Bump version and re-render docs

Author: kheal

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.0.1
 commit = False
 tag = False
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.0`
+ `3.0.1`
 
 ***
 
@@ -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 [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
+Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), 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 3.0.0 (Version v3.0.0), 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 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.0.0"
+__version__ = "3.0.1"
 import time
 import os
 import sys

docs/corems.html

@@ -2401,16 +2401,16 @@ <h6 id="parameters">Parameters</h6>
 
     </div>
     <a class="headerlink" href="#MolecularCombinations.runworker"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="MolecularCombinations.runworker-18"><a href="#MolecularCombinations.runworker-18"><span class="linenos">18</span></a>    <span class="k">def</span> <span class="nf">timed</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
-</span><span id="MolecularCombinations.runworker-19"><a href="#MolecularCombinations.runworker-19"><span class="linenos">19</span></a>        <span class="n">ts</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-</span><span id="MolecularCombinations.runworker-20"><a href="#MolecularCombinations.runworker-20"><span class="linenos">20</span></a>        <span class="n">result</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
-</span><span id="MolecularCombinations.runworker-21"><a href="#MolecularCombinations.runworker-21"><span class="linenos">21</span></a>        <span class="n">te</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-</span><span id="MolecularCombinations.runworker-22"><a href="#MolecularCombinations.runworker-22"><span class="linenos">22</span></a>        <span class="k">if</span> <span class="s2">&quot;log_time&quot;</span> <span class="ow">in</span> <span class="n">kw</span><span class="p">:</span>
-</span><span id="MolecularCombinations.runworker-23"><a href="#MolecularCombinations.runworker-23"><span class="linenos">23</span></a>            <span class="n">name</span> <span class="o">=</span> <span class="n">kw</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;log_name&quot;</span><span class="p">,</span> <span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span>
-</span><span id="MolecularCombinations.runworker-24"><a href="#MolecularCombinations.runworker-24"><span class="linenos">24</span></a>            <span class="n">kw</span><span class="p">[</span><span class="s2">&quot;log_time&quot;</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">)</span>
-</span><span id="MolecularCombinations.runworker-25"><a href="#MolecularCombinations.runworker-25"><span class="linenos">25</span></a>        <span class="k">else</span><span class="p">:</span>
-</span><span id="MolecularCombinations.runworker-26"><a href="#MolecularCombinations.runworker-26"><span class="linenos">26</span></a>            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%r</span><span class="s2">  </span><span class="si">%2.2f</span><span class="s2"> ms&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="p">(</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">))</span>
-</span><span id="MolecularCombinations.runworker-27"><a href="#MolecularCombinations.runworker-27"><span class="linenos">27</span></a>        <span class="k">return</span> <span class="n">result</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="MolecularCombinations.runworker-26"><a href="#MolecularCombinations.runworker-26"><span class="linenos">26</span></a>    <span class="k">def</span> <span class="nf">timed</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+</span><span id="MolecularCombinations.runworker-27"><a href="#MolecularCombinations.runworker-27"><span class="linenos">27</span></a>        <span class="n">ts</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+</span><span id="MolecularCombinations.runworker-28"><a href="#MolecularCombinations.runworker-28"><span class="linenos">28</span></a>        <span class="n">result</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
+</span><span id="MolecularCombinations.runworker-29"><a href="#MolecularCombinations.runworker-29"><span class="linenos">29</span></a>        <span class="n">te</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+</span><span id="MolecularCombinations.runworker-30"><a href="#MolecularCombinations.runworker-30"><span class="linenos">30</span></a>        <span class="k">if</span> <span class="s2">&quot;log_time&quot;</span> <span class="ow">in</span> <span class="n">kw</span><span class="p">:</span>
+</span><span id="MolecularCombinations.runworker-31"><a href="#MolecularCombinations.runworker-31"><span class="linenos">31</span></a>            <span class="n">name</span> <span class="o">=</span> <span class="n">kw</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;log_name&quot;</span><span class="p">,</span> <span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span>
+</span><span id="MolecularCombinations.runworker-32"><a href="#MolecularCombinations.runworker-32"><span class="linenos">32</span></a>            <span class="n">kw</span><span class="p">[</span><span class="s2">&quot;log_time&quot;</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">)</span>
+</span><span id="MolecularCombinations.runworker-33"><a href="#MolecularCombinations.runworker-33"><span class="linenos">33</span></a>        <span class="k">else</span><span class="p">:</span>
+</span><span id="MolecularCombinations.runworker-34"><a href="#MolecularCombinations.runworker-34"><span class="linenos">34</span></a>            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%r</span><span class="s2">  </span><span class="si">%2.2f</span><span class="s2"> ms&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="p">(</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">))</span>
+</span><span id="MolecularCombinations.runworker-35"><a href="#MolecularCombinations.runworker-35"><span class="linenos">35</span></a>        <span class="k">return</span> <span class="n">result</span>
 </span></pre></div>
 
 

docs/corems/molecular_id/factory/MolecularLookupTable.html

@@ -2054,16 +2054,16 @@ <h6 id="returns">Returns</h6>
 
     </div>
     <a class="headerlink" href="#SearchMolecularFormulas.run_molecular_formula"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="SearchMolecularFormulas.run_molecular_formula-18"><a href="#SearchMolecularFormulas.run_molecular_formula-18"><span class="linenos">18</span></a>    <span class="k">def</span> <span class="nf">timed</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-19"><a href="#SearchMolecularFormulas.run_molecular_formula-19"><span class="linenos">19</span></a>        <span class="n">ts</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-20"><a href="#SearchMolecularFormulas.run_molecular_formula-20"><span class="linenos">20</span></a>        <span class="n">result</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-21"><a href="#SearchMolecularFormulas.run_molecular_formula-21"><span class="linenos">21</span></a>        <span class="n">te</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-22"><a href="#SearchMolecularFormulas.run_molecular_formula-22"><span class="linenos">22</span></a>        <span class="k">if</span> <span class="s2">&quot;log_time&quot;</span> <span class="ow">in</span> <span class="n">kw</span><span class="p">:</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-23"><a href="#SearchMolecularFormulas.run_molecular_formula-23"><span class="linenos">23</span></a>            <span class="n">name</span> <span class="o">=</span> <span class="n">kw</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;log_name&quot;</span><span class="p">,</span> <span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-24"><a href="#SearchMolecularFormulas.run_molecular_formula-24"><span class="linenos">24</span></a>            <span class="n">kw</span><span class="p">[</span><span class="s2">&quot;log_time&quot;</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">)</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-25"><a href="#SearchMolecularFormulas.run_molecular_formula-25"><span class="linenos">25</span></a>        <span class="k">else</span><span class="p">:</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-26"><a href="#SearchMolecularFormulas.run_molecular_formula-26"><span class="linenos">26</span></a>            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%r</span><span class="s2">  </span><span class="si">%2.2f</span><span class="s2"> ms&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="p">(</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">))</span>
-</span><span id="SearchMolecularFormulas.run_molecular_formula-27"><a href="#SearchMolecularFormulas.run_molecular_formula-27"><span class="linenos">27</span></a>        <span class="k">return</span> <span class="n">result</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="SearchMolecularFormulas.run_molecular_formula-26"><a href="#SearchMolecularFormulas.run_molecular_formula-26"><span class="linenos">26</span></a>    <span class="k">def</span> <span class="nf">timed</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-27"><a href="#SearchMolecularFormulas.run_molecular_formula-27"><span class="linenos">27</span></a>        <span class="n">ts</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-28"><a href="#SearchMolecularFormulas.run_molecular_formula-28"><span class="linenos">28</span></a>        <span class="n">result</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-29"><a href="#SearchMolecularFormulas.run_molecular_formula-29"><span class="linenos">29</span></a>        <span class="n">te</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-30"><a href="#SearchMolecularFormulas.run_molecular_formula-30"><span class="linenos">30</span></a>        <span class="k">if</span> <span class="s2">&quot;log_time&quot;</span> <span class="ow">in</span> <span class="n">kw</span><span class="p">:</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-31"><a href="#SearchMolecularFormulas.run_molecular_formula-31"><span class="linenos">31</span></a>            <span class="n">name</span> <span class="o">=</span> <span class="n">kw</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;log_name&quot;</span><span class="p">,</span> <span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">upper</span><span class="p">())</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-32"><a href="#SearchMolecularFormulas.run_molecular_formula-32"><span class="linenos">32</span></a>            <span class="n">kw</span><span class="p">[</span><span class="s2">&quot;log_time&quot;</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">)</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-33"><a href="#SearchMolecularFormulas.run_molecular_formula-33"><span class="linenos">33</span></a>        <span class="k">else</span><span class="p">:</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-34"><a href="#SearchMolecularFormulas.run_molecular_formula-34"><span class="linenos">34</span></a>            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%r</span><span class="s2">  </span><span class="si">%2.2f</span><span class="s2"> ms&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">method</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="p">(</span><span class="n">te</span> <span class="o">-</span> <span class="n">ts</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1000</span><span class="p">))</span>
+</span><span id="SearchMolecularFormulas.run_molecular_formula-35"><a href="#SearchMolecularFormulas.run_molecular_formula-35"><span class="linenos">35</span></a>        <span class="k">return</span> <span class="n">result</span>
 </span></pre></div>
 
 

docs/corems/molecular_id/search/molecularFormulaSearch.html

@@ -14,7 +14,7 @@
 # This call to setup() does all the work
 setup(
     name="CoreMS",
-    version="3.0.0",
+    version="3.0.1",
     description="Mass Spectrometry Framework for Small Molecules Analysis",
     long_description=long_description,
     long_description_content_type="text/markdown",