Merge branch 'doc-UP2780' into 'master'

Setup documentation

See merge request !140

doc/getting_started.rst

-``Getting started``
-~~~~~~~~~~~~~~~~~~~
+Getting started
+~~~~~~~~~~~~~~~
 
-Installation
-------------
-The ToolBox may be installed in any environment. However, it depends on the extra_data and the euxfel_bunch_pattern package, which are no official third party python modules. Within environments where the latter are not present, they need to be installed by hand.
+Toolbox Installation
+--------------------
 
-Furthermore, as long as the ToolBox is not yet added to one of our custom environments, it needs to be installed locally. Activate your preferred environment and check installation of scs_toolbox by typing:
+Recommended: Proposal Environment setup
++++++++++++++++++++++++++++++++++++++++
+
+The proposal specific environment is installed by launching in a shell
+terminal on Maxwell:
+
+.. code:: bash
+
+    module load exfel exfel_anaconda3
+    scs-activate-toolbox-kernel --proposal 2780
+
+where in this example 2780 is the proposal number. After this and refreshing the
+browser, a new kernel named ``SCS Toolbox (p002780)`` is available and should
+be used to run jupyter notebooks on the Maxwell Jupyter hub.
+
+Alternative: Manual ToolBox Installation
+++++++++++++++++++++++++++++++++++++++++
+
+The ToolBox may be installed in any environment. However, it depends on the
+extra_data and the euxfel_bunch_pattern package, which are no official third
+party python modules. Within environments where the latter are not present, they
+need to be installed by hand.
+
+Furthermore, as long as the ToolBox is not yet added to one of our custom
+environments, it needs to be installed locally. Activate your preferred
+environment and check installation of scs_toolbox by typing:
 
 .. code:: bash
 
     pip show toolbox_scs
 
-If the toolbox has been installed in your home directory previously, everything is set up. Otherwise it needs to be installed (only once). In that case enter following command from the the ToolBox top-level directory:
+If the toolbox has been installed in your home directory previously, everything
+is set up. Otherwise it needs to be installed (only once). In that case enter
+following command from the the ToolBox top-level directory:
 
 .. code:: bash
 
     pip install --user ".[maxwell]"
 
-Alternatively, use the -e flag for installation to install the package in development mode.
+Alternatively, use the -e flag for installation to install the package in
+development mode.
 
 .. code:: bash
 
     pip install --user -e ".[maxwell]"
+
+Transferring Data
+-----------------
+
+The DAQ system save data on the online cluster. To analyze data on the
+Maxwell offline cluster, they need to be transferred there. This is achieved by
+login at:
+
+https://in.xfel.eu/metadata
+
+and then navigating to the proposal, then to the ``Runs`` tab from where runs can
+be transferred to the offline cluster by marking them as ``Good`` in the
+``Data Assessment``. Depending on the amount of data in the run, this can take a
+while.
+
+.. image:: metadata.png
+
+Processing Data
+---------------
+
+On the Maxwell Jupyter hub:
+
+https://max-jhub.desy.de
+
+notebooks can be executed using the corresponding Proposal Environment
+kernel or the ``xfel`` kernel if the toolbox was manually installed. For quick
+startup, example notebooks (.ipynb files) can be directly downloaded from the
+:ref:`How to's` section by clicking on the ``View page source``.

doc/howtos.rst

-``How to's``
-~~~~~~~~~~~~
+.. _how to's:
+
+How to's
+~~~~~~~~
 
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