Python 3/2 compatibility

ChangeLog

@@ -1,3 +1,12 @@
+2015-06-12  Luiz Irber  <khmer@luizirber.org>
+
+   * *.py: refactor for Python 3 compatibility. Clear separation of Unicode
+   and Byte strings, use __future__ imports for compatibility (print function,
+   absolute imports, unicode_literals), fix tests to consider changes to random
+   number generator between Python versions.
+   * khmer/_khmer.cc: rename file, methods return Unicode strings instead of
+   Bytestrings.
+
 2015-06-12  Luiz Irber  <khmer@luizirber.org>
 
    * khmer/{khmermodule.cc},tests/test_hashbits.py: Add Unicode support to
@@ -83,7 +92,7 @@
    * scripts/normalize-by-median.py: major refactoring to use context
    managers and classes; fixed -R
    * tests/test_scripts.py: added test for normalize's -R arg
-   
+
 2015-06-01  Tamer Mansour <drtamermansour@gmail.com>
 
    * scripts/normalize-by-median.py: changed to count kmers from both PE reads

Makefile

@@ -8,7 +8,7 @@ CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmermodule.cc)
 PYSOURCES=$(wildcard khmer/*.py scripts/*.py)
 SOURCES=$(PYSOURCES) $(CPPSOURCES) setup.py
 DEVPKGS=sphinxcontrib-autoprogram pep8==1.5.7 diff_cover \
-autopep8 pylint coverage gcovr nose screed pep257
+autopep8 pylint coverage gcovr nose pep257 future screed
 
 GCOVRURL=git+https://github.com/nschum/gcovr.git@never-executed-branches
 VERSION=$(shell git describe --tags --dirty | sed s/v//)
@@ -36,7 +36,7 @@ help: Makefile
 install-dep: install-dependencies
 
 install-dependencies:
-	pip2 install --upgrade $(DEVPKGS) || pip install --upgrade $(DEVPKGS)
+	pip install --upgrade $(DEVPKGS)
 
 ## sharedobj   : build khmer shared object file
 sharedobj: khmer/_khmermodule.so

khmer/__init__.py

@@ -6,6 +6,8 @@
 #
 """This is khmer; please see http://khmer.readthedocs.org/."""
 
+from __future__ import print_function
+
 from khmer._khmer import CountingHash
 from khmer._khmer import LabelHash as _LabelHash
 from khmer._khmer import Hashbits as _Hashbits
@@ -179,12 +181,14 @@ def calc_expected_collisions(hashtable, force=False, max_false_pos=.2):
     fp_all = fp_one ** n_ht
 
     if fp_all > max_false_pos:
-        print >>sys.stderr, "**"
-        print >>sys.stderr, "** ERROR: the graph structure is too small for "
-        print >>sys.stderr, "this data set.  Increase k-mer presence table "
-        print >>sys.stderr, "size/num of tables."
-        print >>sys.stderr, "** Do not use these results!!"
-        print >>sys.stderr, "**"
+        print("**", file=sys.stderr)
+        print(
+            "** ERROR: the graph structure is too small for ", file=sys.stderr)
+        print(
+            "this data set.  Increase k-mer presence table ", file=sys.stderr)
+        print("size/num of tables.", file=sys.stderr)
+        print("** Do not use these results!!", file=sys.stderr)
+        print("**", file=sys.stderr)
         if not force:
             sys.exit(1)