Release 1.3.5

README.mkd

@@ -16,7 +16,7 @@ The tool requires a standard [Python](http://python.org/) installation (2.7 and
 3.3 or higher are supported) with the following modules:
 
 1. [numpy](http://www.numpy.org/) version 1.8.2 or latest
-2. [pandas](http://pandas.pydata.org/) version 0.14.1 or latest
+2. [pandas](http://pandas.pydata.org/) version 0.17.1 or latest
 3. [six](https://pythonhosted.org/six/) version 1.9.0 or latest
 
 The tool has been tested on *Linux* only, but should work on *MacOS* and

pyplink/pyplink.py

@@ -198,7 +198,7 @@ def next(self):
     def _read_current_marker(self):
         """Reads the current marker and returns its genotypes."""
         return self._geno_values[
-            np.fromstring(self._bed.read(self._nb_bytes), dtype=np.uint8)
+            np.frombuffer(self._bed.read(self._nb_bytes), dtype=np.uint8)
         ].flatten(order="C")[:self._nb_samples]
 
     def seek(self, n):
@@ -321,8 +321,8 @@ def get_nb_markers(self):
     def get_duplicated_markers(self):
         """Returns the duplicated markers, if any.
 
-        Args:
-            set: The set of duplicated marker (might be empty).
+        Returns:
+            dict: The set of duplicated marker (might be empty).
 
         """
         if self._has_duplicated:
@@ -398,7 +398,7 @@ def _read_bed(self):
             seek_index = self._get_seek_position(self._bim.iloc[-1, :].i)
             bed_file.seek(seek_index)
             geno = self._geno_values[
-                np.fromstring(bed_file.read(self._nb_bytes), dtype=np.uint8)
+                np.frombuffer(bed_file.read(self._nb_bytes), dtype=np.uint8)
             ].flatten(order="C")[:self._nb_samples]
             if geno.shape[0] != self._nb_samples:
                 raise ValueError("invalid number of entries: corrupted BED?")

setup.py

@@ -17,7 +17,7 @@
 
 MAJOR = 1
 MINOR = 3
-MICRO = 4
+MICRO = 5
 VERSION = "{}.{}.{}".format(MAJOR, MINOR, MICRO)
 
 
@@ -42,7 +42,7 @@ def write_version_file(fn=None):
 
 def get_requirements():
     # Initial requirements
-    requirements = ["numpy >= 1.8.2", "pandas >= 0.14.1", "six >= 1.9.0"]
+    requirements = ["numpy >= 1.8.2", "pandas >= 0.17.1", "six >= 1.9.0"]
 
     # Checking if python 2 (requires mock)
     if sys.version_info[0] == 2:
@@ -62,7 +62,7 @@ def setup_package():
         description="Python module to read binary Plink files.",
         author="Louis-Philippe Lemieux Perreault",
         author_email="louis-philippe.lemieux.perreault@statgen.org",
-        url="http://www.statgen.org",
+        url="https://github.com/lemieuxl/pyplink",
         license="MIT",
         packages=["pyplink", "pyplink.tests"],
         package_data={"pyplink.tests": ["data/*"], },