Merge pull request #160 from stevenhua0320/docs-fix

docs: fix sphinx build for manual part fix

Author: sbillinge

docs/source/license.rst

@@ -12,17 +12,19 @@ If you use this program to do productive scientific research that leads
 to publication, we ask that you acknowledge use of the program by citing
 the following paper in your publication:
 
-        C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen
-        and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure
-        in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)
+```
+C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen
+and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure
+in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)
+```
 
 Copyright 2006-2007, Board of Trustees of Michigan State University,
-Copyright 2008-2025, Board of Trustees of Columbia University in the
-city of New York.  (Copyright holder indicated in each source file).
+Copyright 2008-2025, Board of Trustees of Columbia University in the city of New York.
+(Copyright holder indicated in each source file).
 
 For more information please visit the project web-page:
-    http://www.diffpy.org/
-or email Prof. Simon Billinge at [email protected]
+[http://www.diffpy.org/](http://www.diffpy.org/)
+or email Prof. Simon Billinge at [[email protected]](mailto:[email protected])
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

news/docs-fix.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: Fix sphinx warning with manual fix
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/pdffit2/pdffit.py

@@ -214,8 +214,7 @@ def read_data(self, data, stype, qmax, qdamp):
 
         data    -- name of file from which to read data
         stype   -- 'X' (xray) or 'N' (neutron)
-        qmax    -- Q-value cutoff used in PDF calculation.
-                   Use qmax=0 to neglect termination ripples.
+        qmax    -- Q-value cutoff used in PDF calculation. Use qmax=0 to neglect termination ripples.
         qdamp   -- instrumental Q-resolution factor
 
         Raises: IOError when the file cannot be read from disk
@@ -230,8 +229,7 @@ def read_data_string(self, data, stype, qmax, qdamp, name=""):
 
         data    -- string containing the contents of the data file
         stype   -- 'X' (xray) or 'N' (neutron)
-        qmax    -- Q-value cutoff used in PDF calculation.
-                   Use qmax=0 to neglect termination ripples.
+        qmax    -- Q-value cutoff used in PDF calculation. Use qmax=0 to neglect termination ripples.
         qdamp   -- instrumental Q-resolution factor
         name    -- tag with which to label data
         """
@@ -250,8 +248,7 @@ def read_data_lists(
 
         All lists must be of the same length.
         stype       -- 'X' (xray) or 'N' (neutron)
-        qmax        -- Q-value cutoff used in PDF calculation.
-                       Use qmax=0 to neglect termination ripples.
+        qmax        -- Q-value cutoff used in PDF calculation. Use qmax=0 to neglect termination ripples.
         qdamp       -- instrumental Q-resolution factor
         r_data      -- list of r-values
         Gr_data     -- list of G(r) values
@@ -298,9 +295,9 @@ def alloc(self, stype, qmax, qdamp, rmin, rmax, bin):
 
         The structure from which to calculate the PDF must first be imported
         with the read_struct() or read_struct_string() method.
+
         stype   -- 'X' (xray) or 'N' (neutron)
-        qmax    -- Q-value cutoff used in PDF calculation.
-                   Use qmax=0 to neglect termination ripples.
+        qmax    -- Q-value cutoff used in PDF calculation. Use qmax=0 to neglect termination ripples.
         qdamp   -- instrumental Q-resolution factor
         rmin    -- minimum r-value of calculation
         rmax    -- maximum r-value of calculation
@@ -494,24 +491,29 @@ def constrain(self, var, par, fcon=None):
         """Constrain(var, par[, fcon]) --> Constrain a variable to a parameter.
 
         A variable can be constrained to a number or equation string.
-        var     -- variable to constrain, such as x(1)
-        par     -- parameter which to constrain the variable. This can be
-                   an integer or an equation string containing a reference
-                   to another parameter. Equation strings use standard c++
-                   syntax. The value of a constrained parameter is accessed
-                   as @p in an equation string, where p is the parameter.
-                   e.g.
-                   >>>  constrain(x(1), 1)
-                   >>>  constrain(x(2), "0.5+@1")
-        fcon    -- 'USER', 'IDENT', 'FCOMP', or 'FSQR'
-                   this is an optional parameter, and I don't know how it is
-                   used!
 
-        Raises:
-            pdffit2.constraintError if a constraint is bad
-            pdffit2.unassignedError if variable does not yet exist
-            ValueError if variable index does not exist (e.g. lat(7))
+        :param var: variable to constrain, such as x(1)
+        :param par: parameter which to constrain the variable. This can be an
+                    integer or an equation string containing a reference to
+                    another parameter. Equation strings use standard C++
+                    syntax. The value of a constrained parameter is accessed
+                    as ``@p`` in an equation string, where ``p`` is the
+                    parameter.
+        :type par: int or str
+        :param fcon: 'USER', 'IDENT', 'FCOMP', or 'FSQR'. This is an optional
+                     parameter; usage is currently unclear.
+        :type fcon: str
+
+        Example::
+
+            >>> constrain(x(1), 1)
+            >>> constrain(x(2), "0.5+@1")
+
+        :raises pdffit2.constraintError: if a constraint is bad
+        :raises pdffit2.unassignedError: if variable does not yet exist
+        :raises ValueError: if variable index does not exist (e.g. lat(7))
         """
+
         var_ref = self.__getRef(var)
         varnc = _convertCallable(var)
         if fcon: