[skip ci] Updates

ersilia-os · Feb 13, 2025 · ee571d7 · ee571d7
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commit ee571d7
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diff --git a/_modules/ersilia/io/output.html b/_modules/ersilia/io/output.html
@@ -313,7 +313,6 @@
         <article role="main" id="furo-main-content">
           <h1>Source code for ersilia.io.output</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span><span class="w"> </span><span class="nn">collections</span>
-<span class="kn">import</span><span class="w"> </span><span class="nn">csv</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">json</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">random</span>
@@ -463,13 +462,16 @@ <h1>Source code for ersilia.io.output</h1><div class="highlight"><pre>
 <span class="sd">        delimiter : str, optional</span>
 <span class="sd">            The delimiter to use in the text file (default is None).</span>
 <span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">delimiter</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">delimiter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_delimiter</span><span class="p">(</span><span class="n">file_name</span><span class="p">)</span>
+        <span class="n">none_str</span> <span class="o">=</span> <span class="s2">&quot;None&quot;</span>
         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">,</span> <span class="n">newline</span><span class="o">=</span><span class="s2">&quot;&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">delimiter</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="n">delimiter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_delimiter</span><span class="p">(</span><span class="n">file_name</span><span class="p">)</span>
-            <span class="n">writer</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">writer</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="n">delimiter</span><span class="p">)</span>
-            <span class="n">writer</span><span class="o">.</span><span class="n">writerow</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
-            <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">):</span>
-                <span class="n">writer</span><span class="o">.</span><span class="n">writerow</span><span class="p">(</span><span class="n">row</span><span class="p">)</span></div>
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">delimiter</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+                <span class="n">row_str</span> <span class="o">=</span> <span class="n">delimiter</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="n">none_str</span> <span class="k">if</span> <span class="n">val</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="n">val</span><span class="p">)</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">row</span>
+                <span class="p">)</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">row_str</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="DataFrame.write">
@@ -1010,7 +1012,11 @@ <h1>Source code for ersilia.io.output</h1><div class="highlight"><pre>
                     <span class="k">if</span> <span class="n">dtype</span><span class="p">:</span>
                         <span class="n">are_dtypes_informative</span> <span class="o">=</span> <span class="kc">True</span>
                 <span class="k">if</span> <span class="n">output_keys_expanded</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s2">&quot;Output key not expanded: val </span><span class="si">{</span><span class="n">vals</span><span class="si">}</span><span class="s2"> and </span><span class="si">{</span><span class="n">output_keys</span><span class="si">}</span><span class="s2">&quot;</span>
+                    <span class="p">)</span>
                     <span class="n">output_keys_expanded</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__expand_output_keys</span><span class="p">(</span><span class="n">vals</span><span class="p">,</span> <span class="n">output_keys</span><span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Expanded output keys: </span><span class="si">{</span><span class="n">output_keys_expanded</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
                 <span class="k">if</span> <span class="ow">not</span> <span class="n">are_dtypes_informative</span><span class="p">:</span>
                     <span class="n">t</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_guess_pure_dtype_if_absent</span><span class="p">(</span><span class="n">vals</span><span class="p">)</span>
                     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">output_keys</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -1163,18 +1169,9 @@ <h1>Source code for ersilia.io.output</h1><div class="highlight"><pre>
             <span class="n">extension</span> <span class="o">=</span> <span class="s2">&quot;json&quot;</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">extension</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_to_dataframe</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">model_id</span><span class="p">)</span>
         <span class="n">delimiters</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;csv&quot;</span><span class="p">:</span> <span class="s2">&quot;,&quot;</span><span class="p">,</span> <span class="s2">&quot;tsv&quot;</span><span class="p">:</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="s2">&quot;h5&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
-        <span class="k">if</span> <span class="n">extension</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;csv&quot;</span><span class="p">,</span> <span class="s2">&quot;tsv&quot;</span><span class="p">,</span> <span class="s2">&quot;h5&quot;</span><span class="p">]:</span>
-            <span class="n">R</span> <span class="o">=</span> <span class="p">[]</span>
-
-            <span class="c1"># Flatten the JSON object</span>
-            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">result</span><span class="p">):</span>
-                <span class="n">inp</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s2">&quot;input&quot;</span><span class="p">]</span>
-                <span class="n">out</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s2">&quot;output&quot;</span><span class="p">]</span>
-                <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">out</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">out</span><span class="o">.</span><span class="n">keys</span><span class="p">()]</span>
-                <span class="n">R</span> <span class="o">+=</span> <span class="p">[[</span><span class="n">inp</span><span class="p">[</span><span class="s2">&quot;key&quot;</span><span class="p">],</span> <span class="n">inp</span><span class="p">[</span><span class="s2">&quot;input&quot;</span><span class="p">]]</span> <span class="o">+</span> <span class="n">vals</span><span class="p">]</span>
-
-            <span class="n">df</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">R</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;key&quot;</span><span class="p">,</span> <span class="s2">&quot;input&quot;</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">out</span><span class="o">.</span><span class="n">keys</span><span class="p">()])</span>
+        <span class="k">if</span> <span class="n">extension</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;tsv&quot;</span><span class="p">,</span> <span class="s2">&quot;h5&quot;</span><span class="p">,</span> <span class="s2">&quot;csv&quot;</span><span class="p">]:</span>
             <span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">output</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="n">delimiters</span><span class="p">[</span><span class="n">extension</span><span class="p">])</span>
         <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s2">&quot;json&quot;</span><span class="p">:</span>
             <span class="n">data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>