Commit d43acc1b authored by BorjaEst's avatar BorjaEst
Browse files

Index with first document pages

parent d3537892
Local installation
==================================
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Tests
==================================
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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
...
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
...
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
Installation
==================================
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Overview
===================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
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
=========================================
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
----------------
API-reference
==================================
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Reduce data (Skim)
==================================
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