Port ProteoWizard core to .NET 10

.editorconfig

@@ -16,3 +16,10 @@ end_of_line = lf
 
 # IDE0011: Add braces
 csharp_prefer_braces = true
+
+# WFO1000 ("property does not configure the code serialization for its property content")
+# is new in the .NET 9+ WinForms SDK and ships at Error severity, so WarningsNotAsErrors
+# cannot demote it. It fires on runtime-only properties in the vendored ZedGraph fork, the
+# ported SeeMS and MsConvertGUI - none of which are designer-edited, so the designer never
+# serializes them. Demoted to a warning (kept visible) rather than silenced with NoWarn.
+dotnet_diagnostic.WFO1000.severity = warning

.gitattributes

@@ -4,4 +4,17 @@
 *.mzml binary
 *.mzxml binary
 
-*.sh text eol=lf
+*.sh text eol=lf
+
+# cmd.exe tracks its position in a batch file by byte offset, and that accounting
+# drifts on an LF-only file: after a few `call :label` returns the search starts
+# from the wrong place and fails with "The system cannot find the batch label
+# specified". build.bat lost its entire `call :build_one` loop that way - it
+# staged whatever binaries already existed and reported success. Checkouts with
+# core.autocrlf=true happened to be immune, which is why CI never saw it.
+*.bat text eol=crlf
+
+# Fixtures copied verbatim out of the cpp tests are reference data, not source: the whole point
+# is that they are the same bytes pwiz C++ parses, so line endings must survive a checkout
+# unchanged on every platform.
+pwiz-sharp/pwiz/test/**/TestData/** -text

.gitignore

@@ -436,9 +436,16 @@ Version.cpp
 # Skyline generated files
 /pwiz_tools/Skyline/ProtocolBuffers/GeneratedCode/*.cs
 /pwiz_tools/Skyline/ProtocolBuffers/tmp/*.cs
-/pwiz_tools/Skyline/SkylineTester test list.txt
-/pwiz_tools/Skyline/SkylineTester.log
+# Test-run residue. Unanchored on purpose: on net8 these are written from the
+# staging directory and from the test UI's own output directory, not the Skyline
+# root the old entries were pinned to, so anchoring a path just moves the problem.
+SkylineTester test list.txt
+SkylineTester.log
 SkylineTester Results
+TestRunner.log
+SearchControlLog.txt
+DiannSearchControlLog.txt
+*.mzML.log
 /b.bat
 /b64.bat
 /b32.bat
@@ -476,7 +483,6 @@ SkylineTester Results
 /pwiz_tools/Skyline/Test/ProtocolBuffers/GeneratedCode/*.cs
 /pwiz_tools/Skyline/Test/ProtocolBuffers/tmp/*.cs
 /pwiz_tools/Skyline/Test/ProtocolBuffers/tmp
-/SearchControlLog.txt
 
 # created by WIFF2 SDK in working directory
 /UserSettings.data

clean.bat

@@ -1,94 +1,114 @@
-@echo off
-setlocal
-@echo off
-
-set VERBOSE=1
-if /I "%1"=="-quiet" set VERBOSE=0
-if /I "%1"=="-q" set VERBOSE=0
-
-REM # Get the location of quickbuild.bat and drop trailing slash
-set PWIZ_ROOT=%~dp0
-set PWIZ_ROOT=%PWIZ_ROOT:~0,-1%
-pushd "%PWIZ_ROOT%"
-
-if %VERBOSE%==1 echo   Cleaning build directories...
-IF EXIST build-nt-x86 rmdir /s /q build-nt-x86
-IF EXIST build-nt-x86_64 rmdir /s /q build-nt-x86_64
-
-if %VERBOSE%==1 echo   Cleaning libraries...
-git clean -f -x libraries/boost-build/src/engine > nul
-IF EXIST libraries\boost_1_43_0 rmdir /s /q libraries\boost_1_43_0
-IF EXIST libraries\boost_1_54_0 rmdir /s /q libraries\boost_1_54_0
-IF EXIST libraries\boost_1_56_0 rmdir /s /q libraries\boost_1_56_0
-IF EXIST libraries\boost_1_67_0 rmdir /s /q libraries\boost_1_67_0
-IF EXIST libraries\boost_1_76_0 rmdir /s /q libraries\boost_1_76_0
-IF EXIST libraries\boost_1_86_0 rmdir /s /q libraries\boost_1_86_0
-IF EXIST libraries\gd-2.0.33 rmdir /s /q libraries\gd-2.0.33
-IF EXIST libraries\zlib-1.2.3 rmdir /s /q libraries\zlib-1.2.3
-IF EXIST libraries\libgd-2.1.0alpha rmdir /s /q libraries\libgd-2.1.0alpha
-IF EXIST libraries\libpng-1.5.6 rmdir /s /q libraries\libpng-1.5.6
-IF EXIST libraries\freetype-VER-2-13-3 rmdir /s /q libraries\freetype-VER-2-13-3
-IF EXIST libraries\hdf5-1.8.7 rmdir /s /q libraries\hdf5-1.8.7
-IF EXIST libraries\fftw-3.1.2 rmdir /s /q libraries\fftw-3.1.2
-IF EXIST libraries\expat-2.0.1 rmdir /s /q libraries\expat-2.0.1
-
-del /f /q libraries\libfftw3-3.d* > nul 2>&1
-del /f /q libraries\msparser_*_win64 > nul 2>&1
-git clean -f -d -X libraries
-
-del /f /q pwiz\Version.cpp > nul 2>&1
-del /f /q pwiz\data\msdata\Version.cpp > nul 2>&1
-del /f /q pwiz\data\identdata\Version.cpp > nul 2>&1
-del /f /q pwiz\data\tradata\Version.cpp > nul 2>&1
-del /f /q pwiz\data\proteome\Version.cpp > nul 2>&1
-del /f /q pwiz\analysis\Version.cpp > nul 2>&1
-
-if %VERBOSE%==1 echo   Cleaning vendor dlls...
-del /f /q pwiz_aux\msrc\utility\vendor_api\ABI\*.dll > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\ABI\LicenseKey.h > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\ABI\vc10 > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\ABI\vc9 > nul 2>&1
-git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\ABI > nul 2>&1
-
-del /f /q pwiz_aux\msrc\utility\vendor_api\Agilent\*.dll > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\x86 > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\x64 > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Agilent\EULA.MHDAC > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\Documents > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\*.manifest > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\baf2sql_c.h > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\baf2sql_cpp.h > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\schema.h > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\install_pwiz_vendor_api_bruker_stub > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\x86 > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\x64 > nul 2>&1
-IF EXIST pwiz\data\vendor_api\Mobilion git clean -f -d -X pwiz\data\vendor_api\Mobilion > nul
-git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\Mobilion > nul
-del /f /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\EULA.SFCS > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\x86 > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\x64 > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\*.dll > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\ja-JP > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\zh-CN > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Thermo\*.dll > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Thermo\*.manifest > nul 2>&1
-git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\Thermo\x86 > nul
-del /f /q /s pwiz_aux\msrc\utility\vendor_api\Waters\*.dll > nul 2>&1
-del /f /q /s pwiz_aux\msrc\utility\vendor_api\Waters\*.lib > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Waters\vc12_x86 > nul 2>&1
-rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Waters\vc12_x64 > nul 2>&1
-del /f /q pwiz_aux\msrc\utility\vendor_api\Waters\*.h > nul 2>&1
-
-if %VERBOSE%==1 echo   Cleaning vendor test data...
-git clean -f -d -X pwiz\data\vendor_readers\Thermo\Reader_Thermo_Test.data > nul
-rmdir /s /q pwiz\data\vendor_readers\ABI\T2D\Reader_ABI_T2D_Test.data > nul 2>&1
-git clean -f -d -X pwiz\data\vendor_readers\UIMF\Reader_UIMF_Test.data > nul
-git clean -f -d -X pwiz\data\vendor_readers\ABI\Reader_ABI_Test.data > nul
-git clean -f -d -X pwiz\data\vendor_readers\Agilent\Reader_Agilent_Test.data > nul
-git clean -f -d -X pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data > nul
-git clean -f -d -X pwiz\data\vendor_readers\Mobilion\Reader_Mobilion_Test.data > nul
-git clean -f -d -X pwiz\data\vendor_readers\Waters\Reader_Waters_Test.data > nul
-
-IF EXIST pwiz_tools\clean-apps.bat call pwiz_tools\clean-apps.bat
-
-popd
+@echo off
+setlocal
+@echo off
+
+set VERBOSE=1
+set CLEANCPP=0
+
+REM # By default this cleans only the .NET applications and leaves the C++ build alone.
+REM # Wiping the C++ tree means re-extracting and rebuilding boost and the vendor APIs,
+REM # which dominates the cost of a rebuild and is almost never what you want when the
+REM # thing you actually need cleaned is a managed bin/obj or a stale staging directory.
+REM # Pass -cpp (or -all) for the old full clean.
+:parseargs
+if "%~1"=="" goto endparse
+if /I "%~1"=="-quiet" set VERBOSE=0
+if /I "%~1"=="-q" set VERBOSE=0
+if /I "%~1"=="-cpp" set CLEANCPP=1
+if /I "%~1"=="-all" set CLEANCPP=1
+shift
+goto parseargs
+:endparse
+
+REM # Get the location of quickbuild.bat and drop trailing slash
+set PWIZ_ROOT=%~dp0
+set PWIZ_ROOT=%PWIZ_ROOT:~0,-1%
+pushd "%PWIZ_ROOT%"
+
+if %CLEANCPP%==1 goto CLEAN_CPP
+if %VERBOSE%==1 echo   Keeping C++ build ^(pass -cpp to clean it too^)...
+goto SKIP_CPP
+
+:CLEAN_CPP
+if %VERBOSE%==1 echo   Cleaning build directories...
+IF EXIST build-nt-x86 rmdir /s /q build-nt-x86
+IF EXIST build-nt-x86_64 rmdir /s /q build-nt-x86_64
+
+if %VERBOSE%==1 echo   Cleaning libraries...
+git clean -f -x libraries/boost-build/src/engine > nul
+IF EXIST libraries\boost_1_43_0 rmdir /s /q libraries\boost_1_43_0
+IF EXIST libraries\boost_1_54_0 rmdir /s /q libraries\boost_1_54_0
+IF EXIST libraries\boost_1_56_0 rmdir /s /q libraries\boost_1_56_0
+IF EXIST libraries\boost_1_67_0 rmdir /s /q libraries\boost_1_67_0
+IF EXIST libraries\boost_1_76_0 rmdir /s /q libraries\boost_1_76_0
+IF EXIST libraries\boost_1_86_0 rmdir /s /q libraries\boost_1_86_0
+IF EXIST libraries\gd-2.0.33 rmdir /s /q libraries\gd-2.0.33
+IF EXIST libraries\zlib-1.2.3 rmdir /s /q libraries\zlib-1.2.3
+IF EXIST libraries\libgd-2.1.0alpha rmdir /s /q libraries\libgd-2.1.0alpha
+IF EXIST libraries\libpng-1.5.6 rmdir /s /q libraries\libpng-1.5.6
+IF EXIST libraries\freetype-VER-2-13-3 rmdir /s /q libraries\freetype-VER-2-13-3
+IF EXIST libraries\hdf5-1.8.7 rmdir /s /q libraries\hdf5-1.8.7
+IF EXIST libraries\fftw-3.1.2 rmdir /s /q libraries\fftw-3.1.2
+IF EXIST libraries\expat-2.0.1 rmdir /s /q libraries\expat-2.0.1
+
+del /f /q libraries\libfftw3-3.d* > nul 2>&1
+del /f /q libraries\msparser_*_win64 > nul 2>&1
+git clean -f -d -X libraries
+
+del /f /q pwiz\Version.cpp > nul 2>&1
+del /f /q pwiz\data\msdata\Version.cpp > nul 2>&1
+del /f /q pwiz\data\identdata\Version.cpp > nul 2>&1
+del /f /q pwiz\data\tradata\Version.cpp > nul 2>&1
+del /f /q pwiz\data\proteome\Version.cpp > nul 2>&1
+del /f /q pwiz\analysis\Version.cpp > nul 2>&1
+
+if %VERBOSE%==1 echo   Cleaning vendor dlls...
+del /f /q pwiz_aux\msrc\utility\vendor_api\ABI\*.dll > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\ABI\LicenseKey.h > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\ABI\vc10 > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\ABI\vc9 > nul 2>&1
+git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\ABI > nul 2>&1
+
+del /f /q pwiz_aux\msrc\utility\vendor_api\Agilent\*.dll > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\x86 > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\x64 > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Agilent\EULA.MHDAC > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Agilent\Documents > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\*.manifest > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\baf2sql_c.h > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\baf2sql_cpp.h > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Bruker\schema.h > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\install_pwiz_vendor_api_bruker_stub > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\x86 > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Bruker\x64 > nul 2>&1
+IF EXIST pwiz\data\vendor_api\Mobilion git clean -f -d -X pwiz\data\vendor_api\Mobilion > nul
+git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\Mobilion > nul
+del /f /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\EULA.SFCS > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\x86 > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\x64 > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\*.dll > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\ja-JP > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Shimadzu\zh-CN > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Thermo\*.dll > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Thermo\*.manifest > nul 2>&1
+git clean -f -d -X pwiz_aux\msrc\utility\vendor_api\Thermo\x86 > nul
+del /f /q /s pwiz_aux\msrc\utility\vendor_api\Waters\*.dll > nul 2>&1
+del /f /q /s pwiz_aux\msrc\utility\vendor_api\Waters\*.lib > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Waters\vc12_x86 > nul 2>&1
+rmdir /s /q pwiz_aux\msrc\utility\vendor_api\Waters\vc12_x64 > nul 2>&1
+del /f /q pwiz_aux\msrc\utility\vendor_api\Waters\*.h > nul 2>&1
+
+if %VERBOSE%==1 echo   Cleaning vendor test data...
+git clean -f -d -X pwiz\data\vendor_readers\Thermo\Reader_Thermo_Test.data > nul
+rmdir /s /q pwiz\data\vendor_readers\ABI\T2D\Reader_ABI_T2D_Test.data > nul 2>&1
+git clean -f -d -X pwiz\data\vendor_readers\UIMF\Reader_UIMF_Test.data > nul
+git clean -f -d -X pwiz\data\vendor_readers\ABI\Reader_ABI_Test.data > nul
+git clean -f -d -X pwiz\data\vendor_readers\Agilent\Reader_Agilent_Test.data > nul
+git clean -f -d -X pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data > nul
+git clean -f -d -X pwiz\data\vendor_readers\Mobilion\Reader_Mobilion_Test.data > nul
+git clean -f -d -X pwiz\data\vendor_readers\Waters\Reader_Waters_Test.data > nul
+
+:SKIP_CPP
+IF EXIST pwiz_tools\clean-apps.bat call pwiz_tools\clean-apps.bat
+
+popd

global.json

@@ -0,0 +1,6 @@
+{
+  "sdk": {
+    "version": "10.0.100",
+    "rollForward": "latestFeature"
+  }
+}

libraries/SQLite/update3rdPartyDLLs.bat

@@ -1,13 +1,13 @@
-@echo off
-
-REM This script decompiles a given .NET DLL, updates a specific version of an assembly reference to another version, and recompiles the DLL.
-REM Edit the perl one-liner to change the source and target versions.
-
-CALL %~p0..\msvc_setup_script.bat amd64
-
-ildasm /all /out=%~pn1.il %1 || exit /b
-perl -pi.bak -e "s/1:0:105:2/1:0:98:0/g" %~pn1.il || exit /b
-move %1 %1.bak || exit /b
-ilasm /DLL %~pn1.il || exit /b
-
+@echo off
+
+REM This script decompiles a given .NET DLL, updates a specific version of an assembly reference to another version, and recompiles the DLL.
+REM Edit the perl one-liner to change the source and target versions.
+
+CALL %~p0..\msvc_setup_script.bat amd64
+
+ildasm /all /out=%~pn1.il %1 || exit /b
+perl -pi.bak -e "s/1:0:105:2/1:0:98:0/g" %~pn1.il || exit /b
+move %1 %1.bak || exit /b
+ilasm /DLL %~pn1.il || exit /b
+
 del %~pn1.il %~pn1.il.bak %~pn1.res