Restructuring

.github/workflows/VS2019.yml

@@ -7,17 +7,30 @@ on:
 
 jobs:
   build:
-    runs-on: window-2019
+    runs-on: windows-2019
     steps:
     - uses: actions/checkout@v4
+
+    - name: unzip Thermo MSFileReader
+      shell: bash
+      run: unzip -P iacceptthelicense extern/msfreader.zip -d dlls
+
+    - name: register Thermo MSFileReader
+      shell: cmd
+      run: FOR %%G IN (dlls\*.dll) DO regsvr32 /S %%G
 
     - name: msbuild
       uses: microsoft/setup-msbuild@v2
 
     - name: build mstoolkit
-      run: |
-        msbuild VisualStudio/MSToolkit.sln -p:Configuration=Release -p:Platform=x64 -p:PlatformToolset=v142 -tv:Current
+      # use -p:PreDef=/D_NO_THERMORAW to build MSToolkit without Thermo raw support windows 
+      run: msbuild VisualStudio/MSToolkit.sln -p:Configuration=Release -p:Platform=x64 -p:PlatformToolset=v142 -tv:Current
 
     - name: test
       shell: cmd
-      run: D:\a\MSToolkit\VisualStudio\x64\Release\MSSingleScan.exe
+      run: D:\a\mstoolkit\mstoolkit\VisualStudio\x64\Release\MSSingleScan.exe
+
+    - name: test DLL
+      shell: cmd
+      run: D:\a\mstoolkit\mstoolkit\VisualStudio\x64\Release\DLL\MSSingleScan.exe
+

.github/workflows/linux.yml

@@ -0,0 +1,23 @@
+name: linux build
+
+on:
+  push:
+    branches: [ Restructuring ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: build mstoolkit
+      run: make all
+
+    - name: test
+      run: ./MSSingleScan
+
+    - name: test shared lib version
+      run: |
+        export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/runner/work/mstoolkit/mstoolkit/ && \
+        ./MSSingleScanSL

MAKEFILE.nmake

@@ -1,36 +1,41 @@
-MSTOOLKIT_DEFS=/D"_NOSQLITE"
-
 CFLAGS=/permissive- /GS /GL /W3 /Gy /Zc:wchar_t /Zi /Gm- /O2 /sdl /Zc:inline /fp:precise /errorReport:prompt /WX- /Zc:forScope /Gd /Oi /MD /FC /EHsc /nologo /diagnostics:column 
-CDEFS=/D "WIN32" /D "_CRT_SECURE_NO_WARNINGS" /D "_CRT_NONSTDC_NO_DEPRECATE" /D "XML_STATIC" /D "_MBCS"
+CDEFS=/D "NDEBUG" /D "WIN32" /D "_CRT_SECURE_NO_WARNINGS" /D "_CRT_NONSTDC_NO_DEPRECATE" /D "XML_STATIC" /D "_MBCS"
 LIBFLAGS=/LTCG /MACHINE:X64 /NOLOGO
 
 BUILD_INC=.\include
+BUILD_INC_EXT=$(BUILD_INC)\extern
 BUILD_SRC=.\src
+BUILD_EXT=.\extern
 BUILD_DIR=.\x64\Release
+BUILD_DIR_EXT=.\x64\Release\extern
 
 # -- Global build rules -------------------------------
 # Rules for all packages of the MSToolkit.
 #------------------------------------------------------
 .PHONY: all
-all       : output zlib expat mzparser mzid core mstoolkit
+all       : output zlib expat mzparser core mstoolkit mstoolkitextern
 
 
 # -- Output -------------------------------------------
 # Create output directories
 #------------------------------------------------------
 output:
 	@if not exist $(BUILD_DIR) mkdir $(BUILD_DIR)
+	@if not exist $(BUILD_DIR_EXT) mkdir $(BUILD_DIR_EXT)
 
 # -- MSToolkit  ---------------------------------------
 # The core MSToolkit files
 #------------------------------------------------------
 MSTOOLKIT_SRCDIR=$(BUILD_SRC)\MSToolkit
 
 mstoolkit: $(BUILD_DIR)\*.obj
-	lib /OUT:"$(BUILD_DIR)\MSToolkitLite.lib" $(LIBFLAGS) $?
+	lib /OUT:"$(BUILD_DIR)\MSToolkit.lib" $(LIBFLAGS) $?
+
+mstoolkitextern: $(BUILD_DIR_EXT)\*.obj
+	lib /OUT:"$(BUILD_DIR)\MSToolkitExtern.lib" $(LIBFLAGS) $?
 
-core : $(MSTOOLKIT_SRCDIR)\\*.cpp
-	cl $(CFLAGS) $(CDEFS) $(MSTOOLKIT_DEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
+core: $(MSTOOLKIT_SRCDIR)\*.cpp
+	cl $(CFLAGS) $(CDEFS) $(MSTOOLKIT_DEFS) /I"$(BUILD_INC)" /I"$(BUILD_INC_EXT)" /c /Fo$(BUILD_DIR)\ $?
 
 clean:
 	del $(BUILD_DIR)\*.obj
@@ -39,19 +44,20 @@ clean:
 # -- Expat --------------------------------------------
 # XML support
 #------------------------------------------------------
-EXPAT_SRCDIR=$(BUILD_SRC)\expat-2.2.9\lib
+EXPAT_SRCDIR=$(BUILD_EXT)\expat-2.2.9\lib
 
 expat : $(EXPAT_SRCDIR)\\*.c
-	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
+	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR_EXT)\ $?
 
 
+# This tool is deprecated. 
 # -- mzIMLTools ---------------------------------------
 # mzIdentML support
 #------------------------------------------------------
-MZID_SRCDIR=$(BUILD_SRC)\mzIMLTools
-
-mzid : $(MZID_SRCDIR)\\*.cpp
-	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
+#MZID_SRCDIR=$(BUILD_SRC)\mzIMLTools
+#
+#mzid : $(MZID_SRCDIR)\\*.cpp
+#	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
 
 
 # -- mzParser -----------------------------------------
@@ -60,15 +66,15 @@ mzid : $(MZID_SRCDIR)\\*.cpp
 MZP_SRCDIR=$(BUILD_SRC)\mzParser
 
 mzparser : $(MZP_SRCDIR)\\*.cpp
-	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
+	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /I"$(BUILD_INC_EXT)" /c /Fo$(BUILD_DIR)\ $?
 
 
 # -- zlib ---------------------------------------------
 # zlib file compression
 #------------------------------------------------------
-ZLIB_SRCDIR=$(BUILD_SRC)\zlib-1.2.11
+ZLIB_SRCDIR=$(BUILD_EXT)\zlib-1.2.11
 
 zlib : $(ZLIB_SRCDIR)\\*.c
-	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR)\ $?
+	cl $(CFLAGS) $(CDEFS) /I"$(BUILD_INC)" /c /Fo$(BUILD_DIR_EXT)\ $?
 
 

MSSingleScanSrc/MSSingleScan.cpp

@@ -24,7 +24,7 @@ using namespace MSToolkit;
 
 int main(int argc, char *argv[]){
 
-	//Here are all the variable we are going to need
+	//Here are all the variables we are going to need
 	MSReader r;
 	Spectrum s;
   int j;