Added DFTB converter

Update the setup with automatic documentation build

.gitignore

 /.project
 /.pydevproject
+/build/
+*.pyc

MDANSE/App/GUI/MainFrame.py

@@ -31,6 +31,7 @@ Created on Apr 14, 2015
 '''
 
 import collections
+import operator
 import os
 import webbrowser
 
@@ -98,8 +99,10 @@ class MainFrame(wx.Frame):
         fileMenu.AppendSeparator()
         converterMenu = wx.Menu()
         self._converters = {}
-        for job in REGISTRY["job"].values():
-            if issubclass(job, Converter):
+
+        converters = [job for job in REGISTRY["job"].values() if issubclass(job,Converter)]
+        converters = sorted(converters, key = operator.attrgetter('label'))
+        for job in converters:
             item = converterMenu.Append(wx.ID_ANY,job.label)
             self._converters[job.label] = job.type
             self.Bind(wx.EVT_MENU, self.on_open_converter, item)

MDANSE/Framework/Jobs/Converters/DFTB.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 Jun 4, 2015
+
+:author: Eric C. Pellegrini
+'''
+
+from MDANSE.Framework.Jobs.Converters.Forcite import ForciteConverter
+        
+class DFTBConverter(ForciteConverter):
+    """
+    Converts a DFTB trajectory to a MMTK trajectory.
+    """
+
+    type = 'dftb'
+    
+    label = "DFTB"
\ No newline at end of file

MDANSE/Framework/Jobs/Converters/Discover.py

@@ -231,7 +231,7 @@ class DiscoverConverter(Converter):
     
     label = "Discover"
 
-    category = ('Converters',)
+    category = ('Converters','Materials Studio')
     
     ancestor = None
 

MDANSE/Framework/Jobs/Converters/Forcite.py

@@ -281,7 +281,7 @@ class ForciteConverter(Converter):
     
     label = "Forcite"
 
-    category = ('Converters',)
+    category = ('Converters','Materials Studio')
     
     ancestor = None
 

setup.py

@@ -5,15 +5,23 @@ import sys
 
 import numpy
 
-from Cython.Distutils import build_ext
+from Cython.Distutils import build_ext as cython_build_ext
 
-from distutils.core import setup, Extension
 from distutils.command.build import build
-from distutils.command.build_py import build_py
-from distutils.command.build_scripts import build_scripts 
+from distutils.core import setup, Extension
 from distutils.sysconfig import get_config_vars
 from distutils.util import convert_path
 
+try:
+    import sphinx
+except ImportError:
+    sphinx = None
+
+try:
+    import stdeb
+except ImportError:
+    stdeb = None
+
 #################################
 # Modules variables
 #################################
@@ -148,6 +156,7 @@ PACKAGE_DATA = find_package_data(where='MDANSE', package='MDANSE', show_ignored=
 #################################
 
 DATA_FILES = []
+DATA_FILES.extend(find_data('Doc',exclude=[],prefix='conf_'))
 
 #################################
 # Scripts section
@@ -155,23 +164,17 @@ DATA_FILES = []
 
 SCRIPTS = []
 SCRIPTS.append(os.path.join(SCRIPTS_PATH,'mdanse'))
+SCRIPTS.append(os.path.join(SCRIPTS_PATH,'mdanse_gui'))
 
 #################################
 # Documentation
 #################################
 
-import sphinx.apidoc
-import sphinx.setup_command
-
-class BuildDoc(sphinx.setup_command.BuildDoc):
-
-    user_options = sphinx.setup_command.BuildDoc.user_options + [('doctype=',None,'specify the type of documentation to build ("api" or "help")'),]
-
-    def initialize_options(self):
+if sphinx:
+    import sphinx.apidoc
+    import sphinx.setup_command
 
-        sphinx.setup_command.BuildDoc.initialize_options(self)
-        
-        self.doctype='api'
+    class mdanse_build_doc(sphinx.setup_command.BuildDoc):
                               
         def run(self):
             
@@ -179,10 +182,10 @@ class BuildDoc(sphinx.setup_command.BuildDoc):
                     
             buildDir = os.path.abspath(build.build_lib)
 
-        sphinxDir = os.path.join(build.build_base,'sphinx',self.doctype)
-        
             sys.path.insert(0,buildDir)
 
+            sphinxDir = os.path.join(build.build_base,'sphinx',self.doctype)
+                                 
             metadata = self.distribution.metadata
      
             sphinx.apidoc.main(['',
@@ -196,10 +199,12 @@ class BuildDoc(sphinx.setup_command.BuildDoc):
                                 os.path.join(buildDir,'MDANSE'),
                                 os.path.join(buildDir,'MDANSE','Externals')])
                  
+            curDir = os.getcwd()
+                 
             import shutil
-        shutil.copy(os.path.join('Doc','conf_%s.py' % self.doctype),os.path.join(sphinxDir,'conf.py'))
-        shutil.copy(os.path.join('Doc','mdanse_logo.png'),os.path.join(sphinxDir,'_static'))
-        shutil.copy(os.path.join('Doc','layout.html'),os.path.join(sphinxDir,'_templates'))
+            shutil.copy(os.path.join(curDir,'Doc','conf_%s.py' % self.doctype),os.path.join(sphinxDir,'conf.py'))
+            shutil.copy(os.path.join(curDir,'Doc','mdanse_logo.png'),os.path.join(sphinxDir,'_static'))
+            shutil.copy(os.path.join(curDir,'Doc','layout.html'),os.path.join(sphinxDir,'_templates'))
      
             # The directory where the rst files are located.
             self.source_dir = sphinxDir
@@ -211,57 +216,31 @@ class BuildDoc(sphinx.setup_command.BuildDoc):
             
             self.finalize_options()
                                                      
-        try:
             sphinx.setup_command.BuildDoc.run(self)
-        except UnicodeDecodeError:
-            print >>sys.stderr, "ERROR: unable to build documentation because Sphinx do not handle source path with non-ASCII characters. Please try to move the source package to another location (path with *only* ASCII characters)."            
                  
             sys.path.pop(0)
             
-class BuildHelp(sphinx.setup_command.BuildDoc):
-
-    def run(self):
-        
-        build = self.get_finalized_command('build')
+    class mdanse_build_help(mdanse_build_doc):
         
-        buildDir = os.path.abspath(build.build_lib)
+        doctype = 'help'
 
-        HelpDir = os.path.join(build.build_base,'sphinx','Help')
+    class mdanse_build_api(mdanse_build_doc):
         
-        sys.path.insert(0,buildDir)
-        
-        metadata = self.distribution.metadata
+        doctype = 'api'
 
-        sphinx.apidoc.main(['',
-                            '-F',
-                            '--separate',
-                            '-d', '5',
-                            '-H', metadata.name,
-                            '-A', metadata.author,
-                            '-V', metadata.version,
-                            '-R', metadata.version,
-                            '-o', HelpDir,
-                            os.path.join(buildDir,'MDANSE'),
-                            os.path.join(buildDir,'MDANSE','Externals')])
-        
-        import shutil
-        shutil.copy(os.path.join('Doc','conf_help.py'),os.path.join(HelpDir,'conf.py'))
-        shutil.copy(os.path.join('Doc','mdanse_logo.png'),os.path.join(HelpDir,'_static'))
-        shutil.copy(os.path.join('Doc','layout.html'),os.path.join(HelpDir,'_templates'))
+#################################
+# Debian packaging
+#################################
 
-        # The directory where the rst files are located.
-        self.source_dir = HelpDir
-        # The directory where the conf.py file is located.
-        self.config_dir = self.source_dir
-        # The directory where the documentation will be built
-        self.build_dir = os.path.join(buildDir,'MDANSE','Doc','Help')
+class mdanse_build(build):
 
-        try:
-            sphinx.setup_command.BuildDoc.run(self)
-        except UnicodeDecodeError:
-            print >>sys.stderr, "ERROR: unable to build documentation because Sphinx do not handle source path with non-ASCII characters. Please try to move the source package to another location (path with *only* ASCII characters)."            
+    def has_sphinx(self):
+        if sphinx is None:
+            return False
+        setup_dir = os.path.dirname(os.path.abspath(__file__))
+        return os.path.isdir(os.path.join(setup_dir, 'Doc'))
     
-        sys.path.pop(0)
+    sub_commands = build.sub_commands + [('build_api', has_sphinx),('build_help',has_sphinx)]
                         
 #################################
 # Extensions section
@@ -296,47 +275,12 @@ EXTENSIONS = [Extension('MDANSE.Extensions.distance_histogram',
                         define_macros = [('qh_QHpointer','1')])
               ]
 
-class ModifiedBuildScripts(build_scripts):
-    
-    def finalize_options (self):
-
-        build_scripts.finalize_options(self)
-
-        if self.distribution.command_obj['build'].gui:
-            self.scripts.append(os.path.join(SCRIPTS_PATH,'mdanse_gui'))
-                    
-
-class ModifiedBuildPy(build_py):
-
-    def finalize_options(self):
-
-        build_py.finalize_options(self)
-
-        if self.distribution.command_obj['build'].gui:
-            self.packages.append('MDANSE.App.GUI')
-            self.packages.extend(find_packages(path=os.path.join("MDANSE","App","GUI"), base="MDANSE.App.GUI").keys())
-             
-        self.data_files = self.get_data_files()
-
-
-class ModifiedBuild(build):
-    
-    user_options = build.user_options + [('gui',None,'Build MDANSE with GUI [default]'),
-                                         ('no-gui', None, "Build MDANSE without GUI")]
-    
-    boolean_options = build.boolean_options + ['gui']
-
-    negative_opt = {'no-gui' : 'gui'}
-
-    def initialize_options(self):
-        build.initialize_options(self)
-        self.gui = 1
+CMDCLASS = {'build'     : mdanse_build,
+            'build_ext' : cython_build_ext}
 
-CMDCLASS = {'build_ext'     : build_ext,
-            'build'         : ModifiedBuild,
-            'build_py'      : ModifiedBuildPy,
-            'build_scripts' : ModifiedBuildScripts,
-            'build_doc'     : BuildDoc}
+if sphinx:
+    CMDCLASS['build_api'] = mdanse_build_api
+    CMDCLASS['build_help'] = mdanse_build_help
              
 #################################
 # The setup section
@@ -367,5 +311,4 @@ subunits can be studied.
        ext_modules      = EXTENSIONS,
        scripts          = SCRIPTS,
        cmdclass         = CMDCLASS,
-       command_options  = {'build_doc'  : {'builder':('setup.py','html')}}
-       )
+       install_requires = ['Jinja2'])