2to3 all .py files. versioneer.py threw an error

docs/conf.py

@@ -47,8 +47,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'Pydna'
-copyright = u'2015, Björn Johansson'
+project = 'Pydna'
+copyright = '2015, Björn Johansson'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -221,8 +221,8 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'Pydna.tex', u'Pydna Documentation',
-   u'Björn Johansson', 'manual'),
+  ('index', 'Pydna.tex', 'Pydna Documentation',
+   'Björn Johansson', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -251,8 +251,8 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'pydna', u'Pydna Documentation',
-     [u'Björn Johansson'], 1)
+    ('index', 'pydna', 'Pydna Documentation',
+     ['Björn Johansson'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -265,8 +265,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'Pydna', u'Pydna Documentation',
-   u'Björn Johansson', 'Pydna', 'One line description of project.',
+  ('index', 'Pydna', 'Pydna Documentation',
+   'Björn Johansson', 'Pydna', 'One line description of project.',
    'Miscellaneous'),
 ]
 

pydna/__init__.py

@@ -18,13 +18,13 @@
 
 '''
 
-__author__       = u"Björn Johansson"
-__copyright__    = u"Copyright 2013 - 2015 Björn Johansson"
-__credits__      = [u"Björn Johansson", u"Mark Budde"]
-__license__      = u"BSD"
-__maintainer__   = u"Björn Johansson"
-__email__        = u"[email protected]"
-__status__       = u"Development" # "Production" #"Prototype"
+__author__       = "Björn Johansson"
+__copyright__    = "Copyright 2013 - 2015 Björn Johansson"
+__credits__      = ["Björn Johansson", "Mark Budde"]
+__license__      = "BSD"
+__maintainer__   = "Björn Johansson"
+__email__        = "[email protected]"
+__status__       = "Development" # "Production" #"Prototype"
 from ._version import get_versions
 __version__      = get_versions()['version'][:5]
 __long_version__ = get_versions()['version']
@@ -64,7 +64,7 @@
 import errno         as _errno
 import subprocess    as _subprocess
 import appdirs       as _appdirs
-from ConfigParser import SafeConfigParser as _SafeConfigParser
+from configparser import SafeConfigParser as _SafeConfigParser
 
 _os.environ["pydna_config_dir"] = _os.getenv("pydna_config_dir") or _appdirs.user_config_dir("pydna")
 
@@ -266,7 +266,7 @@ def delete_cache(delete=[ "amplify", "assembly", "genbank", "web", "synced" ]):
         try:
             _os.remove( _os.path.join( _os.environ["pydna_data_dir"], file_) )
             msg += " deleted.\n"
-        except OSError, e:
+        except OSError as e:
             if e._errno == _errno.ENOENT:
                 msg += " no file to delete.\n"
     return _pretty_str(msg)

pydna/_orderedset.py

@@ -62,6 +62,6 @@ def __eq__(self, other):
 if __name__ == '__main__':
     s = OrderedSet('abracadaba')
     t = OrderedSet('simsalabim')
-    print(s | t)
-    print(s & t)
-    print(s - t)
+    print((s | t))
+    print((s & t))
+    print((s - t))

pydna/_pretty.py

@@ -8,7 +8,7 @@ class pretty_str(str):
     def _repr_pretty_(self, p, cycle):
         p.text(self)
 
-class pretty_unicode(unicode):
+class pretty_unicode(str):
     def _repr_pretty_(self, p, cycle):
         p.text(self)
 
@@ -19,10 +19,10 @@ def _repr_pretty_(self, p, cycle):
 if __name__=="__main__":
     import pydna
 
-    print pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test.txt").format()
-    print pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test2.txt").format()[3270:3281]
+    print(pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test.txt").format())
+    print(pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test2.txt").format()[3270:3281])
     import sys;sys.exit(42)
-    import StringIO
+    import io
     from Bio import SeqIO
     from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
 
@@ -34,17 +34,17 @@ def _repr_pretty_(self, p, cycle):
 
     rawseq = re.findall(pattern, textwrap.dedent(raw + "\n\n"), flags=re.MULTILINE).pop(0)
 
-    handle = StringIO.StringIO(raw)
+    handle = io.StringIO(raw)
 
     sr = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
 
     s = sr.format("gb").strip()
 
-    print pretty_string(s[:55]+"circular"+s[63:])[3200:3300]
+    print(pretty_string(s[:55]+"circular"+s[63:])[3200:3300])
 
     from pydna import Dseqrecord
 
     v = Dseqrecord(sr)
 
-    print v.format("gb")
+    print(v.format("gb"))
 

pydna/_sequencetrace.py

@@ -95,7 +95,7 @@ def reverseCompSequence(sequence):
     ambiguity codes.
     """
     tmp = list()
-    for cnt in reversed(range(len(sequence))):
+    for cnt in reversed(list(range(len(sequence)))):
         tmp.append(rclookup[sequence[cnt]])
 
     return ''.join(tmp)
@@ -401,7 +401,7 @@ def followDecode(self, cdata):
         udata = list()
         prev = unpack('B', cdata[256])[0]
         udata.append(cdata[256])
-        for cnt in xrange(257, len(cdata)):
+        for cnt in range(257, len(cdata)):
             diff = unpack('b', cdata[cnt])[0]
             actual = table[prev] - diff
 
@@ -460,14 +460,14 @@ def decode8BitDelta(self, cdata):
 
         # first, unpack the 1-byte values
         udata = list()
-        for cnt in xrange(1, len(cdata)):
+        for cnt in range(1, len(cdata)):
             val = unpack('B', cdata[cnt])[0]
             udata.append(val)
 
         # now apply the reverse delta filtering
         for clev in range(levels):
             prev = 0
-            for cnt in xrange(0, len(udata)):
+            for cnt in range(0, len(udata)):
                 actual = udata[cnt] + prev
                 if actual > 255:
                     # simulate 1-byte integer overflow
@@ -488,14 +488,14 @@ def decode16BitDelta(self, cdata):
 
         # first, unpack the 2-byte values
         udata = list()
-        for cnt in xrange(1, len(cdata), 2):
+        for cnt in range(1, len(cdata), 2):
             val = unpack('>H', cdata[cnt:cnt+2])[0]
             udata.append(val)
 
         # now apply the reverse delta filtering
         for clev in range(levels):
             prev = 0
-            for cnt in xrange(0, len(udata)):
+            for cnt in range(0, len(udata)):
                 actual = udata[cnt] + prev
                 if actual > 65535:
                     # simulate 2-byte integer overflow
@@ -516,14 +516,14 @@ def decode32BitDelta(self, cdata):
 
         # first, unpack the 4-byte values (skipping the 2 padding bytes)
         udata = list()
-        for cnt in xrange(3, len(cdata), 4):
+        for cnt in range(3, len(cdata), 4):
             val = unpack('>I', cdata[cnt:cnt+4])[0]
             udata.append(val)
 
         # now apply the reverse delta filtering
         for clev in range(levels):
             prev = 0
-            for cnt in xrange(0, len(udata)):
+            for cnt in range(0, len(udata)):
                 actual = udata[cnt] + prev
                 if actual > 4294967295:
                     # simulate 1-byte integer overflow
@@ -706,13 +706,13 @@ def readABIIndex(self):
     def printABIIndex(self, data_id):
         for entry in self.abiindex:
             if entry['did'] == data_id:
-                print 'entry ID:', entry['did']
-                print 'idv:', entry['idv']
-                print 'data format:', entry['dformat']
-                print 'format size:', entry['fsize']
-                print 'data count:', entry['dcnt']
-                print 'total data length:', entry['dlen']
-                print 'data offset:', entry['offset']
+                print('entry ID:', entry['did'])
+                print('idv:', entry['idv'])
+                print('data format:', entry['dformat'])
+                print('format size:', entry['fsize'])
+                print('data count:', entry['dcnt'])
+                print('total data length:', entry['dlen'])
+                print('data offset:', entry['offset'])
 
     def getIndexEntry(self, data_id, number):
         for row in self.abiindex:

pydna/_simple_paths8.py

@@ -47,15 +47,15 @@ def all_simple_paths_edges(G, source, target, cutoff=None, data=False):
         edge_data = lambda u,v,n,E,I: (u,v)
 
     for path in _all_simple_paths_graph(G,source,target,cutoff=cutoff):
-        edges = zip(path[:-1],path[1:])
+        edges = list(zip(path[:-1],path[1:]))
         E = []  # list: items of each edge
         N = []  # list: number of items of each edge
         for u,v in edges:
-            edge_items = G[u][v].items()
+            edge_items = list(G[u][v].items())
             E += [edge_items]
             N += [len(edge_items)]
         I = [0 for n in N]
-        idx = [i for i in reversed(range(len(I)))]
+        idx = [i for i in reversed(list(range(len(I))))]
         while True:
             path_edges = []
             for n,(u,v) in enumerate(edges):
@@ -70,13 +70,13 @@ def all_simple_paths_edges(G, source, target, cutoff=None, data=False):
 
 def all_circular_paths_edges(G):
     for path in sorted(nx.simple_cycles(G), key=len, reverse =True):
-        edges = zip(path, path[1:]+[path[0]])
+        edges = list(zip(path, path[1:]+[path[0]]))
         N = []
         for u,v in edges:
             n = len(G[u][v])
             N += [n]
         I = [0 for n in N]
-        idx = [i for i in reversed(range(len(I)))]
+        idx = [i for i in reversed(list(range(len(I))))]
         while True:
             path_edges = []
             for i,(u,v) in enumerate(edges):
@@ -103,27 +103,27 @@ def all_circular_paths_edges(G):
     target = 'd'
 
     # MULTIDIGRAPH
-    print 'MULTIDIGRAPH (data=False)'
+    print('MULTIDIGRAPH (data=False)')
     for path in all_simple_paths_edges(G, source, target):
-        print path
+        print(path)
 
-    print
-    print 'MULTIDIGRAPH (data=True)'
+    print()
+    print('MULTIDIGRAPH (data=True)')
     for path in all_simple_paths_edges(G, source, target, data=True):
         #print path
-        total_weight = sum([(I.values()[0]['weight']) for u,v,I in path])
-        print total_weight, '\t', path
+        total_weight = sum([(list(I.values())[0]['weight']) for u,v,I in path])
+        print(total_weight, '\t', path)
 
-    print
+    print()
     # DIGRAPH
     H = nx.DiGraph(G)
-    print 'DIGRAPH (data=False)'
+    print('DIGRAPH (data=False)')
     for path in all_simple_paths_edges(H, source, target):
-        print path
+        print(path)
 
-    print
-    print 'DIGRAPH (data=True)'
+    print()
+    print('DIGRAPH (data=True)')
     for path in all_simple_paths_edges(H, source, target, data=True):
         total_weight = sum([w['weight'] for u,v,w in path])
-        print total_weight, '\t', path
+        print(total_weight, '\t', path)
 

pydna/_version.py

@@ -76,19 +76,19 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
             if e.errno == errno.ENOENT:
                 continue
             if verbose:
-                print("unable to run %s" % dispcmd)
+                print(("unable to run %s" % dispcmd))
                 print(e)
             return None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(("unable to find command, tried %s" % (commands,)))
         return None
     stdout = p.communicate()[0].strip()
     if sys.version_info[0] >= 3:
         stdout = stdout.decode()
     if p.returncode != 0:
         if verbose:
-            print("unable to run %s (error)" % dispcmd)
+            print(("unable to run %s (error)" % dispcmd))
         return None
     return stdout
 
@@ -99,8 +99,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     dirname = os.path.basename(root)
     if not dirname.startswith(parentdir_prefix):
         if verbose:
-            print("guessing rootdir is '%s', but '%s' doesn't start with "
-                  "prefix '%s'" % (root, dirname, parentdir_prefix))
+            print(("guessing rootdir is '%s', but '%s' doesn't start with "
+                  "prefix '%s'" % (root, dirname, parentdir_prefix)))
         raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
     return {"version": dirname[len(parentdir_prefix):],
             "full-revisionid": None,
@@ -155,15 +155,15 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # "stabilization", as well as "HEAD" and "master".
         tags = set([r for r in refs if re.search(r'\d', r)])
         if verbose:
-            print("discarding '%s', no digits" % ",".join(refs-tags))
+            print(("discarding '%s', no digits" % ",".join(refs-tags)))
     if verbose:
-        print("likely tags: %s" % ",".join(sorted(tags)))
+        print(("likely tags: %s" % ",".join(sorted(tags))))
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
             if verbose:
-                print("picking %s" % r)
+                print(("picking %s" % r))
             return {"version": r,
                     "full-revisionid": keywords["full"].strip(),
                     "dirty": False, "error": None
@@ -185,7 +185,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     if not os.path.exists(os.path.join(root, ".git")):
         if verbose:
-            print("no .git in %s" % root)
+            print(("no .git in %s" % root))
         raise NotThisMethod("no .git directory")
 
     GITS = ["git"]
@@ -236,7 +236,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         if not full_tag.startswith(tag_prefix):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
-                print(fmt % (full_tag, tag_prefix))
+                print((fmt % (full_tag, tag_prefix)))
             pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
                                % (full_tag, tag_prefix))
             return pieces