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--- 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
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