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  1. Apr 21, 2020
  2. Feb 11, 2020
    • Benjamin Cumming's avatar
      enable locset names for probe sites in single cell model. (#955) · ec1f7520
      Benjamin Cumming authored
      Use locset names to set probe sites in single cell model.
      
      1. Extend C++ cable_cell interface to provide a concrete list of locations associated with a locset on the cell.
      2. Extend Python single_cell_model to allow placement of probes on locsets.
      3. Remove "debug" output in Python ring example.
      
      The single cell model maintains a trace callback for each probe location, and needs to know the explicit locations before starting the simulation. The first step is required to enumerate and record the locations associated with a locset when attaching probes.
      
      Open issues: 
      
      1. The extension to `cable_cell` won't sufficiently support locsets that rely on random number generators with global seeds (it would require passing additional meta data required to fully instantiate the locset)
      2. Enhancing the probe recipe interface to be able to associate one `probe_id` with all locations in a locset (the number of which is not specified at the time the `probe_id` is created) would support the interface implemented for the `single_cell_model`.
      
      Note: The richer interface on the C++ side will be implemented in time (see #957).
      ec1f7520
  3. Feb 04, 2020
    • Benjamin Cumming's avatar
      Python Interface (#948) · cfad427a
      Benjamin Cumming authored
      A big update that wraps over 90% of the public C++ API, with enough functionality to let Python users to perform useful modelling.
      
      Key features
      - wrapping of cable cell functionality
        - user-defined explicit compartmentalisation not supported
      - `single_cell_model` abstraction unique to the Python wrapper that simplifies developing and testing single cell models
      - one-dimensional cell builder for Python wrapper that simplfies building cells that 
        - in and of itself limited in scope, but a very useful example of mapping a richer morphology builder onto `sample_tree`s.
      - parsing of region and location expressions from strings
        - implements a generic s-expression parser that we can use for other purposes later
      cfad427a
  4. Sep 25, 2019
    • akuesters's avatar
      Python feature probes and samples (#872) · 8e985d40
      akuesters authored
      Adds
      
      * to `recipe.cpp`: 
      `num_probes` and `get_probe` with helper function `cable_probe(kind, id, location)`
      * `sample.cpp`: 
      `sample` type with attributes `time` and `value`; a `sampler` with `samples()` and `clear()` and helper functions `attach_sampler(sim, dt)` for adding all probes as well as `attach_sampler(sim, dt, probe_id)` for adding one probe
      * `morphology.cpp`: 
      `location` as `arb::mlocation` with `branch` and `position` 
      * corresponding docs and example
      * update to new cable cell semantics in c++ validation test
      
      fixes #762
      8e985d40