Restructure user documentation

Jürgen Knödlseder
1 parent 5f76923a
Showing 24 changed files with 36 additions and 578 deletions
doc/source/admin/download.rst
doc/source/admin/index.rst
doc/source/admin/install_conda.rst
doc/source/admin/install_devel.rst
doc/source/admin/install_source.rst
doc/source/admin/release_history/index.rst
doc/source/conf.py
doc/source/develop/coding/coding.rst
doc/source/develop/index.rst
doc/source/help/index.rst
doc/source/users/howto/index.rst
doc/source/users/index.rst
doc/source/users/quickstart.rst
doc/source/users/user_manual/manual/index.rst → doc/source/users/tutorial/index.rst
doc/source/users/user_manual/manual/linalg.rst → doc/source/users/tutorial/linalg.rst
doc/source/users/howto/sky/convert_coordinates.rst → doc/source/users/tutorial/sky/convert_coordinates.rst
doc/source/users/howto/sky/convert_projections.rst → doc/source/users/tutorial/sky/convert_projections.rst
doc/source/users/howto/sky/index.rst → doc/source/users/tutorial/sky/index.rst
doc/source/users/user_manual/getting.rst
doc/source/users/user_manual/index.rst
-.. _sec_download:
+.. _download:
  
 Download
 ========
@@ -7,7 +7,7 @@ The latest GammaLib release is
 `gammalib-1.6.0 <http://cta.irap.omp.eu/ctools/releases/gammalib/gammalib-1.6.0.tar.gz>`_
 (29 May 2019).
  
-Below a list of older GammaLib releases. Please read the :ref:`sec_release` to
+Below a list of older GammaLib releases. Please read the :ref:`release` to
 learn more about new features and corrected bugs in a given release.
  
 To download an older release, click on the corresponding release number:
-.. _sec_admin:
+.. _admin:
  
 Getting GammaLib
 ================
-.. _sec_install_conda:
+.. _install_conda:
  
 Installing via Anaconda
 =======================
-.. _sec_install_devel:
+.. _install_devel:
  
 Installing the development version
 ==================================
@@ -16,7 +16,7 @@ Download the source tarball from the following link
  
 - `GammaLib <http://cta.irap.omp.eu/ctools/releases/gammalib/gammalib-1.7.0.dev.tar.gz>`_
  
-and follow the instructions on :ref:`sec_install_source`.
+and follow the instructions on :ref:`install_source`.
  
  
 Git repository
@@ -62,7 +62,7 @@ the following command sequence (the code will be installed into the
    $ export GAMMALIB=/usr/local/gamma
    $ source $GAMMALIB/bin/gammalib-init.sh
  
-Please read the :ref:`sec_install_source` section if you need more information
+Please read the :ref:`install_source` section if you need more information
 on how to install GammaLib.
  
 .. note::
-.. _sec_install_source:
+.. _install_source:
  
 Installation from source code
 =============================
  
 Compiling GammaLib from source is the recommended method to install the package
 in case that you do not use Anaconda (if you use Anaconda, please follow
-the instructions at :ref:`sec_install_conda`, and better do not try to compile
+the instructions at :ref:`install_conda`, and better do not try to compile
 the source code against your Anaconda Python installation). You also need to
 compile from source if you want to use the development version of GammaLib.
  
-.. _sec_release:
+.. _release:
  
 Release History
 ===============
@@ -48,7 +48,7 @@ master_doc = &#39;contents&#39;
  
 # General information about the project.
 project = u'GammaLib'
-copyright = u'2006-2016, GammaLib developers'
+copyright = u'2006-2019, GammaLib developers'
  
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -177,7 +177,7 @@ The class definition is structured in several sections:
  
 Note that most classes will derive from the abstract interface class
 :doxy:`GBase` which imposes the implementation of the :doxy:`GBase::clear`, the
-:doxy`GBase::clone` and the :doxy:`GBase::print` methods.
+:doxy:`GBase::clone` and the :doxy:`GBase::print` methods.
  
 The definition of pure virtual methods should be done in a section that
 is separate from the methods that are implemented.
@@ -425,4 +425,4 @@ class extensions. Here an example:
 Note that the access operators perform explicit range checking because the
 ``[]`` operators used do not any range checking. In addition, in this was
 the Python operator names ``__getitem__()`` and ``__setitem__()`` can be
-specified in the exception.
 \ No newline at end of file
+specified in the exception.
-.. _sec_develop:
+.. _develop:
  
 Developer documentation
 =======================
-.. _sec_help:
+.. _help:
  
 Getting Help
 ============
-======
-How To
-======
-
-.. toctree::
-   :maxdepth: 1
-
-   sky/index
-
-
-.. _sec_users:
+.. _users:
  
 User Documentation
 ==================
@@ -8,4 +8,4 @@ User Documentation
  
    quickstart
    user_manual/index
-   howto/index
+   tutorial/index
@@ -58,7 +58,6 @@ Now let&#39;s append a model to this container. For this, type:
    === GModelSky ===
     Name ......................:
     Instruments ...............: all
-    Instrument scale factors ..: unity
     Observation identifiers ...: all
     Model type ................: PointSource
     Model components ..........: "PointSource" * "PowerLaw" * "Constant"
@@ -74,13 +73,13 @@ Now let&#39;s append a model to this container. For this, type:
      Normalization ............: 1 (relative value) (fixed,scale=1,gradient)
  
 With this sequence of commands you first defined a sky direction in
-celestial coordinates using ``GSkyDir``. You may recognise that this
+celestial coordinates using :doxy:`GSkyDir`. You may recognise that this
 is the position of the Crab. You then used this position to define the
-spatial component of a sky model using ``GModelSpatialPointSource``. As the name
+spatial component of a sky model using :doxy:`GModelSpatialPointSource`. As the name
 suggests, the spatial component is a point source. Next, you defined the
-spectral component using ``GModelSpactralPlaw``: a power law with
+spectral component using :doxy:`GModelSpactralPlaw`: a power law with
 normalisation of 1 and a spectral index of -2. Then, you combined the spatial
-and spectral components in a sky model using ``GModelSky``. And
+and spectral components in a sky model using :doxy:`GModelSky`. And
 finally you appended the sky model to the model container allocated
 previously using the append method. When you then print the model
 container you see that is contains now one model with 6 parameters.
@@ -99,7 +98,7 @@ Suppose you want to change one of these parameters, such as the
    >>> models[0]['PivotEnergy'].value(1e6)
    >>> print(models)
    ...
-   PivotEnergy ..............: 1e+06 MeV (fixed,scale=100,gradient)
+   PivotEnergy ..............: 1000000 MeV (fixed,scale=100,gradient)
    ...
  
 As the units are MeV, we had to specify a value of 1e6 to set the
-Users manual
-============
+Tutorials
+=========
  
 .. toctree::
    :maxdepth: 2
  
-   intro
+   sky/index
    linalg
-.. _sec_sky_convert_coordinates:
-
 How to convert a sky coordinate from celestial to Galactic?
 ===========================================================
  
-.. _sec_sky_convert_projections:
-
 How to convert sky map projections?
 ===================================
  
-.. _sec_howto_sky:
-
 Sky coordinates, sky maps and sky regions
 -----------------------------------------
  
-.. _um_getting:
-
-Getting GammaLib
-================
-
-Before you start
-----------------
-
-The procedure for building and installing GammaLib is modeled on GNU software
-distributions. You do not need to have system administrator privileges
-to compile and to install GammaLib.
-
-You will need the following to build the software:
-
--  About 200 MB of free disk space.
-
--  An ANSI C++ compiler. We recommend building GammaLib with the GNU g++
-   compiler.
-
--  GNU make
-
--  The cfitsio library for FITS file support together with the developer
-   package that includes the ``cfitsio.h`` header.
-
-Note that GammaLib compiles also in the absence of the cfitsio library, yet
-without cfitsio, FITS file reading or writing is not supported.
-
-Furthermore, the following optional packages are supported but are not
-required to compile :
-
--  Python, including the Python developer package that includes the
-   ``Python.h`` header file. If Python is present, the GammaLib Python module will
-   be built and installed, allowing to script all GammaLib functionalities from
-   within Python.
-
--  readline, including the readline developer package that provides the
-   ``readline.h`` header file. If readline is present, the packages are used
-   to enhance the user interface when entering parameters for ftools
-   applications (see :ref:`this section <sec_app>`).
-
-If you plan to modify or to extend the GammaLib source code, the following
-software is also required on your system:
-
--  GNU `autoconf <http://www.gnu.org/software/autoconf/>`_ and `automake
-   <http://www.gnu.org/software/automake/>`_ is needed to rebuild the
-   configure script and ``Makefile.am`` resource files following
-   configuration modifications.
-
--  `swig <http://www.swig.org/>`_ is needed to rebuild the Python wrappers
-   following Python interface modifications. Make sure to install the
-   latest swig version to guarantee the largest possible
-   compatibility of the Python wrappers.
-
--  `Doxygen <http://www.doxygen.org/>`_ is needed to rebuild the software
-   reference manual following code modifications.
-
-The following sections provide some information about the installation
-of cfitsio and readline.
-
-.. _sec_cfitsio:
-
-Installing cfitsio
-~~~~~~~~~~~~~~~~~~
-
-HEASARC's cfitsio library comes on many Linux distributions as
-pre-compiled binary, and there are good chances that the package is
-already installed on your system. For Mac OS X, cfitsio can be installed
-from `MacPorts <https://www.macports.org/>`_ or
-`Homebrew <http://brew.sh/>`_. If you use a pre-compiled binary, make sure
-that also the developer package is installed on your system. The developer
-package provides the ``cfitsio.h`` header file which is needed to compile
-in FITS file support in GammaLib. Please refer to the documentation of your
-Linux distribution to learn how to install pre-compiled binary packages (note
-that the installation of pre-compiled binary packages usually requires
-system administrator privileges).
-
-If you need (or prefer) to install cfitsio from source, you can download
-the latest source code from http://heasarc.gsfc.nasa.gov/fitsio.
-Detailed installation instructions can also be found on this site. We
-recommend that you install cfitsio as a shared library in the same
-directory in which you will install GammaLib, so that cfitsio is automatically
-found by the GammaLib configure script. By default, GammaLib gets installed
-into the directory ``/usr/local/gamma``.
-
-You can install version 3.290 of cfitsio (the version that was
-available when writing this manual) by executing the following command
-sequence ($ denotes the UNIX shell prompt)::
-
-    $ wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3290.tar.gz
-    $ tar xfz cfitsio3290.tar.gz
-    $ cd cfitsio
-    $ ./configure --prefix=/usr/local/gamma
-    $ make shared
-    $ sudo make install
-
-The ``--prefix=/usr/local/gamma`` option specifies the directory into which
-cfitsio gets installed. We choose here the default GammaLib installation
-directory ``/usr/local/gamma``. As this directory is a system directory, we
-need to use sudo for installation. If you decide to install cfitsio into
-a local directory which is owned by yourself, it is sufficient to type
-make install to install the library.
-
-Installing readline
-~~~~~~~~~~~~~~~~~~~
-
-The readline package comes on all Linux distributions that are known to
-us as pre-compiled binary, and it is almost certain that readline is already
-installed on your system. Very often, however, the readline developer package
-that provides the readline.h header file is not installed, and you need to
-install this package yourself to enable readline support for GammaLib. Please
-refer to the documentation of your Linux distribution to learn how to
-install pre-compiled binary packages (note that the installation of
-pre-compiled binary packages usually requires system administrator
-privileges).
-
-If you need (or prefer) to install readline from source, you need also
-to install the ncurses library that is required by readline. Here is the
-command line sequence that will install ncurses (version 5.9) and
-readline (version 6.2) in the GammaLib default install directory
-``/usr/local/gamma`` from source::
-
-    $ wget http://ftp.gnu.org/gnu/ncurses/ncurses-5.9.tar.gz
-    $ tar xfz ncurses-5.9.tar.gz
-    $ cd ncurses-5.9
-    $ ./configure --prefix=/usr/local/gamma
-    $ make
-    $ sudo make install
-    $ cd ..
-    $ wget http://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz
-    $ tar xfz readline-6.2.tar.gz
-    $ cd readline-6.2
-    $ ./configure --prefix=/usr/local/gamma
-    $ make
-    $ sudo make install
-
-Note that ``sudo`` is only needed if you are not the owner of the install
-directory.
-
-Installing
-----------
-
-Downloading
-~~~~~~~~~~~
-
-You get the latest version of GammaLib :ref:`here <sec_download>`.
-
-.. _sec_configure:
-
-Configuring
-~~~~~~~~~~~
-
-Once you've downloaded and uncompressed GammaLib, step into the GammaLib
-source code directory and type ::
-
-    $ ./configure
-
-to configure the library for compilation. Make sure that you type
-``./configure`` and not simply ``configure`` to ensure that the configuration
-script in the current directory is invoked and not some other
-system-wide configuration script.
-
-If you would like to install GammaLib in a different directory, use the optional
-``--prefix`` argument during the configuration step. For example ::
-
-    $ ./configure --prefix=/home/myname/gamma
-
-installs GammaLib in the gamma directory that will be located in the user's
-myname home directory. You can obtain a full list of configuration
-options using ::
-
-    $ ./configure --help
-
-If configuration was successful, the script will terminate with printing
-information about the configuration. This information is important in
-case that you encounter installation problems, and may help you to
-diagnose the problems. The typical output that you may see is as
-follows::
-
-  GammaLib configuration summary
-  ==============================
-  * FITS I/O support             (yes)    
-  * Readline support             (yes)    
-  * Ncurses support              (yes)   
-  * Developer configuration      (yes)
-  * Make Python binding          (yes)   use swig for updates
-  * Python                       (yes)
-  * Python.h                     (yes)
-  * Python wrappers              (yes)
-  * swig                         (yes)
-  * Multiwavelength interface    (yes)
-  * Fermi-LAT interface          (yes)
-  * CTA interface                (yes)
-  * COMPTEL interface            (yes)
-  * Doxygen                      (yes)   /usr/local/bin/doxygen
-  * Perform NaN/Inf checks       (yes)   (default)
-  * Perform range checking       (yes)   (default)
-  * Optimize memory usage        (yes)   (default)
-  * Support legacy XML format    (yes)   (default)
-  - Enable OpenMP                (no)
-  - Compile in debug code        (no)    (default)
-  - Enable code for profiling    (no)    (default)
-
-The script informs whether cfitsio has been found (and eventually also
-gives the directories in which the cfitsio library and the header file
-resides), whether readline and ncurses have been found, and whether
-Python including the Python.h header file is available. Although none of
-these items is mandatory, we highly recommend to install cfitsio to
-support FITS file reading and writing (see :ref:`sec_cfitsio`), and
-to install Python to enable GammaLib scripting.
-
-If cfitsio is installed on your system but not found by the configure
-script, it may be located in a directory that is not known to the
-configure script. By default, configure will search for cfitsio (in the
-given order) in the GammaLib install directory, in all standard paths (e.g.
-``/usr/lib``, ``/usr/local/lib``, ...), and in some system specific locations,
-including ``/opt/local/lib`` for Mac OS X. Assuming that you installed
-cfitsio on your system in the directory ``/home/myname/cfitsio``, you may
-explicitly specify this location to configure using the ``LDFLAGS`` and
-``CPPFLAGS`` environment variables::
-
-    $ ./configure LDFLAGS=-L/home/myname/cfitsio/lib CPPFLAGS=-I/home/myname/cfitsio/include
-
-Here, ``LDFLAGS`` specifies the path where the shared cfitsio library is
-located, while ``CPPFLAGS`` specifies the path where the ``cfitsio.h`` header
-file is located. Note that ``-L`` has to prefix the library path and that ``-I``
-has to prefix the header file path. With the same method, you may
-specify any non-standard location for the readline and ncurses
-libraries.
-
-The configuration script also checks for the presence of `swig <http://www.swig.org/>`_,
-which is used for building the Python wrapper files. Normally,
-`swig <http://www.swig.org/>`_ is not needed to create the Python bindings as the
-necessary wrapper files are shipped with the GammaLib source code. If you plan, however,
-to modify or to extend the Python interface, you will need `swig <http://www.swig.org/>`_ 
-to rebuild the Python wrappers following changes to the interface.
-
-The configuration summary informs also about all instrument dependent
-interfaces that will be compiled into the GammaLib library. By default, all
-available interfaces (multi-wavelength, Fermi/LAT, COMPTEL and CTA) will be
-compiled into GammaLib. If you wish to disable a particular interface, you may
-use the configure options ``--without-mwl``, ``--without-lat``, 
-``--without-com`` or ``--without-cta``.
-For example, ::
-
-    $ ./configure --without-mwl --without-lat --without-com
-
-will compile GammaLib without the multi-wavelength, the Fermi/LAT and 
-the COMPTEL interfaces. In this case, only CTA data analysis will be supported.
-
-GammaLib uses `Doxygen <http://www.doxygen.org/>`_ for code documentation.
-In case that you want to install the reference manual also locally on your
-machine, `Doxygen <http://www.doxygen.org/>`_ is needed to create the reference
-manual from the source code. `Doxygen <http://www.doxygen.org/>`_ is
-also needed if you plan to modify or extend the GammaLib library to allow
-rebuilding the reference documentation after changes. Please read see
-:ref:`sec_doxygen` to learn how to build and to install the reference
-manual locally.
-
-Finally, there exist a number of options that define how exactly GammaLib
-will be compiled.
-
-By default, GammaLib makes use of OpenMP for multi-core processing. If you 
-want to disable the multi-core processing, you may specify the 
-``--disable-openmp`` option during configuration.
-
-Several methods are able to detect invalid floating point values (either
-``NaN`` or ``Inf``), and by default, these checks will be compiled in the
-library to track numerical problems. If you want to disable these
-checks, you may specify the ``--disable-nan-check`` option during
-configuration.
-
-Range checking is performed by default on all indices that are provided
-to methods or operators (such as vector or matrix element indices, sky
-pixels, event indices, etc.), at the expense of a small speed penalty
-that arises from these verifications. You may disable these range
-checkings by specifying the ``--disable-range-check`` option during
-configuration.
-
-In a few places there exists a trade-off between speed and memory
-requirements, and a choice has to be made whether faster execution or
-smaller memory allocation should be preferred. By default, smaller
-memory allocation is preferred by GammaLib, but if you are not concerned about
-memory allocation you may specify the ``--disable-small-memory`` option
-during configuration to speed up the code.
-
-If you develop code for GammaLib you may be interested in adding some special
-debugging code, and this debugging code can be compiled in the library
-by specifying the ``--enable-debug`` option during configuration. By default,
-no debugging code will be added to GammaLib.
-
-Another developer option concerns profiling, which may be of interest to
-optimize the execution time of your code. If you would like to add
-profiling information to the code (which will be at the expense of
-execution time), you may specify the ``--enable-profiling`` option during
-configuration, which adds the ``-pg`` flags to the compiler. By default,
-profiling is disabled for GammaLib.
-
-Mac OS X options
-^^^^^^^^^^^^^^^^
-
-The Mac OS X environment is special in that it supports different CPU
-architectures (intel, ppc) and different addressing schemes (32-bit and
-64-bit). To cope with different system versions and architectures, you
-can build a universal binary by using the option ::
-
-    $ ./configure --enable-universalsdk[=PATH]
-
-The optional argument ``PATH`` specifies which OSX SDK should be used to
-perform the build. By default, the SDK ``/Developer/SDKs/MacOSX.10.4u.sdk``
-is used. If you want to build a universal binary on Mac OS X 10.5 or
-higher, and in particular if you build 64-bit code, you have to specify
-``--enable-universalsdk=/``.
-
-A second option (which is only valid in combination with the
-``--enable-universalsdk``) allows to specify the kind of universal build that
-should be created::
-
-    $ ./configure --enable-universalsdk[=PATH] --with-univeral-archs=VALUE
-
-Possible options for ``VALUE`` are: ``32-bit``, ``3-way``, ``intel``, or ``all``. By
-default, a 32-bit build will be made.
-
-These options are in particular needed if your Python architecture
-differs from the default architecture of your system. To examine the
-Python architecture you may type::
-
-    $ file `which python`
-
-which will return the architectures that are compiled in the Python
-executable::
-
-      i386     32-bit intel
-      ppc      32-bit powerpc
-      ppc64    64-bit powerpc
-      x86_64   64-bit intel
-
-If Python is 32-bit (``ppc``, ``i386``) but the compiler produces by default
-64-bit code (``ppc64``, ``x86_64``), the Python module will not work. Using ::
-
-    $ ./configure --enable-universalsdk=/
-
-will force a universal 32-bit build which creates code for ``ppc`` and ``i386``
-architectures. If on the other hand Python is 64-bit (``ppc64``, ``x86_64``)
-but the compiler produces by default 32-bit code (``ppc``, ``i386``), the option ::
-
-    $ ./configure --enable-universalsdk=/ --with-univeral-archs=3-way
-
-will generate a universal build which contains 32-bit and 64-bit code.
-
-Building
-~~~~~~~~
-
-Once configured you can build GammaLib by typing ::
-
-    $ make
-
-This compiles all GammaLib code, including the Python wrappers, and builds the
-dynamic library and Python module.
-
-GammaLib building can profit from multi-processor or multi-core machines by
-performing parallel compilation of source code within the modules. You
-can enable this feature by typing ::
-
-    $ make -j<n>
-
-where ``<n>`` is a number that should be twice the number of cores or
-processors that are available on your machine.
-
-In case that you rebuild GammaLib after changing the configuration, we recommend
-to clean the directory from any former build by typing ::
-
-    $ make clean
-
-prior to make. This will remove all existing object and library files
-from the source code directory, allowing for a fresh clean build of the
-library.
-
-Testing
-~~~~~~~
-
-GammaLib comes with an extensive unit test that allows to validate the library
-prior to installation. We highly recommend to run this unit test
-before installing the library (see :ref:`sec_install`).
-
-To run the unit test type::
-
-    $ make check
-
-This will start a test of all GammaLib modules by using dedicated executables
-which will print some progress and success information into the
-console. After completion of all tests (and assuming that all
-instrument dependent modules are enabled), you should see the following
-message in your console::
-
-    ===================
-    All 21 tests passed
-    ===================
-
-(Note that the exact number of tests that is conducted depends on the 
-configuration options).
-
-.. _sec_install:
-
-Installing
-~~~~~~~~~~
-
-GammaLib is finally installed by typing ::
-
-    $ [sudo] make install
-
-By default, GammaLib is installed in the system directory ``/usr/local/gamma``,
-hence sudo needs to be prepended to enable writing in a system-level
-directory. If you install GammaLib, however, in a local directory of which you
-are the owner, or if you install GammaLib under root, you may simply specify
-make install to initiate the installation process.
-
-The installation step will copy all necessary files into the
-installation directory. Information will be copied in the following
-subdirectories:
-
--  ``bin`` contains GammaLib environment configuration scripts (see section
-   [sec:environment])
-
--  ``include`` contains GammaLib header files (subdirectory gammalib)
-
--  ``lib`` contains the GammaLib library and Python module
-
--  ``share`` contains addition GammaLib information, such as a calibration database
-   (subdirectory ``caldb``), documentation (subdirectory ``doc``), and Python
-   interface definition files (subdirectory ``gammalib/swig``)
-
-.. _sec_environment:
-
-Setting up the GammaLib environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Before using GammaLib you have to setup some environment variables. This will be
-done automatically by an initialisation script that has been installed
-in the bin subdirectory of the install directory. Assuming that you have
-installed GammaLib in the default directory ``/usr/local/gamma`` you need to
-add the following to your ``$HOME/.bashrc`` or ``$HOME/.profile`` script on a
-Linux machine::
-
-    export GAMMALIB=/usr/local/gamma
-    source $GAMMALIB/bin/gammalib-init.sh
-
-If you use C shell or a variant then add the following to your
-``$HOME/.cshrc`` or ``$HOME/.tcshrc`` script::
-
-    setenv GAMMALIB /usr/local/gamma
-    source $GAMMALIB/bin/gammalib-init.csh
-
-You then have to source your initialisation script by typing (for
-example) ::
-
-    $ source $HOME/.bashrc
-
-and all environment variables are set correctly to use GammaLib properly.
-
-.. _sec_doxygen:
-
-Generating the reference documentation
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The reference documentation for GammaLib is generated directly from the source
-code using the `Doxygen <http://www.doxygen.org/>`_ documentation system.
-The latest GammaLib reference manual can be found at
-http://cta.irap.omp.eu/gammalib/doxygen/.
-
-The reference documentation is not shipped together with the source code
-as this would considerably increase the size of the tarball. In case
-that you want to install the reference manual also locally on your
-machine, you first have to create the documentation using Doxygen.
-
-Assuming that Doxygen is available on your machine (see :ref:`sec_configure`)
-you can create the reference documentation by typing ::
-
-    $ make doxygen
-
-Once created, you can install the reference manual by typing ::
-
-    $ [sudo] make doxygen-install
-
-By default, GammaLib is installed in the system directory ``/usr/local/gamma``,
-hence sudo needs to be prepended to enable writing in a system-level
-directory. If you install , however, in a local directory of which you
-are the owner, or if you install GammaLib under root, you may simply specify
-make install to initiate the installation process.
-
-The reference manual will be installed in form of web-browsable HTML
-files into the folder ::
-
-      /usr/local/gamma/share/doc/gammalib/html/doxygen
-
-You can access all web-based GammaLib documentation locally using
-``file:///usr/local/gamma/share/doc/gammalib/html/index.html`` (assuming
-that the GammaLib library has been installed in the default directory
-``/usr/local/gamma``).
-
-In addition, the reference manual will also be available as man pages
-that will be installed into ::
-
-      /usr/local/gamma/share/doc/gammalib/man
-
-To access for example the information for the ``GApplication`` class, you
-can type ::
-
-    $ man GApplication
-
-which then returns the synopsis and detailed documentation for the
-requested class.
-.. _sec_user_manual:
+.. _user_manual:
  
 ===========
 User Manual
@@ -7,11 +7,10 @@ User Manual
 .. toctree::
    :maxdepth: 1
  
-   introduction
-   getting
+   scope
+   overview
    modules/index
    internals
-   manual/index
    glossary
  
  
 Under the hood
 ==============
  
-.. _sec_registry:
-
 Registry classes
 ----------------
  
-What is in this section?
-------------------------
-
-This section provides a detailed manual for using the various GammaLib 
-modules.
-.. _um_intro:
-
-Introduction
-============
-
-Scope
------
-
-This User Manual provides a complete description of the GammaLib C++ library
-and its Python module. It is equally well suited for beginners as for
-experienced users.
-
 Overview
---------
+========
  
 GammaLib is a self-contained, instrument independent, open source,
 multi-platform C++ library and Python module that implements all code
@@ -43,7 +31,7 @@ are:
 * Issue tracker: https://cta-redmine.irap.omp.eu/projects/gammalib/issues
 * Documentation: http://cta.irap.omp.eu/gammalib/
  
-The present document applies to GammaLib version 1.4.
+The present document applies to GammaLib version 1.6.
  
 GammaLib is designed to compile on any POSIX compliant platform. So far, 
 GammaLib has been successfully compiled and tested on Mac OS X, OpenBSD, OpenSolaris
+Scope
+=====
+
+This User Manual provides a complete description of the GammaLib C++ library
+and its Python module. It is equally well suited for beginners as for
+experienced users.