#48: fix linter issues

.pre-commit-config.yaml

@@ -11,4 +11,4 @@ repos:
   rev: v0.4.0
   hooks:
     - id: ruff-format
-#    - id: ruff
+    - id: ruff

alpharaw/__init__.py

@@ -6,14 +6,14 @@
 
 
 def register_readers():
-    from .ms_data_base import ms_reader_provider
-    from .legacy_msdata import mgf
-    from .mzml import MzMLReader
-    from .wrappers import alphapept_wrapper
+    from .ms_data_base import ms_reader_provider  # noqa: F401  # TODO remove import side effect
+    from .legacy_msdata import mgf  # noqa: F401  # TODO remove import side effect
+    from .mzml import MzMLReader  # noqa: F401  # TODO remove import side effect
+    from .wrappers import alphapept_wrapper  # noqa: F401  # TODO remove import side effect
 
     try:
-        from .sciex import SciexWiffData
-        from .thermo import ThermoRawData
+        from .sciex import SciexWiffData  # noqa: F401  # TODO remove import side effect
+        from .thermo import ThermoRawData  # noqa: F401  # TODO remove import side effect
     except (RuntimeError, ImportError):
         print("[WARN] pythonnet is not installed")
 

alpharaw/cli.py

@@ -1,14 +1,15 @@
 import click
 import os
 
+import alpharaw
 from alpharaw.ms_data_base import ms_reader_provider
 from alpharaw.legacy_msdata import mgf  # noqa: F401  # TODO remove import side effect
 from alpharaw.mzml import MzMLReader  # noqa: F401  # TODO remove import side effect
 from alpharaw.wrappers import alphapept_wrapper  # noqa: F401  # TODO remove import side effect
 
 try:
-    from alpharaw.sciex import SciexWiffData
-    from alpharaw.thermo import ThermoRawData
+    from alpharaw.sciex import SciexWiffData  # noqa: F401 # TODO remove import side effect
+    from alpharaw.thermo import ThermoRawData  # noqa: F401 # TODO remove import side effect
 except (RuntimeError, ImportError):
     print("[WARN] pythonnet is not installed")
 

alpharaw/feature/hills.py

@@ -1,4 +1,5 @@
 import numpy as np
+import pandas as pd
 from alphatims.utils import threadpool
 from numba import njit
 from alpharaw.feature.centroids import connect_centroids

alpharaw/feature/isotope_pattern.py

@@ -390,13 +390,13 @@ def grow(
 
         y = pattern[seed + relative_pos]  # This is a reference peak
 
-        l = sortindex_[y]
+        ll = sortindex_[y]
 
         mass2 = stats[y, 0]
         delta_mass2 = stats[y, 1]
 
-        start = hill_ptrs[l]
-        end = hill_ptrs[l + 1]
+        start = hill_ptrs[ll]
+        end = hill_ptrs[ll + 1]
         idx_ = hill_data[start:end]
         int_2 = int_data[idx_]
         scans_2 = scan_idx[idx_]
@@ -560,7 +560,6 @@ def plot_pattern(
     pattern: np.ndarray,
     sorted_hills: np.ndarray,
     centroids: np.ndarray,
-    hill_data: np.ndarray,
 ):
     """Helper function to plot a pattern.
 
@@ -570,19 +569,17 @@ def plot_pattern(
         centroids (np.ndarray): 1D Array containing the masses of the centroids.
         hill_data (np.ndarray): Array containing the indices to hills.
     """
+    import matplotlib.pyplot as plt
+
     f, (ax1, ax2) = plt.subplots(2, 1, sharex=True, figsize=(10, 10))
     centroid_dtype = [("mz", float), ("int", float), ("scan_no", int), ("rt", float)]
 
-    mzs = []
-    rts = []
-    ints = []
     for entry in pattern:
         hill = sorted_hills[entry]
         hill_data = np.array(
             [centroids[_[0]][_[1]] for _ in hill], dtype=centroid_dtype
         )
 
-        int_profile = hill_data["int"]
         ax1.plot(hill_data["rt"], hill_data["int"])
         ax2.scatter(hill_data["rt"], hill_data["mz"], s=hill_data["int"] / 5e5)
 
@@ -1102,13 +1099,6 @@ def report_(
     int_max_idx = np.argmax(isotope_data[:, 2])
     mz_most_abundant = isotope_data[:, 0][int_max_idx]
 
-    int_max = isotope_data[:, 2][int_max_idx]
-
-    rt_start = isotope_data[
-        int_max_idx, 4
-    ]  # This is the start of the most abundant trace
-    rt_end = isotope_data[int_max_idx, 5]
-
     rt_min_ = min(isotope_data[:, 4])
     rt_max_ = max(isotope_data[:, 5])
 

alpharaw/match/psm_match.py

@@ -6,7 +6,6 @@
 
 from alpharaw import register_readers
 
-register_readers()
 
 from alphabase.peptide.fragment import (
     create_fragment_mz_dataframe,
@@ -30,6 +29,9 @@
 from alpharaw.dia.normal_dia import NormalDIAGrouper
 
 
+register_readers()  # TODO remove this import side effect
+
+
 class PepSpecMatch:
     """
     Extract fragment ions from MS2 data.

alpharaw/mzml.py

@@ -157,7 +157,7 @@ def parse_mzml_entry(item_dict: dict) -> tuple:
                 nce = float(filter_string.split("@cid")[1].split(" ")[0])
             else:
                 nce = np.nan
-        except:
+        except Exception:
             nce = np.nan
     return (
         rt,

alpharaw/raw_access/clr_utils.py

@@ -1,7 +1,9 @@
-import clr
+# ruff: noqa: E402  #Module level import not at top of file
 import os
 import numpy as np
 
+import clr
+
 clr.AddReference("System")
 # from System.Runtime.InteropServices import Marshal
 # from System import IntPtr, Int64

alpharaw/raw_access/pysciexwifffilereader.py

@@ -1,3 +1,4 @@
+# ruff: noqa: E402  #Module level import not at top of file
 import os
 import numpy as np
 
@@ -7,6 +8,7 @@
 import clr
 
 clr.AddReference("System")
+
 import System  # noqa: F401
 from System.Threading import Thread
 from System.Globalization import CultureInfo

alpharaw/raw_access/pythermorawfilereader.py

@@ -1,3 +1,4 @@
+# ruff: noqa: E402  #Module level import not at top of file
 import os
 import warnings
 
@@ -308,13 +309,6 @@ def GetScanEventStringForScanNum(self, scanNumber):
         """This function returns scan event information as a string for the specified scan number."""
         return self.source.GetScanEventStringForScanNumber(scanNumber)
 
-    def GetStatusLogForRetentionTime(self, rt):
-        logEntry = self.source.GetStatusLogForRetentionTime(rt)
-        return dict(zip(logEntry.Labels, logEntry.Values))
-
-    def GetStatusLogForScanNum(self, scan):
-        return self.GetStatusLogForRetentionTime(self.RTFromScanNum(scan))
-
     def GetScanEventForScanNum(self, scanNumber):
         return IScanEventBase(self.source.GetScanEventForScanNumber(scanNumber))