From 7b3eff27425f15bd5ad6623509fd7676fc31161f Mon Sep 17 00:00:00 2001 From: Paul Sutter Date: Sat, 7 Jun 2014 03:25:42 +0000 Subject: [PATCH 1/3] README edited online with Bitbucket --- README | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README b/README index eb2c9d5..42b3945 100644 --- a/README +++ b/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 \ No newline at end of file From b871f23a200d8a49931da036b54bb5837cb9303c Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Tue, 24 Jun 2014 05:00:06 -0500 Subject: [PATCH 2/3] temporarily disabled patch for kdtree --- external/external_python_build.cmake | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/external/external_python_build.cmake b/external/external_python_build.cmake index e93947a..805d0b5 100644 --- a/external/external_python_build.cmake +++ b/external/external_python_build.cmake @@ -199,15 +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) + #PATCH_COMMAND ${CMAKE_COMMAND} + # -DPATCH_FILE=${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 From bdd3c9ab65d6f718f37aa4aa5bb8212debb59228 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 24 Jun 2014 13:49:11 +0200 Subject: [PATCH 3/3] Updated kdtree-scipy dependency and patch --- external/external_python_build.cmake | 15 +++++++-------- external/patch_kdtree | 19 +++++-------------- 2 files changed, 12 insertions(+), 22 deletions(-) diff --git a/external/external_python_build.cmake b/external/external_python_build.cmake index 805d0b5..bf1907c 100644 --- a/external/external_python_build.cmake +++ b/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) @@ -199,15 +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 ${CMAKE_COMMAND} + -DPATCH_FILE=${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) - #PATCH_COMMAND ${CMAKE_COMMAND} - # -DPATCH_FILE=${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 - - diff --git a/external/patch_kdtree b/external/patch_kdtree index 847a90a..59f8c29 100644 --- a/external/patch_kdtree +++ b/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