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Commit a14839a4 authored by Petra Seibert's avatar Petra Seibert
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Language corrections for the Sections Developers, Support, Changelog, and the... 

Language corrections for the Sections Developers, Support, Changelog, and the home directory (index.html)
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For_developers/Sphinx/source/Developers/gen_docu.rst
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********************
Update Documentation
Updating the documentation
********************
UNDER CONSTRUCTION
Additional Software
Additional software
===================
Developers working on ``flex_extract`` should make extensive use of the prepared test cases, unit tests and update the documentation. For this, some additional software is necessary:
Developers working on ``flex_extract`` should make extensive use of the prepared test cases and unit tests, and should also update the documentation. For this, some additional software is necessary:
.. code-block:: sh
......@@ -26,19 +26,19 @@ Developers working on ``flex_extract`` should make extensive use of the prepared
Online-documentation with Sphinx
On-line documentation with Sphinx
================================
Use the scriot ``gen_docu.sh`` to generate an update of the online documentation of the python component.
Use the script ``gen_docu.sh`` to generate an update of the on-line documentation of the Python component.
It uses ``pyreverse`` to generate a class and a package diagram with graphviz and overwrites the old files in the developers directory.
``pyreverse`` creates ``dot`` files and with the ``dot`` program of the ``graphviz`` software the ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed.
It uses ``pyreverse`` to generate class and package diagrams with ``graphviz`` and overwrites the old files in the developers directory.
``pyreverse`` creates ``dot`` files, and with the ``dot`` program of the ``graphviz`` software, the ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed.
Sequence diagramms
------------------
You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to:
You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to:
.. code-block:: bash
......@@ -49,7 +49,7 @@ You might need to adapt the fonts path for the diagrams to a true type font. Cur
Block diagramms
------------------
You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to:
You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to:
.. code-block:: bash
......
For_developers/Sphinx/source/Support/faq.rst
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......@@ -7,23 +7,22 @@ FAQ - Frequently asked questions
What can I do if I can't install the third party libraries from distribution packages?
What can I do if I can't install the third-party libraries from distribution packages?
======================================================================================
This can be the case if the user does not have admin rights.
It is possible to install the necessary libraries locally from source.
For this case you should follow the following steps:
This can be the case if the user does not have admin rights and the sysadmins would not want to provide the libraries.
In this case, a workaround is to install the necessary libraries from source into a user directory, following these steps:
Installation hints:
Steps to install libraries from source:
1. `Read Emoslib installation instructions <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_
2. `Read ECMWF blog about gfortran <https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran>`_
3. `Install FFTW <http://www.fftw.org>`_
4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ (2 times make! one without any options and one with single precision option)
4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ (execute ``make`` two times! One time without any options, and another time with the single-precision option.)
5. `Install ECCODES <https://software.ecmwf.int/wiki/display/ECC>`_
6. Register at Mars (:ref:`ref-registration`)
6. Register for MARS access (:ref:`ref-registration`)
7. Install Web API's `CDS API <https://cds.climate.copernicus.eu/api-how-to>`_ and `ECMWF Web API <https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home>`_
8. Check LD_LIBRARY_PATH environment variable if it contains all paths to the libs
9. Check available python packages (e.g. import eccodes / import grib_api / import ecmwfapi)
8. Check whether LD_LIBRARY_PATH environment variable contains the paths to all the libs
9. Check available Python packages (e.g. ``import eccodes`` / ``import grib_api`` / ``import ecmwfapi``)
10. Start test retrieval (:ref:`ref-test-local`)
11. Install ``flex_extract`` (:doc:`../installation`)
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For_developers/Sphinx/source/Support/known_bugs_issues.rst
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......@@ -14,18 +14,19 @@ CDS API and ERA5 data
Installation problems with ``GATEWAY`` and ``DESTINATION`` parameters
---------------------------------------------------------------------
See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information.
See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information. Fixed in v7.1.1.
Installation problems with the Fortran program ``calc_etadot``
--------------------------------------------------------------
See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information.
See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information. Fixed in v7.1.1.
ECCODES Error Code 250
----------------------
If you get an error message from ECCODES with code 250, locking like this:
If you get an error message from ECCODES with code 250, looking like this:
.. code-block:: bash
......@@ -37,9 +38,13 @@ If you get an error message from ECCODES with code 250, locking like this:
... FORTRAN PROGRAM FAILED!
then you have set a wrong maximum level in the :literal:`CONTROL` file!
It is important to properly select the maximum level depending on the data set you would like to retrieve. The following model level definitions (number of model levels available) are limited to [16, 19, 31, 40, 50, 60, 62, 91, 137]. The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137. The operational data set uses different model levels depending on the date. For example, on the 25/06/2013 the operational system started to use 137 model levels. Therefore, everytime you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file or define a LEVELLIST=1/to/137. Of course you can stop before the top of the atmosphere, such as 60/to/137, but you have to select the maximum level number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding introducstion date.
It is important to properly select the maximum level depending on the data set you would like to retrieve. Only the following values of the number of model levels available are valid: 16, 19, 31, 40, 50, 60, 62, 91, 137.
The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137.
The operational data sets use different numbers, depending on the date. For example, from 25/06/2013 on, 137 model levels were used in the operational system. Therefore, every time you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file, or you have to define LEVELLIST=1/to/137. Of course, you can stop before the top of the atmosphere, such as 60/to/137, but you have to include the maximum level number (i. e., the lowest level, see note below!) number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding date they were introduced.
.. note::
Remember that model level 1 corresponds to the top of the atmosphere and then increases in the direction of the surface.
Be aware that the ECMWF model counts the levels from the top of the atmosphere downward to the surface. Level 1 is the topmost level, and e.g. 137 would be the level closest to the ground.
For_developers/Sphinx/source/changelog.rst
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......@@ -19,7 +19,7 @@ Bug fixes
#########
* corrected naming of makefiles and Fortran program executable in online documentation
* adapted checking for ``GATEWAY`` and ``DESTINATION`` parameter
* fixed makefiles to use f90 Fortran files for ECMWF server
* fixed Fortran makefiles to use the .f90 files on ECMWF servers
.. _ref-v71:
......@@ -41,9 +41,9 @@ Changes
* upgraded to Python3
* applied PEP8 style guide
* use of genshi templates
* modularization of python source code
* modularization of Python source code
* upgrade from grib_api to ecCodes
* completely revised/refactored python section
* completely revised/refactored Python section
* restructured program directories
* Fortran program name changed from ``CONVERT2`` to ``calc_etadot``
......@@ -59,8 +59,8 @@ New Features
Bug fixes
#########
* diverse problems with ERA 5 retrieval
* diverse problems with CERA-20C retrieval
* various problems with ERA 5 retrieval
* various problems with CERA-20C retrieval
* BASETIME retrieval option
* `CONVERT2` FORTRAN program: initialise fields to 0.
(introduced initialization of :literal:`field` variable in the Fortran program
......@@ -73,7 +73,7 @@ Release v7.0.3
New Features
############
* output of mars requests to an extra file (debugging and documentation)
* output of MARS requests to an extra file (debugging and documentation)
* CERA-20C download
* ERA 5 download
* public user interface with `ECMWF Web API`_
......@@ -86,16 +86,16 @@ Release v7.0.2
New Features
############
* Python based version
* Python-based version
Changes
#######
* korn shell scripts were substituted by python scripts
* korn shell scripts substituted by Python scripts
.. _ref-v60:
Release v0.1 - v6.0
-------------------
* old version which should no longer be used anymore
* old version which should no longer be used
For_developers/Sphinx/source/index.rst
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Welcome to ``flex_extract``'s user documentation!
=================================================
``Flex_extract`` is an open-source software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to serve as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.
``Flex_extract`` is an open-source software to retrieve meteorological fields from the MARS archive of the European Centre for Medium-Range Weather Forecasts (ECMWF) to serve as input for the FLEXTRA/FLEXPART atmospheric transport modelling system.
.. raw:: html
......@@ -31,8 +31,8 @@ Welcome to ``flex_extract``'s user documentation!
<h2><a href="ecmwf_data.html">ECMWF data</a></h2>
<ul>
<li><a href="ecmwf_data.html">Overview</a></li>
<li><a href="Ecmwf/access.html">Access Modes</a></li>
<li><a href="Ecmwf/ec-links.html">Link Collection</a></li>
<li><a href="Ecmwf/access.html">Access modes</a></li>
<li><a href="Ecmwf/ec-links.html">Link collection</a></li>
</ul>
</td>
<td style="width:30%;height:150px;">
......@@ -42,8 +42,8 @@ Welcome to ``flex_extract``'s user documentation!
<h2><a href="documentation.html">Documentation</a></h2>
<ul>
<li><a href="Documentation/overview.html">Overview</a></li>
<li><a href="Documentation/input.html">Control & Input Data</a></li>
<li><a href="Documentation/output.html">Output Data</a></li>
<li><a href="Documentation/input.html">Control & input data</a></li>
<li><a href="Documentation/output.html">Output data</a></li>
</ul>
</td>
</tr>
......@@ -76,9 +76,9 @@ Welcome to ``flex_extract``'s user documentation!
</div>
<h2><a href="dev_guide.html">Developer</a></h2>
<ul>
<li><a href="Developers/gen_docu.html">Update Documentation</a></li>
<li><a href=""></a><Placeholder></li>
<li><a href=""></a><Placeholder></li>
<li><a href="Developers/gen_docu.html">Updateing the documentation</a></li>
<!-- <li><a href=""></a><Placeholder></li>
<li><a href=""></a><Placeholder></li>-->
</ul>
</td>
</tr>
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For_developers/Sphinx/source/support.rst
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......@@ -15,10 +15,10 @@ Ticket system
-------------
.. _ticket system: https://www.flexpart.eu/report/1
The community website http://flexpart.eu contains a
`ticket system`_ which can be used to report any issue or a proposition for a new feature.
The community website https://flexpart.eu/ contains a
`ticket system`_ which can be used to report any issue or to propose new features.
The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials (with some delay).
The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials (possibly with some delay). Event though a category "Support" is available, in most cases asking questions in the mailing list (see next paragraph below) will be more appropriate.
.. _ref-mailing-list:
......@@ -26,11 +26,10 @@ The tickets can be viewed by anyone, to create a ticket a registration is necess
Mailing list
------------
The mailing list is mainly for the ``FLEXPART`` users to ask questions or share experiences regarding the whole ``FLEXPART`` process with the community. This can be a lot faster than asking only the developers for help. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help.
A mailing list exists for the ``FLEXPART`` users to ask questions or share experiences with the community, regarding the whole ``FLEXPART`` process. This may be faster than asking only the developers for help through tickets. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help.
Additionally, from time to time, there will be announcements for all FLEXPART users, such as new release versions of ``FLEXPART`` or ``flex_extract``.
Just write a mail to: ``flexpart[at]lists.univie.ac.at``
New release versions of ``FLEXPART`` or ``flex_extract`` or other important annoucements will also be made through this mailling list.
The subscription process is explained at the bottom of https://www.flexpart.eu/wiki/RegisteredUser. Once subscribed, write e-mail to ``flexpart[at]lists.univie.ac.at`` to post to the list.
.. _ref-reporting:
......@@ -40,12 +39,11 @@ Reporting an issue
To properly report a problem or bug, please provide as much information as possible.
This includes:
* the flex_extract version
* a flex_extract log file (output of submit.py script)
* the CONTROL file
* the commandline arguments or run(_local).sh settings and
* a description of the environment you used (Unix/Linux version, library version, application mode, etc.).
* the ``flex_extract`` version
* a ``flex_extract log`` file (output of ``submit.py`` script)
* the ``CONTROL`` file
* the command-line arguments or ``run(_local).sh`` settings and
* a description of your environment (Unix/Linux version, library version, application mode, etc.).
.. _ref-known-issues:
......
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