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  1. Feb 12, 2021
  2. Feb 11, 2021
    • Brent Huisman's avatar
      Docs reorder cable cell (#1310) · c96ef921
      Brent Huisman authored
      * Sync Cable Cell page names and ordering between sections (concept, python, cpp). Except cpp cable cell page. Is still one big page.
      * Move CV definition across categories to consistent location.
      * Move decor to separate page (cpp currently missing decor documentation) because it's a top-level concept that should be in the TOC like the other ingredients of the cable cell.
      * Slight rework of Concept intro and Cable Cell pages.
      * The Cable Cell page is now basically an intro, and lay out how the other pages/concepts relate to each other.
      c96ef921
    • Sebastian Schmitt's avatar
      Example for a plastic synapse (#1345) · fc5e98ba
      Sebastian Schmitt authored
      Online STDP is implemented in the synapse and
      and demonstrated by recording an STDP curve in
      an example.
      fc5e98ba
    • Nora Abi Akar's avatar
      Modcc: comments & seg fault (#1360) · 2775b3f3
      Nora Abi Akar authored
      * fix nmodl comment parsing
      * proper handling of \r
      * fix segmentation fault when api_state is null
      * add unit tests
      2775b3f3
    • Nora Abi Akar's avatar
      Modcc: parse the unit of `FUNCTION` (#1361) · 89a2f041
      Nora Abi Akar authored
      * add function unit parsing
      * add unit tests
      89a2f041
    • Nora Abi Akar's avatar
      update gitpod cmake (#1363) · 2adcd65c
      Nora Abi Akar authored
      2adcd65c
  3. Feb 10, 2021
  4. Feb 09, 2021
  5. Feb 08, 2021
  6. Feb 06, 2021
    • Nora Abi Akar's avatar
      Use JFrog as a registry and fix build errors (#1350) · e5123942
      Nora Abi Akar authored
      * Make Gitlab CI push images to CSCS' JFrog registry reg.giuv.cscs.ch so that sarus can pull images on Daint again. 
        This URL is probably temporary until JFrog officially goes into production later this month.
        Unfortunately JFrog is currently behind the firewall.
      * Upgrade g++ to g++8 on the Docker image.
      * Only require libxml when compiling with NeuroML support.
      e5123942
  7. Feb 05, 2021
  8. Feb 04, 2021
    • thorstenhater's avatar
    • Nora Abi Akar's avatar
      Add `post events` functionality to support models with STDP synapses (#1255) · 3531f7ee
      Nora Abi Akar authored
      * Added a `POST_EVENTS` procedure to nmodl, that takes an argument that represents the time since the last spike on the cell. In the event of multiple detectors on the cell, and multiple spikes on the detectors within the same integration period, all spikes will be processed by the synapse. Spikes are processed only once and then cleared.
      * Added 3 vectors to the shared state required to dispatch post-events: `cv_to_cell` map, `time_since_spike` holding max(num_detectors) slots per cell, and `src_to_spike` mapping spike sources (detectors) to slots in `time_since_spike`.
      * Renamed `vec_ci_` to `vec_di_` (to better reflect that it stands for **domain index**). Named the new `cv_to_cell` index as `vec_ci_` in the mechanisms.
      * Fixed existing unit tests and added new tests for the new post-events functionality.
      
      Fixes #1206
      3531f7ee
  9. Feb 03, 2021
    • thorstenhater's avatar
      Allow dynamically creating and loading of mechanism catalogue (#1287) · aa1b6f04
      thorstenhater authored
      First phase of dynamically loaded mechanism catalogues.
      
      - Add functionality to load and use catalogues from DSOs in Python and C++.
      - Add documentation and support scripts to build catalogues DSOs.
      - Re-factor CMakeLists.txt for mechanisms
      - Limitations
        - Needs (compatible, preferably identical) arbor sources when building catalogues
        - Can only work on MacOS and Linux (uses dlfnc)
      aa1b6f04
  10. Feb 02, 2021
  11. Jan 28, 2021
  12. Jan 27, 2021
  13. Jan 25, 2021
  14. Jan 22, 2021
  15. Jan 19, 2021
  16. Jan 15, 2021
  17. Jan 14, 2021
    • Brent Huisman's avatar
      Docs: define branch, mlocation, cv default. (#1302) · b10238e0
      Brent Huisman authored
      * Used Sphinx glossary directive to create terms that can be referred to in `concepts/morphology.rst` and `concepts/labels.rst`.
      * Added note box on difference with Neuron, add source for NEURON cylinder discretisation
      * Parameters added to svg generation script: turn off colors, root
      * Fix cpp TOC duplication, match ordering in other sections.
      * State default cv policy
      * center/re -> midpoints
      * Clarify and remove compartment term
      b10238e0
  18. Jan 11, 2021
    • thorstenhater's avatar
      More pythonic membership on mechanism_catalogue. (#1306) · d2623ecf
      thorstenhater authored
      Introduce two minor changes to the Python API
      to handle mechanism_catalogues idiomatically.
      
      Instead of
      
      import arbor as A
      
      cat = A.default_catalogue()
      
      if cat.has('hh'):
        print("Found HH.")
      
      for mech in cat.keys():
         print("*", mech)
      
      we can now write
      
      import arbor as A
      
      cat = A.default_catalogue()
      
      if 'hh' in cat:
        print("Found HH.")
      
      for mech in cat:
         print("*", mech)
      
      which is closer to the expectations of Python users.
      d2623ecf
    • Brent Huisman's avatar
      add numpy as runtime req (#1308) · 54ab542f
      Brent Huisman authored
      54ab542f
  19. Jan 08, 2021
  20. Jan 07, 2021
  21. Jan 06, 2021
  22. Jan 05, 2021