Merge branch '150_requirements' into 'master'

Remove extraneous requirements and fix SciPy import of boxcar function

Closes #150 and #166

See merge request mass-spectrometry/corems!124

Author: corilo

corems/__init__.py

@@ -362,94 +362,6 @@ def __exit__(self, exc_type, exc_val, exc_tb):
         sys.stdout.close()
         sys.stdout = self._original_stdout
 
-def get_filenames(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location, _ = file_dialog.getOpenFileNames()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return file_location
-
-    else:
-
-        return None
-
-def get_filename(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location, _ = file_dialog.getOpenFileName()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return Path(file_location)
-
-    else:
-
-        return None
-
-def get_dirname(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog 
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location = file_dialog.getExistingDirectory()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return Path(file_location)
-
-    else:
-
-        return None
-
-def get_dirnames(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog, QTreeView, QListView, QAbstractItemView
-    from pathlib import Path
-
-    if not app:
-        app = QApplication(sys.argv)
-    # file_dialog = QFileDialog()
-    # file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    # file_location = file_dialog.getOpenFileNames()
-
-    file_dialog = QFileDialog()
-    file_dialog.setFileMode(QFileDialog.DirectoryOnly)
-    file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
-    file_view = file_dialog.findChild(QListView, 'listView')
-
-    # to make it possible to select multiple directories:
-    if file_view:
-        file_view.setSelectionMode(QAbstractItemView.MultiSelection)
-    f_tree_view = file_dialog.findChild(QTreeView)
-    if f_tree_view:
-        f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
-
-    if file_dialog.exec():
-        paths = file_dialog.selectedFiles()
-
-        QCoreApplication.processEvents()
-        for path in paths:
-            yield Path(path)
-
 def chunks(lst, n):
     """Yield successive n-sized chunks from lst."""
     for i in range(0, len(lst), n):
@@ -461,4 +373,4 @@ def corems_md5(fname):
 
     md5_returned = hashlib.sha256(bytes_io).hexdigest()
 
-    return "{}:{}".format("sha256", md5_returned)
+    return "{}:{}".format("sha256", md5_returned)

corems/mass_spectra/calc/SignalProcessing.py

@@ -4,7 +4,8 @@
 
 from pandas import Series, DataFrame
 
-from scipy.signal import savgol_filter, boxcar
+from scipy.signal import savgol_filter
+from scipy.signal.windows import boxcar
 from scipy import interpolate
 from matplotlib import pyplot as plt
 from numpy import abs

examples/scripts/DI HR-MS MassList.py

@@ -21,13 +21,15 @@
 from corems.molecular_id.factory.classification import HeteroatomsClassification
 from corems.mass_spectrum.calc.Calibration import MzDomainCalibration
 from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
-from corems import SuppressPrints, get_filename, get_filenames
+from corems import SuppressPrints
 from corems.transient.input.brukerSolarix import ReadBrukerSolarix
 from corems.mass_spectra.input import rawFileReader
 
 from corems.encapsulation.constant import Atoms
 from corems.encapsulation.factory.parameters import MSParameters
 
+from support_code.filefinder import get_filename, get_filenames
+
 def mzdomain_calibration(mass_spectrum):
 
     mass_spectrum.settings.min_calib_ppm_error = 0

examples/scripts/GC-MS NetCDF.py

@@ -13,7 +13,7 @@
 from corems.mass_spectra.input.andiNetCDF import ReadAndiNetCDF
 from corems.molecular_id.search.compoundSearch import LowResMassSpectralMatch
 from corems.mass_spectra.calc.GC_RI_Calibration import get_rt_ri_pairs
-from corems import get_dirname, get_filename
+from support_code.filefinder import get_dirname, get_filename
 
 import glob
 

requirements.txt

@@ -1,6 +1,5 @@
 beautifulsoup4~=4.12.0
 chardet~=5.1.0
-comtypes~=1.1.14
 h5py~=3.8.0
 IsoSpecPy~=2.2.2
 lmfit~=1.1.0
@@ -10,8 +9,6 @@ netCDF4~=1.6.3
 numpy~=1.24.2
 openpyxl~=3.1.1
 pandas~=1.5.3
-psutil~=5.9.4
-PySide2~=5.15.2.1
 pyswarm~=0.6
 pythonnet~=3.0.1
 s3path~=0.4.1
@@ -21,4 +18,4 @@ seaborn~=0.12.2
 setuptools~=67.3.3
 SQLAlchemy~=1.4.47
 toml~=0.10.2
-tqdm~=4.64.1
+tqdm~=4.64.1

support_code/experimental_codes/LCMS-DataDependent.py

@@ -28,7 +28,7 @@
 from corems.molecular_formula.input.masslist_ref import ImportMassListRef
 from corems.encapsulation.constant import Labels
 from corems.mass_spectra.input import rawFileReader
-from corems import get_dirname, get_filename
+from support_code.filefinder import get_dirname, get_filename
 
 def _write_frame_to_new_sheet(path_to_file=None, sheet_name='sheet', data=None):
 

support_code/experimental_codes/LCMSDatadependentDataModel.py

@@ -29,7 +29,7 @@
 from corems.molecular_formula.input.masslist_ref import ImportMassListRef
 from corems.encapsulation.constant import Labels
 from corems.mass_spectra.input import rawFileReader
-from corems import get_dirname, get_filename
+from support_code.filefinder import get_dirname, get_filename
 
 def _write_frame_to_new_sheet(path_to_file=None, sheet_name='sheet', data=None):
 

support_code/filefinder.py

@@ -0,0 +1,90 @@
+import sys
+import hashlib
+
+def get_filenames(app=None):
+
+    from PySide2.QtCore import Qt, QCoreApplication
+    from PySide2.QtWidgets import QApplication, QFileDialog
+    from pathlib import Path
+
+    app = QApplication(sys.argv)
+    file_dialog = QFileDialog()
+    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
+    file_location, _ = file_dialog.getOpenFileNames()
+
+    if file_location:
+        QCoreApplication.processEvents()
+        return file_location
+
+    else:
+
+        return None
+
+def get_filename(app=None):
+
+    from PySide2.QtCore import Qt, QCoreApplication
+    from PySide2.QtWidgets import QApplication, QFileDialog
+    from pathlib import Path
+
+    app = QApplication(sys.argv)
+    file_dialog = QFileDialog()
+    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
+    file_location, _ = file_dialog.getOpenFileName()
+
+    if file_location:
+        QCoreApplication.processEvents()
+        return Path(file_location)
+
+    else:
+
+        return None
+
+def get_dirname(app=None):
+
+    from PySide2.QtCore import Qt, QCoreApplication
+    from PySide2.QtWidgets import QApplication, QFileDialog 
+    from pathlib import Path
+
+    app = QApplication(sys.argv)
+    file_dialog = QFileDialog()
+    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
+    file_location = file_dialog.getExistingDirectory()
+
+    if file_location:
+        QCoreApplication.processEvents()
+        return Path(file_location)
+
+    else:
+
+        return None
+
+def get_dirnames(app=None):
+
+    from PySide2.QtCore import Qt, QCoreApplication
+    from PySide2.QtWidgets import QApplication, QFileDialog, QTreeView, QListView, QAbstractItemView
+    from pathlib import Path
+
+    if not app:
+        app = QApplication(sys.argv)
+    # file_dialog = QFileDialog()
+    # file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
+    # file_location = file_dialog.getOpenFileNames()
+
+    file_dialog = QFileDialog()
+    file_dialog.setFileMode(QFileDialog.DirectoryOnly)
+    file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
+    file_view = file_dialog.findChild(QListView, 'listView')
+
+    # to make it possible to select multiple directories:
+    if file_view:
+        file_view.setSelectionMode(QAbstractItemView.MultiSelection)
+    f_tree_view = file_dialog.findChild(QTreeView)
+    if f_tree_view:
+        f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
+
+    if file_dialog.exec():
+        paths = file_dialog.selectedFiles()
+
+        QCoreApplication.processEvents()
+        for path in paths:
+            yield Path(path)

support_code/nmdc/metabolomics/gcms_workflow.py

@@ -13,7 +13,7 @@
 from corems.mass_spectra.input.andiNetCDF import ReadAndiNetCDF
 from corems.molecular_id.search.compoundSearch import LowResMassSpectralMatch
 from corems.mass_spectra.calc.GC_RI_Calibration import get_rt_ri_pairs
-from corems import get_dirname, get_filename
+from support_code.filefinder import get_dirname, get_filename
 
 import glob
 from nmdc.metadata.nmdc_registration import NMDC_Metadata

support_code/nmdc/nom/nom_workflow.py

@@ -22,11 +22,12 @@
 from corems.molecular_id.factory.classification import HeteroatomsClassification, Labels
 from corems.molecular_id.search.priorityAssignment import OxygenPriorityAssignment
 from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
-from corems import SuppressPrints, get_filename, get_dirnames
+from corems import SuppressPrints
 from corems.transient.input.brukerSolarix import ReadBrukerSolarix
 from corems.mass_spectra.input import rawFileReader
 from corems.encapsulation.factory.parameters import MSParameters
 from support_code.nmdc.metadata.nmdc_registration import DMS_Mapping, NMDC_Metadata
+from support_code.filefinder import get_dirnames, get_filename
 
 def run_bruker(file_location):