docs

e24931af · lkugler · c9d25da3 · e24931af · e24931af · e24931af
Commit e24931af authored 2 years ago by lkugler
--- a/docs/build/doctrees/dartwrf.doctree
+++ b/docs/build/doctrees/dartwrf.doctree
--- a/docs/build/doctrees/environment.pickle
+++ b/docs/build/doctrees/environment.pickle
--- 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-module">dartwrf.obsseq_to_netcdf module</a></li>
-<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="#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-module">dartwrf.prep_IC_prior module</a></li>
-<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-prepare-namelist-module">dartwrf.prepare_namelist module</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>
+<li><a class="reference internal" href="#dartwrf-prepare-wrfrundir-module">dartwrf.prepare_wrfrundir module</a></li>
-</ul>
+<li><a class="reference internal" href="#dartwrf-run-obs-diag-module">dartwrf.run_obs_diag module</a></li>
-</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="#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">
+<section id="dartwrf-link-dart-rttov-module">
-<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>
+<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">
+<section id="dartwrf-obsseq-to-netcdf-module">
-<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>
+<h2>dartwrf.obsseq_to_netcdf module<a class="headerlink" href="#dartwrf-obsseq-to-netcdf-module" 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>
 <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">
+<section id="dartwrf-prep-ic-prior-module">
-<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>
+<h2>dartwrf.prep_IC_prior module<a class="headerlink" href="#dartwrf-prep-ic-prior-module" 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>
-<section id="module-dartwrf.prepare_namelist">
+<section id="dartwrf-prepare-namelist-module">
-<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>
+<h2>dartwrf.prepare_namelist module<a class="headerlink" href="#dartwrf-prepare-namelist-module" 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>
-<section id="module-dartwrf.prepare_wrfrundir">
+<section id="dartwrf-prepare-wrfrundir-module">
-<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>
+<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">
+<section id="dartwrf-run-obs-diag-module">
-<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>
+<h2>dartwrf.run_obs_diag module<a class="headerlink" href="#dartwrf-run-obs-diag-module" 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>
 <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>

--- 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>

--- 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-l2"><a class="reference internal" href="dartwrf.html#dartwrf-obsseq-to-netcdf-module">dartwrf.obsseq_to_netcdf module</a></li>
-<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#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-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prep-ic-prior-module">dartwrf.prep_IC_prior module</a></li>
-<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-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prepare-namelist-module">dartwrf.prepare_namelist module</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>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-prepare-wrfrundir-module">dartwrf.prepare_wrfrundir module</a></li>
-</ul>
+<li class="toctree-l2"><a class="reference internal" href="dartwrf.html#dartwrf-run-obs-diag-module">dartwrf.run_obs_diag module</a></li>
-</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#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>

--- a/docs/build/html/objects.inv
+++ b/docs/build/html/objects.inv
--- 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">
       <td></td>
@@ -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>
       <em></em></td></tr>
-     <tr class="cg-1">
-       <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;

--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
 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