Modified the atom symbol of MMTK elements database

Fused Configurable and ConfiguratorsDict classes
Improved the docstring of configurators-based classes

Doc/build_help.sh

 #!/bin/sh
 
-rm -rf ../Documentation
+rm -rf ./Documentation
 
-setenv PYTHONPATH=/home/pellegrini/workspace/MDANSE
+mkdir ./Documentation
+mkdir ./Documentation/_static
+mkdir ./Documentation/_templates
 
-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
+sphinx-apidoc -o  ./Documentation -F --separate -d 5 -H MDANSE -A "G. Goret, B. Aoun  & E. Pellegrini"  -V 1.0 -R 1.0 ../MDANSE
 
-cp layout.html _templates/
-cp mdanse_logo.png _static/
-sphinx-build -b htmlhelp ./ ./Help/
+cp conf_help.py ./Documentation/conf.py
+
+cp layout.html ./Documentation/_templates/
+
+cp mdanse_logo.png ./Documentation/_static/
+
+sphinx-build -b htmlhelp ./Documentation ./Documentation/Help/

Doc/conf_help.py

@@ -75,7 +75,7 @@ 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/mdanse_logo.png'
 
@@ -98,22 +98,25 @@ html_theme_options = {'sidebarwidth':250}#, 'nosidebar':True}
 html_show_copyright = False
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mdanseDoc'
+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', 'MDANSE.tex', u'MDANSE Documentation',
+   u'B. Aoun \\& G. Goret \\& E. Pellegrini', 'manual'),
+]
 
-
-#pdf_documents = [
-#  ('index', 'MDANSE', u'MDANSE 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'),]
 
 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.build_doc()
     if(what in members_to_watch):
         # and modify the docstring so the rendered output is highlights the omission
         if lines:

Doc/conf_html.py

@@ -80,12 +80,11 @@ exclude_patterns = ['MDANSE.Externals','_build', '**Tests**']
 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')
 
-
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
@@ -103,7 +102,7 @@ htmlhelp_basename = 'MDANSE_doc'
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
   ('index', 'MDANSE.tex', u'MDANSE Documentation',
-   u'B. Aoun \\& G. Goret \\& E. Pellegrini, G.R. Kneller', 'manual'),
+   u'B. Aoun \\& G. Goret \\& E. Pellegrini', 'manual'),
 ]
 
 pdf_documents = [('index', 'MDANSE', u'MDANSE Documentation', u'B. Aoun & G. Goret & E. Pellegrini'),]
@@ -124,17 +123,17 @@ 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:
-	        lines.insert(0,'**Description:**\n\n')
-	    lines.insert(0,'    .. inheritance-diagram:: %s\n'%name.split('.')[-1])
-	    lines.insert(0,'**inheritance-diagram:**\n\n')
-    	
+	from MDANSE import REGISTRY
+	for kls in REGISTRY["job"].values():
+		kls.__doc__ += kls.build_doc()
+	if(what in members_to_watch):
+		# and modify the docstring so the rendered output is highlights the omission
+		if lines:
+			lines.insert(0,'**Description:**\n\n')
+			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)
+	app.connect('autodoc-process-docstring', flag_onthefly)
 	

MDANSE/Data/Atoms/ac

-name = "actinium"
+name = 'actinium'
 
-symbol = "ac"
+symbol = 'Ac'
 
-mass = 227.0
\ No newline at end of file
+mass = 227.0

MDANSE/Data/Atoms/ag

-name = "silver"
+name = 'silver'
 
-symbol = "ag"
+symbol = 'Ag'
 
-mass = 107.8682
\ No newline at end of file
+mass = 107.8682

MDANSE/Data/Atoms/ag107

-name = "silver"
+name = 'silver'
 
-symbol = "ag107"
+symbol = 'Ag107'
 
-mass = 106.905093
\ No newline at end of file
+mass = 106.905093

MDANSE/Data/Atoms/ag109

-name = "silver"
+name = 'silver'
 
-symbol = "ag109"
+symbol = 'Ag109'
 
-mass = 108.904756
\ No newline at end of file
+mass = 108.904756

MDANSE/Data/Atoms/al

-name = "aluminium"
+name = 'aluminium'
 
-symbol = "al"
+symbol = 'Al'
 
-mass = 26.98153844
\ No newline at end of file
+mass = 26.98153844

MDANSE/Data/Atoms/al27

-name = "aluminium"
+name = 'aluminium'
 
-symbol = "al27"
+symbol = 'Al27'
 
-mass = 26.98153844
\ No newline at end of file
+mass = 26.98153844

MDANSE/Data/Atoms/am

-name = "americium"
+name = 'americium'
 
-symbol = "am"
+symbol = 'Am'
 
-mass = 243.0
\ No newline at end of file
+mass = 243.0

MDANSE/Data/Atoms/am243

-name = "americium"
+name = 'americium'
 
-symbol = "am243"
+symbol = 'Am243'
 
-mass = 243.0
\ No newline at end of file
+mass = 243.0

MDANSE/Data/Atoms/ar

-name = "argon"
+name = 'argon'
 
-symbol = "ar"
+symbol = 'Ar'
 
-mass = 39.948
\ No newline at end of file
+mass = 39.948

MDANSE/Data/Atoms/ar36

-name = "argon"
+name = 'argon'
 
-symbol = "ar36"
+symbol = 'Ar36'
 
-mass = 35.96754628
\ No newline at end of file
+mass = 35.96754628

MDANSE/Data/Atoms/ar38

-name = "argon"
+name = 'argon'
 
-symbol = "ar38"
+symbol = 'Ar38'
 
-mass = 37.9627322
\ No newline at end of file
+mass = 37.9627322

MDANSE/Data/Atoms/ar40

-name = "argon"
+name = 'argon'
 
-symbol = "ar40"
+symbol = 'Ar40'
 
-mass = 39.96238312
\ No newline at end of file
+mass = 39.96238312

MDANSE/Data/Atoms/as

-name = "arsenic"
+name = 'arsenic'
 
-symbol = "as"
+symbol = 'As'
 
-mass = 74.9215964
\ No newline at end of file
+mass = 74.9215964

MDANSE/Data/Atoms/as75

-name = "arsenic"
+name = 'arsenic'
 
-symbol = "as75"
+symbol = 'As75'
 
-mass = 74.9215964
\ No newline at end of file
+mass = 74.9215964

MDANSE/Data/Atoms/at

-name = "astatine"
+name = 'astatine'
 
-symbol = "at"
+symbol = 'At'
 
-mass = 210.0
\ No newline at end of file
+mass = 210.0

MDANSE/Data/Atoms/au

-name = "gold"
+name = 'gold'
 
-symbol = "au"
+symbol = 'Au'
 
-mass = 196.966552
\ No newline at end of file
+mass = 196.966552

MDANSE/Data/Atoms/au197

-name = "gold"
+name = 'gold'
 
-symbol = "au197"
+symbol = 'Au197'
 
-mass = 196.966552
\ No newline at end of file
+mass = 196.966552

MDANSE/Data/Atoms/b

-name = "boron"
+name = 'boron'
 
-symbol = "b"
+symbol = 'B'
 
-mass = 10.811
\ No newline at end of file
+mass = 10.811

MDANSE/Data/Atoms/b10

-name = "boron"
+name = 'boron'
 
-symbol = "b10"
+symbol = 'B10'
 
-mass = 10.012937
\ No newline at end of file
+mass = 10.012937

MDANSE/Data/Atoms/b11

-name = "boron"
+name = 'boron'
 
-symbol = "b11"
+symbol = 'B11'
 
-mass = 11.0093055
\ No newline at end of file
+mass = 11.0093055

MDANSE/Data/Atoms/ba

-name = "barium"
+name = 'barium'
 
-symbol = "ba"
+symbol = 'Ba'
 
-mass = 137.327
\ No newline at end of file
+mass = 137.327

MDANSE/Data/Atoms/ba130

-name = "barium"
+name = 'barium'
 
-symbol = "ba130"
+symbol = 'Ba130'
 
-mass = 129.90631
\ No newline at end of file
+mass = 129.90631

MDANSE/Data/Atoms/ba132

-name = "barium"
+name = 'barium'
 
-symbol = "ba132"
+symbol = 'Ba132'
 
-mass = 131.905056
\ No newline at end of file
+mass = 131.905056

MDANSE/Data/Atoms/ba134

-name = "barium"
+name = 'barium'
 
-symbol = "ba134"
+symbol = 'Ba134'
 
-mass = 133.904503
\ No newline at end of file
+mass = 133.904503

MDANSE/Data/Atoms/ba135

-name = "barium"
+name = 'barium'
 
-symbol = "ba135"
+symbol = 'Ba135'
 
-mass = 134.905683
\ No newline at end of file
+mass = 134.905683

MDANSE/Data/Atoms/ba136

-name = "barium"
+name = 'barium'
 
-symbol = "ba136"
+symbol = 'Ba136'
 
-mass = 135.90457
\ No newline at end of file
+mass = 135.90457

MDANSE/Data/Atoms/ba137

-name = "barium"
+name = 'barium'
 
-symbol = "ba137"
+symbol = 'Ba137'
 
-mass = 136.905821
\ No newline at end of file
+mass = 136.905821

MDANSE/Data/Atoms/ba138

-name = "barium"
+name = 'barium'
 
-symbol = "ba138"
+symbol = 'Ba138'
 
-mass = 137.905241
\ No newline at end of file
+mass = 137.905241

MDANSE/Data/Atoms/be

-name = "beryllium"
+name = 'beryllium'
 
-symbol = "be"
+symbol = 'Be'
 
-mass = 9.0121821
\ No newline at end of file
+mass = 9.0121821

MDANSE/Data/Atoms/be9

-name = "beryllium"
+name = 'beryllium'
 
-symbol = "be9"
+symbol = 'Be9'
 
-mass = 9.0121821
\ No newline at end of file
+mass = 9.0121821

MDANSE/Data/Atoms/bh

-name = "bohrium"
+name = 'bohrium'
 
-symbol = "bh"
+symbol = 'Bh'
 
-mass = 264.12473
\ No newline at end of file
+mass = 264.12473

MDANSE/Data/Atoms/bi

-name = "bismuth"
+name = 'bismuth'
 
-symbol = "bi"
+symbol = 'Bi'
 
-mass = 208.980383
\ No newline at end of file
+mass = 208.980383

MDANSE/Data/Atoms/bi209

-name = "bismuth"
+name = 'bismuth'
 
-symbol = "bi209"
+symbol = 'Bi209'
 
-mass = 208.980383
\ No newline at end of file
+mass = 208.980383

MDANSE/Data/Atoms/bk

-name = "berkelium"
+name = 'berkelium'
 
-symbol = "bk"
+symbol = 'Bk'
 
-mass = 247.0
\ No newline at end of file
+mass = 247.0

MDANSE/Data/Atoms/br

-name = "bromine"
+name = 'bromine'
 
-symbol = "br"
+symbol = 'Br'
 
-mass = 79.904
\ No newline at end of file
+mass = 79.904

MDANSE/Data/Atoms/br79

-name = "bromine"
+name = 'bromine'
 
-symbol = "br79"
+symbol = 'Br79'
 
-mass = 78.9183376
\ No newline at end of file
+mass = 78.9183376

MDANSE/Data/Atoms/br81

-name = "bromine"
+name = 'bromine'
 
-symbol = "br81"
+symbol = 'Br81'
 
-mass = 80.916291
\ No newline at end of file
+mass = 80.916291

MDANSE/Data/Atoms/c

-name = "carbon"
+name = 'carbon'
 
-symbol = "c"
+symbol = 'C'
 
-mass = 12.0107
\ No newline at end of file
+mass = 12.0107

MDANSE/Data/Atoms/c12

-name = "carbon"
+name = 'carbon'
 
-symbol = "c12"
+symbol = 'C12'
 
-mass = 12.0
\ No newline at end of file
+mass = 12.0

MDANSE/Data/Atoms/c13

-name = "carbon"
+name = 'carbon'
 
-symbol = "c13"
+symbol = 'C13'
 
-mass = 13.00335484
\ No newline at end of file
+mass = 13.00335484

MDANSE/Data/Atoms/c14

-name = "carbon"
+name = 'carbon'
 
-symbol = "c14"
+symbol = 'C14'
 
-mass = 14.00324199
\ No newline at end of file
+mass = 14.00324199

MDANSE/Data/Atoms/ca

-name = "calcium"
+name = 'calcium'
 
-symbol = "ca"
+symbol = 'Ca'
 
-mass = 40.078
\ No newline at end of file
+mass = 40.078

MDANSE/Data/Atoms/ca40

-name = "calcium"
+name = 'calcium'
 
-symbol = "ca40"
+symbol = 'Ca40'
 
-mass = 39.9625912
\ No newline at end of file
+mass = 39.9625912

MDANSE/Data/Atoms/ca42

-name = "calcium"
+name = 'calcium'
 
-symbol = "ca42"
+symbol = 'Ca42'
 
-mass = 41.9586183
\ No newline at end of file
+mass = 41.9586183

MDANSE/Data/Atoms/ca43

-name = "calcium"
+name = 'calcium'
 
-symbol = "ca43"
+symbol = 'Ca43'
 
-mass = 42.9587668
\ No newline at end of file
+mass = 42.9587668

MDANSE/Data/Atoms/ca44

-name = "calcium"