diff options
Diffstat (limited to 'sci-biology/biopython/files/biopython-1.47-kdtree.patch')
| -rw-r--r-- | sci-biology/biopython/files/biopython-1.47-kdtree.patch | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/sci-biology/biopython/files/biopython-1.47-kdtree.patch b/sci-biology/biopython/files/biopython-1.47-kdtree.patch new file mode 100644 index 000000000000..5d9563f2dc0c --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.47-kdtree.patch @@ -0,0 +1,43 @@ +--- 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 |