Merge pull request #1876 from jchodera/fix-docs

Fix sphinx errors

docs-source/api-python/process-docstring.py

@@ -14,8 +14,11 @@ def process_docstring(app, what, name, obj, options, lines):
         s = m.group(1)
         if not s.startswith(linesep):
             s = linesep + s
-        newline = '|LINEBREAK|.. admonition:: Deprecated' + linesep
+        newline = '|LINEBREAK|.. admonition::|LINEBREAK|   Deprecated' + linesep
         return newline + '    ' + s.replace(linesep, linesep + '    ')
+    def repl3(m):
+        s = m.group(1)
+        return '*' + s + '*'
 
     linesep = '|LINEBREAK|'
     joined = linesep.join(lines)
@@ -23,6 +26,7 @@ def process_docstring(app, what, name, obj, options, lines):
     joined = re.sub(r'<tt><pre>((|LINEBREAK|)?.*?)</pre></tt>', repl, joined)
     joined = re.sub(r'<tt>(.*?)</tt>', repl, joined)
     joined = re.sub(r'@deprecated(.*?\|LINEBREAK\|)', repl2, joined, flags=re.IGNORECASE)
+    joined = re.sub(r'<i>(.*?)</i>', repl3, joined)
     lines[:] = [(l if not l.isspace() else '') for l in joined.split(linesep)]
 
 

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -117,22 +117,23 @@ class CharmmPsfFile(object):
 
     This structure has numerous attributes that are lists of the elements of
     this structure, including atoms, bonds, torsions, etc. The attributes are
-        - residue_list
-        - atom_list
-        - bond_list
-        - angle_list
-        - dihedral_list
-        - dihedral_parameter_list
-        - improper_list
-        - cmap_list
-        - donor_list    # hbonds donors?
-        - acceptor_list # hbond acceptors?
-        - group_list    # list of nonbonded interaction groups
+
+    - residue_list
+    - atom_list
+    - bond_list
+    - angle_list
+    - dihedral_list
+    - dihedral_parameter_list
+    - improper_list
+    - cmap_list
+    - donor_list    # hbonds donors?
+    - acceptor_list # hbond acceptors?
+    - group_list    # list of nonbonded interaction groups
 
     Additional attribute is available if a CharmmParameterSet is loaded into
     this structure.
 
-        - urey_bradley_list
+    - urey_bradley_list
 
     The lengths of each of these lists gives the pointers (e.g., natom, nres,
     etc.)
@@ -713,7 +714,7 @@ class CharmmPsfFile(object):
             solvent.
         implicitSolventSaltConc : float=0.0*u.moles/u.liter
             Salt concentration for GB simulations. Converted to Debye length
-            `kappa'
+            ``kappa``
         temperature : float=298.15*u.kelvin
             Temperature used in the salt concentration-to-kappa conversion for
             GB salt concentration term

wrappers/python/simtk/openmm/app/forcefield.py

@@ -445,17 +445,19 @@ class ForceField(object):
         generator : function
             A function that will be called when a residue is encountered that does not match an existing forcefield template.
 
-        When a residue without a template is encountered, the `generator` function is called with:
+        When a residue without a template is encountered, the ``generator`` function is called with:
 
         ::
            success = generator(forcefield, residue)
-        ```
 
-        where `forcefield` is the calling `ForceField` object and `residue` is a simtk.openmm.app.topology.Residue object.
+        where ``forcefield`` is the calling ``ForceField`` object and ``residue`` is a simtk.openmm.app.topology.Residue object.
+
+        ``generator`` must conform to the following API:
 
-        `generator` must conform to the following API:
         ::
-          Parameters
+           generator API
+
+           Parameters
            ----------
            forcefield : simtk.openmm.app.ForceField
                The ForceField object to which residue templates and/or parameters are to be added.