deploy: 0bb9d9a

ReactionMechanismGenerator · Aug 11, 2024 · f0e28a8 · f0e28a8
1 parent eb35dec
commit f0e28a8
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/_modules/arc/parser.html b/_modules/arc/parser.html
@@ -395,11 +395,9 @@ <h1>Source code for arc.parser</h1><div class="highlight"><pre>
         <span class="k">raise</span> <span class="n">InputError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Could not find file </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.yml&#39;</span><span class="p">):</span>
         <span class="n">content</span> <span class="o">=</span> <span class="n">read_yaml_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
-            <span class="k">if</span> <span class="s1">&#39;xyz&#39;</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-                <span class="k">return</span> <span class="n">content</span><span class="p">[</span><span class="s1">&#39;xyz&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="s1">&#39;xyz&#39;</span><span class="p">],</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span> <span class="n">str_to_xyz</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="s1">&#39;xyz&#39;</span><span class="p">])</span>
-            <span class="k">elif</span> <span class="s1">&#39;opt_xyz&#39;</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-                <span class="k">return</span> <span class="n">content</span><span class="p">[</span><span class="s1">&#39;opt_xyz&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="s1">&#39;opt_xyz&#39;</span><span class="p">],</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span> <span class="n">str_to_xyz</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="s1">&#39;opt_xyz&#39;</span><span class="p">])</span>
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;xyz&#39;</span><span class="p">,</span> <span class="s1">&#39;opt_xyz&#39;</span><span class="p">]:</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="ow">and</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+                <span class="k">return</span> <span class="n">content</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span> <span class="n">str_to_xyz</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
     <span class="n">software</span> <span class="o">=</span> <span class="n">identify_ess</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
     <span class="n">xyz_str</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
     <span class="k">if</span> <span class="n">software</span> <span class="o">==</span> <span class="s1">&#39;xtb&#39;</span><span class="p">:</span>
@@ -460,6 +458,10 @@ <h1>Source code for arc.parser</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
         <span class="k">raise</span> <span class="n">InputError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Could not find file </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.yml&#39;</span><span class="p">):</span>
+        <span class="n">content</span> <span class="o">=</span> <span class="n">read_yaml_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="ow">and</span> <span class="s1">&#39;T1&#39;</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="k">return</span> <span class="n">content</span><span class="p">[</span><span class="s1">&#39;T1&#39;</span><span class="p">]</span>
     <span class="n">log</span> <span class="o">=</span> <span class="n">ess_factory</span><span class="p">(</span><span class="n">fullpath</span><span class="o">=</span><span class="n">path</span><span class="p">,</span> <span class="n">check_for_errors</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
     <span class="k">try</span><span class="p">:</span>
         <span class="n">t1</span> <span class="o">=</span> <span class="n">log</span><span class="o">.</span><span class="n">get_T1_diagnostic</span><span class="p">()</span>
@@ -519,6 +521,10 @@ <h1>Source code for arc.parser</h1><div class="highlight"><pre>
 <span class="sd">        Optional[str]: The ESS.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">software</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.yml&#39;</span><span class="p">):</span>
+        <span class="n">content</span> <span class="o">=</span> <span class="n">read_yaml_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="ow">and</span> <span class="s1">&#39;adapter&#39;</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="k">return</span> <span class="n">content</span><span class="p">[</span><span class="s1">&#39;adapter&#39;</span><span class="p">]</span>
     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
         <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">25</span><span class="p">):</span>
             <span class="n">line</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>