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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.

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This is list should not serve as a bug-tracker
File Line Todo
cellular_raza/tests/interaction_two_body_problem.rs 56 revisit this test and then enable again
cellular_raza/tests/storage.rs 74 this is currently not working due to a bug in serde or quick_xml
cellular_raza-benchmarks/src/cell_sorting.rs 471 use this
cellular_raza-benchmarks/src/cell_sorting.rs 476 use this
cellular_raza-building-blocks/src/cell_building_blocks/bacterial_rods.rs 370 refactor this with matrix multiplication!!!
cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs 190 remove this entirely or make it somehow work
cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs 805 write function above such that point [1.0, 0.0] is also inside!
cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs 586 include more formulas for this model
cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs 656 this needs to be calculated again
cellular_raza-building-blocks/src/cell_building_blocks/plot_bound_lennard_jones.html 1 Fix color and styling and adapt to theme -->
cellular_raza-building-blocks/src/cell_building_blocks/plot_morse_potential.html 1 Fix color and styling and adapt to theme -->
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 197 think about replacing two variables for one
cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs 247 read out extracellular concentrations of nutrients here
cellular_raza-building-blocks/src/domains/cartesian_cuboid_2_vertex_old.rs 63 write this nicely!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_2_vertex_old.rs 474 FIXUP we need to insert boundary conditions here as last argument
cellular_raza-building-blocks/src/domains/cartesian_cuboid_2_vertex_old.rs 500 optimize this!
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 311 add actual test case here
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 510 finish this test
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 670 Currently we are not splitting the voxels apart efficiently
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 1013 THINK VERY HARD ABOUT THESE TYPES! THEY MIGHT BE CHOSEN STUPIDLY!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n.rs 1042 optimize this!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 73 write this nicely!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 462 optimize this!
cellular_raza-building-blocks/src/domains/cartesian_cuboid_n_old.rs 488 make them only visible if correspoding feature (eg. fluid_mechanics or gradients) is active
cellular_raza-building-blocks/src/domains/mod.rs 4 #[allow(deprecated)]
cellular_raza-building-blocks/src/domains/mod.rs 8 #[allow(deprecated)]
cellular_raza-concepts/src/cell.rs 7 move this module to cpu_os_threads backend except for traits
cellular_raza-concepts/src/cell.rs 13 consider making this an associated type of the Id trait
cellular_raza-concepts/src/cell.rs 151 make this generic with respect to voxel_index
cellular_raza-concepts/src/domain.rs 80 can be use another iterator than Vec<(I, S, Vec)>?
cellular_raza-concepts/src/domain.rs 365
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/errors.rs 143 think about enabling these debug_assertions (performance difference unclear to me)
cellular_raza-concepts/src/interaction.rs 36
cellular_raza-concepts/src/lib.rs 17 #[deprecated]
cellular_raza-concepts/src/plotting.rs 25 implement this as well
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-derive/src/cell_agent.rs 292 consider adding specific import of cellular_raza or
cellular_raza-concepts-derive/src/domain.rs 395 "
cellular_raza-concepts-derive/src/domain.rs 398 DecomposeError::IndexError(IndexError(format!("TODO"))),
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/datastructures.rs 25 make this private
cellular_raza-core/src/backend/chili/datastructures.rs 264 this is not a boundary error!
cellular_raza-core/src/backend/chili/datastructures.rs 319
cellular_raza-core/src/backend/chili/errors.rs 9 use std::sync::Arc; // TODO in the future use core::error::Error (unstable right now)
cellular_raza-core/src/backend/chili/errors.rs 184 implement more of this
cellular_raza-core/src/backend/chili/errors.rs 208 make error handling more nuanced to be valuable
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/setup.rs 342 insert structs and traits for loading from saved results
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/update_mechanics.rs 205 can we do this without memory allocation?
cellular_raza-core/src/backend/chili/update_mechanics.rs 439 use drain_filter when stabilized
cellular_raza-core/src/backend/chili/update_reactions.rs 100 Think about doing this in two passes
cellular_raza-core/src/backend/chili/update_reactions.rs 283 can we do this without memory allocation?
cellular_raza-core/src/backend/chili/update_reactions.rs 299 can we do this without cloning at all?
cellular_raza-core/src/backend/cpu_os_threads/config.rs 59 rethink how to specify time points to save
cellular_raza-core/src/backend/cpu_os_threads/config.rs 76 use something like an iterator in this place to possibly process in parallel
cellular_raza-core/src/backend/cpu_os_threads/config.rs 154
cellular_raza-core/src/backend/cpu_os_threads/config.rs 596 catch these errors!
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 517
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 608 abstract away these trait bounds to more abstract traits
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 651 every voxel should apply its own boundary conditions
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 686 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 735 these reactions are currently on the same timescale as the
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 919 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 958 can we do this without memory allocation?
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1146 use drain_filter when stabilized
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1244 find better function signature to have multiple time-scales
cellular_raza-core/src/backend/cpu_os_threads/domain_decomposition.rs 1309 this currently also does application of domain boundaries and inclusion of new cells
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/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/supervisor.rs 239 this is not always an error in update_mechanics!
cellular_raza-core/src/backend/cpu_os_threads/supervisor.rs 256 Make sure to only call this if the controller type is not ()
cellular_raza-core/src/backend/cpu_os_threads/supervisor.rs 388 do not clone these variables!
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_rayon/concepts.rs 68 this is totally incorrect!
cellular_raza-core/src/backend/cpu_rayon/concepts.rs 93 todo!()
cellular_raza-core/src/backend/cpu_rayon/concepts.rs 97 todo!()
cellular_raza-core/src/backend/cpu_rayon/concepts.rs 101 todo!()
cellular_raza-core/src/backend/cpu_rayon/engine.rs 235 this currently also does application of domain boundaries and inclusion of new cells which is wrong in general!
cellular_raza-core/src/backend/cpu_rayon/engine.rs 259 Make sure to only call this if the controller type is not ()
cellular_raza-core/src/backend/mod.rs 38 deprecate this!
cellular_raza-core/src/storage/concepts.rs 131 fix sled! This is currently not working on multiple threads
cellular_raza-core/src/storage/concepts.rs 797 decide if these functions should be &mut self instead of &self
cellular_raza-core/src/storage/memory_storage.rs 9 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 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 286 this should not be here! Fix it properly (I asked on sled discord)
cellular_raza-core/src/storage/test.rs 20
cellular_raza-core/src/storage/test.rs 57 extend this to test all functions
cellular_raza-core/src/time.rs 226 check this again
cellular_raza-core/src/time.rs 244 Check if a current event should take place
cellular_raza-core-proc-macro/src/run_sim.rs 44 decide if we need to catch this error in the future
cellular_raza-core-proc-macro/src/run_sim.rs 452 see comment at compatibility_tests function in chili backend.
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 48 add option to specify type parameters for individual aspects
cellular_raza-core-proc-macro/src/simulation_aspects.rs 112 this macro does not give the correct error message
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/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-examples/diffusion/src/main.rs 160 In the future we hope to use the component-wise functions
cellular_raza-examples/diffusion/src/main.rs 388
cellular_raza-examples/diffusion/src/main.rs 414 use the border_infos from before here
cellular_raza-examples/pool_model_pyo3/analysis.ipynb 205 Compare Spatial Model to ODE model\n",
cellular_raza-examples/pool_model_pyo3/pool_paper_spatial.py 24 adjust these parameters
cellular_raza-examples/pool_model_pyo3/src/bacteria_properties.rs 73 can we do this without using clone? Ie. without memory allocations?
cellular_raza-examples/pool_model_pyo3/src/bacteria_properties.rs 185 think about replacing two variables for one
cellular_raza-examples/pool_model_pyo3/src/bacteria_properties.rs 231 read out extracellular concentrations of nutrients here
cellular_raza-examples/pool_model_pyo3/src/bacteria_properties.rs 379
cellular_raza-examples/pool_model_pyo3/src/simulation.rs 246 try to avoid this cloning right here!
cellular_raza-examples/puzzle/src/main.rs 98 todo!()
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 345 use this
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 366 introduce 2 radii to obtain the correct boundary_length
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 407 implement this safekeeping mechanism
cellular_raza-examples/puzzle/src/puzzle_mechanics.rs 678 think about using something else than one here
cellular_raza-examples/semi_vertex/src/cell_properties.rs 99 todo!()
cellular_raza-examples/semi_vertex/src/custom_domain.rs 69 refactor this with matrix multiplication!!!
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