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  1. Jul 29, 2021
    • thorstenhater's avatar
      Implement mechanism ABI · ff12bb82
      thorstenhater authored
      Implements #1376.
      
      * Provide a common C linkage ABI for externally compiled mechanisms, for both CPU and GPU.
      * Remove mechanism type hierarchy (`concrete_mechanism` etc.), and move corresponding functionality to the back-end shared state objects. Mechanism catalogue is no longer indexed by type id.
      * Distinguish between SIMD optimal alignment and SIMD width with new `min_align` attribute. Mechanisms provide both pieces of information via ABI.
      ff12bb82
  2. Jul 27, 2021
  3. Jun 18, 2021
    • Nora Abi Akar's avatar
      Labels instead of indices for placeable item identfication. (#1504) · e0e18976
      Nora Abi Akar authored
      New structs and types:
      * `cell_tag_type` (std::string): for labelling placeable items on a cell. The label refers to a number of items placed on a locset, equal to the number of locations in a locset. The number of locations in not always known to the user, so the previous way of using indices for items was no longer sufficient. 
      * `lid_selection_policy`: for allowing a user to select a single item from a group of items sharing a label. Currently only `round_robin` and `assert_univalent` are supported. 
      * `cell_local_label_type` and `cell_global_label_type`: for identifying the target and source of a connection or gap_junction connection. 
      * `cell_label_ranges`, and `cell_labels_and_gids`: for propagating information about the labelled items on the cell from the cell groups back to the simulation and communicator. 
      * `label_resolution_map` and `resolver`: for selecting an item (and retaining state) from a labelled group of items on a cell according to a user-selected policy.
      
      Changes to the model-initialization: 
      * The `communicator` now needs `label_resolution_maps` constructed from the cell group data in order to build the `connections` vectors. 
      * The `simulation_state` object handles the transfer of the information when it is constructed. 
      * Spike exchange at runtime remains unchanged, because `communicator::connections` remains unchanged. 
      
      Changes to cells, cell_groups and recipe:
      * `decor::place` expects a third label parameter, no longer returns an `lid_range`.
      * `lif`, `source`, and `benchmark` cells need source/target labels in their constructors. 
      * A `cell_group` needs to save data about the gid/labels/lid_ranges of each cell, to propagate back to the `communicator` constructor. 
      * Connections/gap junction connections are formed between {label, policy} pairs on cells instead of indices. 
      * `num_sources`, `num_targets`, `num_gap_junction_sites` deleted from `recipe`.
      
      Additional changes:
      * Add MPI wrapper for exchanging vectors of strings. 
      * Corresponding updates to unit tests, Python wrapper, C++ and Python examples, documentation.
      
      Fixes #1394
      e0e18976
  4. May 17, 2021
  5. Mar 30, 2021
  6. Jan 14, 2021
    • Brent Huisman's avatar
      Docs: define branch, mlocation, cv default. (#1302) · b10238e0
      Brent Huisman authored
      * Used Sphinx glossary directive to create terms that can be referred to in `concepts/morphology.rst` and `concepts/labels.rst`.
      * Added note box on difference with Neuron, add source for NEURON cylinder discretisation
      * Parameters added to svg generation script: turn off colors, root
      * Fix cpp TOC duplication, match ordering in other sections.
      * State default cv policy
      * center/re -> midpoints
      * Clarify and remove compartment term
      b10238e0
  7. Dec 14, 2020
    • Benjamin Cumming's avatar
      Decor (#1235) · ac63809f
      Benjamin Cumming authored
      Make the `cable_cell` interface read only by passing the decorations
      to its constructor in a new `decor` type.
      
      C++ library
      * Remove the paint/place/set_default interface from `cable_cell`
      * Create a `decor` type that:
        * stores lists of paintings and placings
        * stores a set of cable cell parameters
        * uses the `paint`, `place`, `set_default` interface that was deprecated
          from `cable_cell`.
      * Create `paintable`, `placeable` and `defaultable` variants that are sum types
        over the respective types that can be painted, placed and defaulted.
      * Remove the overloaded `cable_cell::paint`, `cable_cell::place`,
        `cable_cell::set_default` methods to single methods that consume the sum types.
      
      Unit Tests
      * Many small changes because many many tests use cable cell API.
      * There were no `cable_cell` unit tests! Not such a big deal, since cable_cell
        is tested implicitly in so many other tests
        * but I added cable_cell tests: not much at the moment but will quickly fill
          ...
      ac63809f
  8. Nov 10, 2020
  9. Oct 09, 2020
  10. Oct 07, 2020
  11. Oct 05, 2020
    • Brent Huisman's avatar
      Update Python examples (#1166) · d3e99c23
      Brent Huisman authored
      * Python examples: Updated to use region expressions (quotes)
      * Python examples: Uniform plotting
      * Python examples: Removed tutorial directory (example roughly matches python/example/single_cell_model.py)
      * Python examples: Rewrote flat_cell_builder() to segment_tree()
      d3e99c23