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  1. Jul 27, 2021
  2. 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
  3. Mar 30, 2021
  4. Feb 18, 2021
    • Brent Huisman's avatar
      Tutorials: ring network (#1313) · 506ff916
      Brent Huisman authored
      * Tutorial ring network added. A few typos fixed, crosslinks fixed.
      * MPI tutorial added.
      * Improved SVG generation, added separate label scaling, increased default label size.
      * Bugfix: didnt generate cable region in gen-labels.py used in `concepts/morphology.rst`.
      * Termified Interconnectivity page.
      * Termified probe nomenclature page. Will be moved in [this PR](https://github.com/arbor-sim/arbor/issues/1353) from python/simulation to concepts/probes_samplers.
      506ff916
  5. Dec 18, 2020
    • Nora Abi Akar's avatar
      Docs: Python examples (#1279) · 6ebfb3db
      Nora Abi Akar authored
      * Add 2 new examples to `python/examples` and their corresponding tutorials in the docs. 
          1. `single_cell_detailed.py` : a slightly more complex example using `single_cell_model`
          2. `single_cell_detailed_recipe.py`: equivalent to `single_cell_detailed.py` but using a recipe. 
      * Change `load_swc`-> `load_swc_arbor` for consistency.
      * Run Sphinx with specified PYTHON_EXECUTABLE.
      * Set PYTHONPATH env var in doc/CMakeLists.txt, such that it propagates correctly, including locally.
      * Build pyarb BEFORE html such that docs build can import arbor in Github Actions script.
      6ebfb3db