Changeset 274f9ef in flex_extract.git for documentation


Ignore:
Timestamp:
Oct 22, 2018, 11:44:47 AM (8 months ago)
Author:
Anne Philipp <anne.philipp@…>
Branches:
dev
Children:
db27c09
Parents:
708c667
Message:

Converted docstrings to numpy style and build first structure for sphinxdocumentation (incl API)

Location:
documentation/Sphinx
Files:
75 added
1 deleted
38 edited

Legend:

Unmodified
Added
Removed
  • documentation/Sphinx/build/html/_modules/index.html

    r708c667 r274f9ef  
    150150           
    151151  <h1>All modules for which code is available</h1>
    152 <ul><li><a href="disaggregation.html">disaggregation</a></li>
     152<ul><li><a href="ControlFile.html">ControlFile</a></li>
     153<li><a href="EcFlexpart.html">EcFlexpart</a></li>
     154<li><a href="GribTools.html">GribTools</a></li>
     155<li><a href="MarsRetrieval.html">MarsRetrieval</a></li>
     156<li><a href="UioFiles.html">UioFiles</a></li>
     157<li><a href="disaggregation.html">disaggregation</a></li>
     158<li><a href="get_mars_data.html">get_mars_data</a></li>
     159<li><a href="install.html">install</a></li>
     160<li><a href="prepare_flexpart.html">prepare_flexpart</a></li>
     161<li><a href="submit.html">submit</a></li>
    153162<li><a href="tools.html">tools</a></li>
    154163</ul>
  • documentation/Sphinx/build/html/_modules/tools.html

    r708c667 r274f9ef  
    213213<span class="c1"># ------------------------------------------------------------------------------</span>
    214214
    215 <div class="viewcode-block" id="none_or_str"><a class="viewcode-back" href="../code.html#tools.none_or_str">[docs]</a><span class="k">def</span> <span class="nf">none_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
    216     <span class="sd">&#39;&#39;&#39;</span>
    217 <span class="sd">    @Description:</span>
    218 <span class="sd">        Converts the input string into pythons None-type if the string</span>
    219 <span class="sd">        contains &quot;None&quot;.</span>
    220 
    221 <span class="sd">    @Input:</span>
    222 <span class="sd">        value: string</span>
    223 <span class="sd">            String to be checked for the &quot;None&quot; word.</span>
    224 
    225 <span class="sd">    @Return:</span>
    226 <span class="sd">        None or value:</span>
    227 <span class="sd">            Return depends on the content of the input value. If it was &quot;None&quot;,</span>
    228 <span class="sd">            then the python type None is returned. Otherwise the string itself.</span>
     215<div class="viewcode-block" id="none_or_str"><a class="viewcode-back" href="../api.html#tools.none_or_str">[docs]</a><span class="k">def</span> <span class="nf">none_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
     216    <span class="sd">&#39;&#39;&#39;Converts the input string into pythons None-type if the string</span>
     217<span class="sd">    contains string &quot;None&quot;.</span>
     218
     219<span class="sd">    Parameters</span>
     220<span class="sd">    ----------</span>
     221<span class="sd">    value : :obj:`string`</span>
     222<span class="sd">        String to be checked for the &quot;None&quot; word.</span>
     223
     224<span class="sd">    Return</span>
     225<span class="sd">    ------</span>
     226<span class="sd">    None or value:</span>
     227<span class="sd">        Return depends on the content of the input value. If it was &quot;None&quot;,</span>
     228<span class="sd">        then the python type None is returned. Otherwise the string itself.</span>
    229229<span class="sd">    &#39;&#39;&#39;</span>
    230230    <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;None&#39;</span><span class="p">:</span>
     
    232232    <span class="k">return</span> <span class="n">value</span></div>
    233233
    234 <div class="viewcode-block" id="none_or_int"><a class="viewcode-back" href="../code.html#tools.none_or_int">[docs]</a><span class="k">def</span> <span class="nf">none_or_int</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
    235     <span class="sd">&#39;&#39;&#39;</span>
    236 <span class="sd">    @Description:</span>
    237 <span class="sd">        Converts the input string into pythons None-type if the string</span>
    238 <span class="sd">        contains &quot;None&quot;. Otherwise it is converted to an integer value.</span>
    239 
    240 <span class="sd">    @Input:</span>
    241 <span class="sd">        value: string</span>
    242 <span class="sd">            String to be checked for the &quot;None&quot; word.</span>
    243 
    244 <span class="sd">    @Return:</span>
    245 <span class="sd">        None or int(value):</span>
    246 <span class="sd">            Return depends on the content of the input value. If it was &quot;None&quot;,</span>
    247 <span class="sd">            then the python type None is returned. Otherwise the string is</span>
    248 <span class="sd">            converted into an integer value.</span>
     234<div class="viewcode-block" id="none_or_int"><a class="viewcode-back" href="../api.html#tools.none_or_int">[docs]</a><span class="k">def</span> <span class="nf">none_or_int</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
     235    <span class="sd">&#39;&#39;&#39;Converts the input string into pythons None-type if the string</span>
     236<span class="sd">    contains string &quot;None&quot;. Otherwise it is converted to an integer value.</span>
     237
     238<span class="sd">    Parameters</span>
     239<span class="sd">    ----------</span>
     240<span class="sd">    value : :obj:`string`</span>
     241<span class="sd">        String to be checked for the &quot;None&quot; word.</span>
     242
     243<span class="sd">    Return</span>
     244<span class="sd">    ------</span>
     245<span class="sd">    None or int(value):</span>
     246<span class="sd">        Return depends on the content of the input value. If it was &quot;None&quot;,</span>
     247<span class="sd">        then the python type None is returned. Otherwise the string is</span>
     248<span class="sd">        converted into an integer value.</span>
    249249<span class="sd">    &#39;&#39;&#39;</span>
    250250    <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;None&#39;</span><span class="p">:</span>
     
    252252    <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">value</span><span class="p">)</span></div>
    253253
    254 <div class="viewcode-block" id="get_cmdline_arguments"><a class="viewcode-back" href="../code.html#tools.get_cmdline_arguments">[docs]</a><span class="k">def</span> <span class="nf">get_cmdline_arguments</span><span class="p">():</span>
    255     <span class="sd">&#39;&#39;&#39;</span>
    256 <span class="sd">    @Description:</span>
    257 <span class="sd">        Decomposes the command line arguments and assigns them to variables.</span>
    258 <span class="sd">        Apply default values for non mentioned arguments.</span>
    259 
    260 <span class="sd">    @Input:</span>
    261 <span class="sd">        &lt;nothing&gt;</span>
    262 
    263 <span class="sd">    @Return:</span>
    264 <span class="sd">        args: instance of ArgumentParser</span>
    265 <span class="sd">            Contains the commandline arguments from script/program call.</span>
     254<div class="viewcode-block" id="get_cmdline_arguments"><a class="viewcode-back" href="../api.html#tools.get_cmdline_arguments">[docs]</a><span class="k">def</span> <span class="nf">get_cmdline_arguments</span><span class="p">():</span>
     255    <span class="sd">&#39;&#39;&#39;Decomposes the command line arguments and assigns them to variables.</span>
     256<span class="sd">    Apply default values for non mentioned arguments.</span>
     257
     258<span class="sd">    Parameters</span>
     259<span class="sd">    ----------</span>
     260
     261<span class="sd">    Return</span>
     262<span class="sd">    ------</span>
     263<span class="sd">    args : :obj:`Namespace`</span>
     264<span class="sd">        Contains the commandline arguments from script/program call.</span>
    266265<span class="sd">    &#39;&#39;&#39;</span>
    267266
     
    342341    <span class="k">return</span> <span class="n">args</span></div>
    343342
    344 <div class="viewcode-block" id="read_ecenv"><a class="viewcode-back" href="../code.html#tools.read_ecenv">[docs]</a><span class="k">def</span> <span class="nf">read_ecenv</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
    345     <span class="sd">&#39;&#39;&#39;</span>
    346 <span class="sd">    @Description:</span>
    347 <span class="sd">        Reads the file into a dictionary where the key values are the parameter</span>
    348 <span class="sd">        names.</span>
    349 
    350 <span class="sd">    @Input:</span>
    351 <span class="sd">        filename: string</span>
    352 <span class="sd">            Path to file where the ECMWV environment parameters are stored.</span>
    353 
    354 <span class="sd">    @Return:</span>
    355 <span class="sd">        envs: dict</span>
    356 <span class="sd">            Contains the environment parameter ecuid, ecgid, gateway</span>
    357 <span class="sd">            and destination for ECMWF server environments.</span>
     343<div class="viewcode-block" id="read_ecenv"><a class="viewcode-back" href="../api.html#tools.read_ecenv">[docs]</a><span class="k">def</span> <span class="nf">read_ecenv</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
     344    <span class="sd">&#39;&#39;&#39;Reads the file into a dictionary where the key values are the parameter</span>
     345<span class="sd">    names.</span>
     346
     347<span class="sd">    Parameters</span>
     348<span class="sd">    ----------</span>
     349<span class="sd">    filename : :obj:`string`</span>
     350<span class="sd">        Path to file where the ECMWF environment parameters are stored.</span>
     351
     352<span class="sd">    Return</span>
     353<span class="sd">    ------</span>
     354<span class="sd">    envs : :obj:`dictionary`</span>
     355<span class="sd">        Contains the environment parameter ecuid, ecgid, gateway</span>
     356<span class="sd">        and destination for ECMWF server environments.</span>
    358357<span class="sd">    &#39;&#39;&#39;</span>
    359358    <span class="n">envs</span><span class="o">=</span> <span class="p">{}</span>
     
    366365    <span class="k">return</span> <span class="n">envs</span></div>
    367366
    368 <div class="viewcode-block" id="clean_up"><a class="viewcode-back" href="../code.html#tools.clean_up">[docs]</a><span class="k">def</span> <span class="nf">clean_up</span><span class="p">(</span><span class="n">c</span><span class="p">):</span>
    369     <span class="sd">&#39;&#39;&#39;</span>
    370 <span class="sd">    @Description:</span>
    371 <span class="sd">        Remove all files from intermediate directory</span>
    372 <span class="sd">        (inputdir from CONTROL file).</span>
    373 
    374 <span class="sd">    @Input:</span>
    375 <span class="sd">        c: instance of class ControlFile</span>
    376 <span class="sd">            Contains all the parameters of CONTROL file and</span>
    377 <span class="sd">            command line.</span>
    378 <span class="sd">            For more information about format and content of the parameter</span>
    379 <span class="sd">            see documentation.</span>
    380 
    381 <span class="sd">    @Return:</span>
    382 <span class="sd">        &lt;nothing&gt;</span>
     367<div class="viewcode-block" id="clean_up"><a class="viewcode-back" href="../api.html#tools.clean_up">[docs]</a><span class="k">def</span> <span class="nf">clean_up</span><span class="p">(</span><span class="n">c</span><span class="p">):</span>
     368    <span class="sd">&#39;&#39;&#39;Remove all files from intermediate directory (inputdir).</span>
     369
     370<span class="sd">    Parameters</span>
     371<span class="sd">    ----------</span>
     372<span class="sd">    c : :obj:`ControlFile`</span>
     373<span class="sd">        Contains all the parameters of CONTROL file and</span>
     374<span class="sd">        command line.</span>
     375
     376<span class="sd">    Return</span>
     377<span class="sd">    ------</span>
     378
    383379<span class="sd">    &#39;&#39;&#39;</span>
    384380
     
    397393
    398394
    399 <div class="viewcode-block" id="my_error"><a class="viewcode-back" href="../code.html#tools.my_error">[docs]</a><span class="k">def</span> <span class="nf">my_error</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;ERROR&#39;</span><span class="p">):</span>
    400     <span class="sd">&#39;&#39;&#39;</span>
    401 <span class="sd">    @Description:</span>
    402 <span class="sd">        Prints a specified error message which can be passed to the function</span>
    403 <span class="sd">        before exiting the program.</span>
    404 
    405 <span class="sd">    @Input:</span>
    406 <span class="sd">        user: list of strings</span>
    407 <span class="sd">            Contains all email addresses which should be notified.</span>
    408 <span class="sd">            It might also contain just the ecmwf user name which wil trigger</span>
    409 <span class="sd">            mailing to the associated email address for this user.</span>
    410 
    411 <span class="sd">        message: string, optional</span>
    412 <span class="sd">            Error message. Default value is &quot;ERROR&quot;.</span>
    413 
    414 <span class="sd">    @Return:</span>
    415 <span class="sd">        &lt;nothing&gt;</span>
     395<div class="viewcode-block" id="my_error"><a class="viewcode-back" href="../api.html#tools.my_error">[docs]</a><span class="k">def</span> <span class="nf">my_error</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;ERROR&#39;</span><span class="p">):</span>
     396    <span class="sd">&#39;&#39;&#39;Prints a specified error message which can be passed to the function</span>
     397<span class="sd">    before exiting the program.</span>
     398
     399<span class="sd">    Parameters</span>
     400<span class="sd">    ----------</span>
     401<span class="sd">    user : :obj:`list` of :obj:`string`</span>
     402<span class="sd">        Contains all email addresses which should be notified.</span>
     403<span class="sd">        It might also contain just the ecmwf user name which wil trigger</span>
     404<span class="sd">        mailing to the associated email address for this user.</span>
     405
     406<span class="sd">    message : :obj:`string`, optional</span>
     407<span class="sd">        Error message. Default value is &quot;ERROR&quot;.</span>
     408
     409<span class="sd">    Return</span>
     410<span class="sd">    ------</span>
     411
    416412<span class="sd">    &#39;&#39;&#39;</span>
    417413
     
    443439
    444440
    445 <div class="viewcode-block" id="normal_exit"><a class="viewcode-back" href="../code.html#tools.normal_exit">[docs]</a><span class="k">def</span> <span class="nf">normal_exit</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;Done!&#39;</span><span class="p">):</span>
    446     <span class="sd">&#39;&#39;&#39;</span>
    447 <span class="sd">    @Description:</span>
    448 <span class="sd">        Prints a specific exit message which can be passed to the function.</span>
    449 
    450 <span class="sd">    @Input:</span>
    451 <span class="sd">        user: list of strings</span>
    452 <span class="sd">            Contains all email addresses which should be notified.</span>
    453 <span class="sd">            It might also contain just the ecmwf user name which wil trigger</span>
    454 <span class="sd">            mailing to the associated email address for this user.</span>
    455 
    456 <span class="sd">        message: string, optional</span>
    457 <span class="sd">            Message for exiting program. Default value is &quot;Done!&quot;.</span>
    458 
    459 <span class="sd">    @Return:</span>
    460 <span class="sd">        &lt;nothing&gt;</span>
     441<div class="viewcode-block" id="normal_exit"><a class="viewcode-back" href="../api.html#tools.normal_exit">[docs]</a><span class="k">def</span> <span class="nf">normal_exit</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;Done!&#39;</span><span class="p">):</span>
     442    <span class="sd">&#39;&#39;&#39;Prints a specific exit message which can be passed to the function.</span>
     443
     444<span class="sd">    Parameters</span>
     445<span class="sd">    ----------</span>
     446<span class="sd">    user : :obj:`list` of :obj:`string`</span>
     447<span class="sd">        Contains all email addresses which should be notified.</span>
     448<span class="sd">        It might also contain just the ecmwf user name which wil trigger</span>
     449<span class="sd">        mailing to the associated email address for this user.</span>
     450
     451<span class="sd">    message : :obj:`string`, optional</span>
     452<span class="sd">        Message for exiting program. Default value is &quot;Done!&quot;.</span>
     453
     454<span class="sd">    Return</span>
     455<span class="sd">    ------</span>
    461456
    462457<span class="sd">    &#39;&#39;&#39;</span>
     
    485480
    486481
    487 <div class="viewcode-block" id="product"><a class="viewcode-back" href="../code.html#tools.product">[docs]</a><span class="k">def</span> <span class="nf">product</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
    488     <span class="sd">&#39;&#39;&#39;</span>
    489 <span class="sd">    @Description:</span>
    490 <span class="sd">        This method is taken from an example at the ECMWF wiki website.</span>
    491 <span class="sd">        https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16</span>
    492 
    493 <span class="sd">        This method combines the single characters of the passed arguments</span>
    494 <span class="sd">        with each other. So that each character of each argument value</span>
    495 <span class="sd">        will be combined with each character of the other arguments as a tuple.</span>
    496 
    497 <span class="sd">        Example:</span>
    498 <span class="sd">        product(&#39;ABCD&#39;, &#39;xy&#39;) --&gt; Ax Ay Bx By Cx Cy Dx Dy</span>
    499 <span class="sd">        product(range(2), repeat = 3) --&gt; 000 001 010 011 100 101 110 111</span>
    500 
    501 <span class="sd">    @Input:</span>
    502 <span class="sd">        *args: tuple</span>
    503 <span class="sd">            Positional arguments (arbitrary number).</span>
    504 
    505 <span class="sd">        **kwds: dictionary</span>
    506 <span class="sd">            Contains all the keyword arguments from *args.</span>
    507 
    508 <span class="sd">    @Return:</span>
    509 <span class="sd">        prod: tuple</span>
    510 <span class="sd">            Return will be done with &quot;yield&quot;. A tuple of combined arguments.</span>
    511 <span class="sd">            See example in description above.</span>
     482<div class="viewcode-block" id="product"><a class="viewcode-back" href="../api.html#tools.product">[docs]</a><span class="k">def</span> <span class="nf">product</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
     483    <span class="sd">&#39;&#39;&#39;This method combines the single characters of the passed arguments</span>
     484<span class="sd">    with each other. So that each character of each argument value</span>
     485<span class="sd">    will be combined with each character of the other arguments as a tuple.</span>
     486
     487<span class="sd">    Note</span>
     488<span class="sd">    ----</span>
     489<span class="sd">    This method is taken from an example at the ECMWF wiki website.</span>
     490<span class="sd">    https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16</span>
     491
     492<span class="sd">    Example</span>
     493<span class="sd">    -------</span>
     494<span class="sd">    product(&#39;ABCD&#39;, &#39;xy&#39;) --&gt; Ax Ay Bx By Cx Cy Dx Dy</span>
     495
     496<span class="sd">    product(range(2), repeat = 3) --&gt; 000 001 010 011 100 101 110 111</span>
     497
     498<span class="sd">    Parameters</span>
     499<span class="sd">    ----------</span>
     500<span class="sd">    \*args : :obj:`tuple`</span>
     501<span class="sd">        Positional arguments (arbitrary number).</span>
     502
     503<span class="sd">    \*\*kwds : :obj:`dictionary`</span>
     504<span class="sd">        Contains all the keyword arguments from \*args.</span>
     505
     506<span class="sd">    Return</span>
     507<span class="sd">    ------</span>
     508<span class="sd">    prod : :obj:`tuple`</span>
     509<span class="sd">        Return will be done with &quot;yield&quot;. A tuple of combined arguments.</span>
     510<span class="sd">        See example in description above.</span>
    512511<span class="sd">    &#39;&#39;&#39;</span>
    513512    <span class="n">pools</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">tuple</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">*</span> <span class="n">kwds</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;repeat&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
     
    521520
    522521
    523 <div class="viewcode-block" id="silent_remove"><a class="viewcode-back" href="../code.html#tools.silent_remove">[docs]</a><span class="k">def</span> <span class="nf">silent_remove</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
    524     <span class="sd">&#39;&#39;&#39;</span>
    525 <span class="sd">    @Description:</span>
    526 <span class="sd">        Remove file if it exists.</span>
    527 <span class="sd">        The function does not fail if the file does not exist.</span>
    528 
    529 <span class="sd">    @Input:</span>
    530 <span class="sd">        filename: string</span>
    531 <span class="sd">            The name of the file to be removed without notification.</span>
    532 
    533 <span class="sd">    @Return:</span>
    534 <span class="sd">        &lt;nothing&gt;</span>
     522<div class="viewcode-block" id="silent_remove"><a class="viewcode-back" href="../api.html#tools.silent_remove">[docs]</a><span class="k">def</span> <span class="nf">silent_remove</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
     523    <span class="sd">&#39;&#39;&#39;Remove file if it exists.</span>
     524<span class="sd">    The function does not fail if the file does not exist.</span>
     525
     526<span class="sd">    Parameters</span>
     527<span class="sd">    ----------</span>
     528<span class="sd">    filename : :obj:`string`</span>
     529<span class="sd">        The name of the file to be removed without notification.</span>
     530
     531<span class="sd">    Return</span>
     532<span class="sd">    ------</span>
     533
    535534<span class="sd">    &#39;&#39;&#39;</span>
    536535    <span class="k">try</span><span class="p">:</span>
     
    544543
    545544
    546 <div class="viewcode-block" id="init128"><a class="viewcode-back" href="../code.html#tools.init128">[docs]</a><span class="k">def</span> <span class="nf">init128</span><span class="p">(</span><span class="n">filepath</span><span class="p">):</span>
    547     <span class="sd">&#39;&#39;&#39;</span>
    548 <span class="sd">    @Description:</span>
    549 <span class="sd">        Opens and reads the grib file with table 128 information.</span>
    550 
    551 <span class="sd">    @Input:</span>
    552 <span class="sd">        filepath: string</span>
    553 <span class="sd">            Path to file of ECMWF grib table number 128.</span>
    554 
    555 <span class="sd">    @Return:</span>
    556 <span class="sd">        table128: dictionary</span>
    557 <span class="sd">            Contains the ECMWF grib table 128 information.</span>
    558 <span class="sd">            The key is the parameter number and the value is the</span>
    559 <span class="sd">            short name of the parameter.</span>
     545<div class="viewcode-block" id="init128"><a class="viewcode-back" href="../api.html#tools.init128">[docs]</a><span class="k">def</span> <span class="nf">init128</span><span class="p">(</span><span class="n">filepath</span><span class="p">):</span>
     546    <span class="sd">&#39;&#39;&#39;Opens and reads the grib file with table 128 information.</span>
     547
     548<span class="sd">    Parameters</span>
     549<span class="sd">    ----------</span>
     550<span class="sd">    filepath : :obj:`string`</span>
     551<span class="sd">        Path to file of ECMWF grib table number 128.</span>
     552
     553<span class="sd">    Return</span>
     554<span class="sd">    ------</span>
     555<span class="sd">    table128 : :obj:`dictionary`</span>
     556<span class="sd">        Contains the ECMWF grib table 128 information.</span>
     557<span class="sd">        The key is the parameter number and the value is the</span>
     558<span class="sd">        short name of the parameter.</span>
    560559<span class="sd">    &#39;&#39;&#39;</span>
    561560    <span class="n">table128</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
     
    569568
    570569
    571 <div class="viewcode-block" id="to_param_id"><a class="viewcode-back" href="../code.html#tools.to_param_id">[docs]</a><span class="k">def</span> <span class="nf">to_param_id</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span> <span class="n">table</span><span class="p">):</span>
    572     <span class="sd">&#39;&#39;&#39;</span>
    573 <span class="sd">    @Description:</span>
    574 <span class="sd">        Transform parameter names to parameter ids</span>
    575 <span class="sd">        with ECMWF grib table 128.</span>
    576 
    577 <span class="sd">    @Input:</span>
    578 <span class="sd">        pars: string</span>
    579 <span class="sd">            Addpar argument from CONTROL file in the format of</span>
    580 <span class="sd">            parameter names instead of ids. The parameter short</span>
    581 <span class="sd">            names are sepearted with &quot;/&quot; and they are passed as</span>
    582 <span class="sd">            one single string.</span>
    583 
    584 <span class="sd">        table: dictionary</span>
    585 <span class="sd">            Contains the ECMWF grib table 128 information.</span>
    586 <span class="sd">            The key is the parameter number and the value is the</span>
    587 <span class="sd">            short name of the parameter.</span>
    588 
    589 <span class="sd">    @Return:</span>
    590 <span class="sd">        ipar: list of integer</span>
    591 <span class="sd">            List of addpar parameters from CONTROL file transformed to</span>
    592 <span class="sd">            parameter ids in the format of integer.</span>
     570<div class="viewcode-block" id="to_param_id"><a class="viewcode-back" href="../api.html#tools.to_param_id">[docs]</a><span class="k">def</span> <span class="nf">to_param_id</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span> <span class="n">table</span><span class="p">):</span>
     571    <span class="sd">&#39;&#39;&#39;Transform parameter names to parameter ids with ECMWF grib table 128.</span>
     572
     573<span class="sd">    Parameters</span>
     574<span class="sd">    ----------</span>
     575<span class="sd">    pars : :obj:`string`</span>
     576<span class="sd">        Addpar argument from CONTROL file in the format of</span>
     577<span class="sd">        parameter names instead of ids. The parameter short</span>
     578<span class="sd">        names are sepearted with &quot;/&quot; and they are passed as</span>
     579<span class="sd">        one single string.</span>
     580
     581<span class="sd">    table : :obj:`dictionary`</span>
     582<span class="sd">        Contains the ECMWF grib table 128 information.</span>
     583<span class="sd">        The key is the parameter number and the value is the</span>
     584<span class="sd">        short name of the parameter.</span>
     585
     586<span class="sd">    Return</span>
     587<span class="sd">    ------</span>
     588<span class="sd">    ipar : :obj:`list` of :obj:`integer`</span>
     589<span class="sd">        List of addpar parameters from CONTROL file transformed to</span>
     590<span class="sd">        parameter ids in the format of integer.</span>
    593591<span class="sd">    &#39;&#39;&#39;</span>
    594592    <span class="n">cpar</span> <span class="o">=</span> <span class="n">pars</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span>
     
    604602    <span class="k">return</span> <span class="n">ipar</span></div>
    605603
    606 <div class="viewcode-block" id="get_list_as_string"><a class="viewcode-back" href="../code.html#tools.get_list_as_string">[docs]</a><span class="k">def</span> <span class="nf">get_list_as_string</span><span class="p">(</span><span class="n">list_obj</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">&#39;, &#39;</span><span class="p">):</span>
    607     <span class="sd">&#39;&#39;&#39;</span>
    608 <span class="sd">    @Description:</span>
    609 <span class="sd">        Converts a list of arbitrary content into a single string.</span>
    610 
    611 <span class="sd">    @Input:</span>
    612 <span class="sd">        list_obj: list</span>
    613 <span class="sd">            A list with arbitrary content.</span>
    614 
    615 <span class="sd">        concatenate_sign: string, optional</span>
    616 <span class="sd">            A string which is used to concatenate the single</span>
    617 <span class="sd">            list elements. Default value is &quot;, &quot;.</span>
    618 
    619 <span class="sd">    @Return:</span>
    620 <span class="sd">        str_of_list: string</span>
    621 <span class="sd">            The content of the list as a single string.</span>
     604<div class="viewcode-block" id="get_list_as_string"><a class="viewcode-back" href="../api.html#tools.get_list_as_string">[docs]</a><span class="k">def</span> <span class="nf">get_list_as_string</span><span class="p">(</span><span class="n">list_obj</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">&#39;, &#39;</span><span class="p">):</span>
     605    <span class="sd">&#39;&#39;&#39;Converts a list of arbitrary content into a single string.</span>
     606
     607<span class="sd">    Parameters</span>
     608<span class="sd">    ----------</span>
     609<span class="sd">    list_obj : :obj:`list`</span>
     610<span class="sd">        A list with arbitrary content.</span>
     611
     612<span class="sd">    concatenate_sign : :obj:`string`, optional</span>
     613<span class="sd">        A string which is used to concatenate the single</span>
     614<span class="sd">        list elements. Default value is &quot;, &quot;.</span>
     615
     616<span class="sd">    Return</span>
     617<span class="sd">    ------</span>
     618<span class="sd">    str_of_list : :obj:`string`</span>
     619<span class="sd">        The content of the list as a single string.</span>
    622620<span class="sd">    &#39;&#39;&#39;</span>
    623621
     
    626624    <span class="k">return</span> <span class="n">str_of_list</span></div>
    627625
    628 <div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../code.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
    629     <span class="sd">&#39;&#39;&#39;</span>
    630 <span class="sd">    @Description:</span>
    631 <span class="sd">        Creates a directory and gives a warning if the directory</span>
    632 <span class="sd">        already exists. The program stops only if there is another problem.</span>
    633 
    634 <span class="sd">    @Input:</span>
    635 <span class="sd">        directory: string</span>
    636 <span class="sd">            The directory name including the path which should be created.</span>
    637 
    638 <span class="sd">    @Return:</span>
    639 <span class="sd">        &lt;nothing&gt;</span>
     626<div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../api.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
     627    <span class="sd">&#39;&#39;&#39;Creates a directory and gives a warning if the directory</span>
     628<span class="sd">    already exists. The program stops only if there is another problem.</span>
     629
     630<span class="sd">    Parameters</span>
     631<span class="sd">    ----------</span>
     632<span class="sd">    directory : :obj:`string`</span>
     633<span class="sd">        The directory name including the path which should be created.</span>
     634
     635<span class="sd">    Return</span>
     636<span class="sd">    ------</span>
     637
    640638<span class="sd">    &#39;&#39;&#39;</span>
    641639    <span class="k">try</span><span class="p">:</span>
     
    650648    <span class="k">return</span></div>
    651649
    652 <div class="viewcode-block" id="put_file_to_ecserver"><a class="viewcode-back" href="../code.html#tools.put_file_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">put_file_to_ecserver</span><span class="p">(</span><span class="n">ecd</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">ecuid</span><span class="p">,</span> <span class="n">ecgid</span><span class="p">):</span>
    653     <span class="sd">&#39;&#39;&#39;</span>
    654 <span class="sd">    @Description:</span>
    655 <span class="sd">        Uses the ecaccess-file-put command to send a file to the ECMWF servers.</span>
    656 
    657 <span class="sd">        NOTE:</span>
    658 <span class="sd">        The return value is just for testing reasons. It does not have</span>
    659 <span class="sd">        to be used from the calling function since the whole error handling</span>
    660 <span class="sd">        is done in here.</span>
    661 
    662 <span class="sd">    @Input:</span>
    663 <span class="sd">        ecd: string</span>
    664 <span class="sd">            The path were the file is stored.</span>
    665 
    666 <span class="sd">        filename: string</span>
    667 <span class="sd">            The name of the file to send to the ECMWF server.</span>
    668 
    669 <span class="sd">        target: string</span>
    670 <span class="sd">            The target queue where the file should be sent to.</span>
    671 
    672 <span class="sd">        ecuid: string</span>
    673 <span class="sd">            The user id on ECMWF server.</span>
    674 
    675 <span class="sd">        ecgid: string</span>
    676 <span class="sd">            The group id on ECMWF server.</span>
    677 
    678 <span class="sd">    @Return:</span>
    679 <span class="sd">        rcode: string</span>
    680 <span class="sd">            Resulting code of command execution. If successful the string</span>
    681 <span class="sd">            will be empty.</span>
     650<div class="viewcode-block" id="put_file_to_ecserver"><a class="viewcode-back" href="../api.html#tools.put_file_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">put_file_to_ecserver</span><span class="p">(</span><span class="n">ecd</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">ecuid</span><span class="p">,</span> <span class="n">ecgid</span><span class="p">):</span>
     651    <span class="sd">&#39;&#39;&#39;Uses the ecaccess-file-put command to send a file to the ECMWF servers.</span>
     652
     653<span class="sd">    Note</span>
     654<span class="sd">    ----</span>
     655<span class="sd">    The return value is just for testing reasons. It does not have</span>
     656<span class="sd">    to be used from the calling function since the whole error handling</span>
     657<span class="sd">    is done in here.</span>
     658
     659<span class="sd">    Parameters</span>
     660<span class="sd">    ----------</span>
     661<span class="sd">    ecd : :obj:`string`</span>
     662<span class="sd">        The path were the file is stored.</span>
     663
     664<span class="sd">    filename : :obj:`string`</span>
     665<span class="sd">        The name of the file to send to the ECMWF server.</span>
     666
     667<span class="sd">    target : :obj:`string`</span>
     668<span class="sd">        The target queue where the file should be sent to.</span>
     669
     670<span class="sd">    ecuid : :obj:`string`</span>
     671<span class="sd">        The user id on ECMWF server.</span>
     672
     673<span class="sd">    ecgid : :obj:`string`</span>
     674<span class="sd">        The group id on ECMWF server.</span>
     675
     676<span class="sd">    Return</span>
     677<span class="sd">    ------</span>
     678<span class="sd">    rcode : :obj:`string`</span>
     679<span class="sd">        Resulting code of command execution. If successful the string</span>
     680<span class="sd">        will be empty.</span>
    682681<span class="sd">    &#39;&#39;&#39;</span>
    683682
     
    698697    <span class="k">return</span> <span class="n">rcode</span></div>
    699698
    700 <div class="viewcode-block" id="submit_job_to_ecserver"><a class="viewcode-back" href="../code.html#tools.submit_job_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">submit_job_to_ecserver</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">jobname</span><span class="p">):</span>
    701     <span class="sd">&#39;&#39;&#39;</span>
    702 <span class="sd">    @Description:</span>
    703 <span class="sd">        Uses ecaccess-job-submit command to submit a job to the ECMWF server.</span>
    704 
    705 <span class="sd">        NOTE:</span>
    706 <span class="sd">        The return value is just for testing reasons. It does not have</span>
    707 <span class="sd">        to be used from the calling function since the whole error handling</span>
    708 <span class="sd">        is done in here.</span>
    709 
    710 <span class="sd">    @Input:</span>
    711 <span class="sd">        target: string</span>
    712 <span class="sd">            The target where the file should be sent to, e.g. the queue.</span>
    713 
    714 <span class="sd">        jobname: string</span>
    715 <span class="sd">            The name of the jobfile to be submitted to the ECMWF server.</span>
    716 
    717 <span class="sd">    @Return:</span>
    718 <span class="sd">        rcode: string</span>
    719 <span class="sd">            Resulting code of command execution. If successful the string</span>
    720 <span class="sd">            will contain an integer number, representing the id of the job</span>
    721 <span class="sd">            at the ecmwf server.</span>
     699<div class="viewcode-block" id="submit_job_to_ecserver"><a class="viewcode-back" href="../api.html#tools.submit_job_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">submit_job_to_ecserver</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">jobname</span><span class="p">):</span>
     700    <span class="sd">&#39;&#39;&#39;Uses ecaccess-job-submit command to submit a job to the ECMWF server.</span>
     701
     702<span class="sd">    Note</span>
     703<span class="sd">    ----</span>
     704<span class="sd">    The return value is just for testing reasons. It does not have</span>
     705<span class="sd">    to be used from the calling function since the whole error handling</span>
     706<span class="sd">    is done in here.</span>
     707
     708<span class="sd">    Parameters</span>
     709<span class="sd">    ----------</span>
     710<span class="sd">    target : :obj:`string`</span>
     711<span class="sd">        The target where the file should be sent to, e.g. the queue.</span>
     712
     713<span class="sd">    jobname : :obj:`string`</span>
     714<span class="sd">        The name of the jobfile to be submitted to the ECMWF server.</span>
     715
     716<span class="sd">    Return</span>
     717<span class="sd">    ------</span>
     718<span class="sd">    rcode : :obj:`string`</span>
     719<span class="sd">        Resulting code of command execution. If successful the string</span>
     720<span class="sd">        will contain an integer number, representing the id of the job</span>
     721<span class="sd">        at the ecmwf server.</span>
    722722<span class="sd">    &#39;&#39;&#39;</span>
    723723
  • documentation/Sphinx/build/html/_sources/api.rst.txt

    r708c667 r274f9ef  
    22============================
    33
     4.. contents::
     5    :local:
     6   
     7Porgrams
     8--------
     9
     10install
     11*******
     12
     13.. automodule:: install
     14    :members:
     15   
     16submit
     17******
     18
     19.. automodule:: submit
     20    :members:
     21   
     22Classes
     23-------
     24
     25ControlFile
     26***********
     27
     28.. automodule:: ControlFile
     29    :members:
     30   
     31EcFlexpart
     32**********
     33
     34.. automodule:: EcFlexpart
     35    :members:
     36   
     37GribTools
     38*********
     39
     40.. automodule:: GribTools
     41    :members:
     42
     43MarsRetrieval
     44*************
     45
     46.. automodule:: MarsRetrieval
     47    :members:
     48
     49UioFiles
     50********
     51
     52.. automodule:: UioFiles
     53    :members:
     54
     55
     56
     57Modules
     58-------
     59
     60get_mars_data
     61*************
     62
     63.. automodule:: get_mars_data
     64    :members:
     65 
     66prepare_flexpart
     67****************
     68
     69.. automodule:: prepare_flexpart
     70    :members:   
     71   
     72tools
     73*****
     74
     75.. automodule:: tools
     76    :members:
     77
     78disaggregation
     79**************   
     80   
    481.. automodule:: disaggregation
    582    :members:
  • documentation/Sphinx/build/html/_sources/downloads.rst.txt

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    downloads/tar_balls
     13    downloads/git_repo
     14    downloads/history_changes
     15   
  • documentation/Sphinx/build/html/_sources/index.rst.txt

    r708c667 r274f9ef  
    44   contain the root `toctree` directive.
    55
    6 Welcome to flex_extract's documentation!
    7 ========================================
     6Welcome to flex_extract's user documentation!
     7=============================================
     8
     9flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.
     10
     11
     12.. The scripts can be 1) executed locally using the ECMWF WebMARS interface, or 2) on the ECMWF member
     13.. state gateway server or HPC facility using the ecaccess software package. As another option the scripts can 3)
     14.. also be triggered using ecflow scheduling software used by ECMWF for data dissemination.
     15
     16All required second party software and libraries used within flex_extract is open source and free of charge.
     17
     18
    819.. raw:: html
    920
     
    8798
    8899.. toctree::
    89    :maxdepth: 2
     100   :maxdepth: 3
    90101   :caption: Table of Contents:
    91102
  • documentation/Sphinx/build/html/_sources/installation.rst.txt

    r708c667 r274f9ef  
    11Installation
    22============
    3 
    4 Describe installation process flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    installation/requirements
     11    installation/oper_modes
     12    installation/test_install
     13
     14
     15   
  • documentation/Sphinx/build/html/_sources/program_structure.rst.txt

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    program_structure/prog_overview
     13    program_structure/prog_components
     14    program_structure/prog_flow
  • documentation/Sphinx/build/html/_sources/requirements.rst.txt

    r708c667 r274f9ef  
    22============
    33
    4 Describe the requirements to use flex_extract ....
    54 
    65    UNDER CONSTRUCTION
     6   
  • documentation/Sphinx/build/html/_sources/support.rst.txt

    r708c667 r274f9ef  
    22=======
    33
    4 Describe support options ....
    54 
    65    UNDER CONSTRUCTION
     6   
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    support/ticket_system
     13    support/mailing_list
     14    support/known_bugs_issues
     15    support/faq
     16       
  • documentation/Sphinx/build/html/_sources/user_guide.rst.txt

    r708c667 r274f9ef  
    11User Guide
    22==========
    3 
    4 Describe using flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    user_guide/how_to
     11    user_guide/control_templates
     12   
  • documentation/Sphinx/build/html/api.html

    r708c667 r274f9ef  
    3030    <link rel="search" title="Search" href="search.html" />
    3131    <link rel="next" title="Support" href="support.html" />
    32     <link rel="prev" title="User Guide" href="user_guide.html" />
     32    <link rel="prev" title="CONTROL-file templates" href="user_guide/control_templates.html" />
    3333
    3434 
     
    8989<li class="toctree-l1"><a class="reference internal" href="program_structure.html">Program Structure</a></li>
    9090<li class="toctree-l1"><a class="reference internal" href="user_guide.html">User Guide</a></li>
    91 <li class="toctree-l1 current"><a class="current reference internal" href="#">Auto Generated Documentation</a></li>
     91<li class="toctree-l1 current"><a class="current reference internal" href="#">Auto Generated Documentation</a><ul>
     92<li class="toctree-l2"><a class="reference internal" href="#porgrams">Porgrams</a><ul>
     93<li class="toctree-l3"><a class="reference internal" href="#module-install">install</a></li>
     94<li class="toctree-l3"><a class="reference internal" href="#module-submit">submit</a></li>
     95</ul>
     96</li>
     97<li class="toctree-l2"><a class="reference internal" href="#classes">Classes</a><ul>
     98<li class="toctree-l3"><a class="reference internal" href="#module-ControlFile">ControlFile</a></li>
     99<li class="toctree-l3"><a class="reference internal" href="#module-EcFlexpart">EcFlexpart</a></li>
     100<li class="toctree-l3"><a class="reference internal" href="#module-GribTools">GribTools</a></li>
     101<li class="toctree-l3"><a class="reference internal" href="#module-MarsRetrieval">MarsRetrieval</a></li>
     102<li class="toctree-l3"><a class="reference internal" href="#module-UioFiles">UioFiles</a></li>
     103</ul>
     104</li>
     105<li class="toctree-l2"><a class="reference internal" href="#modules">Modules</a><ul>
     106<li class="toctree-l3"><a class="reference internal" href="#module-get_mars_data">get_mars_data</a></li>
     107<li class="toctree-l3"><a class="reference internal" href="#module-prepare_flexpart">prepare_flexpart</a></li>
     108<li class="toctree-l3"><a class="reference internal" href="#module-tools">tools</a></li>
     109<li class="toctree-l3"><a class="reference internal" href="#module-disaggregation">disaggregation</a></li>
     110</ul>
     111</li>
     112</ul>
     113</li>
    92114<li class="toctree-l1"><a class="reference internal" href="support.html">Support</a></li>
    93115</ul>
     
    155177           <div itemprop="articleBody">
    156178           
    157   <div class="section" id="module-disaggregation">
    158 <span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-disaggregation" title="Permalink to this headline">¶</a></h1>
     179  <div class="section" id="auto-generated-documentation">
     180<h1>Auto Generated Documentation<a class="headerlink" href="#auto-generated-documentation" title="Permalink to this headline">¶</a></h1>
     181<div class="contents local topic" id="contents">
     182<ul class="simple">
     183<li><a class="reference internal" href="#porgrams" id="id1">Porgrams</a><ul>
     184<li><a class="reference internal" href="#module-install" id="id2">install</a></li>
     185<li><a class="reference internal" href="#module-submit" id="id3">submit</a></li>
     186</ul>
     187</li>
     188<li><a class="reference internal" href="#classes" id="id4">Classes</a><ul>
     189<li><a class="reference internal" href="#module-ControlFile" id="id5">ControlFile</a></li>
     190<li><a class="reference internal" href="#module-EcFlexpart" id="id6">EcFlexpart</a></li>
     191<li><a class="reference internal" href="#module-GribTools" id="id7">GribTools</a></li>
     192<li><a class="reference internal" href="#module-MarsRetrieval" id="id8">MarsRetrieval</a></li>
     193<li><a class="reference internal" href="#module-UioFiles" id="id9">UioFiles</a></li>
     194</ul>
     195</li>
     196<li><a class="reference internal" href="#modules" id="id10">Modules</a><ul>
     197<li><a class="reference internal" href="#module-get_mars_data" id="id11">get_mars_data</a></li>
     198<li><a class="reference internal" href="#module-prepare_flexpart" id="id12">prepare_flexpart</a></li>
     199<li><a class="reference internal" href="#module-tools" id="id13">tools</a></li>
     200<li><a class="reference internal" href="#module-disaggregation" id="id14">disaggregation</a></li>
     201</ul>
     202</li>
     203</ul>
     204</div>
     205<div class="section" id="porgrams">
     206<h2><a class="toc-backref" href="#id1">Porgrams</a><a class="headerlink" href="#porgrams" title="Permalink to this headline">¶</a></h2>
     207<div class="section" id="module-install">
     208<span id="install"></span><h3><a class="toc-backref" href="#id2">install</a><a class="headerlink" href="#module-install" title="Permalink to this headline">¶</a></h3>
     209<dl class="function">
     210<dt id="install.delete_convert_build">
     211<code class="descclassname">install.</code><code class="descname">delete_convert_build</code><span class="sig-paren">(</span><em>src_path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#delete_convert_build"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.delete_convert_build" title="Permalink to this definition">¶</a></dt>
     212<dd><p>Clean up the Fortran source directory and remove all
     213build files (e.g. *.o, *.mod and CONVERT2)</p>
     214<table class="docutils field-list" frame="void" rules="none">
     215<col class="field-name" />
     216<col class="field-body" />
     217<tbody valign="top">
     218<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>src_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the fortran source directory.</td>
     219</tr>
     220</tbody>
     221</table>
     222</dd></dl>
     223
     224<dl class="function">
     225<dt id="install.get_install_cmdline_arguments">
     226<code class="descclassname">install.</code><code class="descname">get_install_cmdline_arguments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#get_install_cmdline_arguments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.get_install_cmdline_arguments" title="Permalink to this definition">¶</a></dt>
     227<dd><p>Decomposes the command line arguments and assigns them to variables.
     228Apply default values for non mentioned arguments.</p>
     229<table class="docutils field-list" frame="void" rules="none">
     230<col class="field-name" />
     231<col class="field-body" />
     232<tbody valign="top">
     233<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>args</strong> – Contains the commandline arguments from script/program call.</td>
     234</tr>
     235<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code></td>
     236</tr>
     237</tbody>
     238</table>
     239</dd></dl>
     240
     241<dl class="function">
     242<dt id="install.install_via_gateway">
     243<code class="descclassname">install.</code><code class="descname">install_via_gateway</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#install_via_gateway"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.install_via_gateway" title="Permalink to this definition">¶</a></dt>
     244<dd><p>Perform the actual installation on local machine or prepare data
     245transfer to remote gate and submit a job script which will
     246install everything on the remote gate.</p>
     247<table class="docutils field-list" frame="void" rules="none">
     248<col class="field-name" />
     249<col class="field-body" />
     250<tbody valign="top">
     251<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     252command line.</td>
     253</tr>
     254</tbody>
     255</table>
     256</dd></dl>
     257
     258<dl class="function">
     259<dt id="install.main">
     260<code class="descclassname">install.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.main" title="Permalink to this definition">¶</a></dt>
     261<dd><p>Controls the installation process. Calls the installation function
     262if target is specified.</p>
     263</dd></dl>
     264
     265<dl class="function">
     266<dt id="install.make_convert_build">
     267<code class="descclassname">install.</code><code class="descname">make_convert_build</code><span class="sig-paren">(</span><em>src_path</em>, <em>makefile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#make_convert_build"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.make_convert_build" title="Permalink to this definition">¶</a></dt>
     268<dd><p>Compiles the Fortran code and generates the executable.</p>
     269<table class="docutils field-list" frame="void" rules="none">
     270<col class="field-name" />
     271<col class="field-body" />
     272<tbody valign="top">
     273<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     274<li><strong>src_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the fortran source directory.</li>
     275<li><strong>makefile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the makefile which should be used.</li>
     276</ul>
     277</td>
     278</tr>
     279</tbody>
     280</table>
     281</dd></dl>
     282
     283<dl class="function">
     284<dt id="install.mk_compilejob">
     285<code class="descclassname">install.</code><code class="descname">mk_compilejob</code><span class="sig-paren">(</span><em>makefile</em>, <em>target</em>, <em>ecuid</em>, <em>ecgid</em>, <em>fp_root</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_compilejob"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_compilejob" title="Permalink to this definition">¶</a></dt>
     286<dd><p>Modifies the original job template file so that it is specified
     287for the user and the environment were it will be applied. Result
     288is stored in a new file “job.temp” in the python directory.</p>
     289<table class="docutils field-list" frame="void" rules="none">
     290<col class="field-name" />
     291<col class="field-body" />
     292<tbody valign="top">
     293<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     294<li><strong>makefile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the makefile which should be used to compile FORTRAN
     295CONVERT2 program.</li>
     296<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target where the installation should be done, e.g. the queue.</li>
     297<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     298<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     299<li><strong>fp_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the root directory of FLEXPART environment or flex_extract
     300environment.</li>
     301</ul>
     302</td>
     303</tr>
     304</tbody>
     305</table>
     306</dd></dl>
     307
     308<dl class="function">
     309<dt id="install.mk_env_vars">
     310<code class="descclassname">install.</code><code class="descname">mk_env_vars</code><span class="sig-paren">(</span><em>ecuid</em>, <em>ecgid</em>, <em>gateway</em>, <em>destination</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_env_vars"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_env_vars" title="Permalink to this definition">¶</a></dt>
     311<dd><p>Creates a file named ECMWF_ENV which contains the
     312necessary environmental variables at ECMWF servers.
     313It is based on the template ECMWF_ENV.template.</p>
     314<table class="docutils field-list" frame="void" rules="none">
     315<col class="field-name" />
     316<col class="field-body" />
     317<tbody valign="top">
     318<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     319<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     320<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     321<li><strong>gateway</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The gateway server the user is using.</li>
     322<li><strong>destination</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The remote destination which is used to transfer files
     323from ECMWF server to local gateway server.</li>
     324</ul>
     325</td>
     326</tr>
     327</tbody>
     328</table>
     329</dd></dl>
     330
     331<dl class="function">
     332<dt id="install.mk_job_template">
     333<code class="descclassname">install.</code><code class="descname">mk_job_template</code><span class="sig-paren">(</span><em>ecuid</em>, <em>ecgid</em>, <em>gateway</em>, <em>destination</em>, <em>fp_root</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_job_template"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_job_template" title="Permalink to this definition">¶</a></dt>
     334<dd><p>Modifies the original job template file so that it is specified
     335for the user and the environment were it will be applied. Result
     336is stored in a new file.</p>
     337<table class="docutils field-list" frame="void" rules="none">
     338<col class="field-name" />
     339<col class="field-body" />
     340<tbody valign="top">
     341<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     342<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     343<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     344<li><strong>gateway</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The gateway server the user is using.</li>
     345<li><strong>destination</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The remote destination which is used to transfer files
     346from ECMWF server to local gateway server.</li>
     347<li><strong>fp_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the root directory of FLEXPART environment or flex_extract
     348environment.</li>
     349</ul>
     350</td>
     351</tr>
     352</tbody>
     353</table>
     354</dd></dl>
     355
     356<dl class="function">
     357<dt id="install.mk_tarball">
     358<code class="descclassname">install.</code><code class="descname">mk_tarball</code><span class="sig-paren">(</span><em>tarball_path</em>, <em>target</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_tarball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_tarball" title="Permalink to this definition">¶</a></dt>
     359<dd><p>Creates a tarball with all necessary files which need to be sent to the
     360installation directory.
     361It does not matter if this is local or remote.
     362Collects all python files, the Fortran source and makefiles,
     363the ECMWF_ENV file, the CONTROL files as well as the
     364template files.</p>
     365<table class="docutils field-list" frame="void" rules="none">
     366<col class="field-name" />
     367<col class="field-body" />
     368<tbody valign="top">
     369<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     370<li><strong>tarball_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The complete path to the tar file which will contain all
     371relevant data for flex_extract.</li>
     372<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The queue where the job is submitted to.</li>
     373</ul>
     374</td>
     375</tr>
     376</tbody>
     377</table>
     378</dd></dl>
     379
     380<dl class="function">
     381<dt id="install.un_tarball">
     382<code class="descclassname">install.</code><code class="descname">un_tarball</code><span class="sig-paren">(</span><em>tarball_path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#un_tarball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.un_tarball" title="Permalink to this definition">¶</a></dt>
     383<dd><p>Extracts the given tarball into current directory.</p>
     384<table class="docutils field-list" frame="void" rules="none">
     385<col class="field-name" />
     386<col class="field-body" />
     387<tbody valign="top">
     388<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tarball_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The complete path to the tar file which will contain all
     389relevant data for flex_extract.</td>
     390</tr>
     391</tbody>
     392</table>
     393</dd></dl>
     394
     395</div>
     396<div class="section" id="module-submit">
     397<span id="submit"></span><h3><a class="toc-backref" href="#id3">submit</a><a class="headerlink" href="#module-submit" title="Permalink to this headline">¶</a></h3>
     398<dl class="function">
     399<dt id="submit.main">
     400<code class="descclassname">submit.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/submit.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#submit.main" title="Permalink to this definition">¶</a></dt>
     401<dd><p>Get the arguments from script call and from CONTROL file.
     402Decides from the argument “queue” if the local version
     403is done “queue=None” or the gateway version with “queue=ecgate”
     404or “queue=cca”.</p>
     405</dd></dl>
     406
     407<dl class="function">
     408<dt id="submit.submit">
     409<code class="descclassname">submit.</code><code class="descname">submit</code><span class="sig-paren">(</span><em>jtemplate</em>, <em>c</em>, <em>queue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/submit.html#submit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#submit.submit" title="Permalink to this definition">¶</a></dt>
     410<dd><p>Prepares the job script and submit it to the specified queue.</p>
     411<table class="docutils field-list" frame="void" rules="none">
     412<col class="field-name" />
     413<col class="field-body" />
     414<tbody valign="top">
     415<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     416<li><strong>jtemplate</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Job template file from sub-directory “_templates” for
     417submission to ECMWF. It contains all necessary
     418module and variable settings for the ECMWF environment as well as
     419the job call and mail report instructions.
     420Default is “job.temp”.</li>
     421<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     422command line.</li>
     423<li><strong>queue</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of queue for submission to ECMWF (e.g. ecgate or cca )</li>
     424</ul>
     425</td>
     426</tr>
     427</tbody>
     428</table>
     429</dd></dl>
     430
     431</div>
     432</div>
     433<div class="section" id="classes">
     434<h2><a class="toc-backref" href="#id4">Classes</a><a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
     435<div class="section" id="module-ControlFile">
     436<span id="controlfile"></span><h3><a class="toc-backref" href="#id5">ControlFile</a><a class="headerlink" href="#module-ControlFile" title="Permalink to this headline">¶</a></h3>
     437<dl class="class">
     438<dt id="ControlFile.ControlFile">
     439<em class="property">class </em><code class="descclassname">ControlFile.</code><code class="descname">ControlFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile" title="Permalink to this definition">¶</a></dt>
     440<dd><p>Contains the information which are stored in the CONTROL files.</p>
     441<dl class="method">
     442<dt id="ControlFile.ControlFile.assign_args_to_control">
     443<code class="descname">assign_args_to_control</code><span class="sig-paren">(</span><em>args</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.assign_args_to_control"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.assign_args_to_control" title="Permalink to this definition">¶</a></dt>
     444<dd><p>Overwrites the existing ControlFile instance attributes with
     445the command line arguments.</p>
     446<table class="docutils field-list" frame="void" rules="none">
     447<col class="field-name" />
     448<col class="field-body" />
     449<tbody valign="top">
     450<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code>) – Contains the commandline arguments from script/program call.</td>
     451</tr>
     452</tbody>
     453</table>
     454</dd></dl>
     455
     456<dl class="method">
     457<dt id="ControlFile.ControlFile.assign_envs_to_control">
     458<code class="descname">assign_envs_to_control</code><span class="sig-paren">(</span><em>envs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.assign_envs_to_control"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.assign_envs_to_control" title="Permalink to this definition">¶</a></dt>
     459<dd><p>Assigns the ECMWF environment parameter.</p>
     460<table class="docutils field-list" frame="void" rules="none">
     461<col class="field-name" />
     462<col class="field-body" />
     463<tbody valign="top">
     464<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>envs</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">strings</span></code>) – Contains the ECMWF environment parameternames “ECUID”, “ECGID”,
     465“DESTINATION” and “GATEWAY” with its corresponding values.
     466They were read from the file “ECMWF_ENV”.</td>
     467</tr>
     468</tbody>
     469</table>
     470</dd></dl>
     471
     472<dl class="method">
     473<dt id="ControlFile.ControlFile.check_conditions">
     474<code class="descname">check_conditions</code><span class="sig-paren">(</span><em>queue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.check_conditions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.check_conditions" title="Permalink to this definition">¶</a></dt>
     475<dd><p>Checks a couple of necessary attributes and conditions,
     476such as if they exist and contain values.
     477Otherwise set default values.</p>
     478<table class="docutils field-list" frame="void" rules="none">
     479<col class="field-name" />
     480<col class="field-body" />
     481<tbody valign="top">
     482<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>queue</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the queue if submitted to the ECMWF servers.
     483Used to check if ecuid, ecgid, gateway and destination
     484are set correctly and are not empty.</td>
     485</tr>
     486</tbody>
     487</table>
     488</dd></dl>
     489
     490<dl class="method">
     491<dt id="ControlFile.ControlFile.check_install_conditions">
     492<code class="descname">check_install_conditions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.check_install_conditions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.check_install_conditions" title="Permalink to this definition">¶</a></dt>
     493<dd><p>Checks a couple of necessary attributes and conditions
     494for the installation such as if they exist and contain values.
     495Otherwise set default values.</p>
     496</dd></dl>
     497
     498<dl class="method">
     499<dt id="ControlFile.ControlFile.to_list">
     500<code class="descname">to_list</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.to_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.to_list" title="Permalink to this definition">¶</a></dt>
     501<dd><p>Just generates a list of strings containing the attributes and
     502assigned values except the attributes “_expanded”, “exedir”,
     503“ecmwfdatadir” and “flexpart_root_scripts”.</p>
     504<table class="docutils field-list" frame="void" rules="none">
     505<col class="field-name" />
     506<col class="field-body" />
     507<tbody valign="top">
     508<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>l</strong> – A sorted list of the all ControlFile class attributes with
     509their values except the attributes “_expanded”, “exedir”,
     510“ecmwfdatadir” and “flexpart_root_scripts”.</td>
     511</tr>
     512<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></td>
     513</tr>
     514</tbody>
     515</table>
     516</dd></dl>
     517
     518</dd></dl>
     519
     520</div>
     521<div class="section" id="module-EcFlexpart">
     522<span id="ecflexpart"></span><h3><a class="toc-backref" href="#id6">EcFlexpart</a><a class="headerlink" href="#module-EcFlexpart" title="Permalink to this headline">¶</a></h3>
     523<dl class="class">
     524<dt id="EcFlexpart.EcFlexpart">
     525<em class="property">class </em><code class="descclassname">EcFlexpart.</code><code class="descname">EcFlexpart</code><span class="sig-paren">(</span><em>c</em>, <em>fluxes=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart" title="Permalink to this definition">¶</a></dt>
     526<dd><p>Class to retrieve FLEXPART specific ECMWF data.</p>
     527<dl class="method">
     528<dt id="EcFlexpart.EcFlexpart.create">
     529<code class="descname">create</code><span class="sig-paren">(</span><em>inputfiles</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.create" title="Permalink to this definition">¶</a></dt>
     530<dd><p>An index file will be created which depends on the combination
     531of “date”, “time” and “stepRange” values. This is used to iterate
     532over all messages in each grib file which were passed through the
     533parameter “inputfiles” to seperate specific parameters into fort.*
     534files. Afterwards the FORTRAN program is called to convert
     535the data fields all to the same grid and put them in one file
     536per unique time step (combination of “date”, “time” and
     537“stepRange”).</p>
     538<div class="admonition note">
     539<p class="first admonition-title">Note</p>
     540<p class="last">This method is based on the ECMWF example index.py
     541<a class="reference external" href="https://software.ecmwf.int/wiki/display/GRIB/index.py">https://software.ecmwf.int/wiki/display/GRIB/index.py</a></p>
     542</div>
     543<table class="docutils field-list" frame="void" rules="none">
     544<col class="field-name" />
     545<col class="field-body" />
     546<tbody valign="top">
     547<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     548<li><strong>inputfiles</strong> (<a class="reference internal" href="#module-UioFiles" title="UioFiles"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UioFiles</span></code></a>) – Contains a list of files.</li>
     549<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     550command line.</li>
     551</ul>
     552</td>
     553</tr>
     554</tbody>
     555</table>
     556</dd></dl>
     557
     558<dl class="method">
     559<dt id="EcFlexpart.EcFlexpart.deacc_fluxes">
     560<code class="descname">deacc_fluxes</code><span class="sig-paren">(</span><em>inputfiles</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.deacc_fluxes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.deacc_fluxes" title="Permalink to this definition">¶</a></dt>
     561<dd><p>Goes through all flux fields in ordered time and de-accumulate
     562the fields. Afterwards the fields are disaggregated in time.
     563Different versions of disaggregation is provided for rainfall
     564data (darain, modified linear) and the surface fluxes and
     565stress data (dapoly, cubic polynomial).</p>
     566<table class="docutils field-list" frame="void" rules="none">
     567<col class="field-name" />
     568<col class="field-body" />
     569<tbody valign="top">
     570<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     571<li><strong>inputfiles</strong> (<a class="reference internal" href="#module-UioFiles" title="UioFiles"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UioFiles</span></code></a>) – Contains a list of files.</li>
     572<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     573command line.</li>
     574</ul>
     575</td>
     576</tr>
     577</tbody>
     578</table>
     579</dd></dl>
     580
     581<dl class="method">
     582<dt id="EcFlexpart.EcFlexpart.prepare_fp_files">
     583<code class="descname">prepare_fp_files</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.prepare_fp_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.prepare_fp_files" title="Permalink to this definition">¶</a></dt>
     584<dd><p>Conversion of GRIB files to FLEXPART binary format.</p>
     585<table class="docutils field-list" frame="void" rules="none">
     586<col class="field-name" />
     587<col class="field-body" />
     588<tbody valign="top">
     589<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     590command line.</td>
     591</tr>
     592</tbody>
     593</table>
     594</dd></dl>
     595
     596<dl class="method">
     597<dt id="EcFlexpart.EcFlexpart.process_output">
     598<code class="descname">process_output</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.process_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.process_output" title="Permalink to this definition">¶</a></dt>
     599<dd><p>The grib files are postprocessed depending on the selection in
     600CONTROL file. The resulting files are moved to the output
     601directory if its not equal to the input directory.
     602The following modifications might be done if
     603properly switched in CONTROL file:
     604GRIB2 - Conversion to GRIB2
     605ECTRANS - Transfer of files to gateway server
     606ECSTORAGE - Storage at ECMWF server</p>
     607<table class="docutils field-list" frame="void" rules="none">
     608<col class="field-name" />
     609<col class="field-body" />
     610<tbody valign="top">
     611<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     612command line.</td>
     613</tr>
     614</tbody>
     615</table>
     616</dd></dl>
     617
     618<dl class="method">
     619<dt id="EcFlexpart.EcFlexpart.retrieve">
     620<code class="descname">retrieve</code><span class="sig-paren">(</span><em>server</em>, <em>dates</em>, <em>public</em>, <em>request</em>, <em>inputdir='.'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.retrieve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.retrieve" title="Permalink to this definition">¶</a></dt>
     621<dd><p>Finalizing the retrieval information by setting final details
     622depending on grid type.
     623Prepares MARS retrievals per grid type and submits them.</p>
     624<table class="docutils field-list" frame="void" rules="none">
     625<col class="field-name" />
     626<col class="field-body" />
     627<tbody valign="top">
     628<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     629<li><strong>server</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFService</span></code> or <code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFDataServer</span></code>) – The connection to the ECMWF server. This is different
     630for member state users which have full access and non
     631member state users which have only access to the public
     632data sets. The decision is made from command line argument
     633“public”; for public access its True (ECMWFDataServer)
     634for member state users its False (ECMWFService)</li>
     635<li><strong>dates</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains start and end date of the retrieval in the format
     636“YYYYMMDD/to/YYYYMMDD”</li>
     637<li><strong>request</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Selects the mode of retrieval.
     6380: Retrieves the data from ECMWF.
     6391: Prints the mars requests to an output file.
     6402: Retrieves the data and prints the mars request.</li>
     641<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Path to the directory where the retrieved data is about
     642to be stored. The default is the current directory (‘.’).</li>
     643</ul>
     644</td>
     645</tr>
     646</tbody>
     647</table>
     648</dd></dl>
     649
     650<dl class="method">
     651<dt id="EcFlexpart.EcFlexpart.write_namelist">
     652<code class="descname">write_namelist</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.write_namelist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.write_namelist" title="Permalink to this definition">¶</a></dt>
     653<dd><p>Creates a namelist file in the temporary directory and writes
     654the following values to it: maxl, maxb, mlevel,
     655mlevelist, mnauf, metapar, rlo0, rlo1, rla0, rla1,
     656momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta</p>
     657<table class="docutils field-list" frame="void" rules="none">
     658<col class="field-name" />
     659<col class="field-body" />
     660<tbody valign="top">
     661<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     662<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     663command line.</li>
     664<li><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the namelist file.</li>
     665</ul>
     666</td>
     667</tr>
     668</tbody>
     669</table>
     670</dd></dl>
     671
     672</dd></dl>
     673
     674</div>
     675<div class="section" id="module-GribTools">
     676<span id="gribtools"></span><h3><a class="toc-backref" href="#id7">GribTools</a><a class="headerlink" href="#module-GribTools" title="Permalink to this headline">¶</a></h3>
     677<dl class="class">
     678<dt id="GribTools.GribTools">
     679<em class="property">class </em><code class="descclassname">GribTools.</code><code class="descname">GribTools</code><span class="sig-paren">(</span><em>filenames</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools" title="Permalink to this definition">¶</a></dt>
     680<dd><p>Class for GRIB utilities (new methods) based on GRIB API</p>
     681<dl class="method">
     682<dt id="GribTools.GribTools.copy">
     683<code class="descname">copy</code><span class="sig-paren">(</span><em>filename_in</em>, <em>selectWhere=True</em>, <em>keynames=[]</em>, <em>keyvalues=[]</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.copy" title="Permalink to this definition">¶</a></dt>
     684<dd><p>Add the content of another input grib file to the objects file but
     685only messages corresponding to keys/values passed to the function.
     686The selectWhere switch decides if to copy the keys equal to (True) or
     687different to (False) the keynames/keyvalues list passed to the function.</p>
     688<table class="docutils field-list" frame="void" rules="none">
     689<col class="field-name" />
     690<col class="field-body" />
     691<tbody valign="top">
     692<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     693<li><strong>filename_in</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Filename of the input file to read the grib messages from.</li>
     694<li><strong>selectWhere</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if to copy the keynames and values equal to (True) or
     695different to (False) the keynames/keyvalues list passed to the
     696function. Default is True.</li>
     697<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keynames. Default is an empty list.</li>
     698<li><strong>keyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keynames. Default is an empty list.</li>
     699<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
     700</ul>
     701</td>
     702</tr>
     703</tbody>
     704</table>
     705</dd></dl>
     706
     707<dl class="method">
     708<dt id="GribTools.GribTools.get_keys">
     709<code class="descname">get_keys</code><span class="sig-paren">(</span><em>keynames</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.get_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.get_keys" title="Permalink to this definition">¶</a></dt>
     710<dd><p>Get keyvalues for a given list of keynames a where statement
     711can be given (list of key and list of values)</p>
     712<table class="docutils field-list" frame="void" rules="none">
     713<col class="field-name" />
     714<col class="field-body" />
     715<tbody valign="top">
     716<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     717<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames.</li>
     718<li><strong>wherekeynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     719<li><strong>wherekeyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     720</ul>
     721</td>
     722</tr>
     723<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>return_list</strong> – List of keyvalues for given keynames.</p>
     724</td>
     725</tr>
     726<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     727</td>
     728</tr>
     729</tbody>
     730</table>
     731</dd></dl>
     732
     733<dl class="method">
     734<dt id="GribTools.GribTools.index">
     735<code class="descname">index</code><span class="sig-paren">(</span><em>index_keys=['mars'], index_file='my.idx'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.index" title="Permalink to this definition">¶</a></dt>
     736<dd><p>Create index file from a list of files if it does not exist or
     737read an index file.</p>
     738<table class="docutils field-list" frame="void" rules="none">
     739<col class="field-name" />
     740<col class="field-body" />
     741<tbody valign="top">
     742<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     743<li><strong>index_keys</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Contains the list of key parameter names from
     744which the index is to be created.
     745Default is a list with a single entry string “mars”.</li>
     746<li><strong>index_file</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Filename where the indices are stored.
     747Default is “my.idx”.</li>
     748</ul>
     749</td>
     750</tr>
     751<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>iid</strong> – Grib index id.</p>
     752</td>
     753</tr>
     754<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code></p>
     755</td>
     756</tr>
     757</tbody>
     758</table>
     759</dd></dl>
     760
     761<dl class="method">
     762<dt id="GribTools.GribTools.set_keys">
     763<code class="descname">set_keys</code><span class="sig-paren">(</span><em>fromfile</em>, <em>keynames</em>, <em>keyvalues</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em>, <em>strict=False</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.set_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.set_keys" title="Permalink to this definition">¶</a></dt>
     764<dd><p>Opens the file to read the grib messages and then write
     765them to a new output file. By default all messages are
     766written out. Also, the keyvalues of the passed list of
     767keynames are set or only those meeting the where statement.
     768(list of key and list of values).</p>
     769<table class="docutils field-list" frame="void" rules="none">
     770<col class="field-name" />
     771<col class="field-body" />
     772<tbody valign="top">
     773<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     774<li><strong>fromfile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Filename of the input file to read the grib messages from.</li>
     775<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames. Default is an empty list.</li>
     776<li><strong>keyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames. Default is an empty list.</li>
     777<li><strong>wherekeynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     778<li><strong>wherekeyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     779<li><strong>strict</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if everything from keynames and keyvalues
     780is written out the grib file (False) or only those
     781meeting the where statement (True). Default is False.</li>
     782<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
     783</ul>
     784</td>
     785</tr>
     786</tbody>
     787</table>
     788</dd></dl>
     789
     790</dd></dl>
     791
     792</div>
     793<div class="section" id="module-MarsRetrieval">
     794<span id="marsretrieval"></span><h3><a class="toc-backref" href="#id8">MarsRetrieval</a><a class="headerlink" href="#module-MarsRetrieval" title="Permalink to this headline">¶</a></h3>
     795<dl class="class">
     796<dt id="MarsRetrieval.MarsRetrieval">
     797<em class="property">class </em><code class="descclassname">MarsRetrieval.</code><code class="descname">MarsRetrieval</code><span class="sig-paren">(</span><em>server</em>, <em>public</em>, <em>marsclass='ei'</em>, <em>dataset=''</em>, <em>type=''</em>, <em>levtype=''</em>, <em>levelist=''</em>, <em>repres=''</em>, <em>date=''</em>, <em>resol=''</em>, <em>stream=''</em>, <em>area=''</em>, <em>time=''</em>, <em>step=''</em>, <em>expver='1'</em>, <em>number=''</em>, <em>accuracy=''</em>, <em>grid=''</em>, <em>gaussian=''</em>, <em>target=''</em>, <em>param=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval" title="Permalink to this definition">¶</a></dt>
     798<dd><p>Class for submitting MARS retrievals.</p>
     799<p>A description of MARS keywords/arguments and examples of their
     800values can be found here:
     801<a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/">https://software.ecmwf.int/wiki/display/UDOC/</a>                   Identification+keywords#Identificationkeywords-class</p>
     802<dl class="method">
     803<dt id="MarsRetrieval.MarsRetrieval.data_retrieve">
     804<code class="descname">data_retrieve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.data_retrieve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.data_retrieve" title="Permalink to this definition">¶</a></dt>
     805<dd><p>Submits a MARS retrieval. Depending on the existence of
     806ECMWF Web-API it is submitted via Python or a
     807subprocess in the Shell. The parameter for the mars retrieval
     808are taken from the defined class attributes.</p>
     809</dd></dl>
     810
     811<dl class="method">
     812<dt id="MarsRetrieval.MarsRetrieval.display_info">
     813<code class="descname">display_info</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.display_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.display_info" title="Permalink to this definition">¶</a></dt>
     814<dd><p>Prints all class attributes and their values to the
     815standard output.</p>
     816</dd></dl>
     817
     818<dl class="method">
     819<dt id="MarsRetrieval.MarsRetrieval.print_info">
     820<code class="descname">print_info</code><span class="sig-paren">(</span><em>inputdir</em>, <em>request_number</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.print_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.print_info" title="Permalink to this definition">¶</a></dt>
     821<dd><p>Prints all mars requests to an extra file for debugging and
     822information.</p>
     823<table class="docutils field-list" frame="void" rules="none">
     824<col class="field-name" />
     825<col class="field-body" />
     826<tbody valign="top">
     827<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     828<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path where all data from the retrievals are stored.</li>
     829<li><strong>request_number</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Number of mars requests for flux and non-flux data.</li>
     830</ul>
     831</td>
     832</tr>
     833</tbody>
     834</table>
     835</dd></dl>
     836
     837<dl class="method">
     838<dt id="MarsRetrieval.MarsRetrieval.print_infodata_csv">
     839<code class="descname">print_infodata_csv</code><span class="sig-paren">(</span><em>inputdir</em>, <em>request_number</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.print_infodata_csv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.print_infodata_csv" title="Permalink to this definition">¶</a></dt>
     840<dd><p>Write all request parameter in alpabetical order into a “csv” file.</p>
     841<table class="docutils field-list" frame="void" rules="none">
     842<col class="field-name" />
     843<col class="field-body" />
     844<tbody valign="top">
     845<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     846<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path where all data from the retrievals are stored.</li>
     847<li><strong>request_number</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Number of mars requests for flux and non-flux data.</li>
     848</ul>
     849</td>
     850</tr>
     851</tbody>
     852</table>
     853</dd></dl>
     854
     855</dd></dl>
     856
     857</div>
     858<div class="section" id="module-UioFiles">
     859<span id="uiofiles"></span><h3><a class="toc-backref" href="#id9">UioFiles</a><a class="headerlink" href="#module-UioFiles" title="Permalink to this headline">¶</a></h3>
     860<dl class="class">
     861<dt id="UioFiles.UioFiles">
     862<em class="property">class </em><code class="descclassname">UioFiles.</code><code class="descname">UioFiles</code><span class="sig-paren">(</span><em>path</em>, <em>pattern</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/UioFiles.html#UioFiles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#UioFiles.UioFiles" title="Permalink to this definition">¶</a></dt>
     863<dd><p>Class to manipulate files. At initialisation it has the pattern
     864which stores a regular expression pattern for the files, the path
     865to the files and the files already.</p>
     866<dl class="method">
     867<dt id="UioFiles.UioFiles.delete_files">
     868<code class="descname">delete_files</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/UioFiles.html#UioFiles.delete_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#UioFiles.UioFiles.delete_files" title="Permalink to this definition">¶</a></dt>
     869<dd><p>Deletes the files.</p>
     870</dd></dl>
     871
     872</dd></dl>
     873
     874</div>
     875</div>
     876<div class="section" id="modules">
     877<h2><a class="toc-backref" href="#id10">Modules</a><a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h2>
     878<div class="section" id="module-get_mars_data">
     879<span id="get-mars-data"></span><h3><a class="toc-backref" href="#id11">get_mars_data</a><a class="headerlink" href="#module-get_mars_data" title="Permalink to this headline">¶</a></h3>
     880<dl class="function">
     881<dt id="get_mars_data.do_retrievement">
     882<code class="descclassname">get_mars_data.</code><code class="descname">do_retrievement</code><span class="sig-paren">(</span><em>c</em>, <em>server</em>, <em>start</em>, <em>end</em>, <em>delta_t</em>, <em>fluxes=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#do_retrievement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.do_retrievement" title="Permalink to this definition">¶</a></dt>
     883<dd><p>Divides the complete retrieval period in smaller chunks and
     884retrieves the data from MARS.</p>
     885<table class="docutils field-list" frame="void" rules="none">
     886<col class="field-name" />
     887<col class="field-body" />
     888<tbody valign="top">
     889<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     890<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     891command line.</li>
     892<li><strong>server</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFService</span></code>) – The server connection to ECMWF.</li>
     893<li><strong>start</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – The start date of the retrieval.</li>
     894<li><strong>end</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – The end date of the retrieval.</li>
     895<li><strong>delta_t</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – Delta_t + 1 is the maximal time period of a single
     896retrieval.</li>
     897<li><strong>fluxes</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if the flux parameters are to be retrieved or
     898the rest of the parameter list.
     899Default value is False.</li>
     900</ul>
     901</td>
     902</tr>
     903</tbody>
     904</table>
     905</dd></dl>
     906
     907<dl class="function">
     908<dt id="get_mars_data.get_mars_data">
     909<code class="descclassname">get_mars_data.</code><code class="descname">get_mars_data</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#get_mars_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.get_mars_data" title="Permalink to this definition">¶</a></dt>
     910<dd><p>Retrieves the EC data needed for a FLEXPART simulation.</p>
     911<p>Start and end dates for retrieval period is set. Retrievals
     912are divided into smaller periods if necessary and datechunk parameter
     913is set.</p>
     914<table class="docutils field-list" frame="void" rules="none">
     915<col class="field-name" />
     916<col class="field-body" />
     917<tbody valign="top">
     918<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     919command line.</td>
     920</tr>
     921</tbody>
     922</table>
     923</dd></dl>
     924
     925<dl class="function">
     926<dt id="get_mars_data.main">
     927<code class="descclassname">get_mars_data.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.main" title="Permalink to this definition">¶</a></dt>
     928<dd><p>Controls the program to get data out of mars.</p>
     929<p>This is done if it is called directly from command line.
     930Then it also takes program call arguments and control file input.</p>
     931</dd></dl>
     932
     933</div>
     934<div class="section" id="module-prepare_flexpart">
     935<span id="prepare-flexpart"></span><h3><a class="toc-backref" href="#id12">prepare_flexpart</a><a class="headerlink" href="#module-prepare_flexpart" title="Permalink to this headline">¶</a></h3>
     936<dl class="function">
     937<dt id="prepare_flexpart.main">
     938<code class="descclassname">prepare_flexpart.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/prepare_flexpart.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.main" title="Permalink to this definition">¶</a></dt>
     939<dd><p>Controls the program to prepare flexpart input files from mars data.</p>
     940<p>This is done if it is called directly from command line.
     941Then it also takes program call arguments and control file input.</p>
     942</dd></dl>
     943
     944<dl class="function">
     945<dt id="prepare_flexpart.prepare_flexpart">
     946<code class="descclassname">prepare_flexpart.</code><code class="descname">prepare_flexpart</code><span class="sig-paren">(</span><em>ppid</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/prepare_flexpart.html#prepare_flexpart"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.prepare_flexpart" title="Permalink to this definition">¶</a></dt>
     947<dd><p>Converts the mars data into flexpart ready input files.</p>
     948<p>Specific data fields are converted to a different grid and the flux
     949data are going to be disaggregated. The data fields are collected by
     950hour and stored in a file with a specific FLEXPART relevant naming
     951convention.</p>
     952<table class="docutils field-list" frame="void" rules="none">
     953<col class="field-name" />
     954<col class="field-body" />
     955<tbody valign="top">
     956<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     957<li><strong>ppid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>) – Contains the ppid number of the current ECMWF job. It will be None if
     958the method was called within this module.</li>
     959<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     960command line.</li>
     961</ul>
     962</td>
     963</tr>
     964</tbody>
     965</table>
     966</dd></dl>
     967
     968</div>
     969<div class="section" id="module-tools">
     970<span id="tools"></span><h3><a class="toc-backref" href="#id13">tools</a><a class="headerlink" href="#module-tools" title="Permalink to this headline">¶</a></h3>
     971<dl class="function">
     972<dt id="tools.clean_up">
     973<code class="descclassname">tools.</code><code class="descname">clean_up</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition">¶</a></dt>
     974<dd><p>Remove all files from intermediate directory (inputdir).</p>
     975<table class="docutils field-list" frame="void" rules="none">
     976<col class="field-name" />
     977<col class="field-body" />
     978<tbody valign="top">
     979<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     980command line.</td>
     981</tr>
     982</tbody>
     983</table>
     984</dd></dl>
     985
     986<dl class="function">
     987<dt id="tools.get_cmdline_arguments">
     988<code class="descclassname">tools.</code><code class="descname">get_cmdline_arguments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#get_cmdline_arguments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_cmdline_arguments" title="Permalink to this definition">¶</a></dt>
     989<dd><p>Decomposes the command line arguments and assigns them to variables.
     990Apply default values for non mentioned arguments.</p>
     991<table class="docutils field-list" frame="void" rules="none">
     992<col class="field-name" />
     993<col class="field-body" />
     994<tbody valign="top">
     995<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>args</strong> – Contains the commandline arguments from script/program call.</td>
     996</tr>
     997<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code></td>
     998</tr>
     999</tbody>
     1000</table>
     1001</dd></dl>
     1002
     1003<dl class="function">
     1004<dt id="tools.get_list_as_string">
     1005<code class="descclassname">tools.</code><code class="descname">get_list_as_string</code><span class="sig-paren">(</span><em>list_obj</em>, <em>concatenate_sign='</em>, <em>'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#get_list_as_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_list_as_string" title="Permalink to this definition">¶</a></dt>
     1006<dd><p>Converts a list of arbitrary content into a single string.</p>
     1007<table class="docutils field-list" frame="void" rules="none">
     1008<col class="field-name" />
     1009<col class="field-body" />
     1010<tbody valign="top">
     1011<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1012<li><strong>list_obj</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code>) – A list with arbitrary content.</li>
     1013<li><strong>concatenate_sign</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – A string which is used to concatenate the single
     1014list elements. Default value is “, “.</li>
     1015</ul>
     1016</td>
     1017</tr>
     1018<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>str_of_list</strong> – The content of the list as a single string.</p>
     1019</td>
     1020</tr>
     1021<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1022</td>
     1023</tr>
     1024</tbody>
     1025</table>
     1026</dd></dl>
     1027
     1028<dl class="function">
     1029<dt id="tools.init128">
     1030<code class="descclassname">tools.</code><code class="descname">init128</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#init128"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.init128" title="Permalink to this definition">¶</a></dt>
     1031<dd><p>Opens and reads the grib file with table 128 information.</p>
     1032<table class="docutils field-list" frame="void" rules="none">
     1033<col class="field-name" />
     1034<col class="field-body" />
     1035<tbody valign="top">
     1036<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filepath</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to file of ECMWF grib table number 128.</td>
     1037</tr>
     1038<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>table128</strong> – Contains the ECMWF grib table 128 information.
     1039The key is the parameter number and the value is the
     1040short name of the parameter.</td>
     1041</tr>
     1042<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code></td>
     1043</tr>
     1044</tbody>
     1045</table>
     1046</dd></dl>
     1047
     1048<dl class="function">
     1049<dt id="tools.make_dir">
     1050<code class="descclassname">tools.</code><code class="descname">make_dir</code><span class="sig-paren">(</span><em>directory</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#make_dir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.make_dir" title="Permalink to this definition">¶</a></dt>
     1051<dd><p>Creates a directory and gives a warning if the directory
     1052already exists. The program stops only if there is another problem.</p>
     1053<table class="docutils field-list" frame="void" rules="none">
     1054<col class="field-name" />
     1055<col class="field-body" />
     1056<tbody valign="top">
     1057<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>directory</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The directory name including the path which should be created.</td>
     1058</tr>
     1059</tbody>
     1060</table>
     1061</dd></dl>
     1062
     1063<dl class="function">
     1064<dt id="tools.my_error">
     1065<code class="descclassname">tools.</code><code class="descname">my_error</code><span class="sig-paren">(</span><em>users</em>, <em>message='ERROR'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#my_error"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.my_error" title="Permalink to this definition">¶</a></dt>
     1066<dd><p>Prints a specified error message which can be passed to the function
     1067before exiting the program.</p>
     1068<table class="docutils field-list" frame="void" rules="none">
     1069<col class="field-name" />
     1070<col class="field-body" />
     1071<tbody valign="top">
     1072<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     1073<li><strong>user</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains all email addresses which should be notified.
     1074It might also contain just the ecmwf user name which wil trigger
     1075mailing to the associated email address for this user.</li>
     1076<li><strong>message</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Error message. Default value is “ERROR”.</li>
     1077</ul>
     1078</td>
     1079</tr>
     1080</tbody>
     1081</table>
     1082</dd></dl>
     1083
     1084<dl class="function">
     1085<dt id="tools.none_or_int">
     1086<code class="descclassname">tools.</code><code class="descname">none_or_int</code><span class="sig-paren">(</span><em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#none_or_int"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_int" title="Permalink to this definition">¶</a></dt>
     1087<dd><p>Converts the input string into pythons None-type if the string
     1088contains string “None”. Otherwise it is converted to an integer value.</p>
     1089<table class="docutils field-list" frame="void" rules="none">
     1090<col class="field-name" />
     1091<col class="field-body" />
     1092<tbody valign="top">
     1093<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – String to be checked for the “None” word.</td>
     1094</tr>
     1095<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Return depends on the content of the input value. If it was “None”,
     1096then the python type None is returned. Otherwise the string is
     1097converted into an integer value.</td>
     1098</tr>
     1099<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">None or int(value)</td>
     1100</tr>
     1101</tbody>
     1102</table>
     1103</dd></dl>
     1104
     1105<dl class="function">
     1106<dt id="tools.none_or_str">
     1107<code class="descclassname">tools.</code><code class="descname">none_or_str</code><span class="sig-paren">(</span><em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#none_or_str"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_str" title="Permalink to this definition">¶</a></dt>
     1108<dd><p>Converts the input string into pythons None-type if the string
     1109contains string “None”.</p>
     1110<table class="docutils field-list" frame="void" rules="none">
     1111<col class="field-name" />
     1112<col class="field-body" />
     1113<tbody valign="top">
     1114<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – String to be checked for the “None” word.</td>
     1115</tr>
     1116<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Return depends on the content of the input value. If it was “None”,
     1117then the python type None is returned. Otherwise the string itself.</td>
     1118</tr>
     1119<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">None or value</td>
     1120</tr>
     1121</tbody>
     1122</table>
     1123</dd></dl>
     1124
     1125<dl class="function">
     1126<dt id="tools.normal_exit">
     1127<code class="descclassname">tools.</code><code class="descname">normal_exit</code><span class="sig-paren">(</span><em>users</em>, <em>message='Done!'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#normal_exit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.normal_exit" title="Permalink to this definition">¶</a></dt>
     1128<dd><p>Prints a specific exit message which can be passed to the function.</p>
     1129<table class="docutils field-list" frame="void" rules="none">
     1130<col class="field-name" />
     1131<col class="field-body" />
     1132<tbody valign="top">
     1133<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     1134<li><strong>user</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains all email addresses which should be notified.
     1135It might also contain just the ecmwf user name which wil trigger
     1136mailing to the associated email address for this user.</li>
     1137<li><strong>message</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Message for exiting program. Default value is “Done!”.</li>
     1138</ul>
     1139</td>
     1140</tr>
     1141</tbody>
     1142</table>
     1143</dd></dl>
     1144
     1145<dl class="function">
     1146<dt id="tools.product">
     1147<code class="descclassname">tools.</code><code class="descname">product</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.product" title="Permalink to this definition">¶</a></dt>
     1148<dd><p>This method combines the single characters of the passed arguments
     1149with each other. So that each character of each argument value
     1150will be combined with each character of the other arguments as a tuple.</p>
     1151<div class="admonition note">
     1152<p class="first admonition-title">Note</p>
     1153<p class="last">This method is taken from an example at the ECMWF wiki website.
     1154<a class="reference external" href="https://software.ecmwf.int/wiki/display/GRIB/index.py">https://software.ecmwf.int/wiki/display/GRIB/index.py</a>; 2018-03-16</p>
     1155</div>
     1156<p class="rubric">Example</p>
     1157<p>product(‘ABCD’, ‘xy’) –&gt; Ax Ay Bx By Cx Cy Dx Dy</p>
     1158<p>product(range(2), repeat = 3) –&gt; 000 001 010 011 100 101 110 111</p>
     1159<table class="docutils field-list" frame="void" rules="none">
     1160<col class="field-name" />
     1161<col class="field-body" />
     1162<tbody valign="top">
     1163<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1164<li><strong>*args</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code>) – Positional arguments (arbitrary number).</li>
     1165<li><strong>**kwds</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code>) – Contains all the keyword arguments from *args.</li>
     1166</ul>
     1167</td>
     1168</tr>
     1169<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>prod</strong> – Return will be done with “yield”. A tuple of combined arguments.
     1170See example in description above.</p>
     1171</td>
     1172</tr>
     1173<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
     1174</td>
     1175</tr>
     1176</tbody>
     1177</table>
     1178</dd></dl>
     1179
     1180<dl class="function">
     1181<dt id="tools.put_file_to_ecserver">
     1182<code class="descclassname">tools.</code><code class="descname">put_file_to_ecserver</code><span class="sig-paren">(</span><em>ecd</em>, <em>filename</em>, <em>target</em>, <em>ecuid</em>, <em>ecgid</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#put_file_to_ecserver"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.put_file_to_ecserver" title="Permalink to this definition">¶</a></dt>
     1183<dd><p>Uses the ecaccess-file-put command to send a file to the ECMWF servers.</p>
     1184<div class="admonition note">
     1185<p class="first admonition-title">Note</p>
     1186<p class="last">The return value is just for testing reasons. It does not have
     1187to be used from the calling function since the whole error handling
     1188is done in here.</p>
     1189</div>
     1190<table class="docutils field-list" frame="void" rules="none">
     1191<col class="field-name" />
     1192<col class="field-body" />
     1193<tbody valign="top">
     1194<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1195<li><strong>ecd</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path were the file is stored.</li>
     1196<li><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the file to send to the ECMWF server.</li>
     1197<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target queue where the file should be sent to.</li>
     1198<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     1199<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     1200</ul>
     1201</td>
     1202</tr>
     1203<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>rcode</strong> – Resulting code of command execution. If successful the string
     1204will be empty.</p>
     1205</td>
     1206</tr>
     1207<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1208</td>
     1209</tr>
     1210</tbody>
     1211</table>
     1212</dd></dl>
     1213
     1214<dl class="function">
     1215<dt id="tools.read_ecenv">
     1216<code class="descclassname">tools.</code><code class="descname">read_ecenv</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#read_ecenv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.read_ecenv" title="Permalink to this definition">¶</a></dt>
     1217<dd><p>Reads the file into a dictionary where the key values are the parameter
     1218names.</p>
     1219<table class="docutils field-list" frame="void" rules="none">
     1220<col class="field-name" />
     1221<col class="field-body" />
     1222<tbody valign="top">
     1223<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to file where the ECMWF environment parameters are stored.</td>
     1224</tr>
     1225<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>envs</strong> – Contains the environment parameter ecuid, ecgid, gateway
     1226and destination for ECMWF server environments.</td>
     1227</tr>
     1228<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code></td>
     1229</tr>
     1230</tbody>
     1231</table>
     1232</dd></dl>
     1233
     1234<dl class="function">
     1235<dt id="tools.silent_remove">
     1236<code class="descclassname">tools.</code><code class="descname">silent_remove</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#silent_remove"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.silent_remove" title="Permalink to this definition">¶</a></dt>
     1237<dd><p>Remove file if it exists.
     1238The function does not fail if the file does not exist.</p>
     1239<table class="docutils field-list" frame="void" rules="none">
     1240<col class="field-name" />
     1241<col class="field-body" />
     1242<tbody valign="top">
     1243<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the file to be removed without notification.</td>
     1244</tr>
     1245</tbody>
     1246</table>
     1247</dd></dl>
     1248
     1249<dl class="function">
     1250<dt id="tools.submit_job_to_ecserver">
     1251<code class="descclassname">tools.</code><code class="descname">submit_job_to_ecserver</code><span class="sig-paren">(</span><em>target</em>, <em>jobname</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#submit_job_to_ecserver"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.submit_job_to_ecserver" title="Permalink to this definition">¶</a></dt>
     1252<dd><p>Uses ecaccess-job-submit command to submit a job to the ECMWF server.</p>
     1253<div class="admonition note">
     1254<p class="first admonition-title">Note</p>
     1255<p class="last">The return value is just for testing reasons. It does not have
     1256to be used from the calling function since the whole error handling
     1257is done in here.</p>
     1258</div>
     1259<table class="docutils field-list" frame="void" rules="none">
     1260<col class="field-name" />
     1261<col class="field-body" />
     1262<tbody valign="top">
     1263<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1264<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target where the file should be sent to, e.g. the queue.</li>
     1265<li><strong>jobname</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the jobfile to be submitted to the ECMWF server.</li>
     1266</ul>
     1267</td>
     1268</tr>
     1269<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>rcode</strong> – Resulting code of command execution. If successful the string
     1270will contain an integer number, representing the id of the job
     1271at the ecmwf server.</p>
     1272</td>
     1273</tr>
     1274<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1275</td>
     1276</tr>
     1277</tbody>
     1278</table>
     1279</dd></dl>
     1280
     1281<dl class="function">
     1282<dt id="tools.to_param_id">
     1283<code class="descclassname">tools.</code><code class="descname">to_param_id</code><span class="sig-paren">(</span><em>pars</em>, <em>table</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#to_param_id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.to_param_id" title="Permalink to this definition">¶</a></dt>
     1284<dd><p>Transform parameter names to parameter ids with ECMWF grib table 128.</p>
     1285<table class="docutils field-list" frame="void" rules="none">
     1286<col class="field-name" />
     1287<col class="field-body" />
     1288<tbody valign="top">
     1289<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1290<li><strong>pars</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Addpar argument from CONTROL file in the format of
     1291parameter names instead of ids. The parameter short
     1292names are sepearted with “/” and they are passed as
     1293one single string.</li>
     1294<li><strong>table</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code>) – Contains the ECMWF grib table 128 information.
     1295The key is the parameter number and the value is the
     1296short name of the parameter.</li>
     1297</ul>
     1298</td>
     1299</tr>
     1300<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>ipar</strong> – List of addpar parameters from CONTROL file transformed to
     1301parameter ids in the format of integer.</p>
     1302</td>
     1303</tr>
     1304<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code></p>
     1305</td>
     1306</tr>
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     1310
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    2741429
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    160165<blockquote>
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    162210<h2 id="D">D</h2>
    163211<table style="width: 100%" class="indextable genindextable"><tr>
     
    165213      <li><a href="api.html#disaggregation.dapoly">dapoly() (in module disaggregation)</a>
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    167   </ul></td>
    168   <td style="width: 33%; vertical-align: top;"><ul>
    169215      <li><a href="api.html#disaggregation.darain">darain() (in module disaggregation)</a>
    170216</li>
     217      <li><a href="api.html#MarsRetrieval.MarsRetrieval.data_retrieve">data_retrieve() (MarsRetrieval.MarsRetrieval method)</a>
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     226</li>
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    172228</li>
     229      <li><a href="api.html#MarsRetrieval.MarsRetrieval.display_info">display_info() (MarsRetrieval.MarsRetrieval method)</a>
     230</li>
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     232</li>
     233  </ul></td>
     234</tr></table>
     235
     236<h2 id="E">E</h2>
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     240
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     247
     248<h2 id="G">G</h2>
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     254</li>
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     256</li>
     257      <li><a href="api.html#tools.get_list_as_string">get_list_as_string() (in module tools)</a>
     258</li>
     259  </ul></td>
     260  <td style="width: 33%; vertical-align: top;"><ul>
     261      <li><a href="api.html#module-get_mars_data">get_mars_data (module)</a>
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     263      <li><a href="api.html#get_mars_data.get_mars_data">get_mars_data() (in module get_mars_data)</a>
     264</li>
     265      <li><a href="api.html#GribTools.GribTools">GribTools (class in GribTools)</a>
     266
     267      <ul>
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     269</li>
     270      </ul></li>
    173271  </ul></td>
    174272</tr></table>
     
    178276  <td style="width: 33%; vertical-align: top;"><ul>
    179277      <li><a href="api.html#disaggregation.IA3">IA3() (in module disaggregation)</a>
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     279      <li><a href="api.html#GribTools.GribTools.index">index() (GribTools.GribTools method)</a>
     280</li>
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     282  <td style="width: 33%; vertical-align: top;"><ul>
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     286</li>
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     288</li>
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     291
     292<h2 id="M">M</h2>
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     294  <td style="width: 33%; vertical-align: top;"><ul>
     295      <li><a href="api.html#get_mars_data.main">main() (in module get_mars_data)</a>
     296
     297      <ul>
     298        <li><a href="api.html#install.main">(in module install)</a>
     299</li>
     300        <li><a href="api.html#prepare_flexpart.main">(in module prepare_flexpart)</a>
     301</li>
     302        <li><a href="api.html#submit.main">(in module submit)</a>
     303</li>
     304      </ul></li>
     305      <li><a href="api.html#install.make_convert_build">make_convert_build() (in module install)</a>
     306</li>
     307      <li><a href="api.html#tools.make_dir">make_dir() (in module tools)</a>
     308</li>
     309  </ul></td>
     310  <td style="width: 33%; vertical-align: top;"><ul>
     311      <li><a href="api.html#MarsRetrieval.MarsRetrieval">MarsRetrieval (class in MarsRetrieval)</a>
     312
     313      <ul>
     314        <li><a href="api.html#module-MarsRetrieval">(module)</a>
     315</li>
     316      </ul></li>
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     318</li>
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     320</li>
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     322</li>
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     326</li>
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     329
     330<h2 id="N">N</h2>
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     333      <li><a href="api.html#tools.none_or_int">none_or_int() (in module tools)</a>
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     337      <li><a href="api.html#tools.none_or_str">none_or_str() (in module tools)</a>
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     340</li>
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     344<h2 id="P">P</h2>
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     350</li>
     351      <li><a href="api.html#EcFlexpart.EcFlexpart.prepare_fp_files">prepare_fp_files() (EcFlexpart.EcFlexpart method)</a>
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     358</li>
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     362</li>
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     364</li>
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     368<h2 id="R">R</h2>
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     376</li>
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     380<h2 id="S">S</h2>
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     394</li>
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     398<h2 id="T">T</h2>
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     423      <li><a href="api.html#install.un_tarball">un_tarball() (in module install)</a>
     424</li>
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     428<h2 id="W">W</h2>
     429<table style="width: 100%" class="indextable genindextable"><tr>
     430  <td style="width: 33%; vertical-align: top;"><ul>
     431      <li><a href="api.html#EcFlexpart.EcFlexpart.write_namelist">write_namelist() (EcFlexpart.EcFlexpart method)</a>
    180432</li>
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  • documentation/Sphinx/build/html/index.html

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    1010 
    11   <title>Welcome to flex_extract’s documentation! &mdash; flex_extract 7.1 alpha documentation</title>
     11  <title>Welcome to flex_extract’s user documentation! &mdash; flex_extract 7.1 alpha documentation</title>
    1212 
    1313
     
    135135      <li><a href="#">Docs</a> &raquo;</li>
    136136       
    137       <li>Welcome to flex_extract’s documentation!</li>
     137      <li>Welcome to flex_extract’s user documentation!</li>
    138138   
    139139   
     
    154154           <div itemprop="articleBody">
    155155           
    156   <div class="section" id="welcome-to-flex-extract-s-documentation">
    157 <h1>Welcome to flex_extract’s documentation!<a class="headerlink" href="#welcome-to-flex-extract-s-documentation" title="Permalink to this headline">¶</a></h1>
     156  <div class="section" id="welcome-to-flex-extract-s-user-documentation">
     157<h1>Welcome to flex_extract’s user documentation!<a class="headerlink" href="#welcome-to-flex-extract-s-user-documentation" title="Permalink to this headline">¶</a></h1>
     158<p>flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.</p>
     159<p>All required second party software and libraries used within flex_extract is open source and free of charge.</p>
    158160<table style="width:100%;">
    159161  <tr>
     
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    156163<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
    157 <p>Describe installation process flex_extract ….</p>
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    159165<div>UNDER CONSTRUCTION</div></blockquote>
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    155164  <div class="section" id="requirements">
    156165<h1>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h1>
    157 <p>Describe the requirements to use flex_extract ….</p>
    158166<blockquote>
    159167<div>UNDER CONSTRUCTION</div></blockquote>
     
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     91<li class="toctree-l2"><a class="reference internal" href="user_guide/how_to.html">How to use flex_extract</a></li>
     92<li class="toctree-l2"><a class="reference internal" href="user_guide/control_templates.html">CONTROL-file templates</a></li>
     93</ul>
     94</li>
    9195<li class="toctree-l1"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
    9296<li class="toctree-l1"><a class="reference internal" href="support.html">Support</a></li>
     
    157161  <div class="section" id="user-guide">
    158162<h1>User Guide<a class="headerlink" href="#user-guide" title="Permalink to this headline">¶</a></h1>
    159 <p>Describe using flex_extract ….</p>
    160163<blockquote>
    161164<div>UNDER CONSTRUCTION</div></blockquote>
     165<div class="toctree-wrapper compound">
     166</div>
    162167</div>
    163168
     
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  • documentation/Sphinx/source/api.rst

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    22============================
    33
     4.. contents::
     5    :local:
     6   
     7Porgrams
     8--------
     9
     10install
     11*******
     12
     13.. automodule:: install
     14    :members:
     15   
     16submit
     17******
     18
     19.. automodule:: submit
     20    :members:
     21   
     22Classes
     23-------
     24
     25ControlFile
     26***********
     27
     28.. automodule:: ControlFile
     29    :members:
     30   
     31EcFlexpart
     32**********
     33
     34.. automodule:: EcFlexpart
     35    :members:
     36   
     37GribTools
     38*********
     39
     40.. automodule:: GribTools
     41    :members:
     42
     43MarsRetrieval
     44*************
     45
     46.. automodule:: MarsRetrieval
     47    :members:
     48
     49UioFiles
     50********
     51
     52.. automodule:: UioFiles
     53    :members:
     54
     55
     56
     57Modules
     58-------
     59
     60get_mars_data
     61*************
     62
     63.. automodule:: get_mars_data
     64    :members:
     65 
     66prepare_flexpart
     67****************
     68
     69.. automodule:: prepare_flexpart
     70    :members:   
     71   
     72tools
     73*****
     74
     75.. automodule:: tools
     76    :members:
     77
     78disaggregation
     79**************   
     80   
    481.. automodule:: disaggregation
    582    :members:
  • documentation/Sphinx/source/downloads.rst

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    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
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     11   
     12    downloads/tar_balls
     13    downloads/git_repo
     14    downloads/history_changes
     15   
  • documentation/Sphinx/source/index.rst

    r708c667 r274f9ef  
    44   contain the root `toctree` directive.
    55
    6 Welcome to flex_extract's documentation!
    7 ========================================
     6Welcome to flex_extract's user documentation!
     7=============================================
     8
     9flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.
     10
     11
     12.. The scripts can be 1) executed locally using the ECMWF WebMARS interface, or 2) on the ECMWF member
     13.. state gateway server or HPC facility using the ecaccess software package. As another option the scripts can 3)
     14.. also be triggered using ecflow scheduling software used by ECMWF for data dissemination.
     15
     16All required second party software and libraries used within flex_extract is open source and free of charge.
     17
    818.. raw:: html
    919
     
    8797
    8898.. toctree::
    89    :maxdepth: 2
     99   :maxdepth: 3
    90100   :caption: Table of Contents:
    91101
  • documentation/Sphinx/source/installation.rst

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    11Installation
    22============
    3 
    4 Describe installation process flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    installation/requirements
     11    installation/oper_modes
     12    installation/test_install
     13
     14
     15   
  • documentation/Sphinx/source/program_structure.rst

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    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    program_structure/prog_overview
     13    program_structure/prog_components
     14    program_structure/prog_flow
  • documentation/Sphinx/source/support.rst

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    22=======
    33
    4 Describe support options ....
    54 
    65    UNDER CONSTRUCTION
     6   
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    support/ticket_system
     13    support/mailing_list
     14    support/known_bugs_issues
     15    support/faq
     16       
  • documentation/Sphinx/source/user_guide.rst

    r708c667 r274f9ef  
    11User Guide
    22==========
    3 
    4 Describe using flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    user_guide/how_to
     11    user_guide/control_templates
     12   
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