- Oct 06, 2021
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Brent Huisman authored
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- Oct 05, 2021
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Sebastian Schmitt authored
- `make install` in CI - make `build-catalogue` play nice with Python 3.6 - execute `build-catalogue`
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- Oct 04, 2021
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Brent Huisman authored
Fixes #1666
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Espen Hagen authored
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- Sep 30, 2021
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Sebastian Schmitt authored
Limit poisson schedule with a stop time using the same semantics as the regular schedule. closes #1617
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- Sep 29, 2021
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Thorsten Hater authored
More, subtler fallout of the ABI patchset: When mechanisms are added to empty regions, various, layered segfaults appear. 1. `set_parameter` will receive a `nullptr` upon linear search, throwing `no such parameter` 2. Guarding this for finite `width` uncovers further need in the ABI interface methods 3. This is caused by early exit in `instantiate` on `width == 0` 4. Getting rid of this is better, as we can treat vacuous mechanism painting like all others... 5. ...but causes another segfault, since we default index arrays to `cv_pos.back()` but `cv_pos` is empty. This patch fixes all of the above and in addition removes mechanisms without support before reifying them on the FVM cells. Relevant tests are added.
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- Sep 28, 2021
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Robin De Schepper authored
Expose default (empty) catalogue constructor to Python
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Nora Abi Akar authored
Fixes 2 bugs where modcc expects a range variable but gets a non-range variable instead. PowBinaryExpressions were being handled separately from other BinaryExpressions and as a result, some crucial analysis was being skipped on the analysis of the lhs and rhs arguments. This PR incorporates the analysis and printing of PowBinaryExpression into BinaryExpression. Printing code for a masked AssignmentExpression was not handling the case of a non-range variable on the rhs of the assignment correctly. In that case, an explicit cast to a vector is needed, which is added in this PR.
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- Sep 24, 2021
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Sebastian Schmitt authored
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- Sep 20, 2021
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Robin De Schepper authored
The duplication arose from slightly more complicated composition than usual but could be resolved by proper MRO, it took me a few passes from its original form as well before I figured out the situation is not as complicated as it seems. `super()` is equal to `super(cls, self)` where `cls` is obtained from the current function's class scope. If arg 2 is an object it will start an MRO search of the object, but skipping classes before the 1st arg type is encountered. In our case with the following base classes: `(_command_template, base_command_class)` this means we can define our base logic in `_command_template` and use `super()` calls there to traverse the MRO in `(base_command_class,)`, so by simply defining `class install_command(_command_template, install)` and `bdist_wheel_command(_command_template, bdist_wheel)` our MRO issue is solved and the duplication removed.
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Nora Abi Akar authored
- Allow CV policies to be parsed and written as a `defaultable` in an ACC decor description. - The format used is `(default (cv-policy (_cv-policy-sexpr_)))`. - Add unit tests. - Fix strange white-space formatting. Fixes #1660
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Sam Yates authored
* Filter results of `ls::on_components(1, reg)` to avoid duplicate or coincident locations arising from terminal zero-length cables in region argument.
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- Sep 09, 2021
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Nora Abi Akar authored
* Fielding an add_sampler call while having no probes is not an error.
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- Sep 06, 2021
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Benjamin Cumming authored
Reduce number of parallel build jobs to reduce risk of OOM in CI builds.
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Benjamin Cumming authored
Neurolucida ASCII files store samples as `(x y z diameter)`, which were incorrectly being interpreted as `(x y z radius)`.
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- Sep 01, 2021
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Brent Huisman authored
Emphasize pip as the preferred method of installation.
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Brent Huisman authored
Github seems to dislike spaces in Markdown URLs.
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Brent Huisman authored
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- Aug 27, 2021
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thorstenhater authored
- Fixes a set of undefined value warnings. - merge identical `case`s
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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.
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- Aug 24, 2021
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kanzl authored
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thorstenhater authored
* Categorise ASSIGNED RANGE variables as STATE-ish. * Also use the opportunity to clean up the infoprinter. * Accidentaly fix bug in propagating parameter ranges from NMODL
️ `mechinfo` Fixes #1623.
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- Aug 23, 2021
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thorstenhater authored
* Clean-up AVX SIMD mask setting. * Remove redundant global constant in the memory lib. * Fix 'unused variable' warning in `test_probe.cpp`.
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- Aug 20, 2021
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thorstenhater authored
- Add a set of test cases to check the behaviour - Remove the function `(nil)` from the the DSL - Remove `nil` and `()` as literals - Add functions `(region-nil)` and `(locset-nil)` Fixes an issue where `join` (and likely `intersect`) would not work due to the fact that `nil` values could not be coerced to `region` or `locset`. This occurred while loading a NML files. While investigating it was found that certain calls, eg `(join () ())` are ambiguous and cannot be resolved without changes in no proportion to the gain. The cause here is that we can resolve `()` as region or a locset and at the same time `join` maps a list of locsets or regions to a locset or region, consequently `(join () ())` can be both. For future reference, in `label_parse.cpp::eval` we look for the first match in the `eval_map` of a function name that can be successfully evaluated. However, this might not be the best match (and the ordering depends on the internals of `eval_map`). We _could_ check all successful evaluations, but as eval is recursive, this idea has some obvious issues.
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- Aug 19, 2021
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Nora Abi Akar authored
Fixes hipcc rocm-4.0.1 build for AMD GPU Fixes #1628
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Sebastian Schmitt authored
* Run examples via scripts (closes #1566)
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- Aug 17, 2021
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Sebastian Schmitt authored
- make spack ci run use arbor version information - Cache Spack for GH Actions
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- Aug 16, 2021
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Brent Huisman authored
Latest Pandas versions required unique indices, breaking the plotting in the python examples.
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- Aug 10, 2021
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Brent Huisman authored
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- Aug 02, 2021
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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`.
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Brent Huisman authored
* Bit of review on the copy of the mech abi docs. * Convert api/abi docs to C Domain directives.
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- Jul 29, 2021
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Benjamin Cumming authored
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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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- Jul 23, 2021
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thorstenhater authored
Add clang sanitizer passes to GH CI.
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- Jul 05, 2021
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thorstenhater authored
Closes #1547. - Move `MechCat*Iter` to module instead of catalogue class - Add `keys`, `values`, and `items` - Fix a typo.
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Sebastian Schmitt authored
Run only on Linux and Spack/develop closes #1534
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- Jul 02, 2021
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Nora Abi Akar authored
The visibility of symbols in the python shared library is set to 'hidden'. However, examining the dynamic symbol table of the generated `.so` file revealed that all the symbols of the static arbor libraries are still visible. This causes some issues on the Mac M1. To resolve, all source files are now compiled with `-fvisibility=hidden`.
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Brent Huisman authored
- Minor fixes to python examples. - Fix `mpi.py` to use new label API. - Rename `mpi.py`.
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Brent Huisman authored
- zenodo entry for v0.5.2 - minor formatting update to spack file
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