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Create benchmarks for swiglpk and decide on a C interface #30

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Midnighter opened this issue Jul 29, 2018 · 0 comments
Open

Create benchmarks for swiglpk and decide on a C interface #30

Midnighter opened this issue Jul 29, 2018 · 0 comments
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@Midnighter
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Done: There is a comprehensive set of benchmarks (using e.g. pytest-benchmark that can be used to decide between C bindings.

Binding options in order of feasibility:

  • SWIG (current)
  • CFFI (Lasse has a running version)
  • ctypes
  • Cython
  • Boost Python

N.B.: A "bottleneck" with the current interface is to retrieve the flux values for all reactions from the solver. This could also be in part to using an OrderedDict in optlang.

@Midnighter Midnighter added this to the COBRApy 1.0 milestone Jul 29, 2018
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