Merge pull request #48 from bpuchala/0.2.X

0.2.1

Author: bpuchala

.gitignore

@@ -24,6 +24,9 @@
 *.bkup
 *.old
 
+# Debugging files
+*.bc
+
 # Mac files
 .DS_Store
 
@@ -58,6 +61,7 @@ src/general/populator
 
 #scons
 .sconsign.dblite
+.sconf_temp
 
 #binaries
 bin/*

INSTALL.md

@@ -5,7 +5,7 @@
 
 **C++11**
 
-CASM must be compiled with a compiler that supports the C++11 standard.
+CASM must be compiled with a compiler that supports the C++11 standard. Testing is done with gcc-4.8.5 and clang-800.0.42.1.
 
 **If using Mac OS X - Xcode command-line tools**
 
@@ -44,7 +44,7 @@ Scons can be downloaded and installed from source following instructions found a
 
 ### Boost
 
-CASM uses several Boost libraries, which are often available installed on many computing clusters. you can install Boost yourself via a package management tool, or by downloading from the Boost website: [http://www.boost.org](http://www.boost.org). CASM uses the system, filesystem, program_options, and unit_test_framework libraries, and their dependencies. Most CASM testing has been performed with Boost version 1.54 or later.
+CASM uses several Boost libraries, which are often available installed on many computing clusters. you can install Boost yourself via a package management tool, or by downloading from the Boost website: [http://www.boost.org](http://www.boost.org). CASM uses the system, filesystem, program_options, and unit_test_framework libraries, and their dependencies. Most CASM testing has been performed with Boost version 1.54 or later. Known bugs in version 1.53 and earlier will cause failures.
 
 *Important: Boost should be compiled using the same compiler that you will use to compile CASM.*
 

Makefile.am

@@ -0,0 +1,95 @@
+#===========================================================#
+#To understand why it's structured this way see
+#http://karelzak.blogspot.co.uk/2013/02/non-recursive-automake.html
+
+ACLOCAL_AMFLAGS = -I build-aux/m4
+
+#===========================================================#
+#Start out empty, let the Makemodule.am files fill these in
+lib_LTLIBRARIES=
+noinst_LIBRARIES=
+bin_PROGRAMS=
+check_PROGRAMS=
+man1_MANS=
+dist_bin_SCRIPTS=
+TESTS=
+
+#===========================================================#
+#Define flags for everything ever
+TXT_VERSION:=$(shell cat $(top_srcdir)/build-aux/casm_version.txt)
+
+AM_CXXFLAGS = -DTXT_VERSION='"$(TXT_VERSION)"'\
+			  -DEIGEN_DEFAULT_DENSE_INDEX_TYPE=long\
+			  -DGZSTREAM_NAMESPACE=gz\
+			  -I$(srcdir)/include\
+			  -I$(srcdir)/include/casm/external/gzstream\
+			  -I$(srcdir)/include/casm/external/qhull/libqhullcpp
+
+AM_CPPFLAGS = -I$(srcdir)/include/casm/external/qhull/libqhull_r/\
+			  -I$(srcdir)/include/casm/external/gzstream\
+			  $(BOOST_CPPFLAGS)
+
+AM_LDFLAGS = $(BOOST_LDFLAGS)
+
+BUILT_SOURCES=
+
+#============================================================#
+#Files that arent sources for executalbes or headers that get installed, but are needed in the distribution.
+#Even though the include/casm/external is distributed through headers, the licensing and other files should
+#also be included.
+EXTRA_DIST=
+
+EXTRA_DIST+=./build-aux/casm_version.txt\
+			./man\
+			./casmenv.sh\
+			./sample_input_files
+
+#Extra files that should be cleaned up upon `distclean`
+DISTCLEANFILES=
+
+#============================================================#
+#Always have included modules use paths relative to this
+#parent Makefile.am. Avoid variable expansion in *_SOURCES
+#============================================================#
+#Create shared casm libraries
+include $(srcdir)/src/casm/Makemodule.am
+include $(srcdir)/src/ccasm/Makemodule.am
+
+#============================================================#
+#Take care of all the include headers
+include $(srcdir)/include/casm/Makemodule.am
+include $(srcdir)/include/ccasm/Makemodule.am
+
+#============================================================#
+#Take care of applications
+include $(srcdir)/apps/casm/Makemodule.am
+include $(srcdir)/apps/completer/Makemodule.am
+
+#============================================================#
+#Take care of tests
+include $(srcdir)/tests/Makemodule.am
+
+#============================================================#
+#Take care of python stuff
+include $(srcdir)/python/Makemodule.am
+
+#============================================================#
+#Misc targets
+.FORCE:
+
+test:
+	echo $(srcdir)
+	echo $(top_srcdir)
+	echo $(AM_LDFLAGS)
+	echo $(AM_CXXFLAGS)
+	echo $(AM_CPPFLAGS)
+	echo $(casm_LDFLAGS)
+	echo $(BOOST_LDFLAGS)
+	echo $(BOOST_CXXFLAGS)
+	echo $(BOOST_CPPFLAGS)
+	echo $(TXT_VERSION)
+
+#============================================================#
+#Recurse into these places (must be direct children, don't be fancy)
+#SUBDIRS= ##DO NOT USE THIS. SERIOUSLY.##
+

SConstruct

@@ -172,10 +172,15 @@ def lib_name(prefix, includename, libname):
   Uses re.match('lib(' + libname + '.*)\.(dylib|a|so).*',string) on all files
   in the prefix/lib directory to get the libname to use. If none found, return None.
   """
-  for p in os.listdir(lib_path(prefix, includename)):
-    m = re.match('lib(' + libname + '.*)\.(dylib|a|so).*',p)
-    if m:
-      return m.group(1)
+  try:
+    for p in os.listdir(lib_path(prefix, includename)):
+      if p is None:
+        continue
+      m = re.match('lib(' + libname + '.*)\.(dylib|a|so).*',p)
+      if m:
+        return m.group(1)
+  except TypeError:
+    pass
   return None
 
 def debug_level():
@@ -315,10 +320,16 @@ env['ENV']['TERM'] = os.environ['TERM']
 # set testing environment (for running tests)
 env['ENV']['PATH'] = env['BINDIR'] + ":" + env['ENV']['PATH']
 
-# set LD_LIBRARY_PATH or DYLD_FALLBACK_LIBRARY_PATH (for running configuration tests)
-for x in ['LD_LIBRARY_PATH', 'DYLD_LIBRARY_FALLBACK_PATH']:
-  if x in os.environ:
-    env['ENV'][x] = os.environ[x]
+# set execution environment variables (for running tests)
+casm_var = ['CXX', 'CASM_CXX', 'CASM_CXXFLAGS', 'CASM_SOFLAGS',
+  'CASM_BOOST_PREFIX', 'CASM_BOOST_INCLUDEDIR', 'CASM_BOOST_LIBDIR',
+  'LD_LIBRARY_PATH', 'DYLD_LIBRARY_FALLBACK_PATH']
+for var in casm_var:
+  if var in os.environ:
+    env['ENV'][var] = os.environ[var]
+
+env['ENV']['CASM_INCLUDEDIR'] = env['INCDIR']
+env['ENV']['CASM_LIBDIR'] = env['LIBDIR']
 
 # add methods to use elsewhre
 env.AddMethod(include_path)
@@ -493,6 +504,19 @@ if not env['IS_INSTALL']:
 ##### Configuration checks
 if 'configure' in COMMAND_LINE_TARGETS:
 
+  def CheckCXX11(conf):
+    conf.Message('Checking for c++11... ') 
+    
+    ret = conf.TryRun("""
+    int main() {
+      int a = 1;
+      auto b = a;
+      return 0;
+    }
+    """, '.cpp')[0]
+    conf.Result(ret)
+    return ret
+  
   def CheckBoost_prefix(conf, boost_prefix):
     conf.Message('BOOST_PREFIX: ' + str(boost_prefix) + '\n')
     conf.Message('Checking for boost headers... ') 
@@ -598,6 +622,7 @@ if 'configure' in COMMAND_LINE_TARGETS:
     env.Clone(LIBPATH=install_lib_paths,
               CPPPATH=cpppath),
     custom_tests = {
+      'CheckCXX11' : CheckCXX11,
       'CheckBoost_prefix' : CheckBoost_prefix,
       'CheckBoost_libname' : CheckBoost_libname,
       'CheckBoost_version' : CheckBoost_version,
@@ -610,6 +635,8 @@ if 'configure' in COMMAND_LINE_TARGETS:
 
   # Note: CheckLib with autoadd=1 (default), because some libraries depend on each other
 
+  if not conf.CheckCXX11():
+    if_failed("C++11 is required. Please check your compiler.")
   for x in ['z', 'dl']:
     if not conf.CheckLib(env[x]):
       if_failed("Please check your installation")

apps/casm/Makemodule.am

@@ -0,0 +1,10 @@
+bin_PROGRAMS += casm
+man1_MANS += man/casm.1
+
+casm_SOURCES = ./apps/casm/casm.cpp
+casm_LDADD=libcasm.la\
+           $(BOOST_SYSTEM_LIB)\
+           $(BOOST_FILESYSTEM_LIB)\
+           $(BOOST_PROGRAM_OPTIONS_LIB)\
+           $(BOOST_REGEX_LIB)\
+           $(BOOST_CHRONO_LIB)

apps/completer/Makemodule.am

@@ -0,0 +1,14 @@
+if ENABLE_BASH_COMPLETION
+bashcompletiondir=$(BASH_COMPLETION_DIR)
+dist_bashcompletion_DATA=./apps/completer/casm
+
+bin_PROGRAMS += casm-complete
+
+casm_complete_SOURCES = ./apps/completer/complete.cpp
+casm_complete_LDADD=libcasm.la\
+           $(BOOST_SYSTEM_LIB)\
+           $(BOOST_FILESYSTEM_LIB)\
+           $(BOOST_PROGRAM_OPTIONS_LIB)\
+           $(BOOST_REGEX_LIB)\
+           $(BOOST_CHRONO_LIB)
+endif

bootstrap.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+bash version.sh
+
+if [ ! $# -eq 0  ]; then
+    echo "Applying specified tag to version string: $1"
+
+    version=$(cat build-aux/casm_version.txt)
+    reversion=$1-${version#*-}
+    echo $reversion > build-aux/casm_version.txt
+fi
+
+autoreconf -ivf

casmenv.sh

@@ -1,21 +1,28 @@
 ### Set environment variables recognized by CASM during installation and use
 
-#  Recognized by install scripts and 'casm' CLI executable for CASM install location (headers and shared libraries)
+#  Recognized by scons install scripts and 'casm' CLI executable for CASM install
+#  location assuming $CASM_PREFIX/include for headers and $CASM_PREFIX/lib for libcasm
 #  Order of precedence:
-#    1) $CASM_PREFIX
-#    2) "/usr/local"
+#    1) $CASM_INCLUDEDIR, $CASM_LIBDIR
+#    2) $CASM_PREFIX/include, $CASM_PREFIX/lib
+#    3) "/usr/local"
 #
 #export CASM_PREFIX="/usr/local"
+#export CASM_INCLUDEDIR="/usr/local/include"
+#export CASM_LIBDIR="/usr/local/lib"
 
 
-#  Recognized by install scripts and 'casm' CLI executable for locating boost install location
+#  Recognized by install scripts and 'casm' CLI executable for locating boost 
+#  install location
 #  Order of precedence:
-#    1) $CASM_BOOST_PREFIX
-#    2) "" (default uses system defaults)
+#    1) $CASM_BOOST_INCLUDEDIR, $CASM_BOOST_LIBDIR
+#    2) $CASM_BOOST_PREFIX/include $CASM_BOOST_PREFIX/lib
+#    3) "" (default uses system defaults)
 #
 #export CASM_BOOST_PREFIX=""
-
-# 
+#export CASM_BOOST_INCLUDEDIR=""
+#export CASM_BOOST_LIBDIR=""
+ 
 
 #  Recognized by install scripts. Use this if linking to boost libraries compiled without c++11. If defined, (i.e. CASM_BOOST_NO_CXX11_SCOPED_ENUMS=1) will compile with -DBOOST_NO_CXX11_SCOPED_ENUMS option.
 #  Order of precedence:

configure.ac

@@ -0,0 +1,109 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.69])
+AC_INIT([CASM],
+        m4_esyscmd([tr -d '\n' < ./build-aux/casm_version.txt]),
+        [casm-developers@lists.engr.ucsb.edu],
+        [],
+        [https://github.com/prisms-center/CASMcode])
+AC_CONFIG_AUX_DIR([build-aux]) #This is my doing
+AC_CONFIG_MACRO_DIR([build-aux/m4])
+#Rules to apply to every Makefile.am. Using tar-ustar due to loooooong file names (I'm looking at you Eigen)
+AM_INIT_AUTOMAKE([foreign subdir-objects 1.9 tar-ustar])
+
+
+AC_CONFIG_SRCDIR([src/casm/CASM_global_definitions.cc])
+AC_CONFIG_HEADERS([config.h])
+
+# Checks for programs.
+AC_PROG_CXX
+AC_PROG_CC
+AC_PROG_CPP
+
+## Checks for libraries.
+## FIXME: Replace `main' with a function in `-lgzstream':
+#AC_CHECK_LIB([gzstream], [main])
+## FIXME: Replace `main' with a function in `-lz':
+AC_CHECK_LIB([z], [gzread], [], AC_MSG_ERROR(gzread from z library not found!))
+AC_CHECK_LIB([dl], [dlopen], [], AC_MSG_ERROR(dlopen from dl library not found!))
+#AC_CHECK_LIB([z], [gzwrite])
+#AC_CHECK_LIB([z], [gzopen])
+#AC_CHECK_LIB([z], [gzclose])
+
+#I added this
+LT_INIT([shared disable-static])
+AC_PROG_LIBTOOL
+LT_LIB_DLLOAD
+AC_DISABLE_STATIC
+if test "$enable_static" != "no"; then
+    echo "Sorry Dave, I can't let you do that. Static libraries are currently disabled.";
+    exit 1;
+fi; 
+
+AX_CXX_COMPILE_STDCXX_11
+BOOSTV=1.54
+AX_BOOST_BASE([$BOOSTV],[],AC_MSG_ERROR(You need Boost $BOOSTV libraries or higher.))
+AX_BOOST_FILESYSTEM
+AX_BOOST_SYSTEM
+AX_BOOST_REGEX
+AX_BOOST_CHRONO
+AX_BOOST_PROGRAM_OPTIONS
+AX_BOOST_UNIT_TEST_FRAMEWORK
+
+#Where to install bash completion
+AC_ARG_WITH([bash-completion-dir],
+    AS_HELP_STRING([--with-bash-completion-dir[=PATH]],
+        [Install the bash auto-completion script in this directory. @<:@default=yes@:>@]),
+    [],
+    [with_bash_completion_dir=yes])
+
+if test "x$with_bash_completion_dir" = "xyes"; then
+    PKG_CHECK_MODULES([BASH_COMPLETION], [bash-completion >= 2.0],
+        [BASH_COMPLETION_DIR="`pkg-config --variable=completionsdir bash-completion`"],
+        [BASH_COMPLETION_DIR="$datadir/bash-completion/completions"])
+else
+    BASH_COMPLETION_DIR="$with_bash_completion_dir"
+fi
+
+AC_SUBST([BASH_COMPLETION_DIR])
+AM_CONDITIONAL([ENABLE_BASH_COMPLETION],[test "x$with_bash_completion_dir" != "xno"])
+
+
+#Require at least this version
+AM_PATH_PYTHON([2.6])
+
+# Checks for header files.
+AC_CHECK_HEADERS([float.h limits.h stdlib.h string.h sys/time.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_CHECK_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_INT32_T
+AC_TYPE_INT64_T
+AC_C_RESTRICT
+AC_TYPE_SIZE_T
+AC_TYPE_UINT64_T
+AC_CHECK_TYPES([ptrdiff_t])
+
+# Checks for library functions.
+AC_FUNC_ERROR_AT_LINE
+AC_FUNC_MALLOC
+AC_HEADER_MAJOR
+AC_FUNC_REALLOC
+AC_FUNC_STRTOD
+AC_CHECK_FUNCS([floor iswprint memmove memset mkdir pow rmdir select sqrt strchr strpbrk strrchr strstr strtol])
+
+#Generate all the necessary files from *.in
+AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([tests/unit/App/run_test_App],                          [chmod +x tests/unit/App/run_test_App])
+AC_CONFIG_FILES([tests/unit/casm_io/run_test_casm_io],                  [chmod +x tests/unit/casm_io/run_test_casm_io])
+AC_CONFIG_FILES([tests/unit/clex/run_test_clex],                        [chmod +x tests/unit/clex/run_test_clex])
+AC_CONFIG_FILES([tests/unit/clusterography/run_test_clusterography],    [chmod +x tests/unit/clusterography/run_test_clusterography])
+AC_CONFIG_FILES([tests/unit/container/run_test_container],              [chmod +x tests/unit/container/run_test_container])
+AC_CONFIG_FILES([tests/unit/crystallography/run_test_crystallography],  [chmod +x tests/unit/crystallography/run_test_crystallography])
+AC_CONFIG_FILES([tests/unit/monte_carlo/run_test_monte_carlo],      [chmod +x tests/unit/monte_carlo/run_test_monte_carlo])
+AC_CONFIG_FILES([tests/unit/system/run_test_system],                    [chmod +x tests/unit/system/run_test_system])
+
+
+AC_OUTPUT

configure.mimic.sh

@@ -0,0 +1 @@
+./configure --prefix=$(pwd)/builds/auto CXXFLAGS='-DNDEBUG -O3 --std=c++11 -Wno-deprecated-register -Wno-deprecated-declarations -DEIGEN_DEFAULT_DENSE_INDEX_TYPE=long -Wno-unused-parameter -DGZSTREAM_NAMESPACE=gz -fPIC'