Add chromatogram support

[Copilot]

Adds native support for chromatograms (XIC, TIC, etc.) with a Pythonic interface matching the existing spectrum functionality.

Changes

• New Py_MSChromatogram wrapper (openms_python/py_chromatogram.py)

  • Properties: mz, name, rt, intensity, rt_range, total_ion_current
  • DataFrame conversion: from_dataframe(), to_dataframe()
  • Filtering: filter_by_rt(), filter_by_intensity()
  • Normalization: normalize_intensity(), normalize_to_tic()
  • Dictionary-style metadata access via MetaInfoMappingMixin

• MSExperiment integration (openms_python/py_msexperiment.py)

  • Added chromatogram_count property
  • Added get_chromatogram(index) and chromatograms() iterator
  • Added add_chromatogram() method
  • Updated __repr__() to include chromatogram count

• Documentation (README.md)

  • Added "Working with Chromatograms" section
  • Updated API reference and comparison table

Example Usage

from openms_python import Py_MSExperiment, Py_MSChromatogram
import pandas as pd

# Load experiment with chromatograms
exp = Py_MSExperiment.from_file('data.mzML')
print(f"Chromatograms: {exp.chromatogram_count}")

# Iterate over chromatograms
for chrom in exp.chromatograms():
    print(f"MZ: {chrom.mz:.4f}, Points: {len(chrom)}")

# Create from DataFrame
df = pd.DataFrame({'rt': [10.0, 20.0, 30.0], 'intensity': [1000.0, 5000.0, 3000.0]})
chrom = Py_MSChromatogram.from_dataframe(df, mz=445.12, name="XIC m/z 445.12")

# Filter and normalize
filtered = chrom.filter_by_rt(15.0, 25.0)
normalized = filtered.normalize_to_tic()

# Add to experiment
exp.add_chromatogram(chrom)

Testing

• 22 new tests added (15 for Py_MSChromatogram, 7 for MSExperiment integration)
• All 99 tests pass with 86% overall coverage
• No security vulnerabilities (CodeQL)

Original prompt

Add chromatogram support

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