clean up

(Portage version: 2.1.6.13/cvs/Linux i686)

3 files changed, 0 insertions, 103 deletions

diff --git a/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch b/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch
deleted file mode 100644
index cefb16d7d95d..000000000000
--- a/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- setup.py.old	2007-03-17 15:21:04.000000000 -0400
-+++ setup.py	2007-05-17 14:02:42.000000000 -0400
-@@ -64,6 +64,7 @@
-         _CHECKED = check_dependencies()
-     return _CHECKED
- 
-+USE_KDTREE = False
- def check_dependencies():
-     """Return whether the installation should continue."""
-     # There should be some way for the user to tell specify not to
-@@ -112,15 +113,8 @@
-         
-     
-     # Compile KDTree ? Not compiled by default
--    print "\n*** Bio.KDTree *** NOT built by default "
--    kdtree_msg = """
--The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
--which in turn, depends on C++ code that does not compile cleanly on
--all platforms. Hence, Bio.KDTree is not built by default.
--
--Would you like to build Bio.KDTree ?"""
--
--    if get_yes_or_no (kdtree_msg, 0):
-+    global USE_KDTREE
-+    if USE_KDTREE:
-         NUMPY_PACKAGES.append("Bio.KDTree")
-         NUMPY_EXTENSIONS.append(
-             CplusplusExtension('Bio.KDTree._CKDTree', 
diff --git a/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch b/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
deleted file mode 100644
index 16fc44d77cd0..000000000000
--- a/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- biopython-1.44/Bio/SeqUtils/__init__.py.old	2007-09-14 09:38:35.000000000 -0400
-+++ biopython-1.44/Bio/SeqUtils/__init__.py	2007-12-17 11:07:27.000000000 -0500
-@@ -7,8 +7,7 @@
- # license.  Please see the LICENSE file that should have been included
- # as part of this package.
- 
--import os, sys, getopt, re, time
--from string import maketrans
-+import re, time
- from Bio import SeqIO
- from Bio import Translate
- from Bio.Seq import Seq
-@@ -277,8 +276,9 @@
-    nice looking 6 frame translation with GC content - code from xbbtools
-    similar to DNA Striders six-frame translation
-    """
--   comp = complement(seq)
--   anti = reverse(comp)
-+   from Bio.Seq import reverse_complement
-+   anti = reverse_complement(seq)
-+   comp = anti[::-1]
-    length = len(seq)
-    frames = {}
-    for i in range(0,3):
-@@ -399,6 +399,7 @@
- # {{{ 
- 
- if __name__ == '__main__':
-+   import sys, getopt
-    # crude command line options to use most functions directly on a FASTA file
-    options = {'apply_on_multi_fasta':0,
-               'quick':0,
diff --git a/sci-biology/biopython/files/biopython-1.47-kdtree.patch b/sci-biology/biopython/files/biopython-1.47-kdtree.patch
deleted file mode 100644
index 5d9563f2dc0c..000000000000
--- a/sci-biology/biopython/files/biopython-1.47-kdtree.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- setup.py.old	2007-03-17 15:21:04.000000000 -0400
-+++ setup.py	2007-05-17 14:02:42.000000000 -0400
-@@ -64,6 +64,7 @@
-         _CHECKED = check_dependencies()
-     return _CHECKED
- 
-+USE_KDTREE = False
- def check_dependencies():
-     """Return whether the installation should continue."""
-     # There should be some way for the user to tell specify not to
-@@ -112,15 +113,8 @@
-         
-     
-     # Compile KDTree ? Not compiled by default
--    print "\n*** Bio.KDTree *** NOT built by default "
--    kdtree_msg = """
--The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
--which in turn, depends on C++ code that does not compile cleanly on
--all platforms. Hence, Bio.KDTree is not built by default.
--
--Would you like to build Bio.KDTree ?"""
--
--    if get_yes_or_no (kdtree_msg, 0):
-+    global USE_KDTREE
-+    if USE_KDTREE:
-         NUMPY_PACKAGES.append("Bio.KDTree")
-         NUMPY_EXTENSIONS.append(
-             CplusplusExtension('Bio.KDTree._CKDTree', 
---- Tests/test_KDTree.py.old	2008-07-05 16:32:25.000000000 -0400
-+++ Tests/test_KDTree.py	2008-07-05 16:41:33.000000000 -0400
-@@ -1,4 +1,11 @@
--from Bio.KDTree.KDTree import _neighbor_test, _test
-+from Bio import MissingExternalDependencyError
-+
-+try:
-+	from Bio.KDTree.KDTree import _neighbor_test, _test
-+except ImportError:
-+	message = 'Could not import KDTree module ' \
-+			'(not important if you do not plan to use BIO.KDTree).'
-+	raise MissingExternalDependencyError(message)
- 
- nr_points=5000
- dim=3