Add: from __future__ import print_statement

This is currently redundant as we are carefully only
using this simple print style which is both a print
statement (with redundant brackets) under Python 2
and a print function under Python 3:

print(variable)

However, adding the __future__ import to any file using
a print should catch any accidental usage of the print
statement in the near future (even if not testing under
Python 3 where it would be spotted since we've turned
off the print fixer during the 2to3 conversion).

This was automated as follows:

<python>
MAGIC = "from __future__ import print_function"

import os
import sys

def should_mark(filename):
    handle = open(filename, "rU")
    lines = [line.strip() for line in handle if "print" in line]
    handle.close()
    if MAGIC in lines:
        #print("%s is marked" % filename)
        return False
    if "print" in lines:
        print("TODO - %s has a naked print" % filename)
        sys.exit(1)
    for line in lines:
        if "print" not in line:
            continue
        #print(line)
        line = line.strip(" #")
        if line.startswith(">>>") or line.startswith("..."):
            #doctest
            line = line[3:].strip()
        if line.startswith("print ") or line.startswith("print("):
            return True
    print("%s has no print statements" % filename)
    return False

def mark_file(filename, marker=MAGIC):
    with open(filename, "rU") as h:
        lines = list(h.readlines())
    with open(filename, "w") as h:
        while (lines[0].startswith("#") or not lines[0].strip()):
            h.write(lines.pop(0))
        if lines[0].startswith('"""') or lines[0].startswith('r"""'):
            # Module docstring
            if lines[0].strip() == '"""':
                print("Non-PEP8 module docstring in %s" % filename)
            if lines[0].rstrip().endswith('"""') and lines[0].strip() != '"""':
                # One liner
                print("One line module docstring in %s" % filename)
                h.write(lines.pop(0))
            else:
                h.write(lines.pop(0))
                while not lines[0].strip().endswith('"""'):
                    h.write(lines.pop(0))
                h.write(lines.pop(0))
        while (lines[0].startswith("#") or not lines[0].strip()):
            h.write(lines.pop(0))
        h.write(marker + "\n\n")
        h.write("".join(lines))

for dirpath, dirnames, filenames in os.walk("."):
    if dirpath.startswith("./build/"):
        continue
    for f in filenames:
        if not f.endswith(".py"):
            continue
        f = os.path.join(dirpath, f)
        if should_mark(f):
            print("Marking %s" % f)
            mark_file(f)
</python>

Bio/Align/AlignInfo.py

@@ -10,6 +10,8 @@
 """
 
 # standard library
+from __future__ import print_function
+
 import math
 import sys
 

Bio/Align/Applications/_ClustalOmega.py

@@ -11,6 +11,8 @@
 """Command line wrapper for the multiple alignment program Clustal Omega.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Switch, AbstractCommandline

Bio/Align/Applications/_Clustalw.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program Clustal W.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 import os

Bio/Align/Applications/_Dialign.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program DIALIGN2-2.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline

Bio/Align/Applications/_Mafft.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment programme MAFFT.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 import os

Bio/Align/Applications/_Muscle.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program MUSCLE.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Switch, AbstractCommandline

Bio/Align/Applications/_Prank.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program PRANK.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Switch, AbstractCommandline

Bio/Align/Applications/_Probcons.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program PROBCONS.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline

Bio/Align/Applications/_TCoffee.py

@@ -5,6 +5,8 @@
 """Command line wrapper for the multiple alignment program TCOFFEE.
 """
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Application import _Option, _Switch, AbstractCommandline

Bio/Align/Generic.py

@@ -13,6 +13,8 @@
 Classes:
  - Alignment
 """
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 # biopython

Bio/Align/__init__.py

@@ -9,6 +9,8 @@
 class, used in the Bio.AlignIO module.
 
 """
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
 from Bio.Seq import Seq

Bio/AlignIO/ClustalIO.py

@@ -9,6 +9,8 @@
 Bio.SeqIO functions if you want to work directly with the gapped sequences).
 """
 
+from __future__ import print_function
+
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 from Bio.Align import MultipleSeqAlignment

Bio/AlignIO/EmbossIO.py

@@ -12,6 +12,8 @@
 example from the alignret, water and needle tools.
 """
 
+from __future__ import print_function
+
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 from Bio.Align import MultipleSeqAlignment

Bio/AlignIO/FastaIO.py

@@ -19,6 +19,8 @@
 which can also be used to store a multiple sequence alignments.
 """
 
+from __future__ import print_function
+
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 from Bio.Align import MultipleSeqAlignment

Bio/AlignIO/Interfaces.py

@@ -8,6 +8,8 @@
 use this module.  It provides base classes to try and simplify things.
 """
 
+from __future__ import print_function
+
 from Bio.Alphabet import single_letter_alphabet
 
 # TODO - Review self.next() method for Python 3 support...

Bio/AlignIO/NexusIO.py

@@ -13,6 +13,8 @@
 sequences as SeqRecord objects.
 """
 
+from __future__ import print_function
+
 from Bio.SeqRecord import SeqRecord
 from Bio.Nexus import Nexus
 from Bio.Align import MultipleSeqAlignment

Bio/AlignIO/PhylipIO.py

@@ -31,6 +31,8 @@
 Biopython 1.58 or later treats dots/periods in the sequence as invalid, both
 for reading and writing. Older versions did nothing special with a dot/period.
 """
+from __future__ import print_function
+
 import string
 
 from Bio.Seq import Seq

Bio/AlignIO/StockholmIO.py

@@ -128,6 +128,8 @@
     >>> print(sub_record.letter_annotations['secondary_structure'])
     -------<<<
 """
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # not just plaintext
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord

Bio/AlignIO/__init__.py

@@ -121,6 +121,8 @@
 """
 
 
+from __future__ import print_function
+
 __docformat__ = "epytext en"  # not just plaintext
 
 #TODO

Bio/Application/__init__.py

@@ -19,6 +19,8 @@
 The finished command line strings are then normally invoked via the built-in
 Python module subprocess.
 """
+from __future__ import print_function
+
 import os
 import sys
 import subprocess

Bio/Blast/Applications.py

@@ -32,6 +32,8 @@
 BMC Bioinformatics 2009, 10:421
 doi:10.1186/1471-2105-10-421
 """
+from __future__ import print_function
+
 from Bio import BiopythonDeprecationWarning
 
 from Bio.Application import _Option, AbstractCommandline, _Switch

Bio/Blast/NCBIStandalone.py

@@ -49,6 +49,8 @@
 are likely to be deprecated and then removed in future releases.
 """
 
+from __future__ import print_function
+
 from Bio import BiopythonDeprecationWarning
 import warnings
 warnings.warn("This module has been deprecated. Consider Bio.SearchIO for "

Bio/Blast/NCBIWWW.py

@@ -16,6 +16,8 @@
 qblast        Do a BLAST search using the QBLAST API.
 """
 
+from __future__ import print_function
+
 from Bio._py3k import StringIO
 from Bio._py3k import _as_string, _as_bytes
 

Bio/Blast/NCBIXML.py

@@ -21,6 +21,8 @@
                     Blast records.  It uses the BlastParser internally.
 read                Returns a single Blast record. Uses the BlastParser internally.
 """
+from __future__ import print_function
+
 from Bio.Blast import Record
 import xml.sax
 from xml.sax.handler import ContentHandler

Bio/Data/CodonTable.py

@@ -9,6 +9,8 @@
 Last updated for Version 3.9
 """
 
+from __future__ import print_function
+
 from Bio import Alphabet
 from Bio.Alphabet import IUPAC
 from Bio.Data import IUPACData

Bio/DocSQL.py

@@ -23,6 +23,8 @@
 CreatePeople(message=Success)
 """
 
+from __future__ import print_function
+
 import sys
 
 from Bio import MissingPythonDependencyError

Bio/Emboss/Applications.py

@@ -12,6 +12,8 @@
 programs.
 """
 
+from __future__ import print_function
+
 from Bio.Application import _Option, _Switch, AbstractCommandline
 
 

Bio/Entrez/__init__.py

@@ -68,6 +68,8 @@
 _open        Internally used function.
 
 """
+from __future__ import print_function
+
 import urllib
 import urllib2
 import time

Bio/FSSP/__init__.py

@@ -10,6 +10,8 @@
 tuple of two instances.
 mult_align: returns a Biopython alignment object
 """
+from __future__ import print_function
+
 import re
 import fssp_rec
 from Bio.Align import Generic

Bio/File.py

@@ -15,6 +15,8 @@
 files are also defined under Bio.File but these are not intended for direct
 use.
 """
+from __future__ import print_function
+
 import codecs
 import os
 import contextlib

Bio/GA/Evolver.py

@@ -4,6 +4,8 @@
 for taking care of the transition from one generation to the next.
 """
 # standard modules
+from __future__ import print_function
+
 import sys
 
 

Bio/GenBank/Scanner.py

@@ -26,6 +26,8 @@
 # for more details of this format, and an example.
 # Added by Ying Huang & Iddo Friedberg
 
+from __future__ import print_function
+
 import warnings
 import re
 from Bio.Seq import Seq

Bio/GenBank/__init__.py

@@ -38,6 +38,8 @@
                       location parser.
 
 """
+from __future__ import print_function
+
 import re
 
 # other Biopython stuff

Bio/Geo/Record.py

@@ -13,6 +13,8 @@
 """
 
 
+from __future__ import print_function
+
 class Record(object):
     """Hold GEO information in a format similar to the original record.
 

Bio/Graphics/GenomeDiagram/_AbstractDrawer.py

@@ -40,6 +40,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.lib import pagesizes
 from reportlab.lib import colors
 from reportlab.graphics.shapes import *

Bio/Graphics/GenomeDiagram/_CircularDrawer.py

@@ -12,6 +12,8 @@
 """CircularDrawer module for GenomeDiagram."""
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.graphics.shapes import *
 from reportlab.lib import colors
 from reportlab.pdfbase import _fontdata

Bio/Graphics/GenomeDiagram/_Colors.py

@@ -21,6 +21,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.lib import colors
 
 

Bio/Graphics/GenomeDiagram/_FeatureSet.py

@@ -34,6 +34,8 @@
 # IMPORTS
 
 # ReportLab
+from __future__ import print_function
+
 from reportlab.pdfbase import _fontdata
 from reportlab.lib import colors
 

Bio/Graphics/GenomeDiagram/_Graph.py

@@ -28,6 +28,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.lib import colors
 
 from math import sqrt

Bio/Graphics/GenomeDiagram/_GraphSet.py

@@ -30,6 +30,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.lib import colors
 
 from _Graph import GraphData

Bio/Graphics/GenomeDiagram/_LinearDrawer.py

@@ -27,6 +27,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.graphics.shapes import *
 from reportlab.lib import colors
 

Bio/Graphics/GenomeDiagram/_Track.py

@@ -28,6 +28,8 @@
 """
 
 # ReportLab imports
+from __future__ import print_function
+
 from reportlab.lib import colors
 
 # GenomeDiagram imports

Bio/HMM/Utilities.py

@@ -5,6 +5,8 @@
 """
 
 
+from __future__ import print_function
+
 def pretty_print_prediction(emissions, real_state, predicted_state,
                             emission_title = "Emissions",
                             real_title = "Real State",

Bio/HotRand.py

@@ -8,6 +8,8 @@
    support biosimulations that rely on random numbers.
 """
 
+from __future__ import print_function
+
 import urllib
 from Bio import BiopythonDeprecationWarning
 import warnings