MDANSE MDANSE works at a command line level: the analysis has to be

reintroduced now

Doc/Template.py

@@ -101,8 +101,8 @@ class MainClass1(object):
 
         :Example:
 
-        >>> import template
-        >>> a = template.MainClass1()
+        >>> import Template
+        >>> a = Template.MainClass1()
         >>> a.function1(1,1,1)
         2
 

Doc/build_doc.sh

 #!/bin/sh
 
+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/
+mkdir Documentation
 
-cp doc_utils/conf_html.py ../Documentation/conf.py
+sphinx-apidoc -o  ./Documentation -F --separate -d 5 -H MDANSE -A "B. Aoun & G. Goret & E. Pellegrini"  -V 1.0 -R 1.0 ../MDANSE/
 
+cp conf_html.py ./Documentation/conf.py
 
-cp doc_utils/nMoldyn_logo.png ../Documentation/_static/
+cp mdanse_logo.png ./Documentation/_static/
 
-sphinx-build -b html ../Documentation ../Documentation/_build/html/
+sphinx-build -b html ./Documentation ./Documentation/_build/html/
 
 
 

Doc/build_help.sh

@@ -8,5 +8,5 @@ sphinx-apidoc -o  . -F --separate -d 5 -H mdanse -A "G. Goret, B. Aoun  & E. Pel
 cp conf_help.py conf.py
 
 cp layout.html _templates/
-cp nMoldyn_logo.png _static/
+cp mdanse_logo.png _static/
 sphinx-build -b htmlhelp ./ ./Help/

Doc/conf_help.py

-# -*- coding: utf-8 -*-
+#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
+#goret[at]ill.fr
+#aoun[at]ill.fr
 #
-# nMoldyn documentation build configuration file, created by Gael Goret
-# on Fri Feb 28 10:35:22 2014.
+#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 file is execfile()d with the current directory set to its containing dir.
+#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.
 #
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+#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 30, 2015
+
+@author: goret
+'''
 
 import sys, os
+
 #
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -41,17 +61,17 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'nMoldyn'
-copyright = u'2014, G. Goret & B. Aoun & E. Pellegrini'
+project = u'MDANSE'
+copyright = u'2015, 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
 # built documents.
 #
 # The short X.Y version.
-version = '4.0'
+version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.0'
+release = '1.0'
 
 # List of directories, relative to source directory, that shouldn't be searched
 # for source files.
@@ -65,12 +85,9 @@ inheritance_graph_attrs = dict(rankdir="TB", size='""')
 
 inheritance_node_attrs = dict(color='lightblue', style='filled')
 
-
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-
-
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -80,23 +97,18 @@ html_theme_options = {'sidebarwidth':250}#, 'nosidebar':True}
 
 html_show_copyright = False
 
-
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'mdanseDoc'
 
-
-
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 
 
 #pdf_documents = [
-#  ('index', 'nMoldyn', u'nMoldyn Documentation',
+#  ('index', 'MDANSE', u'MDANSE Documentation',
 #   u'B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller'),
 #]
 
-
-
 exclude_patterns = ['MDANSE.Externals**', 'MDANSE.__pkginfo__']
 
 members_to_watch = ['class']
@@ -109,8 +121,6 @@ def flag_onthefly(app, what, name, obj, options, lines):
 #    	lines.insert(0,'    .. inheritance-diagram:: %s\n'%name.split('.')[-1])
 #    	lines.insert(0,'**inheritance-diagram:**\n\n')
 
-
-
 def autodoc_skip_member(app, what, name, obj, skip, options):
     
     if what in ['method','attribut','function','exception']:
@@ -130,5 +140,3 @@ def autodoc_skip_member(app, what, name, obj, skip, options):
 def setup(app):
     app.connect('autodoc-skip-member', autodoc_skip_member)
     app.connect('autodoc-process-docstring', flag_onthefly)
-
-	

Doc/conf_html.py

-# -*- coding: utf-8 -*-
+#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
+#goret[at]ill.fr
+#aoun[at]ill.fr
 #
-# nMoldyn documentation build configuration file, created by Gael Goret
-# on Fri Feb 28 10:35:22 2014.
+#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 file is execfile()d with the current directory set to its containing dir.
+#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.
 #
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+#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 30, 2015
+
+@author: goret
+'''
+
 
 import sys, os
 #
@@ -17,7 +37,7 @@ 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 -----------------------------------------------------
 
@@ -41,23 +61,23 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'nMoldyn'
-copyright = u'2014, B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller'
+project = u'MDANSE'
+copyright = u'2014, B. Aoun & G. Goret & 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
 # built documents.
 #
 # The short X.Y version.
-version = '4.0'
+version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.0'
+release = '1.0'
 
 # List of directories, relative to source directory, that shouldn't be searched
 # for source files.
-exclude_patterns = ['Externals','_build', '**Tests**']
+exclude_patterns = ['MDANSE.Externals','_build', '**Tests**']
 
-html_logo = '_static/nMoldyn_logo.png'
+html_logo = '_static/mdanse_logo.png'
 
 inheritance_graph_attrs = dict(size='""')
 	
@@ -69,8 +89,6 @@ inheritance_node_attrs = dict(color='lightblue', style='filled')
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-
-
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -78,55 +96,37 @@ pygments_style = 'sphinx'
 html_theme = "nature"
 html_theme_options = {'sidebarwidth':250}#, 'nosidebar':True}
 
-
-
-
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'nMoldyndoc'
-
-
+htmlhelp_basename = 'MDANSE_doc'
 
 # 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',
+  ('index', 'MDANSE.tex', u'MDANSE Documentation',
    u'B. Aoun \\& G. Goret \\& E. Pellegrini, G.R. Kneller', 'manual'),
 ]
 
-#pdf_documents = [
-#  ('index', 'nMoldyn', u'nMoldyn Documentation',
-#   u'B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller'),
-#]
-
+pdf_documents = [('index', 'MDANSE', u'MDANSE Documentation', u'B. Aoun & G. Goret & E. Pellegrini'),]
 
 # -- Options for manual page output --------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'nmoldyn', u'nMoldyn Documentation',
-     [u'B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller'], 1)
-]
-
-
+man_pages = [('index', 'MDANSE', u'MDANSE Documentation', u'B. Aoun & G. Goret & E. Pellegrini'),]
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
-texinfo_documents = [
-  ('index', 'nMoldyn', u'nMoldyn Documentation',
-   u'B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller', 'nMoldyn', 'One line description of project.',
-   'Miscellaneous'),
-]
+texinfo_documents = [('index', 'MDANSE', u'MDANSE Documentation',u'B. Aoun & G. Goret & E. Pellegrini','MDANSE', 'One line description of project.','Miscellaneous'),]
 
-
-
-
-exclude_patterns = ['nMOLDYN.Externals**', 'nMOLDYN.nMOLDYN.__pkginfo__']
+exclude_patterns = ['MDANSE.Externals**', 'MDANSE.__pkginfo__']
 
 members_to_watch = ['class']
 
 def flag_onthefly(app, what, name, obj, options, lines):
+    from MDANSE import REGISTRY
+    for kls in REGISTRY["job"].values():
+    	kls.__doc__ += kls.configurators.build_doc()
     if(what in members_to_watch):
         # and modify the docstring so the rendered output is highlights the omission
 	    if lines:
@@ -134,7 +134,7 @@ def flag_onthefly(app, what, name, obj, options, lines):
 	    lines.insert(0,'    .. inheritance-diagram:: %s\n'%name.split('.')[-1])
 	    lines.insert(0,'**inheritance-diagram:**\n\n')
     	
-    	
 def setup(app):
+
     app.connect('autodoc-process-docstring', flag_onthefly)
 	

Doc/coverage.sh

 #!/bin/sh
 
 cd ../Tests/
-coverage run --source=../nMOLDYN/ ../Tests/AllTests.py
-coverage html --omit=../nMOLDYN/Externals/*,../nMOLDYN/GUI/*,../nMOLDYN/Framework/Plugins/*,../nMOLDYN/Framework/ConfiguratorWidgets/*
\ No newline at end of file
+coverage run --source=../MDANSE/ ../Tests/AllTests.py
+coverage html --omit=../MDANSE/Externals/*,../MDANSE/GUI/*,../MDANSE/Framework/Plugins/*,../MDANSE/Framework/ConfiguratorWidgets/*

Extensions/setup.py

@@ -49,7 +49,7 @@ EXTENSIONS = [Extension('distance_histogram',
 
 
 
-setup (name = "nMolDyn_Extensions",
-           version = "0.1",
+setup (name = "MDANSE_Extensions",
+           version = "1.0",
            ext_modules = EXTENSIONS,                 
            cmdclass = {'build_ext': build_ext})

MANIFEST.in

@@ -3,11 +3,11 @@ include LICENCE
 
 recursive-include Extensions/qhull_lib *.h *c *.pxd
 
-recursive-include nMOLDYN/GUI/Resources/Icons *.png
+recursive-include MDANSE/GUI/Resources/Icons *.png
 
-include nMOLDYN/Data/elements_database.csv
+include MDANSEData/elements_database.csv
 
-include nMOLDYN/Data/Atoms/*
+include MDANSE/Data/Atoms/*
 
 recursive-include UserData *
 

MDANSE/App/HelpFormatter.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
+#goret[at]ill.fr
+#aoun[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 30, 2015
+
+@author: pellegrini
+'''
+
+import optparse
+import textwrap
+
+class IndentedHelp(optparse.IndentedHelpFormatter):
+    '''This class modify slightly the help formatter of the optparse.OptionParser class.
+    
+    This allows to take into account the line feed properly.
+    
+    @note: code taken as it is from an implementation made by Tim Chase
+    (http://groups.google.com/group/comp.lang.python/browse_thread/thread/6df6e6b541a15bc2/09f28e26af0699b1)
+    '''
+
+    def format_description(self, description):
+        if not description: 
+            return ""
+        desc_width = self.width - self.current_indent
+        indent = " "*self.current_indent
+        bits = description.split('\n')
+        formatted_bits = [textwrap.fill(bit,desc_width,initial_indent=indent,subsequent_indent=indent) for bit in bits]
+        result = "\n".join(formatted_bits) + "\n"
+        
+        return result
+
+    def format_option(self, option):
+        
+        result = []
+        opts = self.option_strings[option]
+        opt_width = self.help_position - self.current_indent - 2
+        if len(opts) > opt_width:
+            opts = "%*s%s\n" % (self.current_indent, "", opts)
+            indent_first = self.help_position
+        else: # start help on same line as opts
+            opts = "%*s%-*s  " % (self.current_indent, "", opt_width, opts)
+            indent_first = 0
+        result.append(opts)
+        if option.help:
+            help_text = self.expand_default(option)
+            # Everything is the same up through here
+            help_lines = []
+            for para in help_text.split("\n"):
+                help_lines.extend(textwrap.wrap(para, self.help_width))
+            # Everything is the same after here
+            result.append("%*s%s\n" % (indent_first, "", help_lines[0]))
+            result.extend(["%*s%s\n" % (self.help_position, "", line) for line in help_lines[1:]])
+        elif opts[-1] != "\n":
+            result.append("\n")
+        
+        return "".join(result)
+
+

MDANSE/Core/ClassRegistry.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
+#goret[at]ill.fr
+#aoun[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 30, 2015
+
+@author: pellegrini
+'''
+
 import abc
+import inspect
+import os
 
 class _Meta(type):
     '''
@@ -17,14 +51,11 @@ class _Meta(type):
     
 class ClassRegistry(abc.ABCMeta):
     '''
-    Metaclass that registers the subclasses of bases classes.
-
-    The internal registry is defined as a nested dictionary whose keys 
-    are the |type| class attribute of the base classes and values another dictionary 
-    whose keys are the |type| class attribute of the subclasses and values are the corresponding 
-    class instances.
+    Metaclass that registers the subclasses of all the base classes used in MDANSE framework.
 
-    Hence any base or child class that does not define |type| class attribute will not be resgistered.
+    The subclasses are stored internally in a nested dictionary whose primary key 
+    is the 'type' class attribute of the base class they are inheriting from and secondary key is 
+    their own 'type' class attribute.
     '''
     
     __metaclass__ = _Meta
@@ -38,8 +69,11 @@ class ClassRegistry(abc.ABCMeta):
         Constructor of a class metaclassed by ClassFactory
         
         :param name: the name of the class to be built by this metaclass
+        :type name: str
         :param bases: the base classes of the class to be built by this metaclass
+        :type bases: tuple 
         :param namespace: the attributes and methods of the class to be built by this metaclass
+        :type namespace: dict
         '''
         
         super(ClassRegistry, self).__init__(name, bases, namespace)
@@ -53,9 +87,9 @@ class ClassRegistry(abc.ABCMeta):
         metaClass = namespace.get("__metaclass__", None)
                               
         if metaClass is ClassRegistry:
+            ClassRegistry.__interfaces.append(self)
             if (ClassRegistry._registry.has_key(typ)):
                 return
-            ClassRegistry.__interfaces.append(self)
             ClassRegistry._registry[typ] = {}
 
         else:
@@ -71,15 +105,14 @@ class ClassRegistry(abc.ABCMeta):
         Returns informations about the subclasses of a given base class  stored in the registry.
         
         :param cls: the ClassRegsitry instance
+        :type cls: ClassRegistry
         :param interface: the name of base class of whom information about its subclasses is requested
+        :type interface: str
         '''
                 
         if not cls._registry.has_key(interface):
             return "The interface " + interface + " is not registered"
 
-        import inspect
-        import os
-
         # Dictionnay whose keys are the package names and values and list of (job name, job path) stored in the corresponding package. 
         packages = {}
 
@@ -99,6 +132,8 @@ class ClassRegistry(abc.ABCMeta):
             if modPackage is None:
                 modPackage = os.path.split(os.path.dirname(modFilename))[1]
                 
+            modPackage = modPackage.split(".")[-1]
+        
             # Update the packages dictionary.
             if packages.has_key(modPackage):
                 packages[modPackage].append([k, v.__name__])
@@ -120,3 +155,14 @@ class ClassRegistry(abc.ABCMeta):
     
         return contents
 
+    @classmethod
+    def get_interfaces(cls):
+        '''
+        Returns the interfaces that are currently registered.
+        
+        :param cls: the ClassRegsitry instance
+        :type cls: ClassRegistry
+        '''
+        
+        
+        return sorted(cls._registry.keys())
\ No newline at end of file

MDANSE/Core/MMTKDefinitions.py

+import cPickle
+import os
+
+from MMTK.Biopolymers import defineAminoAcidResidue, defineNucleicAcidResidue
+from MMTK.PDB import defineMolecule
+
+from MDANSE import PLATFORM
+from MDANSE.Core.Error import Error
+from MDANSE.Core.Singleton import Singleton
+
+class MMTKDefinitionsError(Error):
+    pass
+
+class MMTKDefinitions(dict):
+
+    __metaclass__ = Singleton
+    
+    _path = os.path.join(PLATFORM.application_directory(),"mmtk_definitions")
+    
+    _types = ['amino_acid','molecule','nucleic_acid']
+                                                                                 
+    def add(self, name, typ, databaseName):
+        
+        if type not in self._types:
+            raise MMTKDefinitionsError('The type %r is not a valid MMTK definition type. It must be one of %s' % (str(name),MMTKDefinitions._types))
+                        
+        try:
+            if typ == 'molecule':
+                defineMolecule(name,databaseName)
+            elif typ == 'amino_acid':
+                defineAminoAcidResidue(databaseName,name)
+            elif typ == 'nucleic_acid':
+                defineNucleicAcidResidue(databaseName,name)
+        except ValueError as e:
+            raise MMTKDefinitions(str(e))
+        else:
+            self[name] = (typ,databaseName)
+        
+    def load(self):
+        
+        if not os.path.exists(MMTKDefinitions._path):
+            return
+
+        # Try to open the UD file.
+        try:
+            with open(MMTKDefinitions._path, "rb") as f: 
+                mmtkDef = cPickle.load(f)
+                for name,(typ,databaseName) in mmtkDef.items():
+                    self.add(name,typ,databaseName)
+                    
+        # If for whatever reason the pickle file loading failed do not even try to restore it
+        except:
+            raise MMTKDefinitionsError("The mmtk definitions file could not be loaded")
+                    
+    def save(self, path=None):
+        
+        if path is None:
+            path = MMTKDefinitions._path
+            
+        try:                        
+            f = open(path, "wb")
+        except IOError:
+            return
+        else:
+            cPickle.dump(self, f, protocol=2)
+            f.close()
+
+MMTK_DEFINITIONS = MMTKDefinitions()
\ No newline at end of file