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❓ TODO List

❓ TODO List

This is a list of open todos as documented by simple TODO markers in code. The order does not give any hints about the importance of the individual problems. Furthermore, this list is not considered to be persistent accross changes in the code-base. To formally notify us of any bugs, please use the bug-tracker in our repository.

ℹ️
This is list should not serve as a bug-tracker
File Line Todo
cellular_raza/tests/interaction_two_body_problem.rs 61 revisit this test and then enable again
cellular_raza-concepts/src/domain.rs 110 can we use another iterator than Vec<(I, S, Vec)>?
cellular_raza-concepts/src/lib.rs 17 #[deprecated]
cellular_raza-concepts/src/domain_old.rs 38 rename this function and generate SubDomains which then hold a number of voxels.
cellular_raza-concepts/src/domain_old.rs 65 migrate to trait alias when stabilized
cellular_raza-concepts/src/domain_old.rs 96 these functions do NOT capture possible implementations accurately
cellular_raza-concepts/src/domain_old.rs 112 rework this trait. We do not want to make it dependent on the voxel index. But it may be dependent on spatial representation such as Position type.
cellular_raza-concepts/src/domain_old.rs 130 formulate additional trait which does extracellular gradients mechanics and can be linked to this trait
cellular_raza-concepts/src/domain_old.rs 138 formulate additional trait which does extracellular gradients mechanics and can be linked to this trait
cellular_raza-concepts/src/reactions.rs 17 implement random contributions
cellular_raza-concepts/src/reactions.rs 27 do we need this associated type?
cellular_raza-concepts/src/reactions.rs 29 add description
cellular_raza-concepts/src/cell.rs 8 move this module to cpu_os_threads backend except for traits
cellular_raza-concepts/src/errors.rs 145 think about enabling these debug_assertions (performance difference unclear to me)
cellular_raza-concepts/src/plotting.rs 25 implement this as well
cellular_raza-core-proc-macro/src/simulation_aspects.rs 37 add generic aspect which should always be present
cellular_raza-core-proc-macro/src/simulation_aspects.rs 49 add option to specify type parameters for individual aspects
cellular_raza-core-proc-macro/src/simulation_aspects.rs 113 this macro does not give the correct error message
cellular_raza-core-proc-macro/src/run_sim.rs 48 decide if we need to catch this error in the future
cellular_raza-core-proc-macro/src/run_sim.rs 530 see comment at compatibility_tests function in chili backend.
cellular_raza-benchmarks/src/cell_sorting.rs 473 use this
cellular_raza-benchmarks/src/cell_sorting.rs 478 use this
cellular_raza-concepts-derive/src/domain.rs 398 "
cellular_raza-concepts-derive/src/domain.rs 401 DecomposeError::IndexError(IndexError(format!("TODO"))),
cellular_raza-concepts-derive/src/cell_agent.rs 319 consider adding specific import of cellular_raza or
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 346 use this
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 367 introduce 2 radii to obtain the correct boundary_length
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 408 implement this safekeeping mechanism
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 679 think about using something else than one here
cellular_raza-examples/puzzle/src/main.rs 102 todo!()
cellular_raza-examples/bacterial_rods/plotter.py 104 MAGIC NUMBERS
cellular_raza-examples/bacterial_rods/plotter.py 116 MAGIC NUMBERS
cellular_raza-examples/bacterial_rods/plotter.py 155 actually use this
cellular_raza-examples/semi_vertex/src/cell_properties.rs 103 todo!()
cellular_raza-examples/semi_vertex/src/custom_domain.rs 69 refactor this with matrix multiplication!!!
cellular_raza-examples/cellular_raza-template-pyo3/.github/workflows/docs.yml 9 maybe in the future use reusable workflows or composite workflows
cellular_raza-examples/cellular_raza-template-pyo3/docs/conf.py 24 'sphinx.ext.autodoc',
cellular_raza-core/src/time.rs 230 check this again
cellular_raza-core/src/time.rs 248 Check if a current event should take place
cellular_raza-core/src/backend/cpu_os_threads/config.rs 57 rethink how to specify time points to save
cellular_raza-core/src/backend/cpu_os_threads/config.rs 74 use something like an iterator in this place to possibly process in parallel
cellular_raza-core/src/backend/cpu_os_threads/config.rs 152
cellular_raza-core/src/backend/cpu_os_threads/config.rs 599 catch these errors!
cellular_raza-core/src/backend/cpu_os_threads/trait_bounds.rs 7 use trait alias when available
cellular_raza-core/src/backend/cpu_os_threads/trait_bounds.rs 46 use trait alias when available
cellular_raza-core/src/backend/cpu_os_threads/trait_bounds.rs 88 use trait alias when available
cellular_raza-core/src/backend/cpu_os_threads/trait_bounds.rs 167 Define trait aliases for Position and Force
cellular_raza-core/src/backend/cpu_os_threads/trait_bounds.rs 169 use trait alias when available
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 14 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 20 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 24 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 28 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 32 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 36 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 40 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 44 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 48 todo!()
cellular_raza-core/src/backend/cpu_os_threads/logger.rs 52 todo!()
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 504
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 595 abstract away these trait bounds to more abstract traits
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 638 every voxel should apply its own boundary conditions
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 663 make sure that if no extracellular mechanics are in action updating is correct and the
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 712 these reactions are currently on the same timescale as the
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 896 the trait bounds here are too harsh. We should not be required to have Pos: Position
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 936 can we do this without memory allocation?
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1125 use drain_filter when stabilized
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1223 find better function signature to have multiple time-scales
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1288 this currently also does application of domain boundaries and inclusion of new cells
cellular_raza-core/src/backend/cpu_os_threads/supervisor.rs 237 this is not always an error in update_mechanics!
cellular_raza-core/src/backend/cpu_os_threads/supervisor.rs 254 Make sure to only call this if the controller type is not ()
cellular_raza-core/src/backend/cpu_os_threads/supervisor.rs 385 do not clone these variables!
cellular_raza-core/src/backend/cpu_os_threads/errors.rs 6 use std::error::Error; // TODO in the future use core::error::Error (unstable right now)
cellular_raza-core/src/backend/mod.rs 39 deprecate this!
cellular_raza-core/src/backend/elli/mod.rs 12 we should not be selecting the first device by default
cellular_raza-core/src/backend/chili/simulation_flow.rs 99 actually use the specifically designed UDGraph instead of FromMap trait.
cellular_raza-core/src/backend/chili/simulation_flow.rs 310 migrate to FromGraph eventually!
cellular_raza-core/src/backend/chili/simulation_flow.rs 343
cellular_raza-core/src/backend/chili/setup.rs 20 replace this with timestepper in the future
cellular_raza-core/src/backend/chili/setup.rs 50 add a function which will automatically generate the correct number of subdomains
cellular_raza-core/src/backend/chili/setup.rs 62 todo!();
cellular_raza-core/src/backend/chili/update_reactions.rs 104 Think about doing this in two passes
cellular_raza-core/src/backend/chili/update_reactions.rs 287 can we do this without memory allocation?
cellular_raza-core/src/backend/chili/update_reactions.rs 303 can we do this without cloning at all?
cellular_raza-core/src/backend/chili/datastructures.rs 24 make this private
cellular_raza-core/src/backend/chili/datastructures.rs 263 this is not a boundary error!
cellular_raza-core/src/backend/chili/datastructures.rs 316
cellular_raza-core/src/backend/chili/errors.rs 8 use std::sync::atomic::AtomicBool; // TODO in the future use core::error::Error (unstable right now)
cellular_raza-core/src/backend/chili/errors.rs 189 implement more of this
cellular_raza-core/src/backend/chili/errors.rs 213 make error handling more nuanced to be valuable
cellular_raza-core/src/backend/chili/compatibility_tests.rs 51 solve problem where const D: usize from building blocks for interaction
cellular_raza-core/src/backend/chili/update_mechanics.rs 429 use drain_filter when stabilized
cellular_raza-core/src/storage/test.rs 20
cellular_raza-core/src/storage/test.rs 56 extend this to test all functions
cellular_raza-core/src/storage/memory_storage.rs 10 use custom field for config [](https://docs.rs/sled/latest/sled/struct.Config.html) to let the user control these parameters
cellular_raza-core/src/storage/concepts.rs 149 fix sled! This is currently not working on multiple threads
cellular_raza-core/src/storage/concepts.rs 860 decide if these functions should be &mut self instead of &self
cellular_raza-core/src/storage/sled_database.rs 10 use custom field for config [](https://docs.rs/sled/latest/sled/struct.Config.html) to let the user control these parameters
cellular_raza-core/src/storage/sled_database.rs 14 use this buffer
cellular_raza-core/src/storage/sled_database.rs 346 this should not be here! Fix it properly (I asked on sled discord)
cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs 202 remove this entirely or make it somehow work
cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs 884 write function above such that point [1.0, 0.0] is also inside!
cellular_raza-building-blocks/src/cell_building_blocks/bacterial_rods.rs 494 refactor this with matrix multiplication!!!
cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs 580 include more formulas for this model
cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs 650 this needs to be calculated again
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 291 add actual test case here
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 301 add actual test case here
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 520 Currently we are not splitting the voxels apart efficiently
cellular_raza-building-blocks/src/domains/cartesian_2d_diffusion.rs 243 DEBUGGING
cellular_raza-building-blocks/src/domains/cartesian_2d_diffusion.rs 245 // todo!();
cellular_raza-building-blocks/src/domains/mod.rs 5 #[allow(deprecated)]
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 72 write this nicely!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 461 optimize this!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 487 make them only visible if correspoding feature (eg. fluid_mechanics or gradients) is active
cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs 78 can we do this without using clone? Ie. without memory allocations?
cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs 199 think about replacing two variables for one
cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs 249 read out extracellular concentrations of nutrients here
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