Add Py_ExperimentalDesign wrapper with pandas DataFrame and file storage support

[Copilot]

Adds Pythonic wrapper for OpenMS ExperimentalDesign to support multi-sample, fractionated experiment metadata management with pandas DataFrame integration and file storage capabilities.

Implementation

• Py_ExperimentalDesign class with properties: n_samples, n_ms_files, n_fractions, n_fraction_groups, n_labels, is_fractionated, samples
• Factory methods: from_file(), from_consensus_map(), from_feature_map(), from_identifications(), from_dataframe(), from_df()
• DataFrame methods: to_dataframe(), get_df() for seamless pandas integration
• Storage method: store() writes experimental designs to TSV files with full roundtrip support
• Example file: experimental_design.tsv with 2-sample, 3-fraction fractionated design
• Test suite: 21 tests covering load, store, properties, factory methods, DataFrame operations, edge cases
• README section: Documentation and usage examples following idperformance pattern

Usage

from openms_python import Py_ExperimentalDesign
import pandas as pd

# Load from file
design = Py_ExperimentalDesign.from_file("design.tsv")
print(f"Samples: {design.n_samples}, Fractionated: {design.is_fractionated}")

# Create from 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)

# Convert to DataFrame for analysis
df = design.to_dataframe()

# Store to file
design.store("output_design.tsv")

# Create from existing objects
from openms_python import Py_ConsensusMap
consensus = Py_ConsensusMap.from_file("results.consensusXML")
design = Py_ExperimentalDesign.from_consensus_map(consensus)
design.print_summary()

Original prompt

Add support for experimentaldesign test and add to readme

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[timosachsenberg]

@copilot From a Pandas dataframe would be great

[Copilot]

@copilot From a Pandas dataframe would be great

Added DataFrame support with from_dataframe(), from_df(), to_dataframe(), and get_df() methods. You can now create experimental designs from pandas DataFrames and convert them back for analysis. See commit e783d35.

[timosachsenberg]

@copilot also implement store

[timosachsenberg]

@copilot do it! Julianus!!!

[Copilot]

@copilot also implement store

Implemented store() method that writes experimental designs to TSV files with full roundtrip support. See commit f9cb0dc.

@copilot do it! Julianus!!!

Done! The store() method is now implemented. You can save experimental designs to TSV files and reload them perfectly. See commit f9cb0dc.