Merge branch 'master' of github.com:openbabel/openbabel into ruby-reaction

scripts/CMakeLists.txt

@@ -1,5 +1,5 @@
-cmake_minimum_required(VERSION 2.6.0)
-# Library versioning (used in Mac Python bindings)x
+cmake_minimum_required(VERSION 3.12.0)
+# Library versioning (used in Mac Python bindings)
 set(SOVERSION 4)
 
 if (RUN_SWIG)
@@ -22,18 +22,8 @@ if (RUN_SWIG)
 endif (RUN_SWIG)
 
 # The following needs to be kept in synch with ..\CMakeLists.txt
-if(EIGEN3_FOUND)
-  set (eigen_define "-DHAVE_EIGEN" "-DHAVE_EIGEN3")
-  include_directories(${EIGEN3_INCLUDE_DIR})
-  set (CPPFLAGS_VALUE "-I${EIGEN3_INCLUDE_DIR}")
-  set (CPPFLAGS_TEXT "CPPFLAGS=${CPPFLAGS_VALUE}")
-else()
-  if(EIGEN2_FOUND)
-    set (eigen_define "-DHAVE_EIGEN")
-    include_directories(${EIGEN2_INCLUDE_DIR})
-    set (CPPFLAGS_VALUE "-I${EIGEN2_INCLUDE_DIR}")
-    set (CPPFLAGS_TEXT "CPPFLAGS=${CPPFLAGS_VALUE}")
-  endif()
+if(TARGET Eigen3::Eigen)
+  set (eigen_define "-DHAVE_EIGEN3")
 endif()
 
 ###################
@@ -42,24 +32,19 @@ endif()
 
 if (PYTHON_BINDINGS)
   if (EXISTS ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp OR RUN_SWIG)
-    find_package(PythonInterp)
-    if (NOT PYTHONINTERP_FOUND)
+    find_package(Python COMPONENTS Interpreter Development)
+    if (NOT Python_Interpreter_FOUND)
       message(STATUS "Python interpreter NOT found")
-    endif (NOT PYTHONINTERP_FOUND)
+    endif (NOT Python_Interpreter_FOUND)
 
-    if (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
-      set(Python_ADDITIONAL_VERSIONS "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
-    endif (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
-
-    find_package(PythonLibs)
-    if (NOT PYTHONLIBS_FOUND)
+    if (NOT Python_Development_FOUND)
       message(STATUS "Python libraries NOT found")
-    endif (NOT PYTHONLIBS_FOUND)
+    endif (NOT Python_Development_FOUND)
 
-    if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+    if(Python_Development_FOUND AND Python_Interpreter_FOUND)
       set(DO_PYTHON_BINDINGS ON BOOL)
       message(STATUS "Python bindings will be compiled")
-    endif(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+    endif(Python_Development_FOUND AND Python_Interpreter_FOUND)
 
   else ()
     message(STATUS "Warning: Python bindings NOT found. Generate using -DRUN_SWIG=ON.")
@@ -68,9 +53,9 @@ if (PYTHON_BINDINGS)
 endif (PYTHON_BINDINGS)
 
 if (DO_PYTHON_BINDINGS)
-
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
     include_directories(
-        ${PYTHON_INCLUDE_PATH}
+        ${Python_INCLUDE_DIRS}
     )
 
     if(RUN_SWIG)
@@ -96,9 +81,9 @@ if (DO_PYTHON_BINDINGS)
     else()
       # Link against Python library on Linux and Windows
       if(BINDINGS_ONLY)
-        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY})
+        target_link_libraries(bindings_python ${Python_LIBRARIES} ${BABEL_SYSTEM_LIBRARY})
       else()
-        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY})
+        target_link_libraries(bindings_python ${Python_LIBRARIES} ${BABEL_LIBRARY})
       endif()
     endif()
 
@@ -108,24 +93,14 @@ if (DO_PYTHON_BINDINGS)
             PREFIX ""
             LIBRARY_OUTPUT_DIRECTORY "${openbabel_SOURCE_DIR}/scripts/python/openbabel/"
             SUFFIX .so )
-      if( "${PYTHON_INSTDIR}" STREQUAL "" )
-        execute_process(
-          COMMAND
-          ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-          OUTPUT_VARIABLE PYTHON_INSTDIR
-          OUTPUT_STRIP_TRAILING_WHITESPACE
-        )
-	#workaround for https://bugs.launchpad.net/ubuntu/+source/python3-defaults/+bug/1814653
-	if(NOT ${PYTHON_INSTDIR} MATCHES "python[0-9].[0-9]")
-	  execute_process(
-           COMMAND
-           ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,1,prefix='${CMAKE_INSTALL_PREFIX}'))"
-           OUTPUT_VARIABLE PYTHON_INSTDIR
-           OUTPUT_STRIP_TRAILING_WHITESPACE
+	if( "${PYTHON_INSTDIR}" STREQUAL "" )
+          execute_process(
+            COMMAND
+           ${Python_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_path('platlib', vars={'base': '${CMAKE_INSTALL_PREFIX}'}))"
+            OUTPUT_VARIABLE PYTHON_INSTDIR
+            OUTPUT_STRIP_TRAILING_WHITESPACE
           )
-          set(PYTHON_INSTDIR "${PYTHON_INSTDIR}/dist-packages")
-	endif()
-      endif()
+        endif()
         if(NOT BINDINGS_ONLY)
             add_dependencies(bindings_python openbabel)
         endif()
@@ -149,7 +124,7 @@ if (DO_PYTHON_BINDINGS)
             SUFFIX .pyd )
         execute_process(
           COMMAND
-          ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+	  ${Python_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_path('platlib', vars={'base': '${CMAKE_INSTALL_PREFIX}'}))"
           OUTPUT_VARIABLE PYTHON_INSTDIR
           OUTPUT_STRIP_TRAILING_WHITESPACE
         )
@@ -207,6 +182,7 @@ if (JAVA_BINDINGS)
 endif (JAVA_BINDINGS)
 
 if (DO_JAVA_BINDINGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
 
 include_directories(
 	${JNI_INCLUDE_DIRS}
@@ -272,7 +248,7 @@ if (R_BINDINGS)
 endif (R_BINDINGS)
 
 if (DO_R_BINDINGS)
-
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
 
     include_directories(/usr/share/R/include )
     if (RUN_SWIG)
@@ -348,6 +324,7 @@ if (PERL_BINDINGS)
 endif (PERL_BINDINGS)
 
 if (DO_PERL_BINDINGS)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
     include_directories(
         ${PERL_INCLUDE_PATH}
     )
@@ -427,6 +404,7 @@ if (DO_RUBY_BINDINGS)
       )
     endif (RUN_SWIG)
 
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
     include_directories(
         ${RUBY_INCLUDE_PATH}
     )
@@ -498,6 +476,7 @@ if (DO_CSHARP_BINDINGS)
       )
     endif (RUN_SWIG)
 
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
     add_library(bindings_csharp MODULE ${openbabel_SOURCE_DIR}/scripts/csharp/openbabel-csharp.cpp)
     target_link_libraries(bindings_csharp ${BABEL_LIBRARY})
     set_target_properties(bindings_csharp PROPERTIES
@@ -554,6 +533,7 @@ if (PHP_BINDINGS)
 endif (PHP_BINDINGS)
 
 if (DO_PHP_BINDINGS)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
     include_directories(
         ${PHP_CONFIG_INCLUDES}
     )

scripts/openbabel-R.i

@@ -63,7 +63,7 @@
 %}
 
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %{
 #include <openbabel/forcefield.h>
 #include <openbabel/conformersearch.h>
@@ -364,7 +364,7 @@ IGNORE_ITER(OBMol, Residue)
 %ignore OpenBabel::Swab;
 %include <openbabel/rotamer.h>
 %include <openbabel/spectrophore.h>
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 
 // Ignore shadowed methods
 %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);

scripts/openbabel-java.i

@@ -64,7 +64,7 @@
 #include <openbabel/obiter.h>
 %}
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %{
 #include <openbabel/conformersearch.h>
 #include <openbabel/math/align.h>
@@ -304,7 +304,7 @@ IGNORE_ITER(OBMol, Residue)
 %ignore OpenBabel::OBDescriptor::LessThan;
 %include <openbabel/descriptor.h>
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %include <openbabel/conformersearch.h>
 %include <openbabel/math/align.h>
 #else

scripts/openbabel-perl.i

@@ -12,6 +12,12 @@
   #undef seed
 #endif
 
+// workaround perl namespace pollution - handy.h defines Zero(d,n,t) which
+// conflicts with Eigen's Zero() static method declarations
+#ifdef Zero
+  #undef Zero
+#endif
+
 #include <openbabel/obutil.h>
 #include <openbabel/math/vector3.h>
 #include <openbabel/math/matrix3x3.h>
@@ -214,7 +220,11 @@ namespace std { class stringbuf {}; }
 // %include <openbabel/fingerprint.h> // Causes an error (I do not know why)
 %include <openbabel/descriptor.h>
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
+%{
+#include <openbabel/conformersearch.h>
+#include <openbabel/math/align.h>
+%}
 %include <openbabel/conformersearch.h>
 %include <openbabel/math/align.h>
 #else

scripts/openbabel-php.i

@@ -57,7 +57,7 @@
 #include <openbabel/obiter.h>
 %}
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %{
 #include <openbabel/conformersearch.h>
 #include <openbabel/math/align.h>
@@ -281,7 +281,7 @@ IGNORE_ITER(OBMol, Residue)
 %include <openbabel/rotamer.h>
 %include <openbabel/spectrophore.h>
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %include <openbabel/conformersearch.h>
 %include <openbabel/math/align.h>
 #endif

scripts/openbabel-python.i

@@ -88,7 +88,7 @@ if sys.platform.find("linux") != -1:
 %ignore OpenBabel::OBMol::FindChildren(std::vector< OBAtom * > &, OBAtom *, OBAtom *);
 %ignore OpenBabel::OBResidue::GetAtoms;
 
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %{
 #include <openbabel/conformersearch.h>
 #include <openbabel/math/align.h>
@@ -356,8 +356,14 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
 %ignore OpenBabel::Swab;
 %include <openbabel/rotamer.h>
 %include <openbabel/spectrophore.h>
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
+// OBConformerSearch takes ownership of filter/score via SetFilter/SetScore,
+// so tell SWIG to disown the Python wrapper when these are passed.
+%apply SWIGTYPE *DISOWN { OpenBabel::OBConformerFilter *filter };
+%apply SWIGTYPE *DISOWN { OpenBabel::OBConformerScore *score };
 %include <openbabel/conformersearch.h>
+%clear OpenBabel::OBConformerFilter *filter;
+%clear OpenBabel::OBConformerScore *score;
 %include <openbabel/math/align.h>
 #endif
 

scripts/openbabel-ruby.i

@@ -243,7 +243,7 @@ namespace std { class stringbuf {}; }
 // Ignore shadowed methods
 %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);
 %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *);
-#ifdef HAVE_EIGEN
+#ifdef HAVE_EIGEN3
 %{
 #include <openbabel/conformersearch.h>
 #include <openbabel/math/align.h>

scripts/python/openbabel/pybel.py

@@ -672,12 +672,13 @@ class Molecule(object):
         Tkinter and Python Imaging Library are required for image display.
         """
         obconversion = ob.OBConversion()
-        formatok = obconversion.SetOutFormat("_png2")
-        if not formatok:
-            raise ImportError("PNG depiction support not found. You should "
-                              "compile Open Babel with support for Cairo. See "
-                              "installation instructions for more "
-                              "information.")
+        if show or filename:
+            formatok = obconversion.SetOutFormat("_png2")
+            if not formatok:
+                raise ImportError("PNG depiction support not found. You should "
+                                  "compile Open Babel with support for Cairo. See "
+                                  "installation instructions for more "
+                                  "information.")
 
         # Need to copy to avoid removing hydrogens from self
         workingmol = Molecule(ob.OBMol(self.OBMol))
@@ -707,7 +708,8 @@ class Molecule(object):
 
             filedes, filename = tempfile.mkstemp()
 
-        workingmol.write("_png2", filename=filename, overwrite=True)
+        if show or (filedes is None):
+            workingmol.write("_png2", filename=filename, overwrite=True)
 
         if show:
             if sys.platform[:4] == "java":

scripts/python/setup.py

@@ -4,14 +4,12 @@ import os
 import re
 import subprocess
 import sys
-from distutils.command.build import build
-from distutils.command.sdist import sdist
-from distutils.errors import DistutilsExecError
-from distutils.version import StrictVersion
+from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext
 from setuptools.command.install import install
-from setuptools import setup, Extension
-
+from setuptools.command.sdist import sdist
+from setuptools.command.build import build
+from packaging.version import Version
 
 # Path to the directory that contains this setup.py file.
 base_dir = os.path.abspath(os.path.dirname(__file__))
@@ -43,18 +41,18 @@ 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
-        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 {}.{}.x is required. Your version ({}) may not be compatible.'
-                  .format(py_major_ver, py_minor_ver, ob_ver))
+        py_ver = Version(find_version())
+        py_major_ver, py_minor_ver = py_ver.release[:2]
+        pcfile = f'openbabel-{py_major_ver}'
+        ob_ver = Version(pkgconfig(pcfile, '--modversion'))
+        if ob_ver.release[:2] != (py_major_ver, py_minor_ver):
+            print(f'Warning: Open Babel {py_major_ver}.{py_minor_ver}.x is required. '
+                  f'Your version ({ob_ver}) may not be compatible.')
         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)
+        print(f'Warning: {e}.\nGuessing Open Babel location:')
         include_dirs = '/usr/local/include/openbabel3'
         library_dirs = '/usr/local/lib'
     return include_dirs, library_dirs
@@ -64,20 +62,20 @@ class CustomBuild(build):
     """Ensure build_ext runs first in build command."""
     def run(self):
         self.run_command('build_ext')
-        build.run(self)
+        super().run()
 
 
 class CustomInstall(install):
     """Ensure build_ext runs first in install command."""
     def run(self):
         self.run_command('build_ext')
-        install.run(self)
+        super().run()
 
 
 class CustomSdist(sdist):
     """Add swig interface files into distribution from parent directory."""
     def make_release_tree(self, base_dir, files):
-        sdist.make_release_tree(self, base_dir, files)
+        super().make_release_tree(base_dir, files)
         link = 'hard' if hasattr(os, 'link') else None
         pkg_dir = os.path.join(base_dir, 'openbabel')
         self.copy_file(os.path.join('..', 'stereo.i'), pkg_dir, link=link)
@@ -89,7 +87,7 @@ class CustomBuildExt(build_ext):
     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)
+        super().finalize_options()
         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)
@@ -99,22 +97,22 @@ class CustomBuildExt(build_ext):
 
     def swig_sources(self, sources, extension):
         try:
-            return build_ext.swig_sources(self, sources, extension)
-        except DistutilsExecError:
+            return super().swig_sources(sources, extension)
+        except Exception:
             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:',
-                  '  python setup.py build_ext -I{} -L{}'.format(self.ob_include_dir, self.ob_library_dir),
+                  f'  python setup.py build_ext -I{self.ob_include_dir} -L{self.ob_library_dir}',
                   '  python setup.py install',
                   sep='\n')
             sys.exit(1)
 
 
 obextension = Extension(
-    'openbabel._openbabel', [os.path.join('openbabel', 'openbabel-python.i')], libraries=['openbabel']
+    'openbabel._openbabel', [os.path.join('openbabel', 'openbabel-python.i')],
+    libraries=['openbabel']
 )
 
-
 setup(
     name='openbabel',
     version=find_version(),
@@ -125,7 +123,12 @@ setup(
     description='Python interface to the Open Babel chemistry library',
     long_description=open(os.path.join(base_dir, 'README.rst')).read(),
     zip_safe=False,
-    cmdclass={'build': CustomBuild, 'build_ext': CustomBuildExt, 'install': CustomInstall, 'sdist': CustomSdist},
+    cmdclass={
+        'build': CustomBuild,
+        'build_ext': CustomBuildExt,
+        'install': CustomInstall,
+        'sdist': CustomSdist
+    },
     packages=['openbabel'],
     ext_modules=[obextension],
     classifiers=[