chaubold · jakirkham · Apr 22, 2014 · Apr 22, 2014 · Apr 22, 2014 · Apr 22, 2014
diff --git a/README_openblas.txt b/README_openblas.txt
@@ -0,0 +1,15 @@
+If you are having trouble building OpenBLAS out of the box, you may need to specify your CPU Architecture.
+Common architecture options include SandyBridge and Haswell. Even if your build worked correctly, it may
+not be optimal. The default architecture, if not specified, is Nehalem, which is probably not the ideal
+choice unless using an older computer.
+
+To specify the architecture simply use the TARGET flag. For example, TARGET=SANDYBRIDGE will build for
+the SandyBridge architecture. Similarly, TARGET=HASWELL will target the Haswell (or Crystalwell)
+architecture(s). To do this simply modify the BUILD_COMMAND to include this flag ____after____ the call
+to $(MAKE) as it must be an argument to make. It is recommend the same be done for the INSTALL_COMMAND
+as well.
+
+More information can be found on the OpenBLAS GitHub webpage ( https://github.com/xianyi/OpenBLAS/ ). A list
+of architectures supported can be found here ( https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt ).
+Note that at the time of writing this READNME, the list has not been updated in about a year; so, it does not
+list HASWELL even though it is supported by the version we are using.
diff --git a/ann.cmake b/ann.cmake
@@ -15,8 +15,7 @@ external_source (ann
     1.1.2
     ann_1.1.2.tar.gz
     7ffaacc7ea79ca39d4958a6378071365
-    http://www.cs.umd.edu/~mount/ANN/Files/1.1.2
-    FORCE)
+    http://www.cs.umd.edu/~mount/ANN/Files/1.1.2/)
 
 message ("Installing ${ann_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${ann_NAME}

diff --git a/backports-ssl_match_hostname.cmake b/backports-ssl_match_hostname.cmake
@@ -0,0 +1,37 @@
+# Provides match_hostname from Python 3 for Python 2.
+# Required by tornado.
+
+if (NOT backports-ssl_match_hostname_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+
+include (python)
+
+external_source(backports-ssl_match_hostname
+    3.4.0.2
+    backports.ssl_match_hostname-3.4.0.2.tar.gz
+    788214f20214c64631f0859dc79f23c6
+    https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/)
+
+message ("Installing ${backports-ssl_match_hostname_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${backports-ssl_match_hostname_NAME}
+    DEPENDS             ${python_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${backports-ssl_match_hostname_URL}
+    URL_MD5             ${backports-ssl_match_hostname_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${backports-ssl_match_hostname_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT backports-ssl_match_hostname_NAME)
diff --git a/boost.cmake b/boost.cmake
@@ -17,12 +17,13 @@ set (boost_INCLUDE_DIR  ${BUILDEM_INCLUDE_DIR}/boost)
 include_directories (${boost_INCLUDE_DIR})
 
 external_source (boost
-    1_51_0
-    boost_1_51_0.tar.gz
-    6a1f32d902203ac70fbec78af95b3cf8
-    http://downloads.sourceforge.net/project/boost/boost/1.51.0)
+    1_56_0
+    boost_1_56_0.tar.bz2
+    a744cf167b05d72335f27c88115f211d
+    http://hivelocity.dl.sourceforge.net/project/boost/boost/1.56.0)
 
-set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION} 
+set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_container.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_system.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_program_options.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
@@ -42,7 +43,7 @@ ExternalProject_Add(${boost_NAME}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ""
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
-        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-libraries=container,date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
         --with-python=${PYTHON_EXE} 
         --prefix=${BUILDEM_DIR}
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} ./b2

diff --git a/bottleneck.cmake b/bottleneck.cmake
@@ -0,0 +1,41 @@
+# Provides functions to deal with nan in NumPy arrays efficiently.
+#
+# Required by pandas.
+
+
+if (NOT bottleneck_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (TemplateSupport)
+
+include (python)
+include (numpy)
+include (scipy)
+include (nose)
+
+external_git_repo(bottleneck
+	v0.7.0 #4042977fa716f127a2074de011b9ef84caf2e965
+	https://github.com/kwgoodman/bottleneck)
+
+message ("Installing ${bottleneck_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${bottleneck_NAME}
+    DEPENDS             ${python_NAME} ${numpy_NAME} ${scipy_NAME} ${nose_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    GIT_REPOSITORY	${bottleneck_URL}
+    GIT_TAG             ${bottleneck_TAG}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${bottleneck_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT bottleneck_NAME)
diff --git a/cloud_sptheme.cmake b/cloud_sptheme.cmake
@@ -0,0 +1,40 @@
+#
+# Install cloud_sptheme from source. Provides theme for Sphinx.
+#
+
+if (NOT cloud_sptheme_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (TemplateSupport)
+
+include (python)
+include (sphinx)
+
+external_source (cloud_sptheme
+    1.6
+    cloud_sptheme-1.6.tar.gz
+    23d5fce0b87836d9f29573d6ee6a9bc1
+    https://pypi.python.org/packages/source/c/cloud_sptheme/)
+
+message ("Installing ${cloud_sptheme_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${cloud_sptheme_NAME}
+    DEPENDS             ${python_NAME} ${sphinx_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${cloud_sptheme_URL}
+    URL_MD5             ${cloud_sptheme_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${cloud_sptheme_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT cloud_sptheme_NAME)
diff --git a/dlib.cmake b/dlib.cmake
@@ -15,8 +15,7 @@ external_source (dlib
     18.3
     dlib-18.3.tar.bz2
     1ad26ec7bddccf8a605e1edfd0620c65
-    http://downloads.sourceforge.net/project/dclib/dlib/v18.3
-    FORCE)
+    http://downloads.sourceforge.net/project/dclib/dlib/v18.3)
 
 message ("Installing ${dlib_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${dlib_NAME}

diff --git a/ffmpeg.cmake b/ffmpeg.cmake
@@ -0,0 +1,39 @@
+#
+# Install ffmpeg from source.
+# Provides support for audio and video.
+#
+
+if (NOT ffmpeg_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+external_source (ffmpeg
+    2.4.3
+    ffmpeg-2.4.3.tar.bz2
+    8da635baff57d7ab704b1daca5a99b47
+    http://www.ffmpeg.org/releases/
+    FORCE)
+
+message ("Installing ${ffmpeg_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${ffmpeg_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${ffmpeg_URL}
+    URL_MD5             ${ffmpeg_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${ffmpeg_SRC_DIR}/configure
+        --prefix=${BUILDEM_DIR}
+        --disable-yasm
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ${BUILDEM_ENV_STRING} $(MAKE) check
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) install
+)
+
+set_target_properties(${ffmpeg_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT ffmpeg_NAME)
diff --git a/futures.cmake b/futures.cmake
@@ -0,0 +1,41 @@
+#
+# Install futures library from source
+#
+
+if (NOT futures_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+
+external_source (futures
+    2.1.6
+    futures-2.1.6.tar.gz
+    cfab9ac3cd55d6c7ddd0546a9f22f453
+    https://pypi.python.org/packages/source/f/futures)
+
+message ("Installing ${futures_NAME} into ilastik build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${futures_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${futures_URL}
+    URL_MD5             ${futures_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ""
+)
+
+set_target_properties(${futures_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+
+endif (NOT futures_NAME)
+
diff --git a/geos.cmake b/geos.cmake
@@ -0,0 +1,51 @@
+#
+# Install geos from source.
+# Provides an open source geometry engine.
+#
+
+if (NOT geos_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+external_source (geos
+    3.4.2
+    geos-3.4.2.tar.bz2
+    fc5df2d926eb7e67f988a43a92683bae
+    http://download.osgeo.org/geos/)
+
+
+# if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+#     set (GEOS_ENABLE_MACOSX_FRAMEWORK ON)
+#     set (GEOS_ENABLE_MACOSX_FRAMEWORK_UNIXCOMPAT ON)
+# else()
+#     set (GEOS_ENABLE_MACOSX_FRAMEWORK OFF)
+# endif()
+
+
+message ("Installing ${geos_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${geos_NAME}
+    DEPENDS             
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${geos_URL}
+    URL_MD5             ${geos_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+                        # Turns off test that is known failure on Mac and that does not appear to be fixed ( http://trac.osgeo.org/geos/ticket/299 ).
+                        ${geos_SRC_DIR}/tests/unit/geom/CoordinateArraySequenceFactoryTest.cpp ${PATCH_DIR}/geos-CoordinateArraySequenceFactoryTest.cpp.patch
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${geos_SRC_DIR}/configure
+        --prefix=${BUILDEM_DIR}
+        "LDFLAGS=${BUILDEM_LDFLAGS} ${BUILDEM_ADDITIONAL_CXX_FLAGS}"
+        "CPPFLAGS=-I${BUILDEM_DIR}/include ${BUILDEM_ADDITIONAL_CXX_FLAGS}"
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ${BUILDEM_ENV_STRING} $(MAKE) check
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) install
+)
+
+set_target_properties(${geos_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT geos_NAME)
diff --git a/gmp.cmake b/gmp.cmake
@@ -15,7 +15,7 @@ external_source (gmp
     5.0.5
     gmp-5.0.5.tar.bz2
     041487d25e9c230b0c42b106361055fe
-    ftp://ftp.gnu.org/gnu/gmp)
+    ftp://ftp.gnu.org/gnu/gmp/)
 
 message ("Installing ${gmp_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${gmp_NAME}

diff --git a/gmpy.cmake b/gmpy.cmake
@@ -0,0 +1,45 @@
+# Python bindings to the very versatile, established gmp, mpfr, and mpc.
+#
+# Used by SymPy. Though, can be used independently.
+
+
+if (NOT gmpy_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (TemplateSupport)
+
+include (python)
+include (gmp)
+include (mpfr)
+include (mpc)
+
+
+external_source (gmpy
+    2.0.5
+    gmpy2-2.0.5.zip
+    95f008bcab6372164358123f43e3f490
+    http://pypi.python.org/packages/source/g/gmpy2/)
+
+
+message ("Installing ${gmpy_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${gmpy_NAME}
+    DEPENDS             ${python_NAME} ${gmp_NAME} ${mpfr_NAME} ${mpc_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${gmpy_URL}
+    URL_MD5             ${gmpy_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build --prefix=${BUILDEM_DIR}
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install --prefix=${BUILDEM_DIR}
+)
+
+set_target_properties(${gmpy_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT gmpy_NAME)
diff --git a/h5py.cmake b/h5py.cmake
@@ -15,10 +15,10 @@ include (hdf5)
 include (numpy)
 
 external_source (h5py
-    2.1.3
-    h5py-2.1.3.tar.gz
-    afd3c14f763339e186dd9cd24eb2eb74
-    http://h5py.googlecode.com/files)
+    2.3.1
+    h5py-2.3.1.tar.gz
+    8f32f96d653e904d20f9f910c6d9dd91
+    https://pypi.python.org/packages/source/h/h5py)
 
 message ("Installing ${h5py_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${h5py_NAME}