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

Author: corilo

.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>