ivan-krukov / aligning-genealogies

The genealogy-coalescent alignment project
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`Genealogical.predecessors` no longer has `include_self` #10

Closed ivan-krukov closed 4 years ago

ivan-krukov commented 4 years ago

Running the Experiments notebook, I am gitting the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-3-4d9aa12d1c2f> in <module>
      1 algn = DescMatchingAligner(gg, ct)
----> 2 algn.align()
      3 algn.evaluate()

~/work/genealogies/genealogy_aligner/alignment.py in align(self)
     60     def align(self):
     61 
---> 62         ped_ntp = self.ped.get_probands_under(climb_up_step=self.climb_up_step)
     63         ts_ntp = self.ts.get_probands_under(climb_up_step=self.climb_up_step)
     64 

~/work/genealogies/genealogy_aligner/Genealogical.py in get_probands_under(self, nodes, climb_up_step)
    122             ntp[n] = set()
    123 
--> 124             base_set = self.predecessors(n, climb_up_step, include_self=True)
    125             n_set = []
    126             for ns in base_set:

TypeError: predecessors() got an unexpected keyword argument 'include_self'

There is the include_founders parameter. Is that equivalent for the discrete matching algorithm?

shz9 commented 4 years ago

Fixed now.