Merge pull request #2060 from e-kwsm/OB3

Update for Open Babel 3
openbabel · Oct 24, 2019 · f84536d · f84536d
2 parents 6ef538d + 7bf2ec2
commit f84536d
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Showing 30 changed files with 147 additions and 146 deletions.
diff --git a/INSTALL b/INSTALL
@@ -21,9 +21,6 @@ install Open Babel on most systems.  If you are using unique install locations
 and/or libraries are not automatically detected please consult the 'Advanced'
 section.
 
-The following instructions assume that the Open Babel source distribution is in
-the directory ~/openbabel-2.4.0.
-
 1. Create a 'build' directory:
 
    mkdir build

diff --git a/OpenBabel3Config.cmake.in b/OpenBabel3Config.cmake.in
@@ -1,15 +1,15 @@
-# The OpenBabel2 config file. To get the targets include the exports file.
-get_filename_component(OpenBabel2_INSTALL_PREFIX "${OpenBabel2_DIR}@REL_REF@"
+# The OpenBabel3 config file. To get the targets include the exports file.
+get_filename_component(OpenBabel3_INSTALL_PREFIX "${OpenBabel3_DIR}@REL_REF@"
   ABSOLUTE)
 
-set(OpenBabel2_VERSION_MAJOR   "@BABEL_MAJ_VER@")
-set(OpenBabel2_VERSION_MINOR   "@BABEL_MIN_VER@")
-set(OpenBabel2_VERSION_PATCH   "@BABEL_PATCH_VER@")
-set(OpenBabel2_VERSION         "@BABEL_VERSION@")
+set(OpenBabel3_VERSION_MAJOR   "@BABEL_MAJ_VER@")
+set(OpenBabel3_VERSION_MINOR   "@BABEL_MIN_VER@")
+set(OpenBabel3_VERSION_PATCH   "@BABEL_PATCH_VER@")
+set(OpenBabel3_VERSION         "@BABEL_VERSION@")
 
-set(OpenBabel2_INCLUDE_DIRS "@OpenBabel2_INCLUDE_DIRS@")
-set(OpenBabel2_EXPORTS_FILE "@OB_EXPORTS_FILE@")
-set(OpenBabel2_ENABLE_VERSIONED_FORMATS "@ENABLE_VERSIONED_FORMATS@")
+set(OpenBabel3_INCLUDE_DIRS "@OpenBabel3_INCLUDE_DIRS@")
+set(OpenBabel3_EXPORTS_FILE "@OB_EXPORTS_FILE@")
+set(OpenBabel3_ENABLE_VERSIONED_FORMATS "@ENABLE_VERSIONED_FORMATS@")
 
 # Include the exports file to import the exported OpenBabel targets
-include("${OpenBabel2_EXPORTS_FILE}")
+include("${OpenBabel3_EXPORTS_FILE}")
diff --git a/OpenBabel3ConfigVersion.cmake.in b/OpenBabel3ConfigVersion.cmake.in
@@ -1,4 +1,4 @@
-# OpenBabel2 CMake version file - http://www.openbabel.org/
+# OpenBabel3 CMake version file - http://www.openbabel.org/
 
 set(PACKAGE_VERSION @BABEL_MAJ_VER@.@BABEL_MIN_VER@.@BABEL_PATCH_VER@)
 

diff --git a/doc/examples/static_executable/CMakeLists.txt b/doc/examples/static_executable/CMakeLists.txt
@@ -1,10 +1,10 @@
 #
 # This script can be used to create static executables linking to the static
-# OpenBabel2 library.
+# OpenBabel3 library.
 #
 # This script requires OpenBabel to be build and installed. For example:
 #
-#  cd openbabel-2.3
+#  cd openbabel
 #  mkdir build
 #  cd build
 #  cmake -DBUILD_SHARED=OFF -DCMAKE_INSTALL_PREFIX=/home/me/some/path ..
@@ -16,7 +16,7 @@
 #  cd myproject
 #  mkdir build
 #  cd build
-#  cmake -DOpenBabel2_DIR=/home/me/some/path/lib/openbabel ..
+#  cmake -DOpenBabel3_DIR=/home/me/some/path/lib/openbabel ..
 #  make
 #
 # All plugins are inside the static libopenbabel.a but the symbols for the
@@ -53,17 +53,17 @@ else()
   set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
 endif()
 
-# Set the path containing OpenBabel2Config.cmake, needed for find_package below.
-find_path(OpenBabel2_DIR OpenBabel2Config.cmake PATHS
-          ${OpenBabel2_DIR}
+# Set the path containing OpenBabel3Config.cmake, needed for find_package below.
+find_path(OpenBabel3_DIR OpenBabel3Config.cmake PATHS
+          ${OpenBabel3_DIR}
           "/usr/lib/openbabel"
          "/usr/local/lib/openbabel")
 
 #
-# Find and setup OpenBabel2.
+# Find and setup OpenBabel3.
 #
-find_package(OpenBabel2 REQUIRED)
-include_directories(${OpenBabel2_INCLUDE_DIRS})
+find_package(OpenBabel3 REQUIRED)
+include_directories(${OpenBabel3_INCLUDE_DIRS})
 
 # Dependencies
 find_package(LibXml2)

diff --git a/doc/obabel.1 b/doc/obabel.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obabel 1 URM
 .Sh NAME
 .Nm obabel

diff --git a/doc/obchiral.1 b/doc/obchiral.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obchiral 1 URM
 .Sh NAME
 .Nm obchiral

diff --git a/doc/obconformer.1 b/doc/obconformer.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obconformer 1 URM
 .Sh NAME
 .Nm obconformer

diff --git a/doc/obdistgen.1 b/doc/obdistgen.1
@@ -1,5 +1,5 @@
-.Dd October 26, 2017
-.Os "Open Babel" 2.4.1
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obdistgen 1 URM
 .Sh NAME
 .Nm obdistgen

diff --git a/doc/obenergy.1 b/doc/obenergy.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obenergy 1 URM
 .Sh NAME
 .Nm obenergy

diff --git a/doc/obfit.1 b/doc/obfit.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obfit 1 URM
 .Sh NAME
 .Nm obfit

diff --git a/doc/obgen.1 b/doc/obgen.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obgen 1 URM
 .Sh NAME
 .Nm obgen

diff --git a/doc/obgrep.1 b/doc/obgrep.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obgrep 1 URM
 .Sh NAME
 .Nm obgrep

diff --git a/doc/obgui.1 b/doc/obgui.1
@@ -1,5 +1,5 @@
-.Dd June 2, 2012
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obgui 1 URM
 .Sh NAME
 .Nm obgui

diff --git a/doc/obminimize.1 b/doc/obminimize.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obminimize 1 URM
 .Sh NAME
 .Nm obminimize

diff --git a/doc/obprobe.1 b/doc/obprobe.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obprobe 1 URM
 .Sh NAME
 .Nm obprobe

diff --git a/doc/obprop.1 b/doc/obprop.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obprop 1 URM
 .Sh NAME
 .Nm obprop

diff --git a/doc/obrms.1 b/doc/obrms.1
@@ -1,5 +1,5 @@
-.Dd October 26, 2017
-.Os "Open Babel" 2.4.1
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obrms 1 URM
 .Sh NAME
 .Nm obrms

diff --git a/doc/obrotamer.1 b/doc/obrotamer.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obrotamer 1 URM
 .Sh NAME
 .Nm obrotamer

diff --git a/doc/obrotate.1 b/doc/obrotate.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obrotate 1 URM
 .Sh NAME
 .Nm obrotate

diff --git a/doc/obspectrophore.1 b/doc/obspectrophore.1
@@ -1,5 +1,5 @@
-.Dd June 2, 2012
-.Os "Open Babel" 2.3
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obspectrophore 1 URM
 .Sh NAME
 .Nm obspectrophore

diff --git a/doc/obsym.1 b/doc/obsym.1
@@ -1,5 +1,5 @@
-.Dd October 26, 2017
-.Os "Open Babel" 2.4.1
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obsym 1 URM
 .Sh NAME
 .Nm obsym

diff --git a/doc/obtautomer.1 b/doc/obtautomer.1
@@ -1,5 +1,5 @@
-.Dd October 26, 2017
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obtautomer 1 URM
 .Sh NAME
 .Nm obtautomer

diff --git a/doc/obthermo.1 b/doc/obthermo.1
@@ -1,5 +1,5 @@
-.Dd October 26, 2017
-.Os "Open Babel" 2.4.1
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt obthermo 1 URM
 .Sh NAME
 .Nm obthermo

diff --git a/doc/roundtrip.1 b/doc/roundtrip.1
@@ -1,5 +1,5 @@
-.Dd July 4, 2008
-.Os "Open Babel" 2.2
+.Dd Oct 10, 2019
+.Os "Open Babel" 3.0
 .Dt roundtrip 1 URM
 .Sh NAME
 .Nm roundtrip

diff --git a/scripts/java/README b/scripts/java/README
@@ -13,7 +13,7 @@ http://openbabel.org/wiki/Java
 
   First of all, set some environment variables (remember to change the paths to correspond to your system):
 $ export JAVA_HOME=/home/noel/Tools/jdk1.5.0_15
-$ export OB_JAVADIR=/home/noel/Tools/openbabel-2.2.0/scripts/java
+$ export OB_JAVADIR=/home/noel/Tools/openbabel-3.0.0/scripts/java
 $ export OB_LIBDIR=/home/noel/tree/lib # The install location of libopenbabel.so
 
   Next, compile the Java bindings:

diff --git a/scripts/perl/META.yml b/scripts/perl/META.yml
@@ -1,7 +1,7 @@
 # http://module-build.sourceforge.net/META-spec.html
 #XXXXXXX This is a prototype!!!  It will change in the future!!! XXXXX#
 name:         Chemistry-OpenBabel
-version:      1.3
+version:      1.4
 version_from: 
 installdirs:  site
 requires:

diff --git a/scripts/perl/README b/scripts/perl/README
@@ -1,4 +1,4 @@
-Chemistry::OpenBabel version 1.3
+Chemistry::OpenBabel version 1.4
 ================================
 
 This module provides a Perl interface to the Open Babel chemistry library. 
@@ -34,7 +34,7 @@ installed Open Babel):
 DEPENDENCIES
 
      perl-5.6.0 or a more recent version.
-     openbabel-2.1 or a more recent version.
+     openbabel-3 or a more recent version.
 
 Note that if you are trying to build/run this Perl code in the Open
 Babel source/build directory BEFORE you install Open Babel, you may

diff --git a/scripts/python/README.rst b/scripts/python/README.rst
@@ -30,7 +30,7 @@ Dependencies
 ------------
 
 -  Python 2.4 or a more recent version.
--  Open Babel 2.3.0 or a more recent version.
+-  Open Babel 3 or a more recent version.
 
 Installation
 ------------
@@ -45,8 +45,8 @@ Installation
 
 ::
 
-    tar -xzvf openbabel-1.8.1.tar.gz
-    cd openbabel-1.8.1
+    tar -xzvf openbabel-3-0-0.tar.gz
+    cd openbabel-openbabel-3-0-0
     python setup.py install
     
 **Option 3**: While building Open Babel itself.

diff --git a/scripts/python/setup.py b/scripts/python/setup.py
@@ -32,7 +32,8 @@ def find_version():
 def pkgconfig(package, option):
     """Wrapper around pkg-config command line tool."""
     try:
-        return subprocess.check_output(['pkg-config', option, package]).strip()
+        return subprocess.check_output(['pkg-config', option, package],
+                                       universal_newlines=True).strip()
     except subprocess.CalledProcessError:
         raise Exception('Failed to run pkg-config')
 
@@ -41,17 +42,19 @@ def locate_ob():
     """Try use pkgconfig to locate Open Babel, otherwise guess default location."""
     try:
         # Warn if the (major, minor) version of the installed OB doesn't match these python bindings
-        ob_ver = StrictVersion(pkgconfig('openbabel-2.0', '--modversion'))
         py_ver = StrictVersion(find_version())
+        py_major_ver, py_minor_ver = py_ver.version[:2]
+        pcfile = 'openbabel-{}'.format(py_major_ver)
+        ob_ver = StrictVersion(pkgconfig(pcfile, '--modversion'))
         if not ob_ver.version[:2] == py_ver.version[:2]:
-            print('Warning: Open Babel %s.%s.x is required. Your version (%s) may not be compatible.'
-                    % (py_ver.version[0], py_ver.version[1], ob_ver))
-        include_dirs = pkgconfig('openbabel-2.0', '--variable=pkgincludedir')
-        library_dirs = pkgconfig('openbabel-2.0', '--variable=libdir')
+            print('Warning: Open Babel {}.{}.x is required. Your version ({}) may not be compatible.'
+                  .format(py_major_ver, py_minor_ver, ob_ver))
+        include_dirs = pkgconfig(pcfile, '--variable=pkgincludedir')
+        library_dirs = pkgconfig(pcfile, '--variable=libdir')
         print('Open Babel location automatically determined by pkg-config:')
     except Exception as e:
         print('Warning: %s.\nGuessing Open Babel location:' % e)
-        include_dirs = '/usr/local/include/openbabel-2.0'
+        include_dirs = '/usr/local/include/openbabel3'
         library_dirs = '/usr/local/lib'
     return include_dirs, library_dirs
 
@@ -86,9 +89,9 @@ def finalize_options(self):
         # Setting include_dirs, library_dirs, swig_opts here instead of in Extension constructor allows them to be
         # overridden using -I and -L command line options to python setup.py build_ext.
         build_ext.finalize_options(self)
-        include_dirs, library_dirs = locate_ob()
-        self.include_dirs.append(include_dirs)
-        self.library_dirs.append(library_dirs)
+        self.ob_include_dir, self.ob_library_dir = locate_ob()
+        self.include_dirs.append(self.ob_include_dir)
+        self.library_dirs.append(self.ob_library_dir)
         self.swig_opts = ['-c++', '-small', '-O', '-templatereduce', '-naturalvar']
         self.swig_opts += ['-I%s' % i for i in self.include_dirs]
         print('- include_dirs: %s\n- library_dirs: %s' % (self.include_dirs, self.library_dirs))
@@ -97,11 +100,12 @@ def swig_sources(self, sources, extension):
         try:
             return build_ext.swig_sources(self, sources, extension)
         except DistutilsExecError:
-            print('\nError: SWIG failed. Is Open Babel installed?\n'
+            print('\nError: SWIG failed. Is Open Babel installed?',
                   'You may need to manually specify the location of Open Babel include and library directories. '
-                  'For example:\n'
-                  '  python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib\n'
-                  '  python setup.py install')
+                  'For example:',
+                  '  python setup.py build_ext -I{} -L{}'.format(self.ob_include_dir, self.ob_library_dir),
+                  '  python setup.py install',
+                  sep='\n')
             sys.exit(1)