From ea7202ec68051996c7e92414f5dc3c63ee8b7992 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 19 Nov 2025 10:14:56 +0000
Subject: [PATCH 1/5] Initial plan


From 7f8812e3c99df6c6e671563b706b5b8e61947376 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 19 Nov 2025 10:23:37 +0000
Subject: [PATCH 2/5] Add Py_ExperimentalDesign wrapper with tests and README
 documentation

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
---
 README.md                                     |  33 +++
 openms_python/__init__.py                     |   2 +
 .../examples/experimental_design.tsv          |   7 +
 openms_python/py_experimentaldesign.py        | 265 ++++++++++++++++++
 pyproject.toml                                |   2 +-
 tests/test_py_experimentaldesign.py           | 232 +++++++++++++++
 6 files changed, 540 insertions(+), 1 deletion(-)
 create mode 100644 openms_python/examples/experimental_design.tsv
 create mode 100644 openms_python/py_experimentaldesign.py
 create mode 100644 tests/test_py_experimentaldesign.py

diff --git a/README.md b/README.md
index 65f445d..83f5a2d 100644
--- a/README.md
+++ b/README.md
@@ -189,6 +189,39 @@ search engine can be when built with the high-level helpers in
 `openms_python`. Reuse the test as inspiration for bespoke pipelines or as a
 regression harness when experimenting with search-related utilities.
 
+## Experimental design support
+
+Managing multi-sample, multi-fraction experiments? The `Py_ExperimentalDesign`
+wrapper makes it straightforward to work with OpenMS experimental design files
+that describe sample layouts, fractionation schemes, and labeling strategies.
+`tests/test_py_experimentaldesign.py` provides comprehensive examples of loading
+and querying experimental designs, including support for fractionated workflows,
+label-free and labeled quantitation setups, and integration with feature maps,
+consensus maps, and identification results. The wrapper exposes Pythonic
+properties for quick access to sample counts, fraction information, and design
+summaries—perfect for building sample-aware quantitation pipelines or validating
+experimental metadata before analysis.
+
+```python
+from openms_python import Py_ExperimentalDesign
+
+# Load an experimental design from a TSV file
+design = Py_ExperimentalDesign.from_file("design.tsv")
+
+# Quick access to design properties
+print(f"Samples: {design.n_samples}")
+print(f"MS files: {design.n_ms_files}")
+print(f"Fractionated: {design.is_fractionated}")
+
+# Get a summary
+design.print_summary()
+
+# Create from existing OpenMS objects
+from openms_python import Py_ConsensusMap
+consensus = Py_ConsensusMap.from_file("results.consensusXML")
+design = Py_ExperimentalDesign.from_consensus_map(consensus)
+```
+
 ### Iterate over containers and metadata
 
 All sequence-like wrappers (feature maps, consensus maps, identification containers,
diff --git a/openms_python/__init__.py b/openms_python/__init__.py
index 3400c09..750d0d7 100644
--- a/openms_python/__init__.py
+++ b/openms_python/__init__.py
@@ -26,6 +26,7 @@
 from .py_feature import Py_Feature
 from .py_featuremap import Py_FeatureMap
 from .py_consensusmap import Py_ConsensusMap
+from .py_experimentaldesign import Py_ExperimentalDesign
 from .py_identifications import (
     ProteinIdentifications,
     PeptideIdentifications,
@@ -101,6 +102,7 @@ def get_example(name: str, *, load: bool = False, target_dir: Union[str, Path, N
     "Py_Feature",
     "Py_FeatureMap",
     "Py_ConsensusMap",
+    "Py_ExperimentalDesign",
     "ProteinIdentifications",
     "PeptideIdentifications",
     "Identifications",
diff --git a/openms_python/examples/experimental_design.tsv b/openms_python/examples/experimental_design.tsv
new file mode 100644
index 0000000..2d7dac6
--- /dev/null
+++ b/openms_python/examples/experimental_design.tsv
@@ -0,0 +1,7 @@
+Fraction_Group	Fraction	Spectra_Filepath	Label	Sample
+1	1	sample1_fraction1.mzML	1	1
+1	2	sample1_fraction2.mzML	1	1
+1	3	sample1_fraction3.mzML	1	1
+2	1	sample2_fraction1.mzML	1	2
+2	2	sample2_fraction2.mzML	1	2
+2	3	sample2_fraction3.mzML	1	2
diff --git a/openms_python/py_experimentaldesign.py b/openms_python/py_experimentaldesign.py
new file mode 100644
index 0000000..c53a5e5
--- /dev/null
+++ b/openms_python/py_experimentaldesign.py
@@ -0,0 +1,265 @@
+"""Pythonic wrapper for :class:`pyopenms.ExperimentalDesign`."""
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Union, Optional, Set
+import pandas as pd
+
+import pyopenms as oms
+
+from ._io_utils import ensure_allowed_suffix
+
+# 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")
+        >>> print(f"Samples: {design.n_samples}, MS files: {design.n_ms_files}")
+    """
+
+    def __init__(self, native_design: Optional[oms.ExperimentalDesign] = None):
+        """Initialize with an optional native ExperimentalDesign object.
+        
+        Parameters
+        ----------
+        native_design:
+            Optional :class:`pyopenms.ExperimentalDesign` to wrap.
+        """
+        self._design = native_design if native_design is not None else oms.ExperimentalDesign()
+
+    @classmethod
+    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':
+        """Load an experimental design from disk.
+        
+        Parameters
+        ----------
+        filepath:
+            Path to the experimental design TSV file.
+            
+        Returns
+        -------
+        Py_ExperimentalDesign
+            Self for method chaining.
+        """
+        ensure_allowed_suffix(filepath, EXPERIMENTAL_DESIGN_EXTENSIONS, "ExperimentalDesign")
+        edf = oms.ExperimentalDesignFile()
+        self._design = edf.load(str(filepath), False)
+        return self
+
+    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
+            Storage is not yet implemented in pyOpenMS.
+        """
+        ensure_allowed_suffix(filepath, EXPERIMENTAL_DESIGN_EXTENSIONS, "ExperimentalDesign")
+        raise NotImplementedError(
+            "ExperimentalDesign storage is not yet available in pyOpenMS. "
+            "Please use the native pyOpenMS API if this functionality is needed."
+        )
+
+    @property
+    def native(self) -> oms.ExperimentalDesign:
+        """Return the underlying :class:`pyopenms.ExperimentalDesign`."""
+        return self._design
+
+    # ==================== Properties ====================
+
+    @property
+    def n_samples(self) -> int:
+        """Number of samples in the experimental design."""
+        return self._design.getNumberOfSamples()
+
+    @property
+    def n_ms_files(self) -> int:
+        """Number of MS files in the experimental design."""
+        return self._design.getNumberOfMSFiles()
+
+    @property
+    def n_fractions(self) -> int:
+        """Number of fractions in the experimental design."""
+        return self._design.getNumberOfFractions()
+
+    @property
+    def n_fraction_groups(self) -> int:
+        """Number of fraction groups in the experimental design."""
+        return self._design.getNumberOfFractionGroups()
+
+    @property
+    def n_labels(self) -> int:
+        """Number of labels in the experimental design."""
+        return self._design.getNumberOfLabels()
+
+    @property
+    def is_fractionated(self) -> bool:
+        """Whether the experimental design includes fractionation."""
+        return self._design.isFractionated()
+
+    @property
+    def same_n_ms_files_per_fraction(self) -> bool:
+        """Whether all fractions have the same number of MS files."""
+        return self._design.sameNrOfMSFilesPerFraction()
+
+    @property
+    def samples(self) -> Set[str]:
+        """Set of sample identifiers in the design.
+        
+        Returns
+        -------
+        Set[str]
+            Set of sample identifiers.
+        """
+        sample_section = self._design.getSampleSection()
+        samples = sample_section.getSamples()
+        # Convert bytes to str if needed
+        return {s.decode() if isinstance(s, bytes) else str(s) for s in samples}
+
+    # ==================== Summary methods ====================
+
+    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),
+        }
+
+    def print_summary(self) -> None:
+        """Print a formatted summary of the experimental design."""
+        summary = self.summary()
+        print("Experimental Design Summary")
+        print("=" * 40)
+        print(f"Samples: {summary['n_samples']}")
+        print(f"MS Files: {summary['n_ms_files']}")
+        print(f"Fractions: {summary['n_fractions']}")
+        print(f"Fraction Groups: {summary['n_fraction_groups']}")
+        print(f"Labels: {summary['n_labels']}")
+        print(f"Fractionated: {summary['is_fractionated']}")
+        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':
+        """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
+        design = oms.ExperimentalDesign.fromConsensusMap(native_map)
+        return cls(design)
+
+    @classmethod
+    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
+        design = oms.ExperimentalDesign.fromFeatureMap(native_map)
+        return cls(design)
+
+    @classmethod
+    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
+            A new instance derived from the identifications.
+        """
+        design = oms.ExperimentalDesign.fromIdentifications(protein_ids)
+        return cls(design)
+
+    # ==================== Delegation ====================
+
+    def __getattr__(self, name: str):
+        """Delegate attribute access to the underlying ExperimentalDesign."""
+        return getattr(self._design, name)
+
+    def __repr__(self) -> str:
+        """String representation of the ExperimentalDesign."""
+        return (
+            f"Py_ExperimentalDesign(samples={self.n_samples}, "
+            f"ms_files={self.n_ms_files}, fractionated={self.is_fractionated})"
+        )
diff --git a/pyproject.toml b/pyproject.toml
index 0ce5c1c..53b7e32 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ where = ["."]
 include = ["openms_python*"]
 
 [tool.setuptools.package-data]
-"openms_python" = ["examples/*.mzML"]
+"openms_python" = ["examples/*.mzML", "examples/*.tsv"]
 
 [tool.black]
 line-length = 100
diff --git a/tests/test_py_experimentaldesign.py b/tests/test_py_experimentaldesign.py
new file mode 100644
index 0000000..f9b47f7
--- /dev/null
+++ b/tests/test_py_experimentaldesign.py
@@ -0,0 +1,232 @@
+"""Tests for :class:`Py_ExperimentalDesign`."""
+from pathlib import Path
+import tempfile
+
+import pytest
+import pyopenms as oms
+
+from openms_python import Py_ExperimentalDesign, get_example
+
+
+def test_py_experimentaldesign_load_from_file():
+    """Test loading an experimental design from the bundled example."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    assert design.n_samples == 2
+    assert design.n_ms_files == 6
+    assert design.n_fractions == 3
+    assert design.n_fraction_groups == 2
+    assert design.n_labels == 1
+    assert design.is_fractionated is True
+
+
+def test_py_experimentaldesign_properties():
+    """Test that properties work correctly."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    # Test all properties
+    assert isinstance(design.n_samples, int)
+    assert isinstance(design.n_ms_files, int)
+    assert isinstance(design.n_fractions, int)
+    assert isinstance(design.n_fraction_groups, int)
+    assert isinstance(design.n_labels, int)
+    assert isinstance(design.is_fractionated, bool)
+    assert isinstance(design.same_n_ms_files_per_fraction, bool)
+    
+    # Test samples property
+    samples = design.samples
+    assert isinstance(samples, set)
+    assert len(samples) == 2
+    assert '1' in samples
+    assert '2' in samples
+
+
+def test_py_experimentaldesign_summary():
+    """Test summary method returns expected structure."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    summary = design.summary()
+    
+    assert isinstance(summary, dict)
+    assert 'n_samples' in summary
+    assert 'n_ms_files' in summary
+    assert 'n_fractions' in summary
+    assert 'n_fraction_groups' in summary
+    assert 'n_labels' in summary
+    assert 'is_fractionated' in summary
+    assert 'samples' in summary
+    
+    assert summary['n_samples'] == 2
+    assert summary['n_ms_files'] == 6
+    assert summary['samples'] == ['1', '2']
+
+
+def test_py_experimentaldesign_print_summary(capsys):
+    """Test that print_summary produces output."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    design.print_summary()
+    
+    captured = capsys.readouterr()
+    assert "Experimental Design Summary" in captured.out
+    assert "Samples: 2" in captured.out
+    assert "MS Files: 6" in captured.out
+    assert "Fractionated: True" in captured.out
+
+
+def test_py_experimentaldesign_load_method():
+    """Test that load method works and returns self."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign()
+    
+    result = design.load(example_path)
+    
+    assert result is design
+    assert design.n_samples == 2
+
+
+def test_py_experimentaldesign_native_property():
+    """Test that native property returns pyopenms object."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    native = design.native
+    
+    assert isinstance(native, oms.ExperimentalDesign)
+    assert native.getNumberOfSamples() == 2
+
+
+def test_py_experimentaldesign_repr():
+    """Test string representation."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    repr_str = repr(design)
+    
+    assert "Py_ExperimentalDesign" in repr_str
+    assert "samples=2" in repr_str
+    assert "ms_files=6" in repr_str
+    assert "fractionated=True" in repr_str
+
+
+def test_py_experimentaldesign_invalid_extension():
+    """Test that loading a file with wrong extension raises error."""
+    with tempfile.NamedTemporaryFile(suffix='.txt', mode='w', delete=False) as f:
+        f.write("test")
+        temp_path = f.name
+    
+    try:
+        with pytest.raises(ValueError, match="ExperimentalDesign"):
+            Py_ExperimentalDesign.from_file(temp_path)
+    finally:
+        Path(temp_path).unlink()
+
+
+def test_py_experimentaldesign_store_not_implemented():
+    """Test that store method raises NotImplementedError."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    with tempfile.NamedTemporaryFile(suffix='.tsv', delete=False) as f:
+        temp_path = f.name
+    
+    try:
+        with pytest.raises(NotImplementedError, match="not yet available"):
+            design.store(temp_path)
+    finally:
+        Path(temp_path).unlink()
+
+
+def test_py_experimentaldesign_delegation():
+    """Test that methods are delegated to underlying object."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+    
+    # Test delegation of a native method
+    ms_file_section = design.getMSFileSection()
+    assert isinstance(ms_file_section, list)
+    assert len(ms_file_section) == 6
+
+
+def test_py_experimentaldesign_simple_design():
+    """Test with a simple non-fractionated design."""
+    # Create a simple experimental design
+    # Different fraction groups for different samples to avoid conflicts
+    tsv_content = """Fraction_Group\tFraction\tSpectra_Filepath\tLabel\tSample
+1\t1\tfile1.mzML\t1\t1
+2\t1\tfile2.mzML\t1\t2
+"""
+    
+    with tempfile.NamedTemporaryFile(mode='w', suffix='.tsv', delete=False) as f:
+        f.write(tsv_content)
+        temp_path = f.name
+    
+    try:
+        design = Py_ExperimentalDesign.from_file(temp_path)
+        
+        assert design.n_samples == 2
+        assert design.n_ms_files == 2
+        assert design.n_fractions == 1
+        assert design.n_labels == 1
+        
+        samples = design.samples
+        assert len(samples) == 2
+        
+    finally:
+        Path(temp_path).unlink()
+
+
+def test_py_experimentaldesign_from_consensus_map():
+    """Test creating ExperimentalDesign from ConsensusMap."""
+    # Create a minimal consensus map
+    consensus_map = oms.ConsensusMap()
+    
+    # Add some file descriptions
+    file_desc1 = oms.ProteinIdentification()
+    file_desc1.setIdentifier("file1")
+    file_desc2 = oms.ProteinIdentification()
+    file_desc2.setIdentifier("file2")
+    
+    consensus_map.setProteinIdentifications([file_desc1, file_desc2])
+    
+    # Create design from consensus map
+    design = Py_ExperimentalDesign.from_consensus_map(consensus_map)
+    
+    assert isinstance(design, Py_ExperimentalDesign)
+    assert isinstance(design.native, oms.ExperimentalDesign)
+
+
+def test_py_experimentaldesign_from_feature_map():
+    """Test creating ExperimentalDesign from FeatureMap."""
+    # Create a minimal feature map
+    feature_map = oms.FeatureMap()
+    
+    # Add protein identification for the file descriptor
+    prot_id = oms.ProteinIdentification()
+    prot_id.setIdentifier("sample1")
+    feature_map.setProteinIdentifications([prot_id])
+    
+    # Create design from feature map
+    design = Py_ExperimentalDesign.from_feature_map(feature_map)
+    
+    assert isinstance(design, Py_ExperimentalDesign)
+    assert isinstance(design.native, oms.ExperimentalDesign)
+
+
+def test_py_experimentaldesign_from_identifications():
+    """Test creating ExperimentalDesign from identification data."""
+    # Create minimal identification data
+    prot_id = oms.ProteinIdentification()
+    prot_id.setIdentifier("search1")
+    
+    protein_ids = [prot_id]
+    
+    # Create design from identifications
+    design = Py_ExperimentalDesign.from_identifications(protein_ids)
+    
+    assert isinstance(design, Py_ExperimentalDesign)
+    assert isinstance(design.native, oms.ExperimentalDesign)

From 363f7e120685d565bf166f807c878a727a028126 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 19 Nov 2025 10:24:49 +0000
Subject: [PATCH 3/5] Apply black formatting and fix flake8 issues

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
---
 openms_python/py_experimentaldesign.py | 87 ++++++++++++-----------
 tests/test_py_experimentaldesign.py    | 97 +++++++++++++-------------
 2 files changed, 95 insertions(+), 89 deletions(-)

diff --git a/openms_python/py_experimentaldesign.py b/openms_python/py_experimentaldesign.py
index c53a5e5..d9e4871 100644
--- a/openms_python/py_experimentaldesign.py
+++ b/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:
@@ -36,19 +40,19 @@ 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")
         """
@@ -56,14 +60,14 @@ def from_file(cls, filepath: Union[str, Path]) -> 'Py_ExperimentalDesign':
         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
diff --git a/tests/test_py_experimentaldesign.py b/tests/test_py_experimentaldesign.py
index f9b47f7..ab4a8d7 100644
--- a/tests/test_py_experimentaldesign.py
+++ b/tests/test_py_experimentaldesign.py
@@ -1,4 +1,5 @@
 """Tests for :class:`Py_ExperimentalDesign`."""
+
 from pathlib import Path
 import tempfile
 
@@ -12,7 +13,7 @@ def test_py_experimentaldesign_load_from_file():
     """Test loading an experimental design from the bundled example."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     assert design.n_samples == 2
     assert design.n_ms_files == 6
     assert design.n_fractions == 3
@@ -25,7 +26,7 @@ def test_py_experimentaldesign_properties():
     """Test that properties work correctly."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     # Test all properties
     assert isinstance(design.n_samples, int)
     assert isinstance(design.n_ms_files, int)
@@ -34,43 +35,43 @@ def test_py_experimentaldesign_properties():
     assert isinstance(design.n_labels, int)
     assert isinstance(design.is_fractionated, bool)
     assert isinstance(design.same_n_ms_files_per_fraction, bool)
-    
+
     # Test samples property
     samples = design.samples
     assert isinstance(samples, set)
     assert len(samples) == 2
-    assert '1' in samples
-    assert '2' in samples
+    assert "1" in samples
+    assert "2" in samples
 
 
 def test_py_experimentaldesign_summary():
     """Test summary method returns expected structure."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     summary = design.summary()
-    
+
     assert isinstance(summary, dict)
-    assert 'n_samples' in summary
-    assert 'n_ms_files' in summary
-    assert 'n_fractions' in summary
-    assert 'n_fraction_groups' in summary
-    assert 'n_labels' in summary
-    assert 'is_fractionated' in summary
-    assert 'samples' in summary
-    
-    assert summary['n_samples'] == 2
-    assert summary['n_ms_files'] == 6
-    assert summary['samples'] == ['1', '2']
+    assert "n_samples" in summary
+    assert "n_ms_files" in summary
+    assert "n_fractions" in summary
+    assert "n_fraction_groups" in summary
+    assert "n_labels" in summary
+    assert "is_fractionated" in summary
+    assert "samples" in summary
+
+    assert summary["n_samples"] == 2
+    assert summary["n_ms_files"] == 6
+    assert summary["samples"] == ["1", "2"]
 
 
 def test_py_experimentaldesign_print_summary(capsys):
     """Test that print_summary produces output."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     design.print_summary()
-    
+
     captured = capsys.readouterr()
     assert "Experimental Design Summary" in captured.out
     assert "Samples: 2" in captured.out
@@ -82,9 +83,9 @@ def test_py_experimentaldesign_load_method():
     """Test that load method works and returns self."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign()
-    
+
     result = design.load(example_path)
-    
+
     assert result is design
     assert design.n_samples == 2
 
@@ -93,9 +94,9 @@ def test_py_experimentaldesign_native_property():
     """Test that native property returns pyopenms object."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     native = design.native
-    
+
     assert isinstance(native, oms.ExperimentalDesign)
     assert native.getNumberOfSamples() == 2
 
@@ -104,9 +105,9 @@ def test_py_experimentaldesign_repr():
     """Test string representation."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     repr_str = repr(design)
-    
+
     assert "Py_ExperimentalDesign" in repr_str
     assert "samples=2" in repr_str
     assert "ms_files=6" in repr_str
@@ -115,10 +116,10 @@ def test_py_experimentaldesign_repr():
 
 def test_py_experimentaldesign_invalid_extension():
     """Test that loading a file with wrong extension raises error."""
-    with tempfile.NamedTemporaryFile(suffix='.txt', mode='w', delete=False) as f:
+    with tempfile.NamedTemporaryFile(suffix=".txt", mode="w", delete=False) as f:
         f.write("test")
         temp_path = f.name
-    
+
     try:
         with pytest.raises(ValueError, match="ExperimentalDesign"):
             Py_ExperimentalDesign.from_file(temp_path)
@@ -130,10 +131,10 @@ def test_py_experimentaldesign_store_not_implemented():
     """Test that store method raises NotImplementedError."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
-    with tempfile.NamedTemporaryFile(suffix='.tsv', delete=False) as f:
+
+    with tempfile.NamedTemporaryFile(suffix=".tsv", delete=False) as f:
         temp_path = f.name
-    
+
     try:
         with pytest.raises(NotImplementedError, match="not yet available"):
             design.store(temp_path)
@@ -145,7 +146,7 @@ def test_py_experimentaldesign_delegation():
     """Test that methods are delegated to underlying object."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
-    
+
     # Test delegation of a native method
     ms_file_section = design.getMSFileSection()
     assert isinstance(ms_file_section, list)
@@ -160,22 +161,22 @@ def test_py_experimentaldesign_simple_design():
 1\t1\tfile1.mzML\t1\t1
 2\t1\tfile2.mzML\t1\t2
 """
-    
-    with tempfile.NamedTemporaryFile(mode='w', suffix='.tsv', delete=False) as f:
+
+    with tempfile.NamedTemporaryFile(mode="w", suffix=".tsv", delete=False) as f:
         f.write(tsv_content)
         temp_path = f.name
-    
+
     try:
         design = Py_ExperimentalDesign.from_file(temp_path)
-        
+
         assert design.n_samples == 2
         assert design.n_ms_files == 2
         assert design.n_fractions == 1
         assert design.n_labels == 1
-        
+
         samples = design.samples
         assert len(samples) == 2
-        
+
     finally:
         Path(temp_path).unlink()
 
@@ -184,18 +185,18 @@ def test_py_experimentaldesign_from_consensus_map():
     """Test creating ExperimentalDesign from ConsensusMap."""
     # Create a minimal consensus map
     consensus_map = oms.ConsensusMap()
-    
+
     # Add some file descriptions
     file_desc1 = oms.ProteinIdentification()
     file_desc1.setIdentifier("file1")
     file_desc2 = oms.ProteinIdentification()
     file_desc2.setIdentifier("file2")
-    
+
     consensus_map.setProteinIdentifications([file_desc1, file_desc2])
-    
+
     # Create design from consensus map
     design = Py_ExperimentalDesign.from_consensus_map(consensus_map)
-    
+
     assert isinstance(design, Py_ExperimentalDesign)
     assert isinstance(design.native, oms.ExperimentalDesign)
 
@@ -204,15 +205,15 @@ def test_py_experimentaldesign_from_feature_map():
     """Test creating ExperimentalDesign from FeatureMap."""
     # Create a minimal feature map
     feature_map = oms.FeatureMap()
-    
+
     # Add protein identification for the file descriptor
     prot_id = oms.ProteinIdentification()
     prot_id.setIdentifier("sample1")
     feature_map.setProteinIdentifications([prot_id])
-    
+
     # Create design from feature map
     design = Py_ExperimentalDesign.from_feature_map(feature_map)
-    
+
     assert isinstance(design, Py_ExperimentalDesign)
     assert isinstance(design.native, oms.ExperimentalDesign)
 
@@ -222,11 +223,11 @@ def test_py_experimentaldesign_from_identifications():
     # Create minimal identification data
     prot_id = oms.ProteinIdentification()
     prot_id.setIdentifier("search1")
-    
+
     protein_ids = [prot_id]
-    
+
     # Create design from identifications
     design = Py_ExperimentalDesign.from_identifications(protein_ids)
-    
+
     assert isinstance(design, Py_ExperimentalDesign)
     assert isinstance(design.native, oms.ExperimentalDesign)

From e783d356ccafe7640c089ba445c82f13c738cf45 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 19 Nov 2025 10:47:31 +0000
Subject: [PATCH 4/5] Add DataFrame support to Py_ExperimentalDesign
 (from_dataframe/to_dataframe)

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
---
 README.md                              |  14 +++
 openms_python/py_experimentaldesign.py | 144 +++++++++++++++++++++++++
 tests/test_py_experimentaldesign.py    | 122 +++++++++++++++++++++
 3 files changed, 280 insertions(+)

diff --git a/README.md b/README.md
index 83f5a2d..b85f209 100644
--- a/README.md
+++ b/README.md
@@ -204,6 +204,7 @@ experimental metadata before analysis.
 
 ```python
 from openms_python import Py_ExperimentalDesign
+import pandas as pd
 
 # Load an experimental design from a TSV file
 design = Py_ExperimentalDesign.from_file("design.tsv")
@@ -216,6 +217,19 @@ print(f"Fractionated: {design.is_fractionated}")
 # Get a summary
 design.print_summary()
 
+# Convert to pandas DataFrame for analysis
+df = design.to_dataframe()
+
+# Create from a pandas DataFrame
+df = pd.DataFrame({
+    'Fraction_Group': [1, 1, 2, 2],
+    'Fraction': [1, 2, 1, 2],
+    'Spectra_Filepath': ['f1.mzML', 'f2.mzML', 'f3.mzML', 'f4.mzML'],
+    'Label': [1, 1, 1, 1],
+    'Sample': [1, 1, 2, 2]
+})
+design = Py_ExperimentalDesign.from_dataframe(df)
+
 # Create from existing OpenMS objects
 from openms_python import Py_ConsensusMap
 consensus = Py_ConsensusMap.from_file("results.consensusXML")
diff --git a/openms_python/py_experimentaldesign.py b/openms_python/py_experimentaldesign.py
index d9e4871..0679757 100644
--- a/openms_python/py_experimentaldesign.py
+++ b/openms_python/py_experimentaldesign.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 from typing import Union, Optional, Set, TYPE_CHECKING
 
+import pandas as pd
 import pyopenms as oms
 
 from ._io_utils import ensure_allowed_suffix
@@ -256,6 +257,149 @@ def from_identifications(cls, protein_ids: list) -> "Py_ExperimentalDesign":
         design = oms.ExperimentalDesign.fromIdentifications(protein_ids)
         return cls(design)
 
+    @classmethod
+    def from_dataframe(cls, df: pd.DataFrame) -> "Py_ExperimentalDesign":
+        """Create an ExperimentalDesign from a pandas DataFrame.
+
+        Parameters
+        ----------
+        df:
+            DataFrame with columns: Fraction_Group, Fraction, Spectra_Filepath,
+            Label, Sample.
+
+        Returns
+        -------
+        Py_ExperimentalDesign
+            A new instance created from the DataFrame.
+
+        Raises
+        ------
+        ValueError
+            If required columns are missing from the DataFrame.
+
+        Example:
+            >>> import pandas as pd
+            >>> df = pd.DataFrame({
+            ...     'Fraction_Group': [1, 1, 2, 2],
+            ...     'Fraction': [1, 2, 1, 2],
+            ...     'Spectra_Filepath': ['f1.mzML', 'f2.mzML', 'f3.mzML', 'f4.mzML'],
+            ...     'Label': [1, 1, 1, 1],
+            ...     'Sample': [1, 1, 2, 2]
+            ... })
+            >>> design = Py_ExperimentalDesign.from_dataframe(df)
+        """
+        import tempfile
+
+        required_columns = {
+            "Fraction_Group",
+            "Fraction",
+            "Spectra_Filepath",
+            "Label",
+            "Sample",
+        }
+        missing = required_columns - set(df.columns)
+        if missing:
+            missing_str = ", ".join(sorted(missing))
+            raise ValueError(
+                f"DataFrame is missing required columns: {missing_str}. "
+                f"Required columns are: {', '.join(sorted(required_columns))}"
+            )
+
+        # Write DataFrame to a temporary TSV file and load it
+        # This ensures proper sample section setup by the OpenMS loader
+        with tempfile.NamedTemporaryFile(mode="w", suffix=".tsv", delete=False) as f:
+            # Write in the expected format
+            df.to_csv(f, sep="\t", index=False)
+            temp_path = f.name
+
+        try:
+            edf = oms.ExperimentalDesignFile()
+            design = edf.load(temp_path, False)
+            return cls(design)
+        finally:
+            Path(temp_path).unlink()
+
+    @classmethod
+    def from_df(cls, df: pd.DataFrame) -> "Py_ExperimentalDesign":
+        """Alias for :meth:`from_dataframe` matching :meth:`get_df`.
+
+        Parameters
+        ----------
+        df:
+            DataFrame with experimental design data.
+
+        Returns
+        -------
+        Py_ExperimentalDesign
+            A new instance created from the DataFrame.
+        """
+        return cls.from_dataframe(df)
+
+    def to_dataframe(self) -> pd.DataFrame:
+        """Convert the ExperimentalDesign to a pandas DataFrame.
+
+        Returns
+        -------
+        pd.DataFrame
+            DataFrame with columns: Fraction_Group, Fraction, Spectra_Filepath,
+            Label, Sample.
+
+        Example:
+            >>> design = Py_ExperimentalDesign.from_file("design.tsv")
+            >>> df = design.to_dataframe()
+        """
+        ms_files = self._design.getMSFileSection()
+
+        # Get sample IDs from the sample section
+        sample_section = self._design.getSampleSection()
+        sample_ids = sorted(sample_section.getSamples())
+        # Create index-to-id mapping (0-based index to actual sample ID)
+        index_to_sample_id = {}
+        for sample_id in sample_ids:
+            # Decode if bytes
+            if isinstance(sample_id, bytes):
+                sample_id_str = sample_id.decode()
+            else:
+                sample_id_str = str(sample_id)
+            # Try to convert to int if possible
+            try:
+                sample_id_value = int(sample_id_str)
+            except ValueError:
+                sample_id_value = sample_id_str
+            index_to_sample_id[len(index_to_sample_id)] = sample_id_value
+
+        data = {
+            "Fraction_Group": [],
+            "Fraction": [],
+            "Spectra_Filepath": [],
+            "Label": [],
+            "Sample": [],
+        }
+
+        for entry in ms_files:
+            data["Fraction_Group"].append(entry.fraction_group)
+            data["Fraction"].append(entry.fraction)
+            # Decode path if it's bytes
+            path = entry.path
+            if isinstance(path, bytes):
+                path = path.decode()
+            data["Spectra_Filepath"].append(path)
+            data["Label"].append(entry.label)
+            # Map 0-based index back to actual sample ID
+            data["Sample"].append(index_to_sample_id.get(entry.sample, entry.sample))
+
+        return pd.DataFrame(data)
+
+    def get_df(self) -> pd.DataFrame:
+        """Alias for :meth:`to_dataframe`.
+
+        Returns
+        -------
+        pd.DataFrame
+            DataFrame with experimental design data.
+        """
+        return self.to_dataframe()
+
     # ==================== Delegation ====================
 
     def __getattr__(self, name: str):
diff --git a/tests/test_py_experimentaldesign.py b/tests/test_py_experimentaldesign.py
index ab4a8d7..8ebe580 100644
--- a/tests/test_py_experimentaldesign.py
+++ b/tests/test_py_experimentaldesign.py
@@ -3,6 +3,7 @@
 from pathlib import Path
 import tempfile
 
+import pandas as pd
 import pytest
 import pyopenms as oms
 
@@ -231,3 +232,124 @@ def test_py_experimentaldesign_from_identifications():
 
     assert isinstance(design, Py_ExperimentalDesign)
     assert isinstance(design.native, oms.ExperimentalDesign)
+
+
+def test_py_experimentaldesign_from_dataframe():
+    """Test creating ExperimentalDesign from a pandas DataFrame."""
+    import pandas as pd
+
+    # Create a simple DataFrame
+    df = pd.DataFrame(
+        {
+            "Fraction_Group": [1, 1, 2, 2],
+            "Fraction": [1, 2, 1, 2],
+            "Spectra_Filepath": ["f1.mzML", "f2.mzML", "f3.mzML", "f4.mzML"],
+            "Label": [1, 1, 1, 1],
+            "Sample": [1, 1, 2, 2],
+        }
+    )
+
+    design = Py_ExperimentalDesign.from_dataframe(df)
+
+    assert isinstance(design, Py_ExperimentalDesign)
+    assert design.n_ms_files == 4
+    assert design.n_samples == 2
+    assert design.n_fraction_groups == 2
+
+
+def test_py_experimentaldesign_from_df_alias():
+    """Test that from_df is an alias for from_dataframe."""
+    import pandas as pd
+
+    df = pd.DataFrame(
+        {
+            "Fraction_Group": [1],
+            "Fraction": [1],
+            "Spectra_Filepath": ["test.mzML"],
+            "Label": [1],
+            "Sample": [1],
+        }
+    )
+
+    design1 = Py_ExperimentalDesign.from_dataframe(df)
+    design2 = Py_ExperimentalDesign.from_df(df)
+
+    assert design1.n_ms_files == design2.n_ms_files
+
+
+def test_py_experimentaldesign_from_dataframe_missing_columns():
+    """Test that from_dataframe raises error for missing columns."""
+    import pandas as pd
+
+    # Missing Sample column
+    df = pd.DataFrame(
+        {
+            "Fraction_Group": [1],
+            "Fraction": [1],
+            "Spectra_Filepath": ["test.mzML"],
+            "Label": [1],
+        }
+    )
+
+    with pytest.raises(ValueError, match="missing required columns"):
+        Py_ExperimentalDesign.from_dataframe(df)
+
+
+def test_py_experimentaldesign_to_dataframe():
+    """Test converting ExperimentalDesign to DataFrame."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+
+    df = design.to_dataframe()
+
+    assert isinstance(df, pd.DataFrame)
+    assert len(df) == 6
+    assert set(df.columns) == {
+        "Fraction_Group",
+        "Fraction",
+        "Spectra_Filepath",
+        "Label",
+        "Sample",
+    }
+    assert df["Sample"].nunique() == 2
+
+
+def test_py_experimentaldesign_get_df_alias():
+    """Test that get_df is an alias for to_dataframe."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+
+    df1 = design.to_dataframe()
+    df2 = design.get_df()
+
+    assert df1.equals(df2)
+
+
+def test_py_experimentaldesign_dataframe_roundtrip():
+    """Test that DataFrame roundtrip preserves data."""
+    import pandas as pd
+
+    # Create a DataFrame with specific data
+    original_df = pd.DataFrame(
+        {
+            "Fraction_Group": [1, 1, 2],
+            "Fraction": [1, 2, 1],
+            "Spectra_Filepath": ["a.mzML", "b.mzML", "c.mzML"],
+            "Label": [1, 1, 2],
+            "Sample": [1, 1, 2],
+        }
+    )
+
+    # Create design from DataFrame
+    design = Py_ExperimentalDesign.from_dataframe(original_df)
+
+    # Convert back to DataFrame
+    result_df = design.to_dataframe()
+
+    # Check that data is preserved
+    assert len(result_df) == len(original_df)
+    assert result_df["Fraction_Group"].tolist() == original_df["Fraction_Group"].tolist()
+    assert result_df["Fraction"].tolist() == original_df["Fraction"].tolist()
+    assert result_df["Spectra_Filepath"].tolist() == original_df["Spectra_Filepath"].tolist()
+    assert result_df["Label"].tolist() == original_df["Label"].tolist()
+    assert result_df["Sample"].tolist() == original_df["Sample"].tolist()

From f9cb0dc0bf0ae55a64ec68064ee8d47d61787bdd Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 19 Nov 2025 11:16:30 +0000
Subject: [PATCH 5/5] Implement store() method for Py_ExperimentalDesign

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
---
 README.md                              |  3 ++
 openms_python/py_experimentaldesign.py | 20 ++++++------
 tests/test_py_experimentaldesign.py    | 42 +++++++++++++++++++++++---
 3 files changed, 50 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index b85f209..1a2ecb8 100644
--- a/README.md
+++ b/README.md
@@ -230,6 +230,9 @@ df = pd.DataFrame({
 })
 design = Py_ExperimentalDesign.from_dataframe(df)
 
+# Store to file
+design.store("output_design.tsv")
+
 # Create from existing OpenMS objects
 from openms_python import Py_ConsensusMap
 consensus = Py_ConsensusMap.from_file("results.consensusXML")
diff --git a/openms_python/py_experimentaldesign.py b/openms_python/py_experimentaldesign.py
index 0679757..ce399c8 100644
--- a/openms_python/py_experimentaldesign.py
+++ b/openms_python/py_experimentaldesign.py
@@ -80,10 +80,10 @@ def load(self, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
         return self
 
     def store(self, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
-        """Store the experimental design to disk.
+        """Store the experimental design to disk as a TSV file.
 
-        Note: Storage functionality is not available in the current pyOpenMS API.
-        This method is provided for API consistency but will raise NotImplementedError.
+        The design is converted to a DataFrame and written in the format
+        expected by OpenMS ExperimentalDesignFile.
 
         Parameters
         ----------
@@ -95,16 +95,14 @@ def store(self, filepath: Union[str, Path]) -> "Py_ExperimentalDesign":
         Py_ExperimentalDesign
             Self for method chaining.
 
-        Raises
-        ------
-        NotImplementedError
-            Storage is not yet implemented in pyOpenMS.
+        Example:
+            >>> design = Py_ExperimentalDesign.from_file("input.tsv")
+            >>> design.store("output.tsv")
         """
         ensure_allowed_suffix(filepath, EXPERIMENTAL_DESIGN_EXTENSIONS, "ExperimentalDesign")
-        raise NotImplementedError(
-            "ExperimentalDesign storage is not yet available in pyOpenMS. "
-            "Please use the native pyOpenMS API if this functionality is needed."
-        )
+        df = self.to_dataframe()
+        df.to_csv(str(filepath), sep="\t", index=False)
+        return self
 
     @property
     def native(self) -> oms.ExperimentalDesign:
diff --git a/tests/test_py_experimentaldesign.py b/tests/test_py_experimentaldesign.py
index 8ebe580..623daeb 100644
--- a/tests/test_py_experimentaldesign.py
+++ b/tests/test_py_experimentaldesign.py
@@ -128,8 +128,8 @@ def test_py_experimentaldesign_invalid_extension():
         Path(temp_path).unlink()
 
 
-def test_py_experimentaldesign_store_not_implemented():
-    """Test that store method raises NotImplementedError."""
+def test_py_experimentaldesign_store_roundtrip():
+    """Test that store method works and roundtrips correctly."""
     example_path = get_example("experimental_design.tsv")
     design = Py_ExperimentalDesign.from_file(example_path)
 
@@ -137,10 +137,44 @@ def test_py_experimentaldesign_store_not_implemented():
         temp_path = f.name
 
     try:
-        with pytest.raises(NotImplementedError, match="not yet available"):
+        # Store the design
+        result = design.store(temp_path)
+        assert result is design  # Check method chaining
+
+        # Verify file was created
+        assert Path(temp_path).exists()
+
+        # Load it back and verify
+        design2 = Py_ExperimentalDesign.from_file(temp_path)
+        assert design2.n_samples == design.n_samples
+        assert design2.n_ms_files == design.n_ms_files
+        assert design2.n_fractions == design.n_fractions
+        assert design2.n_fraction_groups == design.n_fraction_groups
+        assert design2.n_labels == design.n_labels
+
+        # Verify DataFrame content matches
+        df1 = design.to_dataframe()
+        df2 = design2.to_dataframe()
+        assert df1.equals(df2)
+    finally:
+        if Path(temp_path).exists():
+            Path(temp_path).unlink()
+
+
+def test_py_experimentaldesign_store_invalid_extension():
+    """Test that store rejects invalid file extensions."""
+    example_path = get_example("experimental_design.tsv")
+    design = Py_ExperimentalDesign.from_file(example_path)
+
+    with tempfile.NamedTemporaryFile(suffix=".txt", delete=False) as f:
+        temp_path = f.name
+
+    try:
+        with pytest.raises(ValueError, match="ExperimentalDesign"):
             design.store(temp_path)
     finally:
-        Path(temp_path).unlink()
+        if Path(temp_path).exists():
+            Path(temp_path).unlink()
 
 
 def test_py_experimentaldesign_delegation():