Is there an easy way to avoid these? Preferably one that works in a
standalone python file?

  sage: f = piecewise([[(0,1), x^2]])

  sage: f(0.5)
  /home/mjo/src/sage-4.6.2/local/bin/sage-ipython:1:
  DeprecationWarning: Substitution using function-call syntax and
  unnamed arguments is deprecated and will be removed from a future
  release of Sage; you can use named arguments instead, like
  EXPR(x=..., y=...)
  #!/usr/bin/env python
  0.250000000000000

  sage: f(x=0.5)
  ----------------------------------------------------------------------
  TypeError                            Traceback (most recent call last)

  home/mjo/<ipython console> in <module>()

  TypeError: __call__() got an unexpected keyword argument 'x'

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