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  1. Nov 18, 2020
    • thorstenhater's avatar
      Add readme to examples. (#1228) · 9233b784
      thorstenhater authored
      * Add a readme for the C++ examples
      * Improved readme for dryrun
      
      Fixes #868, #1107.
      9233b784
    • Sam Yates's avatar
      Expose diverse probes in Python API. (#1225) · 1bfe96bc
      Sam Yates authored
      Major changes in Python library and documentation:
      
      * Add global state (immutable after initialization) for the Python module that
        manages the mapping between probe metadata types and the method by which the
        corresponding [sample data can be collected and presented as Python objects.
        This is necessary for decoupling the implementation of the simulation wrapper
        from that of the various cable cell probe types.
      
      * Wrap each of the C++ cable cell probe types with a Python function that
        returns a `probe_info` object.
      
      * Add code for converting and accumulating C++ probe metadata and sample
        data, registered in the module global state against the metadata type info.
      
      * Make the `arbor.simulator` object responsible for recording all spike and
        sample data, with corresponding new methods.
      
      * Use NumPy arrays and structured datatypes for returning spike and
        sample data.
      
      * Place Python schedule proxies under an abstract interface so that consumers
        of the proxies can be made generic over schedule types.
      
      * Add unit tests for the `arbor.simulator` class and its new functionality,
        including distributed spike collection.
      
      * Rework all Python API documentation concerning probes, sampling, and spike
        recording; add information on newly exposed cable cell probe addresses.
      
      * Add new python example `single_cell_recipe.py` which is a generic recipe
        version of `single_cell_model.py`.
      
      * Adjust other code in the wrapper and examples to accommodate these changes.
      
      Minor changes in Python library:
      
      * Add equality tests for `arbor.location` and `arbor.cable` Python classes.
      
      * Use the `py::` namespace shorthand more often in the Python wrapping sources.
      
      * Add an implicit conversion for a pair of numbers to `arbor.cell_member`, so
        that e.g. probe ids can be specified simply as `(gid, index)`.
      
      * Add an implicit conversion from a tuple to `arbor.mpoint` so that a
        morphological point can be specified simply as `(x, y, z, radius)`.
      
      * Modify the interface to `arbor.regular_schedule` so that the overloads
        correspond more closely to the C++ API. In particular,
        `arbor.regular_schedule(dt)` now describes a schedule with times 0, dt, 2*dt,
        etc.
      
      Minor changes in C++ library:
      
      * Change test in FVM lowered cell implementation and exception message for
        `bad_source_description`: assert number of detectors is exactly the number
        of sources promised by the recipe.
      
      * Add comment describing `probe_metadata` object in `sampling.hpp` which
        asserts that the type and value of probe-specific metadata completely
        determines the correct interpretation of sampled data provided to a callback.
      1bfe96bc
  2. Nov 17, 2020
  3. Nov 13, 2020
  4. Nov 11, 2020
  5. Nov 10, 2020
  6. Nov 09, 2020
  7. Nov 06, 2020
  8. 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
  9. Nov 02, 2020
  10. Nov 01, 2020
  11. Oct 28, 2020
  12. Oct 15, 2020
  13. Oct 14, 2020
  14. Oct 09, 2020
  15. Oct 08, 2020
  16. Oct 07, 2020
  17. Oct 06, 2020
  18. 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