- Jul 29, 2021
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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.
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- Jul 27, 2021
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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.
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- Jun 18, 2021
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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
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- May 17, 2021
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Nora Abi Akar authored
Fix mistakes reported by @Helveg in the Python tutorial docs.
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- Mar 30, 2021
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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
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- Jan 14, 2021
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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
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- Dec 14, 2020
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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 ...
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- Nov 10, 2020
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Sebastian Schmitt authored
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Sebastian Schmitt authored
Speed up plotting in seaborn.relplot by disabling calculation of confidence intervals
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- Oct 09, 2020
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Nora Abi Akar authored
* Add some log messages in python examples * Add python examples to CI
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Brent Huisman authored
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- Oct 07, 2020
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Brent Huisman authored
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- Oct 05, 2020
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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()
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