Merge branch '191_decon_corr_patch' into 'master'

Remove hard coded parameter in calculation of deconvoluted MS1 in lc_calc module

Closes #191

See merge request mass-spectrometry/corems!152

Author: corilo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.0
+current_version = 3.2.1
 commit = False
 tag = False
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.2.0`
+ `3.2.1`
 
 ***
 
@@ -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 [3.2.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.0), archived on Zenodo:  
+Version [3.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.1), 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 3.2.0 (Version v3.2.0), 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 3.2.1 (Version v3.2.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.2.0"
+__version__ = "3.2.1"
 import time
 import os
 import sys

corems/mass_spectra/calc/lc_calc.py

@@ -758,7 +758,6 @@ def deconvolute_ms1_mass_features(self):
 
             # Subset the correlation matrix to only include the masses of the mass feature and those with a correlation > 0.8
             decon_corr_min = self.parameters.lc_ms.ms1_deconvolution_corr_min
-            decon_corr_min = 0.9
             corr_subset = corr.loc[mass_feature.mz,]
             corr_subset = corr_subset[corr_subset > decon_corr_min]
 

docs/corems.html

@@ -154,7 +154,7 @@ <h1 id="corems">CoreMS</h1>
 
 <h2 id="current-version">Current Version</h2>
 
-<p><code>3.2.0</code></p>
+<p><code>3.2.1</code></p>
 
 <hr />
 
@@ -487,11 +487,11 @@ <h2 id="citing-corems">Citing CoreMS</h2>
 
 <p>If you use CoreMS in your work, please use the following citation:</p>
 
-<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.0">3.2.0 Release on GitHub</a>, archived on Zenodo:  </p>
+<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.1">3.2.1 Release on GitHub</a>, archived on Zenodo:  </p>
 
 <p><a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI" /></a></p>
 
-<p>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. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
+<p>Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.2.1 (Version v3.2.1), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
 
 <p>```</p>
 
@@ -527,7 +527,7 @@ <h2 id="citing-corems">Citing CoreMS</h2>
                         <label class="view-source-button" for="mod-corems-view-source"><span>View Source</span></label>
 
                         <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Yuri E. Corilo&quot;</span>
-</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.2.0&quot;</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.2.1&quot;</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">time</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span> <span class="nn">os</span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span> <span class="nn">sys</span>

docs/corems/encapsulation/factory/parameters.html

@@ -747,7 +747,7 @@ <h6 id="notes">Notes</h6>
                                 <div class="attr variable">
             <span class="name">molecular_search</span>        =
 <input id="MSParameters.molecular_search-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
-            <label class="view-value-button pdoc-button" for="MSParameters.molecular_search-view-value"></label><span class="default_value">MolecularFormulaSearchSettings(verbose_processing=True, use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=(&#39;Cl&#39;, &#39;Br&#39;), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database=&#39;postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp&#39;, db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=(&#39;Cl&#39;, &#39;Br&#39;), adduct_atoms_pos=(&#39;Na&#39;, &#39;K&#39;), score_methods=(&#39;S_P_lowest_error&#39;, &#39;N_S_P_lowest_error&#39;, &#39;lowest_error&#39;, &#39;prob_score&#39;, &#39;air_filter_error&#39;, &#39;water_filter_error&#39;, &#39;earth_filter_error&#39;), score_method=&#39;prob_score&#39;, output_min_score=0.1, output_score_method=&#39;All Candidates&#39;, isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={&#39;C&#39;: (1, 100), &#39;H&#39;: (1, 200)}, ion_types_excluded=[], ionization_type=&#39;ESI&#39;, min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method=&#39;None&#39;, mz_error_average=0.0, used_atom_valences={&#39;C&#39;: 4, &#39;13C&#39;: 4, &#39;N&#39;: 3, &#39;O&#39;: 2, &#39;S&#39;: 2, &#39;H&#39;: 1, &#39;F&#39;: 1, &#39;Cl&#39;: 1, &#39;Br&#39;: 1, &#39;I&#39;: 1, &#39;At&#39;: 1, &#39;Li&#39;: 1, &#39;Na&#39;: 1, &#39;K&#39;: 1, &#39;Rb&#39;: 1, &#39;Cs&#39;: 1, &#39;Fr&#39;: 1, &#39;B&#39;: 4, &#39;In&#39;: 3, &#39;Al&#39;: 3, &#39;P&#39;: 3, &#39;Ga&#39;: 3, &#39;Mg&#39;: 2, &#39;Be&#39;: 2, &#39;Ca&#39;: 2, &#39;Sr&#39;: 2, &#39;Ba&#39;: 2, &#39;Ra&#39;: 2, &#39;V&#39;: 5, &#39;Fe&#39;: 3, &#39;Si&#39;: 4, &#39;Sc&#39;: 3, &#39;Ti&#39;: 4, &#39;Cr&#39;: 1, &#39;Mn&#39;: 1, &#39;Co&#39;: 1, &#39;Ni&#39;: 1, &#39;Cu&#39;: 2, &#39;Zn&#39;: 2, &#39;Ge&#39;: 4, &#39;As&#39;: 5, &#39;Se&#39;: 6, &#39;Y&#39;: 3, &#39;Zr&#39;: 4, &#39;Nb&#39;: 5, &#39;Mo&#39;: 6, &#39;Tc&#39;: 7, &#39;Ru&#39;: 8, &#39;Rh&#39;: 6, &#39;Pd&#39;: 4, &#39;Ag&#39;: 0, &#39;Cd&#39;: 2, &#39;Sn&#39;: 4, &#39;Sb&#39;: 5, &#39;Te&#39;: 6, &#39;La&#39;: 3, &#39;Hf&#39;: 4, &#39;Ta&#39;: 5, &#39;W&#39;: 6, &#39;Re&#39;: 4, &#39;Os&#39;: 4, &#39;Ir&#39;: 4, &#39;Pt&#39;: 4, &#39;Au&#39;: 3, &#39;Hg&#39;: 1, &#39;Tl&#39;: 3, &#39;Pb&#39;: 4, &#39;Bi&#39;: 3, &#39;Po&#39;: 2, &#39;Ac&#39;: 3})</span>
+            <label class="view-value-button pdoc-button" for="MSParameters.molecular_search-view-value"></label><span class="default_value">MolecularFormulaSearchSettings(verbose_processing=True, use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=(&#39;Cl&#39;, &#39;Br&#39;), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database=&#39;postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp&#39;, db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=(&#39;Cl&#39;, &#39;Br&#39;), adduct_atoms_pos=(&#39;Na&#39;, &#39;K&#39;), score_methods=(&#39;S_P_lowest_error&#39;, &#39;N_S_P_lowest_error&#39;, &#39;lowest_error&#39;, &#39;prob_score&#39;, &#39;air_filter_error&#39;, &#39;water_filter_error&#39;, &#39;earth_filter_error&#39;), score_method=&#39;prob_score&#39;, output_min_score=0.1, output_score_method=&#39;All Candidates&#39;, isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={&#39;C&#39;: (1, 100), &#39;H&#39;: (1, 200)}, ion_types_excluded=[], ionization_type=&#39;ESI&#39;, min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method=&#39;None&#39;, mz_error_average=0.0, used_atom_valences={&#39;C&#39;: 4, &#39;13C&#39;: 4, &#39;N&#39;: 3, &#39;O&#39;: 2, &#39;S&#39;: 2, &#39;H&#39;: 1, &#39;F&#39;: 1, &#39;Cl&#39;: 1, &#39;Br&#39;: 1, &#39;I&#39;: 1, &#39;At&#39;: 1, &#39;Li&#39;: 1, &#39;Na&#39;: 1, &#39;K&#39;: 1, &#39;Rb&#39;: 1, &#39;Cs&#39;: 1, &#39;Fr&#39;: 1, &#39;B&#39;: 4, &#39;In&#39;: 3, &#39;Al&#39;: 3, &#39;P&#39;: 3, &#39;Ga&#39;: 3, &#39;Mg&#39;: 2, &#39;Be&#39;: 2, &#39;Ca&#39;: 2, &#39;Sr&#39;: 2, &#39;Ba&#39;: 2, &#39;Ra&#39;: 2, &#39;V&#39;: 5, &#39;Fe&#39;: 3, &#39;Si&#39;: 4, &#39;Sc&#39;: 3, &#39;Ti&#39;: 4, &#39;Cr&#39;: 1, &#39;Mn&#39;: 1, &#39;Co&#39;: 1, &#39;Ni&#39;: 1, &#39;Cu&#39;: 2, &#39;Zn&#39;: 2, &#39;Ge&#39;: 4, &#39;As&#39;: 5, &#39;Se&#39;: 6, &#39;Y&#39;: 3, &#39;Zr&#39;: 4, &#39;Nb&#39;: 5, &#39;Mo&#39;: 6, &#39;Tc&#39;: 7, &#39;Ru&#39;: 8, &#39;Rh&#39;: 6, &#39;Pd&#39;: 4, &#39;Ag&#39;: 0, &#39;Cd&#39;: 2, &#39;Sn&#39;: 4, &#39;Sb&#39;: 5, &#39;Te&#39;: 6, &#39;La&#39;: 3, &#39;Hf&#39;: 4, &#39;Ta&#39;: 5, &#39;W&#39;: 6, &#39;Re&#39;: 4, &#39;Os&#39;: 4, &#39;Ir&#39;: 4, &#39;Pt&#39;: 4, &#39;Au&#39;: 3, &#39;Hg&#39;: 1, &#39;Tl&#39;: 3, &#39;Pb&#39;: 4, &#39;Bi&#39;: 3, &#39;Po&#39;: 2, &#39;Ac&#39;: 3})</span>
 
 
     </div>