[skip ci] Updates

genindex.html

@@ -2362,8 +2362,6 @@ <h2 id="G">G</h2>
 </li>
  <li><a href="source/autodoc/ersilia.io.readers.html#ersilia.io.readers.file.FileTyper.get_extension">get_extension() (ersilia.io.readers.file.FileTyper method)</a>
 </li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="source/autodoc/ersilia.hub.bundle.html#ersilia.hub.bundle.bundle.BundleDockerfileFile.get_file">get_file() (ersilia.hub.bundle.bundle.BundleDockerfileFile method)</a>
 
  <ul>
@@ -2378,6 +2376,8 @@ <h2 id="G">G</h2>
  <li><a href="source/autodoc/ersilia.hub.bundle.html#ersilia.hub.bundle.repo.ServiceFile.get_file">(ersilia.hub.bundle.repo.ServiceFile method)</a>
 </li>
  </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="source/autodoc/ersilia.core.html#ersilia.core.tracking.RunTracker.get_file_sizes">get_file_sizes() (ersilia.core.tracking.RunTracker method)</a>
 </li>
  <li><a href="source/autodoc/ersilia.serve.html#ersilia.serve.standard_api.StandardCSVRunApi.get_identifier_object_by_input_type">get_identifier_object_by_input_type() (ersilia.serve.standard_api.StandardCSVRunApi method)</a>
@@ -2399,6 +2399,8 @@ <h2 id="G">G</h2>
  <li><a href="source/autodoc/ersilia.hub.fetch.lazy_fetchers.html#ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher.get_metadata">get_metadata() (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method)</a>
 </li>
  <li><a href="source/autodoc/ersilia.hub.bundle.html#ersilia.hub.bundle.repo.RepoUtils.get_model_id">get_model_id() (ersilia.hub.bundle.repo.RepoUtils method)</a>
+</li>
+ <li><a href="source/autodoc/ersilia.core.html#ersilia.core.tracking.get_nan_counts">get_nan_counts() (in module ersilia.core.tracking)</a>
 </li>
  <li><a href="source/autodoc/ersilia.serve.html#ersilia.serve.schema.ApiSchema.get_output_by_api">get_output_by_api() (ersilia.serve.schema.ApiSchema method)</a>
 </li>
@@ -3684,7 +3686,11 @@ <h2 id="R">R</h2>
  <li><a href="source/autodoc/ersilia.hub.fetch.actions.html#ersilia.hub.fetch.actions.get.read_config_yaml_section">read_config_yaml_section() (in module ersilia.hub.fetch.actions.get)</a>
 </li>
  <li><a href="source/autodoc/ersilia.publish.html#ersilia.publish.test.ModelTester.read_csv">read_csv() (ersilia.publish.test.ModelTester method)</a>
+
+ <ul>
+ <li><a href="source/autodoc/ersilia.core.html#ersilia.core.tracking.read_csv">(in module ersilia.core.tracking)</a>
 </li>
+ </ul></li>
  <li><a href="source/autodoc/ersilia.hub.fetch.actions.html#ersilia.hub.fetch.actions.get.read_file_from_path">read_file_from_path() (in module ersilia.hub.fetch.actions.get)</a>
 </li>
  <li><a href="source/autodoc/ersilia.io.readers.html#ersilia.io.readers.file.StandardTabularFileReader.read_header">read_header() (ersilia.io.readers.file.StandardTabularFileReader method)</a>
@@ -3735,6 +3741,8 @@ <h2 id="R">R</h2>
 </li>
  <li><a href="source/autodoc/ersilia.core.html#ersilia.core.session.Session.register_service_class">register_service_class() (ersilia.core.session.Session method)</a>
 </li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="source/autodoc/ersilia.db.environments.html#ersilia.db.environments.managers.DockerManager.remove">remove() (ersilia.db.environments.managers.DockerManager method)</a>
 
  <ul>
@@ -3745,8 +3753,6 @@ <h2 id="R">R</h2>
  <li><a href="source/autodoc/ersilia.utils.html#ersilia.utils.remove.OsfRemover.remove">(ersilia.utils.remove.OsfRemover method)</a>
 </li>
  </ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="source/autodoc/ersilia.utils.html#ersilia.utils.installers.BaseInstaller.remove_from_log">remove_from_log() (ersilia.utils.installers.BaseInstaller method)</a>
 </li>
  <li><a href="source/autodoc/ersilia.lake.html#ersilia.lake.manager.IsauraManager.remove_local_duplicates">remove_local_duplicates() (ersilia.lake.manager.IsauraManager method)</a>

source/autodoc/ersilia.core.html

@@ -312,13 +312,13 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 to Ersilia’s Splunk dashboard.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="ersilia.core.tracking.RunTracker.check_types">
-<span class="sig-name descname"><span class="pre">check_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">result_df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#RunTracker.check_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.RunTracker.check_types" title="Permalink to this definition"></a></dt>
-<dd><p>This class is responsible for checking the types of the output dataframe against the expected types.
-This includes checking the shape of the output dataframe (list vs single) and the types of each column.</p>
+<span class="sig-name descname"><span class="pre">check_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">result</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#RunTracker.check_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.RunTracker.check_types" title="Permalink to this definition"></a></dt>
+<dd><p>This method is responsible for checking the types of the output file against the expected types.
+This includes checking the shape of the output file (list vs single) and the types of each column.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>result_df</strong> – The output dataframe</p></li>
+<li><p><strong>result</strong> – The output file</p></li>
 <li><p><strong>metadata</strong> – The metadata dictionary</p></li>
 </ul>
 </dd>
@@ -330,13 +330,13 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="ersilia.core.tracking.RunTracker.get_file_sizes">
-<span class="sig-name descname"><span class="pre">get_file_sizes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_df</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#RunTracker.get_file_sizes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.RunTracker.get_file_sizes" title="Permalink to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">get_file_sizes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#RunTracker.get_file_sizes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.RunTracker.get_file_sizes" title="Permalink to this definition"></a></dt>
 <dd><p>Calculates the size of the input and output dataframes, as well as the average size of each row.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Input_df<span class="colon">:</span></dt>
+<dt class="field-odd">Input_file<span class="colon">:</span></dt>
 <dd class="field-odd"><p>Pandas dataframe containing the input data</p>
 </dd>
-<dt class="field-even">Output_df<span class="colon">:</span></dt>
+<dt class="field-even">Output_file<span class="colon">:</span></dt>
 <dd class="field-even"><p>Pandas dataframe containing the output data</p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
@@ -394,6 +394,20 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dd><p>Closes the persistent file, renaming it to a unique name.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ersilia.core.tracking.get_nan_counts">
+<span class="sig-prename descclassname"><span class="pre">ersilia.core.tracking.</span></span><span class="sig-name descname"><span class="pre">get_nan_counts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_list</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#get_nan_counts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.get_nan_counts" title="Permalink to this definition"></a></dt>
+<dd><p>Calculates the number of None values in each key of a list of dictionaries.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>data_list</strong> – List of dictionaries containing the data</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Dictionary containing the count of None values for each key</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ersilia.core.tracking.log_files_metrics">
 <span class="sig-prename descclassname"><span class="pre">ersilia.core.tracking.</span></span><span class="sig-name descname"><span class="pre">log_files_metrics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#log_files_metrics"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.log_files_metrics" title="Permalink to this definition"></a></dt>
@@ -415,6 +429,20 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 :param model_id: The currently running model</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ersilia.core.tracking.read_csv">
+<span class="sig-prename descclassname"><span class="pre">ersilia.core.tracking.</span></span><span class="sig-name descname"><span class="pre">read_csv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#read_csv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.read_csv" title="Permalink to this definition"></a></dt>
+<dd><p>Reads a CSV file and returns the data as a list of dictionaries.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>file_path</strong> – Path to the CSV file.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list of dictionaries containing the CSV data.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ersilia.core.tracking.upload_to_cddvault">
 <span class="sig-prename descclassname"><span class="pre">ersilia.core.tracking.</span></span><span class="sig-name descname"><span class="pre">upload_to_cddvault</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">api_key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/ersilia/core/tracking.html#upload_to_cddvault"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ersilia.core.tracking.upload_to_cddvault" title="Permalink to this definition"></a></dt>

source/autodoc/ersilia.html

@@ -295,8 +295,10 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.close_persistent_file"><code class="docutils literal notranslate"><span class="pre">close_persistent_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.get_nan_counts"><code class="docutils literal notranslate"><span class="pre">get_nan_counts()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.log_files_metrics"><code class="docutils literal notranslate"><span class="pre">log_files_metrics()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.open_persistent_file"><code class="docutils literal notranslate"><span class="pre">open_persistent_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.read_csv"><code class="docutils literal notranslate"><span class="pre">read_csv()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.upload_to_cddvault"><code class="docutils literal notranslate"><span class="pre">upload_to_cddvault()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.upload_to_s3"><code class="docutils literal notranslate"><span class="pre">upload_to_s3()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="ersilia.core.html#ersilia.core.tracking.write_persistent_file"><code class="docutils literal notranslate"><span class="pre">write_persistent_file()</span></code></a></li>