Small parsimony#276

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gloriayma wants to merge 20 commits into3.0.0from

small_parsimony

Commits on Oct 23, 2025

rewrote function signatures and docstrings for small_parsimony to take in and output TreeData trees
gloriayma
committed
added get_cell_meta function to utils.py, for use in small_parsimony to allow pass-in of TreeData tree
gloriayma
committed
add helper in utils.py: same as depth_first_traverse_nodes for CassiopeiaTree but now takes in any TreeLike
gloriayma
committed
add helpers in utils.py: same as set_attribute and get_attribute for CassiopeiaTree but now can take in TreeData
gloriayma
committed
add helper in utils.py: same as is_leaf_treelike for CassiopeiaTree but now can take in any treelike
gloriayma
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add helper in utils.py: same as .children attribute for CassiopeiaTree but now can take in any treelike
gloriayma
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fixed depth_first_traverse_nodes_treelike
gloriayma
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fixed function signature for _get_digraph (returns tuple, not nx.DiGraph)
gloriayma
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rewrite of fitch_hartigan_bottom_up to use either CassiopeiaTree or TreeData, using new helper functions in utils.py
gloriayma
committed

Commits on Oct 28, 2025

change helper functions in utils.py: get_attribute_treelike and set_attribute_treelike to work with nx.digraphs. rewrite fitch_hartigan_bottom_up to be in terms of nx.digraphs
gloriayma
committed

Commits on Oct 30, 2025

Commits on Oct 31, 2025

resolved utils.py conflicts
colganwi
committed

Commits on Nov 4, 2025

rewrite of score_small_parsimony to take in any TreeLike
gloriayma
committed