl | 11 + cellular_raza-core/src/storage/concepts.rs | 74 +- cellular_raza-core/src/storage/memory_storage.rs | 33 +- cellular_raza-core/src/storage/ron.rs | 18 +- cellular_raza-core/src/storage/serde_json.rs | 14 +- cellular_raza-core/src/storage/sled_database.rs | 9 + cellular_raza-core/src/time.rs | 12 +- .../bacteria_population/src/bacteria_properties.rs | 4 +- .../bacteria_population/src/main.rs | 6 +- .../bacterial_branching/Cargo.toml | 2 +- .../bacterial_branching/src/bacteria_properties.rs | 6 +- .../bacterial_branching/src/main.rs | 11 +- .../bacterial_branching/src/plotting.py | 2 +- cellular_raza-examples/bacterial_rods/Cargo.toml | 7 +- cellular_raza-examples/bacterial_rods/src/main.rs | 15 +- .../cell_sorting/src/main-brownian.rs | 10 +- .../cell_sorting/src/main-langevin.rs | 10 +- cellular_raza-examples/cell_sorting/src/main.rs | 10 +- cellular_raza-examples/cellular_raza-template | 2 +- cellular_raza-examples/cellular_raza-template-pyo3 | 2 +- cellular_raza-examples/diffusion/Cargo.toml | 18 - cellular_raza-examples/diffusion/src/main.rs | 444 ------------ cellular_raza-examples/getting-started/src/main.rs | 8 +- .../organoid_turing_growth/src/cell_properties.rs | 6 +- .../organoid_turing_growth/src/main.rs | 20 +- cellular_raza-examples/pool_model_pyo3/Cargo.toml | 2 +- .../pool_model_pyo3/materials/summary.typ | 2 +- .../pool_model_pyo3/pyproject.toml | 3 + .../pool_model_pyo3/src/bacteria_properties.rs | 6 +- .../pool_model_pyo3/src/simulation.rs | 4 +- cellular_raza-examples/puzzle/Cargo.toml | 2 +- .../puzzle/src/puzzle_mechanics.rs | 2 +- cellular_raza-examples/semi_vertex/src/main.rs | 2 +- .../sender-receiver/src/controller.rs | 20 +- .../ureter_signalling/Cargo.toml | 2 +- .../ureter_signalling/src/cell_properties.rs | 6 +- .../ureter_signalling/src/main.rs | 20 +- cellular_raza/Cargo.toml | 10 +- .../tests/brownian_diffusion_constant_approx.rs | 55 +- .../tests/determinism_mechanics_interaction.rs | 12 +- cellular_raza/tests/storage.rs | 6 +- update_version.sh | 4 +- 80 files changed, 1156 insertions(+), 2344 deletions(-)