setup.py fix

docs/_pages/gpm.rst

@@ -1,9 +1,9 @@
 GenotypePhenotypeMap
 ====================
 
-The ``GenotypePhenotypeMap`` class is the primary tool provided by the ``gpmap`` package.
-It creates intuitive and useful mapping on the fly. It appends methods and attributes
-to make analyzing genotype-phenotype data easy. We've create other packages that
+The ``GenotypePhenotypeMap`` class is main entry-point to the ``gpmap`` package.
+It offers intuitive and useful methods and attributes
+for analyzing genotype-phenotype data. We've also created a number of other packages that
 easily interact with the ``GenotypePhenotypeMap``.
 
 Example
@@ -31,14 +31,7 @@ Interface
 
 BinaryMap
 ---------
-Attached to the GenotypePhenotypeMap is a ``BinaryMap`` object.
-
-The ``BinaryMap`` class creates a binary representation of all genotypes and maps
-them to a genotype-phenotype map. Binary representations are useful for many reasons,
-like modeling evolutionary paths and analyzing epistatic interactions (see epistasis_)
-
 All ``GenotypePhenotypeMap`` objects append a ``BinaryMap`` instance to a the ``binary``
-attribute. Most attributes in the ``GenotypePhenotypeMap`` also exist in under
-the ``binary`` attribute, updated with the binary genotype representations.
-
-.. _epistasis: http://epicstasis.readthedocs.io/
+attribute. The ``BinaryMap`` class creates a binary representation of all genotypes and maps
+them to a genotype-phenotype map. Most attributes in the ``GenotypePhenotypeMap`` also exist in
+the ``binary`` object, updated with the binary genotype representations.

docs/_pages/tutorials.rst

@@ -38,4 +38,8 @@ Alternatively, you can load data from a json file (using the format defined `her
 Port to NetworkX object
 -----------------------
 
-A useful feature of the ``seqspace`` object
+.. code-block:: python
+
+ Graph = gpm.add_networkx()
+
+.. code-block:: python

gpmap/gpm.py

@@ -221,7 +221,7 @@ def write(self, fname, items, sep="\t", **kwargs):
  f.write(sep.join(row))
 
  def sort(self, genotypes):
- """Sort the genotype-phenotype map by genotypes
+ """Sort the genotype-phenotype map using a list of genotypes.
  """
  if len(genotypes) != self.n:
  raise Exception("""genotypes argument must be the same length.""")

gpmap/graph/draw/base.py

@@ -70,6 +70,13 @@ def path(G, pos, ax, path, scale=1, length=1, **kwargs):
 @checkG
 def network(G, scale=1, vertical=True, figsize=(5,5), **kwargs):
  """Draw a generic plot for a genotype-phenotype map.
+
+ Parameters
+ ----------
+ G : GenotypePhenotypeGraph object
+ genotype-phenotype network to plot
+ scale : 
+
  """
  pos = positions.flattened(G, vertical=vertical, scale=scale)
  # separate keyword args.

gpmap/graph/draw/ellipses.py

@@ -1,3 +1,7 @@
+import numpy
+import matplotlib as mpl
+import networkx as nx
+
 def draw_networkx_nodes_ellipses(G, pos,
  nodelist=None,
  height=20,

gpmap/graph/draw/positions.py

@@ -7,6 +7,8 @@ def flattened(G, scale=1, vertical=False):
  ----------
  G : GenotypePhenotypeGraph object
  A genotype-phenotype objects
+ scale : float (default=1)
+ density of the nodes.
 
  Returns
  -------

gpmap/simulate/__init__.py

@@ -0,0 +1 @@
+from .base import GenotypePhenotypeSimulation

gpmap/simulate/base.py

@@ -18,9 +18,11 @@ def random_mutation_set(length, alphabet_size=2):
  size = [alphabet_size for i in range(length)]
  else:
  size = alphabet_size
-
- alphabet = utils.AMINO_ACIDS[:size]
- mutations = dict([(i, alphabet[i])for i in range(length)])
+ # build mutations dictionary
+ mutations = {}
+ for i in range(length):
+ alphabet = utils.AMINO_ACIDS[:size[i]]
+ mutations[i] = alphabet
  return mutations
 
 class GenotypePhenotypeSimulation(GenotypePhenotypeMap):
@@ -40,7 +42,7 @@ def __init__(self, wildtype, mutations, range=(0,1), *args, **kwargs):
  def set_random(self, range=(0,1)):
  """ Get a set of random
  """
- self.phenotypes = np.random.random(range[0], range[1], size=self.n)
+ self.phenotypes = np.random.uniform(range[0], range[1], size=self.n)
 
  @classmethod
  def from_length(cls, length, alphabet_size=2, *args, **kwargs):
@@ -53,12 +55,11 @@ def from_length(cls, length, alphabet_size=2, *args, **kwargs):
  alphabet_size : int (optional)
  alphabet size
 
-
  Returns
  -------
  self : GenotypePhenotypeSimulation
  """
- mutations = random_mutations_set(lengths, alphabet_size=alphabet_size)
- wildtype = ".join"([m[0] for m in mutations.values()])
+ mutations = random_mutation_set(length, alphabet_size=alphabet_size)
+ wildtype = "".join([m[0] for m in mutations.values()])
  self = cls(wildtype, mutations, *args, **kwargs)
  return self

setup.py

@@ -3,12 +3,21 @@
 except:
  from distutils.core import setup
 
+# Packages and subpackages to install
+packages = [
+ 'gpmap',
+ 'gpmap.evolve',
+ 'gpmap.graph',
+ 'gpmap.graph.draw',
+ 'gpmap.simulate'
+]
+
 setup(name='gpmap',
- version='0.1',
+ version='0.1.1',
  description='Data-structure for analyzing genotype-phenotype map data.',
  author='Zach Sailer',
  author_email='[email protected]',
- packages=['gpmap'],
+ packages=packages,
  url="https://github.com/harmslab/gpmap",
  install_requires=[
  'networkx',