Merge branch 'master' of https://bitbucket.org/cosmicvoids/vide_public

README

@@ -26,7 +26,7 @@ This software is put under the GNU Public License.
 Please see LICENSE for further information.
 
 Mainline VIDE contributions from Ben Wandelt, Nico Hamaus, Alice Pisani, 
-Paul Zibick, and Qingqing Mao.
+Paul Zivick, and Qingqing Mao.
 This toolkit includes ZOBOV, originally developed by Mark Neyrinck. 
 See zobov/zobov_readme.txt for copyright/license information. 
 SDF library provided by Michael S. Warren and John Salmon. 
@@ -48,4 +48,4 @@ cd pipeline/
 Version Summary
 -----------------
 
-v1.0 - Initial Release
+v1.0 - Initial Release

external/external_python_build.cmake

@@ -45,7 +45,7 @@ IF(INTERNAL_SCIPY)
 ENDIF(INTERNAL_SCIPY)
 
 IF(INTERNAL_KDTREE_SCIPY)
-  SET(KDTREE_SCIPY_URL "https://github.com/patvarilly/periodic_kdtree/archive/master.zip" CACHE STRING "URL to download kdtree from")
+  SET(KDTREE_SCIPY_URL "https://github.com/patvarilly/periodic_kdtree/archive/ea2d9e8c9d.zip" CACHE STRING "URL to download kdtree from")
   mark_as_advanced(KDTREE_SCIPY_URL)
 ENDIF(INTERNAL_KDTREE_SCIPY)
 
@@ -200,15 +200,13 @@ IF(INTERNAL_KDTREE_SCIPY)
     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=${CMAKE_SOURCE_DIR}/external/patch_kdtree 
+      -DBUILD_PREFIX=${BUILD_PREFIX}/kdtree-scipy-prefix 
       -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

@@ -1,12 +1,12 @@
---- periodic_kdtree.py.old	2014-04-18 17:30:39.000000000 +0200
-+++ periodic_kdtree.py	2014-04-18 17:31:59.000000000 +0200
+--- periodic_kdtree.py.old	2014-05-31 17:08:00.000000000 +0200
++++ periodic_kdtree.py	2014-06-24 13:42:13.769770000 +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)
+-        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 @@
@@ -18,12 +18,3 @@
  
          # 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