- Dec 14, 2020
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Benjamin Cumming authored
Make the `cable_cell` interface read only by passing the decorations to its constructor in a new `decor` type. C++ library * Remove the paint/place/set_default interface from `cable_cell` * Create a `decor` type that: * stores lists of paintings and placings * stores a set of cable cell parameters * uses the `paint`, `place`, `set_default` interface that was deprecated from `cable_cell`. * Create `paintable`, `placeable` and `defaultable` variants that are sum types over the respective types that can be painted, placed and defaulted. * Remove the overloaded `cable_cell::paint`, `cable_cell::place`, `cable_cell::set_default` methods to single methods that consume the sum types. Unit Tests * Many small changes because many many tests use cable cell API. * There were no `cable_cell` unit tests! Not such a big deal, since cable_cell is tested implicitly in so many other tests * but I added cable_cell tests: not much at the moment but will quickly fill up as we work on reading, writing, etc. Python * Wrap the new decor type. * Update cable cell type to reflect read only API. * Wrap the cv_policy types and implement the same operator overloading.
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Nora Abi Akar authored
Fix segfault in modcc when min/max used in net_receive. * The error occurred when a synapse that use `max` or `min` expressions in the `net_receive` block: we test for linearity to check whether they can be coalesced; we cannot differentiate the expression; an error is raised but not reported; seg fault. * Fixes ` as_c_double` printing which does not print integers as doubles as intended. Fixes #1275
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thorstenhater authored
Fix a latent bug in the Python wrapper that was triggered in pybind11 v2.6.1 These changes ensure that the GIL is acquired before calling functions in C++ that may consume a Python object with reference count 1 as an argument, in which case the object's destructor is called at the end of the function, after any GIL acquired inside the function would have been released. Fixes #1271.
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- Dec 11, 2020
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thorstenhater authored
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- Dec 10, 2020
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Brent Huisman authored
* Move PR message instructions to 'Making a PR' section. * Move coding instructions to 'Write code' section.
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Brent Huisman authored
* Remove mention of the Copyright Transfer Agreement
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- Dec 09, 2020
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thorstenhater authored
* Fix pybind11 issues. * Retract suspicious fix. * Address comments.
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- Dec 08, 2020
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Brent Huisman authored
Replace CMAKE_SOURCE_DIR with PROJECT_SOURCE_DIR to pick up the correct paths when used as a sub-module. Fixes #1266.
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- Dec 07, 2020
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Brent Huisman authored
Update CMake configure to look for svgwrite when building docs. Fixes #1128.
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Brent Huisman authored
Set up contribution guides. Add a contribution guide, as well as * Added contribution section. * Moved content here from the wiki regarding (contribution) processes. Also added some incomplete / placeholder sections that can be improved later. * How to write an example * How to add a test * Coding style guidelines
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- Nov 30, 2020
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Brent Huisman authored
* An explanation of documentation structure. * Added HBP/Ebrains to acknowledgements.
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Nora Abi Akar authored
Fixes #1257
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Nora Abi Akar authored
Fixes a bug caused by swapping the `time` and `time_to` vectors in the `shared_state` and not swapping the corresponding data pointers in the `threshold_watcher` and `mechanism`. - This fix keeps the swapping optimization, and instead, the `threshold_watcher` and `mechanism` hold pointers to the std::vectors (not the underlying arrays) which are dereferenced before use. - The mechanism API functions have been renamed. - A unit test is also added that checks the interpolation behavior of the `threshold_watcher`. Fixes #1251
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- Nov 27, 2020
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Brent Huisman authored
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- Nov 23, 2020
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Nora Abi Akar authored
* Modify `cell kind` concept docs. * Add `cell description` concept docs. * Reorder the docs so that the recipe, cell kind and description, interconnectivity, hardware management, domain decomposition, and simulation are consecutive. Then start the more detailed cable cell docs.
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- Nov 19, 2020
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Nora Abi Akar authored
`pow(double x, int y)` is implemented as of ROCm-3.9 (May have been fixed earlier, don't have access to earlier versions)
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Brent Huisman authored
Change from long double to double for storing floating point values in modcc. WSL, and Windows generally, treats long double differently than Linux, which leads to inconsistencies in literal numeric values in code generated by modcc on the two platforms. Fixes #1245
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- Nov 18, 2020
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thorstenhater authored
* Add a readme for the C++ examples * Improved readme for dryrun Fixes #868, #1107.
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Sam Yates authored
Major changes in Python library and documentation: * Add global state (immutable after initialization) for the Python module that manages the mapping between probe metadata types and the method by which the corresponding [sample data can be collected and presented as Python objects. This is necessary for decoupling the implementation of the simulation wrapper from that of the various cable cell probe types. * Wrap each of the C++ cable cell probe types with a Python function that returns a `probe_info` object. * Add code for converting and accumulating C++ probe metadata and sample data, registered in the module global state against the metadata type info. * Make the `arbor.simulator` object responsible for recording all spike and sample data, with corresponding new methods. * Use NumPy arrays and structured datatypes for returning spike and sample data. * Place Python schedule proxies under an abstract interface so that consumers of the proxies can be made generic over schedule types. * Add unit tests for the `arbor.simulator` class and its new functionality, including distributed spike collection. * Rework all Python API documentation concerning probes, sampling, and spike recording; add information on newly exposed cable cell probe addresses. * Add new python example `single_cell_recipe.py` which is a generic recipe version of `single_cell_model.py`. * Adjust other code in the wrapper and examples to accommodate these changes. Minor changes in Python library: * Add equality tests for `arbor.location` and `arbor.cable` Python classes. * Use the `py::` namespace shorthand more often in the Python wrapping sources. * Add an implicit conversion for a pair of numbers to `arbor.cell_member`, so that e.g. probe ids can be specified simply as `(gid, index)`. * Add an implicit conversion from a tuple to `arbor.mpoint` so that a morphological point can be specified simply as `(x, y, z, radius)`. * Modify the interface to `arbor.regular_schedule` so that the overloads correspond more closely to the C++ API. In particular, `arbor.regular_schedule(dt)` now describes a schedule with times 0, dt, 2*dt, etc. Minor changes in C++ library: * Change test in FVM lowered cell implementation and exception message for `bad_source_description`: assert number of detectors is exactly the number of sources promised by the recipe. * Add comment describing `probe_metadata` object in `sampling.hpp` which asserts that the type and value of probe-specific metadata completely determines the correct interpretation of sampled data provided to a callback.
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- Nov 17, 2020
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Nora Abi Akar authored
* Return `arb::morphology` from `load_swc_xxx` methods for consistency with the NeuroML interface. * Fix unit tests. * Fix documentation
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Brent Huisman authored
Added a CONTRIBUTION.md page for the project. Contains a link to the wiki with more detailed description of the contribution workflow.
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Brent Huisman authored
Fixes #1230
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- Nov 13, 2020
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Benjamin Cumming authored
Fixes #1236
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Nora Abi Akar authored
Fix Python linking errors on some platforms. This appears to be related to the GCC visibility of methods overridden in header files, and is fixed by moving the implementation to the corresponding cpp files. Addresses the Travis CI failure of #1225
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- Nov 11, 2020
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Sebastian Schmitt authored
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- Nov 10, 2020
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Sebastian Schmitt authored
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Nora Abi Akar authored
* Add an example describing the content of a recipe in the recipe concepts page in the docs. * Mention that recipes are necessary, but can be abstracted away using the python `single_cell_model` (Hasn't been documented yet).
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Sebastian Schmitt authored
Speed up plotting in seaborn.relplot by disabling calculation of confidence intervals
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- Nov 09, 2020
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Sebastian Schmitt authored
Update the documentation to mention additional packages used in some python examples.
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Nora Abi Akar authored
Addresses some of the warnings from static analysis tools in #1084 * fix some instances where exceptions were constructed, but not thrown * fix use-after-move in a unit test.
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Sebastian Schmitt authored
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Sebastian Schmitt authored
* Adapt to moved readthedocs account
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Nora Abi Akar authored
* Various DOC changes/updates, most importantly to: * Single Cell Model * Recipe
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- Nov 06, 2020
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Sam Yates authored
* Put generated mechanisms for each built-in catalogue in their own namespace.
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Nora Abi Akar authored
* Remove blank line from `ball_and_stick.swc` * Mention that blank lines in SWC files indicate end of data. * Check for trailing data after parsing in the python interface. * Leave stream in good state if `parse_swc` encounters an empty line indicating end of data.
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- Nov 05, 2020
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Nora Abi Akar authored
* Rename `as_segment_tree` to `load_swc_arbor`. * Remove `swc_mode`: `sort_and_validate_swc` now performs the `relaxed` checks by default, `load_swc_arbor` performs the `strict` checks. * Change `load_swc_xxx` to only accept `swc_data` as an argument * Remove default constructor for `swc_data` and enforce validation of SWC records via `sort_and_validate_swc` at construction. * Add fixes for docs and unit tests.
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- Nov 02, 2020
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thorstenhater authored
* Add interface for querying names. * Add derived mechanisms to list, clean-up. * Add unit tests. * Add python bindings and docs.
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- Nov 01, 2020
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Nora Abi Akar authored
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- Oct 28, 2020
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Sam Yates authored
* Swap arguments in target count check in `fvm_lowered_cell_impl.hpp`. * Update unit test to suit.
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- Oct 15, 2020
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Benjamin Cumming authored
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