Windows updates

COOT_HOME for windows is in USERPROFILE/COOT now.
Installer will move files from InstallDir to new location if exists.
Wincoot batch script searches for CCP4 installed dictionary actually
generally CCP4 in registry and sets up CCP4.

windows/WinCoot_install_masta.nsi

@@ -171,6 +171,39 @@ FunctionEnd
   Call un.ErrorHandlerFunction
 !macroend
 
+; Macro to move files from INSTDIR to USERPROFILE/COOT
+!macro MoveFileToNewHome File isDir
+  ; to avoid duplicate labels...
+  !define ID ${__LINE__}
+  ; check if file exists
+  ClearErrors
+  MessageBox MB_OK `Is "${File}" a dir?`
+  ${If} ${FileExists} "${INSTDIR}\${File}"
+    # your code here
+    MessageBox MB_OK "Try rename"
+    Rename ${INSTDIR}\${File} $%USERPROFILE%\COOT\${File}
+    IfErrors "" skipit_${ID}
+      # somehow couldnt rename, try to copy to dest and remove src
+      # this may be necessary if on different driveletters
+      ClearErrors
+      CopyFiles /Silent ${INSTDIR}\${File} $%USERPROFILE%\COOT\${File}
+      IfErrors "" remove_src_${ID}
+        # couldnt copy, give message
+        MessageBox MB_ICONINFORMATION `"${File}" couldnt be moved from it's old place in \
+        "${INSTDIR}" to new place "$%USERPROFILE%\COOT". \
+        Consider doing it manually if deemed important.`
+        goto skipit_${ID}
+      remove_src_${ID}:
+        ${IF} isDir == "true"
+          RMDir /r ${INSTDIR}\${File}
+        ${Else}
+          Delete ${INSTDIR}\${File}
+        ${EndIf}
+    skipit_${ID}:
+  ${EndIf}
+  !undef ID
+!macroend
+
 ; MUI end ------
 
 Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"
@@ -279,6 +312,8 @@ Section "!WinCoot" SEC01
   File "${src_dir}\bin\gdk-pixbuf-query-loaders.exe"
   ; render (or more?) from raster3d?!
   File "${src_dir}\bin\render.exe"
+  ; clustalw2
+  File "${src_dir}\bin\clustalw2.exe"
   ;gunzip needed?? dont think so
   File "C:\msys64\home\bernhard\autobuild\extras\gunzip"
   File "C:\msys64\home\bernhard\autobuild\extras\gzip.exe"
@@ -456,11 +491,7 @@ Section -AddIcons
 
  exit:
    SetShellVarContext current
-  ; in case we want to install silently (no user intervention)
-  ; we have to call the finish page function, otherwise runwincoot.bat
-  ; won't be edited.
-  IfSilent 0 +2
-    Call FinishPagePreFunction
+  Call FinishPagePreFunction
   IfErrors 0 +5
     ; ${ErrorHandler} 3 "Error in installation. Could not install icons." 0
     DetailPrint "Error in installation. Could not install icons. Continuing."
@@ -470,6 +501,12 @@ Section -AddIcons
 SectionEnd
 
 Section -Post
+  ; first make COOT_HOME in USERPROFILE if it doesnt exist, then move files
+  IfFileExists "$%USERPROFILE%\COOT\*.*" have_usercoot
+    CreateDirectory "$%USERPROFILE%\COOT"
+    Call MoveUserHomeFiles
+  have_usercoot:
+
   ClearErrors
   WriteUninstaller "$INSTDIR\uninst.exe"
 ;  NO MESSING WITH THE REGISTRY!!!!
@@ -562,6 +599,7 @@ Section Uninstall
   Delete "$INSTDIR\bin\lidia.exe"
   Delete "$INSTDIR\bin\mini-rsr-bin.exe"
   Delete "$INSTDIR\bin\render.exe"
+  Delete "$INSTDIR\bin\clustalw2.exe"
   Delete "$INSTDIR\bin\Microsoft.VC90.CRT.manifest"
   Delete "$INSTDIR\bin\pango-querymodules.exe"
   Delete "$INSTDIR\bin\pango-view.exe"
@@ -706,7 +744,7 @@ Function .onInit
 ; no more examples dir (have data dir now)
 ; so default start dir is $INSTDIR
   ${If} $STARTDIR == ""
-    StrCpy $STARTDIR "$INSTDIR"
+    StrCpy $STARTDIR "$%USERPROFILE%"
   ${EndIf}
   IfErrors 0 +6
     ;${ErrorHandler} 6 "Error in installation. Could not initiate installation." 1
@@ -988,9 +1026,9 @@ ${If} $update = 0
   CreateShortCut "$DESKTOP\WinCoot.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\wincoot.bat"' "$INSTDIR\bin\coot-icon.ico" 0 SW_SHOWMINIMIZED
   CreateShortCut "$SMPROGRAMS\$ICONS_GROUP\WinCoot.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\wincoot.bat"' "$INSTDIR\bin\coot-icon.ico" 0 SW_SHOWMINIMIZED
   Sleep 10
-  SetOutPath "$INSTDIR"
   CreateShortCut "$SMPROGRAMS\$ICONS_GROUP\DynaRama.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\bin\dynarama.bat"' "$INSTDIR\bin\rama_all.ico"
   Sleep 10
+  SetOutPath "$INSTDIR"
   WriteIniStr "$INSTDIR\WinCoot.url" "InternetShortcut" "URL" "${PRODUCT_WEB_SITE}"
   WriteIniStr "$INSTDIR\Coot.url" "InternetShortcut" "URL" "${PRODUCT_WEB_SITE_2}"
   CreateShortCut "$SMPROGRAMS\WinCoot\WinCoot Website.lnk" "$INSTDIR\${PRODUCT_NAME}.url"
@@ -1030,3 +1068,23 @@ Function ErrorHandler
   ${EndIf}
 
 FunctionEnd
+
+; Function to move potentially existing WinCoot files and directories from
+; INSTALLDIR to USERPROFILE\COOT
+Function MoveUserHomeFiles
+  ; what shall we move? preferences, backup, downloads dirs, state and history
+  ; state and history files...
+  !insertmacro "MoveFileToNewHome" ".coot-preferences" "true"
+  !insertmacro "MoveFileToNewHome" "coot-backup" "true"
+  !insertmacro "MoveFileToNewHome" "coot-download" "true"
+  !insertmacro "MoveFileToNewHome" "coot-ccp4" "true"
+  !insertmacro "MoveFileToNewHome" "coot-molprobity" "true"
+  !insertmacro "MoveFileToNewHome" "coot-refmac" "true"
+  !insertmacro "MoveFileToNewHome" "coot-acedrg" "true"
+  !insertmacro "MoveFileToNewHome" "coot-pisa" "true"
+  !insertmacro "MoveFileToNewHome" "0-coot-history.scm" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot.state.py" "false"
+  !insertmacro "MoveFileToNewHome" ".coot.py" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot.state.scm" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot-history.scm" "false"
+FunctionEnd

windows/wincoot.bat

@@ -3,34 +3,94 @@
 @set LC_NUMERIC=en
 title WinCoot
 
+REM First try to find a dictionary. Search in the registry for a
+REM CCP4 installation and then setup CCP4.
 
-set COOT_PREFIX=yourWinCootdirectory
+if not exist "%CLIBD_MON%" (
+   echo no $CLIBD_MON found trying to setup CCP4
+   call :setup_ccp4
+)
+
+REM main line
+
+set COOT_PREFIX=%~dp0
 set COOT_GUILE_PREFIX=%COOT_PREFIX:\=/%
 
-set COOT_HOME=%COOT_PREFIX%
+REM New COOT_HOME is in User directory now
+set COOT_HOME=%USERPROFILE%\COOT
 set COOT_BACKUP_DIR=%COOT_PREFIX%\coot-backup
 
 set COOT_SHARE=%COOT_PREFIX%\share
+
 if not exist "%CLIBD_MON%" (
   echo no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
-  set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
+  Call :setup_coot_dictionary
 )
+
 set COOT_SCHEME_DIR=%COOT_SHARE%/coot/scheme
 set COOT_STANDARD_RESIDUES=%COOT_SHARE%\coot\standard-residues.pdb
 set COOT_PIXMAPS_DIR=%COOT_SHARE%\coot\pixmaps
 set COOT_RESOURCES_FILE=%COOT_SHARE%\coot\cootrc
 set COOT_DATA_DIR=%COOT_SHARE%\coot
 set COOT_REF_STRUCTS=%COOT_SHARE%\coot\reference-structures
-set COOT_PYTHON_DIR=%COOT_PREFIX%\python27\lib\site-packages\coot
-REM set COOT_REF_SEC_STRUCTS=%COOT_SHARE%\coot\ss-reference-structures
-
-set PYTHONHOME=%COOT_PREFIX%\python27
+set COOT_PYTHON_DIR=%COOT_PREFIX%\lib\python2.7\site-packages\coot
+REM set PYTHONHOME=%COOT_PREFIX%\python27
 
 set GUILE_LOAD_PATH=%COOT_GUILE_PREFIX%/share/guile/1.8;%COOT_GUILE_PREFIX%/share/guile;%COOT_GUILE_PREFIX%/share/guile/gtk-2.0;%COOT_GUILE_PREFIX%/share/guile/gui;%COOT_GUILE_PREFIX%/share/guile/www;%COOT_GUILE_PREFIX%/share/guile/site
 
 set SYMINFO=%COOT_SHARE%\coot\syminfo.lib
 
-set PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\lib;%COOT_PREFIX%\python27;%PATH%;%COOT_PREFIX%\bin\extras
+set PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\lib;%PATH%;%COOT_PREFIX%\bin\extras
 
 coot-bin.exe %*
 
+Exit /B %ERRORLEVEL%
+
+
+REM function to setup CCP4
+:setup_ccp4
+set /a CCP4_MAJOR=10
+
+:loop_start
+set /a CCP4_MAJOR=CCP4_MAJOR-1
+
+call :find_ccp4 HKCU\SOFTWARE\CCP4-%CCP4_MAJOR%
+if exist "%CLIBD_MON%" (goto :loop_end)
+
+call :find_ccp4 HKLM\SOFTWARE\WOW6432Node\CCP4-%CCP4_MAJOR%
+if exist "%CLIBD_MON%" (goto :loop_end)
+
+if %CCP4_MAJOR% gtr 6 (goto :loop_start)
+:loop_end
+
+Exit /B 0
+
+
+REM Function to find CCP4 in the registry and call ccp4 setup bat
+:find_ccp4
+REM Check in Registry for CCP4 InstallDir
+for /f "skip=1 tokens=3" %%A in (
+  'reg query %1 /v InstallDir 2^>Nul'
+) do set CCP4DIR=%%~A
+if not exist "%CCP4DIR%" (Exit /B 0)
+
+REM find latest dir
+for /f " tokens=*" %%i in (
+  'dir "%CCP4DIR%\%CCP4_MAJOR%.*" /b /ad-h /t:c /od'
+) do set SETUPFILE=%CCP4DIR%\%%i\ccp4.setup.bat
+if not exist "%SETUPFILE%" (Exit /B 0)
+
+REM Finally, setup CCP4
+call "%SETUPFILE%"
+Exit /B 0
+
+:setup_coot_dictionary
+set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
+set WARN=No valid dictionary found, no refinement possible!
+if not exist "%COOT_REFMAC_LIB_DIR%" (
+  REM check for Phenix place too
+  if not exist "%COOT_MONOMER_LIB_DIR%" (
+    msg "%USERNAME%" WinCoot WARNING:: %WARN%
+  )
+)
+Exit /B 0