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  1. Nov 10, 2020
  2. Nov 09, 2020
  3. Nov 06, 2020
  4. Nov 05, 2020
    • Nora Abi Akar's avatar
      Modify SWC loaders (#1214) · 594a365f
      Nora Abi Akar authored
      * Rename `as_segment_tree` to `load_swc_arbor`.
      * Remove `swc_mode`: `sort_and_validate_swc` now performs the `relaxed` checks by default, `load_swc_arbor` performs the `strict` checks. 
      * Change `load_swc_xxx` to only accept `swc_data` as an argument
      * Remove default constructor for `swc_data` and enforce validation of SWC records via `sort_and_validate_swc` at construction.
      * Add fixes for docs and unit tests.
      594a365f
  5. Nov 02, 2020
  6. Nov 01, 2020
  7. Oct 28, 2020
  8. Oct 15, 2020
  9. Oct 14, 2020
  10. Oct 09, 2020
  11. Oct 08, 2020
  12. Oct 07, 2020
  13. Oct 06, 2020
  14. Oct 05, 2020
    • Brent Huisman's avatar
      Update Python examples (#1166) · d3e99c23
      Brent Huisman authored
      * Python examples: Updated to use region expressions (quotes)
      * Python examples: Uniform plotting
      * Python examples: Removed tutorial directory (example roughly matches python/example/single_cell_model.py)
      * Python examples: Rewrote flat_cell_builder() to segment_tree()
      d3e99c23
    • Brent Huisman's avatar
      Docs restructure for 0.4 (#1167) · 67b178cb
      Brent Huisman authored
      * Synced pages between Concepts, Python API and C++ API wherever possible
          * Recipe pages conform between the three section (concepts, python, c++)
          * Cell, Cable Cell and Cell * pages are rearranged and provided with some copy explaining the relationship between them.
      * Moved Python API out of Concepts
      * Renamed Concepts "How does Arbor work?"
      * Added Python Module Index plus mock import of Arbor for RTD build (unfortunately won't show there)
      * Broke out Interconnectivity (synapses) page.
      * Reworked Single Cell Model page into a quick start, with lots of cross referencing.
      * Tweaked logo.
      * Added Spack to install options.
      * Updated blurb.
      * Documentation now follows EU capitalization rules.
      * Assorted typofixes
      67b178cb
    • Benjamin Cumming's avatar
    • Sam Yates's avatar
      Tighten SWC requirements, comments. (#1170) · 4339ffed
      Sam Yates authored
      * Remove contiguous numbering requirement from 'strict' mode SWC
      parsing, as it is not necessary for correct interpretation as a segment
      tree.
      * Describe in the swcio.hpp header how (strict) swc data is interpreted
      as a segment tree.
      * Demonstrate in unit tests that out-of-order and non-contiguously
      numbered records are valid for `parse_swc`.
      * Add unit test for `as_segment_tree`.
      4339ffed
  15. Oct 01, 2020
  16. Sep 30, 2020
    • Sam Yates's avatar
      New SWC parser broke `load_swc_allen`. (#1165) · 09e6e1b5
      Sam Yates authored
      * Minor output formatting fix for `swc_record`.
      * Modify the Python `load_swc_allen` implementation to cope with SWC
      record ids not necessarily being contiguous, and with SWC record parent
      ids corresponding to record ids, not 0-based indices.
      09e6e1b5
  17. Sep 29, 2020
  18. Sep 28, 2020
    • Sam Yates's avatar
      Rewrite SWC reader code. (#1127) · 11a6ef6d
      Sam Yates authored
      * Simplify scanning of SWC records.
      * `parse_swc` now retains metadata read from SWC comments.
      * `parse_swc` is given two modes, relaxed and strict. Strict mode enforces contiguous record numbering and rejects SWC that looks like it has a single-point soma.
      * Subtype `swc_error` according to error mode.
      * Remove `point` class and corresponding unit tests.
      * Add a RAII stream formatting flag saver, used in SWC record output operator.
      * Replace included 1-point soma SWC example with a regular SWC from NeuroMorpho.
      11a6ef6d
  19. Sep 25, 2020
    • Sam Yates's avatar
      Fix error introduced by PR merge. (#1162) · 70e3c902
      Sam Yates authored
      70e3c902
    • Nora Abi Akar's avatar
      Sanitize recipe (#1143) · af4d773b
      Nora Abi Akar authored
      * Raise an exception if:
      1. `recipe.num_souces(gid)` != number of detectors placed on the cell.
      2. `recipe.num_targets(gid)`  != number of synapses placed on the cell.
      3. `recipe.connections_on(gid)` has connections with non-existent source or target gids or lids
      * Raise better exception for gap junctions
      * Fix unit test 
      
      Addresses #681 
      af4d773b
    • Sam Yates's avatar
      Address c++17 TODO comments. (#1159) · 906dd478
      Sam Yates authored
      * Use structured bindings where noted (there are likely other opportunities in the code).
      * Use `if constexpr` to simplify some template-dispatched code.
      * Remove `arb::uitl::get`, as it is no longer required now that util::variant is replaced.
      * Add `_v` utility inline constexpr template values.
      
      Part of the C++17 migration task #1022.
      906dd478