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  1. Jan 05, 2022
  2. Jan 03, 2022
  3. Dec 20, 2021
  4. Dec 15, 2021
  5. Dec 14, 2021
  6. Dec 13, 2021
  7. Dec 08, 2021
  8. Dec 03, 2021
  9. Nov 26, 2021
  10. Nov 22, 2021
    • boeschf's avatar
      Address compiler warnings (#1769) · 99f9ddca
      boeschf authored
      Fix various non-standards compliant code when compiled with elevated warning levels (-Wall -Wpedantic). Here is a list of the problems addressed:
      
      **preprocessor**
      - expansion of empty `__VA_ARGS__` in `ARB_PP_FOREACH`
      - named variadic macro arguments in `TRACE` macro
      
      **glibc** 
      - deprecated `mallinfo` call for newer glibc versions
      
      **simd**
      - non-const C-array sizes
      
      **modcc**
      - generation of C-arrays of size 0
      
      **switch/case**
      - switch-case ranges
      
      **tuple_foreach**
      - compound literals
  11. Nov 17, 2021
  12. Nov 16, 2021
  13. Nov 15, 2021
  14. Nov 12, 2021
  15. Nov 10, 2021
    • Benjamin Cumming's avatar
      Find morphology location from a coordinate (#1751) · 0e8875a9
      Benjamin Cumming authored
      Extend the `pwlin_place` interface to find the location of a morphology that is closest to a 3d coordinate.
      * extend `arb::pwlin_place` interface
      * python wrapper
      * unit tests
      * documentation
      
      Addresses a feature request by @Helveg that I don't think ever had a ticket assigned to it.
      
      Fixes #1661 and #1108.
    • Sam Yates's avatar
      Simplify default proc_allocation generation. (#1725) · e0c13e16
      Sam Yates authored
      * Consolidate default_concurrency, default_gpu functionality into arborenv/default_env.hpp, .cpp.
      * Add new arborenv function `default_allocation()` that uses environment variables ARBENV_NUM_THREADS and ARBENV_GPU_ID to create an `arb::proc_allocation`, with a fallback to `thread_concurrency()`.
      * Use arborenv-specific exceptions instead of generic std::runtime_error etc.
      * Update examples, docs to suit.
      
      Fixes #988 (except for reworking all the unit tests!)
  16. Nov 09, 2021
    • Sam Yates's avatar
      Update/fix tinyopt README.md (#1747) · 2a8878cd
      Sam Yates authored
      tinyopt README.md had an example which was not updated to the 1.0 API. Fixed upstream, and this is a copy.
    • Sam Yates's avatar
      Deal with zero radius points in a morphology (#1719) · 9b35ba52
      Sam Yates authored
      * Add test that is sensitive to small radius loss of precision in ixa computation.
      * Add test that checks for consistent behaviour when there is an (isolated) zero radius point in the morphology.
      * Special case p==1 q==1 case in ratelem so that it can interpolate ixa in the presence of non-finite interpolants.
      * Change naming in pw_element/pw_elements: 'element' refers to the extent+value pairs comprising a 'pw_elements' object; 'value' refers to the value associated with an element; 'extent' refers to the closed interval which is the support of the element.
      * Allow values (but not extents) in a pw_elements object to be mutable, using proxies for iterator access.
      * Write piecewise zip (pw_zip) in terms of a lazy pw_zip_view. Rename zip functions.
      * Document pw_elements more thoroughly.
      * Simplify and document embed_pwlin.cpp routines, expressing everything in terms of simple interpolate/integrate operations.
      * Represent integrated inverse cross-sectional area in the embedding by multiple piecewise-rational functions over a branch, each of which contribute separately to an ixa-based integration, so that precision loss associated with small (or zero) radii can be avoided.
      * Comment embed_pwlin.cpp more thoroughly.
      
      Fixes #1526 
  17. Nov 02, 2021
  18. Oct 29, 2021
  19. Oct 28, 2021
  20. Oct 27, 2021
  21. Oct 22, 2021
    • Nora Abi Akar's avatar
      Solve non-linear systems that are not kinetic schemes. (#1724) · ea25d7aa
      Nora Abi Akar authored
      Some refactoring of the SOLVE statement handling in `module.cpp`. 
      Allow the usage of `SparseNonlinearSolverVisitor` for non-linear systems not only when in the form of a kinetic scheme. 
      Check linearity of kinetic schemes and linear systems (was previously skipped).
    • Nora Abi Akar's avatar
      Gap Junction mechanisms (#1682) · dc371e5d
      Nora Abi Akar authored
      Adds support for user-defined gap junction mechanisms. Fixes #1600.
      
      - API Change: Wrap `mechanism_desc` in one of `density`, `synapse`, `junction` to be able to differentiate the kind of placed mechanism between point and junction mechanisms. 
      - API Change: The `ggap` parameter of a `gap_junction_connection` renamed to `weight` and is not a unit-less parameter. 
      - Mechanism ABI change: New `peer_index` vector which stores the indices of the peer sites of a gap-junction-connection. New mechanism kind. 
      - Internal API change: `shared_state` no longer controls the gap junction current contribution, that is now handled in the mechanism callbacks.
      - Modcc change: Add `JUNCTION_PROCESS` and `v_peer` keywords to nmodl, the first to identify a gap-junction mechanism, the second to access the peer voltage of a gap-junction connection. Modify modcc to be able to compile nmodl and generate correct code.
      - Behavior change: gap-junctions now contribute to both the current and conductance of a CV as opposed to just the current.
      - Add new "gj" mechanism, to replace the built-in constant-conductance based linear gap-junction implementation.
      - Fix unit tests.
      - Fix python wrapper. 
      - Fix docs. 
    • Benjamin Cumming's avatar
      Add locset expressions for proximal and distal translation of locations (#1671) · 5cc7d4dc
      Benjamin Cumming authored
      Add `proximal-translate` and `distal-translate` locset expressions.
      
      Fixes #1662
  22. Oct 21, 2021
  23. Oct 18, 2021
  24. Oct 14, 2021
  25. Oct 13, 2021