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  1. Jul 20, 2022
  2. Jul 19, 2022
  3. Jul 18, 2022
  4. Jul 04, 2022
    • Brent Huisman's avatar
      Move Python build to `pyproject.toml`, bump Python minver to 3.7, fix macos... · 8af6bd27
      Brent Huisman authored
      Move Python build to `pyproject.toml`, bump Python minver to 3.7, fix macos wheel generation (#1916)
      
      * Failing Macos Python wheel builds fixed.
      * Macos Python wheels now come with dual-arch (x86-64 and arm64)
      * Moved (nearly) all Python build instructions to `pyproject.toml`
        * Enables 'build isolation', and need to specify build-deps only once, no need for users or CI scripts to pre-install them.
        * Enables editable `pip` installs (`pip install -e ./arbor`)
        * Compatible with 'build frontends' `pip` and `build`.
        * Passing CMake options actually got shorter
      * Drop Python 3.6 support.
      8af6bd27
  5. Jun 30, 2022
    • Brent Huisman's avatar
      Fix line numbers in tutorials and assorted doc corrections (#1917) · c38db013
      Brent Huisman authored
      - Fix line numbers in tutorials, fallout from #1906
      - Mention arbor-contrib in a few relevant places
      - Correct some fallout from #1904
      - A new hardware and profiling tutorial, and covers things moved out of other examples in #1904
      - Various other documentation fixes
      c38db013
    • Simon Frasch's avatar
      Inhomogeneous parameters (#1887) · 257e625d
      Simon Frasch authored
      Adds the ability to scale parameters of (density) mechanisms based on inhomogeneous properties along a cell.
      Two new types are added:
      - iexpr: An expression describing the scaling factor computation.
      - scaled_mechanism: A wrapper struct around a mechanisms with iexpr attached to selected parameters.
      
      Closes #1650
      257e625d
  6. Jun 23, 2022
  7. Jun 21, 2022
    • Brent Huisman's avatar
      49ae16a9
    • Thorsten Hater's avatar
      Adopt flake8 (#1908) · f685f0e3
      Thorsten Hater authored
      f685f0e3
    • Thorsten Hater's avatar
      Add some convenience to simulation creation. (#1904) · d15afd39
      Thorsten Hater authored
      Encapsulates 80% of cases:
      ```cxx
       rec = recipe()
       ctx = make_context()
       dec = partition_load_balance(rec, ctx)
       sim = simulation(rec, dec, ctx)
      ```
      is now written as
      ```cxx
       rec = recipe()
       sim = simulation(rec)
      ```
      In python we use keyword args to allow
      both to be specified separatly.
      
      Partially fixes #1862 
      d15afd39
    • Thorsten Hater's avatar
      Ionic Diffusion along the Morphology · 4a305b4f
      Thorsten Hater authored
      # Introduction
      
      Plasticity processes are mediated by signalling ions, eg Ca++, which are generated by 
      synapses upon reception of a spike. This adds a quantity `Xd` for any ion `X`
      - initialised as `Xi`
      - read from and written to by NMODL density and point mechanisms.
      - propagates according to a diffusion law `∂_t Xd = ∂_z c X ∂_z Xd + iX/qi`.
      - in contrast to `Xi` and `Xo` there's no buffering and the update in mechanisms
        occurs atomically (and at a different time)
      
      More details can be found in the documentation.
      
      For the future there are some low hanging optimisations
      - per-ion conductivity for the matrix solver could be disabled if no diffusion is computed
      - cable and diffusion solvers store duplicates of the solver state, could be merged
      
      Closes #1651 
      4a305b4f
  8. Jun 20, 2022
  9. Jun 16, 2022
  10. Jun 14, 2022
  11. Jun 13, 2022
  12. Jun 10, 2022
    • Thorsten Hater's avatar
      Isolate external catalogues from libarbor.a. (#1837) · de06afa2
      Thorsten Hater authored
      # Changes
      - Bump ABI to v0.1.1
      - Add `arb_mechanism` to bundle `type` and `interface`s
      - Adjust `generate_catalogue` and `build_catalogue`
      - Return `nullptr` for GPU interfaces if not enabled
      
      # Open Questions
      - How to tell CMake not to link against `libarbor.a` and only use headers?
      - ~~How to get around `#ifdef ARB_GPU_ENABLED`~~ Update: just embrace it.
      
      # Linked Issues
      Fixes #1834 
      de06afa2
    • Brent Huisman's avatar
      random123 submodule added (#1872) · 066dd383
      Brent Huisman authored
      066dd383
  13. Jun 08, 2022
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