Bring mass spec utilities into ViMMS (#331)

Author: joewandy

poetry.lock

@@ -31,10 +31,11 @@ jsonpickle = "^4.1.1"
 statsmodels = "^0.14.4"
 tabulate = "^0.9.0"
 intervaltree = "^3.1.0"
+sortedcontainers = "^2.4.0"
 events = "^0.5"
 pymzml = "^2.5.11"
 psims = "^1.3.5"
-mass-spec-utils = "^0.0.12"
+molmass = "^2025.4.14"
 pysmiles = "^2.0.0"
 numba = "^0.61.2"
 numba-stats = "^1.10.1"

pyproject.toml

@@ -4,7 +4,7 @@
 from pathlib import Path
 
 import pytest
-from mass_spec_utils.library_matching.gnps import load_mgf
+from vimms.mass_spec_utils.library_matching.gnps import load_mgf
 
 from tests.conftest import HMDB, MGF_FILE, MZML_FILE, OUT_DIR, check_mzML, check_non_empty_MS2
 from vimms.ChemicalSamplers import (

tests/test_chemical_generation.py

@@ -2,8 +2,8 @@
 import time
 
 import numpy as np
-from mass_spec_utils.data_import.mzmine import load_picked_boxes, map_boxes_to_scans
-from mass_spec_utils.data_import.mzml import MZMLFile
+from vimms.mass_spec_utils.data_import.mzmine import load_picked_boxes, map_boxes_to_scans
+from vimms.mass_spec_utils.data_import.mzml import MZMLFile
 
 from vimms.Agent import TopNDEWAgent
 from vimms.Box import BoxGrid

vimms/BOMAS.py

@@ -13,7 +13,7 @@
 
 import intervaltree
 import numpy as np
-from mass_spec_utils.data_import.mzmine import PickedBox
+from vimms.mass_spec_utils.data_import.mzmine import PickedBox
 
 
 class Point:

vimms/Box.py

@@ -6,8 +6,8 @@
 
 import numpy as np
 from loguru import logger
-from mass_spec_utils.data_import.mzml import MZMLFile
-from mass_spec_utils.library_matching.gnps import load_mgf
+from vimms.mass_spec_utils.data_import.mzml import MZMLFile
+from vimms.mass_spec_utils.library_matching.gnps import load_mgf
 
 from vimms.Chromatograms import FunctionalChromatogram, ConstantChromatogram, EmpiricalChromatogram
 from vimms.Common import (

vimms/ChemicalSamplers.py

@@ -26,7 +26,7 @@
 from loguru import logger
 from tqdm.auto import tqdm
 
-from mass_spec_utils.data_import.mzml import MZMLFile
+from vimms.mass_spec_utils.data_import.mzml import MZMLFile
 
 ###############################################################################
 # Common constants

vimms/Common.py

@@ -3,7 +3,7 @@
 import csv
 
 import numpy as np
-from mass_spec_utils.adduct_calculator.adduct_rules import AdductTransformer
+from vimms.mass_spec_utils.adduct_calculator.adduct_rules import AdductTransformer
 from molmass import Formula
 
 from vimms.Common import DEFAULT_ISOLATION_WIDTH, ScanParameters

vimms/Controller/targeted.py

@@ -8,8 +8,8 @@
 import pandas as pd
 import seaborn as sns
 from loguru import logger
-from mass_spec_utils.data_import.mzml import MZMLFile
-from mass_spec_utils.data_processing.mzmine import pick_peaks
+from vimms.mass_spec_utils.data_import.mzml import MZMLFile
+from vimms.mass_spec_utils.data_processing.mzmine import pick_peaks
 
 from vimms.Agent import TopNDEWAgent
 from vimms.Box import BoxGrid

vimms/DDA_vs_DIA.py

@@ -4,8 +4,8 @@
 
 # import GPy
 
-from mass_spec_utils.library_matching.spectral_scoring_functions import cosine_similarity
-from mass_spec_utils.library_matching.spectrum import Spectrum
+from vimms.mass_spec_utils.library_matching.spectral_scoring_functions import cosine_similarity
+from vimms.mass_spec_utils.library_matching.spectrum import Spectrum
 
 
 class DriftModel: