corr ref-src links to auto/Examples

hugo/content/ex/sample/particles/core-shell-particle.md

@@ -22,4 +22,4 @@ Scattering from cuboidal core-shell particles.
 {{< highlightfile file="Examples/scatter2d/CoreShellNanoparticles.py" >}}
 
 Validated through an alternative implementation that uses particle composition,
-{{% ref-src "Examples/scatter2d/CoreShellNanoparticles2.py" %}}.
+{{% ref-src "auto/Examples/scatter2d/CoreShellNanoparticles2.py" %}}.

hugo/content/py/fitting/bayesian/_index.md

@@ -16,7 +16,7 @@ To generate these images of the probability distributions of the parameters and
 {{< figscg src="/files/fitted/CornerPlotBayes.png" width="500" class="center">}}
 {{< figscg src="/files/fitted/ReflectivityBayes.png" width="500" class="center">}}
 
-run [this script]({{% ref-src "Examples/bayesian/likelihood_sampling.py" %}}).
+run [this script]({{% ref-src "auto/Examples/bayesian/likelihood_sampling.py" %}}).
 
 
 ### Explanation
@@ -27,7 +27,7 @@ We know the scattering length densities for each, and that in total there are 10
 This sample is created in the `get_sample` function.
 
 Having built the sample, it is necessary to obtain the real experimental data.
-For the above code to work locally, the following [data file]({{% ref-src "Examples/data/genx_interchanging_layers.dat.gz?inline=false" %}}) is required and the Python script (in particular the `get_real_data` function) should be adapted appropriately.
+For the above code to work locally, the following [data file]({{% ref-src "auto/Examples/data/genx_interchanging_layers.dat.gz?inline=false" %}}) is required and the Python script (in particular the `get_real_data` function) should be adapted appropriately.
 This function defined an uncertainty in the reflectivity of 10 %.
 
 The simulation is then defined in the `get_simulation` function, which is passed a series of angles, however, this may be modified to perform a Q-scan as necessary.

hugo/content/py/fitting/extended/fit-specular-data/index.md

@@ -46,4 +46,4 @@ in the BornAgain directory.
 
 {{< highlightfile file="Examples/fit/specular/FitSpecularBasics.py" >}}
 
-Data to be fitted: {{% ref-src "Examples/data/genx_interchanging_layers.dat.gz" %}}
+Data to be fitted: {{% ref-src "auto/Examples/data/genx_interchanging_layers.dat.gz" %}}

hugo/content/py/fitting/extended/fit-with-uncertainties/index.md

@@ -22,4 +22,4 @@ This example follows closely the tutorial on [Fitting reflectometry data](/py/fi
 
 {{< highlightfile file="Examples/fit/specular/FitWithUncertainties.py" >}}
 
-Data to be fitted: {{% ref-src "Examples/data/genx_interchanging_layers.dat.gz" %}}
+Data to be fitted: {{% ref-src "auto/Examples/data/genx_interchanging_layers.dat.gz" %}}

hugo/content/py/fitting/extended/real-life-reflectometry/index.md

@@ -28,4 +28,4 @@ Be patient, since it takes some time to run.
 
 {{< highlightfile file="Examples/fit/specular/RealLifeReflectometryFitting.py" >}}
 
-Data to be fitted: {{% ref-src "Examples/data/mg6a_Merged.txt.gz" %}}
+Data to be fitted: {{% ref-src "auto/Examples/data/mg6a_Merged.txt.gz" %}}

hugo/content/py/fitting/extended/reflectometry-honeycomb/index.md

@@ -148,4 +148,4 @@ As can be seen from the plot of the SLDs, the magnetization is indeed larger for
 
 {{< highlightfile file="Examples/fit/specular/Honeycomb_fit.py" >}}
 
-Reference data: {{% ref-src "Examples/data/honeycomb" %}}
+Reference data: {{% ref-src "auto/Examples/data/honeycomb" %}}

hugo/content/py/fitting/extended/reflectometry-pt-layer/index.md

@@ -100,4 +100,4 @@ a simulation is performed with our fit results and one should obtain the result
 
 {{< highlightfile file="Examples/fit/specular/Pt_layer_fit.py" >}}
 
-Data to be fitted: {{% ref-src "Examples/data/RvsQ_36563_36662.txt.gz" %}}
+Data to be fitted: {{% ref-src "auto/Examples/data/RvsQ_36563_36662.txt.gz" %}}

hugo/content/py/fitting/gisas-fit2d/index.md

@@ -27,7 +27,7 @@ to make the subsequent fitting more difficult and more realistic:
   * Detector x-axis skewed.
 
 The faked data can be found at
-{{% ref-src "Examples/data/faked-gisas1.txt.gz" %}}.
+{{% ref-src "auto/Examples/data/faked-gisas1.txt.gz" %}}.
 
 ## Fit script
 

hugo/content/ref/instr/beam/angular-divergence/index.md

@@ -20,4 +20,4 @@ In this example, a Gaussian distribution is used to spread the incident angle, w
 
 {{< highlightfile file="Examples/specular/VsGenx.py" >}}
 
-Reference data: {{% ref-src "Examples/data/genx_angular_divergence.dat.gz" %}}
+Reference data: {{% ref-src "auto/Examples/data/genx_angular_divergence.dat.gz" %}}

hugo/content/ref/instr/scan/_index.md

@@ -23,7 +23,7 @@ scan = ba.AlphaScan(n, alpha_start, alpha_stop)
 ```
 
 Usage is demonstrated by most examples in
-{{% ref-src "Examples/specular" %}}.
+{{% ref-src "auto/Examples/specular" %}}.
 
 For other sequences of $\alpha\_\text{i}$ values, use the more generic
 ```python

hugo/content/ref/sample/particle/composition/core-shell.md

@@ -32,4 +32,4 @@ opposite argument order, namely `(shell, core)`.
 
 See [Core-and-shell example](/ex/sample/core-shell-particle).
 Validated through an alternative implementation that uses particle composition,
-{{% ref-src "Examples/scatter2d/CoreShellNanoparticles2.py" %}}.
+{{% ref-src "auto/Examples/scatter2d/CoreShellNanoparticles2.py" %}}.

hugo/content/ref/sample/particle/ff/hard/bipyramid4.md

@@ -56,7 +56,7 @@ Scattering by uncorrelated, oriented bipyramids for horizontal incidence. Rotati
 
 <img src="/img/draw/ff/3d/Bipyramid4.png">
 
-Generated by {{% ref-src "Examples/ff/Bipyramid4.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/Bipyramid4.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/box.md

@@ -56,7 +56,7 @@ Scattering by uncorrelated, oriented boxes for horizontal incidence. Rotation ar
 
 <img src="/img/draw/ff/3d/Box.png">
 
-Generated by {{% ref-src "Examples/ff/Box.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/Box.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/cantellatedcube.md

@@ -50,7 +50,7 @@ Scattering by uncorrelated, oriented cantellated cubes for horizontal incidence.
 
 <img src="/img/auto/ff/CantellatedCube.png">
 
-Generated by {{% ref-src "Examples/ff/CantellatedCube.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/CantellatedCube.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/cone.md

@@ -58,7 +58,7 @@ Scattering by uncorrelated, oriented cones for horizontal incidence. Rotation ar
 
 <img src="/img/draw/ff/3d/Cone.png">
 
-Generated by {{% ref-src "Examples/ff/Cone.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/Cone.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/cylinder.md

@@ -53,7 +53,7 @@ Scattering by uncorrelated, oriented cylinders for horizontal incidence. Rotatio
 
 <img src="/img/draw/ff/3d/Cylinder.png">
 
-Generated by {{% ref-src "Examples/ff/Cylinder.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/Cylinder.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/dodecahedron.md

@@ -47,7 +47,7 @@ Scattering by uncorrelated, oriented truncated dodecahedra for horizontal incide
 
 <img src="/img/draw/ff/3d/Dodecahedron.png">
 
-Generated by {{% ref-src "Examples/ff/Dodecahedron.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/Dodecahedron.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/ellipsoidalcylinder.md

@@ -52,7 +52,7 @@ Scattering by uncorrelated, oriented cylinders for horizontal incidence. Rotatio
 
 <img src="/img/draw/ff/3d/EllipsoidalCylinder.png">
 
-Generated by {{% ref-src "Examples/ff/EllipsoidalCylinder.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/EllipsoidalCylinder.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/hemiellipsoid.md

@@ -55,7 +55,7 @@ Scattering by uncorrelated, oriented hemiellipsoids for horizontal incidence. Ro
 
 <img src="/img/draw/ff/3d/HemiEllipsoid.png">
 
-Generated by {{% ref-src "Examples/ff/HemiEllipsoid.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/HemiEllipsoid.py" %}}.
 
 #### History
 

hugo/content/ref/sample/particle/ff/hard/horizontalcylinder.md

@@ -61,7 +61,7 @@ Scattering by uncorrelated, oriented horizontal truncated cylinders for horizont
 
 <img src="/img/auto/ff/HorizontalCylinder.png">
 
-Generated by {{% ref-src "Examples/ff/HorizontalCylinder.py" %}}.
+Generated by {{% ref-src "auto/Examples/ff/HorizontalCylinder.py" %}}.
 
 #### History