diff --git a/docs/build/doctrees/dartwrf.doctree b/docs/build/doctrees/dartwrf.doctree
index 62fc5363038ce2970cf6042833454bca30e74b01..d52c7736296bb7b2bb4ea0e4873b8f796692bb87 100644
Binary files a/docs/build/doctrees/dartwrf.doctree and b/docs/build/doctrees/dartwrf.doctree differ
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index d812b3404cca43b48e5653eb120ec8f17fac4d8a..c7e8250dcd7c750a9a924d230add437fa557bb8d 100644
Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ
diff --git a/docs/build/html/dartwrf.html b/docs/build/html/dartwrf.html
index 5928b3fdea7523f4fca838324afb2972799e6a95..21bb32659c3fbdf8197d6062243702ed079b6414 100644
--- a/docs/build/html/dartwrf.html
+++ b/docs/build/html/dartwrf.html
@@ -85,7 +85,7 @@
 <li><a class="reference internal" href="#module-dartwrf.create_wbubble_wrfinput">dartwrf.create_wbubble_wrfinput module</a></li>
 <li><a class="reference internal" href="#module-dartwrf.evaluate_posterior">dartwrf.evaluate_posterior module</a></li>
 <li><a class="reference internal" href="#module-dartwrf.evaluate_prior">dartwrf.evaluate_prior module</a></li>
-<li><a class="reference internal" href="#module-dartwrf.link_dart_rttov">dartwrf.link_dart_rttov module</a></li>
+<li><a class="reference internal" href="#dartwrf-link-dart-rttov-module">dartwrf.link_dart_rttov module</a></li>
 <li><a class="reference internal" href="#module-dartwrf.obsseq">dartwrf.obsseq module</a><ul>
 <li><a class="reference internal" href="#dartwrf.obsseq.ObsRecord"><code class="docutils literal notranslate"><span class="pre">ObsRecord</span></code></a><ul>
 <li><a class="reference internal" href="#dartwrf.obsseq.ObsRecord.determine_nlayers"><code class="docutils literal notranslate"><span class="pre">ObsRecord.determine_nlayers()</span></code></a></li>
@@ -112,10 +112,7 @@
 </ul>
 </li>
 <li><a class="reference internal" href="#module-dartwrf.obsseq_2dim">dartwrf.obsseq_2dim module</a></li>
-<li><a class="reference internal" href="#module-dartwrf.obsseq_to_netcdf">dartwrf.obsseq_to_netcdf module</a><ul>
-<li><a class="reference internal" href="#dartwrf.obsseq_to_netcdf.listdir_dirs"><code class="docutils literal notranslate"><span class="pre">listdir_dirs()</span></code></a></li>
-</ul>
-</li>
+<li><a class="reference internal" href="#dartwrf-obsseq-to-netcdf-module">dartwrf.obsseq_to_netcdf module</a></li>
 <li><a class="reference internal" href="#module-dartwrf.old_functions">dartwrf.old_functions module</a><ul>
 <li><a class="reference internal" href="#dartwrf.old_functions.create_obsseq_in_separate_obs"><code class="docutils literal notranslate"><span class="pre">create_obsseq_in_separate_obs()</span></code></a></li>
 <li><a class="reference internal" href="#dartwrf.old_functions.obs_operator_nature"><code class="docutils literal notranslate"><span class="pre">obs_operator_nature()</span></code></a></li>
@@ -126,23 +123,10 @@
 <li><a class="reference internal" href="#dartwrf.old_functions.run_Hx"><code class="docutils literal notranslate"><span class="pre">run_Hx()</span></code></a></li>
 </ul>
 </li>
-<li><a class="reference internal" href="#module-dartwrf.prep_IC_prior">dartwrf.prep_IC_prior module</a><ul>
-<li><a class="reference internal" href="#dartwrf.prep_IC_prior.create_updated_wrfinput_from_wrfout"><code class="docutils literal notranslate"><span class="pre">create_updated_wrfinput_from_wrfout()</span></code></a></li>
-<li><a class="reference internal" href="#dartwrf.prep_IC_prior.create_wrfrst_in_WRF_rundir"><code class="docutils literal notranslate"><span class="pre">create_wrfrst_in_WRF_rundir()</span></code></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#module-dartwrf.prepare_namelist">dartwrf.prepare_namelist module</a><ul>
-<li><a class="reference internal" href="#dartwrf.prepare_namelist.run"><code class="docutils literal notranslate"><span class="pre">run()</span></code></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#module-dartwrf.prepare_wrfrundir">dartwrf.prepare_wrfrundir module</a></li>
-<li><a class="reference internal" href="#module-dartwrf.run_obs_diag">dartwrf.run_obs_diag module</a><ul>
-<li><a class="reference internal" href="#dartwrf.run_obs_diag.prepare"><code class="docutils literal notranslate"><span class="pre">prepare()</span></code></a></li>
-<li><a class="reference internal" href="#dartwrf.run_obs_diag.run_obs_seq_to_netcdf"><code class="docutils literal notranslate"><span class="pre">run_obs_seq_to_netcdf()</span></code></a></li>
-<li><a class="reference internal" href="#dartwrf.run_obs_diag.run_obsdiag"><code class="docutils literal notranslate"><span class="pre">run_obsdiag()</span></code></a></li>
-<li><a class="reference internal" href="#dartwrf.run_obs_diag.write_input_filelist"><code class="docutils literal notranslate"><span class="pre">write_input_filelist()</span></code></a></li>
-</ul>
-</li>
+<li><a class="reference internal" href="#dartwrf-prep-ic-prior-module">dartwrf.prep_IC_prior module</a></li>
+<li><a class="reference internal" href="#dartwrf-prepare-namelist-module">dartwrf.prepare_namelist module</a></li>
+<li><a class="reference internal" href="#dartwrf-prepare-wrfrundir-module">dartwrf.prepare_wrfrundir module</a></li>
+<li><a class="reference internal" href="#dartwrf-run-obs-diag-module">dartwrf.run_obs_diag module</a></li>
 <li><a class="reference internal" href="#module-dartwrf.update_IC">dartwrf.update_IC module</a><ul>
 <li><a class="reference internal" href="#dartwrf.update_IC.update_initials_in_WRF_rundir"><code class="docutils literal notranslate"><span class="pre">update_initials_in_WRF_rundir()</span></code></a></li>
 </ul>
@@ -509,8 +493,8 @@ from DART f90 script</p>
 <section id="module-dartwrf.evaluate_prior">
 <span id="dartwrf-evaluate-prior-module"></span><h2>dartwrf.evaluate_prior module<a class="headerlink" href="#module-dartwrf.evaluate_prior" title="Permalink to this heading"></a></h2>
 </section>
-<section id="module-dartwrf.link_dart_rttov">
-<span id="dartwrf-link-dart-rttov-module"></span><h2>dartwrf.link_dart_rttov module<a class="headerlink" href="#module-dartwrf.link_dart_rttov" title="Permalink to this heading"></a></h2>
+<section id="dartwrf-link-dart-rttov-module">
+<h2>dartwrf.link_dart_rttov module<a class="headerlink" href="#dartwrf-link-dart-rttov-module" title="Permalink to this heading"></a></h2>
 </section>
 <section id="module-dartwrf.obsseq">
 <span id="dartwrf-obsseq-module"></span><h2>dartwrf.obsseq module<a class="headerlink" href="#module-dartwrf.obsseq" title="Permalink to this heading"></a></h2>
@@ -663,13 +647,8 @@ self.obstypes (tuple(kind_nr, kind_descriptor)) for each obs type</p>
 <p>Create obs_seq.out files with collapsed vertical dimension
 Specifically, one observation per column which is the maximum of the column</p>
 </section>
-<section id="module-dartwrf.obsseq_to_netcdf">
-<span id="dartwrf-obsseq-to-netcdf-module"></span><h2>dartwrf.obsseq_to_netcdf module<a class="headerlink" href="#module-dartwrf.obsseq_to_netcdf" title="Permalink to this heading"></a></h2>
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.obsseq_to_netcdf.listdir_dirs">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.obsseq_to_netcdf.</span></span><span class="sig-name descname"><span class="pre">listdir_dirs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.obsseq_to_netcdf.listdir_dirs" title="Permalink to this definition"></a></dt>
-<dd></dd></dl>
-
+<section id="dartwrf-obsseq-to-netcdf-module">
+<h2>dartwrf.obsseq_to_netcdf module<a class="headerlink" href="#dartwrf-obsseq-to-netcdf-module" title="Permalink to this heading"></a></h2>
 </section>
 <section id="module-dartwrf.old_functions">
 <span id="dartwrf-old-functions-module"></span><h2>dartwrf.old_functions module<a class="headerlink" href="#module-dartwrf.old_functions" title="Permalink to this heading"></a></h2>
@@ -745,79 +724,17 @@ Creates</p>
 </dd></dl>
 
 </section>
-<section id="module-dartwrf.prep_IC_prior">
-<span id="dartwrf-prep-ic-prior-module"></span><h2>dartwrf.prep_IC_prior module<a class="headerlink" href="#module-dartwrf.prep_IC_prior" title="Permalink to this heading"></a></h2>
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.prep_IC_prior.create_updated_wrfinput_from_wrfout">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.prep_IC_prior.</span></span><span class="sig-name descname"><span class="pre">create_updated_wrfinput_from_wrfout</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prior_init_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prior_path_exp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_start_time</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.prep_IC_prior.create_updated_wrfinput_from_wrfout" title="Permalink to this definition"></a></dt>
-<dd><p>Same as create_wrfout_in_archivedir, but output is <cite>wrfinput</cite> in WRF run directory</p>
-</dd></dl>
-
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.prep_IC_prior.create_wrfrst_in_WRF_rundir">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.prep_IC_prior.</span></span><span class="sig-name descname"><span class="pre">create_wrfrst_in_WRF_rundir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prior_init_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prior_path_exp</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.prep_IC_prior.create_wrfrst_in_WRF_rundir" title="Permalink to this definition"></a></dt>
-<dd><p>copies wrfrst to run_WRF directory (for next WRF run)</p>
-</dd></dl>
-
+<section id="dartwrf-prep-ic-prior-module">
+<h2>dartwrf.prep_IC_prior module<a class="headerlink" href="#dartwrf-prep-ic-prior-module" title="Permalink to this heading"></a></h2>
 </section>
-<section id="module-dartwrf.prepare_namelist">
-<span id="dartwrf-prepare-namelist-module"></span><h2>dartwrf.prepare_namelist module<a class="headerlink" href="#module-dartwrf.prepare_namelist" title="Permalink to this heading"></a></h2>
-<p>Create namelist.input files</p>
-<dl>
-<dt>Usage:</dt><dd><p>prepare_namelist.py &lt;begin&gt; &lt;end&gt; &lt;intv&gt; [–radt=&lt;minutes&gt;] [–restart=&lt;flag&gt;] [–restart_interval=&lt;minutes&gt;]</p>
-</dd>
-<dt>Options:</dt><dd><dl class="option-list">
-<dt><kbd><span class="option">--radt=<var>&lt;minutes&gt;</var></span></kbd></dt>
-<dd><p>Radiation interval [default: 5]</p>
-</dd>
-<dt><kbd><span class="option">--restart=<var>&lt;flag&gt;</var></span></kbd></dt>
-<dd><p>Restart flag (.true., .false.) [default: .false.]</p>
-</dd>
-<dt><kbd><span class="option">--restart_interval=<var>&lt;minutes&gt;</var></span></kbd></dt>
-<dd><p>Restart frequency [default: 720]</p>
-</dd>
-</dl>
-</dd>
-</dl>
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.prepare_namelist.run">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.prepare_namelist.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iens</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">begin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hist_interval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">archive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_interval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">720</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.prepare_namelist.run" title="Permalink to this definition"></a></dt>
-<dd><p>Create namelist.input files</p>
-<p>Args:
-archive (bool): if True, write to archivedir of experiment</p>
-<blockquote>
-<div><p>if False, write to WRF run directory</p>
-</div></blockquote>
-<p>restart (str): fortran bool whether to use wrfinput or wrfrst
-restart_interval (int): output frequency of wrfrst (minutes)</p>
-</dd></dl>
-
+<section id="dartwrf-prepare-namelist-module">
+<h2>dartwrf.prepare_namelist module<a class="headerlink" href="#dartwrf-prepare-namelist-module" title="Permalink to this heading"></a></h2>
 </section>
-<section id="module-dartwrf.prepare_wrfrundir">
-<span id="dartwrf-prepare-wrfrundir-module"></span><h2>dartwrf.prepare_wrfrundir module<a class="headerlink" href="#module-dartwrf.prepare_wrfrundir" title="Permalink to this heading"></a></h2>
+<section id="dartwrf-prepare-wrfrundir-module">
+<h2>dartwrf.prepare_wrfrundir module<a class="headerlink" href="#dartwrf-prepare-wrfrundir-module" title="Permalink to this heading"></a></h2>
 </section>
-<section id="module-dartwrf.run_obs_diag">
-<span id="dartwrf-run-obs-diag-module"></span><h2>dartwrf.run_obs_diag module<a class="headerlink" href="#module-dartwrf.run_obs_diag" title="Permalink to this heading"></a></h2>
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.run_obs_diag.prepare">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.run_obs_diag.</span></span><span class="sig-name descname"><span class="pre">prepare</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obserr_iszero</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.true.'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.run_obs_diag.prepare" title="Permalink to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.run_obs_diag.run_obs_seq_to_netcdf">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.run_obs_diag.</span></span><span class="sig-name descname"><span class="pre">run_obs_seq_to_netcdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filepaths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_out</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'./obs_epoch.nc'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.run_obs_diag.run_obs_seq_to_netcdf" title="Permalink to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.run_obs_diag.run_obsdiag">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.run_obs_diag.</span></span><span class="sig-name descname"><span class="pre">run_obsdiag</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filepaths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_out</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'./obsdiag.nc'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.run_obs_diag.run_obsdiag" title="Permalink to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py function">
-<dt class="sig sig-object py" id="dartwrf.run_obs_diag.write_input_filelist">
-<span class="sig-prename descclassname"><span class="pre">dartwrf.run_obs_diag.</span></span><span class="sig-name descname"><span class="pre">write_input_filelist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filepaths</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dartwrf.run_obs_diag.write_input_filelist" title="Permalink to this definition"></a></dt>
-<dd></dd></dl>
-
+<section id="dartwrf-run-obs-diag-module">
+<h2>dartwrf.run_obs_diag module<a class="headerlink" href="#dartwrf-run-obs-diag-module" title="Permalink to this heading"></a></h2>
 </section>
 <section id="module-dartwrf.update_IC">
 <span id="dartwrf-update-ic-module"></span><h2>dartwrf.update_IC module<a class="headerlink" href="#module-dartwrf.update_IC" title="Permalink to this heading"></a></h2>
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 51f03d2ac247be00bb70b3b0d6a450237d6db6e4..382461efbf1bbc8324cc930cf1f8527a351707f6 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -124,11 +124,11 @@
       <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>
-      <li><a href="dartwrf.html#dartwrf.utils.copy_contents">copy_contents() (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>
@@ -136,10 +136,6 @@
       <li><a href="dartwrf.html#dartwrf.create_obsseq.create_obs_seq_in">create_obs_seq_in() (in module dartwrf.create_obsseq)</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>
@@ -203,13 +199,6 @@
 
       <ul>
         <li><a href="dartwrf.html#module-dartwrf.evaluate_prior">module</a>
-</li>
-      </ul></li>
-      <li>
-    dartwrf.link_dart_rttov
-
-      <ul>
-        <li><a href="dartwrf.html#module-dartwrf.link_dart_rttov">module</a>
 </li>
       </ul></li>
       <li>
@@ -226,6 +215,8 @@
         <li><a href="dartwrf.obs.html#module-dartwrf.obs.calculate_obs_locations">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     dartwrf.obs.error_models
 
@@ -240,20 +231,11 @@
         <li><a href="dartwrf.html#module-dartwrf.obsseq">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     dartwrf.obsseq_2dim
 
       <ul>
         <li><a href="dartwrf.html#module-dartwrf.obsseq_2dim">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>
@@ -261,34 +243,6 @@
 
       <ul>
         <li><a href="dartwrf.html#module-dartwrf.old_functions">module</a>
-</li>
-      </ul></li>
-      <li>
-    dartwrf.prep_IC_prior
-
-      <ul>
-        <li><a href="dartwrf.html#module-dartwrf.prep_IC_prior">module</a>
-</li>
-      </ul></li>
-      <li>
-    dartwrf.prepare_namelist
-
-      <ul>
-        <li><a href="dartwrf.html#module-dartwrf.prepare_namelist">module</a>
-</li>
-      </ul></li>
-      <li>
-    dartwrf.prepare_wrfrundir
-
-      <ul>
-        <li><a href="dartwrf.html#module-dartwrf.prepare_wrfrundir">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>
@@ -388,8 +342,6 @@
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="dartwrf.html#dartwrf.assim_synth_obs.link_nature_to_dart_truth">link_nature_to_dart_truth() (in module dartwrf.assim_synth_obs)</a>
-</li>
-      <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>
@@ -418,8 +370,6 @@
         <li><a href="dartwrf.html#module-dartwrf.evaluate_posterior">dartwrf.evaluate_posterior</a>
 </li>
         <li><a href="dartwrf.html#module-dartwrf.evaluate_prior">dartwrf.evaluate_prior</a>
-</li>
-        <li><a href="dartwrf.html#module-dartwrf.link_dart_rttov">dartwrf.link_dart_rttov</a>
 </li>
         <li><a href="dartwrf.obs.html#module-dartwrf.obs">dartwrf.obs</a>
 </li>
@@ -430,18 +380,8 @@
         <li><a href="dartwrf.html#module-dartwrf.obsseq">dartwrf.obsseq</a>
 </li>
         <li><a href="dartwrf.html#module-dartwrf.obsseq_2dim">dartwrf.obsseq_2dim</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.prepare_namelist">dartwrf.prepare_namelist</a>
-</li>
-        <li><a href="dartwrf.html#module-dartwrf.prepare_wrfrundir">dartwrf.prepare_wrfrundir</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>
@@ -488,8 +428,6 @@
 </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.assim_synth_obs.prepare_nature_dart">prepare_nature_dart() (in module dartwrf.assim_synth_obs)</a>
 </li>
       <li><a href="dartwrf.html#dartwrf.assim_synth_obs.prepare_prior_ensemble">prepare_prior_ensemble() (in module dartwrf.assim_synth_obs)</a>
@@ -521,26 +459,20 @@
       <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>
-      <li><a href="dartwrf.html#dartwrf.create_obsseq.round_to_day">round_to_day() (in module dartwrf.create_obsseq)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="dartwrf.html#dartwrf.create_obsseq.round_to_day">round_to_day() (in module dartwrf.create_obsseq)</a>
+</li>
       <li><a href="dartwrf.html#dartwrf.utils.Shellslurm.run">run() (dartwrf.utils.Shellslurm method)</a>
 
       <ul>
-        <li><a href="dartwrf.html#dartwrf.prepare_namelist.run">(in module dartwrf.prepare_namelist)</a>
-</li>
         <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>
       <li><a href="dartwrf.html#dartwrf.assim_synth_obs.run_perfect_model_obs">run_perfect_model_obs() (in module dartwrf.assim_synth_obs)</a>
 </li>
@@ -605,8 +537,6 @@
       <li><a href="dartwrf.html#dartwrf.utils.ClusterConfig.wrf_rundir">wrf_rundir() (dartwrf.utils.ClusterConfig method)</a>
 </li>
       <li><a href="dartwrf.html#dartwrf.create_obsseq.write_file">write_file() (in module dartwrf.create_obsseq)</a>
-</li>
-      <li><a href="dartwrf.html#dartwrf.run_obs_diag.write_input_filelist">write_input_filelist() (in module dartwrf.run_obs_diag)</a>
 </li>
       <li><a href="dartwrf.html#dartwrf.assim_synth_obs.write_list_of_inputfiles_posterior">write_list_of_inputfiles_posterior() (in module dartwrf.assim_synth_obs)</a>
 </li>
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index b7f9859e5931ce18d6ad12dec2ab3b1d8aaf0fd8..425d20c35d2fd16c0f76b62539d72831fda5a013 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -125,7 +125,7 @@
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.create_wbubble_wrfinput">dartwrf.create_wbubble_wrfinput module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.evaluate_posterior">dartwrf.evaluate_posterior module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.evaluate_prior">dartwrf.evaluate_prior module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.link_dart_rttov">dartwrf.link_dart_rttov module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-link-dart-rttov-module">dartwrf.link_dart_rttov module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.obsseq">dartwrf.obsseq module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.obsseq.ObsRecord"><code class="docutils literal notranslate"><span class="pre">ObsRecord</span></code></a><ul>
 <li class="toctree-l4"><a class="reference internal" href="dartwrf.html#dartwrf.obsseq.ObsRecord.determine_nlayers"><code class="docutils literal notranslate"><span class="pre">ObsRecord.determine_nlayers()</span></code></a></li>
@@ -152,10 +152,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.obsseq_2dim">dartwrf.obsseq_2dim module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.obsseq_to_netcdf">dartwrf.obsseq_to_netcdf module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.obsseq_to_netcdf.listdir_dirs"><code class="docutils literal notranslate"><span class="pre">listdir_dirs()</span></code></a></li>
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-obsseq-to-netcdf-module">dartwrf.obsseq_to_netcdf module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.old_functions">dartwrf.old_functions module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.old_functions.create_obsseq_in_separate_obs"><code class="docutils literal notranslate"><span class="pre">create_obsseq_in_separate_obs()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.old_functions.obs_operator_nature"><code class="docutils literal notranslate"><span class="pre">obs_operator_nature()</span></code></a></li>
@@ -166,23 +163,10 @@
 <li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.old_functions.run_Hx"><code class="docutils literal notranslate"><span class="pre">run_Hx()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.prep_IC_prior">dartwrf.prep_IC_prior module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.prep_IC_prior.create_updated_wrfinput_from_wrfout"><code class="docutils literal notranslate"><span class="pre">create_updated_wrfinput_from_wrfout()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.prep_IC_prior.create_wrfrst_in_WRF_rundir"><code class="docutils literal notranslate"><span class="pre">create_wrfrst_in_WRF_rundir()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.prepare_namelist">dartwrf.prepare_namelist module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.prepare_namelist.run"><code class="docutils literal notranslate"><span class="pre">run()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.prepare_wrfrundir">dartwrf.prepare_wrfrundir module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.run_obs_diag">dartwrf.run_obs_diag module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.run_obs_diag.prepare"><code class="docutils literal notranslate"><span class="pre">prepare()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.run_obs_diag.run_obs_seq_to_netcdf"><code class="docutils literal notranslate"><span class="pre">run_obs_seq_to_netcdf()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.run_obs_diag.run_obsdiag"><code class="docutils literal notranslate"><span class="pre">run_obsdiag()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.run_obs_diag.write_input_filelist"><code class="docutils literal notranslate"><span class="pre">write_input_filelist()</span></code></a></li>
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prep-ic-prior-module">dartwrf.prep_IC_prior module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prepare-namelist-module">dartwrf.prepare_namelist module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prepare-wrfrundir-module">dartwrf.prepare_wrfrundir module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-run-obs-diag-module">dartwrf.run_obs_diag module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dartwrf.html#module-dartwrf.update_IC">dartwrf.update_IC module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="dartwrf.html#dartwrf.update_IC.update_initials_in_WRF_rundir"><code class="docutils literal notranslate"><span class="pre">update_initials_in_WRF_rundir()</span></code></a></li>
 </ul>
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index be2bfc7eee5e9a20c9799f6d2b569af41371d054..0d3b1ba7771a49aeee641befb93be165041ba1ae 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 6e35cb9a17cce85306012aae197c9affb110544a..1dd3cb8a0ee655cab0639863679d1a535e237821 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -81,7 +81,7 @@
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <a href="dartwrf.html#module-dartwrf"><code class="xref">dartwrf</code></a></td><td>
+       <a href="generated/dartwrf.html#module-dartwrf"><code class="xref">dartwrf</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
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@@ -118,11 +118,6 @@
        <td>&#160;&#160;&#160;
        <a href="dartwrf.html#module-dartwrf.evaluate_prior"><code class="xref">dartwrf.evaluate_prior</code></a></td><td>
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-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.link_dart_rttov"><code class="xref">dartwrf.link_dart_rttov</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -148,36 +143,11 @@
        <td>&#160;&#160;&#160;
        <a href="dartwrf.html#module-dartwrf.obsseq_2dim"><code class="xref">dartwrf.obsseq_2dim</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.obsseq_to_netcdf"><code class="xref">dartwrf.obsseq_to_netcdf</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="dartwrf.html#module-dartwrf.old_functions"><code class="xref">dartwrf.old_functions</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.prep_IC_prior"><code class="xref">dartwrf.prep_IC_prior</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.prepare_namelist"><code class="xref">dartwrf.prepare_namelist</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.prepare_wrfrundir"><code class="xref">dartwrf.prepare_wrfrundir</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="dartwrf.html#module-dartwrf.run_obs_diag"><code class="xref">dartwrf.run_obs_diag</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 3fea7d9ba447887d020f2c1b8bbab1c4f2e0f17b..df31179c4d0d69efebf832cc9378b198308b80de 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
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"dartwrf.utils.ClusterConfig.create_job"]], "create_obs_seq_in() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.create_obs_seq_in"]], "create_obsseq_in_separate_obs() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.create_obsseq_in_separate_obs"]], "dartrundir (dartwrf.utils.clusterconfig property)": [[1, "dartwrf.utils.ClusterConfig.dartrundir"]], "dartwrf": [[1, "module-dartwrf"], [4, "module-dartwrf"]], "dartwrf.assim_synth_obs": [[1, "module-dartwrf.assim_synth_obs"]], "dartwrf.cleanup_exp": [[1, "module-dartwrf.cleanup_exp"]], "dartwrf.create_obs_upfront": [[1, "module-dartwrf.create_obs_upfront"]], "dartwrf.create_obsseq": [[1, "module-dartwrf.create_obsseq"]], "dartwrf.create_wbubble_wrfinput": [[1, "module-dartwrf.create_wbubble_wrfinput"]], "dartwrf.evaluate_posterior": [[1, "module-dartwrf.evaluate_posterior"]], "dartwrf.evaluate_prior": [[1, "module-dartwrf.evaluate_prior"]], "dartwrf.obsseq": [[1, "module-dartwrf.obsseq"]], "dartwrf.obsseq_2dim": [[1, "module-dartwrf.obsseq_2dim"]], "dartwrf.old_functions": [[1, "module-dartwrf.old_functions"]], "dartwrf.update_ic": [[1, "module-dartwrf.update_IC"]], "dartwrf.utils": [[1, "module-dartwrf.utils"]], "dartwrf.wrfinput_add_geo": [[1, "module-dartwrf.wrfinput_add_geo"]], "dartwrf.wrfout_add_geo": [[1, "module-dartwrf.wrfout_add_geo"]], "degr_to_rad() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.degr_to_rad"]], "degrees_to_rad() (in module dartwrf.obsseq)": [[1, "dartwrf.obsseq.degrees_to_rad"]], "determine_nlayers() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.determine_nlayers"]], "determine_vert_coords() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.determine_vert_coords"]], "evaluate() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.evaluate"]], "filter() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.filter"]], "generate_obsseq_out() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.generate_obsseq_out"]], "get_dart_date() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.get_dart_date"]], "get_from_cartesian_grid() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.get_from_cartesian_grid"]], "get_lon_lat() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.get_lon_lat"]], "get_obsseq_out() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.get_obsseq_out"]], "get_parametrized_error() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.get_parametrized_error"]], "get_posterior_hx() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.get_posterior_Hx"]], "get_preamble_content() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.get_preamble_content"]], "get_prior_hx() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.get_prior_Hx"]], "get_truth_hx() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.get_truth_Hx"]], "link_contents() (in module dartwrf.utils)": [[1, "dartwrf.utils.link_contents"]], "link_nature_to_dart_truth() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.link_nature_to_dart_truth"]], "mkdir() (in module dartwrf.utils)": [[1, "dartwrf.utils.mkdir"]], "module": [[1, "module-dartwrf"], [1, "module-dartwrf.assim_synth_obs"], [1, "module-dartwrf.cleanup_exp"], [1, "module-dartwrf.create_obs_upfront"], [1, "module-dartwrf.create_obsseq"], [1, "module-dartwrf.create_wbubble_wrfinput"], [1, "module-dartwrf.evaluate_posterior"], [1, "module-dartwrf.evaluate_prior"], [1, "module-dartwrf.obsseq"], [1, "module-dartwrf.obsseq_2dim"], [1, "module-dartwrf.old_functions"], [1, "module-dartwrf.update_IC"], [1, "module-dartwrf.utils"], [1, "module-dartwrf.wrfinput_add_geo"], [1, "module-dartwrf.wrfout_add_geo"], [2, "module-dartwrf.obs"], [2, "module-dartwrf.obs.calculate_obs_locations"], [2, "module-dartwrf.obs.error_models"], [4, "module-dartwrf"]], "obs_operator_nature() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.obs_operator_nature"]], "obs_to_dict() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.obs_to_dict"]], "obskind_read() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.obskind_read"]], "plot() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.plot"]], "plot_box() (in module dartwrf.obsseq)": [[1, "dartwrf.obsseq.plot_box"]], "preamble() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.preamble"]], "prepare_nature_dart() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.prepare_nature_dart"]], "prepare_prior_ensemble() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.prepare_prior_ensemble"]], "print() (in module dartwrf.utils)": [[1, "dartwrf.utils.print"]], "qc_obs() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.qc_obs"]], "rad_to_degrees() (in module dartwrf.obsseq)": [[1, "dartwrf.obsseq.rad_to_degrees"]], "read_preamble() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.read_preamble"]], "read_prior_obs() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.read_prior_obs"]], "read_truth_obs_obsseq() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.read_truth_obs_obsseq"]], "recycle_output() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.recycle_output"]], "replace_errors_obsseqout() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.replace_errors_obsseqout"]], "round_to_day() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.round_to_day"]], "run() (dartwrf.utils.shellslurm method)": [[1, "dartwrf.utils.Shellslurm.run"]], "run() (in module dartwrf.wrfinput_add_geo)": [[1, "dartwrf.wrfinput_add_geo.run"]], "run() (in module dartwrf.wrfout_add_geo)": [[1, "dartwrf.wrfout_add_geo.run"]], "run_hx() (in module dartwrf.old_functions)": [[1, "dartwrf.old_functions.run_Hx"]], "run_perfect_model_obs() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.run_perfect_model_obs"]], "script_to_str() (in module dartwrf.utils)": [[1, "dartwrf.utils.script_to_str"]], "scripts_rundir (dartwrf.utils.clusterconfig property)": [[1, "dartwrf.utils.ClusterConfig.scripts_rundir"]], "sed_inplace() (in module dartwrf.utils)": [[1, "dartwrf.utils.sed_inplace"]], "set_dart_nml() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.set_DART_nml"]], "set_obserr_assimilate_in_obsseqout() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.set_obserr_assimilate_in_obsseqout"]], "setup() (dartwrf.utils.clusterconfig method)": [[1, "dartwrf.utils.ClusterConfig.setup"]], "shell() (in module dartwrf.utils)": [[1, "dartwrf.utils.shell"]], "superob() (dartwrf.obsseq.obsrecord method)": [[1, "dartwrf.obsseq.ObsRecord.superob"]], "symlink() (in module dartwrf.utils)": [[1, "dartwrf.utils.symlink"]], "to_dart() (dartwrf.obsseq.obsseq method)": [[1, "dartwrf.obsseq.ObsSeq.to_dart"]], "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_file() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.write_file"]], "write_list_of_inputfiles_posterior() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.write_list_of_inputfiles_posterior"]], "write_list_of_inputfiles_prior() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.write_list_of_inputfiles_prior"]], "write_list_of_outputfiles() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.write_list_of_outputfiles"]], "write_sat_angle_appendix() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.write_sat_angle_appendix"]], "write_section() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.write_section"]], "write_tuple_to_pickle() (in module dartwrf.create_obsseq)": [[1, "dartwrf.create_obsseq.write_tuple_to_pickle"]], "write_txt() (in module dartwrf.assim_synth_obs)": [[1, "dartwrf.assim_synth_obs.write_txt"]], "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/source/conf.py b/docs/source/conf.py
index e4ce287f71f518675a7b8a44e81a1b3d55dd4e2f..828fa4e760510e91829d16b8840986b51852d68e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -1,6 +1,6 @@
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../dartwrf/'))
+sys.path.insert(0, os.path.abspath('../../'))
 # Configuration file for the Sphinx documentation builder.
 
 # -- Project information