updating to version 0.2.0; docs for some fxns and readme

Author: pblischak

README.rst

@@ -22,7 +22,7 @@ Requirements:
 -  Seaborn
 -  C++ compiler (g++ >= v4.8)
 
-HyDe is a software package that detects a signal for hybridization in phylogenomic
+HyDe is a software package that detects hybridization in phylogenomic
 data sets using phylogenetic invariants. The primary interface for HyDe is a Python
 module called ``phyde`` (**P**\ ythonic **Hy**\ bridization **De**\ tection).
 ``phyde`` provides a suite of tools for performing hypothesis tests on triples of taxa
@@ -51,6 +51,14 @@ as `Miniconda <https://conda.io/miniconda.html>`__.
     # Test the installation
     make test
 
+The ``phyde`` module is also hosted on the Python Package Index (PyPI), and can be installed directly using
+``pip``.
+
+.. code:: py
+
+  # Install from PyPI with pip
+  pip install phyde
+
 Running HyDe from the Command Line
 ----------------------------------
 
@@ -70,7 +78,7 @@ Running HyDe in Python
     import phyde as hd
 
     # Run a hyde analysis
-    hd.run_hyde(...)
+    res = hd.run_hyde("data.txt", "map.txt", "out", 16, 4, 50000, bootReps=100)
 
     # import a data set for testing particular triples
     data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 50000)

phyde/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = "0.1.1"
+__version__ = "0.2.0"
 __author__  = "Paul Blischak and Laura Kubatko"
 
 from phyde.analyze.main import run_hyde

phyde/core/bootstrap.py

@@ -11,12 +11,19 @@ class Bootstrap:
     containing parameter values.
     """
     def __init__(self, bootfile):
+        """
+        Constructor.
+        """
         self.bootfile = bootfile
         self.breps = {}
         self.triples    = []
         self._read_bootstraps(bootfile)
 
     def __call__(self, attr, p1, hyb, p2):
+        """
+        A callable method to access attributes rom a bootstrapped
+        HyDe analysis. Returned as a list.
+        """
         return [t[attr] for t in self.breps[(p1, hyb, p2)]]
 
     def _read_bootstraps(self, bootfile):
@@ -64,7 +71,7 @@ def _boot_info(self, b):
 
     def summarize(self):
         """
-
+        Summarizes the results of a bootsrapped HyDe analysis.
         """
         summaries = {}
         for t in self.triples:
@@ -75,15 +82,28 @@ def summarize(self):
         return summaries
 
     def gamma(self, p1, hyb, p2):
+        """
+        Return the values of gamma for the triple (p1, hyb, p2).
+        """
         return [t['Gamma'] for t in self.breps[(p1, hyb, p2)]]
 
     def zscore(self, p1, hyb, p2):
+        """
+        Return the values of the test statistic for the triple (p1, hyb, p2).
+        """
         return [t['Zscore'] for t in self.breps[(p1, hyb, p2)]]
 
     def pvalue(self, p1, hyb, p2):
+        """
+        Return the p-values for the triple (p1, hyb, p2).
+        """
         return [t['Pvalue'] for t in self.breps[(p1, hyb, p2)]]
 
     def abba_baba(self, p1, hyb, p2):
+        """
+        Calculate Patterson's D-Statistic for all bootstrap replicates
+        for the triple (p1, hyb, p2). Uses vectorization with numpy arrays.
+        """
         return ((np.array([t['ABBA'] for t in self.breps[(p1, hyb, p2)]]) - np.array([t['ABAB'] for t in self.breps[(p1, hyb, p2)]])) /
                 (np.array([t['ABBA'] for t in self.breps[(p1, hyb, p2)]]) + np.array([t['ABAB'] for t in self.breps[(p1, hyb, p2)]])))
 

phyde/core/result.py

@@ -12,19 +12,22 @@ class HydeResult:
     """
     def __init__(self, infile):
         """
-
+        Constructor.
         """
         self.infile = infile
         self.res = {}
         self.triples = []
         self._read_hyde_results(infile)
 
     def __call__(self, attr, p1, hyb, p2):
+        """
+        Callable method for accessing information in a HydeResult object.
+        """
         return self.res[(p1, hyb, p2)][attr]
 
     def _read_hyde_results(self, file):
         """
-
+        Fxn for reading in results file from a hyde_cpp analysis.
         """
         with open(file) as f:
             results = f.read().splitlines()[1:-1]
@@ -40,7 +43,7 @@ def _read_hyde_results(self, file):
 
     def _hyde_info(self, b):
         """
-
+        Store information for HyDe hypothesis test.
         """
         if len(b) != 18:
             raise ValueError("** Warning: length of hyde entry is incorrect. **")
@@ -69,5 +72,8 @@ def _hyde_info(self, b):
         return hyde_info
 
     def abba_baba(self, p1, hyb, p2):
+        """
+        Calculate Patterson's D-Statistic for the triple (p1, hyb, p2).
+        """
         return ((np.array(self.res[(p1,hyb,p2)]['ABBA']) - np.array(self.res[(p1,hyb,p2)]['ABAB'])) /
                 (np.array(self.res[(p1,hyb,p2)]['ABBA']) + np.array(self.res[(p1,hyb,p2)]['ABAB'])))

setup.py

@@ -66,17 +66,23 @@
     print("  Please see the documentation at http://hybridization-detection.rtfd.io/.\n")
     sys.exit()
 else:
-    setup(name="phyde",
-        version="0.1.1",
+    setup(
+        name="phyde",
+        version="0.2.0",
         description="Hybridization detection using phylogenetic invariants",
         long_description=open('README.rst').read(),
         url="https://github.com/pblischak/HyDe",
         author="Paul Blischak & Laura Kubatko",
         author_email="blischak.4@osu.edu",
-        license="GPL",
         packages=find_packages(),
         ext_modules=cythonize("phyde/**/*.pyx", compiler_directives={'--cplus': True}),
         include_dirs=[numpy.get_include()],
         scripts=['scripts/run_hyde.py', 'src/hyde_cpp'],
+        license="GPL",
+        classifiers=[
+            'Programming Language :: Python',
+            'Programming Language :: Python :: 2',
+            'Programming Language :: Python :: 2.7',
+        ],
         zip_safe=False
     )