Restructuring (#32)

* Complete restructuring of the source.
  1. Removed older 3rd party source that I don't think anyone is using anymore.
  2. Separated builds into MSToolkit code and external 3rd party code.
  3. Static builds optionally using the 3rd party code.
  4. Added .dll builds
  5. Users should be able to use their own zlib and expat builds if already installed on their system.
  6. Adding VS projects for validation builds on GitHub.

* Create VS2019.yml (#29) (#30)

Builds MSToolkit on Visual Studio 2019

* Update VS2019.yml

* restore missing files: this was due to rules in the .gitignore, so consider revising...
fix some paths for the visual studio build

* simplifying the expat builds.

* Changes to VS builds

* VS build changes.

* VS changes.

* Update VS2019.yml (#31)

* action update

* VS and action changes.

* VS updates

* VS2019.yml update

* Added another build test.

* Add in Thermo RAW file support on windows builds.

* Create linux.yml

* Updating Makefile for Linux builds.
Updating VS projects for better library builds.
Version update to new numbering system.
Silence some warnings.

* Update linux.yml

* Updated nmake file.

---------

Co-authored-by: mhoopmann <[email protected]>

Author: mhoopmann

.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;