- Nov 15, 2022
-
-
boeschf authored
Addresses #1987 * reproducibility test for random number generator * C++ example demonstrating Ornstein-Uhlenbeck process * Python example featuring stochastic mechanism * stochastic mechanism catalogue The Python example is contributed by Jannik Luboeinski's (@jlubo): https://github.com/jlubo/arbor_ou_lif_example and adapted to fit into Arbor.
-
- Jun 10, 2022
-
-
Thorsten Hater authored
# Changes - Bump ABI to v0.1.1 - Add `arb_mechanism` to bundle `type` and `interface`s - Adjust `generate_catalogue` and `build_catalogue` - Return `nullptr` for GPU interfaces if not enabled # Open Questions - How to tell CMake not to link against `libarbor.a` and only use headers? - ~~How to get around `#ifdef ARB_GPU_ENABLED`~~ Update: just embrace it. # Linked Issues Fixes #1834
-
- Apr 26, 2022
-
-
Thorsten Hater authored
-
- Feb 10, 2022
-
-
Thorsten Hater authored
PyArbor I/O routines now try to cast `filename` arguments to a string. This allows passing `pathlib.Path` objects. Example ```py here = Path(__file__).parent cat = A.load_catalogue(here / 'local-catalogue.so') ```
-
- Oct 06, 2021
-
-
Sebastian Schmitt authored
-
- Oct 04, 2021
-
-
Brent Huisman authored
Fixes #1666
-
- Sep 28, 2021
-
-
Robin De Schepper authored
Expose default (empty) catalogue constructor to Python
-
- Aug 27, 2021
-
-
Nora Abi Akar authored
- Expose `arb_mechanism_kind` to `mechanism_info`. - While building mechanism data in `fvm_build_mechanism_data`, check that synapses, painted region dynamics and reversal potential methods have the expected `arb_mechanism_kind`. - Add unit test.
-
- Aug 02, 2021
-
-
thorstenhater authored
* Fix failure to return value in `py_mech_cat_value_iterator `. * String butchered by formatting. * Join unnecessary separation of string literals in `arborio/cabelio.cpp` * Add missing throw in s_expr code. * Return value, not reference, in `merge_iterator::operator++(int)`. * Check for self-assignment in `mechanism_catalogue`. * Initialize all members of `mechanism`. * Fix index check order in `multi_event_stream` debug output. * Use coordinator_ from base class in `memory::array`.
-
- Jul 05, 2021
-
-
thorstenhater authored
Closes #1547. - Move `MechCat*Iter` to module instead of catalogue class - Add `keys`, `values`, and `items` - Fix a typo.
-
- May 31, 2021
-
-
thorstenhater authored
* Raise KeyError in catalogue. * Raise KeyError in label_dict.
-
- Feb 03, 2021
-
-
thorstenhater authored
First phase of dynamically loaded mechanism catalogues. - Add functionality to load and use catalogues from DSOs in Python and C++. - Add documentation and support scripts to build catalogues DSOs. - Re-factor CMakeLists.txt for mechanisms - Limitations - Needs (compatible, preferably identical) arbor sources when building catalogues - Can only work on MacOS and Linux (uses dlfnc)
-
- Jan 11, 2021
-
-
thorstenhater authored
Introduce two minor changes to the Python API to handle mechanism_catalogues idiomatically. Instead of import arbor as A cat = A.default_catalogue() if cat.has('hh'): print("Found HH.") for mech in cat.keys(): print("*", mech) we can now write import arbor as A cat = A.default_catalogue() if 'hh' in cat: print("Found HH.") for mech in cat: print("*", mech) which is closer to the expectations of Python users.
-
- Dec 14, 2020
-
-
Nora Abi Akar authored
Extend Ptyhon recipe wrapper to support setting of global cell properties. * Rename `pyrecipe::get_probes` to `py_recipe::probes` * Remove `global_properties_shim` : It's easy to make mistakes with the class, as it holds a `mechanism_catalogue` and a `cable_cell_global_properties` which holds a pointer to the catalogue. This would likely have caused issues with the users. * Expose `py_recipe::global_properties`
-
- Nov 02, 2020
-
-
thorstenhater authored
* Add interface for querying names. * Add derived mechanisms to list, clean-up. * Add unit tests. * Add python bindings and docs.
-
- Oct 09, 2020
-
-
Nora Abi Akar authored
Add a catalogue of mechanisms used by the BBP models.
-
- Oct 01, 2020
-
-
Brent Huisman authored
-
- Sep 25, 2020
-
-
Sam Yates authored
* Substitute `std::optional<T>` for `arb::util::optional<T>` for non-reference types T. * Remove reference-deducing `util::value_by_key`; replace usages with new function `util::ptr_by_key`. * Add some missing header includes that were required but included only transitively. * Remove `operator<<` overload for optional in python/strprintf.hpp; replace with utility wrapper class that catches `std::optional<T>`. * Wrap some `std::optional` values with `to_string` in ostream output in python lib. Fixes #1154.
-
- Jul 24, 2020
-
-
thorstenhater authored
Rename import method to avoid Python keyword collision.
-
- Jul 13, 2020
-
-
thorstenhater authored
* Add import method for mechanism catalogues, allowing mechanisms from a second catalogue to be incorporated with a prefix, together with Python interface. * Expose `global_allen_catalogue`. * Extend unit tests to cover mechanism catalogue import and check for name collision error cases.
-
- Jun 24, 2020
-
-
Benjamin Cumming authored
Update core library: * support derivation of named mechanisms in catalogue from a string description of the parent. * fix bug in radois_ge region expression that was finding region_lt. * fix test for radius_ge region expression Add support for mechanism, global properties and catalogue shenanigans to python wrapper
-