Apply black formatting and fix flake8 issues

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>

Author: Copilot

openms_python/py_experimentaldesign.py

@@ -1,24 +1,28 @@
 """Pythonic wrapper for :class:`pyopenms.ExperimentalDesign`."""
+
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Union, Optional, Set
-import pandas as pd
+from typing import Union, Optional, Set, TYPE_CHECKING
 
 import pyopenms as oms
 
 from ._io_utils import ensure_allowed_suffix
 
+if TYPE_CHECKING:
+    from .py_consensusmap import Py_ConsensusMap
+    from .py_featuremap import Py_FeatureMap
+
 # Supported file extensions for experimental design
 EXPERIMENTAL_DESIGN_EXTENSIONS = {".tsv"}
 
 
 class Py_ExperimentalDesign:
     """A Pythonic wrapper around :class:`pyopenms.ExperimentalDesign`.
-    
+
     This class provides convenient methods for loading, storing, and working with
     experimental design files in OpenMS format.
-    
+
     Example:
         >>> from openms_python import Py_ExperimentalDesign
         >>> design = Py_ExperimentalDesign.from_file("design.tsv")
@@ -27,7 +31,7 @@ class Py_ExperimentalDesign:
 
     def __init__(self, native_design: Optional[oms.ExperimentalDesign] = None):
         """Initialize with an optional native ExperimentalDesign object.
-        
+
         Parameters
         ----------
         native_design:
@@ -36,34 +40,34 @@ def __init__(self, native_design: Optional[oms.ExperimentalDesign] = None):
         self._design = native_design if native_design is not None else oms.ExperimentalDesign()
 
     @classmethod
-    def from_file(cls, filepath: Union[str, Path]) -> 'Py_ExperimentalDesign':
+    def from_file(cls, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
         """Load an experimental design from a TSV file.
-        
+
         Parameters
         ----------
         filepath:
             Path to the experimental design TSV file.
-            
+
         Returns
         -------
         Py_ExperimentalDesign
             A new instance with the loaded design.
-            
+
         Example:
             >>> design = Py_ExperimentalDesign.from_file("design.tsv")
         """
         instance = cls()
         instance.load(filepath)
         return instance
 
-    def load(self, filepath: Union[str, Path]) -> 'Py_ExperimentalDesign':
+    def load(self, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
         """Load an experimental design from disk.
-        
+
         Parameters
         ----------
         filepath:
             Path to the experimental design TSV file.
-            
+
         Returns
         -------
         Py_ExperimentalDesign
@@ -74,22 +78,22 @@ def load(self, filepath: Union[str, Path]) -> 'Py_ExperimentalDesign':
         self._design = edf.load(str(filepath), False)
         return self
 
-    def store(self, filepath: Union[str, Path]) -> 'Py_ExperimentalDesign':
+    def store(self, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
         """Store the experimental design to disk.
-        
+
         Note: Storage functionality is not available in the current pyOpenMS API.
         This method is provided for API consistency but will raise NotImplementedError.
-        
+
         Parameters
         ----------
         filepath:
             Path where the experimental design should be saved.
-            
+
         Returns
         -------
         Py_ExperimentalDesign
             Self for method chaining.
-            
+
         Raises
         ------
         NotImplementedError
@@ -146,7 +150,7 @@ def same_n_ms_files_per_fraction(self) -> bool:
     @property
     def samples(self) -> Set[str]:
         """Set of sample identifiers in the design.
-        
+
         Returns
         -------
         Set[str]
@@ -161,20 +165,20 @@ def samples(self) -> Set[str]:
 
     def summary(self) -> dict:
         """Get a summary of the experimental design.
-        
+
         Returns
         -------
         dict
             Dictionary with summary statistics.
         """
         return {
-            'n_samples': self.n_samples,
-            'n_ms_files': self.n_ms_files,
-            'n_fractions': self.n_fractions,
-            'n_fraction_groups': self.n_fraction_groups,
-            'n_labels': self.n_labels,
-            'is_fractionated': self.is_fractionated,
-            'samples': sorted(self.samples),
+            "n_samples": self.n_samples,
+            "n_ms_files": self.n_ms_files,
+            "n_fractions": self.n_fractions,
+            "n_fraction_groups": self.n_fraction_groups,
+            "n_labels": self.n_labels,
+            "is_fractionated": self.is_fractionated,
+            "samples": sorted(self.samples),
         }
 
     def print_summary(self) -> None:
@@ -188,61 +192,62 @@ def print_summary(self) -> None:
         print(f"Fraction Groups: {summary['n_fraction_groups']}")
         print(f"Labels: {summary['n_labels']}")
         print(f"Fractionated: {summary['is_fractionated']}")
-        if summary['samples']:
+        if summary["samples"]:
             print(f"Sample IDs: {', '.join(summary['samples'])}")
 
     # ==================== Factory methods ====================
 
     @classmethod
-    def from_consensus_map(cls, consensus_map: Union['Py_ConsensusMap', oms.ConsensusMap]) -> 'Py_ExperimentalDesign':
+    def from_consensus_map(
+        cls, consensus_map: Union["Py_ConsensusMap", oms.ConsensusMap]
+    ) -> "Py_ExperimentalDesign":
         """Create an ExperimentalDesign from a ConsensusMap.
-        
+
         Parameters
         ----------
         consensus_map:
             A :class:`Py_ConsensusMap` or :class:`pyopenms.ConsensusMap`.
-            
+
         Returns
         -------
         Py_ExperimentalDesign
             A new instance derived from the consensus map.
         """
         # Handle both Py_ConsensusMap and native ConsensusMap
-        native_map = consensus_map.native if hasattr(consensus_map, 'native') else consensus_map
+        native_map = consensus_map.native if hasattr(consensus_map, "native") else consensus_map
         design = oms.ExperimentalDesign.fromConsensusMap(native_map)
         return cls(design)
 
     @classmethod
-    def from_feature_map(cls, feature_map: Union['Py_FeatureMap', oms.FeatureMap]) -> 'Py_ExperimentalDesign':
+    def from_feature_map(
+        cls, feature_map: Union["Py_FeatureMap", oms.FeatureMap]
+    ) -> "Py_ExperimentalDesign":
         """Create an ExperimentalDesign from a FeatureMap.
-        
+
         Parameters
         ----------
         feature_map:
             A :class:`Py_FeatureMap` or :class:`pyopenms.FeatureMap`.
-            
+
         Returns
         -------
         Py_ExperimentalDesign
             A new instance derived from the feature map.
         """
         # Handle both Py_FeatureMap and native FeatureMap
-        native_map = feature_map.native if hasattr(feature_map, 'native') else feature_map
+        native_map = feature_map.native if hasattr(feature_map, "native") else feature_map
         design = oms.ExperimentalDesign.fromFeatureMap(native_map)
         return cls(design)
 
     @classmethod
-    def from_identifications(
-        cls,
-        protein_ids: list
-    ) -> 'Py_ExperimentalDesign':
+    def from_identifications(cls, protein_ids: list) -> "Py_ExperimentalDesign":
         """Create an ExperimentalDesign from protein identification data.
-        
+
         Parameters
         ----------
         protein_ids:
             List of :class:`pyopenms.ProteinIdentification` objects.
-            
+
         Returns
         -------
         Py_ExperimentalDesign