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  1. Apr 03, 2020
  2. Feb 28, 2020
    • Benjamin Cumming's avatar
      pip / setuptools support (#977) · 45885c22
      Benjamin Cumming authored
      Add a `setup.py` for installing Arbor directly with pip/setuptools.
      
      Implement a setuptools extension for CMake in `setup.py`. To be honest, I don't understand entirely how it works, but setuptools is obtuse enough that I don't feel at all guilty about this.
      
      Define additional flags for optionally enabling GPUs, MPI, Vectorization and micro-architecture targets, for more adventurous users.
      
      The documentation is updated with a "howto pip" for more casual users who don't want anything to do with CMake.
      
      Fixes #958 .
  3. Feb 25, 2020
    • Benjamin Cumming's avatar
      More robust Python installation (#971) · b43cd07e
      Benjamin Cumming authored
      Improve the Python wrapper generation and installation:
        - install a proper module that can be extended with Python code;
        - give the user more control over where to install the module (e.g. as a user package or in a virtualenv).
      
      During building, the following sub-directory is built in the build director (`CMAKE_BINARY_DIR`)
      ```
      └── python
          └── arbor
                  ├── __init__.py
                  ├── arbor.so
                  └── VERSION
      ```
      This path can then be copied VERBATIM to the target installation path. By default this will be in `CMAKE_INSTALL_PREFIX/lib/python%d.%d/site-packages`.
      An additional CMake parameter `ARB_PYTHON_PREFIX` can be used to specify an alternative destination for installing the Python module.
      
      The Python part of the wrapper, implemented in `__init__.py` is currently very limited, only providing `__version__` and `__config__` variables.
      
      The installation guide was updated to cover the Python installation.
  4. Feb 04, 2020
    • Benjamin Cumming's avatar
      Python Interface (#948) · cfad427a
      Benjamin Cumming authored
      A big update that wraps over 90% of the public C++ API, with enough functionality to let Python users to perform useful modelling.
      
      Key features
      - wrapping of cable cell functionality
        - user-defined explicit compartmentalisation not supported
      - `single_cell_model` abstraction unique to the Python wrapper that simplifies developing and testing single cell models
      - one-dimensional cell builder for Python wrapper that simplfies building cells that 
        - in and of itself limited in scope, but a very useful example of mapping a richer morphology builder onto `sample_tree`s.
      - parsing of region and location expressions from strings
        - implements a generic s-expression parser that we can use for other purposes later