Deploy preview for PR 57 🛫

C2SM · Feb 7, 2024 · e992cef · e992cef
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diff --git a/pr-preview/pr-57/.doctrees/environment.pickle b/pr-preview/pr-57/.doctrees/environment.pickle
diff --git a/pr-preview/pr-57/.doctrees/functions.doctree b/pr-preview/pr-57/.doctrees/functions.doctree
diff --git a/pr-preview/pr-57/_modules/index.html b/pr-preview/pr-57/_modules/index.html
@@ -94,6 +94,7 @@
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.cosmo.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.emissions.main"><code class="docutils literal notranslate"><span class="pre">jobs.emissions.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.icon.main"><code class="docutils literal notranslate"><span class="pre">jobs.icon.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.icontools.main"><code class="docutils literal notranslate"><span class="pre">jobs.icontools.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.int2lm.main"><code class="docutils literal notranslate"><span class="pre">jobs.int2lm.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.obs_nudging.main"><code class="docutils literal notranslate"><span class="pre">jobs.obs_nudging.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.octe.main"><code class="docutils literal notranslate"><span class="pre">jobs.octe.main()</span></code></a></li>
@@ -102,6 +103,8 @@
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.photo_rate.main"><code class="docutils literal notranslate"><span class="pre">jobs.photo_rate.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.post_cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.post_cosmo.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.post_int2lm.main"><code class="docutils literal notranslate"><span class="pre">jobs.post_int2lm.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.prepare_cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.prepare_cosmo.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.prepare_icon.main"><code class="docutils literal notranslate"><span class="pre">jobs.prepare_icon.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.reduce_output.main"><code class="docutils literal notranslate"><span class="pre">jobs.reduce_output.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../functions.html#jobs.verify_chain.main"><code class="docutils literal notranslate"><span class="pre">jobs.verify_chain.main()</span></code></a></li>
 </ul>
@@ -150,6 +153,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="jobs/cosmo.html">jobs.cosmo</a></li>
 <li><a href="jobs/emissions.html">jobs.emissions</a></li>
 <li><a href="jobs/icon.html">jobs.icon</a></li>
+<li><a href="jobs/icontools.html">jobs.icontools</a></li>
 <li><a href="jobs/int2lm.html">jobs.int2lm</a></li>
 <li><a href="jobs/obs_nudging.html">jobs.obs_nudging</a></li>
 <li><a href="jobs/octe.html">jobs.octe</a></li>
@@ -158,6 +162,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="jobs/photo_rate.html">jobs.photo_rate</a></li>
 <li><a href="jobs/post_cosmo.html">jobs.post_cosmo</a></li>
 <li><a href="jobs/post_int2lm.html">jobs.post_int2lm</a></li>
+<li><a href="jobs/prepare_cosmo.html">jobs.prepare_cosmo</a></li>
+<li><a href="jobs/prepare_icon.html">jobs.prepare_icon</a></li>
 <li><a href="jobs/reduce_output.html">jobs.reduce_output</a></li>
 <li><a href="jobs/tools/cams4int2cosmo.html">jobs.tools.cams4int2cosmo</a></li>
 <li><a href="jobs/tools/check_model.html">jobs.tools.check_model</a></li>

diff --git a/pr-preview/pr-57/_modules/jobs/biofluxes.html b/pr-preview/pr-57/_modules/jobs/biofluxes.html
@@ -94,6 +94,7 @@
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.cosmo.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.emissions.main"><code class="docutils literal notranslate"><span class="pre">jobs.emissions.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.icon.main"><code class="docutils literal notranslate"><span class="pre">jobs.icon.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.icontools.main"><code class="docutils literal notranslate"><span class="pre">jobs.icontools.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.int2lm.main"><code class="docutils literal notranslate"><span class="pre">jobs.int2lm.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.obs_nudging.main"><code class="docutils literal notranslate"><span class="pre">jobs.obs_nudging.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.octe.main"><code class="docutils literal notranslate"><span class="pre">jobs.octe.main()</span></code></a></li>
@@ -102,6 +103,8 @@
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.photo_rate.main"><code class="docutils literal notranslate"><span class="pre">jobs.photo_rate.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.post_cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.post_cosmo.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.post_int2lm.main"><code class="docutils literal notranslate"><span class="pre">jobs.post_int2lm.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.prepare_cosmo.main"><code class="docutils literal notranslate"><span class="pre">jobs.prepare_cosmo.main()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.prepare_icon.main"><code class="docutils literal notranslate"><span class="pre">jobs.prepare_icon.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.reduce_output.main"><code class="docutils literal notranslate"><span class="pre">jobs.reduce_output.main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../functions.html#jobs.verify_chain.main"><code class="docutils literal notranslate"><span class="pre">jobs.verify_chain.main()</span></code></a></li>
 </ul>
@@ -151,10 +154,13 @@ <h1>Source code for jobs.biofluxes</h1><div class="highlight"><pre>
 
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">tools</span><span class="p">,</span> <span class="n">prepare_data</span>
 
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">tools</span><span class="p">,</span> <span class="n">prepare_cosmo</span>
 
-<div class="viewcode-block" id="main"><a class="viewcode-back" href="../../functions.html#jobs.biofluxes.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">cfg</span><span class="p">,</span> <span class="n">model_cfg</span><span class="p">):</span>
+<span class="n">BASIC_PYTHON_JOB</span> <span class="o">=</span> <span class="kc">True</span>
+
+
+<div class="viewcode-block" id="main"><a class="viewcode-back" href="../../functions.html#jobs.biofluxes.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">cfg</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Prepare biofluxes files for COSMO simulations.</span>
 
 <span class="sd">    Copies biofluxes files from the project folder (:attr:`cfg.vprm[&#39;dir&#39;]`)</span>
@@ -164,11 +170,9 @@ <h1>Source code for jobs.biofluxes</h1><div class="highlight"><pre>
 <span class="sd">    ----------</span>
 <span class="sd">    cfg : Config</span>
 <span class="sd">        Object holding all user-configuration parameters as attributes.</span>
-<span class="sd">    model_cfg : dict</span>
-<span class="sd">        Model configuration settings loaded from the ``config/models.yaml`` file.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">tools</span><span class="o">.</span><span class="n">check_model</span><span class="p">(</span><span class="n">cfg</span><span class="p">,</span> <span class="s1">&#39;cosmo-ghg&#39;</span><span class="p">)</span>
-    <span class="n">cfg</span> <span class="o">=</span> <span class="n">prepare_data</span><span class="o">.</span><span class="n">set_cfg_variables</span><span class="p">(</span><span class="n">cfg</span><span class="p">,</span> <span class="n">model_cfg</span><span class="p">)</span>
+    <span class="n">tools</span><span class="o">.</span><span class="n">change_logfile</span><span class="p">(</span><span class="n">cfg</span><span class="o">.</span><span class="n">logfile</span><span class="p">)</span>
+    <span class="n">prepare_cosmo</span><span class="o">.</span><span class="n">set_cfg_variables</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
 
     <span class="n">scratch_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cfg</span><span class="o">.</span><span class="n">int2lm_input</span><span class="p">,</span> <span class="s1">&#39;vprm&#39;</span><span class="p">)</span>