Commit fd0c686c authored by Kelvin Rodriguez's avatar Kelvin Rodriguez
Browse files

updated env

parent af9201e1

environment.yml

0 → 100644
+107 −0
Original line number Diff line number Diff line 
name: isisdeps

channels:

  - anaconda

  - mgckind

  - jlaura

  - defaults

  - conda-forge

  - krodriguez

  - usgs-astrogeology

dependencies:

  - geotiff=1.4.1=0

  - libgcc=4.8.5=1

  - proj4=4.9.2=0

  - blas=1.1=openblas

  - boost=1.65.1=py27_0

  - boost-cpp=1.65.1=1

  - bzip2=1.0.6=1

  - cairo=1.14.6=4

  - cmake=3.9.1=0

  - cspice=66=0

  - curl=7.55.1=0

  - doxygen=1.8.14=0

  - eigen=3.3.3=0

  - expat=2.2.5=0

  - ffmpeg=3.2.4=3

  - flann=1.8.4=0

  - fontconfig=2.12.1=4

  - freetype=2.7=1

  - geos=3.5.1=1

  - gettext=0.19.8.1=0

  - giflib=5.1.4=0

  - glib=2.51.4=0

  - harfbuzz=1.3.4=2

  - hdf5=1.8.18=2

  - icu=58.2=0

  - jasper=1.900.1=4

  - jpeg=9b=2

  - krb5=1.14.2=0

  - lapack=3.6.1=1

  - libffi=3.2.1=3

  - libgfortran=3.0.0=0

  - libiconv=1.15=0

  - libpng=1.6.34=0

  - libssh2=1.8.0=2

  - libtiff=4.0.6=7

  - libuv=1.11.0=0

  - libwebp=0.5.2=7

  - libxcb=1.12=1

  - libxml2=2.9.7=0

  - m4=1.4.17=1

  - metis=5.1.0=3

  - mysql-connector-c=6.1.6=0

  - nanoflann=1.2.2=0

  - ncurses=5.9=10

  - ninja=1.7.2=0

  - nn=1.86.0=2

  - numpy=1.13.3=py27_blas_openblas_200

  - opencv=3.3.0=py27_blas_openblas_200

  - pcre=8.39=0

  - pip=9.0.1=py27_1

  - pixman=0.34.0=1

  - protobuf=3.2.0=py27_0

  - python=2.7.14=4

  - qwt=6.1.3=1

  - readline=7.0=0

  - rhash=1.3.4=0

  - setuptools=38.5.1=py27_0

  - six=1.11.0=py27_1

  - sqlite=3.20.1=2

  - suitesparse=4.5.4=blas_openblas_200

  - superlu=5.2.1=blas_openblas_201

  - tk=8.6.7=0

  - wheel=0.30.0=py27_2

  - x264=20131217=3

  - xorg-kbproto=1.0.7=1

  - xorg-libx11=1.6.4=6

  - xorg-libxau=1.0.8=3

  - xorg-libxdmcp=1.1.2=3

  - xorg-xproto=7.0.31=6

  - xz=5.2.3=0

  - zlib=1.2.11=0

  - ca-certificates=2017.08.26=ha1e5d58_0

  - certifi=2018.1.18=py27_0

  - gsl=2.2.1=h002c638_3

  - libcxx=4.0.1=h579ed51_0

  - libcxxabi=4.0.1=hebd6815_0

  - mysql=5.7.20=h14d89c2_0

  - openblas=0.2.19=1

  - openssl=1.0.2n=hdbc3d79_0

  - qt=5.6.2=h9975529_14

  - isisdeps=7=0

  - bullet=2.86.1=he2aa7b0_0

  - ds9=7.5=h35e3669_0

  - embree=2.16.0=h6834224_0

  - gmm=5.0=h6aef312_0

  - jama=125=hf0e5908_0

  - naif=n0066=h90cdba2_0

  - patchelf=0.9=h879b6ae_0

  - pcl=1.8.1=h7a71350_0

  - qhull=7.2.0=h396fa31_0

  - tbb=4.4=hf7780a4_0

  - tnt=126=h520b23f_0

  - vtk=7.1.1=py27h56fd973_0

  - xalan-c=1.11=h1922a5c_0

  - xerces-c=3.1.4=h10f7eb2_0

prefix: /Users/krodriguez/anaconda3/envs/isisdeps

isis/cmake/AddIsisModule.cmake

+1 −0
Original line number Diff line number Diff line
@@ -44,6 +44,7 @@ function(add_isis_app folder libDependencies) 


  # Have the app install with the real name, not the internal name.

  target_link_libraries(${internalAppName} ${libDependencies})



  set_target_properties(${internalAppName} PROPERTIES OUTPUT_NAME ${appName})

  install(TARGETS ${internalAppName} DESTINATION bin)

isis/cmake/FindAllDependencies.cmake

+28 −291
Original line number Diff line number Diff line
@@ -4,55 +4,9 @@ 
#   go looking for them if they are not?

#===============================================================================



list(APPEND CMAKE_INCLUDE_PATH

  /usgs/pkgs/local/v007/include/

  /usgs/pkgs/local/v007/bin/

  /usgs/pkgs/local/v007/lib/

  /usgs/pkgs/local/v007/objects/

  /usgs/pkgs/local/v007/include/google-protobuf/protobuf2.6.1/

  /usgs/pkgs/local/v007/include/xercesc/xercesc-3.1.2/

  /usgs/pkgs/local/v007/include/tiff/tiff-4.0.5/

  /usr/lib64/

)



set(CMAKE_PREFIX_PATH

  /usgs/pkgs/local/v007/include/

  /usgs/pkgs/local/v007/bin/

  /usgs/pkgs/local/v007/lib/

  /usgs/pkgs/local/v007/libexec/

  /opt/usgs/v007/ports/Library/Frameworks/

  /opt/usgs/v007/ports/libexec/

  /opt/usgs/v007/ports/bin/

  /opt/usgs/v007/ports/lib/

  /opt/usgs/v007/ports/include/

  /opt/usgs/v007/ports/libexec/qt5

  /opt/usgs/v007/ports/libexec/qt5/bin/

  /opt/usgs/v007/ports/libexec/qt5/lib/

  /opt/usgs/v007/3rdparty/bin

  /opt/usgs/v007/3rdparty/include/

  /opt/usgs/v007/3rdparty/lib/

  /opt/usgs/v007/proprietary/

  /opt/usgs/v007/proprietary/include/

  /opt/usgs/v007/proprietary/lib/

  /usr/lib/

  /usr/lib64/

  /usr/local/lib/

)



# Specify top level directories

set(thirdPartyDir "/usgs/pkgs/local/v007")

set(INCLUDE_DIR "${thirdPartyDir}/include")

set(LIB_DIR     "${thirdPartyDir}/lib")

set(PLUGIN_DIR  "${thirdPartyDir}/plugins")

set(BIN_DIR     "${thirdPartyDir}/bin")

set(LIC_DIR     "${thirdPartyDir}/license")



# Set up plugin dir for OSX to correctly find qt5 plugins for installing

if(APPLE)

  set(thirdPartyDir "/opt/usgs/v007")

  set(PLUGIN_DIR "${thirdPartyDir}/ports/libexec/qt5/plugins")

endif(APPLE)



message("CONDA PREFIX: $ENV{CONDA_PREFIX}")

set(CMAKE_LIBRARY_PATH $ENV{$CONDA_PREFIX})

set(CMAKE_INCLUDE_PATH $ENV{$CONDA_PREFIX})



# Add thirdPartyCppFlags

set(thirdPartyCppFlags ${thirdPartyCppFlags} -DGMM_USES_SUPERLU)
@@ -67,15 +21,8 @@ find_program(MOC moc REQUIRED) 
find_program(RCC rcc REQUIRED)

find_program(PROTOC protoc REQUIRED)



# message(STATUS "${CMAKE_PREFIX_PATH}")



include(FindProtobuf)





find_package(Geos 3.5.0 REQUIRED)





if(APPLE)

find_package(Qt5 COMPONENTS

                Core

                Concurrent
@@ -101,61 +48,6 @@ if(APPLE) 
                Widgets

                Xml

                XmlPatterns REQUIRED)

else() # oh god why

  find_path(QT5_CORE_INCLUDE_DIR                 NAMES qchar.h                PATH_SUFFIXES qt/qt5.7.1/QtCore/)

  find_path(QT5_CONCURRENT_INCLUDE_DIR           NAMES qtconcurrentmap.h      PATH_SUFFIXES qt/qt5.7.1/QtConcurrent)

  find_path(QT5_DBUS_INCLUDE_DIR                 NAMES qdbusmacros.h          PATH_SUFFIXES qt/qt5.7.1/QtDBus)

  find_path(QT5_GUI_INCLUDE_DIR                  NAMES qpainter.h             PATH_SUFFIXES qt/qt5.7.1/QtGui)

  find_path(QT5_MULTIMEDIA_INCLUDE_DIR           NAMES qmediacontent.h        PATH_SUFFIXES qt/qt5.7.1/QtMultimedia)

  find_path(QT5_MULTIMEDIAWIDGETS_INCLUDE_DIR    NAMES qvideowidget.h         PATH_SUFFIXES qt/qt5.7.1/QtMultimediaWidgets)

  find_path(QT5_NETWORK_INCLUDE_DIR              NAMES qsslsocket.h           PATH_SUFFIXES qt/qt5.7.1/QtNetwork)

  find_path(QT5_OPENGL_INCLUDE_DIR               NAMES qtopenglglobal.h       PATH_SUFFIXES qt/qt5.7.1/QtOpenGL)

  find_path(QT5_POSITIONING_INCLUDE_DIR          NAMES qgeocoordinate.h       PATH_SUFFIXES qt/qt5.7.1/QtPositioning)

  find_path(QT5_PRINTSUPPORT_INCLUDE_DIR         NAMES qprinter.h             PATH_SUFFIXES qt/qt5.7.1/QtPrintSupport)

  find_path(QT5_QML_INCLUDE_DIR                  NAMES qqmlinfo.h             PATH_SUFFIXES qt/qt5.7.1/QtQml)

  find_path(QT5_QUICK_INCLUDE_DIR                NAMES qquickview.h           PATH_SUFFIXES qt/qt5.7.1/QtQuick)

#  find_path(QT5_SCRIPT_INCLUDE_DIR               NAMES qscriptengine.h        PATH_SUFFIXES qt/qt5.7.1/QtScript)

#find_path(QT5_SCRIPTTOOLS_INCLUDE_DIR          NAMES qtscripttoolsversion.h PATH_SUFFIXES qt/qt5.7.1/QtScriptTools)

  find_path(QT5_SENSORS_INCLUDE_DIR              NAMES qgyroscope.h           PATH_SUFFIXES qt/qt5.7.1/QtSensors)

  find_path(QT5_SQL_INCLUDE_DIR                  NAMES qsql.h                 PATH_SUFFIXES qt/qt5.7.1/QtSql)

  find_path(QT5_SVG_INCLUDE_DIR                  NAMES qsvgwidget.h           PATH_SUFFIXES qt/qt5.7.1/QtSvg)

  find_path(QT5_TEST_INCLUDE_DIR                 NAMES qtest.h                PATH_SUFFIXES qt/qt5.7.1/QtTest)

  find_path(QT5_WEBCHANNEL_INCLUDE_DIR           NAMES qwebchannel.h          PATH_SUFFIXES qt/qt5.7.1/QtWebChannel)

  find_path(QT5_WEBENGINE_INCLUDE_DIR            NAMES qtwebengineglobal.h    PATH_SUFFIXES qt/qt5.7.1/QtWebEngine)

  find_path(QT5_WEBENGINEWIDGETS_INCLUDE_DIR     NAMES qwebenginescript.h     PATH_SUFFIXES qt/qt5.7.1/QtWebEngineWidgets)

  find_path(QT5_WIDGETS_INCLUDE_DIR              NAMES qwidget.h              PATH_SUFFIXES qt/qt5.7.1/QtWidgets)

  find_path(QT5_XML_INCLUDE_DIR                  NAMES qxml.h                 PATH_SUFFIXES qt/qt5.7.1/QtXml)

  find_path(QT5_XMLPATTERNS_INCLUDE_DIR          NAMES qtxmlpatternsglobal.h  PATH_SUFFIXES qt/qt5.7.1/QtXmlPatterns)



  get_filename_component(QT5_ROOT_INCLUDE_DIR "${QT5_CORE_INCLUDE_DIR}" DIRECTORY)



  find_library(QT5_CORE_LIBRARY                  NAMES Qt5Core)

  find_library(QT5_CONCURRENT_LIBRARY            NAMES Qt5Concurrent)

  find_library(QT5_DBUS_LIBRARY                  NAMES Qt5DBus)

  find_library(QT5_GUI_LIBRARY                   NAMES Qt5Gui)

  find_library(QT5_MULTIMEDIA_LIBRARY            NAMES Qt5Multimedia)

  find_library(QT5_MULTIMEDIAWIDGETS_LIBRARY     NAMES Qt5MultimediaWidgets)

  find_library(QT5_NETWORK_LIBRARY               NAMES Qt5Network)

  find_library(QT5_OPENGL_LIBRARY                NAMES Qt5OpenGL)

  find_library(QT5_POSITIONING_LIBRARY           NAMES Qt5Positioning)

  find_library(QT5_PRINTSUPPORT_LIBRARY          NAMES Qt5PrintSupport)

  find_library(QT5_QML_LIBRARY                   NAMES Qt5Qml)

  find_library(QT5_QUICK_LIBRARY                 NAMES Qt5Quick)

  find_library(QT5_SCRIPT_LIBRARY                NAMES Qt5Script)

  find_library(QT5_SCRIPTTOOLS_LIBRARY           NAMES Qt5ScriptTools)

  find_library(QT5_SENSORS_LIBRARY               NAMES Qt5Sensors)

  find_library(QT5_SQL_LIBRARY                   NAMES Qt5Sql)

  find_library(QT5_SVG_LIBRARY                   NAMES Qt5Svg)

  find_library(QT5_TEST_LIBRARY                  NAMES Qt5Test)

  find_library(QT5_WEBCHANNEL_LIBRARY            NAMES Qt5WebChannel)

  find_library(QT5_WEBENGINE_LIBRARY             NAMES Qt5WebEngine)

  find_library(QT5_WEBENGINECORE_LIBRARY         NAMES Qt5WebEngineCore)

  find_library(QT5_WEBENGINEWIDGETS_LIBRARY      NAMES Qt5WebEngineWidgets)

  find_library(QT5_WIDGETS_LIBRARY               NAMES Qt5Widgets)

  find_library(QT5_XML_LIBRARY                   NAMES Qt5Xml)

  find_library(QT5_XMLPATTERNS_LIBRARY           NAMES Qt5XmlPatterns)

endif(APPLE)





# Some of these will have non-traditional installs with version numbers in the paths in v007

# For these, we pass in a version number, and use it in the path suffix
@@ -204,7 +96,6 @@ foreach (_variableName ${_variableNames}) 
      list(APPEND ALLINCDIRS "${${_variableName}}")

    endif(_variableName MATCHES ".+_INCLUDE_DIR$")

endforeach()

list(APPEND ALLINCDIRS "/opt/usgs/v007/ports/include/" "/opt/usgs/v007/3rdParty/include/")



foreach (_variableName ${_variableNames})

    if (_variableName MATCHES "^CMAKE+")
@@ -232,157 +123,3 @@ endforeach() 
list(REMOVE_DUPLICATES ALLLIBDIRS)

list(REMOVE_DUPLICATES ALLLIBS)

list(REMOVE_DUPLICATES ALLINCDIRS)
 


# message(STATUS "ALL LIBS DIRS: ${ALLLIBDIRS}")

# message(STATUS "ALL LIBS: ${ALLLIBS}")

# message(STATUS "ALL INCS: ${ALLINCDIRS}")

#---------------------------------------------------------------------------

#  Define the third party distribution libraries (patterns)

#---------------------------------------------------------------------------



# On OSX we need to include a LOT of extra libraries!

set(EXTRA_DYNAMIC_LIBS)

if(APPLE)

  set(extras

    # QT dependencies

    libpcre16*.dylib

    libgthread-*.dylib

    libpcre.*dylib

    libharfbuzz*.dylib

    libgraphite2.*dylib

    libleveldb*.dylib*

    libsnappy.*dylib

    libwebp*.dylib

    libdbus*.dylib

    libiconv*.dylib

    liblzma*.dylib

    libz*.dylib

    libssl*.dylib

    libcrypto*.dylib

    libpng*.dylib

    libjpeg.*dylib

    libmng.*dylib

    liblcms2.*dylib

    libsqlite3.*dylib

    postgresql*/libpq.*dylib

    mysql56/mysql/libmysqlclient*.dylib

    libiodbc*.dylib

    # OpenCV dependancies

    libtbb*.dylib

    libjasper*.dylib

    libImath*.dylib

    libIlmImf*.dylib

    libIex*.dylib

    libHalf*.dylib

    libIlmThread*.dylib

    libswscale*.dylib

    # Secondary requirements to all OpenCV dependancies

    libSDL-1*.dylib

    libnettle*.dylib

    libhogweed*.dylib

    libgmp*.dylib

    libxvidcore*.dylib

    libx264*.dylib

    libvorbisenc*.dylib

    libvorbis*.dylib

    libogg*.dylib

    libtheoraenc*.dylib

    libtheoradec*.dylib

    libspeex*.dylib

    libschroedinger-1*.dylib

    libopus*.dylib

    libopenjpeg*.dylib

    libmp3lame*.dylib

    libmodplug*.dylib

    libfreetype*.dylib

    libbluray*.dylib

    libass*.dylib

    libgnutls*.dylib

    libbz2*.dylib

    libXrandr*.dylib

    libXext*.dylib

    libXrender*.dylib

    libX11*.dylib

    libxcb*.dylib

    libXau*.dylib

    libXdmcp*.dylib

    liborc-0*.dylib

    libxml2*.dylib

    libfribidi*.dylib

    libfontconfig*.dylib

    libexpat*.dylib

    libintl*.dylib

    libglib-*.dylib

    libp11-kit*.dylib

    libffi*.dylib

    # OpenCV3 dependencies

    libavresample*.dylib

    libxcb-shm*.dylib

    libsoxr*.dylib

    libopenjp2*.dylib

    libOpenNI*.dylib

    libswresample*.dylib

    libidn*.dylib

    libtasn1*.dylib

    libusb*.dylib

    # libxerces-c depends on these libraries

    libicui18n*.dylib

    libicuuc*.dylib

    libicudata*.dylib

    # libgeotiff depends on these libraries

    libproj*.dylib)



else() # Linux

  set(extras libtbb.so*)

endif()



set(EXTRALIBDIR ${LIB_DIR})

foreach(lib ${extras})

  set(EXTRA_DYNAMIC_LIBS ${EXTRA_DYNAMIC_LIBS} ${EXTRALIBDIR}/${lib})

endforeach()



# message("EXTRA_DYNAMIC_LIBS = ${EXTRA_DYNAMIC_LIBS}")



#  Libraries

set(THIRDPARTYLIBS)



set(RAW_DYNAMIC_LIBS ${QT_DYNAMIC_LIBS}

                     ${QWT_DYNAMIC_LIBS}

                     ${XERCES_DYNAMIC_LIBS}

                     ${GEOTIFF_DYNAMIC_LIBS}

                     ${HDF5_DYNAMIC_LIBS}

                     ${TIFF_DYNAMIC_LIBS}

                     ${NAIF_DYNAMIC_LIBS}

                     ${GEOS_DYNAMIC_LIBS}

                     ${GSL_DYNAMIC_LIBS}

                     ${SUPERLU_DYNAMIC_LIBS}

                     ${PROTOBUF_DYNAMIC_LIBS}

                     ${KAKADU_DYNAMIC_LIBS} # Empty if not available

                     ${CHOLMOD_DYNAMIC_LIBS}

                     ${OPENCV_DYNAMIC_LIBS}

                     ${EXTRA_DYNAMIC_LIBS})



# message("THIRDPARTYLIBS = ${RAW_DYNAMIC_LIBS}")



# For each item in this list, expand the wildcard to get the actual library list.

foreach(lib ${RAW_DYNAMIC_LIBS})

  string(FIND "${lib}" "*" position)

  if(${position} EQUAL -1)

    # No wildcard, just add it.

    set(THIRDPARTYLIBS ${THIRDPARTYLIBS} ${lib})

  else()

    # Expand wildcard, then add.

    file(GLOB expandedLibs ${lib})

    set(THIRDPARTYLIBS ${THIRDPARTYLIBS} ${expandedLibs})

  endif()

endforeach()



message("THIRDPARTYLIBS = ${THIRDPARTYLIBS}")



# Plugins

file(GLOB_RECURSE THIRDPARTYPLUGINS "${PLUGIN_DIR}/*${SO}")

file(GLOB THIRDPARTYPLUGINFOLDERS "${PLUGIN_DIR}/*")



# message("third party libs = ${THIRDPARTYLIBS}")

# message("third party plugins = ${THIRDPARTYPLUGINS}")

# message("third party plugins folders = ${THIRDPARTYPLUGINFOLDERS}")

isis/environment.yml

deleted100644 → 0
+0 −104
Original line number Diff line number Diff line 
name: isisdeps

channels:

- anaconda

- krodriguez

- inria-pro-sed

- conda-forge

- usgs-astrogeology

- defaults

dependencies:

- libgcc=4.8.5=1

- blas=1.1=openblas

- boost=1.65.1=py27_0

- boost-cpp=1.65.1=1

- bzip2=1.0.6=1

- ca-certificates=2018.1.18=0

- cairo=1.14.6=4

- certifi=2018.1.18=py27_0

- cmake=3.9.1=0

- cspice=66=0

- curl=7.55.1=0

- dbus=1.10.22=0

- doxygen=1.8.14=0

- eigen=3.3.3=0

- expat=2.2.5=0

- ffmpeg=3.2.4=3

- flann=1.8.4=0

- fontconfig=2.12.1=4

- freetype=2.7=1

- geos=3.5.1=1

- geotiff=1.4.2=1

- gettext=0.19.8.1=0

- giflib=5.1.4=0

- glib=2.51.4=0

- gsl=2.2.1=blas_openblas_3

- harfbuzz=1.3.4=2

- hdf5=1.8.18=3

- icu=58.2=0

- jasper=1.900.1=4

- jpeg=9b=2

- krb5=1.14.2=0

- lapack=3.6.1=1

- libffi=3.2.1=3

- libgfortran=3.0.0=0

- libiconv=1.15=0

- libpng=1.6.28=2

- libssh2=1.8.0=2

- libtiff=4.0.9=0

- libuv=1.11.0=0

- libwebp=0.5.2=7

- libxcb=1.12=1

- libxml2=2.9.7=0

- m4=1.4.17=1

- metis=5.1.0=3

- nanoflann=1.2.2=0

- ncurses=5.9=10

- ninja=1.7.2=0

- nn=1.86.0=2

- numpy=1.13.3=py27_blas_openblas_200

- openblas=0.2.19=2

- opencv=3.3.0=py27_blas_openblas_200

- openssl=1.0.2n=0

- pcre=8.39=0

- pip=9.0.1=py27_1

- pixman=0.34.0=1

- proj4=4.9.3=5

- protobuf=3.2.0=py27_0

- python=2.7.14=4

- qt=5.6.2=h9e3eb04_4

- qwt=6.1.3=1

- readline=7.0=0

- rhash=1.3.4=0

- setuptools=38.5.1=py27_0

- six=1.11.0=py27_1

- sqlite=3.20.1=2

- suitesparse=4.5.4=blas_openblas_200

- superlu=5.2.1=blas_openblas_201

- tk=8.6.7=0

- wheel=0.30.0=py27_2

- x264=20131217=3

- xorg-kbproto=1.0.7=1

- xorg-libx11=1.6.4=6

- xorg-libxau=1.0.8=3

- xorg-libxdmcp=1.1.2=3

- xorg-xproto=7.0.31=6

- xz=5.2.3=0

- zlib=1.2.11=0

- openmpi=1.8.6=4

- parmetis=4.0.3p2=1

- jama=125=0

- tnt=126=0

- bullet=2.86.1=he2aa7b0_0

- ds9=7.5=h35e3669_0

- embree=2.16.0=h6834224_0

- gmm=5.0=h6aef312_0

- naif=n0066=h90cdba2_0

- patchelf=0.9=h879b6ae_0

- pcl=1.8.1=h7a71350_0

- qhull=7.2.0=h396fa31_0

- tbb=4.4=hf7780a4_0

- vtk=7.1.1=py27h56fd973_0

- xalan-c=1.11=h1922a5c_0

- xerces-c=3.1.4=h10f7eb2_0

prefix: /Users/krodriguez-pr/anaconda3/envs/isisdeps