Removed qmean scripts

deployment/linux/create_qmean_bundle.py

-import os
-import shutil
-import subprocess
-import string
-import sys
-
-
-# custom parameters
-
-boost_string='\".so.1.40.0\"'
-system_python_bin='/usr/bin/python2.6'
-name_python_bin='python2.6'
-system_python_libs='/usr/lib/python2.6'
-second_system_python_libs_flag=True
-second_system_python_libs='/usr/lib/pymodules/python2.6'
-qt4_plugins='/usr/lib/qt4/plugins'
-additional_label='ubuntu'
-list_of_excluded_libraries=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL.so','libfontconfig','libfreetype','libdrm','libxcb','libICE']
-
-currdir=os.getcwd()
-if currdir.find('deployment')==-1 or currdir.find('linux')==-1:
-  print '\n'
-  print 'ERROR: Please run this script from the deployment/linux directory'
-  print '\n'
-  sys.exit()
-print '\n'
-print 'WARNING: If this script does not run to completion, please run the reset_repository_qmean.py script before restarting'
-print '\n'
-print 'Detecting architecture and revision'
-uname_output=subprocess.Popen('uname -a', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
-uname_line=uname_output.readlines()
-if uname_line[0].find('x86_64') !=-1:
-  libdir='lib64'
-  archstring='64bit'
-else: 
-  libdir='lib'
-  archstring='32bit'
-svninfo_output=subprocess.Popen('svn info', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
-svninfo_lines=svninfo_output.readlines()
-svninfo_split=string.split(svninfo_lines[4])
-revstring=svninfo_split[1]
-directory_name='qmean-'+archstring+'-'+additional_label+'-rev'+revstring
-print 'Stripping subversion information to avoid accidental commit'
-subprocess.call('rm -rf $(find . -name .svn)',shell=True,cwd='../../')
-print 'Tweaking scripts for bundle use'
-subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" scripts/ost.in.backup > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.prepreprepre > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost.in.pre > scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv modules/scratch/qmean/scripts/qmean.in modules/scratch/qmean/scripts/qmean.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" modules/scratch/qmean/scripts/qmean.in.backup > modules/scratch/qmean/scripts/qmean.in.prepreprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" modules/scratch/qmean/scripts/qmean.in.prepreprepre > modules/scratch/qmean/scripts/qmean.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" modules/scratch/qmean/scripts/qmean.in.preprepre > modules/scratch/qmean/scripts/qmean.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" modules/scratch/qmean/scripts/qmean.in.prepre > modules/scratch/qmean/scripts/qmean.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" modules/scratch/qmean/scripts/qmean.in.pre > modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in scripts/dng.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/dng.in.backup > scripts/dng.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
-print 'Downloading Chemlib dictionary'
-subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
-print 'Compiling Openstructure/Qmean'
-subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DONLY_QMEAN=ON -DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF -DCOMPOUND_LIB=ChemLib/compounds.chemlib', shell=True,cwd='../../')
-subprocess.call('make',shell=True,cwd='../../')
-print 'Converting Chemlib dictionary'
-subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
-print '\nStaging Chemlib dictionary'
-subprocess.call('cmake ./ -DCOMPOUND_LIB=compounds.chemlib',shell=True,cwd='../../')
-subprocess.call('make',shell=True,cwd='../../')
-print 'Removing obsolete packages and package directory'
-subprocess.call('rm -fr qmean-*',shell=True,cwd='../../')
-print 'Creating new package directory'
-subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
-subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
-so_list=[]
-print 'Creating new dependency list'
-walk_list=os.walk('../../stage')
-for dir_entry in walk_list:
-  for file_entry in dir_entry[2]:
-    if file_entry.find('.so')==len(file_entry)-3 or file_entry=='gosty':
-      filepath=os.path.join(dir_entry[0],file_entry)
-      so_list.append(filepath)  
-dep_list=[]
-for so_entry in so_list:
-   dep=subprocess.Popen('perl ./ldd-rec.pl '+so_entry,shell=True,stdout=subprocess.PIPE,cwd='./').stdout
-   dep_so_entry=dep.readlines()
-   for dep_entry in dep_so_entry:
-     dep_list.append(dep_entry[:-1]) 
-sorted_dep_list=sorted(list(set(dep_list)))
-print 'Filtering system libraries from depenedency list'
-filtered_dep_list=[]
-for entry in sorted_dep_list:
-   exclude=False
-   for exclusion in list_of_excluded_libraries:
-     if entry.find(exclusion)!=-1:
-       exclude=True
-   if exclude==False: 
-     filtered_dep_list.append(entry)
-print 'Copy libraries in the package directory structure'
-subprocess.call('mkdir '+directory_name+'/'+libdir,shell=True,cwd='../../')
-for entry in filtered_dep_list:
-  subprocess.call('cp '+entry+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-print 'Copy python executable into package directory structure'
-subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin',shell=True,cwd='../../')
-print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/* '+directory_name+'/'+libdir+'/'+name_python_bin,shell=True,cwd='../../')
-print 'Copy Qt 4 plugins into package directory structure'
-subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../')
-print 'Installing OpenStructure into package directory structure'
-subprocess.call('make install',shell=True,cwd='../../')
-print 'Copy examples into package directory structure'
-subprocess.call('cp -pRL  examples  '+directory_name+'/share/openstructure/',shell=True,cwd='../../')
-print 'Removing headers from package directory structure'
-subprocess.call('rm -fr   '+directory_name+'/include',shell=True,cwd='../../')
-print 'Copying supplementary material into package directory structure'
-subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
-print 'Copy qmean examples into package directory structure'
-subprocess.call('cp -pRL  modules/scratch/qmean/examples '+directory_name+'',shell=True,cwd='../../')
-print 'Copy readme and license files into package directory structure'
-subprocess.call('cp -pRL  modules/scratch/qmean/LICENSE.txt '+directory_name+'',shell=True,cwd='../../')
-subprocess.call('cp -pRL  modules/scratch/qmean/README.txt '+directory_name+'',shell=True,cwd='../../')
-print 'Resetting script to non-bundle versions'
-subprocess.call('rm scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/ost.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('rm modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('rm modules/scratch/qmean/scripts/qmean.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('mv modules/scratch/qmean/scripts/qmean.in.backup modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../')
-

deployment/linux/reset_repository_qmean.py

-import subprocess
-import os
-
-currdir=os.getcwd()
-if currdir.find('deployment')==-1 or currdir.find('linux')==-1:
-  print '\n'
-  print 'ERROR: Please run this script from the deployment/linux directory'
-  print '\n'
-  sys.exit()
-
-subprocess.call('rm -fr scripts/dng.in.pre* scripts/ost_cl.in.pre* modules/scratch/qmean/scripts/qmean.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('mv modules/scratch/qmean/scripts/qmean.in.backup scripts/dng.in modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
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