CHANGES.rst

+Release 4.3.0
+-------------
+
+-   [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.
+-   Added ``sumlabels.py`` application.
+-   BD tree (``dendropy.model.birth_death_tree``) now allows for preservation of extinct tips.
+-   Improved performance of character subset export
+
 Release 4.2.0
 -------------
 

DendroPy.egg-info/PKG-INFO

 Metadata-Version: 1.1
 Name: DendroPy
-Version: 4.2.0
+Version: 4.3.0
 Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
 Home-page: http://packages.python.org/DendroPy/
 Author: Jeet Sukumaran and Mark T. Holder
@@ -115,7 +115,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy
         Current Release
         ===============
         
-        The current release of DendroPy is version 4.2.0 (master-5051a46, 2016-12-28 13:25:19).
+        The current release of DendroPy is version 4.3.0 (master-e251bcf, 2017-07-06 21:23:19).
         
         
 Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics
@@ -131,5 +131,7 @@ Classifier: Programming Language :: Python :: 3.1
 Classifier: Programming Language :: Python :: 3.2
 Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

DendroPy.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ DendroPy.egg-info/entry_points.txt
 DendroPy.egg-info/requires.txt
 DendroPy.egg-info/top_level.txt
 DendroPy.egg-info/zip-safe
+applications/sumlabels/sumlabels.py
 applications/sumtrees/sumtrees.py
 dendropy/__init__.py
 dendropy/__main__.py
@@ -63,6 +64,7 @@ dendropy/interop/genbank.py
 dendropy/interop/muscle.py
 dendropy/interop/paup.py
 dendropy/interop/raxml.py
+dendropy/interop/rspr.py
 dendropy/interop/rstats.py
 dendropy/interop/seqgen.py
 dendropy/legacy/__init__.py

PKG-INFO

 Metadata-Version: 1.1
 Name: DendroPy
-Version: 4.2.0
+Version: 4.3.0
 Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
 Home-page: http://packages.python.org/DendroPy/
 Author: Jeet Sukumaran and Mark T. Holder
@@ -115,7 +115,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy
         Current Release
         ===============
         
-        The current release of DendroPy is version 4.2.0 (master-5051a46, 2016-12-28 13:25:19).
+        The current release of DendroPy is version 4.3.0 (master-e251bcf, 2017-07-06 21:23:19).
         
         
 Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics
@@ -131,5 +131,7 @@ Classifier: Programming Language :: Python :: 3.1
 Classifier: Programming Language :: Python :: 3.2
 Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

applications/sumlabels/sumlabels.py

+#! /usr/bin/env python
+
+##############################################################################
+##  DendroPy Phylogenetic Computing Library.
+##
+##  Copyright 2010 Jeet Sukumaran and Mark T. Holder.
+##  All rights reserved.
+##
+##  See "LICENSE.txt" for terms and conditions of usage.
+##
+##  If you use this work or any portion thereof in published work,
+##  please cite it as:
+##
+##     Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
+##     for phylogenetic computing. Bioinformatics 26: 1569-1571.
+##
+##############################################################################
+
+"""
+Marge labels of splits/branches from different input trees onto corresponding
+splits/branches of a single tree.
+"""
+
+import os
+import sys
+import argparse
+
+import datetime
+import time
+import socket
+try:
+    import getpass
+except:
+    pass
+import platform
+
+import dendropy
+from dendropy.utility.messaging import ConsoleMessenger
+from dendropy.utility.cli import confirm_overwrite, show_splash
+
+_program_name = "SumLabels"
+_program_subtitle = "Phylogenetic Tree Label Concatenation"
+_program_date = "Jan 20 2017"
+_program_version = "Version 2.0.0 (%s)" % _program_date
+_program_author = "Jeet Sukumaran"
+_program_contact = "jeetsukumaran@gmail.com"
+_program_copyright = "Copyright (C) 2017 Jeet Sukumaran.\n" \
+                 "License GPLv3+: GNU GPL version 3 or later.\n" \
+                 "This is free software: you are free to change\nand redistribute it. " \
+                 "There is NO WARRANTY,\nto the extent permitted by law."
+
+def main_cli():
+
+    description =  "%s %s %s" % (_program_name, _program_version, _program_subtitle)
+
+    parser = argparse.ArgumentParser(version =_program_version, description=description)
+
+    parser.add_argument(
+            "sources",
+            metavar="TREEFILE",
+            nargs="+")
+    parser.add_argument("-t","--target",
+            dest="target_tree_filepath",
+            default=None,
+            help="path to file with tree (Newick or NEXUS format) "
+            + "to which labels will be written")
+    parser.add_argument("--preserve-target-labels",
+            action="store_true",
+            dest="preserve_target_labels",
+            default=False,
+            help="keep any existing labels on target tree (by default, these will be cleared before writing the new labels)")
+    parser.add_argument("--rooted",
+            action="store_true",
+            dest="rooted_trees",
+            default=None,
+            help="treat trees as rooted")
+    parser.add_argument("--unrooted",
+            action="store_false",
+            dest="rooted_trees",
+            default=None,
+            help="treat trees as unrooted")
+    parser.add_argument("--ignore-missing-source",
+            action="store_true",
+            dest="ignore_missing_source",
+            default=False,
+            help="ignore missing source tree files (at least one must exist!)")
+    parser.add_argument("-o","--output",
+            dest="output_filepath",
+            default=None,
+            help="path to output file (if not given, will print to standard output)")
+    parser.add_argument("-s","--separator",
+            dest="separator",
+            default="/",
+            help="string to use to separate labels from different source trees (default='%(default)s')")
+    parser.add_argument("--no-taxa-block",
+            action="store_false",
+            dest="include_taxa_block",
+            default=True,
+            help="do not include a taxa block in the output treefile (otherwise will create taxa block by default)")
+    parser.add_argument("-c", "--additional-comments",
+            action="store",
+            dest="additional_comments",
+            default=None,
+            help="additional comments to be added to the summary file")
+    parser.add_argument("--to-newick",
+            action="store_true",
+            dest="to_newick_format",
+            default=False,
+            help="save results in NEWICK (PHYLIP) format (default is to save in NEXUS format)")
+    parser.add_argument("--to-phylip",
+            action="store_true",
+            dest="to_newick_format",
+            default=False,
+            help="same as --to-newick")
+    parser.add_argument("-r", "--replace",
+            action="store_true",
+            dest="replace",
+            default=False,
+            help="replace/overwrite output file without asking if it already exists ")
+    parser.add_argument("-q", "--quiet",
+            action="store_true",
+            dest="quiet",
+            default=False,
+            help="suppress ALL logging, progress and feedback messages")
+
+    args = parser.parse_args()
+    if args.quiet:
+        messaging_level = ConsoleMessenger.ERROR_MESSAGING_LEVEL
+    else:
+        messaging_level = ConsoleMessenger.INFO_MESSAGING_LEVEL
+    messenger = ConsoleMessenger(name="SumLabels", messaging_level=messaging_level)
+
+    # splash
+    if not args.quiet:
+        show_splash(prog_name=_program_name,
+                prog_subtitle=_program_subtitle,
+                prog_version=_program_version,
+                prog_author=_program_author,
+                prog_copyright=_program_copyright,
+                dest=sys.stderr,
+                )
+
+    ###################################################
+    # Source file idiot checking
+
+    source_filepaths = []
+    if len(args.sources) > 0:
+        for fpath in args.sources:
+            fpath = os.path.expanduser(os.path.expandvars(fpath))
+            if not os.path.exists(fpath):
+                if args.ignore_missing_source:
+                    messenger.send_warning("Source file not found: '%s'" % fpath)
+                else:
+                    messenger.error("Terminating due to missing source files. "
+                           + "Use the '--ignore-missing-source' option to continue even "
+                           + "if some files are missing.")
+                    sys.exit(1)
+            else:
+                source_filepaths.append(fpath)
+        if len(source_filepaths) == 0:
+            messenger.error("No valid sources of input trees specified. "
+                    + "Please provide the path to at least one (valid and existing) file "
+                    + "containing trees")
+            sys.exit(1)
+    else:
+        messenger.info("No sources of input trees specified. "
+                + "Please provide the path to at least one (valid and existing) file "
+                + "containing tree samples to summarize. See '--help' for other options.")
+        sys.exit(1)
+
+    ###################################################
+    # Lots of other idiot-checking ...
+
+    # target tree
+    if args.target_tree_filepath is not None:
+        target_tree_filepath = os.path.expanduser(os.path.expandvars(args.target_tree_filepath))
+        if not os.path.exists(target_tree_filepath):
+            messenger.error("Target tree file not found: '%s'" % target_tree_filepath)
+            sys.exit(1)
+    else:
+        messenger.error("Target tree file not specified: use the '-t' or '--target' option to provide path to target tree")
+        sys.exit(1)
+
+    # output
+    if args.output_filepath is None:
+        output_dest = sys.stdout
+    else:
+        output_fpath = os.path.expanduser(os.path.expandvars(args.output_filepath))
+        if confirm_overwrite(filepath=output_fpath, replace_without_asking=args.replace):
+            output_dest = open(output_fpath, "w")
+        else:
+            sys.exit(1)
+
+    # taxon set to handle target trees
+    master_taxon_namespace = dendropy.TaxonNamespace()
+    is_rooted = args.rooted_trees
+    messenger.info("Reading target tree: '%s'" % target_tree_filepath)
+    target_tree = None
+    if is_rooted:
+        rooting = "force-rooted"
+    else:
+        rooting = None
+    for tree in dendropy.Tree.yield_from_files(
+            [target_tree_filepath, "rU",],
+            schema='nexus/newick',
+            taxon_namespace=master_taxon_namespace,
+            rooting=rooting):
+        target_tree = tree
+        break
+    bipartition_labels = {}
+    for src_fpath in source_filepaths:
+        messenger.info("Reading source tree(s) from: '%s'" % src_fpath)
+        for tree in dendropy.Tree.yield_from_files(
+                [src_fpath,],
+                schema='nexus/newick',
+                taxon_namespace=master_taxon_namespace,
+                rooting=rooting):
+            tree.encode_bipartitions()
+            for bipartition, edge in tree.bipartition_edge_map.items():
+                label = edge.head_node.label
+                if not label:
+                    continue
+                try:
+                    bipartition_labels[bipartition].append(label)
+                except KeyError:
+                    bipartition_labels[bipartition] = [label]
+    messenger.info("Mapping labels")
+    target_tree.encode_bipartitions()
+    for bipartition, edge in target_tree.bipartition_edge_map.items():
+        label = []
+        if args.preserve_target_labels and edge.head_node.label:
+            label.append(edge.head_node.label)
+        elif not args.preserve_target_labels:
+            edge.head_node.label = None
+        if bipartition in bipartition_labels:
+            label.extend(bipartition_labels[bipartition])
+        else:
+            pass
+            # messenger.send_warning("Split on target tree not found in source trees: ignoring")
+        if label:
+            edge.head_node.label = args.separator.join(label)
+    output_dataset = dendropy.DataSet()
+    tree_list = output_dataset.new_tree_list(taxon_namespace=master_taxon_namespace)
+    tree_list.append(target_tree)
+    if args.to_newick_format:
+        output_dataset.write(
+                file=output_dest,
+                schema="newick",
+                suppress_rooting=False,
+                suppress_edge_lengths=False,
+                unquoted_underscores=False,
+                preserve_spaces=False,
+                store_tree_weights=False,
+                suppress_annotations=False,
+                annotations_as_nhx=False,
+                suppress_item_comments=False,
+                suppress_leaf_taxon_labels=False,
+                suppress_leaf_node_labels=True,
+                suppress_internal_taxon_labels=False,
+                suppress_internal_node_labels=False,
+                node_label_element_separator=' ',
+                )
+    else:
+        if args.include_taxa_block:
+            simple = False
+        else:
+            simple = True
+        comment = []
+        try:
+            username = getpass.getuser()
+        except:
+            username = "a user"
+        comment.append("%s %s by %s." % (_program_name, _program_version, _program_author))
+        comment.append("Using DendroPy Version %s by Jeet Sukumaran and Mark T. Holder."
+            % dendropy.__version__)
+        python_version = sys.version.replace("\n", "").replace("[", "(").replace("]",")")
+        comment.append("Running under Python %s on %s." % (python_version, sys.platform))
+        comment.append("Executed on %s by %s@%s." % (platform.node(),  username, socket.gethostname()))
+        if args.additional_comments:
+            comment.append("\n")
+            comment.append(args.additional_comments)
+        output_dataset.write(
+                file=output_dest,
+                schema="nexus",
+                simple=simple,
+                file_comments=comment,
+                suppress_rooting=False,
+                unquoted_underscores=False,
+                preserve_spaces=False,
+                store_tree_weights=False,
+                suppress_annotations=False,
+                annotations_as_nhx=False,
+                suppress_item_comments=False,
+                suppress_leaf_taxon_labels=False,
+                suppress_leaf_node_labels=True,
+                suppress_internal_taxon_labels=False,
+                suppress_internal_node_labels=False,
+                node_label_element_separator=' ',
+                )
+    if not args.output_filepath:
+        pass
+    else:
+        messenger.info("Results written to: '%s'." % (output_fpath))
+
+if __name__ == '__main__':
+    main_cli()

applications/sumtrees/sumtrees.py

@@ -1659,6 +1659,7 @@ def main():
         else:
             raise ValueError(args.summary_target)
         _message_and_log(msg, wrap=True)
+        tree.encode_bipartitions()
         target_trees.append(tree)
     else:
         try:

debian/changelog

+python-dendropy (4.3.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * d/rules: do not parse d/changelog
+  * Testsuite: autopkgtest-pkg-python
+
+ -- Andreas Tille <tille@debian.org>  Mon, 19 Feb 2018 09:31:21 +0100
+
 python-dendropy (4.2.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -2,14 +2,15 @@ Source: python-dendropy
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all,
                python-setuptools,
                python3-all,
                python3-setuptools
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-dendropy.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/python-dendropy.git
 Homepage: http://dendropy.org/

debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch

@@ -9,7 +9,7 @@ Subject: [PATCH] Fix bug where encoding for default locale is None.
 
 --- a/dendropy/utility/textprocessing.py
 +++ b/dendropy/utility/textprocessing.py
-@@ -42,6 +42,9 @@ ENCODING = locale.getdefaultlocale()[1]
+@@ -45,6 +45,9 @@ except ValueError:
  if ENCODING == None:
      ENCODING = 'UTF-8'
  

debian/rules

@@ -2,9 +2,6 @@
 
 DH_VERBOSE := 1
 
-DEBPKGNAME:=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-docpkg:=$(DEBPKGNAME)-doc
-
 SUMTREES:=sumtrees
 
 export PYBUILD_NAME=dendropy

dendropy/__init__.py

@@ -104,7 +104,7 @@ import collections
 version_info = collections.namedtuple("dendropy_version_info",
         ["major", "minor", "micro", "releaselevel"])(
                 major=4,
-                minor=2,
+                minor=3,
                 micro=0,
                 releaselevel=""
                 )

dendropy/dataio/newickreader.py

@@ -303,7 +303,8 @@ class NewickReader(ioservice.DataReader):
                     taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
             yield tree
             if tree is None:
-                raise StopIteration
+                # raise StopIteration
+                return
 
     def _read(self,
             stream,

dendropy/dataio/nexuswriter.py

@@ -178,7 +178,7 @@ class NexusWriter(ioservice.DataWriter):
         # and need to be removed so as not to cause problems with our keyword
         # validation scheme
         self.simple = kwargs.pop("simple", False)
-        self.suppress_taxa_blocks = kwargs.pop("suppress_taxa_block", None)
+        self.suppress_taxa_blocks = kwargs.pop("suppress_taxa_blocks", None)
         self.suppress_block_titles = kwargs.pop("suppress_block_titles", None)
         self.file_comments = kwargs.pop("file_comments", [])
         if self.file_comments is None:

dendropy/datamodel/charmatrixmodel.py

@@ -1606,7 +1606,7 @@ class CharacterMatrix(
         # recalculated, which will require some careful and perhaps arbitrary
         # handling of corner cases
         clone.character_subsets = container.OrderedCaselessDict()
-        # clone.clone_from(self)
+        indices = set(indices)
         for vec in clone.values():
             for cell_idx in range(len(vec)-1, -1, -1):
                 if cell_idx not in indices:

dendropy/datamodel/taxonmodel.py

@@ -548,6 +548,7 @@ class TaxonNamespace(
             raise TypeError("TaxonNamespace() takes at most 1 non-keyword argument ({} given)".format(len(args)))
         elif len(args) == 1:
             # special case: construct from argument
+            basemodel.DataObject.__init__(self, label=kwargs_set_label)
             other = args[0]
             for i in other:
                 if isinstance(i, Taxon):

dendropy/datamodel/treemodel.py

@@ -772,6 +772,9 @@ class Edge(
     def __eq__(self, other):
         return self is other
 
+    def __lt__(self, other):
+        return id(self) < id(other)
+
     ###########################################################################
     ### Basic Structure
 
@@ -6103,7 +6106,7 @@ class Tree(
             output.write(s)
         return s
 
-    def as_python_source(self, tree_obj_name=None, tree_args=None, oids=False):
+    def as_python_source(self, tree_obj_name=None, tree_args=None):
         """
         Returns string that will rebuild this tree in Python.
         """
@@ -6119,10 +6122,9 @@ class Tree(
             tree_args = ""
         else:
             tree_args = ", " + tree_args
-        p.append("%s = dendropy.Tree(label=%s%s%s)" \
+        p.append("%s = dendropy.Tree(label=%s%s)" \
             % (tree_obj_name,
                label,
-               oid_str,
                tree_args))
 
         taxon_obj_namer = lambda x: "tax_%s" % id(x)
@@ -6132,11 +6134,11 @@ class Tree(
                 label = "'" + taxon.label + "'"
             else:
                 label = "None"
-            p.append("%s = %s.taxon_namespace.require_taxon(label=%s%s)" \
+            p.append("%s = %s.taxon_namespace.require_taxon(label=%s)" \
                 % (tobj_name,
                    tree_obj_name,
                    label,
-                   oid_str))
+                   ))
 
         node_obj_namer = lambda x: "nd_%s" % id(x)
         for node in self.preorder_node_iter():
@@ -6153,13 +6155,13 @@ class Tree(
                     ct = taxon_obj_namer(child.taxon)
                 else:
                     ct = "None"
-                p.append("%s = %s.new_child(label=%s, taxon=%s, edge_length=%s%s)" %
+                p.append("%s = %s.new_child(label=%s, taxon=%s, edge_length=%s)" %
                         (node_obj_namer(child),
                          nn,
                          label,
                          ct,
                          child.edge.length,
-                         oid_str))
+                         ))
 
         return "\n".join(p)
 

dendropy/interop/rspr.py

+#! /usr/bin/env python
+
+##############################################################################
+##  DendroPy Phylogenetic Computing Library.
+##
+##  Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
+##  All rights reserved.
+##
+##  See "LICENSE.rst" for terms and conditions of usage.
+##
+##  If you use this work or any portion thereof in published work,
+##  please cite it as:
+##
+##     Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
+##     for phylogenetic computing. Bioinformatics 26: 1569-1571.
+##
+##############################################################################
+
+"""
+Wrapper for interacting with RSPR
+"""
+
+import subprocess
+import uuid
+import tempfile
+import socket
+import random
+import os
+import sys
+
+import dendropy
+from dendropy.utility.messaging import get_logger
+from dendropy.utility import processio
+from dendropy.utility import textprocessing
+_LOG = get_logger("interop.rspr")
+
+HOSTNAME = socket.gethostname()
+PID = os.getpid()
+
+class Rspr(object):
+    """
+    This class wraps all attributes and input needed to make a call to RSPR.
+
+        https://github.com/cwhidden/rspr
+
+    RSPR:
+
+    Calculate approximate and exact Subtree Prune and Regraft (rSPR)
+    distances and the associated maximum agreement forests (MAFs) between pairs
+    of rooted binary trees from STDIN in newick format. Supports arbitrary labels.
+    The second tree may be multifurcating.
+
+    Copyright 2009-2014 Chris Whidden
+    whidden@cs.dal.ca
+    http://kiwi.cs.dal.ca/Software/RSPR
+
+    """
+    ###
+    # NOTE ON THE ``--pairwise`` FLAG
+    # -------------------------------
+    # This determines the type of comparisons done.
+    #
+    # Specified without arguments, it does all distinct pairwise comparisons of
+    # the input tree. Output by default is a matrix with only the upper half
+    # filled. So, assuming the source has 4 trees, then:
+    #
+    #   $ cat 4trees.tre | rspr -pairwise
+    #   0,23,24,24
+    #   ,0,5,7
+    #   ,,0,6
+    #
+    # Further (numerical) arguments specify the row/columns to restrict the
+    # comparisons.
+    #
+    # E.g., first row only: first tree to all other trees:
+    #
+    #   $ cat 4trees.tre | rspr -pairwise 0 1
+    #   0,23,24,24
+    #
+    # E.g. first two rows only: first two trees to all other trees:
+    #
+    #   $ cat 4trees.tre | rspr -pairwise 0 2
+    #   0,23,24,24
+    #   ,0,5,7
+    #
+    # E.g. third row only:
+    #
+    #   $ cat 4trees.tre | rspr -pairwise 2 3
+    #   ,,0,6
+    #
+    # E.g. last column only: last tree to all other trees:
+    #
+    #   $ cat 4trees.tre | rspr -pairwise 0 4 3 4
+    #   24
+    #   7
+    #   6
+    #   0
+
+
+    def __init__(self,
+            algorithm="bb",
+            optimizations=None,
+            cc=None,
+            ):
+        """
+
+        Parameters
+        ----------
+        algorithm : str
+            One of "fpt", "bb", "approx".
+        optimizations: list[str] or None
+            Will be passed directly rspr (with each element prefixed by ``-``).
+        cc: bool
+            Calculate a potentially better approximation with a quadratic time
+            algorithm.
+        """
+        self.algorithm = algorithm
+        self.optimizations = optimizations
+
+    def compare_one_to_many(self,
+            ref_tree,
+            comparison_trees,
+            command_args=None,
+            newick_output_kwargs=None,
+            ):
+        """
+
+        Compare ``ref_tree'' to each tree in ``comparison_trees``.
+
+        Parameters
+        ----------
+        ref_tree : |Tree|
+            A |Tree| object to be compared to every tree in ``comparison_trees``.
+        comparison_trees : |Tree|
+            An (ordered) iterable of trees to which ``ref_tree`` should be
+            compared.
+        command_args : list or None
+            An iterable of (string) arguments to be passed to the program.
+        newick_output_kwargs : dict or None
+            A collection of keyword arguments to pass to the tree string
+            composition routines (that will generate the tree strings to be
+            used as input to rspr).
+
+        Returns
+        -------
+        scores : list[numeric]
+            A list of the SPR distances from ``ref_tree'' to
+            ``comparison_trees``, in order of the trees given.
+        """
+        if newick_output_kwargs is None:
+            newick_output_kwargs = {}
+        # tf = tempfile.NamedTemporaryFile("w", delete=True)
+        tf = textprocessing.StringIO()
+        ref_tree.write(file=tf, schema="newick", **newick_output_kwargs)
+        for t in comparison_trees:
+            t.write(file=tf, schema="newick", **newick_output_kwargs)
+        command = []
+        command.append("rspr") # TODO: command path as instance attribute
+        command.extend(["-pairwise", "0", "1"])
+        if command_args is not None:
+            command.extend(command_args)
+        p = subprocess.Popen(command,
+                stdin=subprocess.PIPE,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,)
+        stdout, stderr = processio.communicate(p, commands=tf.getvalue())
+        result_fields = stdout.strip("\n").split(",")
+        assert len(result_fields) == 1 + len(comparison_trees), "Expecting length {} + 1 for results, but received {}: {}".format(len(comparison_trees), len(result_fields), result_fields)
+        return [int(v) for v in result_fields[1:]]
+
+
+
+
+
+
+
+

dendropy/test/test_birthdeath.py

@@ -59,7 +59,7 @@ class BirthDeathTreeTest(unittest.TestCase):
         """test that the birth-death process produces the correct number of tips with GSA."""
         _RNG = MockRandom()
         for num_leaves in range(2, 15):
-            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, ntax=num_leaves, gsa_ntax=3*num_leaves, rng=_RNG)
+            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, num_extant_tips=num_leaves, gsa_ntax=3*num_leaves, rng=_RNG)
             self.assertTrue(t._debug_tree_is_valid())
             self.assertEqual(num_leaves, len(t.leaf_nodes()))
 
@@ -67,7 +67,7 @@ class BirthDeathTreeTest(unittest.TestCase):
         """test that the pure-birth process produces the correct number of tips."""
         _RNG = MockRandom()
         for num_leaves in range(2, 20):
-            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, ntax=num_leaves, rng=_RNG)
+            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, num_extant_tips=num_leaves, rng=_RNG)
             self.assertTrue(t._debug_tree_is_valid())
             self.assertEqual(num_leaves, len(t.leaf_nodes()))
 
@@ -75,7 +75,7 @@ class BirthDeathTreeTest(unittest.TestCase):
         """test that the pure-birth process produces the correct number of tips with GSA."""
         _RNG = MockRandom()
         for num_leaves in range(2, 20):
-            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, ntax=num_leaves, gsa_ntax=4*num_leaves, rng=_RNG)
+            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, num_extant_tips=num_leaves, gsa_ntax=4*num_leaves, rng=_RNG)
             self.assertTrue(t._debug_tree_is_valid())
             self.assertEqual(num_leaves, len(t.leaf_nodes()))
 
@@ -83,7 +83,7 @@ class BirthDeathTreeTest(unittest.TestCase):
         """PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
         _RNG = MockRandom()
         for num_leaves in range(2, 20):
-            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, ntax=num_leaves, rng=_RNG)
+            t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, num_extant_tips=num_leaves, rng=_RNG)
             self.assertTrue(t._debug_tree_is_valid())
             self.assertEqual(num_leaves, len(t.leaf_nodes()))