#172 pymol r4146 needs addition patches to contrib/champ/os_python.h and contrib/champ/champ_module.c

[Jack Howarth]

The current r4146 svn of pymol doesn't build on x86_64-apple-darwin15 against either python 3.4.3 or 3.5.0 due to unresolved symbols....

gcc -bundle -L/sw/lib/python3.5/config-3.5m -lpython3.5m -L/sw/lib -L/sw/lib -L/sw/lib -Wno-c++11-extensions build/temp.macosx-10.11-x86_64-3.5/contrib/champ/champ.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/champ_module.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/chiral.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/err2.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/feedback2.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/list.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/os_memory.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/sort.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/strblock.o build/temp.macosx-10.11-x86_64-3.5/contrib/champ/vla.o -L/sw/lib -o build/lib.macosx-10.11-x86_64-3.5/chempy/champ/_champ.cpython-35m-darwin.so
Undefined symbols for architecture x86_64:
  "_PyCObject_AsVoidPtr", referenced from:
      __memory_dump in champ_module.o
      _insert_pattern_string in champ_module.o
      _insert_model in champ_module.o
      _pattern_free in champ_module.o
      _pattern_clear_tags in champ_module.o
      _pattern_get_cycle in champ_module.o
      _pattern_get_class in champ_module.o
      ...
  "_PyCObject_Check", referenced from:
      __memory_dump in champ_module.o
      _insert_pattern_string in champ_module.o
      _insert_model in champ_module.o
      _pattern_free in champ_module.o
      _pattern_clear_tags in champ_module.o
      _pattern_get_cycle in champ_module.o
      _pattern_get_class in champ_module.o
      ...
  "_PyCObject_FromVoidPtr", referenced from:
      __new in champ_module.o
  "_PyInt_AsLong", referenced from:
      _ChampModelToPat in champ.o
  "_PyInt_Check", referenced from:
      _ChampModelToPat in champ.o
  "_PyInt_FromLong", referenced from:
      _pattern_get_cycle in champ_module.o
      _pattern_get_class in champ_module.o
      _pattern_get_tags in champ_module.o
      _pattern_get_tag_masks in champ_module.o
      _pattern_get_ext_indices_with_tags in champ_module.o
      _list_get_pattern_indices in champ_module.o
      _match_1v1_map in champ_module.o
      ...
  "_PyNumber_Int", referenced from:
      _ChampModelToPat in champ.o
  "_PyString_AsString", referenced from:
      _PConvPyObjectToStrMaxClean in champ.o
      _list_prepend_pattern_strings in champ_module.o
  "_PyString_Check", referenced from:
      _PConvPyObjectToStrMaxClean in champ.o
  "_PyString_FromString", referenced from:
      _pattern_get_codes in champ_module.o
      _pattern_get_string in champ_module.o
      _pattern_get_atom_symbols in champ_module.o
      _pattern_get_atom_names in champ_module.o
      _list_get_pattern_strings in champ_module.o
  "_Py_InitModule", referenced from:
      _init_champ in champ_module.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

These unresolved symbols can be fixed with the following change...

--- pymol-1.8.0.0/contrib/champ/os_python.h.orig        2015-12-12 10:11:29.000000000 -0500
+++ pymol-1.8.0.0/contrib/champ/os_python.h     2015-12-12 10:12:11.000000000 -0500
@@ -18,6 +18,30 @@

 #include"Python.h"

+#if PY_MAJOR_VERSION >= 3
+# define PyInt_Check            PyLong_Check
+# define PyInt_FromLong         PyLong_FromLong
+# define PyInt_AsLong           PyLong_AsLong
+# define PyInt_AS_LONG          PyLong_AS_LONG
+
+# define PyNumber_Int           PyNumber_Long
+
+# define PyString_Check                 PyUnicode_Check
+# define PyString_Size                  PyUnicode_GetLength
+# define PyString_FromString            PyUnicode_FromString
+# define PyString_FromStringAndSize     PyUnicode_FromStringAndSize
+# define PyString_InternFromString      PyUnicode_InternFromString
+# define PyString_AsString              PyUnicode_AsUTF8
+# define PyString_AS_STRING             PyUnicode_AsUTF8
+
+# define PyCObject_AsVoidPtr(capsule)   PyCapsule_GetPointer(capsule, "name")
+# define PyCObject_FromVoidPtr(p, d)    PyCapsule_New(p, "name", (PyCapsule_Destructor) d)
+# define PyCObject_Check                PyCapsule_CheckExact
+
+# define PyEval_EvalCode(o, ...)        PyEval_EvalCode((PyObject*)o, __VA_ARGS__)
+#endif
+
+
 #endif

--- pymol-1.8.0.0/contrib/champ/champ_module.c.orig     2015-12-12 10:23:55.000000000 -0500
+++ pymol-1.8.0.0/contrib/champ/champ_module.c  2015-12-12 10:30:58.000000000 -0500
@@ -1051,6 +1051,17 @@
 void init_champ(void);
 void init_champ(void)
 {
+#if PY_MAJOR_VERSION < 3
   Py_InitModule("_champ", champ_methods);
+#else
+  static struct PyModuleDef moduledef = { PyModuleDef_HEAD_INIT,
+    "_champ", NULL, -1, champ_methods };
+  PyObject * _champ = PyModule_Create(&moduledef);
+  if (_champ) {
+    PyDict_SetItemString(PyImport_GetModuleDict(), "_champ", champ_methods);
+    Py_DECREF(_champ);
+  }
+#endif
+    
 }

and is also attached as pymol-python3.patch.

[Jack Howarth]

Note that failure of the APBS Tools plugin to run under python 3.5.x appears to related to...

https://bugs.python.org/issue23466

and isn't fixed in python 3.5.1. Fortunately, python 3.4.3 doesn't trigger this bug.

[Jack Howarth]

The proposed patch produces the warning...

contrib/champ/champ_module.c:1061:62: warning: incompatible pointer types passing 'PyMethodDef [32]' to parameter of type 'PyObject *'
      (aka 'struct _object *') [-Wincompatible-pointer-types]
    PyDict_SetItemString(PyImport_GetModuleDict(), "_champ", champ_methods);
                                                             ^~~~~~~~~~~~~
/sw/include/python3.5m/dictobject.h:136:79: note: passing argument to parameter 'item' here
PyAPI_FUNC(int) PyDict_SetItemString(PyObject *dp, const char *key, PyObject *item);

so I guess it needs further adjustment.

[Jack Howarth]

Is is valid to just use a cast such as...

PyDict_SetItemString(PyImport_GetModuleDict(), "_champ", (PyObject *)champ_methods);

which suppress the warning?

[Thomas Holder]

fixed in svn rev 4147