v4.1.0-beta

This pre-release includes a new newick parser and other infrastructure-related changes.

The API changes are mainly these:

convert_to_ultrametric() -> to_ultrametric()  (also, new implementation)

topology_only -> topological  (argument in several functions)

feature(s), attribute(s), property(ies) -> prop(s)  (argument in several functions)

popup_prop_keys -> include_props, exclude_props  (in explore() and others)

t & 'A' -> t['A']

tree['A']  (get the node called 'A')
tree[0,1,0]  (get the node that comes from the root's 1st child, then its 2nd child, and then its 1st child)

node.id  (tuple like [0,1,0])
node.level  (number of nodes between node and root)

t.get_tree_root() -> t.root
t.is_root() -> t.is_root
t.is_leaf() -> t.is_leaf

t.get_common_ancestor(n1, n2, n3) -> t.common_ancestor([n1, n2, n3])

t.get_ancestors() -> t.ancestors()

t.get_leaves(), t.iter_leaves() -> t.leaves()

t.get_leaf_names() -> t.leaf_names()

t.get_descendants() , t.iter_descendants() -> t.descendants()

t.get_ascii() -> t.to_str()

t.write(props=[], format=1) -> t.write(props=None, parser=1)

A.get_distance(B) -> t.get_distance(A, B)

Tree(name='Hi', dist=1, support=1) -> Tree({'name': 'Hi', 'dist': 1, 'support': 1})
->
Tree(nw, format=1) -> Tree(nw, parser=1)

nw = t.write(format=f, dist_formatter="%0.1f", name_formatter="TEST-%s", support_formatter="SUP-%0.1f")
->
parser = newick.make_parser(f, dist='%0.1f', name='TEST-%s', support='SUP-%0.1f')
nw = t.write(parser=parser)

props=None (default in some functions) -> write all extended properties
props=[]             -> do not write any extended properties

_FaceContainer -> Grid
_HeaderFaceContainer -> AlignedGrid
get_FaceAreas -> make_faces

smartview/b64pickle.py -> parser/ete_format.py