fixed darglint

noxfile.py

@@ -36,8 +36,7 @@ def activate_virtualenv_in_precommit_hooks(session: Session) -> None:
     session's virtual environment. This allows pre-commit to locate hooks in
     that environment when invoked from git.
 
-    Args:
-        session: The Session object.
+    :param session: The Session object.
     """
     assert session.bin is not None  # noqa: S101
 
@@ -111,6 +110,7 @@ def precommit(session: Session) -> None:
         "flake8-docstrings",
         "flake8-rst-docstrings",
         "isort",
+        "darglint",
         "pep8-naming",
         "pre-commit",
         "pre-commit-hooks",

spectrum_fundamentals/annotation/annotation.py

@@ -12,7 +12,7 @@
 
 def match_peaks(
     fragments_meta_data: List[dict],
-    peaks_intensity: Union[List[float], np.ndarray],
+    peaks_intensity: np.ndarray,
     peaks_masses: np.ndarray,
     tmt_n_term: int,
     unmod_sequence: str,
@@ -29,10 +29,6 @@ def match_peaks(
     :param charge: Precursor charge
     :return: List of matched/annotated peaks
     """
-    # Convert peaks_intensity to numpy array if it's a list
-    if isinstance(peaks_intensity, list):
-        peaks_intensity = np.array(peaks_intensity)
-
     start_peak = 0
     no_of_peaks = len(peaks_intensity)
     max_intensity = 1.0

spectrum_fundamentals/metrics/fragments_ratio.py

@@ -71,13 +71,11 @@ def count_observation_states(
         :param test_state: integer for the test observation state
         :param ion_mask: mask with 1s for the ions that should be counted and 0s for ions that should be ignored, \
                          integer array of length 174
+        :param xl: whether or not the function is executed with xl mode
         :return: number of observation states equal to test_state per row
         """
         state_boolean = observation_state == test_state
-        if xl:
-            return FragmentsRatio.count_with_ion_mask(state_boolean, ion_mask, xl=True)
-        else:
-            return FragmentsRatio.count_with_ion_mask(state_boolean, ion_mask)
+        return FragmentsRatio.count_with_ion_mask(state_boolean, ion_mask, xl=xl)
 
     @staticmethod
     def get_mask_observed_valid(observed_mz: scipy.sparse.csr_matrix) -> scipy.sparse.csr_matrix:

spectrum_fundamentals/metrics/percolator.py

@@ -57,15 +57,14 @@ def __init__(
         all_features_flag: bool = False,
         regression_method: str = "lowess",
         fdr_cutoff: float = 0.01,
-        xl: bool = False,
     ):
         """Initialize a Percolator obj."""
         self.metadata = metadata
         self.input_type = input_type
         self.all_features_flag = all_features_flag
         self.regression_method = regression_method
         self.fdr_cutoff = fdr_cutoff
-        self.xl = xl
+        self.xl = "CROSSLINKER_TYPE" in self.metadata.columns
 
         super().__init__(pred_intensities, true_intensities, mz)
 
@@ -248,7 +247,6 @@ def get_target_decoy_label(reverse: bool):
 
     def add_common_features(self):
         """Add features used by both Andromeda and Prosit feature scoring sets."""
-        self.xl = "CROSSLINKER_TYPE" in self.metadata.columns
         if self.xl:
             self.metrics_val["missedCleavages_A"] = self.metadata["SEQUENCE_A"].apply(Percolator.count_missed_cleavages)
             self.metrics_val["missedCleavages_B"] = self.metadata["SEQUENCE_B"].apply(Percolator.count_missed_cleavages)
@@ -278,7 +276,6 @@ def add_common_features(self):
 
     def add_percolator_metadata_columns(self):
         """Add metadata columns needed by percolator, e.g. to identify a PSM."""
-        self.xl = "CROSSLINKER_TYPE" in self.metadata.columns
         if self.xl:
             spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE_A", "MODIFIED_SEQUENCE_B", "PRECURSOR_CHARGE"]
             self.metrics_val["Peptide"] = (

spectrum_fundamentals/metrics/similarity.py

@@ -57,6 +57,7 @@ def spectral_angle(
         :param predicted_intensities: predicted intensities, see observed_intensities for details, array of length 174
         :param charge: to filter by the peak charges, 0 means everything
         :param xl: whether operating on cleavable crosslinked or linear peptides
+        :raises ValueError: if charge is smaller than 1 or larger than 5
         :return: SA values
         """
         if charge != 0:
@@ -209,6 +210,9 @@ def correlation(
         :param predicted_intensities: predicted intensities, see observed_intensities for details, array of length 174
         :param charge: to filter by the peak charges, 0 means everything
         :param method: either pearson or spearman
+        :param xl: wheter or not to use xl mode
+        :raises ValueError: if charge is smaller than 1 or larger than 5
+
         :return: calculated correlations
         """
         observed_intensities_array = observed_intensities.toarray()