Ticket #49449: pymol_no_cxx11.patch

layer2/AtomInfo.cpp

@@ -1163 +1163 @@
     for (int i = 0; ok && i < 6; ++i)
       ok = CPythonVal_PConvPyFloatToFloat_From_List(G, list, 41 + i, u + i);
     if(ok && (u[0] || u[1] || u[2] || u[3] || u[4] || u[5]))
-      std::copy_n(u, 6, I->get_anisou());
+      memcpy(I->get_anisou(), u, 6 * sizeof(float));
   }
   if(ok && (ll > 47)) {
     OrthoLineType temp;
@@ -1196 +1196 @@
 #endif
   if (src->anisou) {
     dst->anisou = NULL;
-    std::copy_n(src->anisou, 6, dst->get_anisou());
+    memcpy(dst->get_anisou(), src->anisou, 6 * sizeof(float));
   }
 }
 

layer2/CifBondDict.h

@@ -25 +25 @@
 // Working with this limitation is currently reasonable in PyMOL,
 // since cResnLen=5 and cAtomNameLen=4 (see AtomInfo.h).
 
-#include <cstdint>
+#ifdef _PYMOL_NO_CXX11
+#define unordered_map map
+#else
 #include <unordered_map>
+#endif
+
+#include <stdint.h>
 #include <string.h>
 
 // mapped type of bond_dict_t
-class res_bond_dict_t : std::unordered_map<std::int_fast64_t, signed char> {
+class res_bond_dict_t : std::unordered_map<int64_t, signed char> {
   static key_type make_key(const char * name1, const char * name2) {
-    union { char s[4]; std::int32_t i; } u1, u2;
+    union { char s[4]; int32_t i; } u1, u2;
 
     strncpy(u1.s, name1, 4);
     strncpy(u2.s, name2, 4);
@@ -57 +62 @@
 };
 
 // type for mapping: resn -> ((name1, name2) -> bond order)
-class bond_dict_t : public std::map<std::int_fast64_t, res_bond_dict_t> {
+class bond_dict_t : public std::map<int64_t, res_bond_dict_t> {
   static key_type make_key(const char * s_) {
     union { key_type i; char s[sizeof(key_type)]; };
     strncpy(s, s_, sizeof(s));

layer2/CifMoleculeReader.cpp

@@ -195 +195 @@
       I->Bond = bond;
     } else {
       VLASize(I->Bond, BondType, I->NBond + nbond);
-      std::copy(bond, bond + nbond, I->Bond + I->NBond);
+      memcpy(I->Bond + I->NBond, bond, nbond * sizeof(*bond));
       VLAFreeP(bond);
     }
 
@@ -2106 +2106 @@
   }
 
   const char * filename = NULL;
+#ifndef _PYMOL_NO_CXX11
   auto cif = std::make_shared<cif_file>(filename, st);
+#else
+  cif_file _cif_stack(filename, st);
+  auto cif = &_cif_stack;
+#endif
 
   for (auto it = cif->datablocks.begin(); it != cif->datablocks.end(); ++it) {
     ObjectMolecule * obj = ObjectMoleculeReadCifData(G, it->second, discrete);
@@ -2117 +2122 @@
       continue;
     }
 
-#ifndef _PYMOL_NOPY
+#if !defined(_PYMOL_NOPY) && !defined(_PYMOL_NO_CXX11)
     // we only provide access from the Python API so far
     if (SettingGetGlobal_b(G, cSetting_cif_keepinmemory)) {
       obj->m_cifdata = it->second;

layer2/CoordSet.cpp

@@ -978 +978 @@
       char *atomline = (*charVLA) + (*c);
       char *anisoline = atomline + linelen;
       float anisou[6];
-      std::copy_n(ai->anisou, 6, anisou);
+      memcpy(anisou, ai->anisou, 6 * sizeof(float));
 
       if(matrix && !RotateU(matrix, anisou)) {
         PRINTFB(G, FB_CoordSet, FB_Errors) "RotateU failed\n" ENDFB(G);
@@ -1059 +1059 @@
     float tmp_array[6] = { 0.f, 0.f, 0.f, 0.f, 0.f, 0.f };
 
     if (ai->anisou) {
-      std::copy_n(ai->anisou, 6, tmp_array);
+      memcpy(tmp_array, ai->anisou, 6 * sizeof(float));
       if (matrix)
       RotateU(matrix, tmp_array);
     }

layer2/ObjectMolecule.cpp

@@ -22 +22 @@
 #include <algorithm>
 #include <set>
 
+#ifdef _PYMOL_NO_CXX11
+#define STD_MOVE(x) (x)
+#else
+#define STD_MOVE(x) std::move(x)
+#endif
+
 #include"Base.h"
 #include"Debug.h"
 #include"Parse.h"
@@ -7730 +7736 @@
           if(PConvPyListToFloatArrayInPlace(tmp, u, 6)) {
             // only allocate if not all zero
             if(u[0] || u[1] || u[2] || u[3] || u[4] || u[5])
-              std::copy_n(u, 6, ai->get_anisou());
+              memcpy(ai->get_anisou(), u, 6 * sizeof(float));
           }
           Py_DECREF(tmp);
         }
@@ -9600 +9606 @@
   CHECKOK(ok, ai2);
   if (ok){
     for(a = 0; a < cs->NIndex; a++)
-      ai2[a] = std::move(ai[index[a]]);      /* creates a sorted list of atom info records */
+      ai2[a] = STD_MOVE(ai[index[a]]);      /* creates a sorted list of atom info records */
   }
   VLAFreeP(ai);
   ai = ai2;
@@ -9722 +9728 @@
       if(a2 < oldNAtom)
         AtomInfoCombine(G, I->AtomInfo + a2, ai + a1, aic_mask);
       else
-        *(I->AtomInfo + a2) = std::move(*(ai + a1));
+        *(I->AtomInfo + a2) = STD_MOVE(*(ai + a1));
     }
   }
 
@@ -9861 +9867 @@
     dest = I->AtomInfo + I->NAtom;
     src = atInfo;
     for(a = 0; a < cs->NIndex; a++)
-      *(dest++) = std::move(*(src++));
+      *(dest++) = STD_MOVE(*(src++));
     I->NAtom = nAtom;
     VLAFreeP(atInfo);
   } else {
@@ -12561 +12567 @@
   VLAFreeP(I->DiscreteAtmToIdx);
   VLAFreeP(I->DiscreteCSet);
   VLAFreeP(I->CSet);
+#ifndef _PYMOL_NO_CXX11
   I->m_ciffile.reset(); // free data
+#endif
 
   {
     int nAtom = I->NAtom;

layer2/ObjectMolecule.h

@@ -86 +86 @@
   int RepVisCache;     /* for transient storage during updates */
 
   // for reporting available assembly ids after mmCIF loading - SUBJECT TO CHANGE
+#ifndef _PYMOL_NO_CXX11
   std::shared_ptr<cif_file> m_ciffile;
+#endif
   const cif_data * m_cifdata;
 
   // methods

layer2/ObjectMolecule2.cpp

@@ -48 +48 @@
 #include <iostream>
 #include <map>
 
+#ifdef _PYMOL_NO_CXX11
+#define STD_MOVE(x) (x)
+#else
+#define STD_MOVE(x) std::move(x)
+#endif
+
 #define ntrim ParseNTrim
 #define nextline ParseNextLine
 #define ncopy ParseNCopy
@@ -4481 +4487 @@
       if (ok){
         /* autozero here is important */
         for(a = 0; a < i_NAtom; a++)
-          atInfo[a] = std::move(I->AtomInfo[index[a]]);
+          atInfo[a] = STD_MOVE(I->AtomInfo[index[a]]);
       }
       VLAFreeP(I->AtomInfo);
       I->AtomInfo = atInfo;

monkeypatch_distutils.py

@@ -13 +13 @@
 # threaded parallel map (optional)
 pmap = map
 
-if sys.platform == 'darwin':
+try:
     import _osx_support
     _osx_support._UNIVERSAL_CONFIG_VARS += ('CXXFLAGS', 'LDCXXSHARED',)
     _osx_support._COMPILER_CONFIG_VARS += ('LDCXXSHARED',)
+except ImportError:
+    _osx_support = None
 
 distutils.unixccompiler.UnixCCompiler.executables.update({
     'compiler_cxx'      : ["c++"],
@@ -86 +88 @@
     compiler_so = self.compiler_so
     compiler_so_cxx = self.compiler_so_cxx
 
-    if sys.platform == 'darwin':
+    if sys.platform == 'darwin' and _osx_support is not None:
         compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs)
         compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx, cc_args + extra_postargs)
 

setup.py

@@ -149 +149 @@
 pyogl_libs = []
 lib_dirs = []
 ext_comp_args = [
-    "-Wno-narrowing",
     # warnings as errors
     "-Werror=implicit-function-declaration",
     "-Werror=declaration-after-statement",
@@ -213 +212 @@
             ("NO_MMLIBS",None),
             ]
 
+    if sys.platform == 'darwin':
+        import platform
+        if int(platform.mac_ver()[0].split('.')[1]) < 9:
+            # OS X <= 10.8, will still use some C++11 features
+            # like the "auto" keyword, but excludes features which
+            # depend on the C++11 std library.
+            def_macros += [
+                ('_PYMOL_NO_CXX11', None),
+            ]
+
     try:
         import numpy
         inc_dirs += [