Implement store() method for Py_ExperimentalDesign

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

Author: Copilot

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")

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:

tests/test_py_experimentaldesign.py

@@ -128,19 +128,53 @@ 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)
 
     with tempfile.NamedTemporaryFile(suffix=".tsv", delete=False) as f:
         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():