Merge pull request #66 from nlesc-dirac/dev

merge dev into master

.codedocs

@@ -0,0 +1,47 @@
+# CodeDocs.xyz Configuration File
+
+# Optional project name, if left empty the GitHub repository name will be used.
+PROJECT_NAME = "SageCal"
+
+# One or more directories and files that contain example code to be included.
+#EXAMPLE_PATH =
+
+# One or more directories and files to exclude from documentation generation.
+# Use relative paths with respect to the repository root directory.
+EXCLUDE = pkg build
+
+# One or more wildcard patterns to exclude files and directories from document
+# generation.
+#EXCLUDE_PATTERNS =
+
+# One or more symbols to exclude from document generation. Symbols can be
+# namespaces, classes, or functions.
+#EXCLUDE_SYMBOLS =
+
+# Override the default parser (language) used for each file extension.
+EXTENSION_MAPPING =
+
+# Set the wildcard patterns used to filter out the source-files.
+# If left blank the default is:
+# *.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl,
+# *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php,
+# *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox, *.py,
+# *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+FILE_PATTERNS          = *.c \
+                         *.cpp \
+                         *.cxx \                         
+                         *.cu \
+                         *.h \
+                         *.hpp \
+                         *.md
+
+# Hide undocumented class members.
+#HIDE_UNDOC_MEMBERS =
+
+# Hide undocumented classes.
+#HIDE_UNDOC_CLASSES =
+
+# Specify a markdown page whose contents should be used as the main page
+# (index.html). This will override a page marked as \mainpage. For example, a
+# README.md file usually serves as a useful main page.
+USE_MDFILE_AS_MAINPAGE = README.md

.editorconfig

@@ -0,0 +1,16 @@
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+charset = utf-8
+trim_trailing_whitespace = true
+end_of_line = lf
+insert_final_newline = true
+
+# Tab indentation (no size specified)
+[Makefile]
+indent_style = tab
+
+[*.{c,h,cpp,hpp}]
+indent_size = 2

.gitignore

@@ -1,3 +1,5 @@
+build
+
 .idea
 
 */*.png

.travis.yml

@@ -6,18 +6,17 @@ language: cpp
 #env:
 
 before_install:
-  - docker pull ubuntu:xenial
+  - docker pull fdiblen/ubuntu1604-test:latest
-  - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name ubuntu-build ubuntu:xenial
+  - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name ubuntu-build fdiblen/ubuntu1604-test:latest
+  - docker pull fdiblen/sl7-test:latest
+  - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name sl-build fdiblen/sl7-test:latest
+#  - docker pull base/archlinux
+#  - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name arch-build base/archlinux
 
 script:
   - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
   - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
-  - docker exec ubuntu-build apt-get update -y
+  - docker exec -e BRANCH=$BRANCH -e IMAGE='ubuntu' ubuntu-build /bin/bash -c "/travis/workdir/build-tests/compile_sagecal.sh"
-  - docker exec ubuntu-build apt-get install software-properties-common -y
+  - docker exec -e BRANCH=$BRANCH -e IMAGE='sl7' sl-build /bin/bash -c "/travis/workdir/build-tests/compile_sagecal.sh"
-  - docker exec ubuntu-build add-apt-repository -s ppa:kernsuite/kern-3 -y
+#  - docker exec --env BRANCH=$BRANCH arch-build /bin/bash -c "/travis/workdir/build-tests/arch/prepare-arch.sh"
-  - docker exec ubuntu-build apt-add-repository multiverse
+#  - docker exec --env BRANCH=$BRANCH arch-build /bin/bash -c "/travis/workdir/build-tests/arch/compile-arch.sh"
-  - docker exec ubuntu-build apt-get update -y
-  - docker exec ubuntu-build apt-get install -y git cmake g++ pkg-config libcfitsio-bin libcfitsio-dev libopenblas-base libopenblas-dev wcslib-dev wcslib-tools libglib2.0-dev libcasa-casa2 casacore-dev casacore-data casacore-tools
-  - |
-    docker exec --env BRANCH=$BRANCH ubuntu-build /bin/bash -c "/travis/workdir/test-builds/test-ubuntu.sh"
-

CMakeLists.txt

@@ -3,6 +3,13 @@ enable_language(CXX)
 
 #--------------------------------------- project
 project (SageCal)
+
+if (NOT EXISTS ${CMAKE_BINARY_DIR}/CMakeCache.txt)
+  if (NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release" FORCE)
+  endif()
+endif()
+
 set(PROJECT_VERSION_MAJOR 0)
 set(PROJECT_VERSION_MINOR 6)
 set(PROJECT_VERSION_PATCH 0)
@@ -10,6 +17,7 @@ set(PROJECT_VERSION_REVISION 1)
 set(PROJECT_VERSION
   "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
 
+message(STATUS "\n############################\n#   HOST SYSTEM v${CMAKE_HOST_SYSTEM_NAME}\n############################")
 message(STATUS "\n############################\n#   Building SageCal v${PROJECT_VERSION}\n############################")
 
 include(CheckCXXCompilerFlag)
@@ -27,7 +35,6 @@ SET(LIBRARY_OUTPUT_PATH "${MAINFOLDER}/dist/lib")
 set( CMAKE_MODULE_PATH $ENV{CMAKE_MODULE_PATH} )
 set( CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH} )
 
-
 #--------------------------------------- cmake modules
 list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_SOURCE_DIR}/CMakeModules)
 
@@ -49,14 +56,15 @@ IF("${isSystemDir}" STREQUAL "-1")
    SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 ENDIF("${isSystemDir}" STREQUAL "-1")
 
-# libsynthesis has mix of C++ and Fortran which is not handled well by
-# versions before 2.8.
-if(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
-  if(NOT LIB_EXTRA_SYNTHESIS)
-    set(LIB_EXTRA_SYNTHESIS gfortran)
-  endif(NOT LIB_EXTRA_SYNTHESIS)
-endif(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
 
+# # libsynthesis has mix of C++ and Fortran which is not handled well by
+# # versions before 2.8.
+# if(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
+#   if(NOT LIB_EXTRA_SYNTHESIS)
+#     set(LIB_EXTRA_SYNTHESIS gfortran)
+#   endif(NOT LIB_EXTRA_SYNTHESIS)
+# endif(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
+#
 
 
 #--------------------------------------- SageCal dependencies
@@ -72,7 +80,7 @@ include_directories(${CASACORE_INCLUDE_DIR})
 
 #cfitsio
 find_package(CfitsIO REQUIRED)
-include_directories(${CFITSIO_INCLUDE_DIR})
+include_directories(${CFITSIO_INCLUDE})
 
 #lapack
 find_package(LAPACK REQUIRED)
@@ -90,11 +98,22 @@ include_directories(${OpenBLAS_INCLUDE_DIR})
 #find_package(BLAS REQUIRED)
 #include_directories(${BLAS_INCLUDE_DIR})
 
-# FIXME: is this really needed?
+# ##gfortran
-##gfortran
+enable_language(Fortran)
 #find_package(GFortranLibs REQUIRED)
 # include_directories(${GFORTRAN_INCLUDE_DIR})
 
+
+
+
+
+# enable_language(Fortran)
+# # get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
+# set(FC "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
+# set(CMAKE_Fortran_COMPILER "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
+#
+
+
 ##hdf5
 #find_package(HDF5 REQUIRED)
 
@@ -121,11 +140,9 @@ endif()
 
 
 #--------------------------------------- build parameters for all targets
-#set (CMAKE_CXX_FLAGS "-g -O3 -Wall -Wextra -std=c++11 -W -pedantic -ansi -fPIC -fpermissive -fno-omit-frame-pointer -fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -std=c++0x -g -O3")
-# set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall -Wextra -W -pedantic -ansi -fPIC -fpermissive")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -pg -Wall -DNDEBUG -Wextra -Wcast-align -Wpointer-arith -Woverloaded-virtual -Wwrite-strings -Wcast-qual -Wctor-dtor-privacy -Wno-long-long-Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Werror -Wno-unused")
-set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall")
+
-# FIXME: add debug build option
-#set (CMAKE_CXX_FLAGS_DEBUG "-g -pg -pedantic -Wall -DNDEBUG -Wextra -Wcast-align -Wpointer-arith -Woverloaded-virtual -Wwrite-strings -Wcast-qual -Wctor-dtor-privacy -Wno-long-long-Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Werror -Wno-unused")
 
 
 
@@ -133,6 +150,7 @@ set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall")
 #--------------------------------------- summary
 message(STATUS "\n############################\n#   Configuration summary\n############################")
 message (STATUS "CMAKE_SYSTEM .......... = ${CMAKE_SYSTEM}")
+message (STATUS "CMAKE_INSTALL_PREFIX .. = ${CMAKE_INSTALL_PREFIX}")
 message (STATUS "CMAKE_BUILD_TYPE ...... = ${CMAKE_BUILD_TYPE}")
 message (STATUS "BUILD_SHARED_LIBS ..... = ${BUILD_SHARED_LIBS}")
 message (STATUS "CMAKE_INSTALL_NAME_DIR  = ${CMAKE_INSTALL_NAME_DIR}")
@@ -143,30 +161,36 @@ message (STATUS "CMAKE_CXX_FLAGS ....... = ${CMAKE_CXX_FLAGS}")
 message (STATUS "ENABLE_MPI ............ = ${ENABLE_MPI}")
 message (STATUS "ENABLE_CUDA ........... = ${ENABLE_CUDA}")
 
-message (STATUS "CASACORE_INCLUDE_DIR........... = ${CASACORE_INCLUDE_DIR}")
+message (STATUS "CASACORE_INCLUDE_DIR....= ${CASACORE_INCLUDE_DIR}")
-message (STATUS "CASACORE_LIBRARIES........... = ${CASACORE_LIBRARIES}")
+message (STATUS "CASACORE_LIBRARIES......= ${CASACORE_LIBRARIES}")
 
 message (STATUS "OpenBLAS_LIB .......... = ${OpenBLAS_LIB}")
 
-message (STATUS "GLIB_PKG_INCLUDE_DIRS.............. = ${GLIB_PKG_INCLUDE_DIRS}")
+message (STATUS "GLIB_PKG_INCLUDE_DIRS...= ${GLIB_PKG_INCLUDE_DIRS}")
-message (STATUS "GLIB_PKG_LIBRARIES............. = ${GLIB_PKG_LIBRARIES}")
+message (STATUS "GLIB_PKG_LIBRARIES......= ${GLIB_PKG_LIBRARIES}")
 
 #message (STATUS "LAPACK-INC ............ = ${LAPACK_INCLUDE_DIR}")
-message (STATUS "LAPACK_LIBRARIES........... = ${LAPACK_LIBRARIES}")
+message (STATUS "LAPACK_LIBRARIES........= ${LAPACK_LIBRARIES}")
 
 # message (STATUS "GFORTRAN-INC  ......... = ${GFORTRAN_INCLUDE_DIR}")
 # message (STATUS "GFORTRAN-LIBS ......... = ${LIBGFORTRAN_LIBRARIES}")
+message (STATUS "CMAKE_Fortran_COMPILER  = ${CMAKE_Fortran_COMPILER}")
 
-message (STATUS "CFITSIO_INCLUDE_DIR.......... = ${CFITSIO_INCLUDE_DIR}")
+message (STATUS "CFITSIO_ROOT_DIR........= ${CFITSIO_ROOT_DIR}")
-message (STATUS "CFITSIO_LIBRARIES.......... = ${CFITSIO_LIBRARIES}")
+message (STATUS "CFITSIO_INCLUDE.........= ${CFITSIO_INCLUDE}")
+message (STATUS "CFITSIO_LIB.............= ${CFITSIO_LIB}")
 
-message (STATUS "WCSLIB_INCLUDE_DIR........... = ${WCSLIB_INCLUDE_DIR}")
+message (STATUS "WCSLIB_INCLUDE_DIRS.....= ${WCSLIB_INCLUDE_DIRS}")
-message (STATUS "WCSLIB_LIBRARIES ........... = ${WCSLIB_LIBRARIES}")
+message (STATUS "WCSLIB_LIBRARIES .......= ${WCSLIB_LIBRARIES}")
 
-message (STATUS "HDF5_INCLUDE_DIR........... = ${HDF5_INCLUDE_DIRS}")
+message (STATUS "HDF5_INCLUDE_DIR........= ${HDF5_INCLUDE_DIRS}")
-message (STATUS "HDF5_LIBRARIES........... = ${HDF5_LIBRARIES}")
+message (STATUS "HDF5_LIBRARIES..........= ${HDF5_LIBRARIES}")
 
 
+message (STATUS "CMAKE_CURRENT_BINARY_DIR..........= ${CMAKE_CURRENT_BINARY_DIR}")
+message (STATUS "CMAKE_CURRENT_LIST_DIR..........= ${CMAKE_CURRENT_LIST_DIR}")
+message (STATUS "CMAKE_INSTALL_PREFIX..........= ${CMAKE_INSTALL_PREFIX}")
+
 
 #--------------------------------------- include directories
 add_subdirectory(src)
@@ -177,3 +201,5 @@ add_subdirectory(src)
 # FIXME: this will be the final step for testing
 #file(COPY ${PROJECT_SOURCE_DIR}/test DESTINATION ${MAINFOLDER}/dist/test)
 
+
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/dist/ DESTINATION ${CMAKE_INSTALL_PREFIX})

CMakeModules/FindCasaCore.cmake

@@ -71,7 +71,15 @@
 # directly fed to the linker.
 #
 #   Usage: casacore_resolve_dependencies(result components...)
-#
+
+
+if (NOT "$ENV{CASACORE_ROOT_DIR}" STREQUAL "")
+set(CASACORE_ROOT_DIR "$ENV{CASACORE_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
+endif()
+
+
+
+
 macro(casacore_resolve_dependencies _result)
   set(${_result} ${ARGN})
   set(_index 0)

CMakeModules/FindCfitsIO.cmake

@@ -3,11 +3,11 @@
 #  CFITSIO_ROOT_DIR     - CFITSIO root directory
 # Variables defined by this module:
 #  CFITSIO_FOUND        - system has CFITSIO
-#  CFITSIO_INCLUDE_DIR  - the CFITSIO include directory (cached)
+#  CFITSIO_INCLUDE  - the CFITSIO include directory (cached)
-#  CFITSIO_INCLUDE_DIRS - the CFITSIO include directories
+#  CFITSIO_INCLUDES - the CFITSIO include directories
-#                         (identical to CFITSIO_INCLUDE_DIR)
+#                         (identical to CFITSIO_INCLUDE)
 #  CFITSIO_LIBRARY      - the CFITSIO library (cached)
-#  CFITSIO_LIBRARIES    - the CFITSIO libraries
+#  CFITSIO_LIB    - the CFITSIO libraries
 #                         (identical to CFITSIO_LIBRARY)
 #  CFITSIO_VERSION_STRING the found version of CFITSIO, padded to 3 digits
 
@@ -33,12 +33,17 @@
 
 if(NOT CFITSIO_FOUND)
 
-  find_path(CFITSIO_INCLUDE_DIR fitsio.h
+  if (NOT "$ENV{CFITSIO_ROOT_DIR}" STREQUAL "")
+  set(CFITSIO_ROOT_DIR "$ENV{CFITSIO_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
+  endif()
+
+
+  find_path(CFITSIO_INCLUDE fitsio.h
     HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES include include/cfitsio
              include/libcfitsio0)
 
-  if(CFITSIO_INCLUDE_DIR)
+  if(CFITSIO_INCLUDE)
-    FILE(READ "${CFITSIO_INCLUDE_DIR}/fitsio.h" CFITSIO_H)
+    FILE(READ "${CFITSIO_INCLUDE}/fitsio.h" CFITSIO_H)
     set(CFITSIO_VERSION_REGEX ".*#define CFITSIO_VERSION[^0-9]*([0-9]+)\\.([0-9]+).*")
     if ("${CFITSIO_H}" MATCHES ${CFITSIO_VERSION_REGEX})
       # Pad CFITSIO minor version to three digit because 3.181 is older than 3.35
@@ -51,24 +56,24 @@ if(NOT CFITSIO_FOUND)
     else ()
       set(CFITSIO_VERSION_STRING "Unknown")
     endif()
-  endif(CFITSIO_INCLUDE_DIR)
+  endif(CFITSIO_INCLUDE)
 
   find_library(CFITSIO_LIBRARY cfitsio
     HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES lib)
   find_library(M_LIBRARY m)
-  mark_as_advanced(CFITSIO_INCLUDE_DIR CFITSIO_LIBRARY M_LIBRARY)
+  mark_as_advanced(CFITSIO_INCLUDE CFITSIO_LIBRARY M_LIBRARY)
 
   if(CMAKE_VERSION VERSION_LESS "2.8.3")
     find_package_handle_standard_args(CFITSIO DEFAULT_MSG
-      CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE_DIR)
+      CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE)
   else ()
     include(FindPackageHandleStandardArgs)
     find_package_handle_standard_args(CFITSIO
-      REQUIRED_VARS CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE_DIR
+      REQUIRED_VARS CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE
       VERSION_VAR CFITSIO_VERSION_STRING)
   endif ()
 
-  set(CFITSIO_INCLUDE_DIRS ${CFITSIO_INCLUDE_DIR})
+  set(CFITSIO_INCLUDES ${CFITSIO_INCLUDE})
-  set(CFITSIO_LIBRARIES ${CFITSIO_LIBRARY} ${M_LIBRARY})
+  set(CFITSIO_LIB ${CFITSIO_LIBRARY} ${M_LIBRARY})
 
 endif(NOT CFITSIO_FOUND)

CMakeModules/FindGFortranLibs.cmake

@@ -24,120 +24,128 @@ if(NOT CMAKE_REQUIRED_QUIET)
   message(STATUS "Looking for gfortran related libraries...")
 endif()
 
+# enable_language(Fortran)
+# if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+#
+#   # Basically, call "gfortran -v" to dump compiler info to the string
+#   # GFORTRAN_VERBOSE_STR, which will be used to get necessary paths
+#   message(STATUS "Extracting library and header information by calling 'gfortran -v'...")
+#   execute_process(COMMAND "${CMAKE_Fortran_COMPILER}" "-v" ERROR_VARIABLE
+#     GFORTRAN_VERBOSE_STR RESULT_VARIABLE FLAG)
+#
+#   # For debugging
+#   message(STATUS "'gfortran -v' returned:")
+#   message(STATUS "${GFORTRAN_VERBOSE_STR}")
+#
+#   # Detect gfortran version
+#   string(REGEX MATCH "gcc version [^\t\n ]+" GFORTRAN_VER_STR "${GFORTRAN_VERBOSE_STR}")
+#   string(REGEX REPLACE "gcc version ([^\t\n ]+)" "\\1" GFORTRAN_VERSION_STRING "${GFORTRAN_VER_STR}")
+#   message(STATUS "Detected gfortran version ${GFORTRAN_VERSION_STRING}")
+#   unset(GFORTRAN_VER_STR)
+#
+#   set(MATCH_REGEX "[^\t\n ]+[\t\n ]+")
+#   set(REPLACE_REGEX "([^\t\n ]+)")
+#
+#   # Find architecture for compiler
+#   string(REGEX MATCH "Target: [^\t\n ]+"
+#     GFORTRAN_ARCH_STR "${GFORTRAN_VERBOSE_STR}")
+#   message(STATUS "Architecture string: ${GFORTRAN_ARCH_STR}")
+#   string(REGEX REPLACE "Target: ([^\t\n ]+)" "\\1"
+#     GFORTRAN_ARCH "${GFORTRAN_ARCH_STR}")
+#   message(STATUS "Detected gfortran architecture: ${GFORTRAN_ARCH}")
+#   unset(GFORTRAN_ARCH_STR)
+#
+#   # Find install prefix, if it exists; if not, use default
+#   string(REGEX MATCH  "--prefix=[^\t\n ]+[\t\n ]+"
+#     GFORTRAN_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
+#   if(NOT GFORTRAN_PREFIX_STR)
+#     message(STATUS "Detected default gfortran prefix")
+#     set(GFORTRAN_PREFIX_DIR "/usr/local") # default prefix for gcc install
+#   else()
+#     string(REGEX REPLACE "--prefix=([^\t\n ]+)" "\\1"
+#       GFORTRAN_PREFIX_DIR "${GFORTRAN_PREFIX_STR}")
+#   endif()
+#   message(STATUS "Detected gfortran prefix: ${GFORTRAN_PREFIX_DIR}")
+#   unset(GFORTRAN_PREFIX_STR)
+#
+#   # Find install exec-prefix, if it exists; if not, use default
+#   string(REGEX MATCH "--exec-prefix=[^\t\n ]+[\t\n ]+" "\\1"
+#     GFORTRAN_EXEC_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
+#   if(NOT GFORTRAN_EXEC_PREFIX_STR)
+#     message(STATUS "Detected default gfortran exec-prefix")
+#     set(GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_PREFIX_DIR}")
+#   else()
+#     string(REGEX REPLACE "--exec-prefix=([^\t\n ]+)" "\\1"
+#       GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_EXEC_PREFIX_STR}")
+#   endif()
+#   message(STATUS "Detected gfortran exec-prefix: ${GFORTRAN_EXEC_PREFIX_DIR}")
+#   UNSET(GFORTRAN_EXEC_PREFIX_STR)
+#
+#   # Find library directory and include directory, if library directory specified
+#   string(REGEX MATCH "--libdir=[^\t\n ]+"
+#     GFORTRAN_LIB_DIR_STR "${GFORTRAN_VERBOSE_STR}")
+#   if(NOT GFORTRAN_LIB_DIR_STR)
+#     message(STATUS "Found --libdir flag -- not found")
+#     message(STATUS "Using default gfortran library & include directory paths")
+#     set(GFORTRAN_LIBRARIES_DIR
+#       "${GFORTRAN_EXEC_PREFIX_DIR}/lib/gcc/${GFORTRAN_ARCH}/${GFORTRAN_VERSION_STRING}")
+#     string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/include")
+#   else()
+#     message(STATUS "Found --libdir flag -- yes")
+#     string(REGEX REPLACE "--libdir=([^\t\n ]+)" "\\1"
+#       GFORTRAN_LIBRARIES_DIR "${GFORTRAN_LIB_DIR_STR}")
+#     string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/gcc/" "${GFORTRAN_ARCH}" "/" "${GFORTRAN_VERSION_STRING}" "/include")
+#   endif()
+#   message(STATUS "gfortran libraries path: ${GFORTRAN_LIBRARIES_DIR}")
+#   message(STATUS "gfortran include path dir: ${GFORTRAN_INCLUDE_DIR}")
+#   unset(GFORTRAN_LIB_DIR_STR)
+#
+#   # There are lots of other build options for gcc & gfortran. For now, the
+#   # options implemented above should cover a lot of common use cases.
+#
+#   # Clean up be deleting the output string from "gfortran -v"
+#   unset(GFORTRAN_VERBOSE_STR)
+#
+#   # Find paths for libgfortran, libquadmath, libgomp
+#   # libgomp needed for OpenMP support without Clang
+#   find_library(LIBGFORTRAN_LIBRARIES NAMES gfortran libgfortran
+#     HINTS ${GFORTRAN_LIBRARIES_DIR})
+#   find_library(LIBQUADMATH_LIBRARIES NAMES quadmath libquadmath
+#     HINTS ${GFORTRAN_LIBRARIES_DIR})
+#   find_library(LIBGOMP_LIBRARIES NAMES gomp libgomp
+#     HINTS ${GFORTRAN_LIBRARIES_DIR})
+#
+#   # Find OpenMP headers
+#   find_path(LIBGOMP_INCLUDE_DIR NAMES omp.h HINTS ${GFORTRAN_INCLUDE_DIR})
+#
+# else()
+#   message(STATUS "CMAKE_Fortran_COMPILER_ID does not match 'GNU'!")
+# endif()
+#
+# include(FindPackageHandleStandardArgs)
+#
+# # Required: libgfortran, libquadmath, path for gfortran libraries
+# # Optional: libgomp, path for OpenMP headers, path for gcc/gfortran headers
+# find_package_handle_standard_args(GFortranLibs
+#   REQUIRED_VARS LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES GFORTRAN_LIBRARIES_DIR
+#   VERSION_VAR GFORTRAN_VERSION_STRING)
+#
+# if(GFORTRANLIBS_FOUND)
+#   message(STATUS "Looking for gfortran libraries -- found")
+#   message(STATUS "gfortran version: ${GFORTRAN_VERSION_STRING}")
+# else()
+#   message(STATUS "Looking for gfortran libraries -- not found")
+# endif()
+#
+# mark_as_advanced(LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES
+#   LIBGOMP_LIBRARIES LIBGOMP_INCLUDE_DIR
+#   GFORTRAN_LIBRARIES_DIR GFORTRAN_INCLUDE_DIR)
+# # FindGFortranLIBS.cmake ends here
+
+
 enable_language(Fortran)
-if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+# if (NOT "$ENV{FC}" STREQUAL "")
-
+# set(FC "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
-  # Basically, call "gfortran -v" to dump compiler info to the string
+# set(CMAKE_Fortran_COMPILER "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
-  # GFORTRAN_VERBOSE_STR, which will be used to get necessary paths
+# set(GFORTRANLIBS_FOUND "1" CACHE INTERNAL "found environment variable")
-  message(STATUS "Extracting library and header information by calling 'gfortran -v'...")
+# endif()
-  execute_process(COMMAND "${CMAKE_Fortran_COMPILER}" "-v" ERROR_VARIABLE
-    GFORTRAN_VERBOSE_STR RESULT_VARIABLE FLAG)
-
-  # For debugging
-  message(STATUS "'gfortran -v' returned:")
-  message(STATUS "${GFORTRAN_VERBOSE_STR}")
-
-  # Detect gfortran version
-  string(REGEX MATCH "gcc version [^\t\n ]+" GFORTRAN_VER_STR "${GFORTRAN_VERBOSE_STR}")
-  string(REGEX REPLACE "gcc version ([^\t\n ]+)" "\\1" GFORTRAN_VERSION_STRING "${GFORTRAN_VER_STR}")
-  message(STATUS "Detected gfortran version ${GFORTRAN_VERSION_STRING}")
-  unset(GFORTRAN_VER_STR)
-
-  set(MATCH_REGEX "[^\t\n ]+[\t\n ]+")
-  set(REPLACE_REGEX "([^\t\n ]+)")
-
-  # Find architecture for compiler
-  string(REGEX MATCH "Target: [^\t\n ]+"
-    GFORTRAN_ARCH_STR "${GFORTRAN_VERBOSE_STR}")
-  message(STATUS "Architecture string: ${GFORTRAN_ARCH_STR}")
-  string(REGEX REPLACE "Target: ([^\t\n ]+)" "\\1"
-    GFORTRAN_ARCH "${GFORTRAN_ARCH_STR}")
-  message(STATUS "Detected gfortran architecture: ${GFORTRAN_ARCH}")
-  unset(GFORTRAN_ARCH_STR)
-
-  # Find install prefix, if it exists; if not, use default
-  string(REGEX MATCH  "--prefix=[^\t\n ]+[\t\n ]+"
-    GFORTRAN_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
-  if(NOT GFORTRAN_PREFIX_STR)
-    message(STATUS "Detected default gfortran prefix")
-    set(GFORTRAN_PREFIX_DIR "/usr/local") # default prefix for gcc install
-  else()
-    string(REGEX REPLACE "--prefix=([^\t\n ]+)" "\\1"
-      GFORTRAN_PREFIX_DIR "${GFORTRAN_PREFIX_STR}")
-  endif()
-  message(STATUS "Detected gfortran prefix: ${GFORTRAN_PREFIX_DIR}")
-  unset(GFORTRAN_PREFIX_STR)
-
-  # Find install exec-prefix, if it exists; if not, use default
-  string(REGEX MATCH "--exec-prefix=[^\t\n ]+[\t\n ]+" "\\1"
-    GFORTRAN_EXEC_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
-  if(NOT GFORTRAN_EXEC_PREFIX_STR)
-    message(STATUS "Detected default gfortran exec-prefix")
-    set(GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_PREFIX_DIR}")
-  else()
-    string(REGEX REPLACE "--exec-prefix=([^\t\n ]+)" "\\1"
-      GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_EXEC_PREFIX_STR}")
-  endif()
-  message(STATUS "Detected gfortran exec-prefix: ${GFORTRAN_EXEC_PREFIX_DIR}")
-  UNSET(GFORTRAN_EXEC_PREFIX_STR)
-
-  # Find library directory and include directory, if library directory specified
-  string(REGEX MATCH "--libdir=[^\t\n ]+"
-    GFORTRAN_LIB_DIR_STR "${GFORTRAN_VERBOSE_STR}")
-  if(NOT GFORTRAN_LIB_DIR_STR)
-    message(STATUS "Found --libdir flag -- not found")
-    message(STATUS "Using default gfortran library & include directory paths")
-    set(GFORTRAN_LIBRARIES_DIR
-      "${GFORTRAN_EXEC_PREFIX_DIR}/lib/gcc/${GFORTRAN_ARCH}/${GFORTRAN_VERSION_STRING}")
-    string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/include")
-  else()
-    message(STATUS "Found --libdir flag -- yes")
-    string(REGEX REPLACE "--libdir=([^\t\n ]+)" "\\1"
-      GFORTRAN_LIBRARIES_DIR "${GFORTRAN_LIB_DIR_STR}")
-    string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/gcc/" "${GFORTRAN_ARCH}" "/" "${GFORTRAN_VERSION_STRING}" "/include")
-  endif()
-  message(STATUS "gfortran libraries path: ${GFORTRAN_LIBRARIES_DIR}")
-  message(STATUS "gfortran include path dir: ${GFORTRAN_INCLUDE_DIR}")
-  unset(GFORTRAN_LIB_DIR_STR)
-
-  # There are lots of other build options for gcc & gfortran. For now, the
-  # options implemented above should cover a lot of common use cases.
-
-  # Clean up be deleting the output string from "gfortran -v"
-  unset(GFORTRAN_VERBOSE_STR)
-
-  # Find paths for libgfortran, libquadmath, libgomp
-  # libgomp needed for OpenMP support without Clang
-  find_library(LIBGFORTRAN_LIBRARIES NAMES gfortran libgfortran
-    HINTS ${GFORTRAN_LIBRARIES_DIR})
-  find_library(LIBQUADMATH_LIBRARIES NAMES quadmath libquadmath
-    HINTS ${GFORTRAN_LIBRARIES_DIR})
-  find_library(LIBGOMP_LIBRARIES NAMES gomp libgomp
-    HINTS ${GFORTRAN_LIBRARIES_DIR})
-
-  # Find OpenMP headers
-  find_path(LIBGOMP_INCLUDE_DIR NAMES omp.h HINTS ${GFORTRAN_INCLUDE_DIR})
-
-else()
-  message(STATUS "CMAKE_Fortran_COMPILER_ID does not match 'GNU'!")
-endif()
-
-include(FindPackageHandleStandardArgs)
-
-# Required: libgfortran, libquadmath, path for gfortran libraries
-# Optional: libgomp, path for OpenMP headers, path for gcc/gfortran headers
-find_package_handle_standard_args(GFortranLibs
-  REQUIRED_VARS LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES GFORTRAN_LIBRARIES_DIR
-  VERSION_VAR GFORTRAN_VERSION_STRING)
-
-if(GFORTRANLIBS_FOUND)
-  message(STATUS "Looking for gfortran libraries -- found")
-  message(STATUS "gfortran version: ${GFORTRAN_VERSION_STRING}")
-else()
-  message(STATUS "Looking for gfortran libraries -- not found")
-endif()
-
-mark_as_advanced(LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES
-  LIBGOMP_LIBRARIES LIBGOMP_INCLUDE_DIR
-  GFORTRAN_LIBRARIES_DIR GFORTRAN_INCLUDE_DIR)
-# FindGFortranLIBS.cmake ends here

CMakeModules/FindWcsLib.cmake

@@ -32,20 +32,28 @@
 #  WCSLIB_LIBRARIES    - the WCSLIB libraries
 #                        (identical to WCSLIB_LIBRARY)
 
+# find paths
 if(NOT WCSLIB_FOUND)
 
-  find_path(WCSLIB_INCLUDE_DIR wcslib/wcs.h
+  if (NOT "$ENV{WCSLIB_ROOT_DIR}" STREQUAL "")
-    HINTS ${WCSLIB_ROOT_DIR} PATH_SUFFIXES include)
+  set(WCSLIB_ROOT "$ENV{WCSLIB_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
-  find_library(WCSLIB_LIBRARY wcs
+  endif()
-    HINTS ${WCSLIB_ROOT_DIR} PATH_SUFFIXES lib)
+
+  find_path(WCSLIB_INCLUDE wcslib/wcs.h
+    HINTS ${WCSLIB_ROOT} PATH_SUFFIXES include)
+  find_library(WCSLIB_LIB wcs
+    HINTS ${WCSLIB_ROOT} PATH_SUFFIXES lib)
   find_library(M_LIBRARY m)
-  mark_as_advanced(WCSLIB_INCLUDE_DIR WCSLIB_LIBRARY M_LIBRARY)
+  mark_as_advanced(WCSLIB_INCLUDE WCSLIB_LIB M_LIBRARY)
 
   include(FindPackageHandleStandardArgs)
   find_package_handle_standard_args(WCSLIB DEFAULT_MSG
-    WCSLIB_LIBRARY M_LIBRARY WCSLIB_INCLUDE_DIR)
+    WCSLIB_LIB M_LIBRARY WCSLIB_INCLUDE)
 
-  set(WCSLIB_INCLUDE_DIRS ${WCSLIB_INCLUDE_DIR})
+  set(WCSLIB_INCLUDE_DIRS ${WCSLIB_INCLUDE})
-  set(WCSLIB_LIBRARIES ${WCSLIB_LIBRARY} ${M_LIBRARY})
+  set(WCSLIB_LIBRARIES ${WCSLIB_LIB} ${M_LIBRARY})
+
+  set(WCSLIB_INCLUDE ${WCSLIB_INCLUDE})
+  set(WCSLIB_LIB ${WCSLIB_LIB} ${M_LIBRARY})
 
 endif(NOT WCSLIB_FOUND)

CONTRIBUTING.md

@@ -0,0 +1,92 @@
+# Contributing
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment 
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

Docker/build_images.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+version=$(date +"%d%m%Y")
+
+for folder in \
+	sl7-test \
+	ubuntu1604-test
+
+do
+    name=${folder%%/}
+    echo
+    echo "==========================================="
+    echo "Building: "$name
+    echo "==========================================="
+
+    cmd="docker build -t fdiblen/$name:$version -t fdiblen/$name:latest ./$name"
+    echo
+    echo "Running:"
+    echo $cmd
+    echo
+    echo
+    eval $cmd
+
+    if [ $? -eq 0 ]
+    then
+      echo
+      echo "Successfully built the $name image!"
+    else
+      echo
+      echo "Could not build the $name image" >&2
+      exit $?
+    fi
+
+    #docker push fdiblen/$name:$version
+    #docker push fdiblen/$name:latest
+done

Docker/sl7-test/Dockerfile

@@ -0,0 +1,42 @@
+FROM scientificlinux/sl:7
+MAINTAINER f.diblen@esciencecenter.nl
+
+# add EPEL repository for openblas
+RUN yum -y \
+    install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
+
+# install dependencies
+RUN yum -y install \
+    wget git pkgconfig make cmake3 cmake3-gui gcc-gfortran gcc-c++ flex bison \
+    openblas openblas-devel glib2-devel lapack lapack-devel cfitsio cfitsio-devel \
+    wcslib wcslib-devel ncurses ncurses-devel readline readline-devel \
+    python-devel boost boost-devel fftw fftw-devel hdf5 hdf5-devel \
+    numpy boost-python mpich mpich-devel fftw fftw-libs fftw-devel
+
+RUN mkdir /build && cd /build
+
+# compile casacore
+RUN git clone --progress --verbose https://github.com/casacore/casacore.git casacore_src && \
+    cd casacore_src && \
+    mkdir build && cd build && \
+    cmake3 .. -DUSE_FFTW3=ON \
+    -DCMAKE_INSTALL_PREFIX=/opt/casacore \
+    -DDATA_DIR=/opt/casacore/data -DUSE_OPENMP=ON \
+    -DUSE_HDF5=ON \
+    -DBUILD_PYTHON=ON \
+    -DUSE_THREADS=ON && \
+    make -j4 && \
+    make install
+
+
+## compile sagecal
+#RUN cd /build && \
+#    mkdir build-sl && cd build-sl && \
+#    cmake3 .. -DCMAKE_INSTALL_PREFIX=/opt/sagecal \
+#    -DCASACORE_ROOT_DIR=/opt/casacore \
+#    -DCASACORE_INCLUDE=/opt/casacore/include/casacore
+#    make -j4 && \
+#    make install && \
+#
+#RUN ls -alsrt /opt/sagecal && \
+#    /opt/sagecal/bin/sagecal

Docker/ubuntu1604-test/Dockerfile

@@ -0,0 +1,28 @@
+FROM ubuntu:xenial
+MAINTAINER f.diblen@esciencecenter.nl
+
+RUN apt-get update -y && \
+    apt-get install software-properties-common -y && \
+    add-apt-repository -s ppa:kernsuite/kern-3 -y && \
+    apt-add-repository multiverse && \
+    apt-get update -y
+
+RUN apt-get install -y \
+    git cmake g++ pkg-config \
+    libcfitsio-bin libcfitsio-dev \
+    libopenblas-base libopenblas-dev \
+    wcslib-dev wcslib-tools \
+    libglib2.0-dev \
+    libcasa-casa2 casacore-dev casacore-data casacore-tools \
+    mpich \
+    fftw-dev libfftw3-mpi3 libfftw3-bin
+
+
+## compile sagecal
+#RUN mkdir /build && cd /build \
+#    mkdir build-ubuntu && cd build-ubuntu && \
+#    cmake .. -DCMAKE_INSTALL_PREFIX=/opt/sagecal && \
+#    make -j4 && \
+#    make install && \
+#    ls -alsrt /opt/sagecal && \
+#    /opt/sagecal/bin/sagecal

INSTALL.md

@@ -1,6 +1,32 @@
 di 28 aug 2018  9:37:58 CEST
 # SAGECal Installation
 
+
+## das5
+
+Load the modules below before compiling SageCal.
+```
+module load cmake/3.8.2
+module load mpich/ge/gcc/64/3.2
+module load gcc/4.9.3
+module load casacore/2.3.0-gcc-4.9.3
+module load wcslib/5.13-gcc-4.9.3
+module load wcslib/5.16-gcc-4.9.3
+module load cfitsio/3.410-gcc-4.9.3
+```
+
+checkout the source code and compile it with the instructions below(in source folder):
+```
+git clone https://github.com/nlesc-dirac/sagecal.git
+
+cd sagecal && mkdir build && cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH
+make
+make install
+```
+$INSTALL_PATH is where you want to install SageCal.
+
+
 ## Cmake Build
 
 ### Requirements

LICENSE.md

@@ -0,0 +1,339 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

README.md

@@ -4,9 +4,11 @@
 | ------------- | ------------- |
 | [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=master)](https://travis-ci.org/nlesc-dirac/sagecal)  | [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=dev)](https://travis-ci.org/nlesc-dirac/sagecal)  |
 
+[![Documentation](https://codedocs.xyz/nlesc-dirac/sagecal.svg)](https://codedocs.xyz/nlesc-dirac/sagecal/)
 
 # SAGECAL
 
+
 ## Features
 
 - Levenberg-Marquardt, LBFGS, Riemannian Trust Region, Nesterov's accelerated gradient descent algorithms
@@ -23,6 +25,9 @@
 Read INSTALL for installation. This file gives a brief guide to use SAGECal.
 Warning: this file may be obsolete. use sagecal -h to see up-to-date options.
 
+## Code documentation
+Code documentation can be found [here](https://codedocs.xyz/nlesc-dirac/sagecal).
+
 
 ## Step by Step Introduction:
 
@@ -182,3 +187,6 @@ So for this cluster, there will be more than 1 column in the solution file, the
 
 ### Additional Info
 See [LOFAR Cookbook Chapter](https://support.astron.nl/LOFARImagingCookbook/sagecal.html).
+
+Please cite this code using the DOI.
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1289316.svg)](https://doi.org/10.5281/zenodo.1289316)

build-tests/compile_sagecal.sh

@@ -0,0 +1,56 @@
+#!/usr/bin/env bash
+
+echo 'script: ' $0
+
+echo "Building SageCal" && \
+echo "Branch --> $BRANCH" && \
+echo "Image --> $IMAGE"
+
+BUILD_DIR=$IMAGE'-build'
+
+cd /travis/workdir && \
+    mkdir $BUILD_DIR && cd $BUILD_DIR
+
+CMAKE_EXE=''
+OPTS=''
+
+case $IMAGE in
+    ubuntu)
+        echo 'Building for Ubuntu'
+        CMAKE_EXE=$(which cmake)
+        OPTS=''
+        ;;
+    sl7)
+        echo 'Building for Scientific Linux'
+        CMAKE_EXE=$(which cmake3)
+        OPTS='-DCASACORE_ROOT_DIR=/opt/casacore'
+        ;;
+    arch)
+        OPTS=''
+        ;;
+    *)
+        echo 'Unknown image $IMAGE!'
+        exit 1
+        ;;
+esac
+
+echo 'CMAKE_EXE: ' $CMAKE_EXE
+echo 'CMake options: ' $OPTS
+echo 'pwd: ' $PWD
+
+echo 'ls -asl: '
+ls -asl
+
+echo 'ls -asl /travis/workdir: '
+ls -asl /travis/workdir
+
+echo 'ls -asl /travis/workdir/$BUILD_DIR: '
+ls -asl /travis/workdir/$BUILD_DIR
+
+
+$CMAKE_EXE /travis/workdir -DCMAKE_INSTALL_PREFIX=/opt/sagecal $OPTS
+
+make -j4 && \
+make install && \
+ls -alsrt /opt/sagecal && \
+/opt/sagecal/bin/sagecal

src/MPI/CMakeLists.txt

@@ -18,7 +18,7 @@ add_executable(sagecal-mpi ${SRCFILES})
 
 target_link_libraries(sagecal-mpi
  ${CASACORE_LIBRARIES}
- ${CFITSIO_LIBRARIES}
+ ${CFITSIO_LIB}
  ${OpenBLAS_LIB}
  ${LAPACK_LIBRARIES}
  ${WCSLIB_LIBRARIES}
@@ -29,7 +29,6 @@ target_link_libraries(sagecal-mpi
  -lopenblas
  -lgfortran
  -lpthread
- -lcfitsio
  -lm
  -ldirac
  -lradio

src/MPI/data.cpp

@@ -1 +0,0 @@
-../MS/data.cpp

src/MPI/data.h

@@ -1 +0,0 @@
-../MS/data.h

src/MPI/data.h

@@ -0,0 +1,174 @@
+/*
+ *
+ Copyright (C) 2006-2008 Sarod Yatawatta <sarod@users.sf.net>  
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ 
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ 
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ $Id$
+ */
+
+#ifndef __DATA_H__
+#define __DATA_H__
+#include <unistd.h>
+#include <stdio.h>
+#include <iostream>
+#include <casacore/ms/MeasurementSets/MSIter.h>
+#include <casacore/tables/Tables/Table.h>
+#include <casacore/tables/Tables/TableVector.h>
+#include <casacore/tables/Tables/TableRecord.h>
+#include <casacore/tables/Tables/TableColumn.h>
+#include <casacore/tables/Tables/TableIter.h>
+#include <casacore/tables/Tables/ScalarColumn.h>
+#include <casacore/tables/Tables/ArrayColumn.h>
+#include <casacore/casa/Arrays/Array.h>
+#include <casacore/casa/Arrays/Cube.h>
+#include <fstream>
+#include <math.h>
+#include <complex>
+
+
+using namespace casacore;
+
+namespace Data
+{
+
+    struct IOData {
+       int N; /* no of stations */
+       int Nbase; /* baselines, exclude autocorrelations */
+       int tilesz;
+       int Nchan; /* total no of channels */
+       int Nms; /* no. of MS */
+       int *NchanMS; /* total channels per MS : Nms x 1 vector */
+       double deltat; /* integration time (s) */
+       int totalt; /* total no of time slots */
+       double ra0; /* phase center */
+       double dec0; /* phase center */
+       double *u; /* uvw coords, size Nbase*tilesz x 1 */
+       double *v;
+       double *w;
+       double *x; /* averaged data, size Nbase*8*tilez x 1
+       ordered by XX(re,im),XY(re,im),YX(re,im),YY(re,im), baseline, timeslots */
+       double *xo; /* unaveraged data, size Nbase*8*tilesz*Nchan x 1
+       ordered by  XX(re,im),XY(re,im),YX(re,im),YY(re,im), baseline, timeslots, channel */
+       double *freqs; /* channel freqs, size Nchan x 1 */
+       double freq0; /* averaged freq */
+       double *flag; /* double for conforming with old routines size Nbase*tilesz x 1 */
+       double deltaf; /* total bandwidth for freq. smearing */
+
+       double fratio; /* flagged data ratio = flagged/total, not counting data excluded from uv cut */
+                      /* if 1, all usable data are flagged */
+    };
+
+    /* Station beam info */
+    struct LBeam {
+      double *time_utc; /* time coord UTC (s), size tileszx1, 
+                         convert from MJD (s) to JD (days) */
+      int *Nelem; /* no of elements in each station, size Nx1 */
+      /* position (ITRF) of stations (m)
+       later changed to logitude,latitude,height (rad,rad,m) */
+      double *sx; /* x: size Nx1 */
+      double *sy; /* y: ... */
+      double *sz; /* z: ... */
+      /* x,y,z coords of elements, projected, converted to ITRF (m) */
+      double **xx; /* x coord pointer, size Nx1, each *x: x coord of station, size Nelem[]x1 */
+      double **yy; /* y ... */
+      double **zz; /* z ... */
+      /* pointing center of beams (only one) (could be different from phase center) */
+      double p_ra0;
+      double p_dec0;
+    };
+
+
+    /* read Auxilliary info and setup memory */
+    void readAuxData(const char *fname, IOData *data);
+    void readAuxData(const char *fname, IOData *data, LBeam *binfo);
+
+    void readAuxDataList(vector<string> msnames, IOData *data);
+
+    void readMSlist(char *fname, vector<string> *msnames);
+    /* load data using MS Iterator */
+    void loadData(Table t, IOData iodata, double *fratio);
+    void loadData(Table t, IOData iodata, LBeam binfo, double *fratio);
+
+    void loadDataList(vector<MSIter*> msitr, Data::IOData iodata, double *fratio);
+    /* write back data using MS Iterator */
+    void writeData(Table t, IOData iodata);
+    void writeDataList(vector<MSIter*> msitr, IOData iodata);
+    void freeData(IOData data);
+    void freeData(IOData data, LBeam binfo);
+
+    extern int numChannels; 
+    extern unsigned long int numRows;
+
+    struct float2 {
+      float x,y;
+    };
+
+
+    extern char *TableName; /* MS name */
+    extern char *MSlist; /* text file with MS names */
+    extern char *MSpattern; /* pattern to match all MS names used in calibration */
+    extern float min_uvcut;
+    extern float max_uvcut;
+    extern float max_uvtaper;
+    extern casacore::String DataField; /* input column DATA/CORRECTED_DATA */
+    extern casacore::String OutField; /* output column DATA/CORRECTED_DATA */
+    extern int TileSize; //Tile size
+    extern int Nt; /* no of worker threads */
+    extern char *SkyModel; /* sky model file */
+    extern char *Clusters; /* cluster file */
+    extern int format; /* sky model format 0: LSM, 1: LSM with 3 order spec idx*/
+ 
+    /* sagecal paramters */
+    extern int max_emiter;
+    extern int max_iter;
+    extern int max_lbfgs;
+    extern int lbfgs_m;
+    extern int gpu_threads;
+    extern int linsolv;
+    extern int solver_mode;
+    extern int ccid;
+    extern double rho;
+    extern char *solfile;
+    extern char *initsolfile;
+    extern char *ignorefile;
+    extern double nulow,nuhigh;
+    extern int randomize;
+    extern int whiten;
+    extern int DoSim; /* if 1, simulation mode */
+    extern int doChan; /* if 1, solve for each channel in multi channel data */
+    extern int doBeam; /* if 1, predict (LOFAR) beam array factor */
+    extern int DoDiag; /* if >0, enables diagnostics (Leverage) 1: write leverage as output (no residual), 2: only calculate fractions of leverage/noise */
+    extern int phaseOnly; /* if >0, and if any correction is done, extract phase and do phase only correction */
+
+    /* distributed sagecal parameters */
+    extern int Nadmm; /* ADMM iterations >=1 */
+    extern int Npoly; /* polynomial order >=1 */
+    extern int PolyType; /* what kind on polynomials to use 0,1,2,3 */
+    extern double admm_rho; /* regularization */
+    extern char *admm_rho_file; /* text file for regularization of each cluster */
+    extern int aadmm; /* if >0, enable adaptive update of rho */
+    /* for debugging, upper limit on time slots */
+    extern int Nmaxtime;
+    /* skipping initial timeslots */
+    extern int Nskip;
+    extern int verbose; /* if >0, enable verbose output */
+    extern int mdl; /* if given, calculate AIC/MDL for different poly configs and find minimum */
+    extern int GPUpredict; /* if given, use GPU for model calculation */
+    extern int heapsize; /* heap size in GPU (MB), for using malloc() */
+    /* for client server mode */
+    extern int servermode; /* 0: client, 1: server, else default operation */
+    extern char *servername; /* server host name or ip address */
+    extern char *portnumber; /* which port number to use for communication */
+}
+#endif //__DATA_H__

src/MS/CMakeLists.txt

@@ -23,7 +23,7 @@ add_executable(sagecal ${SRCFILES})
 
 target_link_libraries(sagecal
  ${CASACORE_LIBRARIES}
- ${CFITSIO_LIBRARIES}
+ ${CFITSIO_LIB}
  ${OpenBLAS_LIB}
  ${LAPACK_LIBRARIES}
  ${WCSLIB_LIBRARIES}
@@ -32,7 +32,6 @@ target_link_libraries(sagecal
  -lopenblas
  -lgfortran
  -lpthread
- -lcfitsio
  -lm
  -ldirac
  -lradio

src/buildsky/CMakeLists.txt

@@ -1,5 +1,6 @@
 find_package(WcsLib REQUIRED)
-include_directories(${WCSLIB_INCLUDE_DIR}/wcslib)
+include_directories(${WCSLIB_INCLUDE_DIRS}/wcslib)
+include_directories(${WCSLIB_INCLUDE_DIRS})
 include_directories(./)
 
 link_directories(${LIBRARY_OUTPUT_PATH})
@@ -8,7 +9,7 @@ FILE(GLOB SRCFILES *.c)
 add_executable(buildsky ${SRCFILES})
 
 target_link_libraries(buildsky
- ${CFITSIO_LIBRARIES}
+ ${CFITSIO_LIB}
  ${OpenBLAS_LIB}
  ${LAPACK_LIBRARIES}
  ${WCSLIB_LIBRARIES}
@@ -17,7 +18,6 @@ target_link_libraries(buildsky
  -lopenblas
  -lgfortran
  -lpthread
- -lcfitsio
  -lm
 )
 

src/lib/Dirac/lbfgs.c

@@ -423,7 +423,8 @@ cubic_interp(
    }
   }
 
-  return 0;
+  /* fallback value */
+  return (a+b)*0.5;
 }
 
 

src/lib/Dirac/lbfgs_nocuda.c

@@ -187,8 +187,8 @@ cubic_interp(
     return b;
    }
   }
-
+  /* fallback value */
-  return 0;
+  return (a+b)*0.5;
 }
 
 

src/restore/CMakeLists.txt

@@ -1,6 +1,7 @@
 find_package(WcsLib REQUIRED)
 find_package(FFTW REQUIRED)
-include_directories(${WCSLIB_INCLUDE_DIR}/wcslib)
+include_directories(${WCSLIB_INCLUDE_DIRS}/wcslib)
+include_directories(${WCSLIB_INCLUDE_DIRS})
 include_directories(./)
 
 link_directories(${LIBRARY_OUTPUT_PATH})
@@ -9,7 +10,7 @@ FILE(GLOB SRCFILES *.c)
 add_executable(restore ${SRCFILES})
 
 target_link_libraries(restore
- ${CFITSIO_LIBRARIES}
+ ${CFITSIO_LIB}
  ${OpenBLAS_LIB}
  ${LAPACK_LIBRARIES}
  ${WCSLIB_LIBRARIES}
@@ -20,7 +21,6 @@ target_link_libraries(restore
  -lopenblas
  -lgfortran
  -lpthread
- -lcfitsio
  -lm
 )
 

test-builds/test-ubuntu.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-echo "Building SageCal" && \ 
-echo "Branch --> $BRANCH" && \
-cd /travis/workdir && \
-mkdir build && cd build && \
-cmake .. -DENABLE_CUDA=OFF && \
-make -j4 && \
-ls -alsrt ./dist/bin && \
-./dist/bin/sagecal
-

test/Change_freq.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+from pyrap.tables import *
+
+# You can use this script to create different MS data files by copying a single MS
+# into MS with different names and changing their frequencies to unique values
+
+# change freq
+def read_corr(msname,freq):
+  import os
+  import math
+  tf=table(msname+'/SPECTRAL_WINDOW',readonly=False)
+  ch0=tf.getcol('CHAN_FREQ')
+  ch0[0,0]=freq
+  reffreq=tf.getcol('REF_FREQUENCY')
+  reffreq[0]=ch0[0,0]
+  tf.putcol('CHAN_FREQ',ch0)
+  tf.putcol('REF_FREQUENCY',reffreq)
+  tf.close()
+
+
+if __name__ == '__main__':
+  # args MS
+  import sys
+  argc=len(sys.argv)
+  if argc==3:
+   read_corr(sys.argv[1],float(sys.argv[2]))
+  else:
+   print("thisscript MS frequency")
+  exit()

test/dosage-mpi.sh

@@ -0,0 +1,5 @@
+# Before running this, make sure you have at least 2 data files with names matching the pattern '*.ms'
+
+# This command assumes sagecal-mpi binary is at ../src/MPI/sagecal-mpi
+# 'regularization_factors.txt' should exactly match the cluster info given by '3c196.sky.txt.cluster'
+mpirun -np 3 ../src/MPI/sagecal-mpi -f '*.ms' -A 10 -P 2 -Q 2 -G regularization_factors.txt -s 3c196.sky.txt -c 3c196.sky.txt.cluster -p zsol -n 2 -t 10 -e 4 -g 2 -l 10 -m 7 -x 30 -F 1 -j 5 -B 1 -k 1 -K 3 -W 0 -V > sagecal-mpi.ms.output

test/dosage.sh

@@ -1,2 +1,3 @@
 # Before running this, untar sm.ms.tar and build sagecal
+# this command assumes sagecal binary is at ../src/MS/sagecal
 ../src/MS/sagecal -d sm.ms -s extended_source_list.txt -c extended_source_list.txt.cluster -n 4 -t 10 -p sm.ms.solutions -e 4 -g 2 -l 10 -m 7 -x 30 -F 1 -j 2  -k -1 -B 1 -W 0 > sm.ms.output

test/regularization_factors.txt

@@ -0,0 +1,6 @@
+# format
+# cluster_id hybrid admm_rho
+-1 2 4
+2 1 2
+
+# end