- Nov 14, 2016
-
-
Sam Yates authored
* Tokenize strings of the form "7E+X", "2.3E " etc as a number (integer, real) followed by a new token starting with 'E'. Note that this makes the string "1.2E3E4" no longer cause a lexer error status. * Add tests for corresponding numeric disambiguation in `text_lexer.cpp`. * Add tests for stoichiometric expressions that ensure that only otherwise ambiguous phrases such as "7E+2F" fail to parse ("7E+F" should parse correctly as a stoich expression.) * Add missing comma in list of 'good' expressions in the `Parser.parse_line_expressions` test.
-
- Nov 07, 2016
-
-
Sam Yates authored
* Extend stoichiometric expressions to allow negative coefficients. * Check that terms in a reaction expression are all non-negative. * Add CONSERVE keyword. * Add `ConserveExpression` and corresponding parsing behaviour. * Add unit tests for above and for recognition of KINETIC block as a `procedure`.
-
- Nov 04, 2016
-
-
Sam Yates authored
* Make verbose printing in test_modcc a runtime flag `-v`. * Show results of `lexer.parse()` in test_modcc when run with `-v`. * Split numerical lexing and parsing into real and integer categories. * Add expression parsing for KINETIC block and enclosed reaction expressions. Note: does not parse CONSERVE yet; no test for KINETIC block (reactions are covered though.)
-
- Oct 31, 2016
-
-
Sam Yates authored
* Split `tok::number` token into `tok::real` and `tok::integer` * Add new tokens: `tok::tilde`, `tok::arrow` and `tok::kinetic` (keyword) * Add new expressions: `IntegerExpression` (deriving from `NumberExpression`), `ReactionExpression`, `StoichExpression` and `StoichTermExpression`. * Add new `procedureKind`: `kinetic`. * Add parse rules for KINETIC blocks. Note: no real testing yet.
-
Ben Cumming authored
Complex compartments
-
Sam Yates authored
* 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.
-
- Oct 30, 2016
-
-
Sam Yates authored
* 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.
-
- Oct 28, 2016
-
-
Ben Cumming authored
Feature/divided compartments
-
Ben Cumming authored
Consolidate validation tests (issue #41)
-
Sam Yates authored
* 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.
-
Sam Yates authored
* Simplify trace analysis and reporting code in `trace_analysis.hpp` * Consolidate convergence test run procedures into new class `convergence_test_runner`.
-
Ben Cumming authored
Feature/new test model
-
Ben Cumming authored
More range functionality, unit tests.
-
Sam Yates authored
* Add documentation of template parameters for `filter_iterator`. * Document use of `uninitalized<F>` for holding functional objects in `filter_iterator` and `transform_iterator`
-
- Oct 27, 2016
-
-
Sam Yates authored
* Make `test_common_cells.hpp` and `ball_and_taper.py` agree. * Add `ball_and_squiggle` model that has a tapering undulating profile.
-
Sam Yates authored
* 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`
-
Sam Yates authored
* Tests for `math::pi`, `math::lerp`, `math::area_frustrum` and `math::volume_frustrum` * Fix `math:pi<long double>()`.
-
Sam Yates authored
-
Ben Cumming authored
modcc: Support for units syntax within a state block.
-
Vasileios Karakasis authored
-
Ben Cumming authored
Add "lib" to search prefixes for libtbb
-
Ben Cumming authored
Address deprecated use of 'symbol' warning.
-
Sam Yates authored
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
-
Sam Yates authored
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
-
Sam Yates authored
* Fix quoting error in library search. * Add "lib" to prefixes when system is "Linux".
-
- Oct 26, 2016
-
-
Vasileios Karakasis authored
-
Vasileios Karakasis authored
-
Ben Cumming authored
Feature/cable validation
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
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.
-
- Oct 25, 2016
-
-
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.
-
Vasileios Karakasis authored
Address bug in fix for cell clone ctor.
-
Sam Yates authored
* Add test for cell clone semantics. * Fix `1cell::cell(clone_cell_t, const cell&)` for correct copy semantics.
-
Sam Yates authored
Fixes Clang 3.7 failure to compile.
-