Transform LAMMPS Python module into package

- Moves lammps.py into its own package
- Imports entire module in __init__.py
- Changes both how legacy and CMake build systems install
- Added traditional setup.py for Python-only installation

Note: the CMake install target runs setup.py build and install
in a way that produces files in CMAKE_BINARY_DIR/python instead
of python/build. This is to maintain out-of-source compilation
support.

cmake/CMakeLists.txt

@@ -661,7 +661,7 @@ if(BUILD_SHARED_LIBS)
     add_custom_target(
       install-python
       ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-      -m ${LAMMPS_PYTHON_DIR}/lammps.py
+      -p ${LAMMPS_PYTHON_DIR}/lammps
       -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
       COMMENT "Installing LAMMPS Python module")
@@ -691,11 +691,8 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if (Python_EXECUTABLE)
-    execute_process(COMMAND ${Python_EXECUTABLE}
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
-      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
-      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
-    install(FILES ${LAMMPS_PYTHON_DIR}/lammps.py DESTINATION ${PYTHON_INSTDIR})
   endif()
 endif()
 

python/install.py

@@ -1,42 +1,42 @@
 #!/usr/bin/env python
 
 """
-Installer script to install the LAMMPS python module and the corresponding
+Installer script to install the LAMMPS python package and the corresponding
 shared library into either the system-wide site-packages tree, or - failing
 that - into the corresponding user tree. Called from the 'install-python'
 build target in the conventional and CMake based build systems
 """
 
-# copy LAMMPS shared library and lammps.py to system dirs
+# copy LAMMPS shared library and lammps package to system dirs
 
 from __future__ import print_function
 import sys,os,shutil
 from argparse import ArgumentParser
 
 parser = ArgumentParser(prog='install.py',
-                        description='LAMMPS python module installer script')
+                        description='LAMMPS python package installer script')
 
-parser.add_argument("-m", "--module", required=True,
+parser.add_argument("-p", "--package", required=True,
-                    help="path to the source of the LAMMPS Python module")
+                    help="path to the LAMMPS Python package")
 parser.add_argument("-l", "--lib", required=True,
                     help="path to the compiled LAMMPS shared library")
 parser.add_argument("-v", "--version", required=True,
                     help="path to the LAMMPS version.h header file")
 
 parser.add_argument("-d","--dir",
-                    help="Legacy custom installation folder selection for module and library")
+                    help="Legacy custom installation folder selection for package and library")
 
 args = parser.parse_args()
 
 # validate arguments and make paths absolute
 
-if args.module:
+if args.package:
-  if not os.path.exists(args.module):
+  if not os.path.exists(args.package):
-    print( "ERROR: LAMMPS module file %s does not exist" % args.module)
+    print( "ERROR: LAMMPS package %s does not exist" % args.package)
     parser.print_help()
     sys.exit(1)
   else:
-    args.module = os.path.abspath(args.module)
+    args.package = os.path.abspath(args.package)
 
 if args.lib:
   if not os.path.exists(args.lib):
@@ -66,9 +66,9 @@ if args.dir:
 # without any special processing or additional steps to that folder
 
 if args.dir:
-  print("Copying LAMMPS Python module to custom folder %s" % args.dir)
+  print("Copying LAMMPS Python package to custom folder %s" % args.dir)
   try:
-    shutil.copyfile(args.module, os.path.join(args.dir,'lammps.py'))
+    shutil.copytree(args.package, os.path.join(args.dir,'lammps'))
   except shutil.Error:
     pass # fail silently
 
@@ -81,15 +81,19 @@ if args.dir:
   sys.exit()
 
 # extract version string from header
-fp = open(args.version,'r')
+def get_lammps_version(header):
-txt=fp.read().split('"')[1].split()
+    with open(header, 'r') as f:
-verstr=txt[0]+txt[1]+txt[2]
+        line = f.readline()
-fp.close()
+        start_pos = line.find('"')+1
+        end_pos = line.find('"', start_pos)
+        return "".join(line[start_pos:end_pos].split())
 
-print("Installing LAMMPS Python module version %s into site-packages folder" % verstr)
+verstr = get_lammps_version(args.version)
 
-# we need to switch to the folder of the python module
+print("Installing LAMMPS Python package version %s into site-packages folder" % verstr)
-os.chdir(os.path.dirname(args.module))
+
+# we need to switch to the folder of the python package
+os.chdir(os.path.dirname(args.package))
 
 from distutils.core import setup
 from distutils.sysconfig import get_python_lib
@@ -103,10 +107,10 @@ try:
         author = "Steve Plimpton",
         author_email = "sjplimp@sandia.gov",
         url = "https://lammps.sandia.gov",
-        description = "LAMMPS Molecular Dynamics Python module",
+        description = "LAMMPS Molecular Dynamics Python package",
         license = "GPL",
-        py_modules = ["lammps"],
+        packages=['lammps'],
-        data_files = [(get_python_lib(), [args.lib])])
+        data_files = [(os.path.join(get_python_lib(), 'lammps'), [args.lib])])
 except:
   tryuser=True
   print ("Installation into global site-packages folder failed.\nTrying user folder %s now." % site.USER_SITE)
@@ -119,9 +123,9 @@ if tryuser:
           author = "Steve Plimpton",
           author_email = "sjplimp@sandia.gov",
           url = "https://lammps.sandia.gov",
-          description = "LAMMPS Molecular Dynamics Python module",
+          description = "LAMMPS Molecular Dynamics Python package",
           license = "GPL",
-          py_modules = ["lammps"],
+          packages=['lammps'],
-          data_files = [(site.USER_SITE, [args.lib])])
+          data_files = [(os.path.join(site.USER_SITE, 'lammps'), [args.lib])])
   except:
     print("Installation into user site package folder failed.")

python/lammps/__init__.py

@@ -0,0 +1 @@
+from .lammps import *

python/setup.py

@@ -0,0 +1,26 @@
+# this only installs the LAMMPS python package
+# it assumes the LAMMPS shared library is already installed
+from distutils.core import setup
+import os
+
+LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
+LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
+LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
+
+def get_lammps_version():
+    with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
+        line = f.readline()
+        start_pos = line.find('"')+1
+        end_pos = line.find('"', start_pos)
+        return "".join(line[start_pos:end_pos].split())
+
+setup(
+    name = "lammps",
+    version = get_lammps_version(),
+    author = "Steve Plimpton",
+    author_email = "sjplimp@sandia.gov",
+    url = "https://lammps.sandia.gov",
+    description = "LAMMPS Molecular Dynamics Python package",
+    license = "GPL",
+    packages=["lammps"]
+)

src/Makefile

@@ -278,7 +278,7 @@ mpi-stubs:
 sinclude ../lib/python/Makefile.lammps
 install-python:
 	@$(PYTHON) ../python/install.py -v ../src/version.h \
-		-m ../python/lammps.py -l ../src/liblammps.so
+		-p ../python/lammps -l ../src/liblammps.so
 
 # Create a tarball of src dir and packages