import from dgcode ncrystaldev git: candidate for version 3.9.3

CHANGELOG

@@ -1,3 +1,7 @@
+v3.9.3 2024-08-20
+     * Fix NCrystal.cifutils plot labels with underscores in filenames.
+     * Fix MiniMC plotting.
+
 v3.9.2 2024-08-19
      * Prevent rare error in the MiniMC framework, which happened when acos was
        evaluated on a value which due to numerical instabilities was ever so

CMakeLists.txt

@@ -86,7 +86,7 @@ endif()
 
 cmake_policy( SET CMP0048 NEW )#Not sure if this is really needed
 
-project( NCrystal VERSION 3.9.2 ${_project_metadata} )
+project( NCrystal VERSION 3.9.3 ${_project_metadata} )
 
 unset( _project_metadata )
 

NCrystal/__init__.py

@@ -54,7 +54,7 @@
 
 #NB: Synchronize meta-data below with fields in setup.py+template_setup.py.in meta data:
 __license__ = "Apache 2.0, http://www.apache.org/licenses/LICENSE-2.0"
-__version__ = '3.9.2'
+__version__ = '3.9.3'
 __status__ = "Production"
 __author__ = "NCrystal developers (Thomas Kittelmann, Xiao Xiao Cai)"
 __copyright__ = "Copyright 2015-2024 %s"%__author__

NCrystal/_mmc.py

@@ -329,6 +329,8 @@ def plot( self, *,
                 plt.figure()
 
             do_legend = False
+            tot_integral_with_absorption = None#unknown
+
             if breakdown_mode:
 
                 colors = {
@@ -357,7 +359,6 @@ def plot( self, *,
                                              'NOSCAT'].index(h.title))
 
                 integrals = [ h.stats.get('integral',-1.0) for h in hists ]
-                tot_integral_with_absorption = None#unknown
                 tot_integral = ( sum(integrals)
                                  if all( i>=0.0 for i in integrals )
                                  else None )

NCrystal/cifutils.py

@@ -400,7 +400,9 @@ def produce_validation_plots( files, verbose_lbls = True, pdf_target = None,
     embed them in a PDF file. Any plot_kwargs will be passed along to the
     produce_validation_plot(..) function.
     """
-    from .plot import _import_matplotlib_plt, _import_matplotlib_pdfpages, _fakepyplot_mode
+    from .plot import ( _import_matplotlib_plt,
+                        _import_matplotlib_pdfpages,
+                        _fakepyplot_mode )
 
     if pdf_target:
         pdfpages = _import_matplotlib_pdfpages()
@@ -508,7 +510,7 @@ def _extractID(s,pattern):
                 yield int(d)
 
     import re as _re
-    _re_atomdbspecs = _re.compile("\[ *with ([a-zA-Z ]+)->([ a-zA-Z0-9+-\.]+) *\]")
+    _re_atomdbspecs = _re.compile(r"\[ *with ([a-zA-Z ]+)->([ a-zA-Z0-9+-\.]+) *\]")
     def _extractAtomDBSpec(s):
         #Look for remapping specs like "[with H->D]" and return in @ATOMDB format
         #(i.e. "H is D").
@@ -537,7 +539,8 @@ def _extractAtomDBSpec(s):
     ids = newids
 
     def _atomdb_to_remap( atomdb):
-        _atomdb = list( ' '.join(e.strip().split()) for e in (atomdb or '').replace(':',' ').split('@') )
+        _atomdb = list( ' '.join(e.strip().split())
+                        for e in (atomdb or '').replace(':',' ').split('@') )
         _atomdb = list( e for e in _atomdb if e )
         l = []
         for c in _atomdb:
@@ -587,6 +590,9 @@ def _atomdb_to_remap( atomdb):
                     'pink',
                     'gray')]
 
+    def fix_lbl_for_plt(lbl):
+        return lbl.replace('_',"$"+'\\'+"mathrm{\\_}$")
+
     for i,(lbl,mc) in enumerate(cmps):
         lbl = str(lbl)
         if '/' in lbl:
@@ -608,7 +614,7 @@ def _atomdb_to_remap( atomdb):
             natoms_all.add(si['n_atoms'])
 
         plt.plot(wls,mc.scatter.xsect(wl=wls),
-                 label=lbl,
+                 label=fix_lbl_for_plt(lbl),
                  linewidth=lw,
                  alpha=0.5 if i==0 else 0.5,
                  color = col_ordered[i] if i<len(col_ordered) else None,
@@ -1610,7 +1616,9 @@ def guess_elem_name( site_label ):
             if elem_name:
                 _nc_common.warn(f'Assuming atomic symbol "{elem_name}" based on CIF label "{site.label}"')
             else:
-                raise _nc_core.NCBadInput(f'Neither Gemmi nor NCrystal\'s custom code could deduce an atomic symbol for the CIF label "{site.label}"')
+                raise _nc_core.NCBadInput(f'Neither Gemmi nor NCrystal\'s custom'
+                                          ' code could deduce an atomic symbol'
+                                          f' for the CIF label "{site.label}"')
             elem_Z = None
         else:
             elem_name, elem_Z = site_en, int(site.element.atomic_number)

VERSION

@@ -1 +1 @@
-3.9.2
+3.9.3

ncrystal_core/include/NCrystal/NCVersion.hh

@@ -39,9 +39,9 @@
 
 #define NCRYSTAL_VERSION_MAJOR 3
 #define NCRYSTAL_VERSION_MINOR 9
-#define NCRYSTAL_VERSION_PATCH 2
-#define NCRYSTAL_VERSION   3009002 /* (1000000*MAJOR+1000*MINOR+PATCH)   */
-#define NCRYSTAL_VERSION_STR "3.9.2"
+#define NCRYSTAL_VERSION_PATCH 3
+#define NCRYSTAL_VERSION   3009003 /* (1000000*MAJOR+1000*MINOR+PATCH)   */
+#define NCRYSTAL_VERSION_STR "3.9.3"
 
 #include "NCrystal/ncapi.h"
 #include <stdexcept>

ncrystal_core/include/NCrystal/ncrystal.h

@@ -1201,9 +1201,9 @@ extern "C" {
 #endif
 #define NCRYSTAL_VERSION_MAJOR 3
 #define NCRYSTAL_VERSION_MINOR 9
-#define NCRYSTAL_VERSION_PATCH 2
-#define NCRYSTAL_VERSION   3009002 /* (1000000*MAJOR+1000*MINOR+PATCH)             */
-#define NCRYSTAL_VERSION_STR "3.9.2"
+#define NCRYSTAL_VERSION_PATCH 3
+#define NCRYSTAL_VERSION   3009003 /* (1000000*MAJOR+1000*MINOR+PATCH)             */
+#define NCRYSTAL_VERSION_STR "3.9.3"
   NCRYSTAL_API int ncrystal_version(void); /* returns NCRYSTAL_VERSION                  */
   NCRYSTAL_API const char * ncrystal_version_str(void); /* returns NCRYSTAL_VERSION_STR */