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_modules/sssom/cli.html

@@ -129,6 +129,7 @@ <h1>Source code for sssom.cli</h1><div class="highlight"><pre>
     <span class="n">filter_redundant_rows</span><span class="p">,</span>
     <span class="n">invert_mappings</span><span class="p">,</span>
     <span class="n">merge_msdf</span><span class="p">,</span>
+    <span class="n">pandas_set_no_silent_downcasting</span><span class="p">,</span>
     <span class="n">reconcile_prefix_and_data</span><span class="p">,</span>
     <span class="n">remove_unmatched</span><span class="p">,</span>
     <span class="n">sort_df_rows_columns</span><span class="p">,</span>
@@ -201,6 +202,9 @@ <h1>Source code for sssom.cli</h1><div class="highlight"><pre>
 <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">verbose</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">quiet</span><span class="p">:</span> <span class="nb">bool</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Run the SSSOM CLI.&quot;&quot;&quot;</span>
     <span class="n">logger</span> <span class="o">=</span> <span class="n">_logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span>
+
+    <span class="n">pandas_set_no_silent_downcasting</span><span class="p">()</span>
+
     <span class="k">if</span> <span class="n">verbose</span> <span class="o">&gt;=</span> <span class="mi">2</span><span class="p">:</span>
         <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">_logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
     <span class="k">elif</span> <span class="n">verbose</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>

_modules/sssom/parsers.html

@@ -516,9 +516,7 @@ <h1>Source code for sssom.parsers</h1><div class="highlight"><pre>
     <span class="c1"># Need to revisit this solution.</span>
     <span class="c1"># This is to address: A value is trying to be set on a copy of a slice from a DataFrame</span>
     <span class="k">if</span> <span class="n">CONFIDENCE</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
-        <span class="n">df2</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
-        <span class="n">df2</span><span class="p">[</span><span class="n">CONFIDENCE</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;^\s*$&quot;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">regex</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="n">df2</span>
+        <span class="n">df</span><span class="o">.</span><span class="n">replace</span><span class="p">({</span><span class="n">CONFIDENCE</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;^\s*$&quot;</span><span class="p">},</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">regex</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
     <span class="n">mapping_set</span> <span class="o">=</span> <span class="n">_get_mapping_set_from_df</span><span class="p">(</span><span class="n">df</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">meta</span><span class="o">=</span><span class="n">meta</span><span class="p">)</span>
     <span class="n">doc</span> <span class="o">=</span> <span class="n">MappingSetDocument</span><span class="p">(</span><span class="n">mapping_set</span><span class="o">=</span><span class="n">mapping_set</span><span class="p">,</span> <span class="n">converter</span><span class="o">=</span><span class="n">converter</span><span class="p">)</span>

_modules/sssom/util.html

@@ -246,14 +246,9 @@ <h1>Source code for sssom.util</h1><div class="highlight"><pre>
         <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">get_dict_from_mapping</span><span class="p">(</span><span class="n">mapping</span><span class="p">)</span> <span class="k">for</span> <span class="n">mapping</span> <span class="ow">in</span> <span class="n">doc</span><span class="o">.</span><span class="n">mapping_set</span><span class="o">.</span><span class="n">mappings</span><span class="p">)</span>
         <span class="n">meta</span> <span class="o">=</span> <span class="n">_extract_global_metadata</span><span class="p">(</span><span class="n">doc</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="n">pandas_version</span> <span class="o">&gt;=</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">):</span>
-            <span class="c1"># For pandas &gt;= 2.0.0, use the &#39;copy&#39; parameter</span>
-            <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">infer_objects</span><span class="p">(</span><span class="n">copy</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c1"># For pandas &lt; 2.0.0, call &#39;infer_objects()&#39; without any parameters</span>
-            <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">infer_objects</span><span class="p">()</span>
         <span class="c1"># remove columns where all values are blank.</span>
         <span class="n">df</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">infer_objects</span><span class="p">()</span>
         <span class="n">df</span><span class="o">.</span><span class="n">dropna</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;all&quot;</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>  <span class="c1"># remove columns with all row = &#39;None&#39;-s.</span>
 
         <span class="n">slots</span> <span class="o">=</span> <span class="n">_get_sssom_schema_object</span><span class="p">()</span><span class="o">.</span><span class="n">dict</span><span class="p">[</span><span class="s2">&quot;slots&quot;</span><span class="p">]</span>
@@ -1709,6 +1704,18 @@ <h1>Source code for sssom.util</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">compress_or_standardize</span><span class="p">(</span><span class="n">uri</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
 
+
+
+<div class="viewcode-block" id="pandas_set_no_silent_downcasting">
+<a class="viewcode-back" href="../../sssom.html#sssom.util.pandas_set_no_silent_downcasting">[docs]</a>
+<span class="k">def</span> <span class="nf">pandas_set_no_silent_downcasting</span><span class="p">(</span><span class="n">no_silent_downcasting</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Set pandas future.no_silent_downcasting option. Context https://github.com/pandas-dev/pandas/issues/57734.&quot;&quot;&quot;</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">pd</span><span class="o">.</span><span class="n">set_option</span><span class="p">(</span><span class="s2">&quot;future.no_silent_downcasting&quot;</span><span class="p">,</span> <span class="n">no_silent_downcasting</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+        <span class="c1"># Option does not exist in this version of pandas</span>
+        <span class="k">pass</span></div>
+
 </pre></div>
 
            </div>

cli_usage.html

@@ -380,7 +380,7 @@ <h3>convert<a class="headerlink" href="#sssom-convert" title="Link to this headi
 <dd><p>Desired output format.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Options<span class="colon">:</span></dt>
-<dd class="field-odd"><p>tsv | owl | ontoportal_json | fhir_json | json | rdf | nt | xml | turtle | ttl</p>
+<dd class="field-odd"><p>tsv | owl | ontoportal_json | fhir_json | json | rdf | turtle | xml | nt | ttl</p>
 </dd>
 </dl>
 </dd></dl>

developer_docs/api.html

@@ -95,6 +95,7 @@
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.invert_mappings"><code class="docutils literal notranslate"><span class="pre">invert_mappings()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.is_multivalued_slot"><code class="docutils literal notranslate"><span class="pre">is_multivalued_slot()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.merge_msdf"><code class="docutils literal notranslate"><span class="pre">merge_msdf()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#sssom.util.pandas_set_no_silent_downcasting"><code class="docutils literal notranslate"><span class="pre">pandas_set_no_silent_downcasting()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.parse"><code class="docutils literal notranslate"><span class="pre">parse()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.raise_for_bad_path"><code class="docutils literal notranslate"><span class="pre">raise_for_bad_path()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#sssom.util.reconcile_prefix_and_data"><code class="docutils literal notranslate"><span class="pre">reconcile_prefix_and_data()</span></code></a></li>
@@ -1040,6 +1041,12 @@ <h2>Utils<a class="headerlink" href="#utils" title="Link to this heading"></a
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="sssom.util.pandas_set_no_silent_downcasting">
+<span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">pandas_set_no_silent_downcasting</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">no_silent_downcasting</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/sssom/util.html#pandas_set_no_silent_downcasting"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#sssom.util.pandas_set_no_silent_downcasting" title="Link to this definition"></a></dt>
+<dd><p>Set pandas future.no_silent_downcasting option. Context <a class="reference external" href="https://github.com/pandas-dev/pandas/issues/57734">https://github.com/pandas-dev/pandas/issues/57734</a>.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="sssom.util.parse">
 <span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">parse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/sssom/util.html#parse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#sssom.util.parse" title="Link to this definition"></a></dt>

developer_docs/modules.html

@@ -152,6 +152,7 @@ <h1>Technical Documentation<a class="headerlink" href="#technical-documentation"
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.invert_mappings"><code class="docutils literal notranslate"><span class="pre">invert_mappings()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.is_multivalued_slot"><code class="docutils literal notranslate"><span class="pre">is_multivalued_slot()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.merge_msdf"><code class="docutils literal notranslate"><span class="pre">merge_msdf()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.pandas_set_no_silent_downcasting"><code class="docutils literal notranslate"><span class="pre">pandas_set_no_silent_downcasting()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.parse"><code class="docutils literal notranslate"><span class="pre">parse()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.raise_for_bad_path"><code class="docutils literal notranslate"><span class="pre">raise_for_bad_path()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="api.html#sssom.util.reconcile_prefix_and_data"><code class="docutils literal notranslate"><span class="pre">reconcile_prefix_and_data()</span></code></a></li>

developer_docs/sssom.html

@@ -1575,6 +1575,12 @@ <h2>sssom.util module<a class="headerlink" href="#sssom-util-module" title="Link
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py">
+<span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">pandas_set_no_silent_downcasting</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">no_silent_downcasting</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/sssom/util.html#pandas_set_no_silent_downcasting"><span class="viewcode-link"><span class="pre">[source]</span></span></a></dt>
+<dd><p>Set pandas future.no_silent_downcasting option. Context <a class="reference external" href="https://github.com/pandas-dev/pandas/issues/57734">https://github.com/pandas-dev/pandas/issues/57734</a>.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py">
 <span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">parse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/sssom/util.html#parse"><span class="viewcode-link"><span class="pre">[source]</span></span></a></dt>

genindex.html

@@ -1472,6 +1472,8 @@ <h2 id="O">O</h2>
 <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="developer_docs/api.html#sssom.util.pandas_set_no_silent_downcasting">pandas_set_no_silent_downcasting() (in module sssom.util)</a>, <a href="sssom.html#sssom.util.pandas_set_no_silent_downcasting">[1]</a>
+</li>
       <li><a href="developer_docs/api.html#sssom.util.parse">parse() (in module sssom.util)</a>, <a href="sssom.html#sssom.util.parse">[1]</a>
 </li>
       <li><a href="developer_docs/sssom.html#sssom.parsers.parse_alignment_xml">parse_alignment_xml() (in module sssom.parsers)</a>, <a href="sssom.html#sssom.parsers.parse_alignment_xml">[1]</a>

modules.html

@@ -256,6 +256,7 @@ <h1>sssom<a class="headerlink" href="#sssom" title="Link to this heading"></a
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.invert_mappings"><code class="docutils literal notranslate"><span class="pre">invert_mappings()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.is_multivalued_slot"><code class="docutils literal notranslate"><span class="pre">is_multivalued_slot()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.merge_msdf"><code class="docutils literal notranslate"><span class="pre">merge_msdf()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.pandas_set_no_silent_downcasting"><code class="docutils literal notranslate"><span class="pre">pandas_set_no_silent_downcasting()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.parse"><code class="docutils literal notranslate"><span class="pre">parse()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.raise_for_bad_path"><code class="docutils literal notranslate"><span class="pre">raise_for_bad_path()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="sssom.html#sssom.util.reconcile_prefix_and_data"><code class="docutils literal notranslate"><span class="pre">reconcile_prefix_and_data()</span></code></a></li>

sssom.html

@@ -1764,6 +1764,12 @@ <h2>sssom.cliquesummary module<a class="headerlink" href="#sssom-cliquesummary-m
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="sssom.util.pandas_set_no_silent_downcasting">
+<span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">pandas_set_no_silent_downcasting</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">no_silent_downcasting</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/sssom/util.html#pandas_set_no_silent_downcasting"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#sssom.util.pandas_set_no_silent_downcasting" title="Link to this definition"></a></dt>
+<dd><p>Set pandas future.no_silent_downcasting option. Context <a class="reference external" href="https://github.com/pandas-dev/pandas/issues/57734">https://github.com/pandas-dev/pandas/issues/57734</a>.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="sssom.util.parse">
 <span class="sig-prename descclassname"><span class="pre">sssom.util.</span></span><span class="sig-name descname"><span class="pre">parse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/sssom/util.html#parse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#sssom.util.parse" title="Link to this definition"></a></dt>