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Merge branch 'master' into Skyline/work/20240617_MsfAmbiguousSpectra
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@nickshulman
nickshulman authored Jan 9, 2025
2 parents 45ba4d9 + 0292182 commit dcf9c86
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12 changes: 6 additions & 6 deletions .github/workflows/build_and_test.yml
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Expand Up @@ -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 }}
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67 changes: 38 additions & 29 deletions .gitignore
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Expand Up @@ -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*
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
3 changes: 3 additions & 0 deletions .gitmodules
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Expand Up @@ -7,3 +7,6 @@
[submodule "pwiz_tools/Skyline/Executables/BullseyeSharp"]
path = pwiz_tools/Skyline/Executables/BullseyeSharp
url = https://github.com/ProteoWizard/BullseyeSharp
[submodule "pwiz_tools/Skyline/Executables/DevTools/DocumentConverter"]
path = pwiz_tools/Skyline/Executables/DevTools/DocumentConverter
url = https://github.com/ProteoWizard/DocumentConverter
6 changes: 3 additions & 3 deletions Jamroot.jam
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Expand Up @@ -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 $(PWIZ_ROOT_PATH)\\pwiz_aux\\msrc\\utility\\vendor_api_UNIFI.7z" ; }
Expand Down Expand Up @@ -778,7 +778,7 @@ rule install-vendor-api-dependencies-to-locations ( locations + : properties * )
if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI/T2D ] { dependencies += <dependency>$(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) ; }
Expand Down Expand Up @@ -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) ;
}
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1 change: 1 addition & 0 deletions libraries/expat.jam
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Expand Up @@ -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
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Empty file removed libraries/hdf5-1.12.0/HEADERS_ONLY
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13 changes: 0 additions & 13 deletions libraries/hdf5-1.12.0/c++/COPYING
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84 changes: 0 additions & 84 deletions libraries/hdf5-1.12.0/c++/src/H5AbstractDs.h
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27 changes: 0 additions & 27 deletions libraries/hdf5-1.12.0/c++/src/H5Alltypes.h
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68 changes: 0 additions & 68 deletions libraries/hdf5-1.12.0/c++/src/H5ArrayType.h
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