Index with first document pages

docs/dev_guide/local-install.rst

+Local installation
+==================================
\ No newline at end of file

docs/dev_guide/tests.rst

+Tests
+==================================
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docs/getting_started/build.rst

+Build
+===================
+
+Download the repository at the **Build machine** using git.
+
+.. code-block:: bash
+
+    $ git clone git@git.scc.kit.edu:synergy.o3as/o3skim.git
+    Cloning into 'o3skim'...
+    ...
+
+
+Build the container image at the **Build machine** using **docker**.
+
+.. code-block:: bash
+
+    $ docker build --tag o3skim .
+    ...
+    Successfully built 69587025a70a
+    Successfully tagged o3skim:latest
+
+
+If the build process succeded, you should see the image name on the container images list:
+
+.. code-block:: bash
+
+    $ docker images
+    REPOSITORY                         TAG                 IMAGE ID            CREATED              SIZE
+    o3skim                             latest              69587025a70a        xx seconds ago      557MB
+    ...
+

docs/getting_started/cli.rst

+Command Line Interface
+=======================
+
+Finally, run the container. Note the described `data`, `output` and 
+`sources.yaml` have to be provided. Also it is needed to specify the 
+user `application` should run inside the container:
+
+.. code-block:: bash
+
+    $ udocker run \
+      --user=application \
+      --volume=${PWD}/sources.yaml:/app/sources.yaml \
+      --volume=${PWD}/data:/app/data \
+      --volume=${PWD}/output:/app/output \
+      o3skim --verbosity INFO
+    ...
+    executing: main
+    ...
+    2020-08-25 12:42:34,151 - INFO     - Configuration found at: './sources.yaml'
+    2020-08-25 12:42:34,152 - INFO     - Loading data from './data' 
+    2020-08-25 12:42:34,261 - INFO     - Skimming data to './output' 
+
+
+For the main function description and commands help you can call:
+
+.. code-block:: bash
+
+    $ udocker run --user=application o3skim --help
+    ...
+
+

docs/getting_started/deployment.rst

+Deployment
+==================================
+
+To deploy the the application using **udocker** at the **Runtime machine** 
+you need:
+
+ - Input path with data to skim, to be mounter on `/app/data` inside the 
+   container.
+ - Output path for skimmed results, to be mounted on `/app/output` inside
+   the container.
+ - Configuration file with a data structure desctiption at the input path
+   in YAML_ format. This configuration file has to be mounted on 
+   `/app/sources.yaml` inside the container. 
+   See [sources_example.yaml](/sources_example.yaml) for a configuration 
+   example.
+
+.. _YAML: https://yaml.org/
+
+
+Once the requierement are needed, pull the image from the image registry.
+For example, to pull it from the synergy-imk official registry use:
+
+.. code-block:: bash
+
+    $ udocker pull synergyimk/o3skim
+    ...
+    Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
+    ...
+
+
+Once the repository is added and the image downloaded, create the local container: 
+
+.. code-block:: bash
+
+    $ udocker create --name=o3skim synergyimk/o3skim
+    fa42a912-b0d4-3bfb-987f-1c243863802d
+

docs/getting_started/installation.rst

-Installation
-==================================
\ No newline at end of file

docs/getting_started/overview.rst

-Overview
-===================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
-

docs/getting_started/prerequisites.rst

+Prerequisites
+==================================
+
+To run the project as container, you need the following systems and container technologies:
+
+ - **Build machine** with docker_
+ - **Runtime machine** with udocker_
+
+
+.. rubric:: Note udocker_ cannot be used to build containers, only to run them.
+
+.. _docker: https://docs.docker.com/engine/install/
+.. _udocker: https://indigo-dc.gitbook.io/udocker/installation_manual
+

docs/index.rst

 =========================================
-o3skim: Data skiming for ozone assessment
+o3skim
 =========================================
+.. rubric:: Data skiming for ozone assessment.
 
-**o3skim** is an open source project and Python package that allows to reduce
-data from netCDF_ models to analyse and plot the ozone leves in an easy-fast 
-way.
+**o3skim** is an open source project and Python package that provides the 
+tools to preprocess, standarise and reduce ozone data from netCDF_ models to
+simplify and speed up ozone data transfer and plot.
 
 .. _netCDF: http://www.unidata.ucar.edu/software/netcdf
 
@@ -13,41 +14,63 @@ Documentation
 
 **Getting Started**
 
-* :doc:`getting_started/overview`
-* :doc:`getting_started/installation`
+* Which :doc:`getting_started/prerequisites` you need to start.
+* How to :doc:`getting_started/build` your o3skim container.
+* How to :doc:`getting_started/deployment` your o3skim container.
+* How to use the o3skim :doc:`getting_started/cli`
 
 .. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Getting Started
 
-   getting_started/overview
-   getting_started/installation
+   getting_started/prerequisites
+   getting_started/build
+   getting_started/deployment
+   getting_started/cli
 
 **User Guide**
 
 * :doc:`user_guide/source-file`
-* :doc:`user_guide/reduce-data`
+* :doc:`user_guide/API-reference`
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
 
    user_guide/source-file
-   user_guide/reduce-data
+   user_guide/API-reference
+
+
+**Developer Guide**
+
+* :doc:`dev_guide/local-install`
+* :doc:`dev_guide/tests`
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
 
+   dev_guide/local-install
+   dev_guide/tests
 
 
 See also
 --------
 
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
 
-Get in touch
-------------
 
-
-License
+Authors
 -------
+- [@V.Kozlov](https://git.scc.kit.edu/eo9869) - TBD
+- [@T.Kerzenmacher](https://git.scc.kit.edu/px5501) - TBD
+- [@B.Esteban](https://git.scc.kit.edu/zr5094) - TBD
+
 
+Acknowledgements
+----------------
 
 

docs/user_guide/API-reference.rst

+API-reference
+==================================
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docs/user_guide/reduce-data.rst

-Reduce data (Skim)
-==================================
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