Merge branch 'master' into feature/bruker_precursor_2

.github/workflows/build_and_test.yml

@@ -57,12 +57,12 @@ jobs:
 #            compiler: g++-9,
 #            toolset: 'toolset=gcc'
 #          }
-        - {
-            name: "macOS Latest Clang",
-            os:	macos-12,
-            compiler: 'latest clang',
-            toolset: 'toolset=darwin'
-          }
+#        - {
+#            name: "macOS Latest Clang",
+#            os:	macos-12,
+#            compiler: 'latest clang',
+#            toolset: 'toolset=darwin'
+#          }
 
     # Using the value from the matrix above we select the platform (operating system) to run on
     runs-on: ${{ matrix.config.os }}

.gitignore

@@ -360,7 +360,8 @@ ASALocalRun/
 # NVidia Nsight GPU debugger configuration file
 *.nvuser
 
-/build-nt-x86
+build-nt-x86
+/src_subset
 /*.log
 /libraries/boost_1_*
 /libraries/expat*
@@ -379,7 +380,8 @@ Version.cpp
 /pwiz_tools/Bumbershoot/**/AssemblyInfo.cpp
 /pwiz_tools/Bumbershoot/**/AssemblyInfo.cs
 /pwiz_tools/Bumbershoot/idpicker/Resources/Resources.*
-/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/Properties/AssemblyInfo.cs
+/pwiz/utility/bindings/CLI/example/binaries
+/artifact_xml
 
 # Vendor reader test data extracted from tarballs (newer data should be committed directly to git)
 /pwiz/data/vendor_readers/*/Reader*Test.data/**/1SRef
@@ -391,6 +393,7 @@ Version.cpp
 /pwiz_aux/msrc/utility/vendor_api/**/*.dll
 /pwiz_aux/msrc/utility/vendor_api/*/EULA.*
 /pwiz_aux/msrc/utility/vendor_api/ABI/LicenseKey.h
+/pwiz_aux/msrc/utility/vendor_api/ABI/SCIEX.Apis.Data.v1.xml
 /pwiz_aux/msrc/utility/vendor_api/Agilent/x64/
 /pwiz_aux/msrc/utility/vendor_api/Agilent/x86/
 /pwiz_aux/msrc/utility/vendor_api/Bruker/BAF2SQL-README.txt
@@ -399,9 +402,12 @@ Version.cpp
 /pwiz_aux/msrc/utility/vendor_api/Bruker/x64/
 /pwiz_aux/msrc/utility/vendor_api/Bruker/x86/
 /pwiz_aux/msrc/utility/vendor_api/Bruker/**/*.h
+/pwiz_aux/msrc/utility/vendor_api/Bruker/**.SxS.manifest
+/pwiz_aux/msrc/utility/vendor_api/Mobilion/*.h
 /pwiz_aux/msrc/utility/vendor_api/Shimadzu/*.xml
 /pwiz_aux/msrc/utility/vendor_api/Shimadzu/*.txt
 /pwiz_aux/msrc/utility/vendor_api/Waters/MassLynx*.h*
+/pwiz_aux/msrc/utility/vendor_api/thermo/x64
 /pwiz_aux/msrc/utility/vendor_api/thermo/ThermoFisher.CommonCore.RawFileReader.xml
 /pwiz_aux/msrc/utility/vendor_api/thermo/ThermoFisher.CommonCore.MassPrecisionEstimator.xml
 /pwiz_aux/msrc/utility/vendor_api/thermo/ThermoFisher.CommonCore.Data.xml
@@ -419,45 +425,48 @@ SkylineTester Results
 /bs32.bat
 /bso64.bat
 /bso32.bat
+/qb64.bat
 /SignAfterPublishPW.bat
-/OnyxTOFMS.试验.wiff.scan
-/160109_Mix1_calcurve_074_raw.skyl
-/160109_Mix1_calcurve_074_raw.skyd
-/160109_Mix1_calcurve_074_raw
-/160109_Mix1_calcurve_073_mzML.skyl
-/160109_Mix1_calcurve_073_mzML.skyd
-/160109_Mix1_calcurve_073_mzML
-/160109_Mix1_calcurve_071_raw.skyl
-/160109_Mix1_calcurve_071_raw.skyd
-/160109_Mix1_calcurve_071_raw
-/160109_Mix1_calcurve_070_mzML.skyl
-/160109_Mix1_calcurve_070_mzML.skyd
-/160109_Mix1_calcurve_070_mzML
-/REP02_CE_Vantage_15mTorr_0001_REP2_02_raw.skyl
-/REP02_CE_Vantage_15mTorr_0001_REP2_02_raw.skyd
-/REP02_CE_Vantage_15mTorr_0001_REP2_02_raw
-/REP02_CE_Vantage_15mTorr_0001_REP2_01_raw.skyl
-/REP02_CE_Vantage_15mTorr_0001_REP2_01_raw.skyd
-/REP02_CE_Vantage_15mTorr_0001_REP2_01_raw
-/REP01_CE_Vantage_15mTorr_0001_REP1_02_raw.skyl
-/REP01_CE_Vantage_15mTorr_0001_REP1_02_raw.skyd
-/REP01_CE_Vantage_15mTorr_0001_REP1_02_raw
-/REP01_CE_Vantage_15mTorr_0001_REP1_01_raw.skyl
-/REP01_CE_Vantage_15mTorr_0001_REP1_01_raw.skyd
-/REP01_CE_Vantage_15mTorr_0001_REP1_01_raw
+/160109_Mix1_calcurve_074_raw*
+/160109_Mix1_calcurve_073_mzML*
+/160109_Mix1_calcurve_071_raw*
+/160109_Mix1_calcurve_070_mzML*
+/REP02_CE_Vantage_15mTorr_0001_REP2_02_raw*
+/REP02_CE_Vantage_15mTorr_0001_REP2_01_raw*
+/REP01_CE_Vantage_15mTorr_0001_REP1_02_raw*
+/REP01_CE_Vantage_15mTorr_0001_REP1_01_raw*
 /pwiz_tools/Skyline/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/SkylineCmd/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/SkylineNightly/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/SkylineNightlyShim/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/SkylineTester/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/TestRunner/Properties/AssemblyInfo.cs
+/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/Executables/Installer/FileList64.txt
 /pwiz_tools/Skyline/TestSettings_x??.testsettings
 /pwiz_tools/Skyline/SignAfterPublishPW.bat
 /BrowseOnly
 /x64/BrowseOnly
-/qb64.bat
 /pwiz_tools/Skyline/Test/ProtocolBuffers/GeneratedCode/*.cs
 /pwiz_tools/Skyline/Test/ProtocolBuffers/tmp/*.cs
 /pwiz_tools/Skyline/Test/ProtocolBuffers/tmp
-/pwiz_aux/msrc/utility/vendor_api/ABI/SCIEX.Apis.Data.v1.xml
+/SearchControlLog.txt
+
+# created by WIFF2 SDK in working directory
+/UserSettings.data
+/UserSettings.data-journal
+
+# created by TeamCity for Skyline versions that need PrositConfig.xml
+/pwiz_tools/Skyline/Model/Prosit/
+
+# created by older versions of the code in the working directory
+/Enolase_repeats_AQv1.4.2*
+/PressureTrace1*
+/7600ZenoTOFMSMS*
+/swath.api*
+/timstof_prm_scheduler.prmsqlite
+
+# created by tc-perftests.bat
+/perfTestNames.txt
+/tutorialTestNames.txt
+/tests.txt

Jamroot.jam

@@ -605,7 +605,7 @@ if [ modules.peek : NT ]
             if ! --without-sciex in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_ABI.7z" ; }
             if ! --without-agilent in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Agilent.7z" ; }
             if ! --without-bruker in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Bruker.7z" ; }
-# Waiting for CCS<->DT support in .mbi reader #            if ! --without-mobilion in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Mobilion.7z" ; }
+            if ! --without-mobilion in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Mobilion.7z" ; }
             if ! --without-shimadzu in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Shimadzu.7z" ; }
             if ! --without-thermo in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_Thermo.7z" ; }
             #if ! --without-unifi in $(args) { SHELL "$(PWIZ_LIBRARIES_PATH)\\7za.exe x -aoa -pi-agree-to-the-vendor-licenses -o$(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_UNIFI.7z" ; }
@@ -778,7 +778,7 @@ rule install-vendor-api-dependencies-to-locations ( locations + : properties * )
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI/T2D ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI/T2D//install_pwiz_vendor_api_abi_t2d/$(location) ; }
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/Agilent ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Agilent//install_pwiz_vendor_api_agilent/$(location) ; }
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/Bruker ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Bruker//install_pwiz_vendor_api_bruker/$(location) ; }
-    # wait for CCS<->DT support in Mobllion #         if [ path.exists pwiz_aux/msrc/utility/vendor_api/Mobilion ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Mobilion//install_pwiz_vendor_api_mbi/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/Mobilion ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Mobilion//install_pwiz_vendor_api_mbi/$(location) ; }
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/Shimadzu ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Shimadzu//install_pwiz_vendor_api_shimadzu/$(location) ; }
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/thermo ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/thermo//install_pwiz_vendor_api_thermo/$(location) ; }
             if [ path.exists pwiz_aux/msrc/utility/vendor_api/UIMF ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UIMF//install_pwiz_vendor_api_uimf/$(location) ; }
@@ -1129,7 +1129,7 @@ rule mbi-dll-location ( api-path : properties * )
 {
     local result = $(api-path) ;
     if --i-agree-to-the-vendor-licenses in [ modules.peek : ARGV ] &&
-       [ path.exists $(api-path)\\MBICore.dll ]
+       [ path.exists $(api-path)\\MBI_SDK.dll ]
     {
         return $(result) ;
     }

libraries/expat.jam

@@ -108,6 +108,7 @@ rule init ( version ? : location : options * )
             <location-prefix>expat
             <toolset>msvc:<define>_CRT_SECURE_NO_DEPRECATE
             <toolset>msvc:<define>_SCL_SECURE_NO_DEPRECATE
+            <toolset>msvc:<cxxflags>/wd4100 # warning C4100: 'enc': unreferenced formal parameter
             <define>HAVE_EXPAT_CONFIG_H
             <define>XML_LARGE_SIZE
             <implicit-dependency>expat_config.h