Fix/gh actions win64

.github/workflows/build_and_release.yml

@@ -103,18 +103,20 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: create_dirs
-      run: CD .. || MKDIR my_rel my_build
+      run: MKDIR my_rel my_build
     - name: configure_and_make
       run: |
-        CD ..
         SET base_dir=%cd%
         ECHO %base_dir%
-        CALL maracluster\admin\builders\nativew64_build.bat -s %base_dir% -r %base_dir%\my_rel -b %base_dir%\my_build -g
+        CD ..
+        SET src_dir=%cd%
+        ECHO %src_dir%
+        CALL maracluster\admin\builders\nativew64_build.bat -s %src_dir% -r %base_dir%\my_rel -b %src_dir%\my_build -g
     - name: Upload packages
       uses: actions/upload-artifact@v4
       with:
         name: win64-packages
-        path: ..\my_rel
+        path: my_rel
 
   pre-release:
     runs-on: ubuntu-latest

admin/builders/_init_msvc_.bat

@@ -1,6 +1,6 @@
 set BUILD_TARGET=%1
 
-call :downloadfile https://github.com/microsoft/vswhere/releases/download/2.8.4/vswhere.exe vswhere.exe
+call %~dp0\download_file.bat https://github.com/microsoft/vswhere/releases/download/2.8.4/vswhere.exe vswhere.exe
 for /f "usebackq tokens=*" %%i in (`.\vswhere.exe -legacy -latest  -property installationPath`) do (
   set MSVC_INSTALL_DIR=%%i
 )
@@ -58,9 +58,4 @@ if not defined DevEnvDir (
   )
 )
 
-EXIT /B %ERRORLEVEL%
-
-:downloadfile
-echo Downloading %1 to %2
-PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%1','%2')"
-EXIT /B
+EXIT /B %ERRORLEVEL%

admin/builders/_urls_and_file_names_.bat

@@ -3,8 +3,8 @@
 ::: hardcoded in the respective buiding scripts
 
 ::: 7-zip
-set ZIP_BASE=7zi
-set ZIP_URL=https://kumisystems.dl.sourceforge.net/project/sevenzip/7-Zip/19.00/7z1900.exe
+set ZIP_BASE=7zip
+set ZIP_URL=https://sourceforge.net/projects/sevenzip/files/7-Zip/24.09/7z2409.exe/download
 
 ::: CMake
 set CMAKE_VERSION=3.23.1
@@ -14,30 +14,42 @@ set CMAKE_URL=https://github.com/Kitware/CMake/releases/download/v%CMAKE_VERSION
 ::: Proteowizard
 ::: https://teamcity.labkey.org/viewType.html?buildTypeId=bt81 :::
 ::: without-t = without tests :::
-set PWIZ_VERSION_URL=https://teamcity.labkey.org/guestAuth/repository/download/bt81/.lastSuccessful/VERSION
-call :downloadfile %PWIZ_VERSION_URL% %INSTALL_DIR%\VERSION
-set /p PWIZ_VERSION_STRING=<%INSTALL_DIR%\VERSION
-set PWIZ_BASE=pwiz-src-without-t-%PWIZ_VERSION_STRING: =_%
-set PWIZ_URL=https://teamcity.labkey.org/guestAuth/repository/download/bt81/.lastSuccessful/%PWIZ_BASE%.tar.bz2
+set PWIZ_VERSION_URL=https://proteowizard.sourceforge.io/releases/bt81.xml
+call %~dp0\download_file.bat %PWIZ_VERSION_URL% bt81.xml
+call :extractbuildinfo
+echo ✅ PWIZ_BUILD_ID: %PWIZ_BUILD_ID%
+echo ✅ PWIZ_FILE_NAME: %PWIZ_FILE_NAME%
+set PWIZ_URL=https://mc-tca-01.s3.us-west-2.amazonaws.com/ProteoWizard/bt81/%PWIZ_BUILD_ID%/%PWIZ_FILE_NAME%
+
 ::: remember to update the boost and zlib version when ProteoWizard updates their versions
-set BOOST_BASE=boost_1_76_0
+set BOOST_BASE=boost_1_86_0
 set ZLIB_BASE=zlib-1.2.3
 
-::: Boost asio library
-set BOOST_ASIO_BASE=boost_asio_1_18_2
-set BOOST_ASIO_URL=https://sourceforge.net/projects/asio/files/asio/1.18.2 (Stable)/%BOOST_ASIO_BASE%.zip/download
+::: Boost asio library (note the additional %%% before %20 to prevent interpretation as a variable)
+set BOOST_ASIO_BASE=boost_asio_1_30_2
+set BOOST_ASIO_URL=https://sourceforge.net/projects/asio/files/asio/1.30.2%%%%20(Stable)/%BOOST_ASIO_BASE%.zip/download
+
+::: Boost unordered library
+set BOOST_UNORDERED_BASE=unordered-boost-1.86.0
+set BOOST_UNORDERED_URL=https://github.com/boostorg/unordered/archive/refs/tags/boost-1.86.0.zip
 
 ::: Qt
 set QT_BASE=qtbase-opensource-src-5.9.9
 set QT_URL=https://download.qt.io/archive/qt/5.9/5.9.9/submodules/%QT_BASE%.zip
 set JOM_URL=http://download.qt.io/official_releases/jom/jom_1_1_3.zip
 
-::: NSIS
-set NSIS_URL=https://sourceforge.net/projects/nsis/files/NSIS 3/3.04/nsis-3.04-setup.exe/download
+::: NSIS (note the additional %%% before %20 to prevent interpretation as a variable)
+set NSIS_URL=https://sourceforge.net/projects/nsis/files/NSIS%%%%203/3.11/nsis-3.11-setup.exe/download
 
 EXIT /B
 
-:downloadfile
-PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%1','%2')"
-EXIT /B
 
+:: Macro to extract BUILD_ID and FILE_NAME using PowerShell regex
+:extractbuildinfo
+::: Step 1: Run PowerShell and output extracted strings to temp files
+PowerShell "$content = Get-Content -Raw 'bt81.xml'; if ($content -match 'id:(\d+)/artifacts/content/(pwiz-src-without-t-[^<]+?\.tar\.bz2)') { $matches[1] | Out-File -Encoding ASCII 'build_id.tmp' }"
+PowerShell "$content = Get-Content -Raw 'bt81.xml'; if ($content -match 'id:(\d+)/artifacts/content/(pwiz-src-without-t-[^<]+?\.tar\.bz2)') { $matches[2] | Out-File -Encoding ASCII 'file_name.tmp' }"
+::: Step 2: Read from the temp files into batch variables
+set /p PWIZ_BUILD_ID=<build_id.tmp
+set /p PWIZ_FILE_NAME=<file_name.tmp
+EXIT /B

admin/builders/download_file.bat

@@ -0,0 +1,11 @@
+:: download a file using curl or PowerShell
+SET URL=%~1
+SET OUT=%~2
+
+echo Downloading %URL% to %OUT%
+where curl >nul 2>&1
+IF %ERRORLEVEL%==0 (
+    curl -L "%URL%" -o "%OUT%"
+) ELSE (
+    PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%URL%','%OUT%')"
+)

admin/builders/install_proteowizard.bat

@@ -11,7 +11,7 @@ set PWIZ_DIR=%INSTALL_DIR%\proteowizard
 if not exist "%PWIZ_DIR%\lib" (
   echo Downloading and installing ProteoWizard
   if not exist "%PWIZ_DIR%" (
-    call :downloadfile %PWIZ_URL% %INSTALL_DIR%\pwiz.tar.bz2
+    call %~dp0\download_file.bat %PWIZ_URL% %INSTALL_DIR%\pwiz.tar.bz2
     if not exist "%INSTALL_DIR%\pwiz.tar" (
       %ZIP_EXE% x "%INSTALL_DIR%\pwiz.tar.bz2" -o"%INSTALL_DIR%" -aoa > NUL
     )
@@ -28,6 +28,7 @@ if not exist "%PWIZ_DIR%\lib" (
                 pwiz/data/msdata//pwiz_data_msdata ^
                 pwiz/data/msdata//pwiz_data_msdata_version ^
                 pwiz/data/msdata/mz5//pwiz_data_msdata_mz5 ^
+                pwiz/data/msdata/mzmlb//pwiz_data_msdata_mzmlb ^
                 pwiz/data/proteome//pwiz_data_proteome ^
                 pwiz/utility/chemistry//pwiz_utility_chemistry ^
                 pwiz/utility/minimxml//pwiz_utility_minimxml ^
@@ -103,14 +104,13 @@ if not exist "%PWIZ_DIR%\lib" (
   for /r pwiz %%x in (*.hpp, *.h) do copy "%%x" include\ /Y > NUL
 
   ::: copy the boost::asio library, which is not included by the ProteoWizard boost tar but is needed for maracluster
-  call :downloadfile "%BOOST_ASIO_URL%" %INSTALL_DIR%\boost_asio.zip
+  call %~dp0\download_file.bat "%BOOST_ASIO_URL%" %INSTALL_DIR%\boost_asio.zip
   %ZIP_EXE% x "%INSTALL_DIR%\boost_asio.zip" -o"%INSTALL_DIR%" -aoa > NUL
-  PowerShell "Copy-Item -Path '%INSTALL_DIR%\%BOOST_ASIO_BASE%\boost' -Destination '%PWIZ_DIR%\libraries\boost_1_76_0' -Recurse -Force"
-)
-
-EXIT /B
+  PowerShell "Copy-Item -Path '%INSTALL_DIR%\%BOOST_ASIO_BASE%\boost' -Destination '%PWIZ_DIR%\libraries\boost_1_86_0' -Recurse -Force"
 
+  call %~dp0\download_file.bat "%BOOST_UNORDERED_URL%" %INSTALL_DIR%\boost_unordered.zip
+  %ZIP_EXE% x "%INSTALL_DIR%\boost_unordered.zip" -o"%INSTALL_DIR%" -aoa > NUL
+  PowerShell "Copy-Item -Path '%INSTALL_DIR%\%BOOST_UNORDERED_BASE%\include\boost' -Destination '%PWIZ_DIR%\libraries\boost_1_86_0' -Recurse -Force"
+)
 
-:downloadfile
-PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%1','%2')"
 EXIT /B

admin/builders/nativew32_build.bat

@@ -12,6 +12,7 @@
 @echo off
 
 set SRC_DIR=%~dp0..\..\..\
+set SCRIPT_DIR=%~dp0
 set BUILD_DIR=%SRC_DIR%\build\win32
 set RELEASE_DIR=%SRC_DIR%\release\win32
 set BUILD_TYPE=Release
@@ -50,15 +51,15 @@ if not exist "%RELEASE_DIR%" (md "%RELEASE_DIR%")
 set ZIP_DIR=%INSTALL_DIR%\%ZIP_BASE%
 if not exist "%ZIP_DIR%" (
   echo Downloading and installing 7-Zip
-  call :downloadfile %ZIP_URL% %INSTALL_DIR%\7zip.exe
-  "%INSTALL_DIR%\7zip.exe" /S /D=%INSTALL_DIR%\7zip
+  call %SCRIPT_DIR%\download_file.bat %ZIP_URL% %INSTALL_DIR%\7zip.exe
+  "%INSTALL_DIR%\7zip.exe" /S /D=%ZIP_DIR%
 )
 set ZIP_EXE="%ZIP_DIR%\7z.exe"
 
 set CMAKE_DIR=%INSTALL_DIR%\%CMAKE_BASE%
 if not exist "%CMAKE_DIR%" (
   echo Downloading and installing CMake
-  call :downloadfile %CMAKE_URL% %INSTALL_DIR%\cmake.zip
+  call %SCRIPT_DIR%\download_file.bat %CMAKE_URL% %INSTALL_DIR%\cmake.zip
   %ZIP_EXE% x "%INSTALL_DIR%\cmake.zip" -o"%INSTALL_DIR%" -aoa -xr!doc > NUL
 )
 set CMAKE_EXE="%CMAKE_DIR%\bin\cmake.exe"
@@ -70,11 +71,11 @@ if not "%NO_GUI%" == "true" (
   if not exist "%INSTALL_DIR%\Qt-dynamic" (
     ::: use multiple cores with jom instead of single-core nmake :::
     echo Downloading Jom
-    call :downloadfile %JOM_URL% %INSTALL_DIR%\jom.zip
+    call %SCRIPT_DIR%\download_file.bat %JOM_URL% %INSTALL_DIR%\jom.zip
     %ZIP_EXE% x "%INSTALL_DIR%\jom.zip" -o"%INSTALL_DIR%\jom" -aoa > NUL
 
     echo Downloading Qt base
-    call :downloadfile %QT_URL% %INSTALL_DIR%\qt.zip
+    call %SCRIPT_DIR%\download_file.bat %QT_URL% %INSTALL_DIR%\qt.zip
     %ZIP_EXE% x "%INSTALL_DIR%\qt.zip" -o"%INSTALL_DIR%" -aoa > NUL
 
     cd /D "%QT_DIR%"
@@ -97,7 +98,7 @@ if not "%NO_GUI%" == "true" (
 set NSIS_DIR=%INSTALL_DIR%\nsis
 if not exist "%NSIS_DIR%" (
   echo Downloading and installing NSIS installer
-  call :downloadfile "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
+  call %SCRIPT_DIR%\download_file.bat "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
   "%INSTALL_DIR%\nsis.exe" /S /D=%INSTALL_DIR%\nsis
 )
 setlocal
@@ -159,10 +160,6 @@ cd /D "%SRC_DIR%"
 
 EXIT /B %exit_code%
 
-:downloadfile
-echo Downloading %1 to %2
-PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%1','%2')"
-EXIT /B
 
 :copytorelease
 echo Copying "%1" to "%RELEASE_DIR%"

admin/builders/nativew64_build.bat

@@ -15,6 +15,7 @@
 @echo off
 
 set SRC_DIR=%~dp0..\..\..\
+set SCRIPT_DIR=%~dp0
 set BUILD_DIR=%SRC_DIR%\build\win64
 set RELEASE_DIR=%SRC_DIR%\release\win64
 set BUILD_TYPE=Release
@@ -56,15 +57,15 @@ if not exist "%RELEASE_DIR%" (md "%RELEASE_DIR%")
 set ZIP_DIR=%INSTALL_DIR%\%ZIP_BASE%
 if not exist "%ZIP_DIR%" (
   echo Downloading and installing 7-Zip
-  call :downloadfile %ZIP_URL% %INSTALL_DIR%\7zip.exe
-  "%INSTALL_DIR%\7zip.exe" /S /D=%INSTALL_DIR%\7zip
+  call %SCRIPT_DIR%\download_file.bat %ZIP_URL% %INSTALL_DIR%\7zip.exe
+  "%INSTALL_DIR%\7zip.exe" /S /D=%ZIP_DIR%
 )
 set ZIP_EXE="%ZIP_DIR%\7z.exe"
 
 set CMAKE_DIR=%INSTALL_DIR%\%CMAKE_BASE%
 if not exist "%CMAKE_DIR%" (
   echo Downloading and installing CMake
-  call :downloadfile %CMAKE_URL% %INSTALL_DIR%\cmake.zip
+  call %SCRIPT_DIR%\download_file.bat %CMAKE_URL% %INSTALL_DIR%\cmake.zip
   %ZIP_EXE% x "%INSTALL_DIR%\cmake.zip" -o"%INSTALL_DIR%" -aoa -xr!doc > NUL
 )
 set CMAKE_EXE="%CMAKE_DIR%\bin\cmake.exe"
@@ -76,11 +77,11 @@ if not "%NO_GUI%" == "true" (
   if not exist "%INSTALL_DIR%\Qt-dynamic" (
     ::: use multiple cores with jom instead of single-core nmake :::
     echo Downloading Jom
-    call :downloadfile %JOM_URL% %INSTALL_DIR%\jom.zip
+    call %SCRIPT_DIR%\download_file.bat %JOM_URL% %INSTALL_DIR%\jom.zip
     %ZIP_EXE% x "%INSTALL_DIR%\jom.zip" -o"%INSTALL_DIR%\jom" -aoa > NUL
 
     echo Downloading Qt base
-    call :downloadfile %QT_URL% %INSTALL_DIR%\qt.zip
+    call %SCRIPT_DIR%\download_file.bat %QT_URL% %INSTALL_DIR%\qt.zip
     %ZIP_EXE% x "%INSTALL_DIR%\qt.zip" -o"%INSTALL_DIR%" -aoa > NUL
 
     cd /D "%QT_DIR%"
@@ -103,7 +104,7 @@ if not "%NO_GUI%" == "true" (
 set NSIS_DIR=%INSTALL_DIR%\nsis
 if not exist "%NSIS_DIR%" (
   echo Downloading and installing NSIS installer
-  call :downloadfile "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
+  call %SCRIPT_DIR%\download_file.bat "%NSIS_URL%" %INSTALL_DIR%\nsis.exe
   "%INSTALL_DIR%\nsis.exe" /S /D=%INSTALL_DIR%\nsis
 )
 setlocal
@@ -184,10 +185,6 @@ cd /D "%SRC_DIR%"
 
 EXIT /B %exit_code%
 
-:downloadfile
-echo Downloading %1 to %2
-PowerShell "[Net.ServicePointManager]::SecurityProtocol = 'tls12, tls11, tls'; (new-object System.Net.WebClient).DownloadFile('%1','%2')"
-EXIT /B
 
 :copytorelease
 echo Copying "%1" to "%RELEASE_DIR%"