- Apr 03, 2020
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Benjamin Cumming authored
Some small changes to facilitate smooth PyPi integration: * update the Python installation guide * update the license file * add a `setup.cfg` * add a stub for the Python readme
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- Feb 28, 2020
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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 .
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- Feb 25, 2020
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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.
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- Feb 04, 2020
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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
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