Merge pull request #87 from Illumina/update-external-github-repo

Improve regression testing, fixed source version and updated build script
Illumina · Sep 28, 2016 · 7b3926c · 7b3926c
2 parents fe3f798 + 488f529
commit 7b3926c
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Showing 229 changed files with 2,222 additions and 2,053 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,7 @@ packages.config
 interop/version.h
 .idea
 src/ext/csharp/src
+.CMakeLists.txt.bak
 
 # Mac OSX Stuff
 .DS_Store

diff --git a/.travis.yml b/.travis.yml
@@ -165,7 +165,8 @@ branches:
 notifications:
   email: false
 before_deploy:
-- tar czf interop-${BUILD_NAME}.tar.gz ${BUILD_PATH}
+- cd `dirname ${BUILD_PATH}`
+- tar czf interop-${BUILD_NAME}.tar.gz ${BUILD_NAME}
 deploy:
   skip_cleanup: true
   provider: releases

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,6 +4,12 @@ set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
 enable_testing()
 include(${PROJECT_SOURCE_DIR}/cmake/Modules/UseGitVersion.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/InternalUtils.cmake)
+set(ARCHIVE_VERSION "v1.0.11-14-g824273c")
+
+if (NOT CMAKE_BUILD_TYPE)
+    message(STATUS "No build type selected, default to Release")
+    set(CMAKE_BUILD_TYPE "Release")
+endif()
 
 interop_config_compiler_and_linker()
 # TODO: https://help.github.com/articles/creating-project-pages-manually/
@@ -17,16 +23,16 @@ set(INTEROP_DL_LIB interop_fpic_lib)
 option(ENABLE_BACKWARDS_COMPATIBILITY "Compile code for c++98" ON)
 option(ENABLE_DOCS "Build documentation with Doxygen" ON)
 option(ENABLE_SWIG "Build third-party language bindings, e.g. C#" ON)
-option(ENABLE_CSHARP "Build C# language bindings" ON)
 option(ENABLE_TEST "Build unit tests (depends on Boost)" ON)
 option(ENABLE_APPS "Build command line programs" ON)
 option(ENABLE_EXAMPLES "Build example programs" ON)
 option(ENABLE_STATIC "Build static libraries instead of dynamic" ON)
 option(FORCE_X86 "Force 32-bit libraries instead of platform default (Does nothing for Visual Studio)" OFF)
 option(FORCE_SHARED_CRT "Used the shared (DLL) run time lib" ON)
+option(ENABLE_CSHARP "Build C# language bindings" ON)
 
 include_directories(.)
-add_version_target(version ${CMAKE_SOURCE_DIR}/interop/version.h INTEROP_VERSION)
+add_version_target(version ${CMAKE_SOURCE_DIR}/interop/version.h INTEROP_VERSION ${ARCHIVE_VERSION})
 
 if(INTEROP_VERSION)
     string(REGEX REPLACE "[^v]*(v.*)" "\\1" VERSION ${INTEROP_VERSION})
@@ -50,18 +56,12 @@ if(INTEROP_VERSION)
     set(CPACK_PACKAGE_VERSION_MINOR "${VERSION_MINOR}")
     set(CPACK_PACKAGE_VERSION_PATCH "${VERSION_PATCH}")
     set(CPACK_PACKAGE_INSTALL_DIRECTORY "interop_${VERSION_SHORT}")
-    set(CPACK_OUTPUT_FILE_PREFIX "interop/${VERSION_SHORT}")
+    set(CPACK_OUTPUT_FILE_PREFIX "interop/${VERSION}")
 endif()
 
 #Adds the target "package"
 include(CPack)
 
-if(ENABLE_BACKWARDS_COMPATIBILITY)
-    message(STATUS "Using C++11: No")
-else()
-    message(STATUS "Using C++11: Yes")
-endif()
-
 if(ENABLE_STATIC)
     set(LIBRARY_TYPE STATIC)
 else()
@@ -81,9 +81,9 @@ install(FILES README.md docs/src/changes.md DESTINATION .)
 
 find_package(Git)
 if(GIT_FOUND)
-    string(REGEX REPLACE "[^v]*(v[0-9]+.[0-9]+.[0-9])-.*" "\\1" TAG ${INTEROP_VERSION})
+    string(REGEX REPLACE "[^v]*(v[0-9]+.[0-9]+.[0-9]+)-.*" "\\1" TAG ${INTEROP_VERSION})
     add_custom_target(history
-        COMMAND ${GIT_EXECUTABLE};log;${TAG}..HEAD;-m;--first-parent;--date=short;--format='%ad | %b'
+        COMMAND ${GIT_EXECUTABLE};--no-pager;log;${TAG}..HEAD;--date=short;--format='%ad | %B'
         COMMENT "List all commits from last tag - ${TAG}"
         WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
 endif()
diff --git a/cmake/InternalUtils.cmake b/cmake/InternalUtils.cmake
@@ -81,7 +81,8 @@ macro(interop_config_compiler_and_linker)
         set(CXX11_FLAG_ "-std=c++11")
     endif()
 
-    check_cxx_compiler_flag("-std=c89" COMPILER_SUPPORTS_ANSI)
+    set(ANSI_FLAG "-std=c++98")
+    check_cxx_compiler_flag("${ANSI_FLAG}" COMPILER_SUPPORTS_ANSI) #-ansi (does not work on CLang 3.4)
     check_cxx_compiler_flag("${CXX11_FLAG_}" COMPILER_SUPPORTS_CXX11)
     if(COMPILER_SUPPORTS_CXX11)
         set(CXX_CX11_FLAG "${CXX11_FLAG_}")
@@ -104,36 +105,60 @@ macro(interop_config_compiler_and_linker)
             message(FATAL_ERROR "Unsupported compiler")
         endif()
     endif()
-    if(COMPILER_IS_GNUCC_OR_CLANG)
-        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -Wno-c++0x-compat -Wno-error=c++0x-compat -Wextra")
-        if(WIN32 AND MINGW)
-            # Add big object support to Windows Compilers
-            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wa,-mbig-obj")
+
+    set(ENABLE_BIG_OBJ_FLAG "")
+    if(MSVC)
+        set(ENABLE_BIG_OBJ_FLAG "/bigobj")
+    elseif(MINGW)
+        set(ENABLE_BIG_OBJ_FLAG "-Wa,-mbig-obj")
+    endif()
+
+    set(flags_to_check "-Wno-eof-newline;-Wno-maybe-uninitialized;-Wno-strict-aliasing;-Wno-unused-function;-Wno-unused-parameter;-Wno-unnamed-type-template-args;-Wno-c++0x-compat;-Wno-error=c++0x-compat")
+    foreach(flag ${flags_to_check})
+        string(TOUPPER ${flag} FLAG_NAME)
+        string(REPLACE "-" "_" FLAG_NAME ${FLAG_NAME})
+        string(REPLACE "=" "_EQ_" FLAG_NAME ${FLAG_NAME})
+        string(REPLACE "C++" "CPP" FLAG_NAME ${FLAG_NAME})
+        set(${FLAG_NAME} ${flag})
+        check_cxx_compiler_flag(${flag} IS_${FLAG_NAME}_SUPPORTED)
+        if(NOT IS_${FLAG_NAME}_SUPPORTED)
+            set(${FLAG_NAME} "")
         endif()
+    endforeach()
+
+    if(COMPILER_IS_GNUCC_OR_CLANG)
+        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror ${_WNO_CPP0X_COMPAT} ${_WNO_ERROR_EQ_CPP0X_COMPAT} ${_WNO_EOF_NEWLINE}")
     elseif(MSVC)
         # Visual Studio Complains about not being able to create an assignment operator and copy constructor
         # -wd4511 and -wd4512 disable these pointless warnings
         # Add big object support to Windows Compilers
-        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX -wd4511 -wd4512 /bigobj")
+        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX -wd4511 -wd4512")
+        add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_SCL_SECURE_NO_WARNINGS)
     elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
         if(WIN32)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX")
         else()
-            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -Wno-c++0x-compat -Wno-error=c++0x-compat -Wextra")
+            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror ${_WNO_CPP0X_COMPAT} ${_WNO_ERROR_EQ_CPP0X_COMPAT}")
         endif()
     endif()
     if(NOT ENABLE_BACKWARDS_COMPATIBILITY)
         if(COMPILER_IS_GNUCC_OR_CLANG)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_CX11_FLAG}")
+            message(STATUS "Using C++11: Yes")
+        elseif(MSVC)
+            message(STATUS "Using C++11: Yes")
+        else()
+            message(STATUS "Using C++11: Compiler default")
         endif()
     elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
-        #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-local-typedef -Wno-unnamed-type-template-args")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_CX11_FLAG}")
+        message(STATUS "Using C++11: Yes")
     elseif(MINGW)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_CX11_FLAG}")
-        message(WARNING "ENABLE_BACKWARDS_COMPATIBILITY=ON does not work with MinGW, ignoring")
+        message(STATUS "Using C++11: Yes")
     elseif(COMPILER_SUPPORTS_ANSI)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c89")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ANSI_FLAG}")
+        message(STATUS "Using C++11: No")
     endif()
 endmacro()
 
diff --git a/cmake/Modules/UseCSharp.cmake b/cmake/Modules/UseCSharp.cmake
@@ -34,8 +34,10 @@ endif( NOT CSHARP_COMPILER )
 # Include type-based USE_FILE
 if( CSHARP_TYPE MATCHES ".NET" )
   include( ${DotNetFrameworkSdk_USE_FILE} )
+  set(CSHARP_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
 elseif ( CSHARP_TYPE MATCHES "Mono" )
   include( ${Mono_USE_FILE} )
+  set(CSHARP_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_BUILD_TYPE})
 endif ( CSHARP_TYPE MATCHES ".NET" )
 
 macro( CSHARP_ADD_LIBRARY name )
@@ -91,16 +93,14 @@ macro( CSHARP_ADD_PROJECT type name )
   #  MESSAGE( SEND_ERROR "No C# sources were specified for ${type} ${name}" )
   #endif ()
   #list( SORT sources_dep )
-
-  set(CSHARP_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
-
+  file(MAKE_DIRECTORY ${CSHARP_OUTPUT_DIR})
   string (REPLACE ";" "," source_list "${sources}")
   set(CSHARP_${name}_BINARY ${CSHARP_OUTPUT_DIR}/${name}.${output})
   set(CSHARP_${name}_BINARY_NAME ${name}.${output})
   # Add custom target and command
   MESSAGE( STATUS "Adding C# ${type} ${name}: '${CSHARP_COMPILER} /t:${type} /out:${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'" )
   add_custom_command(
-    COMMENT "Compiling C# ${type} ${name}: '${CSHARP_COMPILER} /unsafe /t:${type} /out:${CMAKE_CURRENT_BINARY_DIR}/${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'"
+    COMMENT "Compiling C# ${type} ${name}: '${CSHARP_COMPILER} /unsafe /t:${type} /out:${CSHARP_OUTPUT_DIR}/${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'"
     OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${name}.${output}
     COMMAND ${CMAKE_COMMAND} -DFILES_TO_COPY="${source_list}" -DDESTINATION_DIR="${CMAKE_CURRENT_BINARY_DIR}" -P "${CMAKE_SOURCE_DIR}/cmake/CopyListOfFiles.cmake"
     COMMAND ${CSHARP_COMPILER}

diff --git a/cmake/Modules/UseGitVersion.cmake b/cmake/Modules/UseGitVersion.cmake
@@ -8,7 +8,7 @@
 #   - _macro_name - name of the macro in the header file
 #
 
-function(add_version_target _target _version_file _macro_name)
+function(add_version_target _target _version_file _macro_name _default)
     if(NOT GIT_FOUND)
         find_package(Git REQUIRED)
     endif()
@@ -25,15 +25,18 @@ function(add_version_target _target _version_file _macro_name)
         OUTPUT_STRIP_TRAILING_WHITESPACE
     )
     if(NOT res EQUAL 0)
-        set(VERSION \"Unknown\")
+        set(VERSION \"\${BKUP}\")
     endif()
     configure_file(\${SRC} \${DST} @ONLY)
     "
     )
+    add_custom_command(OUTPUT ${_version_file}
+            COMMAND ${CMAKE_COMMAND} -D SRC=${CMAKE_BINARY_DIR}/${version_base}.in
+            -D DST=${_version_file}
+            -D BKUP=${_default}
+            -P ${CMAKE_BINARY_DIR}/version.cmake)
     add_custom_target(${_target}
-        ${CMAKE_COMMAND} -D SRC=${CMAKE_BINARY_DIR}/${version_base}.in
-                         -D DST=${_version_file}
-                         -P ${CMAKE_BINARY_DIR}/version.cmake
+        DEPENDS ${_version_file}
     )
     execute_process(
             COMMAND ${GIT_EXECUTABLE} describe --tags --dirty=-dirty
@@ -45,7 +48,7 @@ function(add_version_target _target _version_file _macro_name)
             OUTPUT_STRIP_TRAILING_WHITESPACE
     )
     if(NOT res EQUAL 0)
-        set(VERSION \"Unknown\")
+        set(VERSION "${_default}")
     endif()
     set(${_macro_name} ${VERSION} PARENT_SCOPE)
 endfunction()
diff --git a/cmake/package.nuspec.in b/cmake/package.nuspec.in
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="utf-8"?>
+<package xmlns="http://schemas.microsoft.com/packaging/2013/01/nuspec.xsd">
+    <metadata minClientVersion="2.5">
+        <id>illumina_interop_@CSHARP_TYPE@_@PLATFORM@</id>
+        <version>@INTEROP_VERSION@</version>
+        <title>Illumina InterOp Library for @CSHARP_TYPE@ on @PLATFORM@</title>
+        <authors>Illumina Inc.</authors>
+        <owners>Illumina Inc.</owners>
+        <licenseUrl>https://github.com/Illumina/interop/blob/master/LICENSE</licenseUrl>
+        <projectUrl>https://github.com/Illumina/interop</projectUrl>
+        <requireLicenseAcceptance>true</requireLicenseAcceptance>
+        <developmentDependency>false</developmentDependency>
+        <description>
+        The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files
+        produced by Illumina sequencers. These libraries are backwards compatible and capable of supporting prior
+        releases of the software, with one exception: GA systems have been excluded.
+        </description>
+        <summary>
+        High-level C++ binding for Illumina C++ InterOp Library, packaged for
+        @CSHARP_TYPE@ @CSHARP_VERSION@ on @PLATFORM@
+        </summary>
+        <releaseNotes>https://github.com/Illumina/interop/blob/master/README.md</releaseNotes>
+        <copyright>GNU GPL v3</copyright>
+        <tags>native, Illumina, InterOp, C++, C#, @PLATFORM@, @CSHARP_TYPE@ </tags>
+    </metadata>
+    <files>
+        @NUGET_FILE_LIST@
+    </files>
+</package>
+
diff --git a/cmake/package.targets b/cmake/package.targets
@@ -0,0 +1,9 @@
+<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <ItemGroup>
+    <NativeLibs Include="$(MSBuildThisFileDirectory)**\*.dll" />
+    <None Include="@(NativeLibs)">
+      <Link>%(RecursiveDir)%(FileName)%(Extension)</Link>
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
+  </ItemGroup>
+</Project>
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -159,7 +159,7 @@ STRIP_FROM_PATH        =
 # header file to include in order to use a class. If left blank only the name of
 # the header file containing the class definition is used. Otherwise one should
 # specify the list of include paths that are normally passed to the compiler
-# using the -I flag.
+# using the -I test_modifier.
 
 STRIP_FROM_INC_PATH    =
 
@@ -444,15 +444,15 @@ EXTRACT_STATIC         = NO
 
 EXTRACT_LOCAL_CLASSES  = YES
 
-# This flag is only useful for Objective-C code. If set to YES, local methods,
+# This test_modifier is only useful for Objective-C code. If set to YES, local methods,
 # which are defined in the implementation section but not in the interface are
 # included in the documentation. If set to NO, only methods in the interface are
 # included.
 # The default value is: NO.
 
 EXTRACT_LOCAL_METHODS  = NO
 
-# If this flag is set to YES, the members of anonymous namespaces will be
+# If this test_modifier is set to YES, the members of anonymous namespaces will be
 # extracted and appear in the documentation as a namespace called
 # 'anonymous_namespace{file}', where file will be replaced with the base name of
 # the file that contains the anonymous namespace. By default anonymous namespace
@@ -720,7 +720,7 @@ WARNINGS               = YES
 #WARN_AS_ERROR = YES
 
 # If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
-# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this test_modifier
 # will automatically be disabled.
 # The default value is: YES.
 
@@ -1269,7 +1269,7 @@ CHM_FILE               =
 
 HHC_LOCATION           =
 
-# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# The GENERATE_CHI test_modifier controls if a separate .chi index file is generated
 # (YES) or that it should be included in the master .chm file (NO).
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTMLHELP is set to YES.
@@ -1282,15 +1282,15 @@ GENERATE_CHI           = NO
 
 CHM_INDEX_ENCODING     =
 
-# The BINARY_TOC flag controls whether a binary table of contents is generated
+# The BINARY_TOC test_modifier controls whether a binary table of contents is generated
 # (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
 # enables the Previous and Next buttons.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 BINARY_TOC             = NO
 
-# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# The TOC_EXPAND test_modifier can be set to YES to add extra items for group members to
 # the table of contents of the HTML help documentation and to the tree view.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTMLHELP is set to YES.

diff --git a/docs/src/changes.md b/docs/src/changes.md
@@ -1,5 +1,20 @@
 # Changes                                               {#changes}
 
+## v1.0.12
+
+Date       | Description
+---------- | -----------
+2016-09-26 | IPA-5210: Create CSV parsable summary output
+2016-09-23 | IPA-5194: Create nuspec package file
+2016-09-17 | Refactor individual metric unit tests
+2016-09-17 | Refactor metric stream tests
+2016-09-14 | Reorganized code into own stat util file
+2016-09-14 | Fixes error rate at a specific cycle when tiles are at different cycles
+2016-09-14 | Add version information for zip archives
+2016-09-14 | IPA-5070: Add optional flag to skip median for summary
+2016-09-13 | Ensure ANSI build is being tested
+
+
 ## v1.0.11
 
 Date       | Description

diff --git a/docs/src/contribute.md b/docs/src/contribute.md
@@ -66,3 +66,16 @@ git log v1.0.0..HEAD --oneline --decorate --no-merges
 
 In the above example, v1.0.0 was the last tag, you should replace this value with the actual last tag.
 
+## Linking to our git hooks
+
+Windows: 
+
+~~~~~~~~~{.bat}
+mklink .git\hooks\pre-commit <abs-path>\tools\hooks\pre-commit.sh
+~~~~~~~~~
+
+Linux:
+
+~~~~~~~~~{.sh}
+ln -s tools/hooks/pre-commit.sh .git/hooks/pre-commit
+~~~~~~~~~
diff --git a/docs/src/example_sav_analysis.md b/docs/src/example_sav_analysis.md
@@ -18,7 +18,7 @@ Each plot command has an additional set of options that allow the user
 to choose a specific metric to plot or how to filter the data. For
 example, the user can choose to only plot data from lane 1 by specifiying
 the option `--filter-by-lane=1`.  A full list of options for each program
-can be obtained with the `--help` flag.
+can be obtained with the `--help` test_modifier.
 
 ## SAV Analysis Tab
 

diff --git a/docs/src/install.md b/docs/src/install.md
@@ -121,7 +121,7 @@ cmake --help
 ~~~~~~~~~~~~~
 
 The default CMake generator for Windows is 32-bit.  This can be changed by specifying the appropriate generator 
-using the `-G` flag:
+using the `-G` test_modifier:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{.sh}
 cmake ../interop -G “Visual Studio 12 2013 Win64”

diff --git a/interop/constants/enums.h b/interop/constants/enums.h
@@ -343,3 +343,4 @@ namespace illumina { namespace interop { namespace constants
 #undef INTEROP_TUPLE3
 #undef INTEROP_TUPLE4
 
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -343,3 +343,4 @@ namespace illumina { namespace interop { namespace constants
		#undef INTEROP_TUPLE3
		#undef INTEROP_TUPLE4