use os.path.join(), os.symlink(), shutile.copyfile() and tarfile module

lib/latte/Install.py

@@ -4,7 +4,7 @@
 # used to automate the steps described in the README file in this dir
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil
+import sys,os,re,subprocess,shutil,tarfile
 sys.path.append('..')
 from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
@@ -46,13 +46,13 @@ make lib-latte args="-p $HOME/latte"   # use existing LATTE installation
 
 pgroup = parser.add_mutually_exclusive_group()
 pgroup.add_argument("-b", "--build", action="store_true",
-                    help="download and build the Eigen3 library")
+                    help="download and build the LATTE library")
 pgroup.add_argument("-p", "--path",
-                    help="specify folder of existing Eigen installation")
+                    help="specify folder of existing LATTE installation")
 parser.add_argument("-m", "--machine", choices=['gfortran','ifort','linalg','serial','mpi'],
                     help="suffix of a Makefile.lammps.* file used for linking LAMMPS with this library")
 parser.add_argument("-v", "--version", default=version,
-                    help="set version of Eigen to download and build (default: %s)" % version)
+                    help="set version of LATTE to download and build (default: %s)" % version)
 
 args = parser.parse_args()
 
@@ -79,7 +79,7 @@ homedir = "LATTE-%s" % version
 if buildflag:
   url = "https://github.com/lanl/LATTE/archive/v%s.tar.gz" % version
   lattepath = fullpath(homepath)
-  lattedir = "%s/%s" % (lattepath,homedir)
+  lattedir = os.path.join(lattepath,homedir)
 
 # download and unpack LATTE tarball
 
@@ -95,13 +95,14 @@ if buildflag:
   print("Unpacking LATTE ...")
   if os.path.exists(lattedir):
     shutil.rmtree(lattedir)
-  cmd = 'cd "%s"; tar zxvf LATTE.tar.gz' % lattepath
+  if tarfile.is_tarfile('LATTE.tar.gz'):
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    tgz = tarfile.open('LATTE.tar.gz')
-  os.remove("%s/LATTE.tar.gz" % lattepath)
+    tgz.extractall()
+    os.remove('LATTE.tar.gz')
+  else:
+    sys.exit("File LATTE.tar.gz is not a supported archive")
 
   # build LATTE
-
-if buildflag:
   print("Building LATTE ...")
   cmd = 'cd "%s"; make' % lattedir
   try:
@@ -119,17 +120,14 @@ if os.path.isfile("liblink") or os.path.islink("liblink"):
   os.remove("liblink")
 if os.path.isfile("filelink.o") or os.path.islink("filelink.o"):
   os.remove("filelink.o")
-cmd = 'ln -s "%s/src" includelink' % lattedir
+os.symlink(os.path.join(lattedir,'src'),'includelink')
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+os.symlink(lattedir,'liblink')
-cmd = 'ln -s "%s" liblink' % lattedir
+os.symlink(os.path.join(lattedir,'src','latte_c_bind.o'),'filelink.o')
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-cmd = 'ln -s "%s/src/latte_c_bind.o" filelink.o' % lattedir
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
 
 # copy Makefile.lammps.suffix to Makefile.lammps
 
 if suffixflag or not os.path.exists("Makefile.lammps"):
+  if suffix == None: suffix = 'gfortran'
   print("Creating Makefile.lammps")
   if os.path.exists("Makefile.lammps.%s" % suffix):
-    cmd = 'cp Makefile.lammps.%s Makefile.lammps' % suffix
+    shutil.copyfile("Makefile.lammps.%s" % suffix, 'Makefile.lammps')
-    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

lib/smd/Install.py

@@ -4,7 +4,7 @@
 # used to automate the steps described in the README file in this dir
 
 from __future__ import print_function
-import sys,os,re,glob,subprocess,shutil
+import sys,os,re,glob,subprocess,shutil,tarfile
 sys.path.append('..')
 from install_helpers import fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
@@ -57,7 +57,7 @@ if args.build == False and not args.path:
   sys.exit(help)
 
 homepath = fullpath(".")
-eigenpath = "%s/eigen3" % homepath
+eigenpath = os.path.join(homepath,"eigen3")
 
 buildflag = args.build
 pathflag = args.path != None
@@ -73,29 +73,33 @@ if pathflag:
 
 if buildflag:
   print("Downloading Eigen ...")
+  eigentar = os.path.join(homepath,tarball)
   url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version
-  geturl(url,"%s/%s" % (homepath,tarball))
+  geturl(url,eigentar)
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
     print("checking version %s\n" % version)
-    if not checkmd5sum(checksums[version],'%s/%s' % (homepath,tarball)):
+    if not checkmd5sum(checksums[version],eigentar):
       sys.exit("Checksum for Eigen library does not match")
 
 
   print("Cleaning up old folders ...")
-  edir = glob.glob("%s/eigen-eigen-*" % homepath)
+  edir = glob.glob(os.path.join(homepath,"eigen-eigen-*"))
   edir.append(eigenpath)
   for one in edir:
     if os.path.isdir(one):
       shutil.rmtree(one)
 
   print("Unpacking Eigen tarball ...")
-  cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarball)
+  if tarfile.is_tarfile(eigentar):
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    tgz = tarfile.open(eigentar)
-  edir = glob.glob("%s/eigen-eigen-*" % homepath)
+    tgz.extractall(path=homepath)
+    os.remove(eigentar)
+  else:
+    sys.exit("File %s is not a supported archive" % eigentar)
+  edir = glob.glob(os.path.join(homepath,"eigen-eigen-*"))
   os.rename(edir[0],eigenpath)
-  os.remove(tarball)
 
 # create link in lib/smd to Eigen src dir
 
@@ -103,5 +107,4 @@ print("Creating link to Eigen include folder")
 if os.path.isfile("includelink") or os.path.islink("includelink"):
   os.remove("includelink")
 linkdir = eigenpath
-cmd = 'ln -s "%s" includelink' % linkdir
+os.symlink(linkdir,'includelink')
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

lib/voronoi/Install.py

@@ -4,7 +4,7 @@
 # used to automate the steps described in the README file in this dir
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil
+import sys,os,re,subprocess,shutil,tarfile
 sys.path.append('..')
 from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
@@ -61,34 +61,37 @@ pathflag = args.path != None
 voropath = args.path
 
 homepath = fullpath(".")
-homedir = "%s/%s" % (homepath,version)
+homedir = os.path.join(homepath,version)
 
 if pathflag:
     if not os.path.isdir(voropath):
       sys.exit("Voro++ path %s does not exist" % voropath)
-    homedir = voropath
+    homedir = fullpath(voropath)
 
 # download and unpack Voro++ tarball
 
 if buildflag:
   print("Downloading Voro++ ...")
-  geturl(url,"%s/%s.tar.gz" % (homepath,version))
+  vorotar = os.path.join(homepath,version) + '.tar.gz'
+  geturl(url,vorotar)
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
-    if not checkmd5sum(checksums[version],'%s/%s.tar.gz' % (homepath,version)):
+    if not checkmd5sum(checksums[version],vorotar):
       sys.exit("Checksum for Voro++ library does not match")
 
   print("Unpacking Voro++ tarball ...")
-  if os.path.exists("%s/%s" % (homepath,version)):
+  srcpath = os.path.join(homepath,version)
-    shutil.rmtree("%s/%s" % (homepath,version))
+  if os.path.exists(srcpath): shutil.rmtree(srcpath)
-  cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
+  if tarfile.is_tarfile(vorotar):
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    tgz = tarfile.open(vorotar)
-  os.remove("%s/%s.tar.gz" % (homepath,version))
+    tgz.extractall(path=homepath)
+    os.remove(vorotar)
+  else:
+    sys.exit("File %s is not a supported archive" % vorotar)
   if os.path.basename(homedir) != version:
-    if os.path.exists(homedir):
+    if os.path.exists(homedir): shutil.rmtree(homedir)
-      shutil.rmtree(homedir)
+    os.rename(srcpath,homedir)
-    os.rename("%s/%s" % (homepath,version),homedir)
 
 # build Voro++
 
@@ -109,7 +112,5 @@ if os.path.isfile("includelink") or os.path.islink("includelink"):
   os.remove("includelink")
 if os.path.isfile("liblink") or os.path.islink("liblink"):
   os.remove("liblink")
-cmd = 'ln -s "%s/src" includelink' % homedir
+os.symlink(os.path.join(homedir,'src'),'includelink')
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+os.symlink(os.path.join(homedir,'src'),'liblink')
-cmd = 'ln -s "%s/src" liblink' % homedir
-subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)