some cleanups and small bugfixes to conform better with python conventions

lib/Install.py

@@ -1,19 +1,22 @@
 #!/usr/bin/env python
 
-# install.py tool to do a generic build of a library
+"""
-# soft linked to by many of the lib/Install.py files
+Install.py tool to do a generic build of a library
-# used to automate the steps described in the corresponding lib/README
+soft linked to by many of the lib/Install.py files
+used to automate the steps described in the corresponding lib/README
+"""
 
 from __future__ import print_function
-import sys,os,subprocess
+import sys, os, subprocess
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import get_cpus, fullpath
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
-help = """
+HELP = """
 Syntax from src dir: make lib-libname args="-m machine -e suffix"
 Syntax from lib dir: python Install.py -m machine -e suffix
 
@@ -39,10 +42,11 @@ args = parser.parse_args()
 # print help message and exit, if neither build nor path options are given
 if not args.machine and not args.extramake:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 machine = args.machine
-extraflag = args.extramake
+extraflag = not args.extramake
+suffix = args.extramake
 
 # set lib from working dir
 
@@ -53,10 +57,10 @@ lib = os.path.basename(cwd)
 # reset EXTRAMAKE if requested
 
 if not os.path.exists("Makefile.%s" % machine):
-  sys.exit("lib/%s/Makefile.%s does not exist" % (lib,machine))
+  sys.exit("lib/%s/Makefile.%s does not exist" % (lib, machine))
 
-lines = open("Makefile.%s" % machine,'r').readlines()
+lines = open("Makefile.%s" % machine, 'r').readlines()
-fp = open("Makefile.auto",'w')
+fp = open("Makefile.auto", 'w')
 
 has_extramake = False
 for line in lines:
@@ -64,7 +68,7 @@ for line in lines:
   if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
     has_extramake = True
     if extraflag:
-      line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+      line = line.replace(words[2], "Makefile.lammps.%s" % suffix)
   fp.write(line)
 
 fp.close()
@@ -75,14 +79,16 @@ n_cpus = get_cpus()
 print("Building lib%s.a ..." % lib)
 cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
 try:
-  txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
+  txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
   print(txt.decode('UTF-8'))
 except subprocess.CalledProcessError as e:
   print("Make failed with:\n %s" % e.output.decode('UTF-8'))
   sys.exit(1)
 
-if os.path.exists("lib%s.a" % lib): print("Build was successful")
+if os.path.exists("lib%s.a" % lib):
-else: sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+  print("Build was successful")
+else:
+  sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib))
 
 if has_extramake and not os.path.exists("Makefile.lammps"):
   print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib)

lib/gpu/Install.py

@@ -1,20 +1,23 @@
 #!/usr/bin/env python
 
-# Install.py tool to build the GPU library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to build the GPU library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,subprocess,shutil
+import sys, os, subprocess, shutil
+from argparse import ArgumentParser
+
 sys.path.append('..')
 from install_helpers import get_cpus
-from argparse import ArgumentParser
 
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix"
 Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix
 
@@ -41,10 +44,10 @@ parser.add_argument("-b", "--build", action="store_true",
 parser.add_argument("-m", "--machine", default='linux',
                     help="suffix of Makefile.machine used as base for customizing Makefile.auto")
 parser.add_argument("-a", "--arch", default='sm_30',
-                    choices=['sm_12','sm_13','sm_20','sm_21','sm_30','sm_35','sm_37',
+                    choices=['sm_12', 'sm_13', 'sm_20', 'sm_21', 'sm_30', 'sm_35', 'sm_37',
-                             'sm_50','sm_52','sm_60','sm_61','sm_70','sm_75'],
+                             'sm_50', 'sm_52', 'sm_60', 'sm_61', 'sm_70', 'sm_75'],
                     help="set GPU architecture and instruction set (default: 'sm_30')")
-parser.add_argument("-p", "--precision", default='mixed', choices=['single','mixed','double'],
+parser.add_argument("-p", "--precision", default='mixed', choices=['single', 'mixed', 'double'],
                     help="set GPU kernel precision mode (default: mixed)")
 parser.add_argument("-e", "--extramake", default='standard',
                     help="set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.<extramake>")
@@ -56,9 +59,9 @@ parser.add_argument("-o", "--output",
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor output options are given
-if args.build == False and not args.output:
+if not args.build and not args.output:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 hflag = 0
 eflag = 0
@@ -71,9 +74,12 @@ if args.build:
 isuffix = args.machine
 arch = args.arch
 
-if args.precision == "double": precstr = "-D_DOUBLE_DOUBLE"
+if args.precision == "double":
-elif args.precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
+  precstr = "-D_DOUBLE_DOUBLE"
-else: precstr = "-D_SINGLE_SINGLE"
+elif args.precision == "mixed":
+  precstr = "-D_SINGLE_DOUBLE"
+else:
+  precstr = "-D_SINGLE_SINGLE"
 
 lmpsuffix = args.extramake
 
@@ -91,8 +97,8 @@ if args.output:
 if not os.path.exists("Makefile.%s" % isuffix):
   sys.exit("lib/gpu/Makefile.%s does not exist" % isuffix)
 
-lines = open("Makefile.%s" % isuffix,'r').readlines()
+lines = open("Makefile.%s" % isuffix, 'r').readlines()
-fp = open("Makefile.auto",'w')
+fp = open("Makefile.auto", 'w')
 
 for line in lines:
   words = line.split()
@@ -101,13 +107,13 @@ for line in lines:
     continue
 
   if hflag and words[0] == "CUDA_HOME" and words[1] == '=':
-    line = line.replace(words[2],hdir)
+    line = line.replace(words[2], hdir)
   if words[0] == "CUDA_ARCH" and words[1] == '=':
-    line = line.replace(words[2],"-arch=%s" % arch)
+    line = line.replace(words[2], "-arch=%s" % arch)
   if words[0] == "CUDA_PRECISION" and words[1] == '=':
-    line = line.replace(words[2],precstr)
+    line = line.replace(words[2], precstr)
   if eflag and words[0] == "EXTRAMAKE" and words[1] == '=':
-    line = line.replace(words[2],"Makefile.lammps.%s" % lmpsuffix)
+    line = line.replace(words[2], "Makefile.lammps.%s" % lmpsuffix)
 
   fp.write(line)
 fp.close()
@@ -122,7 +128,7 @@ if makeflag:
   n_cpus = get_cpus()
   cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
   try:
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     print("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -138,4 +144,3 @@ if makeflag:
 if outflag:
   print("Creating new Makefile.%s" % osuffix)
   shutil.copyfile("Makefile.auto", "Makefile.%s" % osuffix)
-

lib/kim/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# install.py tool to download, compile, and setup the kim-api library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, compile, and setup the kim-api library
+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, subprocess, shutil
-sys.path.append('..')
-from install_helpers import fullpath,geturl
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -19,7 +22,7 @@ version = "kim-api-v1.9.5"
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-kim args="-b -v version  -a kim-name"
                  or: make lib-kim args="-b -a everything"
                  or: make lib-kim args="-n -a kim-name"
@@ -64,13 +67,13 @@ parser.add_argument("-vv", "--verbose", action="store_true",
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path and args.nobuild == False:
+if not args.build and not args.path and not args.nobuild:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
-addflag = args.add != None
+addflag = args.add is not None
 addmodelname = args.add
 everythingflag = False
 if addflag and addmodelname == "everything":
@@ -81,7 +84,8 @@ verboseflag = args.verbose
 if pathflag:
   buildflag = False
   kimdir = args.path
-  if not os.path.isdir(kimdir): sys.exit("KIM API path %s does not exist" % kimdir)
+  if not os.path.isdir(kimdir):
+    sys.exit("KIM API path %s does not exist" % kimdir)
   kimdir = fullpath(kimdir)
 
 url = "https://s3.openkim.org/kim-api/%s.txz" % version
@@ -96,7 +100,7 @@ if pathflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
+  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir, kimdir))
 else:
   kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
   if args.nobuild and not os.path.isdir(kimdir):
@@ -119,55 +123,60 @@ if buildflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
+  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir, kimdir))
 
   # download entire kim-api tarball
 
   print("Downloading kim-api tarball ...")
-  geturl(url,"%s/%s.txz" % (thisdir,version))
+  geturl(url, "%s/%s.txz" % (thisdir, version))
   print("Unpacking kim-api tarball ...")
-  cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir,version,version)
+  cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir, version, version)
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   # configure kim-api
 
   print("Configuring kim-api ...")
-  cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir,version,kimdir)
+  cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir, version, kimdir)
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   # build kim-api
   print("Building kim-api ...")
-  cmd = 'cd "%s/%s"; make' % (thisdir,version)
+  cmd = 'cd "%s/%s"; make' % (thisdir, version)
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-  if verboseflag: print(txt.decode("UTF-8"))
+  if verboseflag:
+    print(txt.decode("UTF-8"))
 
   # install kim-api
 
   print("Installing kim-api ...")
-  cmd = 'cd "%s/%s"; make install' % (thisdir,version)
+  cmd = 'cd "%s/%s"; make install' % (thisdir, version)
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-  if verboseflag: print(txt.decode("UTF-8"))
+  if verboseflag:
+    print(txt.decode("UTF-8"))
 
   # remove source files
 
   print("Building and installing example Models")
-  cmd = 'cd "%s/%s/examples"; make model-drivers-all-system' % (thisdir,version)
+  cmd = 'cd "%s/%s/examples"; make model-drivers-all-system' % (thisdir, version)
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-  if verboseflag: print (txt.decode("UTF-8"))
+  if verboseflag:
-  cmd = 'cd "%s/%s/examples"; make models-all-system' % (thisdir,version)
+    print(txt.decode("UTF-8"))
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  cmd = 'cd "%s/%s/examples"; make models-all-system' % (thisdir, version)
-  if verboseflag: print (txt.decode("UTF-8"))
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
+  if verboseflag:
+    print(txt.decode("UTF-8"))
 
   print("Removing kim-api source and build files ...")
-  cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir,version,version)
+  cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version)
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   # add all OpenKIM models, if desired
   if everythingflag:
     print("Adding all OpenKIM models, this will take a while ...")
     cmd = '%s/bin/kim-api-v1-collections-management install system OpenKIM' % (kimdir)
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-    if verboseflag: print(txt.decode("UTF-8"))
+    if verboseflag:
+      print(txt.decode("UTF-8"))
 
 # add single OpenKIM model
 if addflag:
@@ -175,12 +184,13 @@ if addflag:
   makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR")
   if os.path.isfile(makefile_path):
     cmd = 'make --no-print-directory -f %s print_dir' % makefile_path
-    kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    kimdir = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   if not os.path.isdir(kimdir):
     sys.exit("\nkim-api is not installed")
 
   # download single model
   cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-  if verboseflag: print (txt.decode("UTF-8"))
+  if verboseflag:
+    print(txt.decode("UTF-8"))

lib/latte/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, build, and link to the LATTE library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, build, and link to the LATTE library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil,tarfile
+import sys, os, subprocess, shutil, tarfile
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl, checkmd5sum
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -26,7 +29,7 @@ checksums = { \
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-latte args="-b"
                  or: make lib-latte args="-p /usr/local/latte"
                  or: make lib-latte args="-m gfortran"
@@ -49,7 +52,7 @@ pgroup.add_argument("-b", "--build", action="store_true",
                     help="download and build the LATTE library")
 pgroup.add_argument("-p", "--path",
                     help="specify folder of existing LATTE installation")
-parser.add_argument("-m", "--machine", choices=['gfortran','ifort','linalg','serial','mpi'],
+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 LATTE to download and build (default: %s)" % version)
@@ -57,21 +60,22 @@ parser.add_argument("-v", "--version", default=version,
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 homepath = fullpath(".")
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
 version = args.version
-suffixflag = args.machine != None
+suffixflag = args.machine is not None
 suffix = args.machine
 
 if pathflag:
   lattedir = args.path
-  if not os.path.isdir(lattedir): sys.exit("LATTE path %s does not exist" % lattedir)
+  if not os.path.isdir(lattedir):
+    sys.exit("LATTE path %s does not exist" % lattedir)
   lattedir = fullpath(lattedir)
 
 homedir = "LATTE-%s" % version
@@ -79,17 +83,17 @@ homedir = "LATTE-%s" % version
 if buildflag:
   url = "https://github.com/lanl/LATTE/archive/v%s.tar.gz" % version
   lattepath = fullpath(homepath)
-  lattedir = os.path.join(lattepath,homedir)
+  lattedir = os.path.join(lattepath, homedir)
 
 # download and unpack LATTE tarball
 
 if buildflag:
   print("Downloading LATTE ...")
-  geturl(url,"LATTE.tar.gz")
+  geturl(url, "LATTE.tar.gz")
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
-    if not checkmd5sum(checksums[version],'LATTE.tar.gz'):
+    if not checkmd5sum(checksums[version], 'LATTE.tar.gz'):
       sys.exit("Checksum for LATTE library does not match")
 
   print("Unpacking LATTE ...")
@@ -106,7 +110,7 @@ if buildflag:
   print("Building LATTE ...")
   cmd = 'cd "%s"; make' % lattedir
   try:
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -120,14 +124,15 @@ 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")
-os.symlink(os.path.join(lattedir,'src'),'includelink')
+os.symlink(os.path.join(lattedir, 'src'), 'includelink')
-os.symlink(lattedir,'liblink')
+os.symlink(lattedir, 'liblink')
-os.symlink(os.path.join(lattedir,'src','latte_c_bind.o'),'filelink.o')
+os.symlink(os.path.join(lattedir, 'src', 'latte_c_bind.o'), 'filelink.o')
 
 # copy Makefile.lammps.suffix to Makefile.lammps
 
 if suffixflag or not os.path.exists("Makefile.lammps"):
-  if suffix == None: suffix = 'gfortran'
+  if suffix is None:
+    suffix = 'gfortran'
   print("Creating Makefile.lammps")
   if os.path.exists("Makefile.lammps.%s" % suffix):
     shutil.copyfile("Makefile.lammps.%s" % suffix, 'Makefile.lammps')

lib/message/Install.py

@@ -1,20 +1,23 @@
 #!/usr/bin/env python
 
-# Install.py tool to build the CSlib library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to build the CSlib library
+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, subprocess, shutil
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-message args="-m"
                  or: make lib-message args="-s -z"
 Syntax from lib dir: python Install.py -m
@@ -37,9 +40,9 @@ parser.add_argument("-z", "--zmq", default=False, action="store_true",
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.mpi == False and args.serial == False:
+if not args.mpi and not args.serial:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 mpiflag = args.mpi
 serialflag = args.serial
@@ -50,7 +53,7 @@ zmqflag = args.zmq
 # copy appropriate Makefile.lammps.* to Makefile.lammps
 
 print("Building CSlib ...")
-srcdir = fullpath(os.path.join("cslib","src"))
+srcdir = fullpath(os.path.join("cslib", "src"))
 
 if mpiflag and zmqflag:
   cmd = "make -C %s lib_parallel" % srcdir
@@ -60,20 +63,22 @@ elif not mpiflag and zmqflag:
   cmd = "make -C %s lib_serial" % srcdir
 elif not mpiflag and not zmqflag:
   cmd = "make -C %s lib_serial zmq=no" % srcdir
-  
+
 print(cmd)
 try:
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   print(txt.decode('UTF-8'))
 except subprocess.CalledProcessError as e:
     print("Make failed with:\n %s" % e.output.decode('UTF-8'))
     sys.exit(1)
 
-slb=os.path.join(srcdir,"libcsnompi.a")
+slb = os.path.join(srcdir, "libcsnompi.a")
-if mpiflag: slb = os.path.join(srcdir,"libcsmpi.a")
+if mpiflag:
-shutil.copyfile(slb,os.path.join(srcdir,"libmessage.a"))
+  slb = os.path.join(srcdir, "libcsmpi.a")
+shutil.copyfile(slb, os.path.join(srcdir, "libmessage.a"))
 
-smk="Makefile.lammps.nozmq"
+smk = "Makefile.lammps.nozmq"
-if zmqflag: smk="Makefile.lammps.zmq"
+if zmqflag:
-shutil.copyfile(smk,"Makefile.lammps")
+  smk = "Makefile.lammps.zmq"
+shutil.copyfile(smk, "Makefile.lammps")
 print("Using %s for Makefile.lammps" % smk)

lib/mscg/Install.py

@@ -1,15 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, build, and link to the MS-CG library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, build, and link to the MS-CG library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil,tarfile
+import sys, os, subprocess, shutil, tarfile
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath,get_cpus,geturl
-
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -20,7 +22,7 @@ machine = "g++_simple"
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-mscg args="-p [path] -m [suffix] -v [version]"
                  or: make lib-mscg args="-b -m [suffix]"
 Syntax from lib dir: python Install.py -p [path]  -m [suffix] -v [version]
@@ -47,19 +49,19 @@ pgroup.add_argument("-p", "--path",
                     help="specify folder of existing MSCG installation")
 parser.add_argument("-v", "--version", default=version, choices=checksums.keys(),
                     help="set version of MSCG to download and build (default: %s)" % version)
-parser.add_argument("-m", "--machine", default=machine, choices=['mpi','serial','g++_simple','intel_simple','lapack', 'mac'],
+parser.add_argument("-m", "--machine", default=machine, choices=['mpi', 'serial', 'g++_simple', 'intel_simple', 'lapack', 'mac'],
                     help="set machine suffix specifies which src/Make/Makefile.suffix to use. (default: %s)" % machine)
 
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
-mscgpath= args.path
+mscgpath = args.path
 msuffix = args.machine
 mscgver = args.version
 
@@ -70,7 +72,7 @@ tarname = "MS-CG-%s.tar.gz" % mscgver
 tardir = "MSCG-release-%s" % mscgver
 
 homepath = fullpath('.')
-homedir = os.path.join(homepath,tardir)
+homedir = os.path.join(homepath, tardir)
 
 if pathflag:
     if not os.path.isdir(mscgpath):
@@ -81,41 +83,41 @@ if pathflag:
 
 if buildflag:
   print("Downloading MS-CG ...")
-  tarname = os.path.join(homepath,tarname)
+  tarname = os.path.join(homepath, tarname)
-  geturl(url,tarname)
+  geturl(url, tarname)
 
   print("Unpacking MS-CG tarfile ...")
 
-  if os.path.exists(os.path.join(homepath,tardir)):
+  if os.path.exists(os.path.join(homepath, tardir)):
-    shutil.rmtree(os.path.join(homepath,tardir))
+    shutil.rmtree(os.path.join(homepath, tardir))
-  
+
   if tarfile.is_tarfile(tarname):
     tgz = tarfile.open(tarname)
     tgz.extractall(path=homepath)
     os.remove(tarname)
   else:
-    sys.exit("File %s is not a supported archive",tarname)
+    sys.exit("File %s is not a supported archive", tarname)
 
   if os.path.basename(homedir) != tardir:
     if os.path.exists(homedir):
       shutil.rmtree(homedir)
-    os.rename(os.path.join(homepath,tardir),homedir)
+    os.rename(os.path.join(homepath, tardir), homedir)
 
 # build MS-CG
 
 if buildflag:
   print("Building MS-CG ...")
-  mkf="Makefile.%s" % msuffix
+  mkf = "Makefile.%s" % msuffix
-  mkp=os.path.join(homedir,'src','Make',mkf)
+  mkp = os.path.join(homedir, 'src', 'Make', mkf)
   if os.path.exists(mkp):
-    shutil.copyfile(mkp,os.path.join(homedir,'src',mkf))
+    shutil.copyfile(mkp, os.path.join(homedir, 'src', mkf))
   elif os.path.exists("Makefile.%s" % msuffix):
-    shutil.copyfile("Makefile.%s" % msuffix,os.path.join(homedir,'src',mkf))
+    shutil.copyfile("Makefile.%s" % msuffix, os.path.join(homedir, 'src', mkf))
   else:
     sys.exit("Cannot find Makefile.%s" % msuffix)
   try:
-    cmd = 'make -C %s -f Makefile.%s' % (os.path.join(homedir,'src'),msuffix)
+    cmd = 'make -C %s -f Makefile.%s' % (os.path.join(homedir, 'src'), msuffix)
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     print("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -124,9 +126,9 @@ if buildflag:
   if not os.path.exists("Makefile.lammps"):
     print("Creating Makefile.lammps")
     if os.path.exists("Makefile.lammps.%s" % msuffix):
-      shutil.copyfile('Makefile.lammps.%s' % msuffix,'Makefile.lammps')
+      shutil.copyfile('Makefile.lammps.%s' % msuffix, 'Makefile.lammps')
     else:
-      shutil.copyfile('Makefile.lammps.default','Makefile.lammps')
+      shutil.copyfile('Makefile.lammps.default', 'Makefile.lammps')
   else: print("Makefile.lammps exists. Please check its settings")
 
 # create 2 links in lib/mscg to MS-CG src dir
@@ -136,5 +138,5 @@ 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")
-os.symlink(os.path.join(homedir,'src'),'includelink')
+os.symlink(os.path.join(homedir, 'src'), 'includelink')
-os.symlink(os.path.join(homedir,'src'),'liblink')
+os.symlink(os.path.join(homedir, 'src'), 'liblink')

lib/plumed/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, build, and link to the plumed2 library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, build, and link to the plumed2 library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,re,subprocess,hashlib,shutil
+import sys, os, subprocess, shutil
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import get_cpus, fullpath, geturl, checkmd5sum
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -19,7 +22,7 @@ mode = "static"
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-plumed args="-b"
                  or: make lib-plumed args="-b -v 2.4.3"
                  or: make lib-plumed args="-p /usr/local/plumed2 -m shared"
@@ -57,13 +60,13 @@ parser.add_argument("-m", "--mode", default=mode, choices=['static', 'shared', '
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
-plumedpath= args.path
+plumedpath = args.path
 
 homepath = fullpath('.')
 homedir = "%s/plumed2" % (homepath)
@@ -76,31 +79,31 @@ if pathflag:
 # download and unpack plumed2 tarball
 
 if buildflag:
-  url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
+  url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version, version)
   filename = "plumed-src-%s.tar.gz" %version
   print("Downloading plumed  ...")
-  geturl(url,filename)
+  geturl(url, filename)
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
-    if not checkmd5sum(checksums[version],filename):
+    if not checkmd5sum(checksums[version], filename):
       sys.exit("Checksum for plumed2 library does not match")
 
   print("Unpacking plumed2 source tarball ...")
-  if os.path.exists("%s/plumed-%s" % (homepath,version)):
+  if os.path.exists("%s/plumed-%s" % (homepath, version)):
-    shutil.rmtree("%s/plumed-%s" % (homepath,version))
+    shutil.rmtree("%s/plumed-%s" % (homepath, version))
   if os.path.exists(homedir):
     shutil.rmtree(homedir)
-  cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)
+  cmd = 'cd "%s"; tar -xzvf %s' % (homepath, filename)
-  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
-  os.remove(os.path.join(homepath,filename))
+  os.remove(os.path.join(homepath, filename))
 
   # build plumed
   print("Building plumed ...")
   n_cpus = get_cpus()
-  cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-modules=all --enable-static-patch ; make -j%d ; make install' % (homepath,version,homedir,n_cpus)
+  cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-modules=all --enable-static-patch ; make -j%d ; make install' % (homepath, version, homedir, n_cpus)
   try:
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     print("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -113,20 +116,20 @@ 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")
-os.symlink(os.path.join(homedir,'include'),'includelink')
+os.symlink(os.path.join(homedir, 'include'), 'includelink')
-libpath=os.path.join(homedir,'lib64')
+libpath = os.path.join(homedir, 'lib64')
-if not os.path.exists(libpath): libpath=os.path.join(homedir,'lib')
+if not os.path.exists(libpath):
-os.symlink(libpath,'liblink')
+  libpath = os.path.join(homedir, 'lib')
+os.symlink(libpath, 'liblink')
 if os.path.isfile("Makefile.lammps.%s" % mode):
   print("Creating Makefile.lammps")
-  plumedinc = os.path.join('liblink','plumed','src','lib','Plumed.inc.' + mode)
+  plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode)
-  lines1 = open(plumedinc,'r').readlines()
+  lines1 = open(plumedinc, 'r').readlines()
-  lines2 = open("Makefile.lammps.%s" % mode,'r').readlines()
+  lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines()
-  fp = open("Makefile.lammps",'w')
+  fp = open("Makefile.lammps", 'w')
-  fp.write(os.path.join("PLUMED_LIBDIR=",homedir,"lib\n"))
+  fp.write(os.path.join("PLUMED_LIBDIR=", homedir, "lib\n"))
   for line in lines1:
     fp.write(line)
   for line in lines2:
     fp.write(line)
   fp.close()
-

lib/pylint.rc

@@ -0,0 +1,564 @@
+# pylint configuration for checking Install.py files in the lib folder and its subdirs
+
+[MASTER]
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code.
+extension-pkg-whitelist=
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Add files or directories matching the regex patterns to the blacklist. The
+# regex matches against base names, not paths.
+ignore-patterns=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+init-hook=sys.path.append('..')
+
+# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
+# number of processors available to use.
+jobs=1
+
+# Control the amount of potential inferred values when inferring a single
+# object. This can help the performance when dealing with large functions or
+# complex, nested conditions.
+limit-inference-results=100
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# Specify a configuration file.
+#rcfile=
+
+# When enabled, pylint would attempt to guess common misconfiguration and emit
+# user-friendly hints instead of false-positive error messages.
+suggestion-mode=yes
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=no
+
+
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED.
+confidence=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once). You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use "--disable=all --enable=classes
+# --disable=W".
+disable=print-statement,
+        parameter-unpacking,
+        unpacking-in-except,
+        old-raise-syntax,
+        backtick,
+        long-suffix,
+        old-ne-operator,
+        old-octal-literal,
+        import-star-module-level,
+        non-ascii-bytes-literal,
+        raw-checker-failed,
+        bad-inline-option,
+        locally-disabled,
+        locally-enabled,
+        file-ignored,
+        suppressed-message,
+        useless-suppression,
+        deprecated-pragma,
+        use-symbolic-message-instead,
+        apply-builtin,
+        basestring-builtin,
+        buffer-builtin,
+        cmp-builtin,
+        coerce-builtin,
+        execfile-builtin,
+        file-builtin,
+        long-builtin,
+        raw_input-builtin,
+        reduce-builtin,
+        standarderror-builtin,
+        unicode-builtin,
+        xrange-builtin,
+        coerce-method,
+        delslice-method,
+        getslice-method,
+        setslice-method,
+        no-absolute-import,
+        old-division,
+        dict-iter-method,
+        dict-view-method,
+        next-method-called,
+        metaclass-assignment,
+        indexing-exception,
+        raising-string,
+        reload-builtin,
+        oct-method,
+        hex-method,
+        nonzero-method,
+        cmp-method,
+        input-builtin,
+        round-builtin,
+        intern-builtin,
+        unichr-builtin,
+        map-builtin-not-iterating,
+        zip-builtin-not-iterating,
+        range-builtin-not-iterating,
+        filter-builtin-not-iterating,
+        using-cmp-argument,
+        eq-without-hash,
+        div-method,
+        idiv-method,
+        rdiv-method,
+        exception-message-attribute,
+        invalid-str-codec,
+        sys-max-int,
+        bad-python3-import,
+        deprecated-string-function,
+        deprecated-str-translate-call,
+        deprecated-itertools-function,
+        deprecated-types-field,
+        next-method-defined,
+        dict-items-not-iterating,
+        dict-keys-not-iterating,
+        dict-values-not-iterating,
+        deprecated-operator-function,
+        deprecated-urllib-function,
+        xreadlines-attribute,
+        deprecated-sys-function,
+        exception-escape,
+        comprehension-escape,
+        invalid-name,
+        bad-indentation,
+        multiple-imports,
+        line-too-long
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=c-extension-no-member
+
+
+[REPORTS]
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details.
+#msg-template=
+
+# Set the output format. Available formats are text, parseable, colorized, json
+# and msvs (visual studio). You can also give a reporter class, e.g.
+# mypackage.mymodule.MyReporterClass.
+output-format=text
+
+# Tells whether to display a full report or only the messages.
+reports=no
+
+# Activate the evaluation score.
+score=yes
+
+
+[REFACTORING]
+
+# Maximum number of nested blocks for function / method body
+max-nested-blocks=5
+
+# Complete name of functions that never returns. When checking for
+# inconsistent-return-statements if a never returning function is called then
+# it will be considered as an explicit return statement and no message will be
+# printed.
+never-returning-functions=sys.exit
+
+
+[FORMAT]
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+expected-line-ending-format=
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\S+>?$
+
+# Number of spaces of indent required inside a hanging  or continued line.
+indent-after-paren=4
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module.
+max-module-lines=1000
+
+# List of optional constructs for which whitespace checking is disabled. `dict-
+# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
+# `trailing-comma` allows a space between comma and closing bracket: (a, ).
+# `empty-line` allows space-only lines.
+no-space-check=trailing-comma,
+               dict-separator
+
+# Allow the body of a class to be on the same line as the declaration if body
+# contains single statement.
+single-line-class-stmt=no
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+single-line-if-stmt=no
+
+
+[VARIABLES]
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+# Tells whether unused global variables should be treated as a violation.
+allow-global-unused-variables=yes
+
+# List of strings which can identify a callback function by name. A callback
+# name must start or end with one of those strings.
+callbacks=cb_,
+          _cb
+
+# A regular expression matching the name of dummy variables (i.e. expected to
+# not be used).
+dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore.
+ignored-argument-names=_.*|^ignored_|^unused_
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# List of qualified module names which can have objects that can redefine
+# builtins.
+redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io
+
+
+[SIMILARITIES]
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+
+[SPELLING]
+
+# Limits count of emitted suggestions for spelling mistakes.
+max-spelling-suggestions=4
+
+# Spelling dictionary name. Available dictionaries: none. To make it working
+# install python-enchant package..
+spelling-dict=
+
+# List of comma separated words that should not be checked.
+spelling-ignore-words=
+
+# A path to a file that contains private dictionary; one word per line.
+spelling-private-dict-file=
+
+# Tells whether to store unknown words to indicated private dictionary in
+# --spelling-private-dict-file option instead of raising a message.
+spelling-store-unknown-words=no
+
+
+[LOGGING]
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format.
+logging-modules=logging
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,
+      XXX,
+      TODO
+
+
+[TYPECHECK]
+
+# List of decorators that produce context managers, such as
+# contextlib.contextmanager. Add to this list to register other decorators that
+# produce valid context managers.
+contextmanager-decorators=contextlib.contextmanager
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+generated-members=
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# Tells whether to warn about missing members when the owner of the attribute
+# is inferred to be None.
+ignore-none=yes
+
+# This flag controls whether pylint should warn about no-member and similar
+# checks whenever an opaque object is returned when inferring. The inference
+# can return multiple potential results while evaluating a Python object, but
+# some branches might not be evaluated, which results in partial inference. In
+# that case, it might be useful to still emit no-member and other checks for
+# the rest of the inferred objects.
+ignore-on-opaque-inference=yes
+
+# List of class names for which member attributes should not be checked (useful
+# for classes with dynamically set attributes). This supports the use of
+# qualified names.
+ignored-classes=optparse.Values,thread._local,_thread._local
+
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis. It
+# supports qualified module names, as well as Unix pattern matching.
+ignored-modules=
+
+# Show a hint with possible names when a member name was not found. The aspect
+# of finding the hint is based on edit distance.
+missing-member-hint=yes
+
+# The minimum edit distance a name should have in order to be considered a
+# similar match for a missing member name.
+missing-member-hint-distance=1
+
+# The total number of similar names that should be taken in consideration when
+# showing a hint for a missing member.
+missing-member-max-choices=1
+
+
+[BASIC]
+
+# Naming style matching correct argument names.
+argument-naming-style=snake_case
+
+# Regular expression matching correct argument names. Overrides argument-
+# naming-style.
+#argument-rgx=
+
+# Naming style matching correct attribute names.
+attr-naming-style=snake_case
+
+# Regular expression matching correct attribute names. Overrides attr-naming-
+# style.
+#attr-rgx=
+
+# Bad variable names which should always be refused, separated by a comma.
+bad-names=foo,
+          bar,
+          baz,
+          toto,
+          tutu,
+          tata
+
+# Naming style matching correct class attribute names.
+class-attribute-naming-style=any
+
+# Regular expression matching correct class attribute names. Overrides class-
+# attribute-naming-style.
+#class-attribute-rgx=
+
+# Naming style matching correct class names.
+class-naming-style=PascalCase
+
+# Regular expression matching correct class names. Overrides class-naming-
+# style.
+#class-rgx=
+
+# Naming style matching correct constant names.
+const-naming-style=UPPER_CASE
+
+# Regular expression matching correct constant names. Overrides const-naming-
+# style.
+#const-rgx=
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+docstring-min-length=-1
+
+# Naming style matching correct function names.
+function-naming-style=snake_case
+
+# Regular expression matching correct function names. Overrides function-
+# naming-style.
+#function-rgx=
+
+# Good variable names which should always be accepted, separated by a comma.
+good-names=i,
+           j,
+           k,
+           ex,
+           Run,
+           _
+
+# Include a hint for the correct naming format with invalid-name.
+include-naming-hint=no
+
+# Naming style matching correct inline iteration names.
+inlinevar-naming-style=any
+
+# Regular expression matching correct inline iteration names. Overrides
+# inlinevar-naming-style.
+#inlinevar-rgx=
+
+# Naming style matching correct method names.
+method-naming-style=snake_case
+
+# Regular expression matching correct method names. Overrides method-naming-
+# style.
+#method-rgx=
+
+# Naming style matching correct module names.
+module-naming-style=snake_case
+
+# Regular expression matching correct module names. Overrides module-naming-
+# style.
+#module-rgx=
+
+# Colon-delimited sets of names that determine each other's naming style when
+# the name regexes allow several styles.
+name-group=
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+no-docstring-rgx=^_
+
+# List of decorators that produce properties, such as abc.abstractproperty. Add
+# to this list to register other decorators that produce valid properties.
+# These decorators are taken in consideration only for invalid-name.
+property-classes=abc.abstractproperty
+
+# Naming style matching correct variable names.
+variable-naming-style=snake_case
+
+# Regular expression matching correct variable names. Overrides variable-
+# naming-style.
+#variable-rgx=
+
+
+[IMPORTS]
+
+# Allow wildcard imports from modules that define __all__.
+allow-wildcard-with-all=no
+
+# Analyse import fallback blocks. This can be used to support both Python 2 and
+# 3 compatible code, which means that the block might have code that exists
+# only in one or another interpreter, leading to false positives when analysed.
+analyse-fallback-blocks=no
+
+# Deprecated modules which should not be used, separated by a comma.
+deprecated-modules=optparse,tkinter.tix
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled).
+ext-import-graph=
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled).
+import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled).
+int-import-graph=
+
+# Force import order to recognize a module as part of the standard
+# compatibility libraries.
+known-standard-library=
+
+# Force import order to recognize a module as part of a third party library.
+known-third-party=enchant
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method.
+max-args=5
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Maximum number of boolean expressions in an if statement.
+max-bool-expr=5
+
+# Maximum number of branch for function / method body.
+max-branches=12
+
+# Maximum number of locals for function / method body.
+max-locals=15
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+# Maximum number of return / yield for function / method body.
+max-returns=6
+
+# Maximum number of statements in function / method body.
+max-statements=50
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+
+[CLASSES]
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,
+                      __new__,
+                      setUp
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected=_asdict,
+                  _fields,
+                  _replace,
+                  _source,
+                  _make
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=cls
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception".
+overgeneral-exceptions=Exception

lib/scafacos/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, build, and link to the ScaFaCoS library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, build, and link to the ScaFaCoS library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil,tarfile
+import sys, os, subprocess, shutil, tarfile
-sys.path.append('..')
-from install_helpers import fullpath,geturl,get_cpus,checkmd5sum
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl, get_cpus, checkmd5sum
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -24,7 +27,7 @@ checksums = { \
 
 # extra help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-scafacos args="-b"
                  or: make lib-scafacos args="-p /usr/local/scafacos"
 Syntax from lib dir: python Install.py -b
@@ -49,23 +52,23 @@ parser.add_argument("-v", "--version", default=version,
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
 version = args.version
 
 homepath = fullpath(".")
-scafacospath = os.path.join(homepath,"scafacos-%s" % version)
+scafacospath = os.path.join(homepath, "scafacos-%s" % version)
 
 if pathflag:
   scafacospath = args.path
-  if not os.path.isdir(os.path.join(scafacospath,"include")):
+  if not os.path.isdir(os.path.join(scafacospath, "include")):
     sys.exit("ScaFaCoS include path for %s does not exist" % scafacospath)
-  if (not os.path.isdir(os.path.join(scafacospath,"lib64"))) \
+  if (not os.path.isdir(os.path.join(scafacospath, "lib64"))) \
-     and (not os.path.isdir(os.path.join(scafacospath,"lib"))):
+     and (not os.path.isdir(os.path.join(scafacospath, "lib"))):
     sys.exit("ScaFaCoS lib path for %s does not exist" % scafacospath)
   scafacospath = fullpath(scafacospath)
 
@@ -73,19 +76,19 @@ if pathflag:
 
 if buildflag:
   print("Downloading ScaFaCoS ...")
-  geturl(url,"%s/scafacos-%s.tar.gz" % (homepath,version))
+  geturl(url, "%s/scafacos-%s.tar.gz" % (homepath, version))
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
-    if not checkmd5sum(checksums[version],'%s/scafacos-%s.tar.gz' % (homepath,version)):
+    if not checkmd5sum(checksums[version], '%s/scafacos-%s.tar.gz' % (homepath, version)):
       sys.exit("Checksum for ScaFaCoS library does not match")
 
   print("Unpacking ScaFaCoS tarball ...")
   if os.path.exists(scafacospath):
     shutil.rmtree(scafacospath)
-  tarname = os.path.join(homepath,"%s.tar.gz" % scafacospath)
+  tarname = os.path.join(homepath, "%s.tar.gz" % scafacospath)
   if tarfile.is_tarfile(tarname):
-    tgz=tarfile.open(tarname)
+    tgz = tarfile.open(tarname)
     tgz.extractall(path=homepath)
     os.remove(tarname)
   else:
@@ -94,9 +97,9 @@ if buildflag:
   # build ScaFaCoS
   print("Building ScaFaCoS ...")
   n_cpu = get_cpus()
-  cmd = 'cd "%s"; ./configure --prefix="%s" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77=; make -j%d; make install' % (scafacospath,os.path.join(homepath,'build'),n_cpu)
+  cmd = 'cd "%s"; ./configure --prefix="%s" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77=; make -j%d; make install' % (scafacospath, os.path.join(homepath, 'build'), n_cpu)
   try:
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -109,11 +112,11 @@ if os.path.isfile("includelink") or os.path.islink("includelink"):
 if os.path.isfile("liblink") or os.path.islink("liblink"):
   os.remove("liblink")
 if buildflag:
-  os.symlink(os.path.join(homepath,'build','include'),'includelink')
+  os.symlink(os.path.join(homepath, 'build', 'include'), 'includelink')
-  os.symlink(os.path.join(homepath,'build','lib'),'liblink')
+  os.symlink(os.path.join(homepath, 'build', 'lib'), 'liblink')
 else:
-  os.symlink(os.path.join(scafacospath,'include'),'includelink')
+  os.symlink(os.path.join(scafacospath, 'include'), 'includelink')
-  if os.path.isdir(os.path.join(scafacospath,"lib64")):
+  if os.path.isdir(os.path.join(scafacospath, "lib64")):
-    os.symlink(os.path.join(scafacospath,'lib64'),'liblink')
+    os.symlink(os.path.join(scafacospath, 'lib64'), 'liblink')
   else:
-    os.symlink(os.path.join(scafacospath,'lib'),'liblink')
+    os.symlink(os.path.join(scafacospath, 'lib'), 'liblink')

lib/smd/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, and point to the Eigen library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, and point to the Eigen library
+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,tarfile
+import sys, os, glob, shutil, tarfile
-sys.path.append('..')
-from install_helpers import fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl, checkmd5sum
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -27,7 +30,7 @@ checksums = { \
 
 # help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-smd args="-b"
                  or: make lib-smd args="-p /usr/include/eigen3"
 
@@ -52,20 +55,21 @@ parser.add_argument("-v", "--version", default=version,
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 homepath = fullpath(".")
-eigenpath = os.path.join(homepath,"eigen3")
+eigenpath = os.path.join(homepath, "eigen3")
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
 version = args.version
 
 if pathflag:
   eigenpath = args.path
-  if not os.path.isdir(eigenpath): sys.exit("Eigen path %s does not exist" % eigenpath)
+  if not os.path.isdir(eigenpath):
+    sys.exit("Eigen path %s does not exist" % eigenpath)
   eigenpath = fullpath(eigenpath)
 
 # download and unpack Eigen tarball
@@ -73,19 +77,19 @@ if pathflag:
 
 if buildflag:
   print("Downloading Eigen ...")
-  eigentar = os.path.join(homepath,tarball)
+  eigentar = os.path.join(homepath, tarball)
   url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version
-  geturl(url,eigentar)
+  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],eigentar):
+    if not checkmd5sum(checksums[version], eigentar):
       sys.exit("Checksum for Eigen library does not match")
 
 
   print("Cleaning up old folders ...")
-  edir = glob.glob(os.path.join(homepath,"eigen-eigen-*"))
+  edir = glob.glob(os.path.join(homepath, "eigen-eigen-*"))
   edir.append(eigenpath)
   for one in edir:
     if os.path.isdir(one):
@@ -98,8 +102,8 @@ if buildflag:
     os.remove(eigentar)
   else:
     sys.exit("File %s is not a supported archive" % eigentar)
-  edir = glob.glob(os.path.join(homepath,"eigen-eigen-*"))
+  edir = glob.glob(os.path.join(homepath, "eigen-eigen-*"))
-  os.rename(edir[0],eigenpath)
+  os.rename(edir[0], eigenpath)
 
 # create link in lib/smd to Eigen src dir
 
@@ -107,4 +111,4 @@ print("Creating link to Eigen include folder")
 if os.path.isfile("includelink") or os.path.islink("includelink"):
   os.remove("includelink")
 linkdir = eigenpath
-os.symlink(linkdir,'includelink')
+os.symlink(linkdir, 'includelink')

lib/voronoi/Install.py

@@ -1,14 +1,17 @@
 #!/usr/bin/env python
 
-# Install.py tool to download, unpack, build, and link to the Voro++ library
+"""
-# used to automate the steps described in the README file in this dir
+Install.py tool to download, unpack, build, and link to the Voro++ library
+used to automate the steps described in the README file in this dir
+"""
 
 from __future__ import print_function
-import sys,os,re,subprocess,shutil,tarfile
+import sys, os, subprocess, shutil, tarfile
-sys.path.append('..')
-from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
 from argparse import ArgumentParser
 
+sys.path.append('..')
+from install_helpers import fullpath, geturl, checkmd5sum
+
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
@@ -24,7 +27,7 @@ checksums = { \
 
 # extra help message
 
-help = """
+HELP = """
 Syntax from src dir: make lib-voronoi args="-b"
                  or: make lib-voronoi args="-p /usr/local/voro++-0.4.6"
                  or: make lib-voronoi args="-b -v voro++-0.4.6"
@@ -52,16 +55,16 @@ parser.add_argument("-v", "--version", default=version,
 args = parser.parse_args()
 
 # print help message and exit, if neither build nor path options are given
-if args.build == False and not args.path:
+if not args.build and not args.path:
   parser.print_help()
-  sys.exit(help)
+  sys.exit(HELP)
 
 buildflag = args.build
-pathflag = args.path != None
+pathflag = args.path is not None
 voropath = args.path
 
 homepath = fullpath(".")
-homedir = os.path.join(homepath,version)
+homedir = os.path.join(homepath, version)
 
 if pathflag:
     if not os.path.isdir(voropath):
@@ -72,17 +75,18 @@ if pathflag:
 
 if buildflag:
   print("Downloading Voro++ ...")
-  vorotar = os.path.join(homepath,version) + '.tar.gz'
+  vorotar = os.path.join(homepath, version) + '.tar.gz'
-  geturl(url,vorotar)
+  geturl(url, vorotar)
 
   # verify downloaded archive integrity via md5 checksum, if known.
   if version in checksums:
-    if not checkmd5sum(checksums[version],vorotar):
+    if not checkmd5sum(checksums[version], vorotar):
       sys.exit("Checksum for Voro++ library does not match")
 
   print("Unpacking Voro++ tarball ...")
-  srcpath = os.path.join(homepath,version)
+  srcpath = os.path.join(homepath, version)
-  if os.path.exists(srcpath): shutil.rmtree(srcpath)
+  if os.path.exists(srcpath):
+    shutil.rmtree(srcpath)
   if tarfile.is_tarfile(vorotar):
     tgz = tarfile.open(vorotar)
     tgz.extractall(path=homepath)
@@ -90,8 +94,9 @@ if buildflag:
   else:
     sys.exit("File %s is not a supported archive" % vorotar)
   if os.path.basename(homedir) != version:
-    if os.path.exists(homedir): shutil.rmtree(homedir)
+    if os.path.exists(homedir):
-    os.rename(srcpath,homedir)
+      shutil.rmtree(homedir)
+    os.rename(srcpath, homedir)
 
 # build Voro++
 
@@ -99,7 +104,7 @@ if buildflag:
   print("Building Voro++ ...")
   cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir
   try:
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+    txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     print(txt.decode('UTF-8'))
   except subprocess.CalledProcessError as e:
     print("Make failed with:\n %s" % e.output.decode('UTF-8'))
@@ -112,5 +117,5 @@ 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")
-os.symlink(os.path.join(homedir,'src'),'includelink')
+os.symlink(os.path.join(homedir, 'src'), 'includelink')
-os.symlink(os.path.join(homedir,'src'),'liblink')
+os.symlink(os.path.join(homedir, 'src'), 'liblink')