Merge branch '302_requirements_sys_fix' into 'master'

Restructure the way rawFileReader sources dotnet library and fix requirements

Closes #180 and #177

See merge request mass-spectrometry/corems!143

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.2
+current_version = 3.1.0
 commit = False
 tag = False
 

Makefile

@@ -23,8 +23,12 @@ patch:
 
 	@bumpversion patch --allow-dirty
 
+pypi_test:
+	@rm -rf build dist *.egg-info
+	@python3 setup.py sdist
+
 pypi:	
-
+	@rm -rf build dist *.egg-info
 	@python3 setup.py sdist
 	@twine upload dist/*
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.2`
+ `3.1.0`
 
 ***
 
@@ -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 [3.0.2 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.2), archived on Zenodo:  
+Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), 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 3.0.2 (Version v3.0.2), 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 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.0.2"
+__version__ = "3.1.0"
 import time
 import os
 import sys

corems/mass_spectra/input/massList.py

@@ -3,7 +3,6 @@
 
 import sys
 
-sys.path.append(".")  # Why?
 from pathlib import Path
 from threading import Thread
 import warnings

corems/mass_spectra/input/rawFileReader.py

@@ -14,6 +14,8 @@
 import site
 from pathlib import Path
 import datetime
+import importlib.util
+import os
 
 import clr
 import pandas as pd
@@ -31,9 +33,9 @@
 from corems.encapsulation.factory.parameters import LCMSParameters, default_parameters
 from corems.mass_spectra.input.parserbase import SpectraParserInterface
 
-# do not change the order from the imports statements and reference ThermoFisher below
-sys.path.append(site.getsitepackages()[0] + "/ext_lib/dotnet/")
-sys.path.append("ext_lib/dotnet/")
+# Add the path of the Thermo .NET libraries to the system path
+spec = importlib.util.find_spec("corems")
+sys.path.append(str(Path(os.path.dirname(spec.origin)).parent) + "/ext_lib/dotnet/")
 
 clr.AddReference("ThermoFisher.CommonCore.RawFileReader")
 clr.AddReference("ThermoFisher.CommonCore.Data")

corems/molecular_formula/input/masslist_ref.py

@@ -9,8 +9,6 @@
 
 import pandas as pd
 
-sys.path.append(".")
-
 from corems.encapsulation.constant import Atoms, Labels
 from corems.molecular_formula.factory.MolecularFormulaFactory import (
     LCMSLibRefMolecularFormula,

corems/molecular_id/factory/molecularSQL.py

@@ -1,6 +1,5 @@
 import sys
 
-sys.path.append(".")
 import json
 import os
 

corems/molecular_id/search/priorityAssignment.py

@@ -1,7 +1,6 @@
 import os
 import sys
 
-sys.path.append(".")
 from copy import deepcopy
 from threading import Thread
 from itertools import product

docs/corems.html

@@ -154,7 +154,7 @@ <h1 id="corems">CoreMS</h1>
 
 <h2 id="current-version">Current Version</h2>
 
-<p><code>3.0.2</code></p>
+<p><code>3.1.0</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/v3.0.2">3.0.2 Release on GitHub</a>, archived on Zenodo:  </p>
+<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0">3.1.0 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 3.0.2 (Version v3.0.2), 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 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
 
 <p>```</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;3.0.2&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;3.1.0&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

@@ -713,7 +713,7 @@ <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(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(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;sqlite:///db/molformula.db&#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>