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cellular_raza-building-blocks/src/domains/mod.rs | 10 +- cellular_raza-building-blocks/src/lib.rs | 2 +- cellular_raza-concepts-derive/src/cell_agent.rs | 303 ++++++++-- cellular_raza-concepts-derive/src/domain.rs | 19 +- cellular_raza-concepts-derive/src/lib.rs | 6 +- cellular_raza-concepts/Cargo.toml | 2 +- cellular_raza-concepts/src/cell.rs | 34 +- cellular_raza-concepts/src/cycle.rs | 2 +- cellular_raza-concepts/src/domain.rs | 480 +++++++++------ cellular_raza-concepts/src/domain_new.rs | 310 ---------- cellular_raza-concepts/src/domain_old.rs | 201 ++++++ cellular_raza-concepts/src/interaction.rs | 11 +- cellular_raza-concepts/src/lib.rs | 14 +- cellular_raza-concepts/src/mechanics.rs | 32 +- cellular_raza-concepts/src/reactions.rs | 482 +++++++++++++++ .../src/test_derive_cell_agent.rs | 54 +- cellular_raza-concepts/tests/derive_domain.rs | 3 +- cellular_raza-concepts/tests/derive_subdomain.rs | 3 +- cellular_raza-core-proc-macro/src/aux_storage.rs | 293 ++++++--- cellular_raza-core-proc-macro/src/communicator.rs | 41 +- cellular_raza-core-proc-macro/src/lib.rs | 3 +- cellular_raza-core-proc-macro/src/run_sim.rs | 64 +- .../src/simulation_aspects.rs | 12 +- cellular_raza-core/Cargo.toml | 6 +- .../src/backend/chili/aux_storage.rs | 66 +- .../src/backend/chili/compatibility_tests.rs | 11 +- .../src/backend/chili/datastructures.rs | 24 +- cellular_raza-core/src/backend/chili/errors.rs | 4 +- cellular_raza-core/src/backend/chili/mod.rs | 11 +- cellular_raza-core/src/backend/chili/proc_macro.rs | 8 +- cellular_raza-core/src/backend/chili/setup.rs | 11 +- .../src/backend/chili/simulation_flow.rs | 55 +- cellular_raza-core/src/backend/chili/solvers.rs | 281 ++++++--- .../src/backend/chili/update_cycle.rs | 2 +- .../src/backend/chili/update_mechanics.rs | 159 +++-- .../src/backend/chili/update_reactions.rs | 372 +++++++++++- .../src/backend/cpu_os_threads/config.rs | 11 +- .../backend/cpu_os_threads/domain_decomposition.rs | 92 +-- 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cellular_raza-examples/cellular_raza-template-pyo3 | 2 +- cellular_raza-examples/diffusion/src/main.rs | 143 +++-- .../organoid_turing_growth/src/main.rs | 3 + .../organoid_turing_growth/src/plotting.rs | 2 + .../pool_model_pyo3/pool_paper_spatial.py | 4 +- .../pool_model_pyo3/src/bacteria_properties.rs | 24 +- .../pool_model_pyo3/src/simulation.rs | 3 + cellular_raza-examples/puzzle/Cargo.toml | 19 + cellular_raza-examples/puzzle/plot.py | 123 ++++ cellular_raza-examples/puzzle/src/main.rs | 236 ++++++++ .../puzzle/src/puzzle_mechanics.rs | 664 ++++++++++++++++++++ cellular_raza-examples/semi_vertex/plot.py | 104 ++++ .../src/alternative_vertex_mechanics.rs | 189 ++++-- .../semi_vertex/src/cell_properties.rs | 122 ++-- .../semi_vertex/src/custom_domain.rs | 11 +- cellular_raza-examples/semi_vertex/src/main.rs | 126 ++-- cellular_raza-examples/semi_vertex/src/plotting.rs | 8 +- .../sender-receiver/src/controller.rs | 2 +- cellular_raza-examples/sender-receiver/src/main.rs | 3 + .../sender-receiver/src/plotting.rs | 2 + cellular_raza-examples/template/src/main.rs | 4 +- .../ureter_signalling/src/main.rs | 3 + .../ureter_signalling/src/plotting.rs | 2 + cellular_raza-homepage/content/internals/_index.md | 4 + .../content/internals/releases.md | 6 + .../content/internals/roadmap.md | 7 +- .../content/showcase/cell-sorting.md | 18 +- .../layouts/shortcodes/load_table.html | 1 + cellular_raza-homepage/static/hextra.css | 1 + cellular_raza/Cargo.toml | 6 +- ...an.rs => brownian_diffusion_constant_approx.rs} | 0 cellular_raza/tests/storage.rs | 113 ++++ 221 files changed, 6558 insertions(+), 2517 deletions(-)