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diff --git a/docs/build/doctrees/dev-notes.doctree b/docs/build/doctrees/dev-notes.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/help.doctree b/docs/build/doctrees/help.doctree
diff --git a/docs/build/doctrees/hqtb/about-pipeline.doctree b/docs/build/doctrees/hqtb/about-pipeline.doctree
diff --git a/docs/build/doctrees/hqtb/hqtb-config.doctree b/docs/build/doctrees/hqtb/hqtb-config.doctree
diff --git a/docs/build/doctrees/hqtb/run-pipeline.doctree b/docs/build/doctrees/hqtb/run-pipeline.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/analysis.doctree b/docs/build/doctrees/hqtb/step-desc/analysis.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/bidirect_blast.doctree b/docs/build/doctrees/hqtb/step-desc/bidirect_blast.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/gen_draft.doctree b/docs/build/doctrees/hqtb/step-desc/gen_draft.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/annot.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/annot.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/cleanup.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/cleanup.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/extension.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/extension.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/smooth.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/smooth.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refinement.doctree b/docs/build/doctrees/hqtb/step-desc/refinement.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/validation.doctree b/docs/build/doctrees/hqtb/step-desc/validation.doctree
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/installation.doctree b/docs/build/doctrees/installation.doctree
diff --git a/docs/build/doctrees/modules/classes.doctree b/docs/build/doctrees/modules/classes.doctree
diff --git a/docs/build/doctrees/modules/cmd.doctree b/docs/build/doctrees/modules/cmd.doctree
diff --git a/docs/build/doctrees/modules/cmpb.doctree b/docs/build/doctrees/modules/cmpb.doctree
diff --git a/docs/build/doctrees/modules/core.doctree b/docs/build/doctrees/modules/core.doctree
diff --git a/docs/build/doctrees/modules/hqtb.doctree b/docs/build/doctrees/modules/hqtb.doctree
diff --git a/docs/build/doctrees/modules/util.doctree b/docs/build/doctrees/modules/util.doctree
diff --git a/docs/build/doctrees/overview-pipes.doctree b/docs/build/doctrees/overview-pipes.doctree
diff --git a/docs/build/doctrees/specimen.doctree b/docs/build/doctrees/specimen.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e6df1f6e9c96870d3ba9c601c63df629
+config: 0fb85034dd4ee52eca935a0038112cc8
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -18,7 +18,7 @@
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -81,7 +81,19 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="specimen/util/util.html">specimen.util.util</a></li>
+<ul><li><a href="specimen/classes/reports.html">specimen.classes.reports</a></li>
+<li><a href="specimen/cmpb/workflow.html">specimen.cmpb.workflow</a></li>
+<li><a href="specimen/hqtb/core/analysis.html">specimen.hqtb.core.analysis</a></li>
+<li><a href="specimen/hqtb/core/bidirectional_blast.html">specimen.hqtb.core.bidirectional_blast</a></li>
+<li><a href="specimen/hqtb/core/generate_draft_model.html">specimen.hqtb.core.generate_draft_model</a></li>
+<li><a href="specimen/hqtb/core/refinement/annotation.html">specimen.hqtb.core.refinement.annotation</a></li>
+<li><a href="specimen/hqtb/core/refinement/cleanup.html">specimen.hqtb.core.refinement.cleanup</a></li>
+<li><a href="specimen/hqtb/core/refinement/extension.html">specimen.hqtb.core.refinement.extension</a></li>
+<li><a href="specimen/hqtb/core/refinement/smoothing.html">specimen.hqtb.core.refinement.smoothing</a></li>
+<li><a href="specimen/hqtb/core/validation.html">specimen.hqtb.core.validation</a></li>
+<li><a href="specimen/hqtb/workflow.html">specimen.hqtb.workflow</a></li>
+<li><a href="specimen/util/set_up.html">specimen.util.set_up</a></li>
+<li><a href="specimen/util/util.html">specimen.util.util</a></li>
 </ul>
 
            </div>

diff --git a/docs/build/html/_modules/specimen/classes/reports.html b/docs/build/html/_modules/specimen/classes/reports.html
diff --git a/docs/build/html/_modules/specimen/cmpb/workflow.html b/docs/build/html/_modules/specimen/cmpb/workflow.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/analysis.html b/docs/build/html/_modules/specimen/hqtb/core/analysis.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/bidirectional_blast.html b/docs/build/html/_modules/specimen/hqtb/core/bidirectional_blast.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/generate_draft_model.html b/docs/build/html/_modules/specimen/hqtb/core/generate_draft_model.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/annotation.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/annotation.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/cleanup.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/cleanup.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/extension.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/extension.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/validation.html b/docs/build/html/_modules/specimen/hqtb/core/validation.html
@@ -0,0 +1,190 @@
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+  <title>specimen.hqtb.core.validation &mdash; SPECIMEN 1.0.0 documentation</title>
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+
+  <h1>Source code for specimen.hqtb.core.validation</h1><div class="highlight"><pre>
+<span></span><span class="sd">&quot;&quot;&quot;Validate a model (part 4 of the workflow).</span>
+
+<span class="sd">Implemented tests in include:</span>
+<span class="sd">- cobra/sbml check using cobrapy</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="n">__author__</span> <span class="o">=</span> <span class="s1">&#39;Carolin Brune&#39;</span>
+
+<span class="c1">################################################################################</span>
+<span class="c1"># requirements</span>
+<span class="c1">################################################################################</span>
+
+<span class="kn">import</span> <span class="nn">cobra</span>
+<span class="kn">import</span> <span class="nn">pprint</span>
+<span class="kn">import</span> <span class="nn">time</span>
+
+<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="c1">################################################################################</span>
+<span class="c1"># functions</span>
+<span class="c1">################################################################################</span>
+
+<span class="c1"># @TODO: add more validation options.´</span>
+
+<div class="viewcode-block" id="run">
+<a class="viewcode-back" href="../../../../modules/core.html#specimen.hqtb.core.validation.run">[docs]</a>
+<span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="nb">dir</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">model_path</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">tests</span><span class="p">:</span><span class="kc">None</span><span class="o">|</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;cobra&#39;</span><span class="p">]</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">run_all</span><span class="p">:</span><span class="nb">bool</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;SPECIMEN Step 4: Validate the model.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        - dir (str): </span>
+<span class="sd">            Path to the output directory.</span>
+<span class="sd">        - model_path (str): </span>
+<span class="sd">            Path to the model to be validated</span>
+<span class="sd">        - tests (None | Literal[&#39;cobra&#39;], optional): </span>
+<span class="sd">            Tests to perform. </span>
+<span class="sd">            Defaults to None.</span>
+<span class="sd">        - run_all (bool, optional): </span>
+<span class="sd">            Run al available tests. If True, overwrites</span>
+<span class="sd">            the previous parameter.</span>
+<span class="sd">            Defaults to True.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">total_time_s</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+
+    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">validation</span><span class="se">\n</span><span class="s1">################################################################################</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="c1"># -----------------------</span>
+    <span class="c1"># create output directory</span>
+    <span class="c1"># -----------------------</span>
+
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">Path</span><span class="p">(</span><span class="nb">dir</span><span class="p">,</span><span class="s2">&quot;04_validation&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+        <span class="nb">print</span><span class="p">(</span><span class="sa">F</span><span class="s1">&#39;Creating new directory </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="nb">dir</span><span class="p">,</span><span class="s2">&quot;04_validation&quot;</span><span class="p">))</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">FileExistsError</span><span class="p">:</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Given directory already has required structure.&#39;</span><span class="p">)</span>
+
+    <span class="c1"># --------------</span>
+    <span class="c1"># validate model</span>
+    <span class="c1"># --------------</span>
+
+    <span class="k">if</span> <span class="n">run_all</span> <span class="ow">or</span> <span class="p">(</span><span class="n">tests</span> <span class="ow">and</span> <span class="s1">&#39;cobra&#39;</span> <span class="ow">in</span> <span class="n">tests</span><span class="p">):</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1"># ---------------------------------</span><span class="se">\n</span><span class="s1"># validate model - cobra validation</span><span class="se">\n</span><span class="s1"># ---------------------------------&#39;</span><span class="p">)</span>
+        <span class="n">start</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+
+        <span class="c1"># validate using cobra</span>
+        <span class="n">cobra_report</span> <span class="o">=</span> <span class="n">cobra</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">validate_sbml_model</span><span class="p">(</span><span class="n">model_path</span><span class="p">)</span>
+        <span class="n">pprint</span><span class="o">.</span><span class="n">pprint</span><span class="p">(</span><span class="n">cobra_report</span><span class="p">)</span>
+
+        <span class="n">end</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+        <span class="nb">print</span><span class="p">(</span><span class="sa">F</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">time: </span><span class="si">{</span><span class="n">end</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="n">start</span><span class="si">}</span><span class="s1">s&#39;</span><span class="p">)</span>
+
+    <span class="n">total_time_e</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">F</span><span class="s1">&#39;total runtime: </span><span class="si">{</span><span class="n">total_time_e</span><span class="o">-</span><span class="n">total_time_s</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span></div>
+
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
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+    <p>&#169; Copyright 2024, Carolin Brune.</p>
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