when both taxon_namespaces are empty (not equals None)
so does dendropy.calculate.treesum.consensus_tree (calls count_splits_on_trees)
[x] add is_mutable to docstring for Bipartition __init__
[x] dendropy.interop.ete and dendropy.interop.biopython have required imports to test, worth adding to CI?
[x] dendropy.model.discrete.simulate_discrete_chars and dendropy.model.discrete.simulate_discrete_char_dataset don't seem to work with a DiscreteCharacterEvolutionModel type argument as specified, because no stationary_sample attribute (works with NucleotideCharacterEvolutionModel)
dendropy.simulate.popgenism.FragmentedPopulations.generate_sequences
(revisit)dendropy.model.coalescent.discrete_time_to_coalescence
pop_size = None
(default), ifn_genes <= 1
(integer), orpop_size < 1
(integer)dendropy.model.coalescent.log_probability_of_coalescent_frames
gcd()
as deprecated and remove internal use (calculate.mathfn
)factorial()
incalculate.combinatorics
dendropy.calculate.treesum.summarize_node_ages_on_tree
allow_negative_edges
dendropy.calculate.treesum.count_splits_on_trees
(revisit)dendropy.calculate.treesum.consensus_tree
(callscount_splits_on_trees
)is_mutable
to docstring for Bipartition__init__
dendropy.interop.ete
anddendropy.interop.biopython
have required imports to test, worth adding to CI?dendropy.model.discrete.simulate_discrete_chars
anddendropy.model.discrete.simulate_discrete_char_dataset
don't seem to work with aDiscreteCharacterEvolutionModel
type argument as specified, because nostationary_sample
attribute (works withNucleotideCharacterEvolutionModel
)dendropy.model.parismony.fitch_up_pass
requires an argumentpreorder_node_list
but calls itpostorder_nodes
in docstring https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/parsimony.py#L226preorder_nodes
topreorder_node_iter
and deprecate old kwargdendropy.model.reconcile.ContainingTree.clear
https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/model/reconcile.py#L180domain_taxa
doesn't seem to exist anywhere else in the codedendropy.utility.bibtex.BibTexEntry
initialization breaks on https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/bibtex.py#L115__getattr__
too fancyBibTexEntry
and updatebasemodel.add_bibtex
dendropy.utility.container.NormalizedBitmaskDict
https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/container.py#L266fill_bitmask=None
dendropy.utility.messaging.log_lines
https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/messaging.py#L155level=None
dendropy.utility.processing.enqueue_stream
https://github.com/jeetsukumaran/DendroPy/blob/cc82ab774ed83831b5c5125278d88c3c614c2d8a/src/dendropy/utility/processio.py#L77dendropy.calculate.treesum.TopologyCounter.hash_topology