Merge pull request #134 from Roestlab/fix/scipy-bump

Minor Fixes

massdash/loaders/access/MzMLDataAccess.py

@@ -391,14 +391,14 @@ def msExperimentToFeatureMap(self, msExperiment: po.MSExperiment, feature: Trans
             spec = msExperiment.getSpectrum(k)
             mz, intensity = spec.get_peaks()
             if (len(mz) == 0 and len(intensity) == 0):
-                LOGGER.warn(
+                LOGGER.warning(
                     f"MS{spec.getMSLevel()} spectrum native id {spec.getNativeID()} had no m/z or intensity array, skipping this spectrum")
                 continue
             rt = np.full([mz.shape[0]], spec.getRT(), float)
 
             if not self.has_im:
                 if config.im_window is not None:
-                    LOGGER.warn(
+                    LOGGER.warning(
                         f"MS{spec.getMSLevel()} spectrum native id {spec.getNativeID()} had no ion mobility array")
                 im = np.full([mz.shape[0]], np.nan, float)
             else:
@@ -420,7 +420,7 @@ def msExperimentToFeatureMap(self, msExperiment: po.MSExperiment, feature: Trans
             annotation_mz_mapping = pd.concat([annotation_mz_mapping, pd.DataFrame({'Annotation': ['prec'], 'product_mz': [feature.precursor_mz]})])
             results_df = results_df.merge(annotation_mz_mapping, on='Annotation', how='left')
         else:
-            LOGGER.warn(f"No spectra found for peptide: {feature.sequence}{feature.precursor_charge}. Try adjusting the extraction parameters")
+            LOGGER.warning(f"No spectra found for peptide: {feature.sequence}{feature.precursor_charge}. Try adjusting the extraction parameters")
             results_df = pd.DataFrame(columns=['rt', 'int', 'Annotation'])
 
         return FeatureMap(results_df, feature.sequence, feature.precursor_charge, config)

massdash/plotting/InteractivePlotter.py

@@ -8,7 +8,8 @@
 
 # Data modules
 import numpy as np
-from scipy.signal import savgol_filter, gaussian, convolve
+from scipy.signal import savgol_filter, convolve
+from scipy.signal.windows import gaussian
 
 # Plotting modules
 from bokeh.plotting import figure

massdash/plotting/InteractiveTwoDimensionPlotter.py

@@ -8,7 +8,7 @@
 # Data modules
 import numpy as np
 import pandas as pd
-from scipy.ndimage.filters import gaussian_filter
+from scipy.ndimage import gaussian_filter
 
 # Plotting modules
 from bokeh.models import HoverTool, CrosshairTool, Title
@@ -20,7 +20,7 @@
 from .GenericPlotter import PlotConfig
 # Structs
 from ..structs.FeatureMap import FeatureMap
-#Transofmrations
+#Transformations
 from ..dataProcessing.transformations import equalize2D
 
 class InteractiveTwoDimensionPlotter:

massdash/structs/TransitionGroup.py

@@ -248,7 +248,7 @@ def plot(self,
             transitionGroupFeatures (Optional[List[TransitionGroupFeature]], optional): list of transition group features include in plot. Defaults to None.
             smoothing (Optional[Literal['none', 'sgolay', 'gauss']], optional): Smoothing to apply on the plot. Defaults to 'none'.
             gaussian_sigma (float, optional): sigma for gaussian plotting, ignored if smoothing is not 'gauss'. Defaults to 2.0.
-            gaussian_window (int, optional): window for guassian plotting, ignored if smoothing is not 'gauss'. Defaults to 11.
+            gaussian_window (int, optional): window for gaussian plotting, ignored if smoothing is not 'gauss'. Defaults to 11.
             sgolay_polynomial_order (int, optional): Polynomial order for sgolay, ignored if smoothing is not 'sgolay'. Defaults to 3.
             sgolay_frame_length (int, optional): Frame length for sgolay, ignored if smoothing is not 'sgolay'. Defaults to 11.
 

pyproject.toml

@@ -30,7 +30,7 @@ requires = [
     "plotly",
     "psutil",
     "pyopenms",
-    "scipy",
+    "scipy>=1.12.0",
     "streamlit>=1.30.0",
     "streamlit-javascript",
     "tk",

setup.cfg

@@ -47,7 +47,7 @@ install_requires =
     plotly
     psutil
     pyopenms
-    scipy
+    scipy>=1.12.0
     streamlit>=1.30.0
     streamlit-javascript
     tk