re #9649 A few warnings, but more importanly a catergory for functions

Code/Mantid/docs/source/algorithms/Fit-v1.rst

@@ -48,7 +48,7 @@ set before any other.
 
 The function and the initial values for its parameters are set with the
 Function property. A function can be simple or composite. A `simple
-function <:Category:Fit_functions>`__ has a name registered with Mantid
+function <../categories/Functions.html>`__ has a name registered with Mantid
 framework. The Fit algorithm creates an instance of a function by this
 name. A composite function is an arithmetic sum of two or more functions
 (simple or composite). Each function has a number of named parameters,
@@ -74,7 +74,7 @@ To use a simple function for a fit set its name and initial parameter
 values using the Function property. This property is a comma separated
 list of name=value pairs. The name of the first name=value pairs must be
 "name" and it must be set equal to the name of one of a `simple
-function <:Category:Fit_functions>`__. This name=value pair is followed
+function <../categories/Functions.html>`__. This name=value pair is followed
 by name=value pairs specifying values for the parameters of this
 function. If a parameter is not set in Function it will be given its
 default value defined by the function. All names are case sensitive. For
@@ -96,7 +96,7 @@ are created when the Formula attribute is set. It is important that
 Formula is defined before initializing the parameters.
 
 A list of the available simple functions can be found
-`here <:Category:Fit_functions>`__.
+`here <../categories/Functions.html>`__.
 
 Setting a composite function
 ############################
@@ -105,11 +105,11 @@ A composite function is a sum of simple functions. It does not have a
 name. To define a composite function set a number of simple functions in
 the Function property. Each simple function definition must be separated
 by a semicolon ';'. For example fitting two Gaussians on a linear
-background might look like this:
+background might look like this::
 
-| ``Function: "name=LinearBackground, A0=0.3; ``
-| ``           name=Gaussian, PeakCentre=4.6, Height=10, Sigma=0.5;``
-| ``           name=Gaussian, PeakCentre=7.6, Height=8, Sigma=0.5"``
+   Function: "name=LinearBackground, A0=0.3; 
+              name=Gaussian, PeakCentre=4.6, Height=10, Sigma=0.5;
+              name=Gaussian, PeakCentre=7.6, Height=8, Sigma=0.5"
 
 Setting ties
 ############

Code/Mantid/docs/source/algorithms/IQTransform-v1.rst

@@ -67,6 +67,7 @@ Usage
 
    print 'Output Y:', output.readY(0)
    print 'Output X:', output.readX(0)
+
 Output:
 
 .. testoutput:: ExZimm
@@ -88,6 +89,7 @@ Output:
 
    print 'Output Y:', output.readY(0)
    print 'Output X:', output.readX(0)
+
 Output:
 
 .. testoutput:: ExZimmBg
@@ -112,6 +114,7 @@ Output:
 
    print 'Output Y:', output.readY(0)
    print 'Output X:', output.readX(0)
+   
 Output:
 
 .. testoutput:: ExGeneral

Code/Mantid/docs/source/algorithms/Rebin2D-v1.rst

@@ -38,6 +38,7 @@ Usage
     rb = Rebin2D(wsc,[0,100,20000],[0,0.01,1.2],UseFractionalArea=True)
     print ("Bins in the X axis: %i" % rb.blocksize())
     print ("Bins in the Y axis: %i" % rb.getNumberHistograms())
+
 Output:
 
 .. testoutput:: ExUseFractionalArea
@@ -56,6 +57,7 @@ Output:
     rb = Rebin2D(wsc,[0,100,20000],[0,0.01,1.2],Transpose=True)
     print ("Bins in the X axis: %i" % rb.blocksize())
     print ("Bins in the Y axis: %i" % rb.getNumberHistograms())
+    
 Output:
 
 .. testoutput:: ExTranspose

Code/Mantid/docs/source/functions/Abragam.rst

@@ -9,3 +9,5 @@ Description
 Abragam fitting function for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times cos( 2 \pi \times {Omega} \times {x} + {Phi} ) \times \exp(-{Sigma}^2 \times Tau^2 \times {x}^2 \times ( exp ( {x} / Tau ) - 1 + {x} / Tau ) )
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/BSpline.rst

@@ -17,3 +17,5 @@ first attrbiute is 'n' which has integer type and sets the number of
 interpolation points. The parameter names have the form 'yi' where 'y'
 is letter 'y' and 'i' is the parameter's index starting from 0 and have
 the type double. Likewise, the attribute names have the form 'xi'.
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/BackToBackExponential.rst

@@ -45,3 +45,5 @@ Properties
 *Note the initial default guesses for in particular A and B are only
 based on fitting a couple of peaks in a dataset collected on the ISIS's
 HRPD instrument.*
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/BivariateNormal.rst

@@ -60,3 +60,5 @@ square or contiguous subregion of a panel
 
 The values for out in function1D are, for each pixel, the difference of
 V(see formula) and dataY(0).
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/Chebyshev.rst

@@ -31,3 +31,5 @@ index starting from 0.
 
 The other two attributes are doubles 'StartX' and 'EndX' which define
 the expansion (fitting) interval.
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/CompositeFunction.rst

@@ -61,3 +61,5 @@ To define a composite function inside a composite function enclose the
 inner one in brackets:
 
 ``name=LinearBackground;(composite=Convolution;name=Resolution;name=Lorentzian)``
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/Convolution.rst

@@ -37,3 +37,5 @@ Note that the box function is defined on interval [-5, 5]:
    :alt: Box.png
 
    Box.png
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/CubicSpline.rst

@@ -17,3 +17,5 @@ The first attrbiute is 'n' which has integer type and sets the number of
 interpolation points. The parameter names have the form 'yi' where 'y'
 is letter 'y' and 'i' is the parameter's index starting from 0 and have
 the type double. Likewise, the attribute names have the form 'xi'.
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/DiffRotDiscreteCircle.rst

@@ -129,3 +129,5 @@ Properties
 +---------+-------------+-----------+-----------------------------------------------------------------------------------------+
 
 Category:Fit_functions
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/DiffSphere.rst

@@ -63,3 +63,5 @@ Properties
 +---------+-------------+-----------+----------------------------------------------------------------------------+
 
 Category:Fit_functions
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/ExpDecay.rst

@@ -9,3 +9,5 @@ Description
 Exponential decay function is defined by
 
 .. math:: \mbox{Height}\times \exp(-\frac{x}{\mbox{Lifetime}})
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/ExpDecayMuon.rst

@@ -9,3 +9,5 @@ Description
 Exponential decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Lambda} \times {x})
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/ExpDecayOsc.rst

@@ -9,3 +9,5 @@ Description
 Oscillation exponential decay function is defined by
 
 .. math:: \mbox{A}\times \exp(-{Lambda} \times {x}) \times cos( 2 \pi \times {Frequency} \times {x} + {Phi} )
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/FlatBackground.rst

@@ -9,3 +9,5 @@ Description
 A Flat background function is defined as:
 
 :math:`y = A_0`
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/GausDecay.rst

@@ -9,3 +9,5 @@ Description
 Gaussian decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Sigma}^2 \times {x}^2 )
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/GausOsc.rst

@@ -9,3 +9,5 @@ Description
 Oscillating Gaussian decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Sigma}^2 \times {x}^2) \times cos( 2 \pi \times {Frequency} \times {x} + {Phi} )
+
+.. categories:: Functions
\ No newline at end of file

Code/Mantid/docs/source/functions/Gaussian.rst

@@ -27,3 +27,5 @@ a TOF peak:
    :alt: GaussianWithConstBackground.png
 
    GaussianWithConstBackground.png
+
+.. categories:: Functions
\ No newline at end of file