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CovingtonResearchGroup · Aug 30, 2023 · 484944d · 484944d
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diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
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: 04ea74231bf22a48d2b0eb7d6d5c4b50
+config: 52c128f2412b016c396a5d410f8a834c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Overview: module code &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/classic.css" />
 
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
     <script src="../_static/jquery.js"></script>
@@ -88,7 +88,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>

diff --git a/docs/_build/html/_modules/olm/USGS/DataRetrieval.html b/docs/_build/html/_modules/olm/USGS/DataRetrieval.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>olm.USGS.DataRetrieval &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/classic.css" />
 
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -57,7 +57,7 @@ <h1>Source code for olm.USGS.DataRetrieval</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="GetSiteData"><a class="viewcode-back" href="../../../olm.USGS.DataRetrieval.GetSiteData.html#olm.USGS.DataRetrieval.GetSiteData">[docs]</a><span class="k">def</span> <span class="nf">GetSiteData</span><span class="p">(</span><span class="n">location</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieves meta data about a Water Quality portal site using the site identifier.</span>
 
 
@@ -84,7 +84,7 @@ <h1>Source code for olm.USGS.DataRetrieval</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">GetNWISSiteData</span><span class="p">(</span><span class="n">location</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieves meta data about a USGS site using the full site identifier.</span>
 
 
@@ -226,7 +226,7 @@ <h1>Source code for olm.USGS.DataRetrieval</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="GetDailyDischarge"><a class="viewcode-back" href="../../../olm.USGS.DataRetrieval.GetDailyDischarge.html#olm.USGS.DataRetrieval.GetDailyDischarge">[docs]</a><span class="k">def</span> <span class="nf">GetDailyDischarge</span><span class="p">(</span><span class="n">location</span><span class="p">,</span> <span class="n">date</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieve daily average discharge value from USGS database for given date and USGS site.</span>
 
 <span class="sd">    Parameters</span>
@@ -291,7 +291,7 @@ <h1>Source code for olm.USGS.DataRetrieval</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="GetDailyDischargeRecord"><a class="viewcode-back" href="../../../olm.USGS.DataRetrieval.GetDailyDischargeRecord.html#olm.USGS.DataRetrieval.GetDailyDischargeRecord">[docs]</a><span class="k">def</span> <span class="nf">GetDailyDischargeRecord</span><span class="p">(</span><span class="n">location</span><span class="p">,</span> <span class="n">start_date</span><span class="p">,</span> <span class="n">end_date</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieve daily average discharge values from USGS database for given date range and USGS site.</span>
 
 <span class="sd">    Parameters</span>
@@ -400,7 +400,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>

diff --git a/docs/_build/html/_modules/olm/USGS/PhreeqcPandas.html b/docs/_build/html/_modules/olm/USGS/PhreeqcPandas.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>olm.USGS.PhreeqcPandas &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/classic.css" />
 
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -72,7 +72,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="readPhreeqcOutput"><a class="viewcode-back" href="../../../olm.USGS.PhreeqcPandas.readPhreeqcOutput.html#olm.USGS.PhreeqcPandas.readPhreeqcOutput">[docs]</a><span class="k">def</span> <span class="nf">readPhreeqcOutput</span><span class="p">(</span><span class="n">phreeqcOutputFile</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Reads the output file from a PHREEQC simulation run.</span>
 
 <span class="sd">    Parameters</span>
@@ -172,7 +172,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
     <span class="n">datetext</span><span class="o">=</span><span class="s2">&quot;&quot;</span><span class="p">,</span>
     <span class="n">charge</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Writes a PHREEQC input file using the row from a site DataFrame.</span>
 
 <span class="sd">    Parameters</span>
@@ -241,7 +241,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="phreeqcRunSetPCO2"><a class="viewcode-back" href="../../../olm.USGS.PhreeqcPandas.phreeqcRunSetPCO2.html#olm.USGS.PhreeqcPandas.phreeqcRunSetPCO2">[docs]</a><span class="k">def</span> <span class="nf">phreeqcRunSetPCO2</span><span class="p">(</span>
     <span class="n">logPCO2</span><span class="p">,</span> <span class="n">phreeqcInputFile</span><span class="p">,</span> <span class="n">PHREEQC_PATH</span><span class="p">,</span> <span class="n">DATABASE_FILE</span><span class="p">,</span> <span class="n">newInputFile</span><span class="o">=</span><span class="kc">None</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Reads a PHREEQC input file, modifies it to a set PCO2 and runs the modified file.</span>
 
 <span class="sd">    Parameters</span>
@@ -328,7 +328,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="calciteSaturationAtFixedPCO2"><a class="viewcode-back" href="../../../olm.USGS.PhreeqcPandas.calciteSaturationAtFixedPCO2.html#olm.USGS.PhreeqcPandas.calciteSaturationAtFixedPCO2">[docs]</a><span class="k">def</span> <span class="nf">calciteSaturationAtFixedPCO2</span><span class="p">(</span>
     <span class="n">logPCO2</span><span class="p">,</span> <span class="n">phreeqcInputFile</span><span class="p">,</span> <span class="n">PHREEQC_PATH</span><span class="p">,</span> <span class="n">DATABASE_FILE</span><span class="p">,</span> <span class="n">newInputFile</span><span class="o">=</span><span class="kc">None</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Function used in root finding of saturation PCO2.</span>
 
 <span class="sd">    Function is used by findPCO2atCalciteSaturation(). As a stand alone function, it&#39;s</span>
@@ -370,7 +370,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="findPCO2atCalciteSaturation"><a class="viewcode-back" href="../../../olm.USGS.PhreeqcPandas.findPCO2atCalciteSaturation.html#olm.USGS.PhreeqcPandas.findPCO2atCalciteSaturation">[docs]</a><span class="k">def</span> <span class="nf">findPCO2atCalciteSaturation</span><span class="p">(</span>
     <span class="n">phreeqcInputFile</span><span class="p">,</span> <span class="n">PHREEQC_PATH</span><span class="p">,</span> <span class="n">DATABASE_FILE</span><span class="p">,</span> <span class="n">newInputFile</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">units</span><span class="o">=</span><span class="s2">&quot;atm&quot;</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Finds the PCO2 where calcite would be saturated by modifing PCO2 of a PHREEQC input</span>
 <span class="sd">    file.</span>
 
@@ -419,7 +419,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
     <span class="n">phreeqcDict</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
     <span class="n">force_balance</span><span class="o">=</span><span class="s2">&quot;&quot;</span><span class="p">,</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Takes a WQXtoPandas site multi-indexed DataFrame and runs all samples through</span>
 <span class="sd">    PHREEQC, returning a DataFrame of the outputs that is indexed by date. Will</span>
 <span class="sd">    run automatically within WQXtoPandas if specified in the excel start file.</span>
@@ -622,7 +622,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
     <span class="n">bracket_charge_balance</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">process_regular</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Processes all data from site directories in PHREEQC.</span>
 
 <span class="sd">    Parameters</span>
@@ -712,7 +712,7 @@ <h1>Source code for olm.USGS.PhreeqcPandas</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">runPHREEQC</span><span class="p">(</span><span class="n">startfilename</span><span class="p">,</span> <span class="n">process_regular</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Process all samples within a site directory using information from the start file.</span>
 
 <span class="sd">    Parameters</span>
@@ -807,7 +807,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>

diff --git a/docs/_build/html/_modules/olm/USGS/WQXtoPandas.html b/docs/_build/html/_modules/olm/USGS/WQXtoPandas.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>olm.USGS.WQXtoPandas &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/classic.css" />
 
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -86,7 +86,7 @@ <h1>Source code for olm.USGS.WQXtoPandas</h1><div class="highlight"><pre>
     <span class="n">max_xml_query_tries</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span>
     <span class="n">restart</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Processes a WQX xml data file and loads data for each site in the WQX file into</span>
 <span class="sd">    Pandas data objects that are stored in directories for each site.</span>
 
@@ -729,7 +729,7 @@ <h1>Source code for olm.USGS.WQXtoPandas</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="runWQXtoPandas"><a class="viewcode-back" href="../../../olm.USGS.WQXtoPandas.runWQXtoPandas.html#olm.USGS.WQXtoPandas.runWQXtoPandas">[docs]</a><span class="k">def</span> <span class="nf">runWQXtoPandas</span><span class="p">(</span><span class="n">startfilename</span><span class="p">,</span> <span class="n">autosplitnum</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">restart</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Runs WQXtoPandas on an excel format input file where parameters can be set for an automatic query of data from</span>
 <span class="sd">    the USGS NWIS database.</span>
 
@@ -1020,7 +1020,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>

diff --git a/docs/_build/html/_modules/olm/USGS/loadWaterQualityData.html b/docs/_build/html/_modules/olm/USGS/loadWaterQualityData.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>olm.USGS.loadWaterQualityData &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/classic.css" />
 
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -59,7 +59,7 @@ <h1>Source code for olm.USGS.loadWaterQualityData</h1><div class="highlight"><pr
     <span class="n">loadPhreeqc</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">loadMetaData</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
 <span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieves site data for multiple sites within a processed sites directory.</span>
 
 <span class="sd">    Parameters</span>
@@ -192,7 +192,7 @@ <h1>Source code for olm.USGS.loadWaterQualityData</h1><div class="highlight"><pr
 
 
 <div class="viewcode-block" id="loadSiteData"><a class="viewcode-back" href="../../../olm.USGS.loadWaterQualityData.loadSiteData.html#olm.USGS.loadWaterQualityData.loadSiteData">[docs]</a><span class="k">def</span> <span class="nf">loadSiteData</span><span class="p">(</span><span class="n">site</span><span class="p">,</span> <span class="n">processedSitesDir</span><span class="o">=</span><span class="n">DEFAULT_DIR</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieves site data for an individual site from a directory of processed sites.</span>
 
 <span class="sd">    Parameters</span>
@@ -225,7 +225,7 @@ <h1>Source code for olm.USGS.loadWaterQualityData</h1><div class="highlight"><pr
 
 
 <div class="viewcode-block" id="loadSitePhreeqcData"><a class="viewcode-back" href="../../../olm.USGS.loadWaterQualityData.loadSitePhreeqcData.html#olm.USGS.loadWaterQualityData.loadSitePhreeqcData">[docs]</a><span class="k">def</span> <span class="nf">loadSitePhreeqcData</span><span class="p">(</span><span class="n">site</span><span class="p">,</span> <span class="n">processedSitesDir</span><span class="o">=</span><span class="n">DEFAULT_DIR</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Retrieves site PHREEQC data for an individual site from a directory of processed</span>
 <span class="sd">    sites.</span>
 
@@ -336,7 +336,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>

diff --git a/docs/_build/html/_modules/olm/USGS/siteListExtraction.html b/docs/_build/html/_modules/olm/USGS/siteListExtraction.html
@@ -7,7 +7,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>olm.USGS.siteListExtraction &#8212; olm 0.39 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="/default.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/classic.css" />
 
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -107,7 +107,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-        &#169; Copyright 2014-2022 Matthew Covington.
+        &#169; Copyright 2014-2023 Matthew Covington.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
     </div>
   </body>