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v1.0b1

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1 parent fafe2f7 commit a89a74bfff3d4253e918da061b3843e765836325 @bielcardona committed Mar 17, 2012
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@@ -1,10 +1,15 @@
from setuptools import setup, find_packages
setup(name="PhyloNetwork",
- version="0.9",
- author="Gabriel Cardona",
- author_email="bielcardona@gmail.com",
- license="BSD",
- keywords="phylogenetic trees networks",
- packages=['PhyloNetwork'],
- package_dir = {'PhyloNetwork': 'src/PhyloNetwork'}
+ version="1.0b1",
+ author="Gabriel Cardona, David Sanchez",
+ author_email="bielcardona@gmail.com, dscharles@gmail.com",
+ license="BSD",
+ keywords="phylogenetic trees networks",
+ packages=['pyphylonetwork'],
+ package_dir = {'pyphylonetwork': 'src/pyphylonetwork'},
+ install_requires = [
+ 'networkx',
+ 'pyparsing',
+ 'numpy'
+ ]
)
@@ -2,12 +2,13 @@
Class for phylogenetic networks... with nested taxa
"""
-from PhyloNetwork.classes import *
-from PhyloNetwork.distances import *
-from PhyloNetwork.memoize import *
-from PhyloNetwork.permutations import *
-from PhyloNetwork.eNewick import *
-from PhyloNetwork.generators import *
+from .classes import *
+from .distances import *
+from .memoize import *
+from .permutations import *
+from .eNewick import *
+from .generators import *
+from .exceptions import *
def eNewick_reader(filename,ignore_prefix=None):
f = open(filename,'r')
@@ -1,11 +1,4 @@
-'''
-Created on Dec 24, 2011
-
-@author: cardona
-'''
-
from networkx import DiGraph, is_directed_acyclic_graph, dfs_successors
-#from networkx.exception import NetworkXException, NetworkXError
from networkx import single_source_shortest_path_length,all_pairs_shortest_path_length,dijkstra_path_length
import numpy,pyparsing,copy
@@ -1,9 +1,3 @@
-'''
-Created on Dec 24, 2011
-
-@author: cardona
-'''
-
from utils import total_cmp
from .exceptions import TaxaException
@@ -44,8 +38,8 @@ def nodal_distance_splitted(net1,net2,p=1,take_root=False, check=False):
if check:
if not net1.taxa() == net2.taxa():
- raise TaxaException("Networks over different set of taxa")
-
+ raise TaxaException("Networks over different set of taxa")
+
try:
mat=net1.nodal_matrix()-net2.nodal_matrix()
except:
File renamed without changes.
@@ -1,5 +1,3 @@
-
-
class MalformedNewickException(Exception):
"""
Raised when creating a new network from a malformed eNewick string.
@@ -1,9 +1,3 @@
-'''
-Created on Jan 16, 2012
-
-@author: cardona
-'''
-
from .classes import PhyloNetwork
from .operations import push_and_hang,hold_and_hang,push_and_label,hold_and_label
from .utils import random_weighted
@@ -1,9 +1,3 @@
-'''
-Created on Dec 24, 2011
-
-@author: cardona
-'''
-
import functools
class memoize_method(object):
@@ -1,9 +1,3 @@
-'''
-Created on Jan 16, 2012
-
-@author: cardona
-'''
-
import copy
def push_and_hang(net,u,newtaxa):
@@ -1,9 +1,3 @@
-'''
-Created on Dec 24, 2011
-
-@author: cardona
-'''
-
from random import randint
def total_cmp(x,y):

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