- Jun 16, 2021
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Sebastian Schmitt authored
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- May 17, 2021
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Nora Abi Akar authored
Fix mistakes reported by @Helveg in the Python tutorial docs.
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- Mar 30, 2021
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Charl Linssen authored
Co-authored-by:
C.A.P. Linssen <charl@turingbirds.com>
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- Mar 29, 2021
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Nora Abi Akar authored
Remove `gid` attribute of target of a connection, and local gap-junction site of a gap-junction connection (#1467) * Change the type of the target of a `connection` from `cell_member_type` to `cell_lid_type`. The target cell's gid is always known in both the recipe and simulation. * Change the type of the local site of a `gap_junction_connection` from `cell_member_type` to `cell_lid_type`, and make it such that the first argument of the connection is the peer site, and the second the local site. The local cell's gid is always known in both the recipe and simulation. * Change the type of the target of an `event_generator` from `cell_member_type` to `cell_lid_type`. The target cell's gid is always known in both the recipe and simulation. * New `cell_spike_events` and `cse_vector` for `simulation::inject_events`. * Simplify recipe sanity checks and remove associated exception types. * Fix unit tests, examples, docs
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- Mar 17, 2021
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Brent Huisman authored
* Add Python version of brunel.cpp example. * Enforce consistency in units: both C++ and Python APIs use unit `kHz` for all frequencies. * Align Python version `poisson_schedule` signature with C++ equivalent. * Update unit tests to suit API changes. * Update documentation to suit, along with minor additions related to networks and interconnectivity. * Add `brunel.py` to `basic.yml` tests
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- Feb 22, 2021
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Brent Huisman authored
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- Feb 18, 2021
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Brent Huisman authored
* Tutorial ring network added. A few typos fixed, crosslinks fixed. * MPI tutorial added. * Improved SVG generation, added separate label scaling, increased default label size. * Bugfix: didnt generate cable region in gen-labels.py used in `concepts/morphology.rst`. * Termified Interconnectivity page. * Termified probe nomenclature page. Will be moved in [this PR](https://github.com/arbor-sim/arbor/issues/1353) from python/simulation to concepts/probes_samplers.
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- Jan 22, 2021
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Sebastian Schmitt authored
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- Jan 15, 2021
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Nora Abi Akar authored
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- Jan 14, 2021
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Brent Huisman authored
* Used Sphinx glossary directive to create terms that can be referred to in `concepts/morphology.rst` and `concepts/labels.rst`. * Added note box on difference with Neuron, add source for NEURON cylinder discretisation * Parameters added to svg generation script: turn off colors, root * Fix cpp TOC duplication, match ordering in other sections. * State default cv policy * center/re -> midpoints * Clarify and remove compartment term
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- Jan 08, 2021
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Brent Huisman authored
* Add docs tutorial page for single_cell_recipe.py example * Adapted single_cell_recipe.py slightly * Improved labels and fixed some broken cross-linking * Fixed a typo here and there
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- Dec 18, 2020
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Nora Abi Akar authored
* Add 2 new examples to `python/examples` and their corresponding tutorials in the docs. 1. `single_cell_detailed.py` : a slightly more complex example using `single_cell_model` 2. `single_cell_detailed_recipe.py`: equivalent to `single_cell_detailed.py` but using a recipe. * Change `load_swc`-> `load_swc_arbor` for consistency. * Run Sphinx with specified PYTHON_EXECUTABLE. * Set PYTHONPATH env var in doc/CMakeLists.txt, such that it propagates correctly, including locally. * Build pyarb BEFORE html such that docs build can import arbor in Github Actions script.
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Nora Abi Akar authored
Add API for `single_cell_model` and `label_dict`
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- 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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- Nov 30, 2020
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Brent Huisman authored
* An explanation of documentation structure. * Added HBP/Ebrains to acknowledgements.
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- Nov 10, 2020
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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
* Various DOC changes/updates, most importantly to: * Single Cell Model * Recipe
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- Oct 09, 2020
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Brent Huisman authored
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