Merge branch 'master' into feature/update-to-boost-1.86

.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
@@ -399,10 +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
@@ -420,45 +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

pwiz/analysis/chromatogram_processing/ChromatogramList_LockmassRefiner.cpp

@@ -41,29 +41,30 @@ ChromatogramList_LockmassRefiner::ChromatogramList_LockmassRefiner(const msdata:
 : ChromatogramListWrapper(inner), mzPositiveScans_(lockmassMzPosScans), mzNegativeScans_(lockmassMzNegScans), tolerance_(lockmassTolerance)
 {
 
-    // add processing methods to the copy of the inner ChromatogramList's data processing
-    ProcessingMethod method;
-    method.order = dp_->processingMethods.size();
-    method.set(MS_m_z_calibration);
-
-    if (!dp_->processingMethods.empty())
-        method.softwarePtr = dp_->processingMethods[0].softwarePtr;
-
     detail::ChromatogramList_Waters* waters = dynamic_cast<detail::ChromatogramList_Waters*>(&*inner);
     if (waters)
     {
+        // add processing methods to the copy of the inner ChromatogramList's data processing
+        ProcessingMethod method;
+        method.order = dp_->processingMethods.size();
+        method.set(MS_m_z_calibration);
+
+        if (!dp_->processingMethods.empty())
+            method.softwarePtr = dp_->processingMethods[0].softwarePtr;
+
         method.userParams.push_back(UserParam("Waters lockmass correction"));
+        dp_->processingMethods.push_back(method);
     }
     else
     {
-        cerr << "Warning: lockmass refinement was requested, but is unavailable";
+        cerr << "Warning: lockmass refinement for chromatogram data was requested, but is unavailable";
 #ifdef WIN32
         cerr << " for non-Waters input data. ";
 #else
         cerr << " as it depends on Windows DLLs.  ";
 #endif
+        cerr << endl;
     }
-    dp_->processingMethods.push_back(method);
 }
 
 

pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.cpp

@@ -41,31 +41,30 @@ PWIZ_API_DECL
 SpectrumList_LockmassRefiner::SpectrumList_LockmassRefiner(const msdata::SpectrumListPtr& inner, double lockmassMzPosScans, double lockmassMzNegScans, double lockmassTolerance)
 : SpectrumListWrapper(inner), mzPositiveScans_(lockmassMzPosScans), mzNegativeScans_(lockmassMzNegScans), tolerance_(lockmassTolerance)
 {
-
-    // add processing methods to the copy of the inner SpectrumList's data processing
-    ProcessingMethod method;
-    method.order = dp_->processingMethods.size();
-    method.set(MS_m_z_calibration);
-
-    if (!dp_->processingMethods.empty())
-        method.softwarePtr = dp_->processingMethods[0].softwarePtr;
-
-    SpectrumList_PeakPicker* peakPicker = dynamic_cast<SpectrumList_PeakPicker*>(&*inner);
+    SpectrumList_PeakPicker* peakPicker = dynamic_cast<SpectrumList_PeakPicker*>(&*inner); // If there's a peak picker, it will be outermost
     detail::SpectrumList_Waters* waters = dynamic_cast<detail::SpectrumList_Waters*>(peakPicker ? &*peakPicker->inner() : &*inner);
     if (waters)
     {
+        // add processing methods to the copy of the inner SpectrumList's data processing
+        ProcessingMethod method;
+        method.order = dp_->processingMethods.size();
+        method.set(MS_m_z_calibration);
+
+        if (!dp_->processingMethods.empty())
+            method.softwarePtr = dp_->processingMethods[0].softwarePtr;
         method.userParams.push_back(UserParam("Waters lockmass correction"));
+        dp_->processingMethods.push_back(method);
     }
     else
     {
-        cerr << "Warning: lockmass refinement was requested, but is unavailable";
+        cerr << "Warning: lockmass refinement for spectrum data was requested, but is unavailable";
 #ifdef WIN32
         cerr << " for non-Waters input data. ";
 #else
         cerr << " as it depends on Windows DLLs.  ";
 #endif
+        cerr << endl;
     }
-    dp_->processingMethods.push_back(method);
 }
 
 

pwiz/data/vendor_readers/Mobilion/ChromatogramList_Mobilion.cpp

@@ -98,7 +98,6 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_Mobilion::chromatogram(size_t ind
     if (!result.get())
         throw std::runtime_error("[ChromatogramList_Mobilion::chromatogram()] Allocation error.");
 
-    boost::lock_guard<boost::mutex> lock(processWideHdf5Mutex);  // lock_guard will unlock mutex when out of scope or when exception thrown (during destruction)
     result->index = index;
     result->id = ie.id;
     result->set(ie.chromatogramType);

pwiz/data/vendor_readers/Mobilion/Reader_Mobilion.cpp

@@ -183,8 +183,6 @@ void Reader_Mobilion::read(const string& filename,
         throw ReaderFail(string("[Reader_Mobilion::read()] Mobilion API does not support Unicode in filepaths ('") + utf8CharAsString(unicodeCharItr, filename.end()) + "')");
     }
 
-    boost::lock_guard<boost::mutex> lock(processWideHdf5Mutex); // mutex unlocks when out of scope or when exception thrown (during destruction)
-
     MBIFilePtr rawdata(new MBIFileWrapper(filename.c_str()));
     result.run.spectrumListPtr = SpectrumListPtr(new SpectrumList_Mobilion(result, rawdata, config));
     result.run.chromatogramListPtr = ChromatogramListPtr(new ChromatogramList_Mobilion(rawdata, config));

pwiz/data/vendor_readers/Mobilion/Reader_Mobilion_Detail.hpp

@@ -36,18 +36,23 @@ namespace pwiz {
 namespace msdata {
 namespace detail {
 namespace Mobilion {
+
+extern boost::mutex processWideHdf5Mutex; // HDF5 library isn't thread-safe: allow just one at a time
+
 PWIZ_API_DECL class MBIFileWrapper
 {
     public:
     MBIFileWrapper(const std::string& filepath)
     : file(filepath.c_str())
     {
+        processWideHdf5Mutex.lock(); // HDF5 library isn't thread-safe: allow just one at a time
         file.Init();
     }
 
     ~MBIFileWrapper()
     {
         file.Close();
+        processWideHdf5Mutex.unlock(); // HDF5 library isn't thread-safe: allow just one at a time
     }
 
     MBIFile file;
@@ -65,7 +70,6 @@ PWIZ_API_DECL CVID translatePolarity(const std::string& polarity);
 PWIZ_API_DECL CVID translateAsInletType(IonizationType ionizationType);
 PWIZ_API_DECL CVID translate(ActivationType activationType);*/
 
-extern boost::mutex processWideHdf5Mutex; // HDF5 library isn't thread-safe
 } // Mobilion
 
 using namespace Mobilion;

pwiz/data/vendor_readers/Mobilion/SpectrumList_Mobilion.cpp

@@ -76,7 +76,6 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_Mobilion::spectrum(size_t index, bool get
 
 PWIZ_API_DECL SpectrumPtr SpectrumList_Mobilion::spectrum(size_t index, DetailLevel detailLevel) const
 {
-    boost::lock_guard<boost::mutex> lock(processWideHdf5Mutex);  // lock_guard will unlock mutex when out of scope or when exception thrown (during destruction)
     if (index >= size_)
         throw runtime_error("[SpectrumList_Mobilion::spectrum()] Bad index: "
                             + lexical_cast<string>(index));

pwiz/data/vendor_readers/Shimadzu/SpectrumList_Shimadzu.cpp

@@ -176,16 +176,17 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_Shimadzu::spectrum(size_t index, DetailLe
             spectrum->getPrecursorInfo(selectedMz, intensity, charge);
 
             Precursor precursor;
-            /*if (spectrum->getHasIsolationInfo())
+            if (spectrum->getHasIsolationInfo())
             {
                 double centerMz, lowerLimit, upperLimit;
                 spectrum->getIsolationInfo(centerMz, lowerLimit, upperLimit);
                 precursor.isolationWindow.set(MS_isolation_window_target_m_z, centerMz, MS_m_z);
-                precursor.isolationWindow.set(MS_isolation_window_lower_offset, centerMz - lowerLimit, MS_m_z);
-                precursor.isolationWindow.set(MS_isolation_window_upper_offset, upperLimit - centerMz, MS_m_z);
-				selectedMz = centerMz;
-            }*/
-            precursor.isolationWindow.set(MS_isolation_window_target_m_z, selectedMz, MS_m_z);
+                precursor.isolationWindow.set(MS_isolation_window_lower_offset, lowerLimit, MS_m_z);
+                precursor.isolationWindow.set(MS_isolation_window_upper_offset, upperLimit, MS_m_z);
+                selectedMz = centerMz;
+            }
+            else
+                precursor.isolationWindow.set(MS_isolation_window_target_m_z, selectedMz, MS_m_z);
 
             SelectedIon selectedIon;
 

pwiz/utility/bindings/CLI/timstof_prm_scheduler/PrmSchedulerTest.cpp

@@ -666,6 +666,7 @@ int main(int argc, char* argv[])
 
     try
     {
+        bfs::current_path(bfs::path(testArgs[0]).parent_path()); // set working directory to test exe location
         if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
         if (os_) *os_ << "PrmSchedulerTest\n";
 

pwiz/utility/misc/VendorReaderTestHarness.cpp

@@ -560,6 +560,7 @@ void testRead(const Reader& reader, const string& rawpath, const bfs::path& pare
     bfs::path::string_type unicodeTestString(boost::locale::conv::utf_to_utf<bfs::path::value_type>(L"-试验"));
     bfs::path rawpathPath(rawpath);
     bfs::path newRawPath = bfs::current_path() / rawpathPath.filename();
+    vector<bfs::path> extraCopiedPaths;
     const auto& oldExtension = newRawPath.extension().native();
     newRawPath = newRawPath.replace_extension().native() + unicodeTestString + newRawPath.extension().native();
     if (bfs::exists(newRawPath))
@@ -571,37 +572,19 @@ void testRead(const Reader& reader, const string& rawpath, const bfs::path& pare
         // special case for wiff files with accompanying .scan files
         if (bal::iends_with(rawpath, ".wiff") || bal::iends_with(rawpath, ".wiff2"))
         {
-            bfs::path wiffscanPath(rawpathPath);
-            wiffscanPath.replace_extension(".wiff.scan");
-            if (bfs::exists(wiffscanPath))
+            for (auto ext : { L".wiff.scan", L".dad.scan", L".dad.sidx" })
             {
-                bfs::path newWiffscanPath = bfs::current_path() / rawpathPath.filename(); // replace_extension won't work as desired on wiffscanPath
-                newWiffscanPath = newWiffscanPath.replace_extension().native() + unicodeTestString + boost::locale::conv::utf_to_utf<bfs::path::value_type>(L".wiff.scan");
-                if (bfs::exists(newWiffscanPath))
-                    bfs::remove(newWiffscanPath);
-                bfs::copy_file(wiffscanPath, newWiffscanPath);
-            }
-
-            wiffscanPath = rawpathPath;
-            wiffscanPath.replace_extension(".dad.scan");
-            if (bfs::exists(wiffscanPath))
-            {
-                bfs::path newWiffscanPath = bfs::current_path() / rawpathPath.filename(); // replace_extension won't work as desired on wiffscanPath
-                newWiffscanPath = newWiffscanPath.replace_extension().native() + unicodeTestString + boost::locale::conv::utf_to_utf<bfs::path::value_type>(L".dad.scan");
-                if (bfs::exists(newWiffscanPath))
-                    bfs::remove(newWiffscanPath);
-                bfs::copy_file(wiffscanPath, newWiffscanPath);
-            }
-
-            wiffscanPath = rawpathPath;
-            wiffscanPath.replace_extension(".dad.sidx");
-            if (bfs::exists(wiffscanPath))
-            {
-                bfs::path newWiffscanPath = bfs::current_path() / rawpathPath.filename(); // replace_extension won't work as desired on wiffscanPath
-                newWiffscanPath = newWiffscanPath.replace_extension().native() + unicodeTestString + boost::locale::conv::utf_to_utf<bfs::path::value_type>(L".dad.sidx");
-                if (bfs::exists(newWiffscanPath))
-                    bfs::remove(newWiffscanPath);
-                bfs::copy_file(wiffscanPath, newWiffscanPath);
+                bfs::path wiffscanPath(rawpathPath);
+                wiffscanPath.replace_extension(ext);
+                if (bfs::exists(wiffscanPath))
+                {
+                    bfs::path newWiffscanPath = bfs::current_path() / rawpathPath.filename(); // replace_extension won't work as desired on wiffscanPath
+                    newWiffscanPath = newWiffscanPath.replace_extension().native() + unicodeTestString + boost::locale::conv::utf_to_utf<bfs::path::value_type>(ext);
+                    if (bfs::exists(newWiffscanPath))
+                        bfs::remove(newWiffscanPath);
+                    bfs::copy_file(wiffscanPath, newWiffscanPath);
+                    extraCopiedPaths.emplace_back(newWiffscanPath);
+                }
             }
         }
         bfs::copy_file(rawpathPath, newRawPath);
@@ -682,17 +665,8 @@ void testRead(const Reader& reader, const string& rawpath, const bfs::path& pare
         bfs::remove_all(newRawPath); // remove the copy of the RAW file with non-ASCII characters
 
         // special case for wiff files with accompanying .scan files
-        if (bal::iequals(rawpathPath.extension().string(), ".wiff"))
-        {
-            bfs::path wiffscanPath(rawpathPath);
-            wiffscanPath.replace_extension(".wiff.scan");
-            if (bfs::exists(wiffscanPath))
-            {
-                bfs::path newWiffscanPath = bfs::current_path() / rawpathPath.filename(); // replace_extension won't work as desired on wiffscanPath
-                newWiffscanPath.replace_extension(unicodeTestString + boost::locale::conv::utf_to_utf<bfs::path::value_type>(L".wiff.scan"));
-                bfs::remove(newWiffscanPath);
-            }
-        }
+        for (auto extraPath : extraCopiedPaths)
+            bfs::remove(extraPath);
     }
     catch (bfs::filesystem_error& e)
     {

pwiz_aux/msrc/utility/vendor_api/Bruker/Jamfile.jam

@@ -233,4 +233,6 @@ explicit install_pwiz_vendor_api_bruker ;
 install install_pwiz_vendor_api_bruker_stub
     : [ path.glob $(API_PATH) : *.manifest ]
     ;
+
+explicit install_pwiz_vendor_api_bruker_stub ;
 }