Bump version and regenerate documentation

Author: kheal

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.0
+current_version = 3.2.0
 commit = False
 tag = False
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.1.0`
+ `3.2.0`
 
 ***
 
@@ -335,11 +335,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), archived on Zenodo:  
+Version [3.2.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.2.0 (Version v3.2.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.1.0"
+__version__ = "3.2.0"
 import time
 import os
 import sys

docs/corems.html

@@ -1531,7 +1531,7 @@ <h1 class="modulename">
                     <div class="attr variable">
             <span class="name">spec</span>        =
 <input id="spec-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
-            <label class="view-value-button pdoc-button" for="spec-view-value"></label><span class="default_value">ModuleSpec(name=&#39;corems&#39;, loader=&lt;_frozen_importlib_external.SourceFileLoader object&gt;, origin=&#39;/Users/heal742/LOCAL/corems_dev/corems/corems/__init__.py&#39;, submodule_search_locations=[&#39;/Users/heal742/LOCAL/corems_dev/corems/corems&#39;])</span>
+            <label class="view-value-button pdoc-button" for="spec-view-value"></label><span class="default_value">ModuleSpec(name=&#39;corems&#39;, loader=&lt;_frozen_importlib_external.SourceFileLoader object&gt;, origin=&#39;/Users/heal742/LOCAL/corems_dev/corems/./corems/__init__.py&#39;, submodule_search_locations=[&#39;/Users/heal742/LOCAL/corems_dev/corems/./corems&#39;])</span>
 
 
     </div>

docs/corems/encapsulation/factory/parameters.html

@@ -194,12 +194,12 @@ <h1 class="modulename">
 </span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
 </span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a>    <span class="k">def</span> <span class="nf">calc_error_dist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 </span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate the error distribution.&quot;&quot;&quot;</span>
-</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a>
-</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
-</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a>        <span class="c1"># loop trough mass spectrum</span>
-</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a>
-</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)):</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a>        <span class="n">verbose</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">mass_spectrum</span><span class="o">.</span><span class="n">verbose_processing</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a>        <span class="c1"># loop trough mass spectrum</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">),</span> <span class="n">disable</span><span class="o">=</span><span class="ow">not</span> <span class="n">verbose</span><span class="p">):</span>
 </span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>            <span class="c1"># access ms peaks triplets ( peak_obj_idx -1, peak_obj_idx, and peak_obj_idx + 1)</span>
 </span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>            <span class="c1"># check lower and upper boundaries to not excesses mass spectrum range</span>
 </span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>
@@ -636,12 +636,12 @@ <h1 class="modulename">
 </span><span id="MassErrorPrediction-91"><a href="#MassErrorPrediction-91"><span class="linenos"> 91</span></a>
 </span><span id="MassErrorPrediction-92"><a href="#MassErrorPrediction-92"><span class="linenos"> 92</span></a>    <span class="k">def</span> <span class="nf">calc_error_dist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 </span><span id="MassErrorPrediction-93"><a href="#MassErrorPrediction-93"><span class="linenos"> 93</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate the error distribution.&quot;&quot;&quot;</span>
-</span><span id="MassErrorPrediction-94"><a href="#MassErrorPrediction-94"><span class="linenos"> 94</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="MassErrorPrediction-95"><a href="#MassErrorPrediction-95"><span class="linenos"> 95</span></a>
-</span><span id="MassErrorPrediction-96"><a href="#MassErrorPrediction-96"><span class="linenos"> 96</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
-</span><span id="MassErrorPrediction-97"><a href="#MassErrorPrediction-97"><span class="linenos"> 97</span></a>        <span class="c1"># loop trough mass spectrum</span>
-</span><span id="MassErrorPrediction-98"><a href="#MassErrorPrediction-98"><span class="linenos"> 98</span></a>
-</span><span id="MassErrorPrediction-99"><a href="#MassErrorPrediction-99"><span class="linenos"> 99</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)):</span>
+</span><span id="MassErrorPrediction-94"><a href="#MassErrorPrediction-94"><span class="linenos"> 94</span></a>        <span class="n">verbose</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">mass_spectrum</span><span class="o">.</span><span class="n">verbose_processing</span>
+</span><span id="MassErrorPrediction-95"><a href="#MassErrorPrediction-95"><span class="linenos"> 95</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="MassErrorPrediction-96"><a href="#MassErrorPrediction-96"><span class="linenos"> 96</span></a>
+</span><span id="MassErrorPrediction-97"><a href="#MassErrorPrediction-97"><span class="linenos"> 97</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
+</span><span id="MassErrorPrediction-98"><a href="#MassErrorPrediction-98"><span class="linenos"> 98</span></a>        <span class="c1"># loop trough mass spectrum</span>
+</span><span id="MassErrorPrediction-99"><a href="#MassErrorPrediction-99"><span class="linenos"> 99</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">),</span> <span class="n">disable</span><span class="o">=</span><span class="ow">not</span> <span class="n">verbose</span><span class="p">):</span>
 </span><span id="MassErrorPrediction-100"><a href="#MassErrorPrediction-100"><span class="linenos">100</span></a>            <span class="c1"># access ms peaks triplets ( peak_obj_idx -1, peak_obj_idx, and peak_obj_idx + 1)</span>
 </span><span id="MassErrorPrediction-101"><a href="#MassErrorPrediction-101"><span class="linenos">101</span></a>            <span class="c1"># check lower and upper boundaries to not excesses mass spectrum range</span>
 </span><span id="MassErrorPrediction-102"><a href="#MassErrorPrediction-102"><span class="linenos">102</span></a>
@@ -1230,12 +1230,12 @@ <h6 id="methods">Methods</h6>
     <a class="headerlink" href="#MassErrorPrediction.calc_error_dist"></a>
             <div class="pdoc-code codehilite"><pre><span></span><span id="MassErrorPrediction.calc_error_dist-92"><a href="#MassErrorPrediction.calc_error_dist-92"><span class="linenos"> 92</span></a>    <span class="k">def</span> <span class="nf">calc_error_dist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 </span><span id="MassErrorPrediction.calc_error_dist-93"><a href="#MassErrorPrediction.calc_error_dist-93"><span class="linenos"> 93</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate the error distribution.&quot;&quot;&quot;</span>
-</span><span id="MassErrorPrediction.calc_error_dist-94"><a href="#MassErrorPrediction.calc_error_dist-94"><span class="linenos"> 94</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="MassErrorPrediction.calc_error_dist-95"><a href="#MassErrorPrediction.calc_error_dist-95"><span class="linenos"> 95</span></a>
-</span><span id="MassErrorPrediction.calc_error_dist-96"><a href="#MassErrorPrediction.calc_error_dist-96"><span class="linenos"> 96</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
-</span><span id="MassErrorPrediction.calc_error_dist-97"><a href="#MassErrorPrediction.calc_error_dist-97"><span class="linenos"> 97</span></a>        <span class="c1"># loop trough mass spectrum</span>
-</span><span id="MassErrorPrediction.calc_error_dist-98"><a href="#MassErrorPrediction.calc_error_dist-98"><span class="linenos"> 98</span></a>
-</span><span id="MassErrorPrediction.calc_error_dist-99"><a href="#MassErrorPrediction.calc_error_dist-99"><span class="linenos"> 99</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)):</span>
+</span><span id="MassErrorPrediction.calc_error_dist-94"><a href="#MassErrorPrediction.calc_error_dist-94"><span class="linenos"> 94</span></a>        <span class="n">verbose</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">mass_spectrum</span><span class="o">.</span><span class="n">verbose_processing</span>
+</span><span id="MassErrorPrediction.calc_error_dist-95"><a href="#MassErrorPrediction.calc_error_dist-95"><span class="linenos"> 95</span></a>        <span class="n">results_list</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="MassErrorPrediction.calc_error_dist-96"><a href="#MassErrorPrediction.calc_error_dist-96"><span class="linenos"> 96</span></a>
+</span><span id="MassErrorPrediction.calc_error_dist-97"><a href="#MassErrorPrediction.calc_error_dist-97"><span class="linenos"> 97</span></a>        <span class="n">indexes_without_results</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">)))</span>
+</span><span id="MassErrorPrediction.calc_error_dist-98"><a href="#MassErrorPrediction.calc_error_dist-98"><span class="linenos"> 98</span></a>        <span class="c1"># loop trough mass spectrum</span>
+</span><span id="MassErrorPrediction.calc_error_dist-99"><a href="#MassErrorPrediction.calc_error_dist-99"><span class="linenos"> 99</span></a>        <span class="k">for</span> <span class="n">peak_obj_idx</span><span class="p">,</span> <span class="n">peak_obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mass_spectrum_obj</span><span class="p">),</span> <span class="n">disable</span><span class="o">=</span><span class="ow">not</span> <span class="n">verbose</span><span class="p">):</span>
 </span><span id="MassErrorPrediction.calc_error_dist-100"><a href="#MassErrorPrediction.calc_error_dist-100"><span class="linenos">100</span></a>            <span class="c1"># access ms peaks triplets ( peak_obj_idx -1, peak_obj_idx, and peak_obj_idx + 1)</span>
 </span><span id="MassErrorPrediction.calc_error_dist-101"><a href="#MassErrorPrediction.calc_error_dist-101"><span class="linenos">101</span></a>            <span class="c1"># check lower and upper boundaries to not excesses mass spectrum range</span>
 </span><span id="MassErrorPrediction.calc_error_dist-102"><a href="#MassErrorPrediction.calc_error_dist-102"><span class="linenos">102</span></a>