Merge pull request #153 from OpenMS/fix_fix

Fix fix

Author: poshul

.github/workflows/main.yml

@@ -20,6 +20,7 @@ jobs:
     needs: prepare
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:

CMakeLists.txt

@@ -186,7 +186,7 @@ set (PATCH_DIR "${PROJECT_SOURCE_DIR}/patches/" CACHE STRING "Directory containi
 # project specific source directories
 ## Warning: ensure these are all upper-case names!
 set(BZIP2_DIR ${CONTRIB_BIN_SOURCE_DIR}/bzip2-1.0.5)
-set(ZLIB_DIR ${CONTRIB_BIN_SOURCE_DIR}/zlib-1.2.11)
+set(ZLIB_DIR ${CONTRIB_BIN_SOURCE_DIR}/zlib-1.3.1)
 set(BOOST_DIR ${CONTRIB_BIN_SOURCE_DIR}/boost_1_78_0)
 set(XERCES_DIR ${CONTRIB_BIN_SOURCE_DIR}/Xerces-C_3_2_0)
 set(LIBSVM_DIR ${CONTRIB_BIN_SOURCE_DIR}/libsvm-3.12)
@@ -215,34 +215,14 @@ set(ARCHIVE_BZIP2 bzip2-1.0.5.tar.gz)
 set(ARCHIVE_BZIP2_TAR bzip2-1.0.5.tar)
 set(ARCHIVE_BZIP2_SHA1 "8b02713ea0c8eb501cc8bdac4432d7f29700f767")
 
-# set(ARCHIVE_ZLIB zlib-1.2.5.tar.gz)
-# set(ARCHIVE_ZLIB_TAR  zlib-1.2.5.tar)
-# set(ARCHIVE_ZLIB_SHA1 "8e8b93fa5eb80df1afe5422309dca42964562d7e")
-
-#set(ARCHIVE_ZLIB zlib-1.2.8.tar.gz)
-#set(ARCHIVE_ZLIB_TAR  zlib-1.2.8.tar)
-#set(ARCHIVE_ZLIB_SHA1 "a4d316c404ff54ca545ea71a27af7dbc29817088")
-
-set(ARCHIVE_ZLIB zlib-1.2.11.tar.gz)
-set(ARCHIVE_ZLIB_TAR  zlib-1.2.11.tar)
-set(ARCHIVE_ZLIB_SHA1 "56559d4c03beaedb0be1c7481d6a371e2458a496")
+set(ARCHIVE_ZLIB zlib-1.3.1.tar.gz)
+set(ARCHIVE_ZLIB_TAR  zlib-1.3.1.tar)
+set(ARCHIVE_ZLIB_SHA1 "f535367b1a11e2f9ac3bec723fb007fbc0d189e5")
 
 set(ARCHIVE_BOOST boost_1_78_0.tar.gz)
 set(ARCHIVE_BOOST_TAR  boost_1_78_0.tar)
 set(ARCHIVE_BOOST_SHA1 "ff717ea23af2900e0ad3cae616b3e4ae43e68ad7")
 
-#set(ARCHIVE_BOOST boost_1_71_0.tar.gz)
-#set(ARCHIVE_BOOST_TAR  boost_1_71_0.tar)
-#set(ARCHIVE_BOOST_SHA1 "4f3846b0cd92ecdd56961484d757388fb07a2ada")
-
-#set(ARCHIVE_BOOST boost_1_67_0.tar.gz)
-#set(ARCHIVE_BOOST_TAR  boost_1_67_0.tar)
-#set(ARCHIVE_BOOST_SHA1 "77e73c9fd7bf85b14067767b9e8fdc39b49ee0f2")
-
-# set(ARCHIVE_XERCES xerces-c-3.1.1-vs17.tar.gz)
-# set(ARCHIVE_XERCES_TAR  xerces-c-3.1.1.tar)
-# set(ARCHIVE_XERCES_SHA1 "af2bd237b8272f92dc6486f703b921a864f3006e")
-
 set(ARCHIVE_XERCES Xerces-C_3_2_0.tar.gz)
 set(ARCHIVE_XERCES_TAR  Xerces-C_3_2_0.tar)
 set(ARCHIVE_XERCES_SHA1 "da64ed4065694a88378cad340c8382d15a614837")

libraries.cmake/boost.cmake

@@ -100,6 +100,8 @@ MACRO( OPENMS_CONTRIB_BUILD_BOOST)
 
     # use proper toolchain (random guesses. There is not proper documentation)
     if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+      # Modern Clang chokes on boost 1.78 unless we pass this (https://github.com/boostorg/mpl/issues/74)
+      set(BOOST_EXTRA_CXXFLAGS "-Wno-enum-constexpr-conversion")
       # since around boost 1.70 there is not bootstrap toolset called darwin anymore
       set(_boost_bootstrap_toolchain "clang")
       if(APPLE)
@@ -163,7 +165,7 @@ MACRO( OPENMS_CONTRIB_BUILD_BOOST)
       set(BOOST_DEBUG_FLAGS "--debug-configuration -d+2")
     endif()
     # boost cmd (use b2 since sometimes the copying/symlinking from b2 to bjam fails)
-    set (BOOST_CMD "./b2 ${BOOST_DEBUG_FLAGS} architecture=x86 toolset=${_boost_toolchain} -j ${NUMBER_OF_JOBS} --disable-icu link=${BOOST_BUILD_TYPE} cxxflags=-fPIC ${OSX_LIB_FLAG} ${OSX_DEPLOYMENT_FLAG} ${BOOST_LINKER_FLAGS} install --build-type=complete --layout=tagged --threading=single,multi")
+    set (BOOST_CMD "./b2 ${BOOST_DEBUG_FLAGS} architecture=x86 toolset=${_boost_toolchain} -j ${NUMBER_OF_JOBS} --disable-icu link=${BOOST_BUILD_TYPE} cxxflags=-fPIC ${BOOST_EXTRA_CXXFLAGS} ${OSX_LIB_FLAG} ${OSX_DEPLOYMENT_FLAG} ${BOOST_LINKER_FLAGS} install --build-type=complete --layout=tagged --threading=single,multi")
 
     # boost install
     message(STATUS "Installing Boost libraries (${BOOST_CMD}) ...")
@@ -172,7 +174,7 @@ MACRO( OPENMS_CONTRIB_BUILD_BOOST)
                     --disable-icu
                     -s NO_LZMA=1
                     -s NO_ZSTD=1
-                    link=${BOOST_BUILD_TYPE} "cxxflags=-fPIC ${OSX_LIB_FLAG} ${OSX_DEPLOYMENT_FLAG}" ${BOOST_LINKER_FLAGS}  install 
+                    link=${BOOST_BUILD_TYPE} "cxxflags=-fPIC ${BOOST_EXTRA_CXXFLAGS} ${OSX_LIB_FLAG} ${OSX_DEPLOYMENT_FLAG}" ${BOOST_LINKER_FLAGS}  install 
                     --build-type=complete
                     --layout=tagged
                     --threading=single,multi

libraries.cmake/zlib.cmake

@@ -12,10 +12,6 @@ else()
 endif()
 OPENMS_SMARTEXTRACT(ZIP_ARGS ARCHIVE_ZLIB "ZLIB" "README")
 
-set(_PATCH_FILE "${PATCH_DIR}/zlib/zlib_mind_libtype.patch")
-set(_PATCHED_FILE "${ZLIB_DIR}/CMakeLists.txt")
-OPENMS_PATCH( _PATCH_FILE ZLIB_DIR _PATCHED_FILE)
-
 ## build the obj/lib
 if (MSVC)
   message(STATUS "Generating zlib build system .. ")

macros.cmake

@@ -78,7 +78,7 @@ endmacro()
 ## downloads the archive for the given library
 ## @param libname The library that should be downloaded
 macro(download_contrib_archive libname)
-  set(_BASE_URL "https://github.com/OpenMS/contrib-sources/releases/download/2024-04-29-000000/")
+  set(_BASE_URL "https://github.com/OpenMS/contrib-sources/releases/download/3.5.0pre1/")
 
   # the files/folders where downloads are stored
   set(_archive_folder "${PROJECT_BINARY_DIR}/archives")