Autogenerate more, and switch themes

docs-source/python-api/app.rst.jinja2

@@ -7,16 +7,9 @@ Loaders and Setup
     :toctree: generated/
     :template: class.rst
 
-    ~simtk.openmm.app.pdbfile.PDBFile
-    ~simtk.openmm.app.pdbxfile.PDBxFile
-    ~simtk.openmm.app.gromacsgrofile.GromacsGroFile
-    ~simtk.openmm.app.gromacstopfile.GromacsTopFile
-    ~simtk.openmm.app.amberinpcrdfile.AmberInpcrdFile
-    ~simtk.openmm.app.amberprmtopfile.AmberPrmtopFile
-    ~simtk.openmm.app.charmmpsffile.CharmmPsfFile
-    ~simtk.openmm.app.charmmcrdfiles.CharmmRstFile
-    ~simtk.openmm.app.charmmparameterset.CharmmParameterSet
-    ~simtk.openmm.app.desmonddmsfile.DesmondDMSFile
+{% for fileclass in fileclasses %}
+    ~{{ fileclass }}
+{% endfor %}
 
 
 Representation and Manipulation
@@ -47,4 +40,14 @@ Reporting Output
 {% for reporter in reporters %}
     ~{{ reporter }}
 {% endfor %}
-    ~simtk.openmm.app.dcdfile.DCDFile
+
+
+Extras
+~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    {% for extra in app_extras %}
+    ~{{ extra }}
+    {% endfor %}

docs-source/python-api/conf.py

@@ -44,14 +44,15 @@ pygments_style = 'sphinx'
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
 html_theme_options = {
-    'logo': 'OPENMMLogo.png',
-    'description': 'A high performance GPU molecular simulation toolkit',
-    'github_user': 'pandegroup',
-    'github_repo': 'openmm',
-    'travis_button': True,
+    # 'logo': 'OPENMMLogo.png',
+    #'description': 'A high performance GPU molecular simulation toolkit',
+    #'github_user': 'pandegroup',
+    #'github_repo': 'openmm',
+    #'travis_button': True,
 }
+html_logo = 'OPENMMLogo.png'
 
 
 # Add any paths that contain custom themes here, relative to this directory.

docs-source/python-api/library.rst.jinja2

@@ -11,6 +11,7 @@ Core Objects
     ~simtk.openmm.openmm.System
     ~simtk.openmm.openmm.Context
     ~simtk.openmm.openmm.Platform
+    ~simtk.openmm.openmm.State
 
 
 Forces

docs-source/python-api/render.py

@@ -10,23 +10,19 @@ def fullname(klass):
     return klass.__module__ + '.' + klass.__name__
 
 
-def template_variables():
+#        'integrators': [],
+#        'library_extras': [],
+#         'forces': [],
+
+def library_template_variables():
     data = {
-        'reporters': [],
-        'forces': [],
         'integrators': [],
-        'library_extras': []
+        'library_extras': [],
+        'forces': [],
     }
 
-
-    app_klasses = inspect.getmembers(app, predicate=inspect.isclass)
     mm_klasses = inspect.getmembers(mm, predicate=inspect.isclass)
 
-    # gather all Reporters
-    for name, klass in app_klasses:
-        if name.endswith('Reporter'):
-            data['reporters'].append(fullname(klass))
-
     # gather all Force subclasses
     for name, klass in mm_klasses:
         if issubclass(klass, mm.Force):
@@ -37,23 +33,54 @@ def template_variables():
         if issubclass(klass, mm.Integrator):
             data['integrators'].append(fullname(klass))
 
-    # gather all extra subclasses
+    # gather all extra subclasses in simtk.openmm.openmm
+    exclude = ['simtk.openmm.openmm.Platform', 'simtk.openmm.openmm.Context',
+              'simtk.openmm.openmm.System', 'simtk.openmm.openmm.State']
+    exclude.extend(data['forces'])
+    exclude.extend(data['integrators'])
+    exclude.extend([
+        'simtk.openmm.openmm.SwigPyIterator',
+        'simtk.openmm.openmm.OpenMMException'])
+
     for _, klass in mm_klasses:
         full = fullname(klass)
+        if full not in exclude and not klass.__name__[0].islower():
+            data['library_extras'].append(full)
 
-        if full in data['forces']:
-            continue
-        if full in data['integrators']:
-            continue
-        if full in ('simtk.openmm.openmm.Platform', 'simtk.openmm.openmm.Context',
-                    'simtk.openmm.openmm.System'):
-            continue
-        if klass.__name__[0].islower():
-            continue
-        if klass.__name__ in ['SwigPyIterator', 'OpenMMException']:
-            continue
+    return data
 
-        data['library_extras'].append(full)
+
+def app_template_variables():
+    data = {
+        'reporters': [],
+        'fileclasses': [],
+        'app_extras': [],
+    }
+
+    app_klasses = inspect.getmembers(app, predicate=inspect.isclass)
+
+    # gather all Reporters
+    for name, klass in app_klasses:
+        if name.endswith('Reporter'):
+            data['reporters'].append(fullname(klass))
+
+    # gather all classes with "File" in the name
+    for name, klass in app_klasses:
+        if 'File' in name:
+            data['fileclasses'].append(fullname(klass))
+
+    # gather all extra subclasses in simtk.openmm.app
+    exclude = ['simtk.openmm.app.topology.Topology',
+               'simtk.openmm.app.modeller.Modeller',
+               'simtk.openmm.app.forcefield.ForceField',
+               'simtk.openmm.app.simulation.Simulation']
+    exclude.extend(data['reporters'])
+    exclude.extend(data['fileclasses'])
+
+    for _, klass in app_klasses:
+        full = fullname(klass)
+        if full not in exclude and not klass.__name__[0].islower():
+            data['app_extras'].append(full)
 
     return data
 
@@ -62,7 +89,8 @@ def main():
     here = dirname(__file__)
     templateLoader = jinja2.FileSystemLoader(here)
     templateEnv = jinja2.Environment(loader=templateLoader)
-    data = template_variables()
+    data = library_template_variables()
+    data.update(app_template_variables())
 
     for template_fn in glob(join(here, '*.jinja2')):
         output_fn = splitext(template_fn)[0]