- Oct 26, 2016
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Sam Yates authored
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Sam Yates authored
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Sam Yates authored
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Sam Yates authored
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Sam Yates authored
* Implement Rallpack1 validation test (with a workaround for inability to set membrane conductance). * Fix bug in L≠1 case in PassiveCable.jl (this may still be wrong). * Fix bug in peak delta computation in trace analysis when both traces have no local maxima. * Gentle failure on missing `numeric_soma.json` * Allow multiple `-s` selection operations for `tsplot`, acting disjunctively.
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- Oct 25, 2016
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Sam Yates authored
* Amend data directory path in validation tests. * Enmodulate `hh_soma.jl` * Add HH channel reference data generations script. * Switch `validate_soma.cpp` to numeric reference data. * Consolidate common code in `validate_ball_and_stick.cpp` * Add (nearly) Rallpack1 validation test (see below). * Gentle failure on absence of reference data in `validate_ball_and_stick.cpp` Can't yet override mechanism default parameter values, so the cable cell model added to `test_common_cells.hpp` lets the default stand; validation script will have to use the default membrane conductance rather than that given by Rallpack1.
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- Oct 24, 2016
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Sam Yates authored
* Use consistent scaling for y[1] scalar voltage in hh_soma.jl * Also: add more reserved target names to CMakeLists.txt helper function.
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Sam Yates authored
* Move generation and data to top-level validation directory. * Make BUILD_VALIDATION_DATA and VALIDATION_DATA_DIR cache vars. * Add helper CMake functions for data generation. Note `validation/ref/numeric/foo.sh` is just a placeholder.
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Sam Yates authored
* Align defaults with values used in most of the NEURON validation scripts. * Use consistent 100 Ω·m bulk resistivity across both NEURON test models and basic validation cells.
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Sam Yates authored
Also: * Ensure intrinsic and passive properties properly set on test cells.
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- Oct 20, 2016
- Oct 19, 2016
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Sam Yates authored
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Sam Yates authored
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Sam Yates authored
* New file (Julia module): PassiveCable.jl * Update script documentation for profstats * Add (too brief) documentation for PassiveCable.jl * Fix `env`, `python` invocation on python scripts.
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Sam Yates authored
add reference solution for hh soma test
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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
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Ben Cumming authored
Update README.md with current installation procedure.
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klijn1 authored
- changed back a non-typo (that will tech me to use spell checking...) - Output result of test-function as exit value
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klijn1 authored
Add Julia installation steps and example run Silence variable not used warning in validate.cpp Add missing include to rangeutil.hpp
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- Oct 14, 2016
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Ben Cumming authored
Make lambda transform iterators copy-assignable.
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Ben Cumming authored
Enhanced validation tests.
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- Oct 13, 2016
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Sam Yates authored
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Sam Yates authored
* Add unit test that demonstrates need for non-const version of `max_element_by` * Rename file stream member variable from `f_` to `out_` in `validation_data.hpp`.
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Ben Cumming authored
Fixes support of scientific notation in modcc.
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- Oct 12, 2016
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Vasileios Karakasis authored
Also the corresponding unit test was rewritten in a less repetitive manner.
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- Oct 11, 2016
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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 `mode...
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- Oct 08, 2016
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Ben Cumming authored
modcc: support for comments starting with '?'
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- Oct 07, 2016
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Vasileios Karakasis authored
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Sam Yates authored
add unit test that shows bug in fvm
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Benjamin Cumming authored
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Benjamin Cumming authored
* add unit test fvm_multi.mechanism_indexes that fails to show bug in ticket #20 * add interface to fvm_multicell for getting list of stimuli * add unit test that checks stimuli are correctly added to lowered cell
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Vasileios Karakasis authored
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- Oct 06, 2016
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Ben Cumming authored
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- Oct 05, 2016
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Vasileios Karakasis authored
update modcc to latest modparser trunk
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- Oct 04, 2016
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Benjamin Cumming authored
* update the out of date version of modparser was added to the repository * fix some warnings about unused static functions in a modcc test header * move modcc/src path contents to modcc, because there was little point having the additional sub directory.
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Ben Cumming authored
Moved over modcc unit tests.
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