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  1. Jun 16, 2021
  2. May 17, 2021
  3. Mar 30, 2021
  4. Mar 29, 2021
    • Nora Abi Akar's avatar
      Remove `gid` attribute of target of a connection, and local gap-junction site... · db0041a5
      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
      db0041a5
  5. Mar 17, 2021
    • Brent Huisman's avatar
      Port of Brunel example (#1404) · c326ab3b
      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
      c326ab3b
  6. Feb 22, 2021
  7. Feb 18, 2021
    • Brent Huisman's avatar
      Tutorials: ring network (#1313) · 506ff916
      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.
      506ff916
  8. Jan 22, 2021
  9. Jan 15, 2021
  10. Jan 14, 2021
    • Brent Huisman's avatar
      Docs: define branch, mlocation, cv default. (#1302) · b10238e0
      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
      b10238e0
  11. Jan 08, 2021
  12. Dec 18, 2020
    • Nora Abi Akar's avatar
      Docs: Python examples (#1279) · 6ebfb3db
      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.
      6ebfb3db
    • Nora Abi Akar's avatar
      Docs: Add missing class descriptions (#1280) · fdd30bda
      Nora Abi Akar authored
      Add API for `single_cell_model` and `label_dict`
      fdd30bda
  13. Dec 14, 2020
    • Benjamin Cumming's avatar
      Decor (#1235) · ac63809f
      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.
      ac63809f
  14. Nov 30, 2020
  15. Nov 10, 2020
  16. Nov 09, 2020
  17. Oct 09, 2020