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Consolidate and simply common validation testing code #41

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halfflat opened this issue Oct 27, 2016 · 1 comment
Closed

Consolidate and simply common validation testing code #41

halfflat opened this issue Oct 27, 2016 · 1 comment
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@halfflat
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Partially done already, but address:

  • Duplicate convergence testing code across validation tests.
  • Poor clarity in assert_convergence code.
@halfflat halfflat self-assigned this Oct 27, 2016
halfflat added a commit to halfflat/arbor that referenced this issue Oct 27, 2016
@halfflat
Consolidate validation test code (issue arbor-sim#41)
eae3e68 
* Simplify trace analysis and reporting code in
  `trace_analysis.hpp`
* Consolidate convergence test run procedures into
  new class `convergence_test_runner`.
halfflat added a commit to halfflat/arbor that referenced this issue Oct 28, 2016
@halfflat
Consolidate validation test code (issue arbor-sim#41)
1b929ff 
* Simplify trace analysis and reporting code in
  `trace_analysis.hpp`
* Consolidate convergence test run procedures into
  new class `convergence_test_runner`.
bcumming added a commit that referenced this issue Oct 28, 2016
@bcumming
Merge pull request #48 from halfflat/feature/consolidate-validation-t…
550da10 
…ests

Consolidate validation tests (issue #41)
@halfflat
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Resolved PR#48

bcumming pushed a commit that referenced this issue Nov 4, 2016
@Ivanmartinezperez @bcumming
Omp (#38)
0ded25a 
* first version of openmp threading back end

* adding openmp parallel sort implementation

* OpenMP sort working

* Support for units syntax within state block.

* Add soma-less cable cell to test cells.

Also:
* Ensure intrinsic and passive properties properly set on test cells.

* Change bulk resistivity default.

* 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.

* OpenMP back end working

* Add Extrae+paraver support, needs to fix compilation warnings

* Reorganize validation data generation

* 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.

* Bugfix: hh_soma.jl

* Use consistent scaling for y[1] scalar voltage in hh_soma.jl
* Also: add more reserved target names to CMakeLists.txt
  helper function.

* Refactor convergence tests; add numeric soma ref.

* 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.

* Add Rallpack1 validation, plus bugfix, clean

* 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.

* Remove errant test file.

* file's cleanup

* Remove tabs

* Use correct routine in numeric_rallpack1.jl x0.3

* Configure-time test for julia

* `math::infinity<>()` wrapper for infinity

* Use name `i_e` for Stim current density

* Use `math::infinity<>()` for infinite value

* Adds unit tests for the STATE block.

* Add "lib" to search prefixes for libtbb

* Fix quoting error in library search.
* Add "lib" to prefixes when system is "Linux".

* Address deprecated use of 'symbol' warning.

Julia 0.5 deprecates use of `symbol` instead of
`Symbol`. This patch just substitutes the
correct call.

* Address deprecated use of 'symbol' warning.

Julia 0.5 deprecates use of `symbol` instead of
`Symbol`. This patch just substitutes the
correct call.

* Addresses PR comments.

* Unit tests for math.hpp

* Tests for `math::pi`, `math::lerp`, `math::area_frustrum`
  and `math::volume_frustrum`
* Fix `math:pi<long double>()`.

* Extend range, view functionality.

* New `filter` view: lazily selects based on predicate.
* Generic `front` and `back` for sequences.
* New rangeutil STL wrappers `stable_sort_by`, `all_of`, `any_of`.
* Consolidate common utility unit testing structures into
  `tests/unit/common.hpp`

* Add `ball_and_squiggle` model; fix `ball_and_taper`.

* Make `test_common_cells.hpp` and `ball_and_taper.py` agree.
* Add `ball_and_squiggle` model that has a tapering undulating
  profile.

* Address PR#46 review comments.

* Add documentation of template parameters for `filter_iterator`.
* Document use of `uninitalized<F>` for holding functional objects
  in `filter_iterator` and `transform_iterator`

* Consolidate validation test code (issue #41)

* Simplify trace analysis and reporting code in
  `trace_analysis.hpp`
* Consolidate convergence test run procedures into
  new class `convergence_test_runner`.

* New compartment info structure for FVM.

* Make `algorithm::sum`, `algorithm::mean` more generic,
  allowing use with array types.
* Add `div_compartment` compartment representation, that
  holds geometric information for each half of a compartment
  that will then be used in calculating control volumes.
* Add three compartmentalisation schemes/policies that
  discretize a segment into `div_compartment` objects:
    * `div_compartment_by_ends` divides based only on the
      segment end points and radii.
    * `div_compartment_sampler` forms frusta by sampling
      the segment radius at each compartment boundary
    * `div_compartment_integrator` computes the compartment
      areas and volumes exactly by summing all frustra
      in the intersection of the segment and the compartmnet
      span.

* Extrae linked at execution time

* cleaning project

* Complex compartments

* Use divided compartments to determine FVM coefficients.
* Pick correct control volume in FVM from sgement position (avoids
  off-by-half error.)
* Add colour override functionality to tsplot: `--colour` option.
* Add const accessor for cell soma.
* Source formatting, comments in `math.hpp`
* Fix `range_view`: was using incorrectly named type trait.
* Add unit test for `range_view`.
* Allow points of discontinuity to be omitted from L-infinity norm
  calculations.
* Add `-d, --min-dt` option to `validate.exe` to control time
  step in validation convergence tests.
* Add validation test: confirm divided compartment policy does
  not effect results on simple frustrum dendrites.
* Change default max compartments on validation tests to 100
  (ad hoc observed convergence limit at dt circa 0.001 ms;
  finder spatial division would required much finer dt.)
* Make NEURON validation data generation scripts use CVODE by
  default, and with `secondorder=2` when non-zero `dt` is given.

* Remove division policy type parameter.

* Use only `div_compartment_integrator` for compartmentalization in
  `fvm_multicell`. The policy will later be moved to a backend
  policy class.
* For now, disable validation tests that test different division
  policies (see above).
* Tweak comments and remove redundant `using`, following comments
  on PR#54.

* Minor twicks and corrections
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