Fix static lapack

azure-pipelines.yml

@@ -0,0 +1,87 @@
+# Starter pipeline
+# Start with a minimal pipeline that you can customize to build and deploy your code.
+# Add steps that build, run tests, deploy, and more:
+# https://aka.ms/yaml
+
+trigger:
+- master
+
+pr:
+- master
+
+jobs:
+- job: Build
+  timeoutInMinutes: 360
+
+  strategy:
+    matrix:
+      linux:
+        imageName: 'ubuntu-16.04'
+        CXX: '/usr/bin/clang++'
+        CC: '/usr/bin/clang'
+        buildPlatform: 'linux'
+      mac:
+        imageName: 'macos-10.13'
+        DEVELOPER_DIR: '/Applications/Xcode_9.4.1.app'
+        buildPlatform: 'osx'
+
+      windows:
+        imageName: 'vs2017-win2016'
+        buildPlatform: 'windows'
+
+  variables:
+    VCPKG_ROOT: '$(Build.SourcesDirectory)/vcpkg'
+    archiveFile: '$(Build.ArtifactStagingDirectory)/flimfit-env-$(buildPlatform).zip'
+
+  pool:
+    vmImage: $(imageName)
+
+  steps:
+
+    - task: UsePythonVersion@0
+      inputs:
+        versionSpec: '3.6'
+        architecture: 'x64'
+
+    - script: brew install gcc6 p7zip
+      displayName: 'Install brew dependencies'
+      condition: eq(variables['buildPlatform'],'osx')
+
+    - task: CopyFiles@2
+      inputs:
+        contents: '**'
+        targetFolder: '$(Build.SourcesDirectory)/vcpkg'
+
+    - script: python build-flimfit-env.py
+      workingDirectory: 'vcpkg'
+      displayName: 'Build vcpkg ports'
+
+    - task: CopyFiles@2
+      condition: always() 
+      inputs:
+        contents: 'vcpkg/buildtrees/**/*.log'
+        targetFolder: '$(Build.ArtifactStagingDirectory)/logs'
+
+    - task: PublishBuildArtifacts@1
+      condition: always() 
+      inputs:
+        pathtoPublish: '$(Build.ArtifactStagingDirectory)/logs'
+        artifactName: 'vcpkg-logs-$(buildPlatform)'
+
+    - task: ArchiveFiles@2
+      inputs:
+        rootFolderOrFile: '$(Build.SourcesDirectory)/vcpkg'
+        archiveType: 'zip'
+        archiveFile: '$(archiveFile)'
+
+    - task: PublishBuildArtifacts@1
+      inputs:
+        pathtoPublish: '$(archiveFile)'
+        artifactName: 'flimfit-env-$(buildPlatform)'
+
+    - task: GithubRelease@0
+      displayName: 'Create GitHub Release'
+      inputs:
+        githubConnection: seanwarren
+        repositoryName: seanwarren/vcpkg
+        assets: $(archiveFile)

build-flimfit-env.py

@@ -0,0 +1,35 @@
+import json
+import subprocess
+import platform
+import os
+import re
+import shutil
+
+# Get vcpkg directory
+vcpkg_dir = os.path.dirname(os.path.realpath(__file__))
+
+# Get system and setup extension
+system = platform.system()
+if system == "Windows":
+   script_ext = ".bat"
+   exec_ext = ".exe"
+else:
+   script_ext = ".sh"
+   exec_ext = ""
+
+# Bootstrap vcpkg
+subprocess.run([os.path.join(vcpkg_dir, "bootstrap-vcpkg" + script_ext)], check=True)
+
+# Read configuration
+json_file = open(os.path.join(vcpkg_dir, 'flimfit-env-config.json'))
+config = json.load(json_file)
+
+# Setup ports
+triplet_ext = ":" + config["default_triplet"][system]
+ports = [port + triplet_ext for port in config["ports"]]
+
+# Build ports
+subprocess.run([os.path.join(vcpkg_dir, "vcpkg" + exec_ext), "install", "--clean-after-build"] + ports, 
+   cwd=vcpkg_dir, check=True)
+
+shutil.rmtree(os.path.join(vcpkg_dir, "downloads"))

flimfit-env-config.json

@@ -0,0 +1,30 @@
+{
+   "default_triplet": {
+      "Windows": "x64-windows-static",
+      "Darwin":  "x64-osx",
+      "Linux":   "x64-linux"   
+   },
+
+   "ports" :
+   [
+      "qt5-serialport",
+      "boost",
+      "dlib",
+      "opencv",
+      "fftw3",
+      "omefiles",
+      "bioimage[opencv]",
+      "libics",
+      "hdf5",
+      "boost-random",
+      "boost-serialization",
+      "boost-align",
+      "boost-interprocess",
+      "boost-bind",
+      "boost-function",
+      "boost-math",
+      "boost-accumulators",
+      "boost-filesystem",
+      "boost-property-tree"
+   ]
+}

ports/bioimage/CONTROL

@@ -0,0 +1,8 @@
+Source: bioimage
+Version: 2.5.2 
+Description: LibBioImage is a C++ library for access and process biological 3D images. It supports many input and output formats and basic image processing operations.
+Build-Depends: tiff, libraw, eigen3, proj4, libjpeg-turbo, libgeotiff, exiv2[unicode]
+
+Feature: opencv
+Description: opencv functionality for bioimage
+Build-Depends: opencv[core]

ports/bioimage/bioimageconvert.patch

@@ -0,0 +1,204 @@
+--- CMakeLists.txt
++++ CMakeLists.txt
+@@ -67,6 +67,11 @@
+     cmake_policy(SET CMP0060 NEW)
+ endif()
+
++# Make IMPORTED_LINK_INTERFACE_LIBRARIES per configuration when exported
++if(POLICY CMP0022)
++   cmake_policy(SET CMP0022 OLD)
++endif()
++
+
+ #---------------------------------------------------------------------
+ # Set project information
+--- cmake/bioimageConfig.cmake.in
++++ cmake/bioimageConfig.cmake.in
+@@ -1,4 +1,8 @@
+ @PACKAGE_INIT@
+
++include(CMakeFindDependencyMacro)
++find_dependency(PROJ4)
++find_dependency(GeoTIFF)
++find_dependency(Exiv2)
+ include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@Targets.cmake")
+ check_required_components("@PROJECT_NAME@")
+
+--- cmake/Modules/FindLCMS2.cmake
++++ cmake/Modules/FindLCMS2.cmake
+@@ -29,18 +29,32 @@
+    PATH_SUFFIXES lcms2 liblcms2
+ )
+
+-find_library(LCMS2_LIBRARIES NAMES lcms2 liblcms2 lcms-2 liblcms-2
++find_library(LCMS2_RELEASE_LIBRARY NAMES lcms2
+    PATHS     
+    ${PC_LCMS2_LIBDIR}
+    ${PC_LCMS2_LIBRARY_DIRS}
+    PATH_SUFFIXES lcms2
+ )
+
+-if(LCMS2_INCLUDE_DIR AND LCMS2_LIBRARIES)
++find_library(LCMS2_DEBUG_LIBRARY NAMES lcms2d
++   PATHS     
++   ${PC_LCMS2_LIBDIR}
++   ${PC_LCMS2_LIBRARY_DIRS}
++   PATH_SUFFIXES lcms2
++)
++
++
++if(LCMS2_INCLUDE_DIR AND LCMS2_RELEASE_LIBRARY)
+    set(LCMS2_FOUND TRUE)
+-else(LCMS2_INCLUDE_DIR AND LCMS2_LIBRARIES)
++else()
+    set(LCMS2_FOUND FALSE)
+-endif(LCMS2_INCLUDE_DIR AND LCMS2_LIBRARIES)
++endif()
++
++if (LCMS2_DEBUG_LIBRARY)
++   set(LCMS2_LIBRARIES optimized "${LCMS2_RELEASE_LIBRARY}" debug "${LCMS2_DEBUG_LIBRARY}")
++else()
++   set(LCMS2_LIBRARIES ${LCMS2_RELEASE_LIBRARY})
++endif()
+
+ if(LCMS2_FOUND)
+    file(READ ${LCMS2_INCLUDE_DIR}/lcms2.h LCMS2_VERSION_CONTENT)
+--- cmake/Modules/FindTIFF.cmake
++++ cmake/Modules/FindTIFF.cmake
+@@ -47,14 +47,55 @@
+ endforeach()
+
+ if(NOT TIFF_LIBRARY)
+-    find_library(TIFF_LIBRARY_RELEASE NAMES ${TIFF_NAMES})
+-    find_library(TIFF_LIBRARY_DEBUG NAMES ${TIFF_NAMES_DEBUG})
++    find_library(TIFF_LIBRARY_RELEASE 
++        NAMES ${TIFF_NAMES}
++        PATH_SUFFIXES "lib" "local/lib")
++    find_library(TIFF_LIBRARY_DEBUG 
++        NAMES ${TIFF_NAMES_DEBUG}
++        PATH_SUFFIXES "debug/lib" "lib" "local/lib")
++
++    if(TIFF_LIBRARY_RELEASE)
++
++        get_filename_component(TIFF_LIBRARY_NAME ${TIFF_LIBRARY_RELEASE} NAME_WE)
++        get_filename_component(TIFF_LIBRARY_EXTENSION ${TIFF_LIBRARY_RELEASE} EXT)
++        get_filename_component(TIFF_LIBRARY_PATH ${TIFF_LIBRARY_RELEASE} DIRECTORY)
++        get_filename_component(TIFF_DEBUG_LIBRARY_PATH ${TIFF_LIBRARY_DEBUG} DIRECTORY)
++
++        message("searching for: "${TIFF_LIBRARY_NAME}xx${TIFF_LIBRARY_EXTENSION}" in ${TIFF_LIBRARY_PATH}")
++
++        find_library(TIFFXX_LIBRARY_RELEASE 
++            NAMES "${TIFF_LIBRARY_NAME}xx${TIFF_LIBRARY_EXTENSION}"
++            PATHS ${TIFF_LIBRARY_PATH}
++            NO_DEFAULT_PATH)
++        find_library(TIFFXX_LIBRARY_DEBUG
++            NAMES "${TIFF_LIBRARY_NAME}xxd${TIFF_LIBRARY_EXTENSION}"
++            PATHS ${TIFF_DEBUG_LIBRARY_PATH}
++            NO_DEFAULT_PATH)
++
++        if(TIFFXX_LIBRARY_RELEASE)
++            list(APPEND TIFF_LIBRARY_RELEASE ${TIFFXX_LIBRARY_RELEASE})
++            list(APPEND TIFF_LIBRARY_DEBUG ${TIFFXX_LIBRARY_DEBUG})
++            set(CPP_TIFF_LIBRARY optimised  ${TIFFXX_LIBRARY_RELEASE} debug  ${TIFFXX_LIBRARY_DEBUG})
++            set(TIFF_CXX_FOUND TRUE)
++        else()
++            message(FATAL_ERROR "Could NOT find TIFF/C++ library ${CPP_TIFF_LIBRARY}.")
++        endif()
++
++    endif()
++
+     include(SelectLibraryConfigurations)
+     select_library_configurations(TIFF)
+     mark_as_advanced(TIFF_LIBRARY_RELEASE TIFF_LIBRARY_DEBUG)
++
+ endif()
+ unset(TIFF_NAMES)
+ unset(TIFF_NAMES_DEBUG)
++unset(TIFF_LIBRARY_NAME)
++unset(TIFF_LIBRARY_PATH)
++unset(TIFF_LIBRARY_EXTENSION)
++
++message("${TIFF_FOUND} ==== ${TIFF_LIBRARY} ==== ${TIFF_LIBRARY_RELEASE} ==== ${TIFF_LIBRARY_DEBUG}")
++message("TIFF_LIBRARY: ${TIFF_LIBRARY}")
+
+ if(TIFF_INCLUDE_DIR AND EXISTS "${TIFF_INCLUDE_DIR}/tiffvers.h")
+     file(STRINGS "${TIFF_INCLUDE_DIR}/tiffvers.h" tiff_version_str
+@@ -101,49 +142,6 @@
+         endif()
+     endif()
+
+-    # looking for C++ version of library libtiffxx.so
+-    set(TIFF_CXX_FOUND FALSE)
+-    foreach(TIFF_LIBRARY ${TIFF_LIBRARIES})
+-        # We do not want just any tiffxx library, we specifically want
+-        # the one that belongs to the tiff library we found before. So we
+-        # expect the same path and extension.
+-        get_filename_component(TIFF_LIBRARY_NAME ${TIFF_LIBRARY} NAME_WE)
+-        get_filename_component(TIFF_LIBRARY_PATH ${TIFF_LIBRARY} DIRECTORY)
+-        get_filename_component(TIFF_LIBRARY_EXTENSION ${TIFF_LIBRARY} EXT)
+-        if(TIFF_LIBRARY_NAME MATCHES "d$")
+-            # Check for libtiffdxx:
+-            set(CPP_TIFF_LIBRARY "${TIFF_LIBRARY_PATH}/${TIFF_LIBRARY_NAME}xx${TIFF_LIBRARY_EXTENSION}")
+-            if(NOT EXISTS ${CPP_TIFF_LIBRARY})
+-                message("-- Could NOT find (debug) TIFF/C++ library ${CPP_TIFF_LIBRARY}.")
+-                # Check for libtiffxxd:
+-                string(REGEX REPLACE "d$" "" TIFF_LIBRARY_NAME ${TIFF_LIBRARY_NAME})
+-                set(CPP_TIFF_LIBRARY "${TIFF_LIBRARY_PATH}/${TIFF_LIBRARY_NAME}xxd${TIFF_LIBRARY_EXTENSION}")
+-                if(NOT EXISTS ${CPP_TIFF_LIBRARY})
+-                    message("-- Could NOT find (debug) TIFF/C++ library ${CPP_TIFF_LIBRARY}.")
+-                    continue()
+-                endif()
+-            endif()
+-        else()
+-            # Check for libtiffxx:
+-            set(CPP_TIFF_LIBRARY "${TIFF_LIBRARY_PATH}/${TIFF_LIBRARY_NAME}xx${TIFF_LIBRARY_EXTENSION}")
+-            if(NOT EXISTS ${CPP_TIFF_LIBRARY})
+-                message("-- Could NOT find TIFF/C++ library ${CPP_TIFF_LIBRARY}.")
+-                continue()
+-            endif()
+-        endif()
+-
+-        message("-- Found TIFF/C++ library ${CPP_TIFF_LIBRARY}")
+-        set(TIFF_CXX_FOUND TRUE)
+-        list(APPEND TIFF_LIBRARIES "${CPP_TIFF_LIBRARY}")
+-        unset(TIFF_LIBRARY)
+-        unset(TIFF_LIBRARY_NAME)
+-        unset(TIFF_LIBRARY_PATH)
+-        unset(TIFF_LIBRARY_EXTENSION)
+-        break()
+-    endforeach()
+-    if(NOT TIFF_CXX_FOUND)
+-        message(FATAL_ERROR "Could NOT find TIFF/C++ library ${CPP_TIFF_LIBRARY}.")
+-    endif()
+ endif()
+
+-mark_as_advanced(TIFF_INCLUDE_DIR TIFF_LIBRARY)
+\ No newline at end of file
++mark_as_advanced(TIFF_INCLUDE_DIR TIFF_LIBRARY)
+--- libsrc/libbioimg/core_lib/xtypes.h
++++ libsrc/libbioimg/core_lib/xtypes.h
+@@ -52,7 +52,12 @@
+ typedef	short int16;
+ typedef	unsigned short uint16;
+
+-#if defined(WIN32) || defined(WIN64) || defined(_WIN32) || defined(_WIN64) || defined(_MSVC)
++#if defined(__APPLE__)
++typedef int32_t int32;
++typedef long int64;
++typedef uint32_t uint32;
++typedef unsigned long uint64;
++#elif defined(WIN32) || defined(WIN64) || defined(_WIN32) || defined(_WIN64) || defined(_MSVC)
+ typedef __int32 int32;
+ typedef __int64 int64;
+ typedef unsigned __int32 uint32;
+--- libsrc/libbioimg/formats_api/bim_image.h
++++ libsrc/libbioimg/formats_api/bim_image.h
+@@ -67,7 +67,7 @@
+ #endif //BIM_USE_EIGEN
+
+ #ifdef BIM_USE_OPENCV
+-#include <opencv2/core/core.hpp>
++namespace cv { class Mat; }
+ #endif //BIM_USE_OPENCV
+
+ #ifdef BIM_USE_NUMPY