* added check in tcbuild.bat that clean script does not make the repo…

…sitory dirty (#3240)

* added check in tcbuild.bat that clean script does not make the repository dirty
* fixed removing WIFF auxiliary files for Unicode testing
* changed timstof_prm_scheduler.prmsqlite to be written to test directory instead of repo root
* updated .gitignore for SearchControlLog.txt and UserSettings.data (from WIFF2 SDK)
* added error message immediately after clean script for dirty repo
* added Thermo/x64 subdir to .gitignore
* added CleanBumbershoot.bat
* added src_subset to .gitignore (automatically cleaning it when the build is successful would be an alternative, but then if the build fails, it would be dirty for subsequent builds of different configs)
* added files to .gitignore either created by TeamCity or by older versions of the code (e.g. without the fixes to delete WIFF auxiliary files for Unicode testing)

.gitignore

@@ -361,6 +361,7 @@ ASALocalRun/
 *.nvuser
 
 /build-nt-x86
+/src_subset
 /*.log
 /libraries/boost_1_*
 /libraries/expat*
@@ -391,6 +392,7 @@ 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
@@ -403,6 +405,7 @@ Version.cpp
 /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
@@ -420,32 +423,16 @@ 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
@@ -457,8 +444,24 @@ SkylineTester Results
 /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*
+/timstof_prm_scheduler.prmsqlite
+
+# created by tc-perftests.bat
+/perfTestNames.txt
+/tutorialTestNames.txt
+/tests.txt

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_tools/Bumbershoot/CleanBumbershoot.bat

@@ -0,0 +1,24 @@
+@echo off
+setlocal
+@echo off
+
+REM # Get the location of this script and drop trailing slash
+set SCRIPT_ROOT=%~dp0
+set SCRIPT_ROOT=%SCRIPT_ROOT:~0,-1%
+pushd %SCRIPT_ROOT%
+
+FOR /r %%I IN (*Version.cpp) DO del "%%I"
+IF EXIST idpicker\build-nt-x86 rmdir /s /q idpicker\build-nt-x86
+IF EXIST idpicker\packages rmdir /s /q idpicker\packages
+
+IF EXIST greazy\GUI\Properties\AssemblyInfo.cs del /q greazy\GUI\Properties\AssemblyInfo.cs
+IF EXIST idpicker\Controls\Properties\AssemblyInfo.cs del /q idpicker\Controls\Properties\AssemblyInfo.cs
+IF EXIST idpicker\CustomDataSourceDialog\Properties\AssemblyInfo.cs del /q idpicker\CustomDataSourceDialog\Properties\AssemblyInfo.cs
+IF EXIST idpicker\Model\Properties\AssemblyInfo.cs del /q idpicker\Model\Properties\AssemblyInfo.cs
+IF EXIST idpicker\Qonverter\CLI\AssemblyInfo.cpp del /q idpicker\Qonverter\CLI\AssemblyInfo.cpp
+IF EXIST idpicker\Util\Properties\AssemblyInfo.cs del /q idpicker\Util\Properties\AssemblyInfo.cs
+IF EXIST idpicker\Properties\AssemblyInfo.cs del /q idpicker\Properties\AssemblyInfo.cs
+IF EXIST idpicker\Resources\Resources.rc del /q idpicker\Resources\Resources.rc
+IF EXIST idpicker\Resources\Resources.res del /q idpicker\Resources\Resources.res
+
+popd

pwiz_tools/clean-apps.bat

@@ -12,12 +12,14 @@ call :CleanBinaries Shared
 call :CleanBinaries Skyline
 call :CleanBinaries SeeMS
 call :CleanBinaries MSConvertGUI
+call :CleanBinaries Bumbershoot
 
 IF EXIST Shared\CommonTest rmdir /s/q Shared\CommonTest
 
 IF EXIST SeeMS\CleanSeeMS.bat call SeeMS\CleanSeeMS.bat
 IF EXIST Skyline\CleanSkyline.bat call Skyline\CleanSkyline.bat
 IF EXIST BiblioSpec\CleanBiblioSpec.bat call BiblioSpec\CleanBiblioSpec.bat
+IF EXIST Bumbershoot\CleanBumbershoot.bat call Bumbershoot\CleanBumbershoot.bat
 
 popd
 rem Exit the script

scripts/misc/tcbuild-apps.bat

@@ -34,6 +34,11 @@ call clean.bat
 set EXIT=%ERRORLEVEL%
 if %EXIT% NEQ 0 set ERROR_TEXT=Error performing clean & goto error
 
+REM # check clean did not dirty repo (but postpone error until after quickbuild)
+set CLEAN_EXIT=0
+git status --porcelain | findstr . && set CLEAN_EXIT=1
+if %CLEAN_EXIT% NEQ 0 echo Repository is dirty after clean script >&2
+
 REM # the -p1 argument overrides bjam's default behavior of merging stderr into stdout
 REM # the --abbreviate-paths argument abbreviates paths like .../ftr1-value/ftr2-value/...
 
@@ -43,6 +48,7 @@ echo quickbuild.bat %ALL_ARGS% -p1 --abbreviate-paths --teamcity-test-decoration
 call quickbuild.bat %ALL_ARGS% -p1 --abbreviate-paths --teamcity-test-decoration --without-compassxtract
 set EXIT=%ERRORLEVEL%
 if %EXIT% NEQ 0 set ERROR_TEXT=Error running quickbuild & goto error
+if %CLEAN_EXIT% NEQ 0 set EXIT=%CLEAN_EXIT% & set ERROR_TEXT=Repository was dirty after clean script & goto error
 
 popd
 

scripts/misc/tcbuild.bat

@@ -10,6 +10,7 @@ pushd %SCRIPTS_MISC_ROOT%\..\..
 set EXIT=0
 set ALL_ARGS=%*
 set CLEAN=1
+set CLEAN_EXIT=0
 
 if "%ALL_ARGS: no-clean=%" neq "%ALL_ARGS%" (
     set CLEAN=0
@@ -22,6 +23,10 @@ if %CLEAN%==1 (
   call clean.bat
   set EXIT=%ERRORLEVEL%
   if %EXIT% NEQ 0 set ERROR_TEXT=Error performing clean & goto error
+
+  REM # check clean did not dirty repo (but postpone error until after quickbuild)
+  git status --porcelain | findstr . && set CLEAN_EXIT=1
+  if %CLEAN_EXIT% NEQ 0 echo Repository is dirty after clean script >&2
 )
 
 REM # the -p1 argument overrides bjam's default behavior of merging stderr into stdout
@@ -32,6 +37,7 @@ echo ##teamcity[progressMessage 'Running quickbuild...']
 call quickbuild.bat -p1 --abbreviate-paths --teamcity-test-decoration --verbose-test %ALL_ARGS%
 set EXIT=%ERRORLEVEL%
 if %EXIT% NEQ 0 set ERROR_TEXT=Error running quickbuild & goto error
+if %CLEAN_EXIT% NEQ 0 set EXIT=%CLEAN_EXIT% & set ERROR_TEXT=Repository was dirty after clean script & goto error
 
 REM # uncomment this to test that test failures and error output are handled properly
 REM call quickbuild.bat -p1 --teamcity-test-decoration pwiz/utility/misc//FailUnitTest pwiz/utility/misc//FailRunTest