KATRIN-Experiment · Gon-na · Dec 7, 2023 · Dec 14, 2023 · Nov 16, 2023 · Dec 19, 2023
diff --git a/Documentation/gh-pages/source/compiling.rst b/Documentation/gh-pages/source/compiling.rst
@@ -1,4 +1,4 @@
-Getting starting with Kassiopiea
+Getting started with Kassiopiea
 **********************************
 
 .. contents:: On this page

diff --git a/Documentation/gh-pages/source/conf.py b/Documentation/gh-pages/source/conf.py
@@ -11,7 +11,21 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-# import sys
+
+import sys
+
+sys.path.insert(0, os.path.abspath('/Gon-na/Kassiopeia/Kassiopeia/LICENSEtest.rst'))
+
+sys.path.insert(0, os.path.abspath('/Gon-na/Kassiopeia/LICENSEtest.rst'))
+
+sys.path.insert(0, os.path.abspath('/Kassiopeia/LICENSEtest.rst'))
+
+sys.path.insert(0, os.path.abspath('/Kassiopeia/Kassiopeia/LICENSEtest.rst'))
+
+sys.path.insert(0, os.path.abspath('/home/runner/work/Kassiopeia/Kassiopeia/LICENSEtest.rst'))
+
+
+
 # sys.path.insert(0, os.path.abspath('.'))
 
 

diff --git a/Documentation/gh-pages/source/contact.rst b/Documentation/gh-pages/source/contact.rst
@@ -0,0 +1,46 @@
+
+Contact, Meeting and References
+*********************************
+
+You can `contribute changes <https://github.com/KATRIN-Experiment/Kassiopeia/compare>`_, `report issues <https://github.com/KATRIN-Experiment/Kassiopeia/issues/new>`_ and `join discussions <https://github.com/KATRIN-Experiment/Kassiopeia/discussions>`_ on Github.
+
+Join the Kassiopeia community on `Gitter <https://gitter.im/kassiopeia-simulation/community>`_.
+
+Contact
+=======
+
+*  Kasper development list: katrin-kasper@lists.kit.edu
+*  Richard Salomon: richardsalomon@uni-muenster.de
+*  Benedikt Bieringer: benedikt.b@uni-muenster.de
+
+
+
+Regular Meeting
+=======
+
+We also organize a regular meeting via Zoom. 
+
+Kassiopeia **users as well as developers** can join, ask questions, raise issues and discuss development topics. 
+It does not matter whether you are already an expert or a complete beginner. **Everyone is welcome!** 
+
+The meeting is announced via email. 
+Please register for the `mailing list <https://www.lists.kit.edu/sympa/subscribe/kassiopeia-user>`_ if you are interested. 
+
+
+References and Citation
+==========
+
+**Cite** |our paper|_\ **:**
+
+.. |our paper| replace:: **our paper**
+.. _our paper: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
+
+.. code-block:: bash
+
+    D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950)
+
+
+In addition to this user guide, *Kassiopeia* and its associated libraries have been documented extensively in several
+PhD theses. Many of these can be found under the list of KATRIN publications_.
+
+.. _publications: https://www.katrin.kit.edu/375.php
diff --git a/Documentation/gh-pages/source/external_documentation.rst b/Documentation/gh-pages/source/external_documentation.rst
diff --git a/Documentation/gh-pages/source/index.rst b/Documentation/gh-pages/source/index.rst
@@ -40,8 +40,8 @@ Welcome to Kassiopeia's documentation!
  .. toctree::
     :maxdepth: 4
 
-    Introduction <introduction.rst>
-    References, Citation and Contact <external_documentation.rst>
+    Contact, Meeting and References <contact.rst>
+    Introduction <introduction.rst> 
     Getting Started <compiling.rst>
     Examples and Tests <examples.rst>
     Configuring Your Own Simulation <configuration.rst>
@@ -52,9 +52,10 @@ Welcome to Kassiopeia's documentation!
     Visualization Techniques <visualization.rst>
     XML Bindings <bindings.rst>
     License <license.rst>
+    LicenseTEST <linktolicense.rst>
     Authors <authors.rst>
-
 
+
 
 
 
@@ -94,6 +95,9 @@ to run your first simulation! *Note: A VTK error indicates that the "VNC (Deskto
     D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950)
 
 
+In addition to this user guide, *Kassiopeia* and its associated libraries have been documented extensively in several
+PhD theses. Many of these can be found under the list of KATRIN publications_.
+
 **Docker images**
 --------------
 
@@ -106,6 +110,6 @@ The `kassiopeia/full` image comes with a JupyterLab installation, can run on Kub
 
 .. |More information| replace:: **More information**
 .. _More information: https://github.com/KATRIN-Experiment/Kassiopeia/blob/main/Docker/README.md
-
+.. _publications: https://www.katrin.kit.edu/375.php
 
 
diff --git a/Documentation/gh-pages/source/licensetest.rst b/Documentation/gh-pages/source/licensetest.rst
@@ -0,0 +1 @@
+/home/runner/work/Kassiopeia
diff --git a/Documentation/gh-pages/source/linktolicense.rst b/Documentation/gh-pages/source/linktolicense.rst
@@ -0,0 +1,23 @@
+
+
+.. include:: ../Gon-na/Kassiopeia/LICENSEtest.rst
+
+.. include:: ../Gon-na/Kassiopeia/blob/main/LICENSEtest.rst
+
+.. include:: ../Gon-na/Kassiopeia/Kassiopeia/blob/main/LICENSEtest.rst
+
+.. include:: ../Kassiopeia/LICENSEtest.rst
+
+BREAKER 0
+
+.. include:: licensetest.rst
+
+BREAKER 1
+
+.. include:: ../home/runner/work/Kassiopeia/Kassiopeia/LICENSEtest.rst
+
+
+BREAKER 2
+
+
+.. include:: license.rst
diff --git a/LICENSEtest.rst b/LICENSEtest.rst
@@ -0,0 +1,6 @@
+testlicense file
+no content HOWEVER
+
+fieldsd
+fieldsf
+fields
diff --git a/README.md b/README.md
@@ -14,8 +14,6 @@
 This simulation package by [the KATRIN collaboration](https://katrin.kit.edu) allows to run highly customizable particle tracking simulations
 along with calculations of electric and magnetic fields.
 
-**Full user guide:** http://katrin-experiment.github.io/Kassiopeia/index.html
-
 **Quick start:** [**Try it out online**](https://mybinder.org/v2/gh/KATRIN-Experiment/KassiopeiaBinder/HEAD)
 in an interactive Binder session. Open a "VNC (Desktop)" tab and a terminal tab and run
 
@@ -31,159 +29,15 @@ to run your first simulation! *Note: A VTK error indicates that the "VNC (Deskto
 D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950)
 ```
 
- Docker images
---------------
-
-**All images:** https://github.com/orgs/KATRIN-Experiment/packages
-
-The `kassiopeia/full` image comes with a JupyterLab installation, can run on Kubernetes based JupyterHubs and is also used for the "try it out online" link above.
-
-**More information:** [Docker README](Docker/README.md)
-
- System requirements:
-----------------------
-
-NOTE: Kasper requires Linux/MacOS. Windows+cygwin should work too, but has not been tested.
-
-Some dependencies are only required if certain module are compiled in.
-
-Dependencies:
-*   CMake (https://www.cmake.org) version 3.14 or higher
-*   G++ (https://gcc.gnu.org) version 6.1 or higher (if compiling with GCC)
-*   Clang++ (https://clang.llvm.org) version 3.4 or higher (if compiling with clang)
-*   Boost (https://www.boost.org) version 1.65 or higher
-*   GSL (https://www.gnu.org/software/gsl)
-*   ROOT (https://www.cern.ch/root) version 6.16 or higher
-    +   --enable-minuit2 (if you want to use KaFit)
-    +   --enable-fftw3 (if you want to use KEMField)
-
-Optional Dependencies:
-*   FFTW (https://fftw.org) version 3.3.4 or higher
-*   HDF5 (https://support.hdfgroup.org/HDF5/)
-*   Log4CXX (https://logging.apache.org/log4cxx)
-*   MPI (https://www.open-mpi.org or mpich.org)
-*   OpenCL (https://www.khronos.org/opencl), installation details depend on your system
-*   PETSc (https://mcs.anl.gov/petsc)
-*   VTK (https://www.vtk.org) version 6.1 or higher
-*   pdflatex (for making the documentation; minimum version not known)
-*   doxygen (for making the documentation; minimum version not known)
-
-### Ubuntu Linux 18.04 LTS (bionic)
-
-* Make sure to update CMake to version 3.13 or newer. See www.cmake.org or use this
-    [direct link](https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz).
-* Download ROOT libraries from cern.root.ch or use this
-    [direct link](https://root.cern/download/root_v6.18.04.Linux-ubuntu18-x86_64-gcc7.4.tar.gz).
-    Another option is to build your own version from the source files.
-* To install all build dependencies:
-    ```
-    > apt-get update -y && apt-get install -y \
-        build-essential cmake cmake-curses-gui \
-        libqt4-dev libx11-dev libxext-dev libxft-dev  libxpm-dev \
-        libboost-all-dev libfftw3-dev libgsl0-dev libhdf5-dev liblog4cxx-dev libomp-dev libopenmpi-dev \
-        libpcl-dev libsqlite3-dev libssl-dev libvtk6-dev libxml2-dev ocl-icd-opencl-dev zlib1g-dev
-    ```
-
-### Fedora Linux 31
-
-* The ROOT libraries can be installed easily with the package manager.
-* To install all build dependencies:
-    ```
-    > dnf install -y \
-        @development-tools cmake cmake-gui \
-        root-core root-io-xmlparser root-minuit2 root-spectrum \
-        vtk vtk-qt vtk-java \
-        boost-devel fftw-devel gsl-devel hdf5-devel libomp-devel libxml2-devel log4cxx-devel \
-        ocl-icd-devel openmpi-devel openssl-devel pcl-devel sqlite-devel vtk-devel zlib-devel
-    ```
-
- Installation
---------------
-
-1. Make a separate directory for the build tree, and enter that directory:
-    ```
-    > mkdir build
-    > cd build
-    ```
-
-    * Consider setting important environmental variables now.
-      Selecting a specific compiler to be configured by CMake is done for example by
-        ```
-        > export CXX=clang++
-        > export CC=clang
-        ```
-    to use the Clang/LLVM compiler, or
-        ```
-        > export CXX=g++
-        > export CC=gcc
-        ```
-    to use the GNU compiler (GCC).
-
-2. Run cmake (or ccmake, or cmake-gui, if you prefer):
-    ```
-    > cmake ..
-    > ccmake ..
-    ```
-
-    * If applicable, make any changes you need to the configuration, and
-        (re)generate the makefiles. e.g. You may want to change the install
-        prefix. (NOTE: Most users will probably want to do this.)
-
-        The default is `<Source-Directory>/install`. If you're not doing
-        a general install for your system, or if you just want to use a
-        different location, you should change `CMAKE_INSTALL_PREFIX` to
-        your desired location. Also note the `CMAKE_BUILD_TYPE`. If you
-        do not plan to debug Kasper applications, 'Release' will give you
-        the best execution performance.
-
-        If you use one of the GUI variants (ccmake or cmake-gui), you can
-        just go through a list of all the available build options. Most
-        options also have a short description. Note that some variables
-        have dependencies (e.g. `BUILD_KASSIOPEIA` will also enable
-        `BUILD_KEMFIELD`).
-
-3. Then type
-    ```
-    > make
-    ```
-    to start the build process. This can take some time, depending on the
-    modules you activated in CMake. If you have more than one CPU core on
-    your system, you can build several files in parallel:
-    ```
-        > make -j2
-    ```
-    Make sure to keep the number passed to 'make' smaller than the number
-    of actual CPU cores. Instead of 'make' you could also use 'ninja'
-    or any other build tool that works with CMake.
-
-4. Install the executables and libraries with
-    ```
-    > make install
-    ```
-    Executables are installed in the `bin/` directory, and libraries are
-    installed in the `lib/` directory (or `lib64/` on some systems.)
-
-5. Include `kasperenv.sh` in your `~/.bashrc` (or similar, depending on
-    your shell) with
-    ```
-    > source /path/to/Kasper/install/bin/kasperenv.sh
-    ```
-    This script adds the `bin/` directory to your `$PATH` so you can call
-    any Kasper executables directly from the commandline. Furthermore this
-    sets the `$KASPERSYS` environment variable to the install directory.
-
-
- Documentation
----------------
-
-1. Documentation distributed with Kasper
-    1. This `README.md` file
-    2. The Kassiopeia documentation is an HTML page hosted on GitHub
-        that will guide you through the installation process and
-        explains how to get started with your first simulation:
-        http://katrin-experiment.github.io/Kassiopeia/index.html
-
- Open Source
+**[Documentation](http://katrin-experiment.github.io/Kassiopeia/index.html)** 
+=============================================================================================
+
+* **[System requirements & installation](https://katrin-experiment.github.io/Kassiopeia/compiling.html)**
+* **[Docker images](https://github.com/orgs/KATRIN-Experiment/packages), [more information](Docker/README.md)**
+* **[Meeting & Getting help](https://katrin-experiment.github.io/Kassiopeia/discussion.html)**
+
+
+Open source
 -------------
 
 This software is distributed "as-is" under an open source license
@@ -196,24 +50,15 @@ Kassiopeia includes the following open-source libraries:
 * stl_reader (https://github.com/sreiter/stl_reader)
 
 
- Getting help
---------------
+Contact
+-----------------------
 
-Join the Kassiopeia community on Gitter: https://gitter.im/kassiopeia-simulation/community
+*  Kasper development list: katrin-kasper@lists.kit.edu
+*  Richard Salomon: richardsalomon@uni-muenster.de
+*  Benedikt Bieringer: benedikt.b@uni-muenster.de
 
-You can [contribute changes](https://github.com/KATRIN-Experiment/Kassiopeia/compare), [report issues](https://github.com/KATRIN-Experiment/Kassiopeia/issues/new) and [join discussions](https://github.com/KATRIN-Experiment/Kassiopeia/discussions) on Github.
 
-### Regular Meeting
 
-We also organize a regular meeting via Zoom. 
 
-Kassiopeia **users as well as developers** can join, ask questions, raise issues and discuss development topics. 
-It does not matter whether you are already an expert or a complete beginner. **Everyone is welcome!** 
 
-The meeting is announced via email. 
-Please register for the [mailing list](https://www.lists.kit.edu/sympa/subscribe/kassiopeia-user) if you are interested. 
 
-Primary email contacts:
-*    Kasper development list: katrin-kasper@lists.kit.edu
-*    Richard Salomon: richardsalomon@uni-muenster.de
-*    Benedikt Bieringer: benedikt.b@uni-muenster.de