Merge branch 'percolator:master' into master

statisticalbiotechnology · Aug 13, 2024 · e2af0ec · e2af0ec
2 parents fa3328a + 2105687
commit e2af0ec
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,54 +10,53 @@ jobs:
   build-ubuntu:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: preinstall
       run: sudo apt-get update && sudo apt-get install -y -o Acquire::Retries=3 libxml2-utils
     - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
+      run: mkdir -p ../release ../build
     - name: configure_and_make
-      run: ./admin/builders/ubuntu64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+      run: ./admin/builders/ubuntu64_build.sh -s `pwd`/.. -r `pwd`/../release -b `pwd`/../build
     - name: unit_tests
-      run: cd ../my_build/percolator && make test
+      run: cd ../build/percolator && make test
     - name: system_test  
-      run: cd ../my_build/percolator && sudo make install && make test-install
+      run: cd ../build/percolator && sudo make install && make test-install
 
-  build-centos:
-    runs-on: ubuntu-latest
-    container: 'lukall/centos_runner:latest'
-    steps:
-    - uses: actions/checkout@v2
-    - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
-    - name: configure_and_make
-      run: ./admin/builders/centos64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
-    - name: unit_tests
-      run: cd ../my_build/percolator-test && make test
-      # Decend into percolator-test, with an alternative install directory
-    - name: system_test  
-      run: cd ../my_build/percolator-test && make install && make test-install
+#  build-centos:
+#    runs-on: ubuntu-latest
+#    container: 'lukall/centos_runner:latest'
+#    steps:
+#    - uses: actions/checkout@v4
+#    - name: create_dirs
+#      run: mkdir -p ../my_rel ../my_build
+#    - name: configure_and_make
+#      run: ./admin/builders/centos64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+#    - name: unit_tests
+#      run: cd ../my_build/percolator-test && make test
+#      # Decend into percolator-test, with an alternative install directory
+#    - name: system_test  
+#      run: cd ../my_build/percolator-test && make install && make test-install
 
   build-osx:
     runs-on: macos-12
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
+      run: mkdir -p ../release ../build
     - name: configure_and_make
-      run: admin/builders/osx64_build.sh  -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+      run: admin/builders/osx64_build.sh  -s `pwd`/.. -r `pwd`/../release -b `pwd`/../build
     - name: unit_tests
-      run: cd ../my_build/percolator && make test
+      run: cd ../build/percolator && make test
     - name: system_test  
-      run: cd ../my_build/percolator && sudo make install && make test-install
-
+      run: cd ../build/percolator && sudo make install && make test-install
 
   build-windows:
     runs-on: windows-2019
     defaults:
       run:
         shell: cmd
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: create_dirs
       run: CD .. || MKDIR my_rel my_build
     - name: configure_and_make

diff --git a/.github/workflows/triggered_build.yml b/.github/workflows/triggered_build.yml
@@ -6,81 +6,80 @@ jobs:
   build-ubuntu:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: preinstall
       run: sudo apt-get update && sudo apt-get install -y -o Acquire::Retries=3 libxml2-utils
     - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
+      run: mkdir -p ${{ github.workspace }}/../release ${{ github.workspace }}/../build
     - name: configure_and_make
-      run: ./admin/builders/ubuntu64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+      run: ./admin/builders/ubuntu64_build.sh -s ${{ github.workspace }}/.. -r ${{ github.workspace }}/../release -b ${{ github.workspace }}/../build
     - name: test
-      run: cd ../my_build/percolator && sudo make install && make test ARGS="-V"
+      run: cd ${{ github.workspace }}/../build/percolator && sudo make install && make test ARGS="-V"
     - name: zip raw binary
-      run: zip -j ../my_rel/percolator-noxml-ubuntu-portable.zip ../my_build/percolator-noxml/src/percolator
+      run: zip -j ${{ github.workspace }}/../release/percolator-noxml-ubuntu-portable.zip ${{ github.workspace }}/../build/percolator-noxml/src/percolator
     - name: Upload packages
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: ubuntu-packages
-        path: ../my_rel
+        path: ${{ github.workspace }}/../release
 
-  build-centos:
-    runs-on: ubuntu-latest
-    container: 'lukall/centos_runner:latest'
-    steps:
-    - uses: actions/checkout@v2
-    - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
-    - name: configure_and_make
-      run: ./admin/builders/centos64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
-    - name: test
-      run: cd ../my_build/percolator && make install && make test ARGS="-V"
-    - name: zip raw binary
-      run: zip -j ../my_rel/percolator-noxml-linux-portable.zip ../my_build/percolator-noxml/src/percolator
-    - name: Upload packages
-      uses: actions/upload-artifact@v1
-      with:
-        name: centos-packages
-        path: ../my_rel
+#  build-centos:
+#    runs-on: ubuntu-latest
+#    container: 'lukall/centos_runner:latest'
+#    steps:
+#    - uses: actions/checkout@v4
+#    - name: create_dirs
+#      run: mkdir -p ../my_rel ../my_build
+#    - name: configure_and_make
+#      run: ./admin/builders/centos64_build.sh -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+#    - name: test
+#      run: cd ../my_build/percolator && make install && make test ARGS="-V"
+#    - name: zip raw binary
+#      run: zip -j ../my_rel/percolator-noxml-linux-portable.zip ../my_build/percolator-noxml/src/percolator
+#    - name: Upload packages
+#      uses: actions/upload-artifact@v3
+#      with:
+#        name: centos-packages
+#        path: ../my_rel
 
   build-osx:
     runs-on: macos-12
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: create_dirs
-      run: mkdir -p ../my_rel ../my_build
+      run: mkdir -p ${{ github.workspace }}/../release ${{ github.workspace }}/../build
     - name: configure_and_make
-      run: admin/builders/osx64_build.sh  -s `pwd`/.. -r `pwd`/../my_rel -b `pwd`/../my_build
+      run: ./admin/builders/osx64_build.sh -s ${{ github.workspace }}/.. -r ${{ github.workspace }}/../release -b ${{ github.workspace }}/../build
     - name: test
-      run: cd ../my_build/percolator && sudo make install && make test ARGS="-V"
+      run: cd ${{ github.workspace }}/../build/percolator && sudo make install && make test ARGS="-V"
     - name: zip raw binary
-      run: zip ../my_rel/percolator-noxml-osx-portable.zip ../my_build/percolator-noxml/src/percolator
+      run: zip ${{ github.workspace }}/../release/percolator-noxml-osx-portable.zip ${{ github.workspace }}/../build/percolator-noxml/src/percolator
     - name: Upload packages
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: osx-packages
-        path: ../my_rel
-
+        path: ${{ github.workspace }}/../release
 
   build-windows:
     runs-on: windows-2019
     defaults:
       run:
         shell: cmd
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: create_dirs
-      run: MKDIR %homedrive%%homepath%\my_rel %homedrive%%homepath%\my_build
+      run: MKDIR %GITHUB_WORKSPACE%\..\my_rel %GITHUB_WORKSPACE%\..\my_build
     - name: configure_and_make
       run: |
-        CD ..
+        CD %GITHUB_WORKSPACE%
         SET base_dir=%cd%
         ECHO %base_dir%
-        CALL percolator\admin\builders\nativew64_build.bat -s %base_dir% -r %homedrive%%homepath%\my_rel -b %homedrive%%homepath%\my_build
+        CALL percolator\admin\builders\nativew64_build.bat -s %base_dir% -r %GITHUB_WORKSPACE%\..\my_rel -b %GITHUB_WORKSPACE%\..\my_build
     - name: zip raw binary
       shell: pwsh
-      run: Compress-Archive -Path ${env:homedrive}${env:homepath}\my_build\percolator-noxml\src\Release\*.exe -Destination ${env:homedrive}${env:homepath}\my_rel\percolator-noxml-windows-portable.zip
+      run: Compress-Archive -Path "${env:GITHUB_WORKSPACE}\..\my_build\percolator-noxml\src\Release\*.exe" -DestinationPath "${env:GITHUB_WORKSPACE}\..\my_rel\percolator-noxml-windows-portable.zip"
     - name: Upload packages
       uses: actions/upload-artifact@v3
       with:
         name: windows-packages
-        path: ~/my_rel/
+        path: ${GITHUB_WORKSPACE}\..\my_rel\percolator-noxml-windows-portable.zip
diff --git a/CommonCMake.txt b/CommonCMake.txt
@@ -50,8 +50,8 @@ set(CMAKE_MODULE_PATH ${PERCOLATOR_SOURCE_DIR}/cmake)
 
 # VERSION AND NAMESPACES
 set(CPACK_PACKAGE_VERSION_MAJOR "3")
-set(CPACK_PACKAGE_VERSION_MINOR "06")
-set(CPACK_PACKAGE_VERSION_PATCH "5")
+set(CPACK_PACKAGE_VERSION_MINOR "07")
+set(CPACK_PACKAGE_VERSION_PATCH "0")
 set(PIN_VERSION_MAJOR "1")
 set(PIN_VERSION_MINOR "3")
 set(POUT_VERSION_MAJOR "1")
@@ -114,9 +114,9 @@ if(APPLE)
 endif()
 if(MINGW OR WIN32 OR APPLE)
   OPTION(BUILD_SHARED_LIBS "build static binaries." OFF)
-  OPTION(STATIC "build a static binaries. This is mainly intended for the win32-package and the MACOSX-bundle." ON )
+  OPTION(STATIC "build static binaries. This is mainly intended for the win32-package and the MACOSX-bundle." ON )
 else(MINGW OR WIN32 OR APPLE)
-  OPTION(STATIC "build a static binaries. This is mainly intended for the win32-package and the MACOSX-bundle." OFF )
+  OPTION(STATIC "build static binaries. This is mainly intended for the win32-package and the MACOSX-bundle." OFF )
 endif()
 
 # Link Boost static and single threaded
@@ -131,8 +131,9 @@ set(Boost_ADDITIONAL_VERSIONS "1.46" "1.47.0" "1.47"
 # SET COMPILER OPTIONS
 ###############################################################################
 
-set (CMAKE_CXX_STANDARD 11)
+set (CMAKE_CXX_STANDARD 14)
 set (CMAKE_CXX_STANDARD_REQUIRED YES)
+set (CMAKE_CXX_EXTENSIONS OFF)
 
 IF(APPLE)
   add_definitions(-Dxdr_uint16_t=xdr_u_int16_t -Dxdr_uint32_t=xdr_u_int32_t -Dxdr_uint64_t=xdr_u_int64_t)

diff --git a/admin/builders/_urls_and_file_names_.bat b/admin/builders/_urls_and_file_names_.bat
@@ -33,8 +33,12 @@ set XERCES_64_BASE=xerces-c-3.1.1-x86_64-windows-vc-10.0
 set XERCES_64_URL=https://archive.apache.org/dist/xerces/c/3/binaries/%XERCES_64_BASE%.zip
 
 ::: XSD
-set XSD_BASE=xsd-3.3.0-i686-windows
-set XSD_URL=https://www.codesynthesis.com/download/xsd/3.3/windows/i686/%XSD_BASE%.zip
+::: set XSD_BASE=xsd-3.3.0-i686-windows
+::: set XSD_URL=https://www.codesynthesis.com/download/xsd/3.3/windows/i686/%XSD_BASE%.zip
+set XSD_BASE=xsd-4.2.0-x86_64-windows10
+set XSD_URL=https://www.codesynthesis.com/download/xsd/4.2/windows/windows10/x86_64/%XSD_BASE%.zip
+set LIBXSD_BASE=libxsd-4.2.0-windows
+set LIBXSD_URL=https://www.codesynthesis.com/download/xsd/4.2/windows/windows10/x86_64/%LIBXSD_BASE%.zip
 
 ::: SQLite3
 set SQLITE_SRC_BASE=sqlite-amalgamation-3080200

diff --git a/admin/builders/_urls_and_file_names_.sh b/admin/builders/_urls_and_file_names_.sh
@@ -9,7 +9,7 @@
 mac_os_xsd='xsd-4.0.0+dep'
 mac_os_xsd_url='https://www.codesynthesis.com/download/xsd/4.0/'${mac_os_xsd}'.tar.bz2'
 # -- xerces --
-mac_os_xerces='xerces-c-3.2.3'
+mac_os_xerces='xerces-c-3.2.5'
 mac_os_xerces_url='https://archive.apache.org/dist/xerces/c/3/sources/'${mac_os_xerces}'.tar.gz'
 
 #

diff --git a/admin/builders/nativew64_build.bat b/admin/builders/nativew64_build.bat
@@ -108,6 +108,10 @@ if not exist "%XSD_DIR%" (
   echo Downloading and installing CodeSynthesis XSD
   call :downloadfile %XSD_URL% %INSTALL_DIR%\xsd.zip
   %ZIP_EXE% x "%INSTALL_DIR%\xsd.zip" -o"%INSTALL_DIR%" > NUL
+  call :downloadfile %LIBXSD_URL% %INSTALL_DIR%\libxsd.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\libxsd.zip" -o"%INSTALL_DIR%" > NUL
+  echo Moving files from %LIBXSD_BASE%\include\ to %XSD_BASE%
+  xcopy "%INSTALL_DIR%\%LIBXSD_BASE%\include\*" "%INSTALL_DIR%\%XSD_BASE%\" /s /e /y /i
 )
 
 ::: Needed for converters package :::

diff --git a/admin/builders/osx64_build.sh b/admin/builders/osx64_build.sh
@@ -106,17 +106,17 @@ mkdir -p ${build_dir}
 cd ${build_dir}
 
 # XercesC installation
-if [[ -d /usr/local/include/xercesc ]] # this implies homebrew installation ...
-	then
-	echo "Xerces is already installed."
-else
+#if [[ -d /usr/local/include/xercesc ]] # this implies homebrew installation ...
+#	then
+#	echo "Xerces is already installed."
+#else
 	curl -k -O ${mac_os_xerces_url}
 	tar xzf ${mac_os_xerces}.tar.gz
 	cd ${mac_os_xerces}/
 	./configure CFLAGS="-arch x86_64" CXXFLAGS="-arch x86_64" --disable-dynamic --enable-transcoder-iconv --disable-network --disable-threads
 	make -j 2
 	sudo make install
-fi
+#fi
 
 cd ${build_dir}