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  1. Dec 09, 2020
  2. Nov 18, 2020
    • Sam Yates's avatar
      Expose diverse probes in Python API. (#1225) · 1bfe96bc
      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...
  3. Oct 02, 2019
    • akuesters's avatar
      Python wrapper: thread safe recipe (#882) · f30c4204
      akuesters authored and Benjamin Cumming's avatar Benjamin Cumming committed
      Ensure that errors in Python callbacks that are called from multithreaded C++ code propogate the correct Python error back to the parent Python callback site, and that no callbacks are called from other threads if an error has already ocurred.
      - protects each recipe callback with a mutex, stores python exception, catches and throws python exception if occured
      - methods calling recipe (in simulation and partition_load_balance) are protected as well by try catch, resets and rethrows python exception (if occured) or else throws C++ exception
      
      fixes #792
      f30c4204
  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
  5. Jul 02, 2019
    • akuesters's avatar
      Python wrapper: documentation (#799) · 1f4eacd2
      akuesters authored and Benjamin Cumming's avatar Benjamin Cumming committed
      Add docs for Python wrapper to ReadTheDocs:
      
      - Overview, Common Types, Hardware Management, Recipes, Domain Decomposition, Simulations, Metering
      - Installing Arbor: Optional Requirements (Python), Buidling and Installing (Python Frontend), and Installation (Python Module)
      
      Missing (, since not implemented yet): 
      
      - probes
      - arbor-sup 
      - hint maps in domain_decomposition
      - reset, events, empty schedule in event_generator
      Also does not cover unit testing (since doc is user-centric).
      
      Makes also defaults and units in wrapper consistent.
      
      Fixes  #766
      1f4eacd2
  6. Jun 24, 2019
    • Benjamin Cumming's avatar
      Python spikes (#788) · 726328c4
      Benjamin Cumming authored
      Support for recording spikes generated by a simulation in the Python wrapper
      * Implement a `spike_recorder` that holds a shared pointer to a `std::vector` of spikes, and a callback for the `arb::simulation` spike recording API.
      * Add `python/example/ring.py` that creates a ring network, then records and prints spikes.
      * Some fixes to get the full `recipe` -> `domain_decomposition` -> `simulation` -> `spikes` workflow to work
        * always use default `global_parameters`: user customization of global parameters for cable cells can wait until the ion species interface is finished.
        * change the Python recipe interface for `recipe::connections_on` to use `pybind11::objects` because of shim.
      * Some small improvements to error and help messages.
      
      Fixes #764 
      726328c4
  7. Jun 12, 2019