- Nov 18, 2020
-
-
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 tha...
-
- Nov 17, 2020
-
-
Nora Abi Akar authored
* Return `arb::morphology` from `load_swc_xxx` methods for consistency with the NeuroML interface. * Fix unit tests. * Fix documentation
-
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.
-
Brent Huisman authored
Fixes #1230
-
- Nov 13, 2020
-
-
Benjamin Cumming authored
Fixes #1236
-
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
-
- Nov 11, 2020
-
-
Sebastian Schmitt authored
-
- Nov 10, 2020
-
-
Sebastian Schmitt authored
-
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).
-
Sebastian Schmitt authored
Speed up plotting in seaborn.relplot by disabling calculation of confidence intervals
-
- Nov 09, 2020
-
-
Sebastian Schmitt authored
Update the documentation to mention additional packages used in some python examples.
-
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.
-
Sebastian Schmitt authored
-
Sebastian Schmitt authored
* Adapt to moved readthedocs account
-
Nora Abi Akar authored
* Various DOC changes/updates, most importantly to: * Single Cell Model * Recipe
-
- Nov 06, 2020
-
-
Sam Yates authored
* Put generated mechanisms for each built-in catalogue in their own namespace.
-
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.
-
- Nov 05, 2020
-
-
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.
-
- 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.
-
- Nov 01, 2020
-
-
Nora Abi Akar authored
-
- Oct 28, 2020
-
-
Sam Yates authored
* Swap arguments in target count check in `fvm_lowered_cell_impl.hpp`. * Update unit test to suit.
-
- Oct 15, 2020
-
-
Benjamin Cumming authored
-
Benjamin Cumming authored
-
Benjamin Cumming authored
-
- Oct 14, 2020
-
-
thorstenhater authored
Memory access optimization for the fine matrix GPU solver.
-
thorstenhater authored
Optimise the hh NMODL implementation to reduce unnecessary loads/stores and memory overheads.
-
- Oct 09, 2020
-
-
Brent Huisman authored
-
Nora Abi Akar authored
Add a catalogue of mechanisms used by the BBP models.
-
Nora Abi Akar authored
* Add some log messages in python examples * Add python examples to CI
-
Nora Abi Akar authored
* Fix some broken links and typos. * Fix out-of-date documentation. * Reword some of the existing sections.
-
Brent Huisman authored
-
Nora Abi Akar authored
-
- Oct 08, 2020
-
-
Brent Huisman authored
Remove Python API ref page, Spack Install, fix some links
-
- Oct 07, 2020
-
-
Brent Huisman authored
Remove imported dependencies in the documentation generation.
-
Brent Huisman authored
-
- Oct 06, 2020
-
-
Sebastian Schmitt authored
-
Benjamin Cumming authored
-
- Oct 05, 2020
-
-
Brent Huisman authored
* Python examples: Updated to use region expressions (quotes) * Python examples: Uniform plotting * Python examples: Removed tutorial directory (example roughly matches python/example/single_cell_model.py) * Python examples: Rewrote flat_cell_builder() to segment_tree()
-
Brent Huisman authored
* Synced pages between Concepts, Python API and C++ API wherever possible * Recipe pages conform between the three section (concepts, python, c++) * Cell, Cable Cell and Cell * pages are rearranged and provided with some copy explaining the relationship between them. * Moved Python API out of Concepts * Renamed Concepts "How does Arbor work?" * Added Python Module Index plus mock import of Arbor for RTD build (unfortunately won't show there) * Broke out Interconnectivity (synapses) page. * Reworked Single Cell Model page into a quick start, with lots of cross referencing. * Tweaked logo. * Added Spack to install options. * Updated blurb. * Documentation now follows EU capitalization rules. * Assorted typofixes
-
Benjamin Cumming authored
-