Prepare documentation for release

Jürgen Knödlseder
1 parent f048c13b
Showing 6 changed files with 70 additions and 141 deletions
doc/source/_templates/index.html
doc/source/about.rst
doc/source/admin/install_source.rst
doc/source/users/reference_manual/csspec.rst
doc/source/users/reference_manual/csviscube.rst
doc/source/users/tutorials/1dc/getting_data.rst
@@ -19,7 +19,7 @@ Besides CTA, GammaLib supports also the analysis of Fermi/LAT and COMPTEL data,
 and extensions to support further gamma-ray instruments are planned. An
 interface to virtual observatory ressources does also exist. By making use of
 the GammaLib multi-instrument capabilities, ctools supports the joint analysis
-of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT and COMPTEL data.
+of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT, INTEGRAL/SPI and COMPTEL data.
 {%endtrans%}</p>
 <p>{%trans%} ctools are developed by a team of enthousiastic gamma-ray
@@ -15,12 +15,13 @@ Creation of shell or Python scripts and pipelines is supported as well.
 ctools are based on GammaLib, a versatile toolbox for the scientific
 analysis of astronomical gamma-ray data. 
-Besides CTA, GammaLib supports also the analysis of Fermi/LAT and COMPTEL 
-data, and extensions to support further gamma-ray instruments are planned. 
+Besides CTA, GammaLib supports also the analysis of Fermi/LAT, INTEGRAL/SPI
+and COMPTEL data, and extensions to support further gamma-ray instruments are
+planned.
 An interface to virtual observatory ressources does also exist.
 By making use of the GammaLib multi-instrument capabilities, ctools 
-supports the joint analysis of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT and
-COMPTEL data.
+supports the joint analysis of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT,
+INTEGRAL/SPI and COMPTEL data.
 ctools are developed by a team of enthousiastic gamma-ray astronomers with
 support from engineers. We regularily organise
@@ -17,7 +17,7 @@ The procedure for building and installing ctools is modeled on GNU
 software distributions. You will need the following to build the
 software:
--  About 25 MB of free disk space.
+-  About 50 MB of free disk space.
 -  An ANSI C++ compiler. ctools builds well using GNU g++ or clang.
@@ -42,7 +42,7 @@ section and continue with the :ref:`sec_building_ctools` section.
 You will need the following to build the GammaLib:
--  About 200 MB of free disk space.
+-  About 300 MB of free disk space.
 -  An ANSI C++ compiler. We recommend building GammaLib with the GNU g++
    or the clang compilers.
@@ -66,7 +66,7 @@ in an appropriate location (for example ``$HOME/builds``), and type
 .. code-block:: bash
-  $ tar xvfz gammalib-1.2.0.tar.gz
+   $ tar xvfz gammalib-1.7.0.tar.gz
 (the ``$`` symbol indicates the console prompt and is not part of the
 command that you should type in).
@@ -76,25 +76,25 @@ typing
 .. code-block:: bash
-  $ cd gammalib-1.2.0
-  $ ./configure
-  $ make
-  $ make check
-  $ make install
+   $ cd gammalib-1.7.0
+   $ ./configure
+   $ make
+   $ make check
+   $ make install
 The last step may require system administator privileges. In this case,
 use
 .. code-block:: bash
-  $ sudo make install
+   $ sudo make install
 If you do not have system administrator privileges, change the install
 directory by typing for example
 .. code-block:: bash
-  $ ./configure --prefix=$HOME/gamma
+   $ ./configure --prefix=$HOME/gamma
 which then installs GammaLib in the ``gamma`` folder of your home
 directory.
@@ -114,16 +114,16 @@ machine:
 .. code-block:: bash
-  export GAMMALIB=/usr/local/gamma
-  source $GAMMALIB/bin/gammalib-init.sh
+   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:
 .. code-block:: csh
-  setenv GAMMALIB /usr/local/gamma
-  source $GAMMALIB/bin/gammalib-init.csh
+   setenv GAMMALIB /usr/local/gamma
+   source $GAMMALIB/bin/gammalib-init.csh
 .. _sec_building_ctools:
@@ -136,7 +136,7 @@ an appropriate location (for example ``$HOME/builds``), and type
 .. code-block:: bash
-  $ tar xvfz ctools-1.2.0.tar.gz
+   $ tar xvfz ctools-1.7.0.tar.gz
 (the ``$`` symbol indicates the console prompt and is not part of the
 command that you should type in).
@@ -145,9 +145,9 @@ Step in the directory and build the ctools by typing
 .. code-block:: bash
-  $ cd ctools-1.2.0
-  $ ./configure
-  $ make
+   $ cd ctools-1.7.0
+   $ ./configure
+   $ make
 at the operating system prompt. The ``./configure`` command customizes
 the Makefiles for the particular system, the ``make`` command compiles
@@ -159,7 +159,7 @@ You can get the full list of configuration options by typing
 .. code-block:: bash
-  $ ./configure --help
+   $ ./configure --help
 Testing ctools
@@ -170,7 +170,7 @@ make sure that ctools have been built correctly. For this, type
 .. code-block:: bash
-  $ make check
+   $ make check
 If you have automake version 1.13 or newer installed, you should see the
 following output at the end of the unit testing:
@@ -181,7 +181,7 @@ following output at the end of the unit testing:
    PASS: test_python_cscripts.sh
    PASS: test_examples.py
    ============================================================================
-   Testsuite summary for ctools 1.2.0
+   Testsuite summary for ctools 1.7.0
    ============================================================================
    # TOTAL: 3
    # PASS:  3
@@ -199,34 +199,36 @@ For older automake version, you should see
    ***********************
    * ctools unit testing *
    ***********************
-   Test ctobssim on command line: ..... ok
-   Test ctobssim from Python: ................................................. ok
-   Test ctselect on command line: ....... ok
-   Test ctselect from Python: ..... ok
-   Test ctbin on command line: ..... ok
-   Test ctbin from Python: ............................................. ok
+   Test ctobssim on command line: ...... ok
+   Test ctobssim from Python: ........................................... ok
+   Test ctselect on command line: ........ ok
+   Test ctselect from Python: .............................................................. ok
+   Test ctphase on command line: ...... ok
+   Test ctphase from Python: .............. ok
    ...
    PASS test_python_ctools.sh
    *************************
    * cscripts unit testing *
    *************************
-   Test cscaldb on command line: .. ok
-   Test cscaldb from Python: . ok
-   Test cslightcrv on command line: ............... ok
-   Test cslightcrv from Python: ................................................. ok
-   Test csmodelinfo on command line: ..... ok
-   Test csmodelinfo from Python: ..... ok
+   Test cscript base class: ............................................................................................................................... ok
+   Test ctobservation base class: ............................................. ok
+   Test ctlikelihood base class: ... ok
+   Test csbkgmodel on command line: ..... ok
+   Test csbkgmodel from Python: ........... ok
+   Test csbkgmodel pickeling: ...... ok
    ...
    PASS test_python_cscripts.sh
    ********************
    * Examples testing *
    ********************
-   Test generate_prod3_irfs.py: .. ok
    Test make_pointings.py: ....... ok
-   Test make_spectrum.py: .. ok
-   Test make_ts_distributions.py: .. ok
+   Test show_butterfly.py: .. ok
+   Test show_irf.py: .. ok
+   Test show_lightcurve.py: .. ok
+   Test show_model.py: ... ok
+   Test show_obs.py: ... ok
    ...
    PASS test_examples.py
    ==================
@@ -239,9 +241,9 @@ versions, but there it is written in log files that you can find in the
 .. code-block:: bash
-  test_python_ctools.sh.log
-  test_python_cscripts.sh.log
-  test_examples.py.log
+   test_python_ctools.sh.log
+   test_python_cscripts.sh.log
+   test_examples.py.log
 If you do not see the same output, but a failure message, please check
 first the :ref:`issues` section. If you cannot fix the problem, please
@@ -256,7 +258,7 @@ Now you are ready to install the ctools by typing
 .. code-block:: bash
-  $ make install
+   $ make install
 If the destination directory is owned by ``root`` (which is normally the 
 case when using the default), administrator privileges are needed for
@@ -264,7 +266,7 @@ installation. In this case, type
 .. code-block:: bash
-  $ sudo make install
+   $ sudo make install
 By default, the install directory is set to ``/usr/local/gamma``. To 
 change the install directory (for example in case that you do not
@@ -273,7 +275,7 @@ can be given, for example:
 .. code-block:: bash
-  $ ./configure --prefix=$HOME/gamma
+   $ ./configure --prefix=$HOME/gamma
 Setting up the ctools environment
@@ -288,16 +290,16 @@ on a Linux machine:
 .. code-block:: bash
-  export CTOOLS=/usr/local/gamma
-  source $CTOOLS/bin/ctools-init.sh
+   export CTOOLS=/usr/local/gamma
+   source $CTOOLS/bin/ctools-init.sh
 If you use C shell or a variant then add the following to your 
 ``$HOME/.cshrc`` or ``$HOME/.tcshrc`` script:
 .. code-block:: csh
-  setenv CTOOLS /usr/local/gamma
-  source $CTOOLS/bin/ctools-init.csh
+   setenv CTOOLS /usr/local/gamma
+   source $CTOOLS/bin/ctools-init.csh
 Checking your setup
@@ -309,17 +311,17 @@ As a quick check that your setup is okay you can run ``csinfo check``:
 .. code-block:: bash
-  $ csinfo check
+   $ csinfo check
-  Gammalib / ctools setup check:
+   Gammalib / ctools setup check:
-     GAMMALIB environment variable ... ok
-     CTOOLS   environment variable ... ok
-     gammalib Python import .......... ok
-     ctools   Python import .......... ok
-     cscripts Python import .......... ok
+      GAMMALIB environment variable ... ok
+      CTOOLS   environment variable ... ok
+      gammalib Python import .......... ok
+      ctools   Python import .......... ok
+      cscripts Python import .......... ok
-     ===> Your Gammalib / ctools setup is OK.
+      ===> Your Gammalib / ctools setup is OK.
 If the setup is not okay, run the ``csinfo info`` command to print
 detailed information about your setup. There's also a ``csinfo list``
@@ -158,7 +158,7 @@ General parameters
 ``(dll_sigmax = 5.0) [real]``
     Maximum number of standard deviations for log-like profiles. The final number
     of bins generated in the likelihood profile will be:
-       2*(dll_sigmax/dll_sigstep) + 1
+    ``2*(dll_sigmax/dll_sigstep) + 1``
     ensuring that the central flux will always be evaluated.
 ``(dll_freenodes = no) [boolean]``
@@ -15,6 +15,7 @@ that a given position on the sky is observable under a given zenith angle
 by an IACT array during a given time period.
 For the moment, the script takes into account:
+
 - a Sun constraint, specified as a minimum zenith angle of the Sun (hidden
   parameter ``sunzenith``). If the Sun is higher in the sky than this zenith
   angle the corresponding times are excluded
@@ -3,89 +3,14 @@
 Getting the data
 ================
-The
+The data for the
 :ref:`first CTA Data Challenge <glossary_1dc>`
-data are available on the
-`CTA ownCloud server <https://owncloud.cta-observatory.org>`_.
-Only CTA Consortium members are entitled to access the data.
-You need your usual CTA credentials to download the data.
+are only available to members of the CTA Consortium.
+Instructions for CTA Consortium of how to download the data can be found
+`here <https://forge.in2p3.fr/projects/data-challenge-1-dc-1/wiki/Getting_data>`_
+(access to the instructions are restricted).
-The release contains simulated data for the Galactic Plane Survey, the
-Galactic Centre Survey, the Extragalactic Survey and the AGN monitoring program,
-:ref:`instrument response functions (IRFs) <glossary_irf>`, and the
-:ref:`model definition files <glossary_moddef>`
-that were used for the simulation.
-
-The data were split into the separate files that can be downloaded
-by clicking on the following links:
-
-* `Galactic Plane Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gps.tar.gz>`_ (8.3 GB)
-* `Galactic Centre Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gc.tar.gz>`_ (4.4 GB)
-* `Extragalactic Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/egal.tar.gz>`_ (2.5 GB)
-* `AGN monitoring program <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/agn.wobble.tar.gz>`_ (4.7 GB)
-* `Instrument Response Functions <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/caldb.tar.gz>`_ (1.2 MB)
-* `Sky and background models <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/models.tar.gz>`_ (0.9 GB)
-
-You can also download the files using the ``wget`` tool from the command
-line by typing:
-
-.. code-block:: bash
-
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gps.tar.gz --user=<user> --ask-password
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gc.tar.gz --user=<user> --ask-password
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/egal.tar.gz --user=<user> --ask-password
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/agn.wobble.tar.gz --user=<user> --ask-password
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/caldb.tar.gz --user=<user> --ask-password
-   $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/models.tar.gz --user=<user> --ask-password
-
-.. warning::
-   ``<user>`` needs to be replaced by your CTA user name.
-   Don't type the ``$`` symbol. It indicates that a command should be typed
-   on the command line of your terminal.
-
-.. note::
-   You may need to add the ``--no-check-certificate`` option to download the
-   files using ``wget``.
-
-.. note::
-   In case you encounter the following error message
-
-   .. code-block:: bash
-
-      HTTP request sent, awaiting response... 401 Unauthorized
-      Authentication selected: Basic realm="ownCloud"
-      Reusing existing connection to owncloud.cta-observatory.org:443.
-      HTTP request sent, awaiting response... 404 Not Found
-      2017-06-06 14:43:33 ERROR 404: Not Found.
-
-   or any other problems with the download, please contact
-   sstober@cta-observatory.org.
-
-To make sure that you have the relevant files you may check the MD5 checksums
-after downloading by typing for example
-
-.. code-block:: bash
-
-   $ md5 gps.tar.gz
-
-on Mac OS X or
-
-.. code-block:: bash
-
-   $ md5sum gps.tar.gz
-
-on Linux. Below the expected results:
-
-.. code-block:: bash
-
-   gps.tar.gz         c7129c71e911920f82273270c9d7c818
-   gc.tar.gz          07aa46bb2d67cd64fa4685078643b043
-   egal.tar.gz        4ea5f2ff8312b700dcc133a89d9fd096
-   agn.wobble.tar.gz  df8fc4f9de22ac36a86023ccbfd0cf89
-   caldb.tar.gz       ce718128e1b2fe19c4b8dc79b688d113
-   models.tar.gz      87662cf53a2988522f485cad984d8810
-
-Now uncompress the files at any place by typing
+Once downloaded, uncompress the files at any place by typing
 .. code-block:: bash