diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
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diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
index 2bf2672ee88514435c26768885baec1e08c080b6..8c57b541b73c9e4cee4cdfd5ef2b9f57b71bf7a7 100644
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diff --git a/docs/build/doctrees/index2.doctree b/docs/build/doctrees/index2.doctree
deleted file mode 100644
index 797f03dfd3d268169e139908104ec455be0e1e70..0000000000000000000000000000000000000000
Binary files a/docs/build/doctrees/index2.doctree and /dev/null differ
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
index 3b23e27aadb68ffba9a22833a3fc5cd92f1deb04..7d932e88b9f1c2b6b4af1631e907d6f3b061f50d 100644
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@@ -5,12 +5,17 @@ DART-WRF is a Python package to run an Ensemble Data Assimilation system with th
+.. toctree::
+:maxdepth: 2
+:caption: Contents:
-Contents
---------
-.. toctree::
- api
- example
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/docs/build/html/_sources/index2.rst.txt b/docs/build/html/_sources/index2.rst.txt
deleted file mode 100644
index 993e6a3d7d8874f0d3c9ad84933439de14a57f7c..0000000000000000000000000000000000000000
--- a/docs/build/html/_sources/index2.rst.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-.. DART-WRF documentation master file, created by
- sphinx-quickstart on Fri Feb 17 17:22:54 2023.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to DART-WRF's documentation!
-====================================
-
-.. toctree::
- :maxdepth: 2
- :caption: Contents:
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/build/html/_static/alabaster.css b/docs/build/html/_static/alabaster.css
deleted file mode 100644
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- display: block;
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- -moz-box-shadow: 2px 2px 4px #EEE;
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diff --git a/docs/build/html/_static/custom.css b/docs/build/html/_static/custom.css
deleted file mode 100644
index 2a924f1d6a8bc930c5296bdb2d5c2d3e39b04a1c..0000000000000000000000000000000000000000
--- a/docs/build/html/_static/custom.css
+++ /dev/null
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diff --git a/docs/build/html/api.html b/docs/build/html/api.html
index 2e25becbef3b575856aa5435712b212681133008..be268dd4210289368b317eea01303da497a8b266 100644
--- a/docs/build/html/api.html
+++ b/docs/build/html/api.html
@@ -17,9 +17,7 @@
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
- <link rel="search" title="Search" href="search.html" />
- <link rel="next" title="dartwrf" href="generated/dartwrf.html" />
- <link rel="prev" title="Welcome to the DART-WRF documentation!" href="index.html" />
+ <link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
@@ -41,10 +39,8 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="generated/dartwrf.html">dartwrf</a></li>
-</ul>
-
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
</div>
</div>
</nav>
@@ -80,10 +76,7 @@
</div>
</div>
- <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
- <a href="index.html" class="btn btn-neutral float-left" title="Welcome to the DART-WRF documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
- <a href="generated/dartwrf.html" class="btn btn-neutral float-right" title="dartwrf" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
- </div>
+ <footer>
<hr/>
diff --git a/docs/build/html/example.html b/docs/build/html/example.html
index e1d61b95a097b68b38fef2f671442c51b1f03fcb..74b0b342f4693f635c63fd4d359aaa54629bdf74 100644
--- a/docs/build/html/example.html
+++ b/docs/build/html/example.html
@@ -17,8 +17,7 @@
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
- <link rel="search" title="Search" href="search.html" />
- <link rel="prev" title="dartwrf" href="generated/dartwrf.html" />
+ <link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
@@ -40,11 +39,11 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="generated/dartwrf.html">dartwrf</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Workflow</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Workflow</a></li>
</ul>
-
+</div>
</div>
</div>
</nav>
@@ -170,9 +169,7 @@ clusterB.userdir = ‘/home/pathB/myuser/’
</div>
</div>
- <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
- <a href="generated/dartwrf.html" class="btn btn-neutral float-left" title="dartwrf" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
- </div>
+ <footer>
<hr/>
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 42493693a4ed5956d7d48d7797661b5bdc2346ac..7e8a1fefc34825d2204d98852251fb65cb92b47f 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -38,11 +38,8 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="generated/dartwrf.html">dartwrf</a></li>
-<li class="toctree-l1"><a class="reference internal" href="example.html">Workflow</a></li>
-</ul>
-
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
</div>
</div>
</nav>
@@ -70,33 +67,388 @@
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
- <a href="#D"><strong>D</strong></a>
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
+ | <a href="#O"><strong>O</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#W"><strong>W</strong></a>
</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.append_file">append_file() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.archivedir">archivedir (dartwrf.utils.ClusterConfig property)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.backup_scripts">backup_scripts() (dartwrf.utils.ClusterConfig method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.error_models.calc_obserr_WV">calc_obserr_WV() (in module dartwrf.obs.error_models)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.clean_wrfdir">clean_wrfdir() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.error_models.cloudimpact">cloudimpact() (in module dartwrf.obs.error_models)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig">ClusterConfig (class in dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.copy">copy() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.copy_contents">copy_contents() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.copy_scp_srvx8">copy_scp_srvx8() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.create_job">create_job() (dartwrf.utils.ClusterConfig method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.create_obsseq_in_separate_obs">create_obsseq_in_separate_obs() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.prep_IC_prior.create_updated_wrfinput_from_wrfout">create_updated_wrfinput_from_wrfout() (in module dartwrf.prep_IC_prior)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.prep_IC_prior.create_wrfrst_in_WRF_rundir">create_wrfrst_in_WRF_rundir() (in module dartwrf.prep_IC_prior)</a>
+</li>
+ </ul></td>
+</tr></table>
+
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.dartrundir">dartrundir (dartwrf.utils.ClusterConfig property)</a>
+</li>
<li>
dartwrf
<ul>
- <li><a href="generated/dartwrf.html#module-dartwrf">module</a>
+ <li><a href="dartwrf.html#module-dartwrf">module</a>, <a href="generated/dartwrf.html#module-dartwrf">[1]</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.obs
+
+ <ul>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.obs.calculate_obs_locations
+
+ <ul>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs.calculate_obs_locations">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.obs.error_models
+
+ <ul>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs.error_models">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.obsseq
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.obsseq">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.obsseq_to_netcdf
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.obsseq_to_netcdf">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.old_functions
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.old_functions">module</a>
</li>
</ul></li>
</ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li>
+ dartwrf.prep_IC_prior
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.prep_IC_prior">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.run_obs_diag
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.run_obs_diag">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.update_IC
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.update_IC">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.utils
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.utils">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.wrfinput_add_geo
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.wrfinput_add_geo">module</a>
+</li>
+ </ul></li>
+ <li>
+ dartwrf.wrfout_add_geo
+
+ <ul>
+ <li><a href="dartwrf.html#module-dartwrf.wrfout_add_geo">module</a>
+</li>
+ </ul></li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.degrees_to_rad">degrees_to_rad() (in module dartwrf.obsseq)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.determine_nlayers">determine_nlayers() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.calculate_obs_locations.evenly_on_grid">evenly_on_grid() (in module dartwrf.obs.calculate_obs_locations)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.ExperimentConfiguration">ExperimentConfiguration (class in dartwrf.utils)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.get_from_cartesian_grid">get_from_cartesian_grid() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.get_lon_lat">get_lon_lat() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.get_posterior_Hx">get_posterior_Hx() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.get_preamble_content">get_preamble_content() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.get_prior_Hx">get_prior_Hx() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.get_truth_Hx">get_truth_Hx() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.link_contents">link_contents() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq_to_netcdf.listdir_dirs">listdir_dirs() (in module dartwrf.obsseq_to_netcdf)</a>
+</li>
+ </ul></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.mkdir">mkdir() (in module dartwrf.utils)</a>
+</li>
<li>
module
<ul>
- <li><a href="generated/dartwrf.html#module-dartwrf">dartwrf</a>
+ <li><a href="dartwrf.html#module-dartwrf">dartwrf</a>, <a href="generated/dartwrf.html#module-dartwrf">[1]</a>
+</li>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs">dartwrf.obs</a>
+</li>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs.calculate_obs_locations">dartwrf.obs.calculate_obs_locations</a>
+</li>
+ <li><a href="dartwrf.obs.html#module-dartwrf.obs.error_models">dartwrf.obs.error_models</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.obsseq">dartwrf.obsseq</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.obsseq_to_netcdf">dartwrf.obsseq_to_netcdf</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.old_functions">dartwrf.old_functions</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.prep_IC_prior">dartwrf.prep_IC_prior</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.run_obs_diag">dartwrf.run_obs_diag</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.update_IC">dartwrf.update_IC</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.utils">dartwrf.utils</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.wrfinput_add_geo">dartwrf.wrfinput_add_geo</a>
+</li>
+ <li><a href="dartwrf.html#module-dartwrf.wrfout_add_geo">dartwrf.wrfout_add_geo</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
+
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.old_functions.obs_operator_nature">obs_operator_nature() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.obs_to_dict">obs_to_dict() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord">ObsRecord (class in dartwrf.obsseq)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq">ObsSeq (class in dartwrf.obsseq)</a>
+</li>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.error_models.OE_model_harnisch_WV62">OE_model_harnisch_WV62() (in module dartwrf.obs.error_models)</a>
+</li>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.error_models.OE_model_harnisch_WV73">OE_model_harnisch_WV73() (in module dartwrf.obs.error_models)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.plot">plot() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.plot_box">plot_box() (in module dartwrf.obsseq)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.run_obs_diag.prepare">prepare() (in module dartwrf.run_obs_diag)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.print">print() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.rad_to_degrees">rad_to_degrees() (in module dartwrf.obsseq)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.read_preamble">read_preamble() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.read_prior_obs">read_prior_obs() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.read_truth_obs_obsseq">read_truth_obs_obsseq() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.recycle_output">recycle_output() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.replace_errors_obsseqout">replace_errors_obsseqout() (in module dartwrf.old_functions)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.Shellslurm.run">run() (dartwrf.utils.Shellslurm method)</a>
+
+ <ul>
+ <li><a href="dartwrf.html#dartwrf.wrfinput_add_geo.run">(in module dartwrf.wrfinput_add_geo)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.wrfout_add_geo.run">(in module dartwrf.wrfout_add_geo)</a>
</li>
</ul></li>
+ <li><a href="dartwrf.html#dartwrf.old_functions.run_Hx">run_Hx() (in module dartwrf.old_functions)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.run_obs_diag.run_obs_seq_to_netcdf">run_obs_seq_to_netcdf() (in module dartwrf.run_obs_diag)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.run_obs_diag.run_obsdiag">run_obsdiag() (in module dartwrf.run_obs_diag)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.script_to_str">script_to_str() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.scripts_rundir">scripts_rundir (dartwrf.utils.ClusterConfig property)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.sed_inplace">sed_inplace() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.setup">setup() (dartwrf.utils.ClusterConfig method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.shell">shell() (in module dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.Shellslurm">Shellslurm (class in dartwrf.utils)</a>
+</li>
+ <li><a href="dartwrf.obs.html#dartwrf.obs.calculate_obs_locations.square_array_from_domaincenter">square_array_from_domaincenter() (in module dartwrf.obs.calculate_obs_locations)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsRecord.superob">superob() (dartwrf.obsseq.ObsRecord method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.symlink">symlink() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.to_dart">to_dart() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.obsseq.ObsSeq.to_pandas">to_pandas() (dartwrf.obsseq.ObsSeq method)</a>
+</li>
+ <li><a href="dartwrf.html#dartwrf.utils.try_remove">try_remove() (in module dartwrf.utils)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.update_IC.update_initials_in_WRF_rundir">update_initials_in_WRF_rundir() (in module dartwrf.update_IC)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.wrf_rundir">wrf_rundir() (dartwrf.utils.ClusterConfig method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="dartwrf.html#dartwrf.run_obs_diag.write_input_filelist">write_input_filelist() (in module dartwrf.run_obs_diag)</a>
+</li>
</ul></td>
</tr></table>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 741af69e45e7a35b9e2be41247449fc57b9b8af8..2ccfe02b30c9a5d6fcff49542da350e83f59cc3a 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -17,8 +17,7 @@
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
- <link rel="search" title="Search" href="search.html" />
- <link rel="next" title="<no title>" href="api.html" />
+ <link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
@@ -40,11 +39,12 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="generated/dartwrf.html">dartwrf</a></li>
-<li class="toctree-l1"><a class="reference internal" href="example.html">Workflow</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Welcome to the DART-WRF documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
-
+</div>
</div>
</div>
</nav>
@@ -72,23 +72,30 @@
<section id="welcome-to-the-dart-wrf-documentation">
<h1>Welcome to the DART-WRF documentation!<a class="headerlink" href="#welcome-to-the-dart-wrf-documentation" title="Permalink to this heading"></a></h1>
<p>DART-WRF is a Python package to run an Ensemble Data Assimilation system with the software packages DART and WRF.</p>
-<section id="contents">
-<h2>Contents<a class="headerlink" href="#contents" title="Permalink to this heading"></a></h2>
<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="generated/dartwrf.html">dartwrf</a></li>
-<li class="toctree-l1"><a class="reference internal" href="example.html">Workflow</a></li>
-</ul>
</div>
+<dl class="field-list simple">
+<dt class="field-odd">maxdepth<span class="colon">:</span></dt>
+<dd class="field-odd"><p>2</p>
+</dd>
+<dt class="field-even">caption<span class="colon">:</span></dt>
+<dd class="field-even"><p>Contents:</p>
+</dd>
+</dl>
</section>
+<section id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading"></a></h1>
+<ul class="simple">
+<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
+<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
+<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
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- <a href="api.html" class="btn btn-neutral float-right" title="<no title>" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/docs/build/html/index2.html b/docs/build/html/index2.html
deleted file mode 100644
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- <div class="bodywrapper">
-
-
- <div class="body" role="main">
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- <section id="welcome-to-dart-wrf-s-documentation">
-<h1>Welcome to DART-WRF’s documentation!<a class="headerlink" href="#welcome-to-dart-wrf-s-documentation" title="Permalink to this heading">¶</a></h1>
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"to_pandas() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.to_pandas"]], "try_remove() (in module dartwrf.utils)": [[1, "dartwrf.utils.try_remove"]], "update_initials_in_wrf_rundir() (in module dartwrf.update_ic)": [[1, "dartwrf.update_IC.update_initials_in_WRF_rundir"]], "wrf_rundir() (dartwrf.utils.clusterconfig method)": [[1, "dartwrf.utils.ClusterConfig.wrf_rundir"]], "write_input_filelist() (in module dartwrf.run_obs_diag)": [[1, "dartwrf.run_obs_diag.write_input_filelist"]], "oe_model_harnisch_wv62() (in module dartwrf.obs.error_models)": [[2, "dartwrf.obs.error_models.OE_model_harnisch_WV62"]], "oe_model_harnisch_wv73() (in module dartwrf.obs.error_models)": [[2, "dartwrf.obs.error_models.OE_model_harnisch_WV73"]], "calc_obserr_wv() (in module dartwrf.obs.error_models)": [[2, "dartwrf.obs.error_models.calc_obserr_WV"]], "cloudimpact() (in module dartwrf.obs.error_models)": [[2, "dartwrf.obs.error_models.cloudimpact"]], "dartwrf.obs": [[2, "module-dartwrf.obs"]], "dartwrf.obs.calculate_obs_locations": [[2, "module-dartwrf.obs.calculate_obs_locations"]], "dartwrf.obs.error_models": [[2, "module-dartwrf.obs.error_models"]], "evenly_on_grid() (in module dartwrf.obs.calculate_obs_locations)": [[2, "dartwrf.obs.calculate_obs_locations.evenly_on_grid"]], "square_array_from_domaincenter() (in module dartwrf.obs.calculate_obs_locations)": [[2, "dartwrf.obs.calculate_obs_locations.square_array_from_domaincenter"]]}})
\ No newline at end of file
diff --git a/docs/pyproject.toml b/docs/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..fbc33db517970cc0c5766217a8f94da4be16c889
--- /dev/null
+++ b/docs/pyproject.toml
@@ -0,0 +1,9 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "dartwrf"
+authors = [{name = "Lukas Kugler", email = "lukas.kugler@univie.ac.at"}]
+dynamic = ["version", "description"]
+
diff --git a/docs/source/dartwrf.obs.rst b/docs/source/dartwrf.obs.rst
new file mode 100644
index 0000000000000000000000000000000000000000..79a1e0e57472de8c7562aacda2720bb20ffb10f3
--- /dev/null
+++ b/docs/source/dartwrf.obs.rst
@@ -0,0 +1,29 @@
+dartwrf.obs package
+===================
+
+Submodules
+----------
+
+dartwrf.obs.calculate\_obs\_locations module
+--------------------------------------------
+
+.. automodule:: dartwrf.obs.calculate_obs_locations
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.obs.error\_models module
+--------------------------------
+
+.. automodule:: dartwrf.obs.error_models
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: dartwrf.obs
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/source/dartwrf.rst b/docs/source/dartwrf.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7353c0e5b69833543bf910bd45bda9b97f58c2c3
--- /dev/null
+++ b/docs/source/dartwrf.rst
@@ -0,0 +1,182 @@
+dartwrf package
+===============
+
+Subpackages
+-----------
+
+.. toctree::
+ :maxdepth: 4
+
+ dartwrf.config
+ dartwrf.obs
+
+Submodules
+----------
+
+dartwrf.assim\_synth\_obs module
+--------------------------------
+
+.. automodule:: dartwrf.assim_synth_obs
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.cleanup\_exp module
+---------------------------
+
+.. automodule:: dartwrf.cleanup_exp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.create\_obs\_upfront module
+-----------------------------------
+
+.. automodule:: dartwrf.create_obs_upfront
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.create\_obsseq module
+-----------------------------
+
+.. automodule:: dartwrf.create_obsseq
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.create\_wbubble\_wrfinput module
+----------------------------------------
+
+.. automodule:: dartwrf.create_wbubble_wrfinput
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.evaluate\_posterior module
+----------------------------------
+
+.. automodule:: dartwrf.evaluate_posterior
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.evaluate\_prior module
+------------------------------
+
+.. automodule:: dartwrf.evaluate_prior
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.link\_dart\_rttov module
+--------------------------------
+
+.. automodule:: dartwrf.link_dart_rttov
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.obsseq module
+---------------------
+
+.. automodule:: dartwrf.obsseq
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.obsseq\_2dim module
+---------------------------
+
+.. automodule:: dartwrf.obsseq_2dim
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.obsseq\_to\_netcdf module
+---------------------------------
+
+.. automodule:: dartwrf.obsseq_to_netcdf
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.old\_functions module
+-----------------------------
+
+.. automodule:: dartwrf.old_functions
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.prep\_IC\_prior module
+------------------------------
+
+.. automodule:: dartwrf.prep_IC_prior
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.prepare\_namelist module
+--------------------------------
+
+.. automodule:: dartwrf.prepare_namelist
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.prepare\_wrfrundir module
+---------------------------------
+
+.. automodule:: dartwrf.prepare_wrfrundir
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.run\_obs\_diag module
+-----------------------------
+
+.. automodule:: dartwrf.run_obs_diag
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.update\_IC module
+-------------------------
+
+.. automodule:: dartwrf.update_IC
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.utils module
+--------------------
+
+.. automodule:: dartwrf.utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.wrfinput\_add\_geo module
+---------------------------------
+
+.. automodule:: dartwrf.wrfinput_add_geo
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.wrfout\_add\_geo module
+-------------------------------
+
+.. automodule:: dartwrf.wrfout_add_geo
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: dartwrf
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 3b23e27aadb68ffba9a22833a3fc5cd92f1deb04..7d932e88b9f1c2b6b4af1631e907d6f3b061f50d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -5,12 +5,17 @@ DART-WRF is a Python package to run an Ensemble Data Assimilation system with th
+.. toctree::
+:maxdepth: 2
+:caption: Contents:
-Contents
---------
-.. toctree::
- api
- example
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d2417a80236590c7d565d3c2f36e15d0fa95cfdc
--- /dev/null
+++ b/docs/source/modules.rst
@@ -0,0 +1,7 @@
+dartwrf
+=======
+
+.. toctree::
+ :maxdepth: 4
+
+ dartwrf