Added a patch to scipy-kdtree to fix a np.min bug in query

external/check_and_apply_patch.cmake

@@ -0,0 +1,19 @@
+SET(STAMP ${BUILD_PREFIX}/patch_applied)
+
+SET(RESULT "not ok")
+
+IF (EXISTS ${STAMP})
+  FILE(READ ${STAMP} RESULT)
+ENDIF (EXISTS ${STAMP})
+
+IF(NOT "${RESULT}" STREQUAL "ok")
+  EXECUTE_PROCESS(COMMAND patch -p0 -i ${PATCH_FILE}
+                  WORKING_DIRECTORY ${SOURCE_PREFIX}
+                  RESULT_VARIABLE okcode)
+  IF(NOT "${okcode}" STREQUAL "0")
+    FILE(WRITE ${STAMP} "not-applied")
+    MESSAGE(FATAL_ERROR "Patch not applied")
+  ELSE(NOT "${okcode}" STREQUAL "0")
+    FILE(WRITE ${STAMP} "ok")
+  ENDIF(NOT "${okcode}" STREQUAL "0")
+ENDIF(NOT "${RESULT}" STREQUAL "ok")

external/external_python_build.cmake

@@ -199,7 +199,14 @@ IF(INTERNAL_KDTREE_SCIPY)
     BUILD_IN_SOURCE 1
     BUILD_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
     INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
+    PATCH_COMMAND  ${CMAKE_COMMAND} 
+      -DBUILD_PREFIX=${BUILD_PREFIX}/kdtree-scipy-prefix 
+      -DPATCH_FILE=${CMAKE_SOURCE_DIR}/external/patch_kdtree 
+      -DSOURCE_PREFIX=${BUILD_PREFIX}/kdtree-scipy-prefix/src/kdtree-scipy
+      -P ${CMAKE_SOURCE_DIR}/external/check_and_apply_patch.cmake
+
    )
+  SET(AUXILIARY_PYTHON_DEPEND ${AUXILIARY_PYTHON_DEPEND} kdtree-scipy)
 ENDIF(INTERNAL_KDTREE_SCIPY)
 
 

external/patch_kdtree

@@ -0,0 +1,29 @@
+--- periodic_kdtree.py.old	2014-04-18 17:30:39.000000000 +0200
++++ periodic_kdtree.py	2014-04-18 17:31:59.000000000 +0200
+@@ -102,7 +102,7 @@
+         # all neighbors within the given distance_upper_bound".
+ 
+         # Cap distance_upper_bound
+-        distance_upper_bound = np.min(distance_upper_bound,
++        distance_upper_bound = min(distance_upper_bound,
+                                       self.max_distance_upper_bound)
+ 
+         # Run queries over all relevant images of x
+@@ -128,7 +128,7 @@
+         # is a single point, not an array of points
+         
+         # Cap r
+-        r = np.min(r, self.max_distance_upper_bound)
++        r = min(r, self.max_distance_upper_bound)
+ 
+         # Run queries over all relevant images of x
+         results = []
+@@ -213,7 +213,7 @@
+         # all neighbors within the given distance_upper_bound".
+ 
+         # Cap distance_upper_bound
+-        distance_upper_bound = np.min(distance_upper_bound,
++        distance_upper_bound = min(distance_upper_bound,
+                                       self.max_distance_upper_bound)
+ 
+         # Run queries over all relevant images of x