Remove with_statement imports required under Python 2.5

Removed all the with statement imports (and any comment lines associated with them); from __future__ import with_statement
DunbrackLab · Aug 28, 2013 · eeab501 · eeab501
1 parent d134b3a
commit eeab501
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Showing 27 changed files with 2 additions and 64 deletions.
diff --git a/Bio/AlignIO/__init__.py b/Bio/AlignIO/__init__.py
@@ -120,8 +120,6 @@
 same length.
 """
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
 
 __docformat__ = "epytext en"  # not just plaintext
 

diff --git a/Bio/File.py b/Bio/File.py
@@ -15,8 +15,6 @@
 files are also defined under Bio.File but these are not intended for direct
 use.
 """
-# For with statement in Python 2.5
-from __future__ import with_statement
 import codecs
 import os
 import contextlib

diff --git a/Bio/Nexus/Nexus.py b/Bio/Nexus/Nexus.py
@@ -9,9 +9,6 @@
 Based upon 'NEXUS: An extensible file format for systematic information'
 Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
 """
-# For with in Python/Jython 2.5
-from __future__ import with_statement
-
 import copy
 import math
 import random

diff --git a/Bio/PDB/DSSP.py b/Bio/PDB/DSSP.py
@@ -20,8 +20,6 @@
     - -        None
 """
 
-from __future__ import with_statement
-
 import re
 from StringIO import StringIO
 import subprocess

diff --git a/Bio/PDB/PDBList.py b/Bio/PDB/PDBList.py
@@ -20,9 +20,6 @@
 
 """ Access the PDB over the internet (e.g. to download structures). """
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import contextlib
 import gzip
 import os

diff --git a/Bio/PDB/PDBParser.py b/Bio/PDB/PDBParser.py
@@ -5,9 +5,6 @@
 
 """Parser for PDB files."""
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import warnings
 
 try:

diff --git a/Bio/PDB/parse_pdb_header.py b/Bio/PDB/parse_pdb_header.py
@@ -23,8 +23,6 @@
 
 """Parse the header of a PDB file."""
 
-# For 'with' on Python 2.5/Jython 2.5
-from __future__ import with_statement
 import re
 
 from Bio import File

diff --git a/Bio/Phylo/PAML/baseml.py b/Bio/Phylo/PAML/baseml.py
@@ -3,9 +3,6 @@
 # license. Please see the LICENSE file that should have been included
 # as part of this package.
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import os
 import os.path
 from _paml import Paml, _relpath

diff --git a/Bio/Phylo/PAML/codeml.py b/Bio/Phylo/PAML/codeml.py
@@ -3,9 +3,6 @@
 # license. Please see the LICENSE file that should have been included
 # as part of this package.
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import os
 import os.path
 from _paml import Paml, _relpath

diff --git a/Bio/Phylo/_io.py b/Bio/Phylo/_io.py
@@ -8,8 +8,6 @@
 This API follows the same semantics as Biopython's `SeqIO` and `AlignIO`.
 """
 
-# For with on Python/Jython 2.5
-from __future__ import with_statement
 __docformat__ = "restructuredtext en"
 
 from Bio import File

diff --git a/Bio/SearchIO/__init__.py b/Bio/SearchIO/__init__.py
@@ -194,9 +194,6 @@
 
 """
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 __docformat__ = 'epytext en'
 
 import sys

diff --git a/Bio/SeqIO/PdbIO.py b/Bio/SeqIO/PdbIO.py
@@ -2,8 +2,6 @@
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
-from __future__ import with_statement
-
 import collections
 import warnings
 

diff --git a/Bio/SeqIO/__init__.py b/Bio/SeqIO/__init__.py
@@ -259,9 +259,6 @@
 making up each alignment as SeqRecords.
 """
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 __docformat__ = "epytext en"  # not just plaintext
 
 #TODO

diff --git a/Doc/Tutorial.tex b/Doc/Tutorial.tex
@@ -2675,11 +2675,10 @@ \section{Parsing sequences from compressed files}
 
 \noindent
 Here we use a file handle instead, using the \verb|with| statement
-(Python 2.5 or later) to close the handle automatically:
+to close the handle automatically:
 
-%This doctest won't work on Python 2.5, even with the __future__ import. Odd.
+%doctest examples
 \begin{verbatim}
->>> from __future__ import with_statement #Needed on Python 2.5
 >>> from Bio import SeqIO
 >>> with open("ls_orchid.gbk") as handle:
 ...     print sum(len(r) for r in SeqIO.parse(handle, "gb"))

diff --git a/Tests/test_Application.py b/Tests/test_Application.py
@@ -9,8 +9,6 @@
 stdin/stdout/stderr handling.
 """
 
-from __future__ import with_statement
-
 import os
 import unittest
 

diff --git a/Tests/test_BWA_tool.py b/Tests/test_BWA_tool.py
@@ -5,8 +5,6 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-from __future__ import with_statement
-
 from Bio import MissingExternalDependencyError
 import sys
 import os

diff --git a/Tests/test_File.py b/Tests/test_File.py
@@ -3,8 +3,6 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-from __future__ import with_statement
-
 import os.path
 import unittest
 import shutil

diff --git a/Tests/test_Phylo_NeXML.py b/Tests/test_Phylo_NeXML.py
@@ -6,8 +6,6 @@
 
 """Unit tests for the NeXML and NeXMLIO modules.
 """
-from __future__ import with_statement
-
 import os
 import tempfile
 import unittest

diff --git a/Tests/test_SearchIO_blast_tab.py b/Tests/test_SearchIO_blast_tab.py
@@ -5,9 +5,6 @@
 
 """Tests for SearchIO BlastIO parsers."""
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import os
 import unittest
 

diff --git a/Tests/test_SearchIO_blast_text.py b/Tests/test_SearchIO_blast_text.py
@@ -5,9 +5,6 @@
 
 """Tests for SearchIO BlastIO plain text parsers."""
 
-# For using with statement in Python 2.5 or Jython
-from __future__ import with_statement
-
 import os
 import unittest
 

diff --git a/Tests/test_SeqIO_FastaIO.py b/Tests/test_SeqIO_FastaIO.py
@@ -4,8 +4,6 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-from __future__ import with_statement
-
 import unittest
 from StringIO import StringIO
 

diff --git a/Tests/test_SeqIO_QualityIO.py b/Tests/test_SeqIO_QualityIO.py
@@ -5,8 +5,6 @@
 
 """Additional unit tests for Bio.SeqIO.QualityIO (covering FASTQ and QUAL)."""
 
-from __future__ import with_statement
-
 import os
 import unittest
 import warnings

diff --git a/Tests/test_SeqIO_features.py b/Tests/test_SeqIO_features.py
@@ -8,8 +8,6 @@
 Initially this takes matched tests of GenBank and FASTA files from the NCBI
 and confirms they are consistent using our different parsers.
 """
-from __future__ import with_statement
-
 import os
 import unittest
 from Bio.Alphabet import generic_dna, generic_rna, generic_protein

diff --git a/Tests/test_SeqUtils.py b/Tests/test_SeqUtils.py
@@ -3,8 +3,6 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-from __future__ import with_statement
-
 import os
 import unittest
 

diff --git a/Tests/test_SubsMat.py b/Tests/test_SubsMat.py
@@ -2,8 +2,6 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-from __future__ import with_statement
-
 try:
     from numpy import corrcoef
     del corrcoef

diff --git a/Tests/test_TogoWS.py b/Tests/test_TogoWS.py
@@ -6,8 +6,6 @@
 """Testing Bio.TogoWS online code.
 """
 
-from __future__ import with_statement
-
 import unittest
 from StringIO import StringIO
 

diff --git a/Tests/test_Uniprot.py b/Tests/test_Uniprot.py
@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 """Test for the Uniprot parser on Uniprot XML files.
 """
-from __future__ import with_statement
-
 import os
 import unittest