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Merge pull request #12 from vincefn/upstream-objcryst
Merge upstream objcryst changes (upstream-objcryst branch)
2 parents e7c354a + c0a6bb8 commit d9fed52

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‎.gitignore

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@@ -9,7 +9,8 @@ project.xcworkspace
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*.app
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build
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*.log
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/cctbx
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/cctbx/cctbx
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/cctbx/include
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/newmat
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/freeglut*
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/fftw*
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*.tar.bz2
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*.tar.gz
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cctbx_install_script.csh
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cctbx_sources
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newmat11
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.idea
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/wxWidgets*
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*.pyc
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/ObjCryst/rules.mak
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JOB*.xml*
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/Fox/src/Fox
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/Fox/src/Fox-nogui
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/Fox/example/client
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*.dmg
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Fox/wikihtml
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*.pov
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boost_1_68_0
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GridRslt
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‎ChangeLog.txt

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#### 2020.1 (January 2021)
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NEW FEATURES
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* Add cylindrical absorption correction (mu*R)
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* Access to Crystallography Open Database now uses an http access without
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need for MySQL, and should work through firewalls
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IMPROVEMENTS
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* Switched to wxWidgets 3.1
9+
* When using --cif2pattern, do not convert atoms to a Molecule (faster)
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* Fox grid allows a working directory with spaces in the path.
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BUG FIXES
13+
* Correct EstimateCellVolume estimation for orthorombic F
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* + several minor issues
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#### 2017.2 (28 June 2017)
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NEW FEATURES
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* 3D crystal view: add 'M' shortcut to allow forcing the full display

‎Fox/Fox-Info.plist

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<string>Fox.icns</string>
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<key>CFBundleTypeName</key>
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<string>Crystallographic Information File</string>
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<key>CFBundleTypeRole</key>
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<string>Viewer</string>
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<key>LSItemContentTypes</key>
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<array>
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<string></string>
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<false/>
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<key>NSPersistentStoreTypeKey</key>
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<string>XML</string>
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<key>CFBundleTypeRole</key>
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<string>Viewer</string>
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</dict>
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<dict>
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<key>CFBundleTypeExtensions</key>
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<key>CFBundleSignature</key>
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<string>????</string>
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<key>CFBundleVersion</key>
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<string>2016.1</string>
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<string>2020.1</string>
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</dict>
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</plist>

‎Fox/Fox.xcodeproj/project.pbxproj

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‎Fox/Fox_vc12.sln

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Microsoft Visual Studio Solution File, Format Version 12.00
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# Visual Studio 2013
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VisualStudioVersion = 12.0.31101.0
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# Visual Studio Version 16
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VisualStudioVersion = 16.0.30804.86
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Fox", "Fox_vc12.vcxproj", "{2775CD9F-FFF3-4373-A229-94DD4B6D7747}"
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ProjectSection(ProjectDependencies) = postProject
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GlobalSection(SolutionProperties) = preSolution
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HideSolutionNode = FALSE
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EndGlobalSection
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GlobalSection(ExtensibilityGlobals) = postSolution
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SolutionGuid = {92D2EBD0-0BED-4254-8D3C-BB238046D064}
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EndGlobalSection
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EndGlobal

‎Fox/Fox_vc12.vcxproj

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<?xml version="1.0" encoding="utf-8"?>
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<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<Project DefaultTargets="Build" ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<ItemGroup Label="ProjectConfigurations">
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<ProjectConfiguration Include="Debug|Win32">
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<Configuration>Debug</Configuration>
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<Keyword>Win32Proj</Keyword>
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<RootNamespace>Fox</RootNamespace>
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<ProjectName>Fox</ProjectName>
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<WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
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</PropertyGroup>
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<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
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<ConfigurationType>Application</ConfigurationType>
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<UseDebugLibraries>true</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v142</PlatformToolset>
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<CharacterSet>Unicode</CharacterSet>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
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<ConfigurationType>Application</ConfigurationType>
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<UseDebugLibraries>false</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v142</PlatformToolset>
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<WholeProgramOptimization>true</WholeProgramOptimization>
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<CharacterSet>Unicode</CharacterSet>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_XP_NoCOD|Win32'" Label="Configuration">
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<ConfigurationType>Application</ConfigurationType>
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<UseDebugLibraries>false</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v141_xp</PlatformToolset>
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<WholeProgramOptimization>true</WholeProgramOptimization>
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<CharacterSet>Unicode</CharacterSet>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
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<LinkIncremental>false</LinkIncremental>
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<IntDir>$(Configuration)\$(ProjectName)\</IntDir>
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<GenerateManifest>false</GenerateManifest>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_XP_NoCOD|Win32'">
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<LinkIncremental>false</LinkIncremental>
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<Optimization>Disabled</Optimization>
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<PreprocessorDefinitions>WIN32;_CRT_SECURE_NO_WARNINGS;_DEBUG;_WINDOWS;%(PreprocessorDefinitions);__WX__CRYST__;HAVE_SSE_MATHFUN;USE_SSE2;OBJCRYST_GL;HAVE_FFTW;__FOX_COD__;__DEBUG__</PreprocessorDefinitions>
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<SDLCheck>false</SDLCheck>
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<AdditionalIncludeDirectories>$(SolutionDir)..\;$(SolutionDir)..\cctbx\include;$(SolutionDir)..\ObjCryst;$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\include;$(SolutionDir)..\fftw\api;$(SolutionDir)..\mysql-connector-c-src\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<AdditionalIncludeDirectories>$(SolutionDir)..\;$(SolutionDir)..\cctbx\include;$(SolutionDir)..\ObjCryst;$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\lib\vc_lib\mswu;$(SolutionDir)..\wxWidgets\include;$(SolutionDir)..\fftw\api;$(ProjectDir)\..\boost;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<ObjectFileName>$(IntDir)\%(RelativeDir)</ObjectFileName>
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<RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
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<EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
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<Link>
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<SubSystem>Windows</SubSystem>
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<GenerateDebugInformation>true</GenerateDebugInformation>
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<AdditionalLibraryDirectories>$(SolutionDir)..\wxWidgets\lib\vc_lib;$(SolutionDir)$(Configuration);$(SolutionDir)..\fftw\fftw-3.3-libs\Static-Release;$(SolutionDir)..\mysql-connector-c-src\libmysql\Debug;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
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<AdditionalDependencies>newmat.lib;cctbx.lib;libfftwf-3.3.lib;mysqlclient.lib;%(AdditionalDependencies)</AdditionalDependencies>
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<IgnoreSpecificDefaultLibraries>libboost_date_time-vc100-mt-sgd-1_47.lib;MSVCRT.lib;LIBCMT.lib</IgnoreSpecificDefaultLibraries>
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<AdditionalLibraryDirectories>$(SolutionDir)..\wxWidgets\lib\vc_lib;$(SolutionDir)$(Configuration);$(SolutionDir)..\fftw\fftw-3.3-libs\Static-Release;$(ProjectDir)\..\boost\stage\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
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<AdditionalDependencies>newmat.lib;cctbx.lib;libfftwf-3.3.lib;%(AdditionalDependencies)</AdditionalDependencies>
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<IgnoreSpecificDefaultLibraries>MSVCRT.lib;LIBCMT.lib</IgnoreSpecificDefaultLibraries>
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</Link>
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<ResourceCompile>
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<AdditionalIncludeDirectories>$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<IntrinsicFunctions>true</IntrinsicFunctions>
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<PreprocessorDefinitions>WIN32;_CRT_SECURE_NO_WARNINGS;NDEBUG;_WINDOWS;%(PreprocessorDefinitions);__WX__CRYST__;HAVE_SSE_MATHFUN;USE_SSE2;OBJCRYST_GL;HAVE_FFTW;__FOX_COD__</PreprocessorDefinitions>
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<SDLCheck>false</SDLCheck>
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<AdditionalIncludeDirectories>$(SolutionDir)..\;$(SolutionDir)..\cctbx\include;$(SolutionDir)..\ObjCryst;$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\include;$(SolutionDir)..\fftw\api;$(SolutionDir)..\mysql-connector-c-src\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<AdditionalIncludeDirectories>$(SolutionDir)..\;$(SolutionDir)..\cctbx\include;$(SolutionDir)..\ObjCryst;$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\include;$(SolutionDir)..\fftw\api;$(ProjectDir)\..\boost;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<ObjectFileName>$(IntDir)\%(RelativeDir)</ObjectFileName>
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<RuntimeLibrary>MultiThreaded</RuntimeLibrary>
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<EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
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<FloatingPointModel>Fast</FloatingPointModel>
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<FloatingPointExceptions>
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</FloatingPointExceptions>
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<MultiProcessorCompilation>true</MultiProcessorCompilation>
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<FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
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<EnableParallelCodeGeneration>true</EnableParallelCodeGeneration>
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<InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
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<BufferSecurityCheck>false</BufferSecurityCheck>
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</ClCompile>
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<Link>
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<SubSystem>Windows</SubSystem>
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<GenerateDebugInformation>true</GenerateDebugInformation>
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<GenerateDebugInformation>false</GenerateDebugInformation>
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<EnableCOMDATFolding>true</EnableCOMDATFolding>
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<OptimizeReferences>true</OptimizeReferences>
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<AdditionalLibraryDirectories>$(SolutionDir)..\wxWidgets\lib\vc_lib;$(SolutionDir)$(Configuration);$(SolutionDir)..\fftw\fftw-3.3-libs\Static-Release;$(SolutionDir)..\mysql-connector-c-src\libmysql\Release;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
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<IgnoreSpecificDefaultLibraries>libboost_date_time-vc100-mt-s-1_47.lib;MSVCRT.lib</IgnoreSpecificDefaultLibraries>
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<AdditionalDependencies>newmat.lib;cctbx.lib;libfftwf-3.3.lib;mysqlclient.lib;%(AdditionalDependencies)</AdditionalDependencies>
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<AdditionalLibraryDirectories>$(SolutionDir)..\wxWidgets\lib\vc_lib;$(SolutionDir)$(Configuration);$(SolutionDir)..\fftw\fftw-3.3-libs\Static-Release;$(ProjectDir)\..\boost\stage\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
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<IgnoreSpecificDefaultLibraries>
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</IgnoreSpecificDefaultLibraries>
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<AdditionalDependencies>newmat.lib;cctbx.lib;libfftwf-3.3.lib;%(AdditionalDependencies)</AdditionalDependencies>
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<ShowProgress>LinkVerbose</ShowProgress>
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<LinkTimeCodeGeneration>UseLinkTimeCodeGeneration</LinkTimeCodeGeneration>
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</Link>
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<ResourceCompile>
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<AdditionalIncludeDirectories>$(SolutionDir)..\wxWidgets\include\msvc;$(SolutionDir)..\wxWidgets\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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<ClCompile Include="..\ObjCryst\ObjCryst\ScatteringPowerSphere.cpp" />
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<ClCompile Include="..\ObjCryst\ObjCryst\SpaceGroup.cpp" />
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<ClCompile Include="..\ObjCryst\ObjCryst\test.cpp" />
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<ClCompile Include="..\ObjCryst\ObjCryst\Undo.cpp" />
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<ClCompile Include="..\ObjCryst\ObjCryst\UnitCell.cpp" />
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<ClCompile Include="..\ObjCryst\ObjCryst\ZScatterer.cpp" />
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<ClCompile Include="..\ObjCryst\Quirks\ci_string.cpp" />
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<ClCompile Include="src\FoxClient.cpp" />
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<ClCompile Include="src\FoxJob.cpp" />
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<ClCompile Include="src\FoxServer.cpp" />
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<ClCompile Include="src\FoxServerThread.cpp" />
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<ClCompile Include="src\GridResult.cpp" />
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<ClCompile Include="src\IOSocket.cpp" />
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<ClCompile Include="src\WXFoxClient.cpp" />

‎Fox/Fox_vc12.vcxproj.filters

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<ClCompile Include="src\FoxServer.cpp">
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<Filter>Source Files\Fox</Filter>
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</ClCompile>
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<ClCompile Include="src\FoxServerThread.cpp">
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<Filter>Source Files\Fox</Filter>
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</ClCompile>
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<ClCompile Include="src\GridResult.cpp">
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<Filter>Source Files\Fox</Filter>
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</ClCompile>
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<ClCompile Include="src\WXGridWindow.cpp">
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<Filter>Source Files\Fox</Filter>
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</ClCompile>
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<ClCompile Include="..\ObjCryst\ObjCryst\Undo.cpp">
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<Filter>Source Files\ObjCryst</Filter>
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</ClCompile>
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</ItemGroup>
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<ItemGroup>
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<None Include="src\Fox.icns">

‎Fox/cctbx_vc12.vcxproj

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<?xml version="1.0" encoding="utf-8"?>
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<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<Project DefaultTargets="Build" ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<ItemGroup Label="ProjectConfigurations">
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<ProjectConfiguration Include="Debug|Win32">
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<Configuration>Debug</Configuration>
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<ProjectGuid>{BA6FA16F-837D-4869-90B9-44ACCD4EC001}</ProjectGuid>
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<RootNamespace>cctbx</RootNamespace>
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<ProjectName>cctbx</ProjectName>
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<WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
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</PropertyGroup>
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<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
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<ConfigurationType>StaticLibrary</ConfigurationType>
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<UseDebugLibraries>true</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v142</PlatformToolset>
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<CharacterSet>MultiByte</CharacterSet>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
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<ConfigurationType>StaticLibrary</ConfigurationType>
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<UseDebugLibraries>false</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v142</PlatformToolset>
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<WholeProgramOptimization>true</WholeProgramOptimization>
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<CharacterSet>MultiByte</CharacterSet>
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</PropertyGroup>
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<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_XP_NoCOD|Win32'" Label="Configuration">
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<ConfigurationType>StaticLibrary</ConfigurationType>
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<UseDebugLibraries>false</UseDebugLibraries>
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<PlatformToolset>v120_xp</PlatformToolset>
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<PlatformToolset>v141_xp</PlatformToolset>
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<WholeProgramOptimization>true</WholeProgramOptimization>
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<CharacterSet>MultiByte</CharacterSet>
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</PropertyGroup>
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<WarningLevel>Level3</WarningLevel>
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<Optimization>Disabled</Optimization>
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<SDLCheck>false</SDLCheck>
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<AdditionalIncludeDirectories>$(ProjectDir)\..\cctbx\include</AdditionalIncludeDirectories>
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<AdditionalIncludeDirectories>$(ProjectDir)\..\boost;$(ProjectDir)\..\cctbx\include</AdditionalIncludeDirectories>
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<PreprocessorDefinitions>_CRT_SECURE_NO_WARNINGS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
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<RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
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<MultiProcessorCompilation>true</MultiProcessorCompilation>
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<FunctionLevelLinking>true</FunctionLevelLinking>
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<IntrinsicFunctions>true</IntrinsicFunctions>
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<SDLCheck>false</SDLCheck>
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<AdditionalIncludeDirectories>$(ProjectDir)\..\cctbx\include</AdditionalIncludeDirectories>
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<AdditionalIncludeDirectories>$(ProjectDir)\..\boost;$(ProjectDir)\..\cctbx\include</AdditionalIncludeDirectories>
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<PreprocessorDefinitions>_CRT_SECURE_NO_WARNINGS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
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<RuntimeLibrary>MultiThreaded</RuntimeLibrary>
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<MultiProcessorCompilation>true</MultiProcessorCompilation>

‎Fox/gnu.mak

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clean: tidy
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$(MAKE) -f gnu.mak -C src clean
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$(MAKE) -f gnu.mak -C $(BUILD_DIR)/ObjCryst clean
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${RM} -Rf ${BUILD_DIR}/static-libs/* ${BUILD_DIR}/fftw-3.3.4 ${BUILD_DIR}/newmat ${BUILD_DIR}/wxWidgets-3.0.2
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${RM} -Rf ${BUILD_DIR}/static-libs/*
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tidy:
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$(MAKE) -f gnu.mak -C src tidy
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$(MAKE) -f gnu.mak -C ${BUILD_DIR}/ObjCryst tidy
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${RM} -Rf ${BUILD_DIR}/fftw-3.3.4 ${BUILD_DIR}/newmat ${BUILD_DIR}/wxWidgets-3.0.2
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${RM} -Rf ${BUILD_DIR}/fftw-3.3.4 ${BUILD_DIR}/newmat ${BUILD_DIR}/wxWidgets-3.1.4
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#install Fox in /usr/local/bin
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‎Fox/macosx.mak

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libfftw: ../static-libs/lib/libfftw3f.a
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# MySQL
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../mysql-5.6.24.tar.gz:
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cd .. && $(DOWNLOAD_COMMAND) http://dev.mysql.com/get/Downloads/MySQL-5.6/mysql-5.6.24.tar.gz
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#:TODO: find a way to only compile the static version of libmysqlclient ?
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../static-libs/lib/libmysqlclient.a: ../mysql-5.6.24.tar.gz
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cd .. && tar -xzf mysql-5.6.24.tar.gz
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cd ../mysql-5.6.24 && MACOSX_DEPLOYMENT_TARGET=10.5 cmake -DCMAKE_INSTALL_PREFIX=$(PWD)/../static-libs && MACOSX_DEPLOYMENT_TARGET=10.5 $(MAKE) -j4 install
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rm -f $(PWD)/../static-libs/lib/libmysql*.dylib
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rm -Rf ../mysql-5.6.24
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../wxWidgets-3.1.4.tar.bz2:
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cd .. && $(DOWNLOAD_COMMAND) https://github.com/wxWidgets/wxWidgets/releases/download/v3.1.4/wxWidgets-3.1.4.tar.bz2
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libmysql: ../static-libs/lib/libmysqlclient.a
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../wxWidgets-3.0.2.tar.bz2:
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cd .. && curl -O ftp://ftp.wxwidgets.org/pub/3.0.2/wxWidgets-3.0.2.tar.bz2
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../static-libs/bin/wx-config: ../wxWidgets-3.0.2.tar.bz2
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cd .. && tar -xjf wxWidgets-3.0.2.tar.bz2
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cd ../wxWidgets-3.0.2 && ./configure --with-opengl --disable-webviewwebkit --enable-optimise --disable-shared --enable-monolithic --prefix=$(PWD)/../static-libs && make -j4 install
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rm -Rf ../wxWidgets-3.0.2
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../static-libs/bin/wx-config: ../wxWidgets-3.1.4.tar.bz2
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cd .. && tar -xjf wxWidgets-3.1.4.tar.bz2
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cd ../wxWidgets-3.1.4 && ./configure --with-opengl --disable-debug --disable-webviewwebkit --enable-optimise --disable-shared --enable-monolithic --disable-mediactrl --without-libtiff --enable-cxx11 --prefix=$(PWD)/../static-libs && make -j4 install
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rm -Rf ../wxWidgets-3.1.4
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libwx: ../static-libs/bin/wx-config
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default: Fox
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Fox: libfftw libwx ../cctbx ../newmat libmysql
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Fox: libfftw libwx ../cctbx ../newmat
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xcodebuild -project Fox.xcodeproj -target Fox -configuration Deployment
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Fox-nogui: ../cctbx ../newmat

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