Support py37 public GitHub (#180)

Support packaging Python 3.7 wheels

CMakeLists.txt

@@ -171,12 +171,25 @@ find_package(Git)
 if(GIT_FOUND)
     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'"
-        COMMENT "List all commits from last tag - ${TAG}"
+        COMMAND ${GIT_EXECUTABLE} log ${TAG}..HEAD -m --first-parent --date=short --format='%ad | %s'
+        COMMENT "${GIT_EXECUTABLE} log ${TAG}..HEAD -m --first-parent --date=short --format=%ad | %s"
         WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
 endif()
 
 set_target_properties(bundle PROPERTIES EXCLUDE_FROM_ALL 1 EXCLUDE_FROM_DEFAULT_BUILD 1)
 
 configure_file(interop/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/include/interop/config.h @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/interop/config.h DESTINATION include/interop)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/interop/config.h DESTINATION include/interop)
+
+
+message(STATUS "Supported Languages")
+message(STATUS "    C++") # Version
+if(PYTHON_BUILD_AVAILABLE)
+    message(STATUS "    ${PYTHON_BUILD_AVAILABLE}")
+endif()
+if(CSHARP_BUILD_AVAILABLE)
+    message(STATUS "    ${CSHARP_BUILD_AVAILABLE}")
+endif()
+if(JAVA_BUILD_AVAILABLE)
+    message(STATUS "    ${JAVA_BUILD_AVAILABLE}")
+endif()

appveyor.yml

@@ -93,7 +93,7 @@ environment:
       PACKAGE_TARGET: package_wheel
       ADDIONAL_CONFIG_OPTIONS: -DENABLE_APPS=OFF -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=OFF
       PYTHON_PATH_DIR: C:\Miniconda36-x64
-      PYTHON_VERSION: 3.5
+      PYTHON_VERSION: 3.7
       configuration: Release
 
 matrix:
@@ -157,7 +157,6 @@ deploy:
     configuration: Release
     config_type: win64
 
-
 ########################################################################################################################
 #
 # These settings allow one to Remote Desktop into the VM and check what went wrong:

cmake/InternalUtils.cmake

@@ -68,6 +68,8 @@ macro(interop_config_compiler_and_linker)
 
     if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang" OR CMAKE_COMPILER_IS_GNUCC OR "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
         set(COMPILER_IS_GNUCC_OR_CLANG ON)
+    elseif(NOT WIN32 AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+        set(COMPILER_IS_GNUCC_OR_CLANG ON)
     else()
         set(COMPILER_IS_GNUCC_OR_CLANG OFF)
     endif()

cmake/Modules/FindCSBuild.cmake

@@ -68,13 +68,15 @@ if(DOTNET_FOUND)
     message(STATUS "Found .NET: ${DOTNET_EXECUTABLE_VERSION}")
     set(CSHARP_INTERPRETER "")
     set(CSHARP_TYPE "net${_version}")
+    set(CSHARP_BUILDER_VERSION ".NET ${DOTNET_EXECUTABLE_VERSION} - net${_version}")
 elseif(MONO_FOUND)
     message(STATUS "Found Mono: ${MONO_VERSION}")
     set(CSBUILD_EXECUTABLE "${XBUILD_EXECUTABLE}")
     set(CSBUILD_CSPROJ "msbuild.csproj")
     set(CSBUILD_OUPUT_PREFIX "")
     set(CSHARP_INTERPRETER "${MONO_EXECUTABLE}")
     set(CSHARP_TYPE "net${_version}")
+    set(CSHARP_BUILDER_VERSION "Mono ${MONO_VERSION} - net${_version}")
 elseif(DOTNET_CORE_FOUND)
     message(STATUS "Found .NET Core: ${DOTNET_CORE_VERSION}")
     set(CSBUILD_EXECUTABLE "${DOTNET_CORE_EXECUTABLE}")
@@ -84,6 +86,7 @@ elseif(DOTNET_CORE_FOUND)
     set(CSHARP_INTERPRETER "${DOTNET_CORE_EXECUTABLE}")
     set(CSBUILD_RESTORE_FLAGS "restore")
     set(CSHARP_TYPE "${CSHARP_TARGET_FRAMEWORK}")
+    set(CSHARP_BUILDER_VERSION ".NET Standard ${DOTNET_CORE_VERSION} - ${CSHARP_TARGET_FRAMEWORK}")
 else()
     set(CSBUILD_FOUND FALSE)
 endif()

docs/src/changes.md

@@ -1,9 +1,10 @@
 # Changes                                               {#changes}
 
-## v1.1.5 (Master)
+## v1.1.5
 
 Date       | Description
 ---------- | -----------
+2018-07-22 | Add Python 3.7 support
 2018-06-28 | Future proof throw specification
 2018-06-27 | Fix bug in example example_populate_qmetricset.pp
 2018-05-07 | Fix C++ Linking bug with inconsistent macros

src/ext/csharp/CMakeLists.txt

@@ -216,4 +216,6 @@ if(NUGET_EXE)
 
 else()
     message(STATUS "NuGet not found, nupack target will not be available")
-endif()
+endif()
+
+set(CSHARP_BUILD_AVAILABLE ${CSHARP_BUILDER_VERSION} CACHE INTERNAL "All dependencies are satisfied for the C# Build" FORCE)

src/ext/python/CMakeLists.txt

@@ -153,6 +153,8 @@ endif()
 
 if(NOT PYTHON_WHEEL_PREFIX)
     set(PYTHON_WHEEL_PREFIX "${PACKAGE_OUTPUT_FILE_PREFIX}")
+else()
+    get_filename_component(PYTHON_WHEEL_PREFIX ${PYTHON_WHEEL_PREFIX} ABSOLUTE)
 endif()
 add_custom_target(package_wheel
         COMMENT "Creating Python wheel package in ${PYTHON_WHEEL_PREFIX}"
@@ -164,4 +166,5 @@ if(NOT SKIP_PACKAGE_ALL_WHEEL)
     add_dependencies(bundle package_wheel)
 endif()
 
-set(PYTHON_TARGET_FOUND ON CACHE INTERNAL "Python target is available" FORCE)
+
+set(PYTHON_BUILD_AVAILABLE "Python ${PYTHON_VERSION_STRING}" CACHE INTERNAL "All dependencies are satisfied for the Java Build" FORCE)

src/tests/python/CMakeLists.txt

@@ -9,7 +9,7 @@ if(swig_major_ver LESS "3")
 endif()
 
 find_package(PythonInterp)
-if(NOT PYTHON_TARGET_FOUND)
+if(NOT PYTHON_BUILD_AVAILABLE)
     return()
 endif()
 

tools/docker/DockerFile_Centos5

@@ -1,4 +1,4 @@
-# docker build --rm -t ezralanglois/interop -f ./tools/DockerFile tools
+# sudo docker build --rm -t docker-bioinformatics.dockerhub.illumina.com/interop_centos5 -f ./tools/docker/DockerFile_Centos6 tools
 
 FROM quay.io/pypa/manylinux1_x86_64
 

tools/package.sh

@@ -45,6 +45,15 @@ elif [ ! -z $SOURCE_PATH ]; then
     ARTIFACT_PATH=$SOURCE_PATH/dist
 fi
 
+# ARTIFACT_PATH="$(echo $(cd $(dirname "$ARTIFACT_PATH") && pwd -P)/$(basename "$ARTIFACT_PATH"))"
+
+if hash greadlink  2> /dev/null; then
+    readlink="greadlink"
+else
+    readlink="readlink"
+fi
+ARTIFACT_PATH=`$readlink -f $ARTIFACT_PATH`
+
 if [ ! -z $3 ] ; then
     BUILD_SERVER=$3
     DISABLE_SUBDIR=OFF
@@ -105,6 +114,8 @@ else
     mkdir $ARTIFACT_PATH
 fi
 
+
+
 if [ "$PYTHON_VERSION" == "None" ] ; then
     PYTHON_VERSION=
 fi
@@ -132,7 +143,7 @@ fi
 
 if [ "$PYTHON_VERSION" != "" ] ; then
     if [ "$PYTHON_VERSION" == "ALL" ] ; then
-        python_versions="2.7.11 3.4.4 3.5.1 3.6.0"
+        python_versions="2.7.11 3.4.4 3.5.1 3.6.0 3.7.0"
     else
         python_versions="$PYTHON_VERSION"
     fi
@@ -158,14 +169,15 @@ if [ "$PYTHON_VERSION" != "" ] ; then
             pip install numpy
             pip install wheel
         fi
-        run "Configure $py_ver" cmake $SOURCE_PATH -B${BUILD_PATH} ${CMAKE_EXTRA_FLAGS} -DENABLE_PYTHON_DYNAMIC_LOAD=ON -DPYTHON_EXECUTABLE=`which python` -DPYTHON_WHEEL_PREFIX=${ARTIFACT_PATH}/tmp
+        run "Configure $py_ver" cmake $SOURCE_PATH -B${BUILD_PATH} ${CMAKE_EXTRA_FLAGS} -DENABLE_PYTHON_DYNAMIC_LOAD=ON -DPYTHON_EXECUTABLE=`which python` -DSKIP_PACKAGE_ALL_WHEEL=ON -DPYTHON_WHEEL_PREFIX=${ARTIFACT_PATH}/tmp
         run "Build $py_ver" cmake --build $BUILD_PATH -- -j${THREAD_COUNT}
         run "Test $py_ver" cmake --build $BUILD_PATH --target check_python -- -j${THREAD_COUNT}
         run "Build Wheel $py_ver" cmake --build $BUILD_PATH --target package_wheel -- -j${THREAD_COUNT}
 
         if hash delocate-wheel 2> /dev/null; then
+            ls ${ARTIFACT_PATH}/tmp/*.whl
             delocate-listdeps ${ARTIFACT_PATH}/tmp/*.whl
-            delocate-wheel $ARTIFACT_PATH/tmp/*.whl
+            delocate-wheel ${ARTIFACT_PATH}/tmp/*.whl
             delocate-addplat -c --rm-orig -x 10_9 -x 10_10 $ARTIFACT_PATH/tmp/*.whl -w $ARTIFACT_PATH
         elif hash auditwheel 2> /dev/null; then
             auditwheel --version

tools/package_docker.sh

@@ -24,8 +24,8 @@ fi
 sudo systemctl status docker || sudo systemctl start docker || true
 
 docker ps 1>/dev/null 2>&1 || prefix=sudo;
-#${prefix} docker rmi $(docker images --filter "dangling=true") >/dev/null 2>&1 || true
-${prefix} docker rmi $(docker images) >/dev/null 2>&1 || true
-${prefix} docker rm $(docker ps -a) >/dev/null 2>&1 || true
+#${prefix} docker rmi $(${prefix} docker images --filter "dangling=true") >/dev/null 2>&1 || true
+${prefix} docker rmi $(${prefix} docker images) >/dev/null 2>&1 || true
+${prefix} docker system prune -f >/dev/null 2>&1 || true
 ${prefix} docker pull $image
 ${prefix} docker run --rm -w /tmp --user `id -u`:`id -g` -v `pwd`:/src:ro -v `pwd`/dist:/dist:rw $image sh /src/tools/package.sh /src /dist teamcity OFF Release $pyver $build_number "$extra"

tools/prereqs/docker-centos5-install.sh

@@ -38,6 +38,7 @@ NUNIT_HOME=${PROG_HOME}/nunit
 if hash cmake  2> /dev/null; then
     echo "Found CMake"
 else
+    echo "Installing CMake"
     wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C /usr
 
 
@@ -56,9 +57,31 @@ else
     "/opt/python/cp36-cp36m/bin/pip" install auditwheel==1.5.0
 fi
 
+
+if [ -e /usr/include/gtest/gtest.h ]; then
+    echo "Found GTest and GMock"
+else
+    echo "Installing GTest and GMock"
+    mkdir /gtest
+    curl -L ${GOOGLETEST_URL} -o release-1.8.0.tar.gz
+
+    tar --strip-components=1 -xzf release-1.8.0.tar.gz -C /gtest
+    #curl ${GOOGLETEST_URL} | tar --strip-components=1 -xz -C /gtest
+    mkdir /gtest/build
+    cmake -H/gtest -B/gtest/build
+    cmake --build /gtest/build -- -j4
+    cp -r /gtest/googletest/include/gtest /usr/include/
+    cp -r /gtest/googlemock/include/gmock /usr/include/
+    cp /gtest/build/googlemock/gtest/lib*.a /usr/lib/
+    cp /gtest/build/googlemock/lib*.a /usr/lib/
+
+    rm -fr /gtest release-1.8.0.tar.gz
+fi
+
 if hash swig  2> /dev/null; then
-    echo "Found Swig"
+    echo "Found SWIG"
 else
+    echo "Installing SWIG"
     if [ ! -e ${SWIG_HOME} ]; then
         mkdir ${SWIG_HOME}
     fi
@@ -82,6 +105,7 @@ fi
 if hash mono  2> /dev/null; then
     echo "Found mono"
 else
+    echo "Installing Mono"
     PATH_OLD=$PATH
     export PATH=/opt/python/cp27-cp27mu/bin/:$PATH
     yum install automake autoconf libtool  -y
@@ -123,33 +147,19 @@ else
     nuget help
 fi
 
-if [ -e /usr/include/gtest/gtest.h ]; then
-    echo "Found GTest and GMock"
-else
-    mkdir /gtest
-    wget --no-check-certificate --quiet -O - ${GOOGLETEST_URL} | tar --strip-components=1 -xz -C /gtest
-    mkdir /gtest/build
-    cmake -H/gtest -B/gtest/build
-    cmake --build /gtest/build -- -j4
-    cp -r /gtest/googletest/include/gtest /usr/include/
-    cp -r /gtest/googlemock/include/gmock /usr/include/
-    cp /gtest/build/googlemock/gtest/lib*.a /usr/lib/
-    cp /gtest/build/googlemock/lib*.a /usr/lib/
-
-    rm -fr /gtest
-fi
-
 if hash java  2> /dev/null; then
     echo "Found Java"
 else
+    echo "Installing Java"
     wget --quiet --no-cookies --no-check-certificate --header "Cookie: gpw_e24=http%3A%2F%2Fwww.oracle.com%2F; oraclelicense=accept-securebackup-cookie" "${JAVA_URL}" -O ${JAVA_URL##*/}
     rpm -Uvh ${JAVA_URL##*/}
     rm -f  ${JAVA_URL##*/}
 fi
 
 if [ ! -e ${NUNIT_HOME}/NUnit-2.6.4 ]; then
+    echo "Installing NUnit"
     mkdir ${NUNIT_HOME}
-    wget --no-check-certificate --quiet ${NUNIT_URL} -O  ${NUNIT_HOME}/${NUNIT_URL##*/}
+    curl -L ${NUNIT_URL} -o ${NUNIT_HOME}/${NUNIT_URL##*/}
     unzip ${NUNIT_HOME}/${NUNIT_URL##*/} -d ${NUNIT_HOME}
     rm -f ${NUNIT_HOME}/${JUNIT_URL##*/}
 else
@@ -158,12 +168,14 @@ fi
 NUNIT_HOME=${NUNIT_HOME}/NUnit-2.6.4
 
 if [ ! -e ${JUNIT_HOME}/${JUNIT_URL##*/} ]; then
+    echo "Installing JUnit"
     mkdir ${JUNIT_HOME}
     wget --no-check-certificate --quiet ${JUNIT_URL} -O  ${JUNIT_HOME}/${JUNIT_URL##*/}
 else
     echo "Found JUnit at ${JUNIT_HOME}/${JUNIT_URL##*/}"
 fi
 
+echo "Installing Valgrind"
 mkdir tmp_build
 wget --no-check-certificate --quiet -O - ${VALGRIND_URL} | tar --strip-components=1 -xj -C ./tmp_build
 cd tmp_build