- Jul 27, 2021
-
-
Brent Huisman authored
* added notes re literal_include to python examples * merged changes in #1504 * deduped and includified (https://github.com/arbor-sim/arbor/pull/1558) tutorials. * First divergence of tutorial and code spotted! * Added some contrib documentation for examples and docs.
-
- Jun 18, 2021
-
-
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
-
- Mar 30, 2021
-
-
Nora Abi Akar authored
* Fix the regular schedule generated in `single_cell_model::run` * Adjust frequency of probes in python examples to the correct unit (KHz). Fixes #1457
-
- Feb 18, 2021
-
-
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.
-
- Dec 18, 2020
-
-
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.
-