add feature to python lib install script to support existing installation and use links

                 or: make lib-plumed args="-b -v 2.4.2"

Syntax from lib dir: python Install.py -b -v 2.4.2

                 or: python Install.py -b

                 or: python Install.py -p /usr/local/plumed-2.4.2

specify one or more options, order does not matter

  -b = download and build the plumed2 library

  -v = set version of Voro++ to download and build (default: latest stable version)

  -p = specify folder of existing plumed2 installation

  -v = set version of plumed2 to download and build (default: 2.4.2)

Example:

make lib-plumed args="-b"   # download/build in lib/plumed/plumed2

make lib-plumed args="-p $HOME/plumed-2.4.2" # use existing Plumed2 installation in $HOME/plumed-2.4.2

"""

# settings

homepath = "."

buildflag = False

pathflag = False

suffixflag = False

linkflag = True

    if iarg+2 > nargs: error()

    version = args[iarg+1]

    iarg += 2

  elif args[iarg] == "-p":

    if iarg+2 > nargs: error()

    plumedpath = fullpath(args[iarg+1])

    pathflag = True

    iarg += 2

  elif args[iarg] == "-b":

    buildflag = True

    iarg += 1

homepath = fullpath(homepath)

# download and unpack plumed  tarball

if (pathflag):

    if not os.path.isdir(plumedpath): error("Plumed2 path does not exist")

    homedir = plumedpath

if (buildflag and pathflag):

    error("Cannot use -b and -p flag at the same time")

if (not buildflag and not pathflag):

    error("Have to use either -b or -p flag")

# download and unpack plumed2 tarball

if buildflag:

  url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version

  geturl(url,filename) 

  print("Unpacking plumed tarball ...")

  if os.path.exists("%s/%s" % (homepath,version)):

    cmd = 'rm -rf "%s/%s"' % (homepath,version)

  if os.path.exists("%s/plumed2-%s" % (homepath,version)):

    cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)

    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  if os.path.exists("%s/plumed2" % (homepath)):

    cmd = 'rm -rf "%s/plumed2"' % (homepath)

    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)

  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

if buildflag:

   print("Building plumed ...")

   cmd = 'cd %s/plumed2-%s; ./configure ; make' % (homepath,version)

   cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 ; make ; make install' % (homepath,version,homepath)

   txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

   print(txt.decode('UTF-8'))

# 

# # create 2 links in lib/voronoi to Voro++ src dir

# 

# if linkflag:

#   print("Creating links to Voro++ include and lib files")

#   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

#   subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

#   cmd = 'ln -s "%s/src" liblink' % homedir

#   subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

# create 2 links in lib/plumed to plumed2 installation dir

if linkflag:

  print("Creating links to plumed2 include and lib files")

  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/plumed2/include" includelink' % homepath

  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  cmd = 'ln -s "%s/plumed2/lib" liblink' % homepath

  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)