Update zlib for Linux compilations and make MSToolkit compile on MacOS

.github/workflows/VS2019.yml

@@ -2,7 +2,10 @@ name: windows-2019 build
 
 on:
   push:
-    branches: [ Restructuring ]
+    branches: [ master, Restructuring ]
+  pull_request:
+  release:
+    types: [ created ]
   workflow_dispatch:
 
 jobs:

.github/workflows/linux.yml

@@ -2,14 +2,23 @@ name: linux build
 
 on:
   push:
-    branches: [ Restructuring ]
+    branches: [ master ]
+  pull_request:
+  release:
+    types: [ created ]
   workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-24.04
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
+
+    - name: install dependencies
+      run: |
+        apt-get update
+        apt-get install -y unzip
+        apt-get install -y build-essential
 
     - name: build mstoolkit
       run: make all

.gitignore

@@ -2,4 +2,7 @@ include/expat_config.h
 build/
 .vs/
 lib/
-*.json
+*.json
+.DS_Store
+CMakeCache.txt
+CMakeFiles/

CMakeLists.txt

@@ -28,7 +28,7 @@ set(MSTOOLKIT_SRC_DIR ${PROJECT_SOURCE_DIR}/src/MSToolkit)
 set(EXPAT_SRC_DIR ${PROJECT_SOURCE_DIR}/src/expat-2.2.9/lib)
 set(MZID_SRC_DIR ${PROJECT_SOURCE_DIR}/src/mzIMLTools)
 set(MZP_SRC_DIR ${PROJECT_SOURCE_DIR}/src/mzParser)
-set(ZLIB_SRC_DIR ${PROJECT_SOURCE_DIR}/src/zlib-1.2.11)
+set(ZLIB_SRC_DIR ${PROJECT_SOURCE_DIR}/src/zlib-1.3.1)
 
 # Library output directory
 set(LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/lib)

MAKEFILE.nmake

@@ -72,7 +72,7 @@ mzparser : $(MZP_SRCDIR)\\*.cpp
 # -- zlib ---------------------------------------------
 # zlib file compression
 #------------------------------------------------------
-ZLIB_SRCDIR=$(BUILD_EXT)\zlib-1.2.11
+ZLIB_SRCDIR=$(BUILD_EXT)\zlib-1.3.1
 
 zlib : $(ZLIB_SRCDIR)\\*.c
 	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR_EXT)\ $?

Makefile

@@ -12,13 +12,29 @@
 C = gcc
 CC = g++
 
-CFLAGS = -O3 -std=c++11
+CFLAGS = -O3 -std=c++14
 SLFLAGS = -shared -fPIC -g
 INCLUDE = -I./include
 INCLUDE_EXT = -I./include/extern
 DFLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC
 DFLAGS_EXT = -DHAVE_EXPAT_CONFIG_H
 
+
+# -- Libraries  ----------------------------------------------------------
+#
+# Linux and MacOS compatibility
+#
+#
+UNAME_S := $(shell uname -s)
+ifeq ($(UNAME_S),Linux)
+    RELRO = -Wl,-z,relro
+endif
+
+ifeq ($(UNAME_S),Darwin)
+    RELRO =
+endif
+
+
 # -- Need to fix HDF5
 #ifdef HDF5
 #CFLAGS = -O3 -std=c++11 -I. -I./include -I$(HDF5_DIR)/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H $(HDF5)
@@ -105,7 +121,7 @@ expat-realclean : expat-clean
 #
 # http://zlib.net/
 #
-ZLIB_VER := zlib-1.2.11
+ZLIB_VER := zlib-1.3.1
 ZLIB_SRC := $(BUILD_EXT)/$(ZLIB_VER)
 ZLIB_SRCB := $(wildcard $(ZLIB_SRC)/*.c)
 ZLIB_DST := $(BUILD_DIR)/libz.a
@@ -117,7 +133,7 @@ ZLIB_DSO := $(patsubst ${ZLIB_SRC}/%.c, ${ZLIB_SRC}/%.lo, $(ZLIB_SRCB))
 zlib : $(ZLIB_DST) $(ZLIB_LIC)
 
 $(ZLIB_DST) : | $(BUILD_DIR)/ $(ZLIB_SRC)/
-	cd $(BUILD_EXT); unzip -o zlib1211.zip
+	cd $(BUILD_EXT); unzip -o zlib131.zip
 	cd $(ZLIB_SRC); ./configure --prefix=$(BUILD_DIR) --includedir $(SRC_DIR)/include --libdir $(BUILD_DIR) 
 	make -C $(ZLIB_SRC) install
 
@@ -152,7 +168,11 @@ mstoolkit : $(MSTOOLKIT_DST) $(MSTOOLKIT_DSO)
 
 $(MSTOOLKIT_DST) : | $(BUILD_DIR)/
 $(MSTOOLKIT_DST) : $(MSTOOLKIT_DSTDIR)%.o : $(MSTOOLKIT_SRCDIR)%.cpp
+ifeq ($(UNAME_S),Darwin)
+	$(CC) $(CFLAGS) $(INCLUDE) $(DFLAGS) $< -c -o $@
+else
 	$(CC) $(CFLAGS) -static $(INCLUDE) $(DFLAGS) $< -c -o $@
+endif
 
 $(MSTOOLKIT_DSO) : $(MSTOOLKIT_DSTDIR)%.lo : $(MSTOOLKIT_SRCDIR)%.cpp
 	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) $< -c -o $@
@@ -179,10 +199,15 @@ MZPARSER_DSO = $(patsubst ${MZPARSER_SRCDIR}%.cpp, ${MZPARSER_DSTDIR}%.lo, $(MZP
 
 mzparser : $(MZPARSER_DST) $(MZPARSER_DSO)
 	ar rcs $(BUILD_DIR)/libmzparser.a $(MZPARSER_DST)
-	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o $(BUILD_DIR)/libmzparser.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmzparser.so.$(SOVER) $(MZPARSER_DSO)
+ifeq ($(UNAME_S),Linux)
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o $(BUILD_DIR)/libmzparser.so.$(RELVER) $(RELRO) -Wl,-soname,libmzparser.so.$(SOVER) $(MZPARSER_DSO)
 	ln -sf $(BUILD_DIR)/libmzparser.so.$(RELVER) $(BUILD_DIR)/libmzparser.so.$(SOVER)
 	ln -sf $(BUILD_DIR)/libmzparser.so.$(SOVER) $(BUILD_DIR)/libmzparser.so
-
+endif
+ifeq ($(UNAME_S),Darwin)
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o $(BUILD_DIR)/libmzparser.dylib $(RELRO) -Wl,-install_name,libmzparser.dylib $(MZPARSER_DSO) -lz -lexpat -Lextern/zlib-1.3.1 -Lextern/expat-2.2.9
+endif
+
 $(MZPARSER_DST) : | $(BUILD_DIR)/
 $(MZPARSER_DST) : $(MZPARSER_DSTDIR)%.o : $(MZPARSER_SRCDIR)%.cpp
 	$(CC) $(CFLAGS) -static $(INCLUDE) $(DFLAGS) $< -c -o $@
@@ -214,10 +239,15 @@ ifdef HDF5
 endif
 	$(file >>mstoolkit.mri,save)
 	$(file >>mstoolkit.mri,end)
+ifeq ($(UNAME_S),Linux)
 	ar -M <mstoolkit.mri
-	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkit.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkit.so.$(SOVER) $(MSTOOLKIT_DSO) $(MZPARSER_DSO)
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkit.so.$(RELVER) $(RELRO) -Wl,-soname,libmstoolkit.so.$(SOVER) $(MSTOOLKIT_DSO) $(MZPARSER_DSO)
 	ln -sf libmstoolkit.so.$(RELVER) libmstoolkit.so.$(SOVER)
 	ln -sf libmstoolkit.so.$(SOVER) libmstoolkit.so
+endif
+ifeq ($(UNAME_S),Darwin)
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkit.dylib $(RELRO) -Wl,-install_name,libmstoolkit.dylib $(MSTOOLKIT_DSO) $(MZPARSER_DSO) -lz -lexpat -Lextern/zlib-1.3.1 -Lextern/expat-2.2.9
+endif
 
 lib-clean :
 	rm -rf libmstoolkit.a libmstoolkit.so*
@@ -243,10 +273,15 @@ ifdef HDF5
 endif
 	$(file >>mstoolkitextern.mri,save)
 	$(file >>mstoolkitextern.mri,end)
+ifeq ($(UNAME_S),Linux)
 	ar -M <mstoolkitextern.mri
-	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkitextern.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkitextern.so.$(SOVER) $(ZLIB_DSO) $(EXPAT_DSO) 
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkitextern.so.$(RELVER) $(RELRO) -Wl,-soname,libmstoolkitextern.so.$(SOVER) $(ZLIB_DSO) $(EXPAT_DSO) 
 	ln -sf libmstoolkitextern.so.$(RELVER) libmstoolkitextern.so.$(SOVER)
 	ln -sf libmstoolkitextern.so.$(SOVER) libmstoolkitextern.so
+endif
+ifeq ($(UNAME_S),Darwin)
+	$(CC) $(CFLAGS) $(SLFLAGS) $(INCLUDE) $(DFLAGS) -o libmstoolkitextern.dylib $(RELRO) -Wl,-install_name,libmstoolkitextern.dylib $(ZLIB_DSO) $(EXPAT_DSO) 
+endif
 
 libextern-clean :
 	rm -rf libmstoolkitextern.a libmstoolkitextern.so*
@@ -265,9 +300,13 @@ MSSingleScan : lib
 ifdef HDF5
 	$(CC) $(CFLAGS) -static $(INCLUDE) $(DFLAGS) $(SRC_DIR)/MSSingleScanSrc/MSSingleScan.cpp -L. -l:libmstoolkit.a -l:libmstoolkitextern.a -ldl -o MSSingleScan
 else
+ifeq ($(UNAME_S),Linux)
 	$(CC) $(CFLAGS) -static $(INCLUDE) $(INCLUDE_EXT) $(DFLAGS) $(SRC_DIR)/MSSingleScanSrc/MSSingleScan.cpp -L. -lmstoolkit -lmstoolkitextern -o MSSingleScan
+endif
+ifeq ($(UNAME_S),Darwin)
 	$(CC) $(CFLAGS) $(INCLUDE) $(INCLUDE_EXT) $(DFLAGS) $(SRC_DIR)/MSSingleScanSrc/MSSingleScan.cpp -L. -lmstoolkit -lmstoolkitextern -o MSSingleScanSL
 endif
+endif
 
 MSSingleScan-clean :
 	rm -rf MSSingleScan MSSingleScanSL

VisualStudio/extern/zlibdll.vcxproj

@@ -543,7 +543,7 @@ bld_ml64.bat</Command>
     </Midl>
     <ClCompile>
       <InlineFunctionExpansion>OnlyExplicitInline</InlineFunctionExpansion>
-      <AdditionalIncludeDirectories>..\extern\zlib-1.2.11;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <AdditionalIncludeDirectories>..\extern\zlib-1.3.1;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <PreprocessorDefinitions>_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;ZLIB_DLL;%(PreprocessorDefinitions)</PreprocessorDefinitions>
       <StringPooling>true</StringPooling>
       <ExceptionHandling>