- Jul 19, 2022
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Brent Huisman authored
- Generate timestamped VERSION once, to properly group on Test.PyPI. Example: - https://github.com/arbor-sim/arbor/actions/runs/2696804929 - https://test.pypi.org/project/arbor/0.7rc20220719101015/ - Update/simplify release documentation. - Update to v0.7
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- Jul 18, 2022
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Brent Huisman authored
* - Weekly CI Python wheel build pushes to Test.PyPI.org - Easy availability at https://test.pypi.org/project/arbor/ - Small change in documentation around VERSION - Delete superfluous setup.py file.
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- Jul 04, 2022
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Brent Huisman authored
Move Python build to `pyproject.toml`, bump Python minver to 3.7, fix macos wheel generation (#1916) * Failing Macos Python wheel builds fixed. * Macos Python wheels now come with dual-arch (x86-64 and arm64) * Moved (nearly) all Python build instructions to `pyproject.toml` * Enables 'build isolation', and need to specify build-deps only once, no need for users or CI scripts to pre-install them. * Enables editable `pip` installs (`pip install -e ./arbor`) * Compatible with 'build frontends' `pip` and `build`. * Passing CMake options actually got shorter * Drop Python 3.6 support.
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- Jun 30, 2022
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Brent Huisman authored
- Fix line numbers in tutorials, fallout from #1906 - Mention arbor-contrib in a few relevant places - Correct some fallout from #1904 - A new hardware and profiling tutorial, and covers things moved out of other examples in #1904 - Various other documentation fixes
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Simon Frasch authored
Adds the ability to scale parameters of (density) mechanisms based on inhomogeneous properties along a cell. Two new types are added: - iexpr: An expression describing the scaling factor computation. - scaled_mechanism: A wrapper struct around a mechanisms with iexpr attached to selected parameters. Closes #1650
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- Jun 23, 2022
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Thorsten Hater authored
Post-Merge clean-up for the diffusion PR - remove redundant `WRITE`s in mechanisms - diffusion.py is now closer in functionality to diffusion.cpp - diffusion.py now prints a table of results
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Thorsten Hater authored
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- Jun 21, 2022
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Brent Huisman authored
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Thorsten Hater authored
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Thorsten Hater authored
Encapsulates 80% of cases: ```cxx rec = recipe() ctx = make_context() dec = partition_load_balance(rec, ctx) sim = simulation(rec, dec, ctx) ``` is now written as ```cxx rec = recipe() sim = simulation(rec) ``` In python we use keyword args to allow both to be specified separatly. Partially fixes #1862
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Thorsten Hater authored
# Introduction Plasticity processes are mediated by signalling ions, eg Ca++, which are generated by synapses upon reception of a spike. This adds a quantity `Xd` for any ion `X` - initialised as `Xi` - read from and written to by NMODL density and point mechanisms. - propagates according to a diffusion law `∂_t Xd = ∂_z c X ∂_z Xd + iX/qi`. - in contrast to `Xi` and `Xo` there's no buffering and the update in mechanisms occurs atomically (and at a different time) More details can be found in the documentation. For the future there are some low hanging optimisations - per-ion conductivity for the matrix solver could be disabled if no diffusion is computed - cable and diffusion solvers store duplicates of the solver state, could be merged Closes #1651
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- Jun 20, 2022
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Benjamin Cumming authored
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- Jun 16, 2022
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Benjamin Cumming authored
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Thorsten Hater authored
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- Jun 14, 2022
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Jannik Luboeinski authored
Introduces the new policy `round_robin_halt`. This enables to halt at the current item until the policy `round_robin` is called again. Related to issue #1749.
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- Jun 13, 2022
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Thorsten Hater authored
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Thorsten Hater authored
Fix a number of small issues regarding performance and correctness found by PVS Studio in the quest for a better code base.
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- Jun 10, 2022
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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
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Brent Huisman authored
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- Jun 08, 2022
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Brent Huisman authored
Add tutorial on how to integrate a specific Allen Institute cell DB into Arbor. Use the example shown at Bernstein'20.
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Brent Huisman authored
Add tutorial on using all logical cores on a machine, facilitated by the new flag to context creation.
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- Jun 03, 2022
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Sebastian Schmitt authored
Extend the probe demo example with point probes sampling the conductance of two synapses. Co-authored-by:
Brent Huisman <brenthuisman@users.noreply.github.com>
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- Jun 02, 2022
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Brent Huisman authored
As per #1731, this PR adds a dependencies version policy to the docs. It also includes a file containing a list of all configure-time deps. Obsoletes wiki page.
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- May 26, 2022
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Thorsten Hater authored
Add a first round of developer documentation, evolving from the older `internal` part of the docs.
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- May 24, 2022
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boeschf authored
Remove checks for move ctor when it could be elided
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- May 18, 2022
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Thorsten Hater authored
Add accessors for the following items in `global_properties` - ion_species (name -> valence) RO - ion_data (name -> initial values) RO - ion_rev_pot (name -> rev pot mech) RO - Vm, rL, TK, Cm: RW Fixes: #1802
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Brent Huisman authored
Upstream bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006615 Currently affects Ubuntu 22.04 users. Co-authored-by:
Simon Frasch <simon.frasch@cscs.ch>
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- May 05, 2022
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Brent Huisman authored
EOM
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Nora Abi Akar authored
Ensure all indices into ABI variables are generated in dependency order, eg ``` idx = indices[iy] foo = foos[ix] ```
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Nora Abi Akar authored
Fix a crash in GPU code when threshold detector is used for the first time and its internal state is allocated with a wrong size.
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Benjamin Cumming authored
- Add a callback to be executed between epochs. - Add example: print progress indicator
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- May 04, 2022
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Thorsten Hater authored
TL;DR: Simple change for ~2% gain on GPU in a typical workload.
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- Apr 27, 2022
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Thorsten Hater authored
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- Apr 26, 2022
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Thorsten Hater authored
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Thorsten Hater authored
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Robin De Schepper authored
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Espen Hagen authored
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- Mar 24, 2022
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Benjamin Cumming authored
* add support for parsing markers defined in asc files * add hitherto unknown "High" leaf branch type
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- Mar 22, 2022
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Sebastian Schmitt authored
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Thorsten Hater authored
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