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  1. Oct 19, 2016
    • Benjamin Cumming's avatar
      add reference solution for hh soma test · a20f2acb
      Benjamin Cumming authored
      * julia script that uses SUNDIALS to solve the single compartment
        model with HH channel. The model has 4 variables (voltage and
        3 gating variables), which are coupled in the solver (i.e. not
        split like in Neuron / nest-mc.
      * SUNDIALS uses variable order stepping and variable size time steps
        with error detection to accurately integrate in time
      a20f2acb
    • Ben Cumming's avatar
      Merge pull request #31 from w-klijn/master · 14c6c1a8
      Ben Cumming authored
      Update README.md with current installation procedure.
      14c6c1a8
    • klijn1's avatar
      Fix review comments: · 787357c5
      klijn1 authored
       - changed back a non-typo (that will tech me to use spell checking...)
       - Output result of test-function as exit value
      787357c5
    • klijn1's avatar
      Update README.md with current installation procedure. · f4564b2f
      klijn1 authored
      Add Julia installation steps and example run
      
      Silence variable not used warning in validate.cpp
      Add missing include to rangeutil.hpp
      f4564b2f
  2. Oct 14, 2016
  3. Oct 13, 2016
  4. Oct 12, 2016
  5. Oct 11, 2016
    • Sam Yates's avatar
      Enhanced validation tests. · ee3b83c5
      Sam Yates authored
      Validation of simulation results by comparing L-infinity distance and maximum peak displacement in voltage traces taken at mid-points and end-points of sections.
      
      Note that these tests will broadly _fail_ at this point.
      
      Reference data generation and visualization:
      * Use voltage traces as validation data from NEURON; refactor generation scripts.
      * Generate validation data as a dependency of `validation.exe`.
      * Store validation data in a `tsplot`-compatible format.
      * Extend `tsplot` to handle multiple time series per file, a non-time 'time' axis (see `-A` option), filtering of time series by meta data queries (see `-s` option).
      * Remove pre-generated spike-time validation data files.
      
      Core extensions:
      * Add a single-cell `singleton_recipe` recipe wrapper.
      * Allow cell descriptions to be cloned (explicitly) for use with this wrapper.
      * Add `simple_sampler` which maintains a trace of scalar observables as a vector of (time, value) pairs.
      * Allow cell groups to be exposed from `model` (used for post-synaptic event injection in synapse validation test.)
      
      Utility extensions:
      * Add `math::signum` function.
      * Fix `value_type` determination in `util::transform_iterator` where the underlying iterator dereferences to a reference type.
      * Add `util::max_element_by` and `util::max_value` sequence utilities to `rangeutil.hpp`.
      * Small bug fixes for `util::optional` (one const correctness case, and proper behaviour for implicit conversion of `nothing_t` to `optional<void>`.)
      * Generic `util::first` and `util::second` accessor functional objects for reference access to `std::pair` fields in the absence of generic lambda functions.
      * Add `util::path` for path manipulation, corresponding to a subset of C++17 `std::filesystem::path` functionality. Only POSIX path semantics supported at this point.
      
      Validation tests:
      * Rework all validation tests as comparisons of voltage trace data against a (presumably converged) reference trace generated by NEURON.
      * Add options to `validation.exe` driver for verbose output of test results (`-v`), limiting the compartment number in convergence tests (`-m`) and saving the generated traces to a `tsplot`-compatilble JSONfile (`-o`).
      * Gather trace comparison metrics and analysis into `trace_analysis.hpp` and `trace_analysis.cpp`.
      * Add super simple command line argument parsing utility `tinyopt.hpp`.
      * Make a consistent naming of `ball_and_3stick` model across sources.
      * New `ball_and_taper` model.
      ee3b83c5
  6. Oct 08, 2016
  7. Oct 07, 2016
  8. Oct 06, 2016
  9. Oct 05, 2016
  10. Oct 04, 2016
  11. Oct 03, 2016