Merge pull request #17 from diffpy/windows

Windows

Author: vincefn

SConstruct

@@ -17,18 +17,27 @@ SCons construction environment can be customized in sconscript.local script.
 """
 
 import os
+from os.path import join as pjoin
 import platform
 
+
 def subdictionary(d, keyset):
     return dict(kv for kv in d.items() if kv[0] in keyset)
 
+
+def getsyspaths(*names):
+    pall = sum((os.environ.get(n, '').split(os.pathsep) for n in names), [])
+    rv = [p for p in pall if os.path.exists(p)]
+    return rv
+
+
 # copy system environment variables related to compilation
 DefaultEnvironment(ENV=subdictionary(os.environ, '''
     PATH CPATH CPLUS_INCLUDE_PATH LIBRARY_PATH LD_RUN_PATH
     LD_LIBRARY_PATH DYLD_LIBRARY_PATH DYLD_FALLBACK_LIBRARY_PATH
     MACOSX_DEPLOYMENT_TARGET
     '''.split())
-)
+                   )
 
 # Create construction environment
 env = DefaultEnvironment().Clone()
@@ -39,21 +48,54 @@ env.EnsureSConsVersion(0, 98, 1)
 # Customizable compile variables
 vars = Variables('sconsvars.py')
 
-vars.Add(PathVariable(
-    'prefix',
-    'installation prefix directory',
-    '/usr/local'))
-vars.Update(env)
-vars.Add(PathVariable(
-    'libdir',
-    'installation directory for compiled library [prefix/lib]',
-    env['prefix'] + '/lib',
-    PathVariable.PathAccept))
-vars.Add(PathVariable(
-    'includedir',
-    'installation directory for C++ header files [prefix/include]',
-    env['prefix'] + '/include',
-    PathVariable.PathAccept))
+# TODO: also amend paths when VIRTUAL_ENV variable exists,
+#  if CONDA_PREFIX does not exist ?
+if 'CONDA_PREFIX' in os.environ:
+    # building for a conda environment
+    vars.Add(PathVariable(
+        'prefix',
+        'installation prefix directory',
+        os.environ['CONDA_PREFIX']))
+    vars.Update(env)
+    if platform.system().lower() == "windows":
+        vars.Add(PathVariable(
+            'libdir',
+            'installation directory for compiled library [prefix/Library/lib]',
+            pjoin(env['prefix'], 'Library', 'Lib'),
+            PathVariable.PathAccept))
+        vars.Add(PathVariable(
+            'includedir',
+            'installation directory for C++ header files [prefix/Library/include]',
+            pjoin(env['prefix'], 'Library', 'include'),
+            PathVariable.PathAccept))
+    else:
+        vars.Add(PathVariable(
+            'libdir',
+            'installation directory for compiled library [prefix/lib]',
+            pjoin(env['prefix'], 'lib'),
+            PathVariable.PathAccept))
+        vars.Add(PathVariable(
+            'includedir',
+            'installation directory for C++ header files [prefix/include]',
+            pjoin(env['prefix'], 'include'),
+            PathVariable.PathAccept))
+else:
+    vars.Add(PathVariable(
+        'prefix',
+        'installation prefix directory',
+        '/usr/local'))
+    vars.Update(env)
+    vars.Add(PathVariable(
+        'libdir',
+        'installation directory for compiled library [prefix/lib]',
+        env['prefix'] + '/lib',
+        PathVariable.PathAccept))
+    vars.Add(PathVariable(
+        'includedir',
+        'installation directory for C++ header files [prefix/include]',
+        env['prefix'] + '/include',
+        PathVariable.PathAccept))
+
 vars.Add(EnumVariable(
     'build',
     'compiler settings',
@@ -68,9 +110,38 @@ vars.Add(BoolVariable(
 vars.Add(BoolVariable(
     'with_shared_cctbx',
     'compile and link with the shared cctbx library', False))
+
 vars.Update(env)
 env.Help(MY_SCONS_HELP % vars.GenerateHelpText(env))
 
+if platform.system().lower() == "windows":
+    # See https://scons.org/faq.html#Linking_on_Windows_gives_me_an_error
+    env['ENV']['TMP'] = os.environ['TMP']
+    # Prevent the generation of an import lib (.lib) in addition to the dll
+    # Unused as we are using as static library for windows
+    # env.AppendUnique(no_import_lib=1)
+    if 'CONDA_PREFIX' in os.environ:
+        env.Append(CPPPATH=[pjoin(os.environ['CONDA_PREFIX'], 'include')])
+        env.Append(CPPPATH=[pjoin(os.environ['CONDA_PREFIX'], 'Library', 'include')])
+        env.Append(LIBPATH=pjoin(os.environ['CONDA_PREFIX'], 'Library', 'lib'))
+else:
+    if 'CONDA_PREFIX' in os.environ:
+        env.Append(CPPPATH=pjoin(os.environ['CONDA_PREFIX'], 'include'))
+        env.Append(LIBPATH=pjoin(os.environ['CONDA_PREFIX'], 'lib'))
+    # Specify minimum C++ standard.  Allow later standard from sconscript.local.
+    # In case of multiple `-std` options the last option holds.
+    env.PrependUnique(CXXFLAGS='-std=c++11', delete_existing=1)
+
+# the CPPPATH directories are checked by scons dependency scanner
+cpppath = getsyspaths('CPLUS_INCLUDE_PATH', 'CPATH')
+env.AppendUnique(CPPPATH=cpppath)
+# Insert LIBRARY_PATH explicitly because some compilers
+# ignore it in the system environment.
+env.PrependUnique(LIBPATH=getsyspaths('LIBRARY_PATH'))
+# This disable automated versioned named e.g. libboost_date_time-vc142-mt-s-x64-1_73.lib
+# so we can use conda-installed libraries
+env.AppendUnique(CPPDEFINES='BOOST_ALL_NO_LIB')
+
 builddir = env.Dir('build/%s-%s' % (env['build'], platform.machine()))
 
 Export('env')

conda-recipe/bld.bat

@@ -0,0 +1,4 @@
+scons -j%CPU_COUNT%
+if errorlevel 1 exit 1
+scons install prefix=%PREFIX%
+if errorlevel 1 exit 1

conda-recipe/conda_build_config.yaml

@@ -1,2 +1,6 @@
 boost:
-  - 1.67
+  - 1.73
+
+# only for local build ? see https://github.com/conda/conda-build/issues/4064#issuecomment-702983257
+#CONDA_BUILD_SYSROOT:
+#  - /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk

conda-recipe/meta.yaml

@@ -7,6 +7,7 @@ package:
 source:
   # git_url: https://github.com/diffpy/libobjcryst.git
   git_url: ..
+  # path: ..  # To build from modified local tree
 
 build:
   number: 0
@@ -17,12 +18,12 @@ requirements:
   build:
     - {{ compiler('cxx') }}
     - scons
-  host:
-    - libboost {{ boost }}
+    - boost-cpp {{ boost }}
+    - python
 
 test:
-  commands:
-    - test -f $PREFIX/lib/libObjCryst${SHLIB_EXT}
+  commands: # [not win]
+    - test -f $PREFIX/lib/libObjCryst${SHLIB_EXT} # [not win]
 
 about:
   home: https://github.com/diffpy/libobjcryst/

conda-recipe/sconscript.local

@@ -3,17 +3,19 @@
 Import('env')
 
 import os
+import platform
 
-# Apply environment settings for Anaconda compilers
-env.Replace(CXX=os.environ['CXX'])
-env.MergeFlags(os.environ['CFLAGS'])
-env.MergeFlags(os.environ['CPPFLAGS'])
-env.MergeFlags(os.environ['CXXFLAGS'])
-env.MergeFlags(os.environ['LDFLAGS'])
+if platform.system() != 'Darwin':
+    # Apply environment settings for Anaconda compilers
+    env.Replace(CXX=os.environ['CXX'])
+    env.MergeFlags(os.environ['CFLAGS'])
+    env.MergeFlags(os.environ['CPPFLAGS'])
+    env.MergeFlags(os.environ['CXXFLAGS'])
+    env.MergeFlags(os.environ['LDFLAGS'])
 
-# Use the default c++98 language standard
-cxxflags98 = [f for f in env['CXXFLAGS'] if not f.startswith('-std=')]
-env.Replace(CXXFLAGS=cxxflags98)
+    # Use the default c++98 language standard
+    cxxflags98 = [f for f in env['CXXFLAGS'] if not f.startswith('-std=')]
+    env.Replace(CXXFLAGS=cxxflags98)
 
 # Silence copious warnings from the boost headers.
 P = os.environ['PREFIX']

site_scons/fallback_version.py

@@ -7,4 +7,4 @@
 Update FALLBACK_VERSION when tagging a new release.
 '''
 
-FALLBACK_VERSION = '2021.1.1.post0'
+FALLBACK_VERSION = '2022.1.post0'

src/ObjCryst/ObjCryst/Molecule.cpp

@@ -25,6 +25,7 @@
 #include <algorithm>
 #include <iomanip>
 #include <ctime>
+#include <boost/format.hpp>
 
 #include "ObjCryst/Quirks/VFNStreamFormat.h"
 #include "ObjCryst/ObjCryst/Molecule.h"
@@ -2292,8 +2293,12 @@ void Molecule::XMLOutput(ostream &os,int indent)const
       for(pos=mvRigidGroup.begin();pos!=mvRigidGroup.end();++pos)
       {
          XMLCrystTag tagg("RigidGroup",false,true);
-         for(set<MolAtom *>::const_iterator at=(*pos)->begin();at!=(*pos)->end();++at)
-            tagg.AddAttribute("Atom",(*at)->GetName());
+         // Need to use Atom1, Atom2 etc.. so a valid XML is produced
+         // See https://github.com/vincefn/objcryst/issues/52
+         // This won't be backwards-compatible
+         int idx = 0;
+         for (set<MolAtom*>::const_iterator at = (*pos)->begin(); at != (*pos)->end(); ++at)
+             tagg.AddAttribute((boost::format("Atom%d") %idx++).str(), (*at)->GetName());
          /*
          tagg.AddAttribute("Q0",(*pos)->mQuat.Q0());
          tagg.AddAttribute("Q1",(*pos)->mQuat.Q1());
@@ -2384,7 +2389,7 @@ void Molecule::XMLInput(istream &is,const XMLCrystTag &tag)
       {
          RigidGroup s;
          for(unsigned int i=0;i<tagg.GetNbAttribute();i++)
-            if("Atom"==tagg.GetAttributeName(i))
+            if(tagg.GetAttributeName(i).rfind("Atom", 0)==0)
                s.insert(&(this->GetAtom(tagg.GetAttributeValue(i))));
          this->AddRigidGroup(s);
       }

src/ObjCryst/ObjCryst/PowderPattern.cpp

@@ -1298,6 +1298,19 @@ unsigned int PowderPatternDiffraction::GetProfileFitNetNbObs()const
    return nb;
 }
 
+bool PowderPatternDiffraction::HasFhklObsSq() const
+{
+  if(mpLeBailData==NULL) return false;
+  return mpLeBailData->GetFhklObsSq().size() > 0;
+}
+
+const CrystVector_REAL& PowderPatternDiffraction::GetFhklObsSq() const
+{
+  if(mpLeBailData==NULL)
+    throw ObjCrystException("PowderPatternDiffraction::GetFhklObsSq(): no extracted intensities available");
+   return mpLeBailData->GetFhklObsSq();
+}
+
 void PowderPatternDiffraction::CalcPowderPattern() const
 {
    this->GetNbReflBelowMaxSinThetaOvLambda();
@@ -6559,7 +6572,7 @@ void PowderPattern::PrepareIntegratedRfactor()const
       for(int i=0;i<mPowderPatternComponentRegistry.GetNb();i++)
       {
          const CrystVector_long vLim=mPowderPatternComponentRegistry.GetObj(i).GetBraggLimits();
-         for(i=0;i<vLim.numElements();i++) vLimits.push_back(vLim(i));
+         for(int j=0;j<vLim.numElements();j++) vLimits.push_back(vLim(j));
       }
       if(vLimits.size()<2)
       {

src/ObjCryst/ObjCryst/PowderPattern.h

@@ -420,6 +420,16 @@ class PowderPatternDiffraction : virtual public PowderPatternComponent,public Sc
       * No over paremeters (profile, background) are taken into account
       */
       unsigned int GetProfileFitNetNbObs()const;
+      /// Return true if there are extracted (le Bail) squared structure factors, false otherwise
+      bool HasFhklObsSq() const;
+      /** Get the extracted structure factors modulus (squared), e.g. using the Le Bail method.
+      *
+      * Note that the number of reflections listed is limited to the evaluated ones,
+      *which is usually smaller than the H,K and L arrays.
+      *
+      * Raises an exception if this is not available.
+      */
+      const CrystVector_REAL& GetFhklObsSq() const;
    protected:
       virtual void CalcPowderPattern() const;
       virtual void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

src/ObjCryst/RefinableObj/RefinableObj.h

@@ -736,19 +736,19 @@ template<class T> class ObjRegistry
        * but the objects themselves can be modified.
        * This iterator should remain valid even if an object is removed.
        */
-      typename list<T*>::const_iterator list_begin() const;
+      typename std::list<T*>::const_iterator list_begin() const;
       /** low-level access to the underlying list end().
        * Const access as we do not want the number and order of objects to change,
        * but the objects themselves can be modified.
        * This iterator should remain valid even if an object is removed.
        */
-      typename list<T*>::const_iterator list_end() const;
+      typename std::list<T*>::const_iterator list_end() const;
    private:
       /// The registry of objects
       vector<T*> mvpRegistry;
       /// Another view of the registry of objects - this time as a std::list, which
       /// will not be invalidated if one object is deleted
-      list<T*> mvpRegistryList;
+      std::list<T*> mvpRegistryList;
       /// Name of this registry
       string mName;
       /// Last time an object was added or removed