Repository: matchms/matchms

Issue:
Allow `load_from_mgf` to accept StringIO
This is a first small issue for the matchms developer workshop 2025. 

So far `load_from_mgf` does not accept StringIO inputs. It could be nice if it did. 

A pull request will follow shortly to add the feature.

Discussion:

Solution patch:
diff --git a/matchms/importing/load_from_mgf.py b/matchms/importing/load_from_mgf.py
index 1a7bead3..ca69683f 100644
--- a/matchms/importing/load_from_mgf.py
+++ b/matchms/importing/load_from_mgf.py
@@ -5,8 +5,9 @@ from matchms.importing.parsing_utils import parse_spectrum_dict
 from matchms.Spectrum import Spectrum
 
 
-def load_from_mgf(filename: Union[str, TextIO],
-                  metadata_harmonization: bool = True) -> Generator[Spectrum, None, None]:
+def load_from_mgf(
+    filename: Union[str, TextIO], metadata_harmonization: bool = True
+) -> Generator[Spectrum, None, None]:
     """Load spectrum(s) from mgf file.
 
     This function will create ~matchms.Spectrum for every spectrum in the given
@@ -34,7 +35,7 @@ def load_from_mgf(filename: Union[str, TextIO],
         Set to False if metadata harmonization to default keys is not desired.
         The default is True.
     """
-    if not os.path.isfile(filename):
+    if isinstance(filename, str) and not os.path.isfile(filename):
         raise FileNotFoundError(f"The specified file: {filename} doesn't exist.")
 
     def parse_file():
@@ -42,6 +43,7 @@ def load_from_mgf(filename: Union[str, TextIO],
             for pyteomics_spectrum in reader:
                 yield parse_spectrum_dict(
                     spectrum=pyteomics_spectrum,
-                    metadata_harmonization=metadata_harmonization)
+                    metadata_harmonization=metadata_harmonization,
+                )
 
     return parse_file()


Test patch:
diff --git a/tests/importing/test_load_from_mgf.py b/tests/importing/test_load_from_mgf.py
index 26596417..7a5f559a 100644
--- a/tests/importing/test_load_from_mgf.py
+++ b/tests/importing/test_load_from_mgf.py
@@ -1,4 +1,5 @@
 import os
+from io import StringIO
 import pytest
 from matchms import Spectrum
 from matchms.importing import load_from_mgf
@@ -16,4 +17,92 @@ def test_load_from_mgf_using_filepath():
 
 def test_load_missing_mgf_raises():
     with pytest.raises(FileNotFoundError):
-        load_from_mgf('does-not-exist.mgf')
+        load_from_mgf("does-not-exist.mgf")
+
+
+def test_load_from_stream():
+    spectra = list(load_from_mgf(TEXT_IO))
+
+    assert len(spectra) > 0
+    assert isinstance(spectra[0], Spectrum)
+
+
+TEXT_IO = StringIO(
+    """
+BEGIN IONS
+PEPMASS=183.057
+CHARGE=1
+MSLEVEL=2
+SOURCE_INSTRUMENT= -Q-Exactive Plus Orbitrap Res 70k
+FILENAME=Pesticide_Mix6_neg.mzXML
+SEQ=*..*
+IONMODE=negative
+ORGANISM=GNPS-COLLECTIONS-PESTICIDES-NEGATIVE
+NAME=Pesticide6_Fuberidazole_C11H8N2O_2-(2-Furyl)-1H-benzimidazole M-H
+PI=Dorrestein/Touboul
+DATACOLLECTOR=lfnothias
+SMILES=C1=CC=C2C(=C1)NC(=N2)C3=CC=CO3
+INCHI=InChI=1S/C11H8N2O/c1-2-5-9-8(4-1)12-11(13-9)10-6-3-7-14-10/h1-7H,(H,12,13)
+INCHIAUX=N/A
+PUBMED=n/a
+SUBMITUSER=mwang87
+TAGS=
+LIBRARYQUALITY=1
+SPECTRUMID=CCMSLIB00001058235
+SCANS=675
+70.786774	213.612045
+72.976173	241.782242
+73.493057	210.330109
+73.515923	211.937332
+74.17305	209.306686
+75.004799	313.5
+77.80809	210.065475
+82.050003	216.289841
+82.620819	261.580231
+82.860512	222.143372
+88.244919	209.090591
+89.454147	229.945343
+94.881096	219.268311
+94.917038	10964.588867
+94.918587	462.001892
+94.993851	322.640625
+102.743492	237.246567
+106.645241	249.806686
+106.876747	269.230896
+109.907501	269.221008
+112.186974	237.601974
+112.985817	2100.576172
+113.004906	236.479034
+115.000427	1164.228882
+115.333664	267.86319
+116.995949	5871.84668
+117.046104	1942.958862
+117.763412	227.911606
+122.933907	268.506836
+125.587662	259.168152
+126.956421	319.40094
+133.029556	431.949585
+133.420456	231.658493
+133.435806	278.857513
+136.894592	413.464294
+138.90712	4373.975098
+138.965378	330.018127
+141.046158	365.30246
+142.99292	855.966187
+142.995346	1030.517456
+146.785355	272.870209
+154.053802	3683.994141
+154.951416	443.910065
+154.992584	1055.799194
+155.061676	147161.03125
+163.001526	2383.76001
+170.366013	283.286346
+182.987579	1709.164062
+183.007996	5187.443359
+183.056702	285898.9375
+183.121933	448.362885
+190.211334	244.807159
+202.308212	327.976257
+END IONS
+    """
+)