Documentation: Seperate file for links

Gon-na · Apr 12, 2024 · f5ad1cc · f5ad1cc
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diff --git a/Documentation/gh-pages/source/conf.py b/Documentation/gh-pages/source/conf.py
@@ -63,7 +63,15 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+
+# Exclude link file
+exclude_patterns = ['links.rst']
+
+# make rst_epilog a variable, so you can add other epilog parts to it
+rst_epilog =""
+# Read link all targets from file
+with open('links.rst') as f:
+     rst_epilog += f.read()
 
 highlight_language = ''
 

diff --git a/Documentation/gh-pages/source/configuring_simulation.rst b/Documentation/gh-pages/source/configuring_simulation.rst
@@ -65,15 +65,3 @@ declared before their first use.
      configuring_simulation_messagingsystem
      configuring_simulation_pitfalls
 
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
diff --git a/Documentation/gh-pages/source/configuring_simulation_expressions.rst b/Documentation/gh-pages/source/configuring_simulation_expressions.rst
@@ -79,16 +79,3 @@ natively understood by TinyExpr_. The standard functions (and mathematical const
 +-------------+---------------+--------------------------+------------------------------------------------+
 | ``pi``      | ``M_PI``      | ``TMath::E()``           | Fundamental constant.                          |
 +-------------+---------------+--------------------------+------------------------------------------------+
-
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
diff --git a/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst b/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst
@@ -162,14 +162,3 @@ redirecting output to a log file, or customizing the message format.
     In *Kassiopeia*, *KEMField* and *KGeoBag*, most messages use the *KMessage* interface.
 
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
diff --git a/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst b/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst
@@ -41,15 +41,3 @@ the message::
 Depening on where the element is referenced, the error may look different. For example::
 
     [KSOBJECT ERROR MESSAGE] component <Y> could not build command named <X> (invalid child component)
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
diff --git a/Documentation/gh-pages/source/configuring_simulation_statements.rst b/Documentation/gh-pages/source/configuring_simulation_statements.rst
@@ -256,17 +256,6 @@ included by the syntax:
 As shown above, a comment can span multiple lines. Any text between ``<!-- ... -->`` is ignored by the XML initializer,
 including any XML elements. This makes it possible to quickly comment out parts of the file, e.g. for debugging.
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
 
 
 .. rubric:: Footnotes

diff --git a/Documentation/gh-pages/source/contact.rst b/Documentation/gh-pages/source/contact.rst
@@ -48,6 +48,3 @@ In addition to this user guide, *Kassiopeia* and its associated libraries have b
 PhD theses. Many of these can be found under the list of KATRIN publications_.
 
 
-
-.. _publications: https://www.katrin.kit.edu/375.php
-.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
diff --git a/Documentation/gh-pages/source/examples.rst b/Documentation/gh-pages/source/examples.rst
@@ -196,13 +196,4 @@ also distributed with Kassiopeia, and are described in the following table.
 +-----------------------------------------+---------------------------------------------------------------+
 
 
-
-
-.. _VTK: http://www.vtk.org/
-.. _Paraview: http://www.paraview.org/
-.. _TBrowser: https://root.cern.ch/doc/master/classTBrowser.html
-.. _PyROOT: https://root.cern/manual/python/
-.. _uproot: https://pypi.org/project/uproot/
-.. _STL: https://en.wikipedia.org/wiki/STL_%28file_format%29
-
 .. [*] D. Furse *et al.* (2017) New J. Phys. **19** 053012, `doi:10.1088/1367-2630/aa6950 <https://doi.org/10.1088/1367-2630/aa6950>`_
diff --git a/Documentation/gh-pages/source/index.rst b/Documentation/gh-pages/source/index.rst
@@ -129,10 +129,3 @@ For more information and a guide on how to set up `Kassiopeia` see chapter :ref:
 
 
 
-
-.. _`Try it out online`: https://mybinder.org/v2/gh/KATRIN-Experiment/KassiopeiaBinder/HEAD
-.. _`the KATRIN collaboration`: https://katrin.kit.edu
-.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
-.. _publications: https://www.katrin.kit.edu/375.php
-
-
diff --git a/Documentation/gh-pages/source/introduction.rst b/Documentation/gh-pages/source/introduction.rst
@@ -45,5 +45,3 @@ Furthermore, the object oriented approach of *Kassiopeia* provides a clear path
 certain specific features in their own novel applications. Code contributions that extend *Kassiopeia's* functionality
 can be submitted through GitHub and are always welcome.
 
-
-.. _KATRIN: https://www.katrin.kit.edu
diff --git a/Documentation/gh-pages/source/kassiopeia_generation.rst b/Documentation/gh-pages/source/kassiopeia_generation.rst
@@ -233,16 +233,3 @@ pre-existing terminator might be useful for their purpose. As will be explained
 terminators dynamically during the simulation. This allows a very flexible configuration of particle termination.
 
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
diff --git a/Documentation/gh-pages/source/kassiopeia_navigation.rst b/Documentation/gh-pages/source/kassiopeia_navigation.rst
@@ -118,17 +118,3 @@ nesting of the navigation elements should follow the same order as the underlyin
 
 
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kassiopeia_output.rst b/Documentation/gh-pages/source/kassiopeia_output.rst
@@ -476,18 +476,3 @@ The following suffixes are available for the vector and matrix types.
 | Trace              | ``trace``                           | ``KThreeMatrix`` |
 +--------------------+-------------------------------------+------------------+
 
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kassiopeia_propagation.rst b/Documentation/gh-pages/source/kassiopeia_propagation.rst
@@ -278,18 +278,3 @@ Similarly, one may use the following code to employ fully specular reflection:
 
 In order for this interaction to operate on any particles it must be associated with a surface in the simulation command
 structure.
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kassiopeia_simulation.rst b/Documentation/gh-pages/source/kassiopeia_simulation.rst
@@ -37,18 +37,3 @@ modify the actual objects used during the course of a simulation.
 Following the declaration of ``ks_simulation``, the closing tag ``</kassiopeia>`` is placed to complete the simulation
 configuration. When this tag is encountered by the XML parser, it triggers the simulation to run.
 
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kassiopeia_visualization.rst b/Documentation/gh-pages/source/kassiopeia_visualization.rst
@@ -130,19 +130,3 @@ Using Python
 
 The track painters export VTK_ output files that can be visualized in Python with the PyVista_ module, as shown in :ref:`kgeobag-visualization`.
 
-
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _Gnuplot: http://www.gnuplot.info/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kemfield_fields.rst b/Documentation/gh-pages/source/kemfield_fields.rst
@@ -138,18 +138,6 @@ A complete list and set of examples of the XML bindings for magnetic fields can
 Further documentation on the exact methods and parameters used in *KEMField* can be found in [2] and [3].
 
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _PyVista: https://www.pyvista.org/
 
 
 .. rubric:: Footnotes

diff --git a/Documentation/gh-pages/source/kemfield_visualization.rst b/Documentation/gh-pages/source/kemfield_visualization.rst
@@ -96,19 +96,3 @@ the dimensions is equal to zero.) To speed up the computation, it is possible to
 (``compute_gradient``) or electric field (``compute_field``), or to make use of existing symmetries in either dimension.
 Note that the symmetry is not checked against the actual geometry, so it's a responsibility of the user to set this up
 correctly.
-
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _PyVista: https://www.pyvista.org/
-
-
diff --git a/Documentation/gh-pages/source/kgeobag_complex_shapes.rst b/Documentation/gh-pages/source/kgeobag_complex_shapes.rst
@@ -451,17 +451,3 @@ An XML example is as follows:
 
 
 
-
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-
diff --git a/Documentation/gh-pages/source/kgeobag_geometry.rst b/Documentation/gh-pages/source/kgeobag_geometry.rst
@@ -317,17 +317,3 @@ supported shapes are the cylinder surface, describing a simple coil, and the rod
 For further demonstrations of the possible geometry extensions please see the provided example XML files located
 at :gh-code:`KGeoBag/Source/XML/Examples`.
 
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _PyVista: https://www.pyvista.org/
-
diff --git a/Documentation/gh-pages/source/kgeobag_simple_shapes.rst b/Documentation/gh-pages/source/kgeobag_simple_shapes.rst
@@ -1052,15 +1052,3 @@ The parameters are:
 - z_mesh_count: z mesh count
 - z_mesh_power: z mesh power
 
-
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
diff --git a/Documentation/gh-pages/source/kgeobag_visualization.rst b/Documentation/gh-pages/source/kgeobag_visualization.rst
@@ -77,15 +77,3 @@ create a slice that transforms the 3D surfaces into 2D lines.
     plt.ylim(ylim)
 
 
-.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
-.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
-.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
-.. _Paraview: http://www.paraview.org/
-.. _ROOT: https://root.cern.ch/
-.. _VTK: http://www.vtk.org/
-.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
-.. _XML: https://www.w3.org/TR/xml11/
-.. _Xpath: https://www.w3.org/TR/xpath-10/
-.. _TinyExpr: https://github.com/codeplea/tinyexpr/
-.. _Log4CXX: https://logging.apache.org/log4cxx/
-.. _PyVista: https://www.pyvista.org/
Original file line number	Diff line number	Diff line change
Expand Up		@@ -48,6 +48,3 @@ In addition to this user guide, Kassiopeia and its associated libraries have b
		PhD theses. Many of these can be found under the list of KATRIN publications_.



		.. _publications: https://www.katrin.kit.edu/375.php
		.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
Original file line number	Diff line number	Diff line change
Expand Up		@@ -45,5 +45,3 @@ Furthermore, the object oriented approach of Kassiopeia provides a clear path
		certain specific features in their own novel applications. Code contributions that extend Kassiopeia's functionality
		can be submitted through GitHub and are always welcome.


		.. _KATRIN: https://www.katrin.kit.edu