- Oct 04, 2022
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Thorsten Hater authored
* remove storage of RHS and face-conductance in solvers * elide copy RHS->U and RHS->Xd respectively -> solve will now directly mangly U and Xd * fix tests accordingly * Introduce wrapper macro for __restrict__ to Isolate against compiler specifics.
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boeschf authored
use std variants of sqrt and move (removes warnings, and is safer)
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- Sep 27, 2022
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Thorsten Hater authored
Fix a typo preventing the generation of GPU mechs.
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- Sep 20, 2022
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Thorsten Hater authored
* Add pybind11 version to config. * Add version check for PB11. * Bump CMake a tiny bit.
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lukasgd authored
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Thorsten Hater authored
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Thorsten Hater authored
This is prep for meson in addition to simplifying (ie reducing) the amount of scripting we have. In the long run, I'd like to remove `BuildModules.cmake` too, but this might be superseded by meson and this PR is self-contained. # Changes - `modcc` accepts now a list of NMODL files - likewise, `modcc` is now able to spit out a catalogue.cpp file - remove the `generate-catalogue` script, simplify a-b-c - remove some options from `modcc` we never use - No longer allow external modcc
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- Sep 16, 2022
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Thorsten Hater authored
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Thorsten Hater authored
- BREAKING: Rename spike detector -> threshold detector in Python - `spike_detector` is still around, will throw a deprecation error; will be removed 0.9 - this brings Python closer to the C++ API and removes lots of ambiguities in the docs.
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- Sep 07, 2022
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Thorsten Hater authored
* Add segment tree editing: join and split * Add equivalence and equality on trees * Apply isometries to trees * Add raw loaders to NeuroLucida ASC and SWC that return segment trees instead of morphologies
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Thorsten Hater authored
Spike source cells can now generate events based on the interleaving of arbitrarily many schedules. This should simplify the required connectivity.
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- Sep 06, 2022
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Brent Huisman authored
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Thorsten Hater authored
Until now, point mechanisms applied a weighting factor when updating internal/external concentrations. This was an oversight and is only correct in density mechanisms. This has been rectified, but might change point mechanism semantics for injecting/modifying Xi/Xo values.
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- Sep 05, 2022
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Thorsten Hater authored
- Print better modcc errors - Catch errors in symbolic diff in linearity test - Abort upon such errors and advise for a different solver
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Thorsten Hater authored
- Remove the old, multi-target `event_generator` class in favour of `schedule_generator(tgt, weight, explicit_schedule)` - Much simplification ensues, `event_generator` is no longer a type-erasing container, but just what `schedule_generator` was before - Make the label resolution in generators a bit more eager, no longer at simulation time, but now during setup (bit give a wee bit of perf as well) Closes #1488
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Thorsten Hater authored
Add functionality, docs, and examples on editing the connection table. This is a first, small PR on the topic, further functionality will come as requested. Teaser example ```cxx // This recipe -- omitted -- implements a mutable connection table // and returns it via the `connections_on` callback. New entries are // added using `add_connection` which makes one link from a central // `spike_source_cell` to the given `gid` auto rec = recipe(); rec.add_connection(1); auto sim = arb::simulation(rec, ctx); // Record spikes std::vector<arb::spike> spikes; sim.set_local_spike_callback([&spikes](const auto& s) { spikes.insert(spikes.end(), s.begin(), s.end()); }); // Run and print all spikes per gid sim.run(0.25, 0.025); show_spikes(spikes); // Add a new connection rec.add_connection(2); sim.update_connections(rec); // Run and print all spikes per gid sim.run(0.5, 0.025); show_spikes(spikes); ``` # Update July '22 - added re-wiring of Event Generators - implemented a split between a recipe and a recipe-update (cheekily dubbed `topping` until further notice) - `recipes` are `toppings` via inheritance
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Thorsten Hater authored
**BREAKING** Remove access to time `t` in NMODL.
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- Sep 01, 2022
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Thorsten Hater authored
- Enhance `run_cpp_examples.sh` to do some very basic checking of spikes counts - Add a script to check all releases - The former must succeed for all commits to master Here's the expected spike counts as of 0.7 - brunel 6998 - bench 972 - ring 94 (19 pre-v0.7) - gap_junctions 30
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- Aug 26, 2022
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Brent Huisman authored
- allow arbor to be build against py3.11 - modernise!
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- Aug 25, 2022
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Thorsten Hater authored
Document use and care of spike detectors.
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- Aug 23, 2022
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Thorsten Hater authored
Enable pyArborio input routines to consume Stream objects in addition to files by name. - NML - NeuroLucida ASC - SWC Closes #1459
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Thorsten Hater authored
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Thorsten Hater authored
Do not abuse `pybind::arg_v("name", T default, "description")` as `pybind::arg_v("name", "description")`. Use descriptive names and `pybind::arg` instead. Closes #1754
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Thorsten Hater authored
Functionality to - delete ions from global properties - peek into global properties - expose painted, placed, and defaulted items - expose voltage limit to python - make voltage limit an optional to allow for arbitrary values. - Add ion_settings view to python = (valence, ion_data, rev_pot_method) Documentation - cable cell properties in python Closes #1578 Closes #1577 Closes #1607
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- Aug 22, 2022
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Thorsten Hater authored
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Thorsten Hater authored
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- Aug 11, 2022
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Thorsten Hater authored
* Add find_private_gpu and arbor.env.
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- Aug 10, 2022
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Thorsten Hater authored
- Add stacktraces to 1. arbor_exception (and all derived) as `where` 2. arbor_internal_error as `where` 3. arb_assert - Propagate stacktraces to Python exceptions derived from the above. - Expand dev/doc on debugging
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- Aug 09, 2022
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Thorsten Hater authored
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Thorsten Hater authored
* Clean up the bundled mechanisms. Closes #1155
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Thorsten Hater authored
Remove the redundant fvm_(value|size|index)_type aliases and replace them with the raw ABI types.
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Thorsten Hater authored
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Thorsten Hater authored
Throw error if WATCH encountered in NMODL.
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Thorsten Hater authored
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- Aug 05, 2022
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Brent Huisman authored
- elaborate probing API - add definitions for different kinds of probes (vector, scalar, set). - add sketches and example for data layout
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- Aug 04, 2022
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Thorsten Hater authored
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Thorsten Hater authored
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- Aug 02, 2022
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Thorsten Hater authored
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Brent Huisman authored
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- Aug 01, 2022
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Thorsten Hater authored
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