repopulate MDANSE

Doc/build_help.sh

@@ -2,7 +2,11 @@
 
 rm -rf ../Documentation
 
-sphinx-apidoc -o  ../Documentation -F --separate -d 5 -H nMoldyn -A "B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller"  -V 4.0 -R 4.0 ../nMOLDYN/
-cp doc_utils/conf_help.py ../Documentation/conf.py
-cp doc_utils/layout.html ../Documentation/_templates/
-sphinx-build -b htmlhelp ../Documentation ../nMOLDYN/GUI/Help/
+setenv PYTHONPATH=/home/pellegrini/workspace/MDANSE
+
+sphinx-apidoc -o  . -F --separate -d 5 -H mdanse -A "G. Goret, B. Aoun  & E. Pellegrini"  -V 4.0 -R 4.0 ../MDANSE
+cp conf_help.py conf.py
+
+cp layout.html _templates/
+cp nMoldyn_logo.png _static/
+sphinx-build -b htmlhelp ./ ./Help/

Doc/conf_help.py

@@ -17,7 +17,7 @@ import sys, os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-sys.path.append(os.path.abspath('../nMOLDYN'))
+sys.path.append(os.path.abspath('../MDANSE'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -42,7 +42,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'nMoldyn'
-copyright = u'2014, B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller'
+copyright = u'2014, G. Goret & B. Aoun & E. Pellegrini'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -57,10 +57,10 @@ release = '4.0'
 # for source files.
 exclude_patterns = ['Externals','_build', '**Tests**']
 
-html_logo = '_static/nMoldyn_logo.png'
+html_logo = '_static/mdanse_logo.png'
 
 inheritance_graph_attrs = dict(size='""')
-	
+
 inheritance_graph_attrs = dict(rankdir="TB", size='""')
 
 inheritance_node_attrs = dict(color='lightblue', style='filled')
@@ -82,16 +82,13 @@ html_show_copyright = False
 
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'nMoldyndoc'
+htmlhelp_basename = 'mdanseDoc'
 
 
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
-  ('index', 'nMoldyn.tex', u'nMoldyn Documentation',
-   u'B. Aoun \\& G. Goret \\& E. Pellegrini, G.R. Kneller', 'manual'),
-]
+
 
 #pdf_documents = [
 #  ('index', 'nMoldyn', u'nMoldyn Documentation',
@@ -100,7 +97,7 @@ latex_documents = [
 
 
 
-exclude_patterns = ['nMOLDYN.Externals**', 'nMOLDYN.nMOLDYN.__pkginfo__']
+exclude_patterns = ['MDANSE.Externals**', 'MDANSE.__pkginfo__']
 
 members_to_watch = ['class']
 

MDANSE/Core/ClassRegistry.py

@@ -24,7 +24,7 @@ class ClassRegistry(abc.ABCMeta):
     whose keys are the |type| class attribute of the subclasses and values are the corresponding 
     class instances.
 
-    Hence any base or child class that does not define |type| class attribute will not be registered.
+    Hence any base or child class that does not define |type| class attribute will not be resgistered.
     '''
     
     __metaclass__ = _Meta

MDANSE/Data/ElementsDatabase.py

+'''
+MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+------------------------------------------------------------------------------------------
+Copyright (C)
+2015- Eric C. Pellegrini Institut Laue-Langevin
+BP 156
+6, rue Jules Horowitz
+38042 Grenoble Cedex 9
+France
+pellegrini[at]ill.fr
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ 
+Created on Mar 23, 2015
+
+@author: pellegrini
+'''
+
 import _abcoll
-import ast
 import copy
 import csv
 import numbers
 import os
 import xml.etree.ElementTree as etree
 
-from MMTK import Atom
-
-from nMOLDYN import PLATFORM
-from nMOLDYN.Core.Error import Error
-from nMOLDYN.Core.Singleton import Singleton
+from MDANSE.Core.Platform import PLATFORM
+from MDANSE.Core.Error import Error
+from MDANSE.Core.Singleton import Singleton
 
 class ElementsDatabaseError(Error):
     pass
@@ -138,6 +165,8 @@ class SortedCaselessDict(dict):
 
 class ElementsDatabase(object):
     
+    __metaclass__ = Singleton
+    
     _DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__), "elements_database.csv")
 
     _USER_DATABASE = os.path.join(PLATFORM.application_directory(), "elements_database.csv")
@@ -350,10 +379,6 @@ class ElementsDatabase(object):
         
         return SortedCaselessDict([(k,self[k,pname]) for k in self._data.iterkeys()])
 
-    def get_property(self,pname):
-        
-        return SortedCaselessDict([(k,self[k,pname]) for k in self._data.iterkeys()])
-
     def get_property_settings(self,pname):
 
         return copy.deepcopy(self._properties[pname])
@@ -461,3 +486,4 @@ class ElementsDatabase(object):
             f.write('mass = %s' % props["atomic_weight"])
             f.close()
             
+ELEMENTS = ElementsDatabase()
\ No newline at end of file

MDANSE/__init__.py

-'''
-MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
------------------------------------------------------------------------
-
-MDANSE is a library/application for the analysis of molecular dynamics simulation data. 
-
-It uses some concepts of nMolDyn program historically designed by Gerald Kneller 
-for the computation and decomposition of neutron scattering spectra. 
-
------------------------------------------------------------------------
-
-Copyright (C)
-2015- Eric C. Pellegrini Institut Laue-Langevin
-BP 156
-6, rue Jules Horowitz
-38042 Grenoble Cedex 9
-France
-pellegrini[at]ill.fr
-
-This library is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or (at your option) any later version.
-
-This library is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library; if not, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- 
-Created on Mar 23, 2015
-
-@author: Eric C. Pellegrini
-'''
-
-from __pkginfo__ import __version__, __author__, __date__
-
-from MDANSE.Core.ClassRegistry import ClassRegistry as REGISTRY
-from MDANSE.Core.Platform import PLATFORM
-from MDANSE.Data.ElementsDatabase import ELEMENTS
-from MDANSE.Framework.Configurables.UserDefinable import USER_DEFINITIONS
\ No newline at end of file