- Jun 10, 2022
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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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- Mar 16, 2022
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Brent Huisman authored
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Thorsten Hater authored
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Nora Abi Akar authored
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Thorsten Hater authored
Since we have support for ACC loading, the errors thrown by `paint` are no longer sufficiently informative. Even before that it was already hard to correlate source and locus of painting errors. Example ``` $> python3 main.C51A.py Traceback (most recent call last): File "main.C51A.py", line 33, in <module> cell = A.cable_cell(morph, labels, decor) RuntimeError: cable_cell: cable (cable 6 0 1) overpaints ``` This adds more details to the error message ``` $> python3 main.C51A.py Traceback (most recent call last): File "main.C51A.py", line 33, in <module> cell = A.cable_cell(morph, labels, decor) RuntimeError: cable_cell: Setting property 'ion-reversal-potential' on region '(region "soma_group")' overpaints at '(cable 6 0 1)' ```
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- Mar 11, 2022
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Thorsten Hater authored
* Make brunel.py setup faster. * Use one generator for both populations.
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- Mar 08, 2022
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boeschf authored
filter out death test on daint single_node_release
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- Mar 04, 2022
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boeschf authored
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- Feb 28, 2022
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Sebastian Schmitt authored
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- Feb 24, 2022
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boeschf authored
Exports all symbols so arbor can be compiled as set of shared libraries. In order to export all symbols correctly, one macro per library and one global macro are added. The content of the macros is determined at configure time depending on build variant (static/shared), compiler, and platforms (linux, mac os) and goes into the library's include directory as `export.hpp` when installed (at build time it resides at cmake's temporary build directory). The per-library macro is named `ARB_LIBNAME_API` and goes in front of to-be-exported symbols. The global macro is `ARB_SYMBOL_VISIBLE`. This PR adds the annotation in all of the places where it is required. Most of them are in the public headers (and corresponding sources) but some are also added in internal headers, which were required for the unit tests to link properly. Fixes #1752
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Thorsten Hater authored
Half-half dev and user docs on NMODL optimisation. Actually apply that advice in hh.mod
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- Feb 14, 2022
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Sebastian Schmitt authored
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- Feb 10, 2022
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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') ```
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Brent Huisman authored
* Some badges corrected (build) and added (Gitter) * Minor Spack backports * Small updates to `release.rst`
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Nora Abi Akar authored
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Espen Hagen authored
Closes #1822. Adds a separate tutorial for extracellular signal predictions using LFPykit to the docs. Adds some minor improvements to the corresponding python example file. Introduces Intersphinx for linking to other documentation.
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- Feb 07, 2022
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Thorsten Hater authored
* Users may not give dt < 0 to simulation.run() * Add and throw domain_error.
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- Jan 27, 2022
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Brent Huisman authored
* Update VERSION to `v0.6.1-dev` * Updates to `doc/release.rst` * Update Zenodo citation info for v0.6 * Update copyright info and maintainers in `spack/package.py` from upstream * Fix error in build-badge docs
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Brent Huisman authored
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