matsengrp / gctree

GCtree: phylogenetic inference of genotype-collapsed trees
https://matsengrp.github.io/gctree
GNU General Public License v3.0
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Add full inference test and remove mutation model ignore_ualabel call #97

Closed willdumm closed 2 years ago

willdumm commented 2 years ago

Fixes incomplete refactor in #91 after upgrade to historydag v1, and adds a test that runs inference with all criteria via the cli.

willdumm commented 2 years ago

Inspired by:

number of trees with integer branch lengths: 396
  Isotype parsimony will be used as a ranking criterion
  Mutation model parsimony will be used as a ranking criterion
  Traceback (most recent call last):
    File "/opt/miniconda3/bin/gctree", line 8, in <module>
      sys.exit(main())
    File "/opt/miniconda3/lib/python3.9/site-packages/gctree/cli.py", line 734, in main
      args.func(args)
    File "/opt/miniconda3/lib/python3.9/site-packages/gctree/cli.py", line 202, in infer
      trimmed_forest, _ = forest.filter_trees(
    File "/opt/miniconda3/lib/python3.9/site-packages/gctree/branching_processes.py", line 916, in wrapper
      return func(self, *args, **kwargs)
    File "/opt/miniconda3/lib/python3.9/site-packages/gctree/branching_processes.py", line 1174, in filter_trees
      mut_funcs = _mutability_dagfuncs(
    File "/opt/miniconda3/lib/python3.9/site-packages/gctree/mutation_model.py", line 432, in _mutability_dagfuncs
      @hdag.utils.ignore_ualabel(0)
  AttributeError: module 'historydag.utils' has no attribute 'ignore_ualabel'