Merge branch '165_MSParams_fix' into 'master'

Add ability to instantiate MSParameters

Closes #165

See merge request mass-spectrometry/corems!127

Author: corilo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.10
+current_version = 2.1.0
 commit = False
 tag = False
 

README.md

@@ -50,7 +50,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.10`
+ `2.1.0`
 
 ***
 
@@ -323,7 +323,7 @@ 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 [2.0.10 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.10), archived on Zenodo:  
+Version [2.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.1.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.0.10'
+__version__ = '2.1.0'
 __doc__ = '''
 <div align="left">
 

corems/encapsulation/factory/parameters.py

@@ -1,12 +1,40 @@
+import dataclasses
+
 from corems.encapsulation.factory.processingSetting  import LiquidChromatographSetting, MolecularFormulaSearchSettings, TransientSetting, MassSpecPeakSetting, MassSpectrumSetting
 from corems.encapsulation.factory.processingSetting  import CompoundSearchSettings, GasChromatographSetting
 from corems.encapsulation.factory.processingSetting  import DataInputSetting
 
+def reset_ms_parameters():
+    """Reset the MSParameter class to the default values"""
+    MSParameters.molecular_search = MolecularFormulaSearchSettings()
+    MSParameters.transient = TransientSetting()
+    MSParameters.mass_spectrum = MassSpectrumSetting()
+    MSParameters.ms_peak = MassSpecPeakSetting()
+    MSParameters.data_input = DataInputSetting()
+
+def reset_gcms_parameters():
+    """Reset the GCMSParameters class to the default values"""
+    GCMSParameters.molecular_search = CompoundSearchSettings()
+    GCMSParameters.gc_ms = GasChromatographSetting()
+
+def reset_lcms_parameters():
+    """Reset the LCMSParameters class to the default values"""
+    LCMSParameters.lc_ms = LiquidChromatographSetting()
+    LCMSParameters.mass_spectrum = MassSpectrumSetting()
+    LCMSParameters.ms_peak = MassSpecPeakSetting()
+    LCMSParameters.ms1_molecular_search = MolecularFormulaSearchSettings()
+    LCMSParameters.ms2_molecular_search = MolecularFormulaSearchSettings()
+
 class MSParameters:
     """MSParameters class is used to store the parameters used for the processing of the mass spectrum
     
     Each attibute is a class that contains the parameters for the processing of the mass spectrum, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     molecular_search: MolecularFormulaSearchSettings
@@ -19,6 +47,11 @@ class MSParameters:
         MassSpecPeakSetting object
     data_input: DataInputSetting
         DataInputSetting object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
 
     molecular_search = MolecularFormulaSearchSettings()
@@ -27,27 +60,64 @@ class MSParameters:
     ms_peak = MassSpecPeakSetting()
     data_input = DataInputSetting()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.molecular_search = dataclasses.replace(MSParameters.molecular_search)
+            self.transient = dataclasses.replace(MSParameters.transient)
+            self.mass_spectrum = dataclasses.replace(MSParameters.mass_spectrum)
+            self.ms_peak = dataclasses.replace(MSParameters.ms_peak)
+            self.data_input = dataclasses.replace(MSParameters.data_input)
+        else:
+            self.molecular_search = MolecularFormulaSearchSettings()
+            self.transient = TransientSetting()
+            self.mass_spectrum = MassSpectrumSetting()
+            self.ms_peak = MassSpecPeakSetting()
+            self.data_input = DataInputSetting()
+
 class GCMSParameters:
     """GCMSParameters class is used to store the parameters used for the processing of the gas chromatograph mass spectrum
 
     Each attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     molecular_search: MolecularFormulaSearchSettings
         MolecularFormulaSearchSettings object
     gc_ms: GasChromatographSetting
         GasChromatographSetting object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
 
     molecular_search = CompoundSearchSettings()
     gc_ms = GasChromatographSetting()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.molecular_search = dataclasses.replace(GCMSParameters.molecular_search)
+            self.gc_ms = dataclasses.replace(GCMSParameters.gc_ms)
+        else:
+            self.molecular_search = CompoundSearchSettings()
+            self.gc_ms = GasChromatographSetting()
+
 class LCMSParameters:
     """LCMSParameters class is used to store the parameters used for the processing of the liquid chromatograph mass spectrum
 
     Each attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     lc_ms: LiquidChromatographSetting
@@ -60,17 +130,32 @@ class LCMSParameters:
         MolecularFormulaSearchSettings object
     ms2_molecular_search: MolecularFormulaSearchSettings
         MolecularFormulaSearchSettings object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
     lc_ms = LiquidChromatographSetting()
-    
     mass_spectrum = MassSpectrumSetting()
-
     ms_peak = MassSpecPeakSetting()
-
     ms1_molecular_search = MolecularFormulaSearchSettings()
-    
     ms2_molecular_search = MolecularFormulaSearchSettings()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.lc_ms = dataclasses.replace(LCMSParameters.lc_ms)
+            self.mass_spectrum = dataclasses.replace(LCMSParameters.mass_spectrum)
+            self.ms_peak = dataclasses.replace(LCMSParameters.ms_peak)
+            self.ms1_molecular_search = dataclasses.replace(LCMSParameters.ms1_molecular_search)
+            self.ms2_molecular_search = dataclasses.replace(LCMSParameters.ms2_molecular_search)
+        else:
+            self.lc_ms = LiquidChromatographSetting()
+            self.mass_spectrum = MassSpectrumSetting()
+            self.ms_peak = MassSpecPeakSetting()
+            self.ms1_molecular_search = MolecularFormulaSearchSettings()
+            self.ms2_molecular_search = MolecularFormulaSearchSettings()
+
 def default_parameters(file_location):  # pragma: no cover
     """Generate parameters dictionary with the default parameters for data processing
        To gather parameters from instrument data during the data parsing step, a parameters dictionary with the default parameters needs to be generated.

docs/corems.html

@@ -502,7 +502,7 @@ <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="s1">&#39;Yuri E. Corilo&#39;</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="s1">&#39;2.0.5&#39;</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="s1">&#39;2.1.0&#39;</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos">  3</span></a><span class="vm">__doc__</span> <span class="o">=</span> <span class="s1">&#39;&#39;&#39;</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos">  4</span></a><span class="s1">&lt;div align=&quot;left&quot;&gt;</span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos">  5</span></a>