- Oct 27, 2016
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Sam Yates authored
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
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- Oct 26, 2016
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Ben Cumming authored
Feature/cable validation
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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
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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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Vasileios Karakasis authored
Address bug in fix for cell clone ctor.
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Sam Yates authored
* Add test for cell clone semantics. * Fix `1cell::cell(clone_cell_t, const cell&)` for correct copy semantics.
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Sam Yates authored
Fixes Clang 3.7 failure to compile.
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Ben Cumming authored
Add analytic simple cable solver.
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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 22, 2016
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Vasileios Karakasis authored
The problem described in previous commit was caused only inside the cell's copy constructor, where an assignemt for `std::unique_ptr` was attempted. Since `std::unique_ptr`'s cannot be copy-assigned, I have made that assignment manually moving the just cloned other's segment to the cell being constructed. The original `assign_by` method, relying on STL's `assign()` cannot accommodate this without changing its semantics (as pointed out by @halfflat), which would then also conflict with STL's semantics.
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- Oct 20, 2016
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Sam Yates authored
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Sam Yates authored
Left out a factor of λ in equation 4.
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Sam Yates authored
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Sam Yates authored
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Sam Yates authored
* Expand comments, function documentation in Julia script. * Use '#' for top level headers in `README.md`
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Ben Cumming authored
Fix markdown of README.md
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klijn1 authored
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klijn1 authored
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- 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 17, 2016
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Vasileios Karakasis authored
* Container assignment requires that the elements of the target container are copy constructible, whereas `unique_ptr`s in Clang 7.0 are only move constructible, preventing `rangeutil.hpp` from compiling. * Includes correct header (`<numeric>`) that provides `std::accumulate()`.
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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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