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What's New in PyReduce 0.8 ?

Unified Trace Data Model

The Trace dataclass now holds all trace-related data in one place: position polynomial, slit curvature, and wavelength calibration. Pipeline steps update traces in-place as they run, eliminating separate .curve.npz and .wavecal.npz files. All trace data is saved to a single .traces.fits file.

See docs/redesign.md for a full summary of all architectural changes in 0.7/0.8.

New Spectra Format

Extracted spectra use a new per-trace FITS format with NaN masking, replacing the legacy Echelle class. Each spectrum row includes order number, group ID, and extraction metadata.

See docs/output_formats.md for the file format specification.

What's New in PyReduce 0.7 ?

Multi-Fiber Instrument Support

New fibers configuration in instrument YAML for IFU and multi-fiber spectrographs:

  • Named groups: Define fiber ranges (e.g., science A/B, calibration) with merge strategies
  • Bundle patterns: For repeating fiber bundles (e.g., 7 fibers per IFU target)
  • Per-order grouping: For echelle instruments with fiber groups repeated across orders
  • Missing fiber handling: bundle_centers_file assigns traces by proximity when fibers are broken
  • Per-step trace selection (science: [A, B], wavecal: [cal], etc.)

See docs/fiber_bundle_tracing.md for details.

New Instruments

  • MOSAIC (ELT) with multi-fiber bundle support, VIS quadrants (VIS1-VIS4)
  • ANDES_YJH with multi-channel support
  • NEID with multi-amplifier support

See docs/instruments.md for the full list.

Configuration Changes

  • Instrument configs now use YAML (validated by Pydantic)
  • Files reorganized into instruments/{NAME}/ directories
  • Settings cascade: defaults → instrument → runtime overrides
  • Per-channel settings: settings_{channel}.json for channel-specific parameters

See docs/configuration_file.md for details.

Terminology Changes

  • mode → channel (e.g., mode="middle" is now channel="middle")
  • orders step → trace step
  • OrderTracing class → Trace, output .orders.npz → .traces.npz
  • extraction_width → extraction_height
  • Output files: .ech → .fits
  • Mask convention: Now uses numpy standard (1=bad, 0=good)

Plotting

  • PYREDUCE_PLOT_DIR saves plots as PNG files
  • PYREDUCE_PLOT_SHOW=defer accumulates plots for batch viewing
  • Extraction animation with pause/step controls and residual panel
  • Trace overlay on calibration plots

New Pipeline API

from pyreduce.pipeline import Pipeline

result = Pipeline.from_instrument(
    instrument="UVES",
    target="HD132205",
    steps=("bias", "flat", "trace", "science"),
).run()

The old pyreduce.reduce.main() still works but shows a deprecation warning. See docs/examples.md for more.

New CLI

The old argparse CLI is replaced with a cleaner Click-based interface. See docs/cli.md for the full reference.

Extraction Improvements

  • Preset slit function: In some occasions it is useful to extract with a fixed slit function (e.g. from norm_flat step) for single-pass extraction (faster, more robust for faint sources)
  • Per-trace extraction heights: Stored in traces file, computed automatically for fiber bundles
  • Convergence based on spectrum change, outlier rejection improved.

Installation & Build

  • Now uses uv package manager (uv sync, uv run reduce ...), but pip install pyreduce-astro still works
  • Python 3.13+ required
  • Build system migrated from setuptools to Hatchling

See docs/installation.md for details.