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@github-actions github-actions released this 11 Jan 12:47
· 181 commits to master since this release
v0.7b3
195f9e8

Changelog

[0.7b3] - 2026-01-11

Added

  • MOSAIC instrument support with fiber group detection and curvature step
  • Extraction animation controls: pause/step buttons and speed control (PYREDUCE_PLOT_ANIMATION_SPEED)
  • --plot-dir and --plot-show CLI options for flexible plot output

Changed

  • Rename orders to traces in rectify and slit_curve modules for consistency
  • Downgrade extraction max-iterations message from ERROR to WARNING
  • Only warn about missing files for steps that are actually requested

Fixed

  • Handle channel mismatch gracefully in CLI
  • Curvature plotting index error when peaks need int casting

[0.7b2] - 2026-01-09

Changed

  • Reorganize instrument files: All instrument-related files now in per-instrument directories
    • instruments/{name}.py → instruments/{NAME}/__init__.py
    • instruments/{name}.yaml → instruments/{NAME}/config.yaml
    • settings/settings_{NAME}.json → instruments/{NAME}/settings.json
    • wavecal/{name}_*.npz → instruments/{NAME}/wavecal_*.npz
    • masks/mask_{name}_*.fits.gz → instruments/{NAME}/mask_*.fits.gz
  • Base settings and schema moved to instruments/defaults/
  • Wavelength atlas files moved to instruments/defaults/atlas/

Removed

  • Orphan mask files for undefined instruments (elodie, sarg, hds, etc.)

[0.7b1] - 2026-01-06

Changed

  • Curvature algorithm rewrite: Replace 2D model fitting with row-tracking method for better robustness
  • Rename make_shear.py to slit_curve.py
  • Rename curvature coefficients: tilt/shear → p1/p2 throughout codebase
  • Rename arc_extraction to simple_extraction
  • Split curvature extraction_height into separate extraction_height and curve_height parameters
  • Save file renamed from .shear.npz to .curve.npz

Added

  • discover_channels() for automatic channel detection from data files
  • CLI: --target is now optional; loops over all targets if not specified
  • CLI: Uses $REDUCE_DATA for base_dir, reads default input_dir from config
  • Comprehensive CLI test coverage

Fixed

  • Curvature step index error when traces are removed during processing
  • Validate base_dir and input_dir exist with clear error messages
  • File sorting to correctly loop over all nights when not specified
  • CLI dynamic dependency loading for step commands

[0.7a7] - 2026-01-04

Added

  • --settings option for CLI to override reduction parameters from JSON file

Changed

  • Rename extraction_width to extraction_height in settings (clarifies coordinate system)
  • Rename orders to traces in extract.py internal API

[0.7a6] - 2026-01-03

Added

  • --file option for CLI step commands to bypass file discovery
  • NEID instrument with multi-amplifier support

Changed

  • Rename orders step to trace throughout codebase (CLI, API, configs)

Fixed

  • test_normflat to use column_range returned by extract

[0.7a5] - 2025-12-30

Changed

  • Rename arm to channel throughout codebase (API, CLI, configs)
  • Remove decker from CRIRES+ channel format (J1228_det1 instead of J1228_Open_det1)
  • Example scripts now use $REDUCE_DATA env var instead of hardcoded paths

[0.7a4] - 2025-12-23

Added

  • reduce examples --run flag to download and execute examples directly
  • PEP 723 inline metadata in examples for uv run compatibility

[0.7a3] - 2025-12-23

Added

  • reduce examples command to list/download examples from GitHub matching installed version

Changed

  • CLI startup 12x faster via lazy imports (1.2s -> 0.1s)

[0.7a2] - 2025-12-23

Added

  • Manual API calls documentation (manual_calls.md)

Fixed

  • ReadTheDocs build failing due to missing myst_parser
  • Trace module reference in documentation

Changed

  • Docs Makefile now uses uv
  • pyproject.toml cleanup

[0.7a1] - 2025-12-22

Added

  • New Pipeline API with Pipeline.from_instrument() for simplified usage
  • Click-based CLI replacing argparse (uv run reduce run UVES HD132205)
  • Pydantic models for instrument configuration validation
  • YAML instrument configs replacing JSON
  • IPython startup script for interactive development
  • plot_dir option to save plots as PNG files
  • Fiber bundle tracing support for multi-fiber instruments
  • filter_x and filter_type options for order tracing

Changed

  • Rename mode to channel terminology throughout
  • Output extension changed from .ech to .fits
  • Documentation converted from RST to Markdown
  • Trace detection parameters renamed (opower -> degree, filter_size -> filter_y)

Fixed

  • Plotting issues with non-finite values
  • Use interpolate_replace_nans for masked pixels

[0.6.0] - 2025-12-22

Added

  • JSON schema validation test for instrument configurations
  • GitHub workflow creates GitHub Release on tag push

Fixed

  • Fix test_wavecal to match WavelengthCalibration.execute() signature
  • Fix spec fixture to match ScienceExtraction.run() signature
  • Fix instrument schema: replace invalid 'value' keyword with standard JSON Schema 'type'

[0.6.0b5] - 2025-10-04

Fixed

  • Include *.pyd files for Windows builds
  • Remove redundant build test from workflow

[0.6.0b4] - 2025-10-03

Changed

  • workflow builds multi-arch wheels
  • minor fixes to make build pass

[0.6.0b3] - 2025-10-02

Added

  • Test organization with pytest markers (unit, instrument, slow, downloads)
  • ANDES instrument configuration and settings

Changed

  • CI now runs fast tests (~7s) on every push to master
  • Test suite optimized with slow marker for tests >3s

Fixed

  • ANDES instrument configuration errors (missing decker fields, regex pattern)
  • NIRSPEC FITS header errors with illegal keywords containing dots
  • Pre-commit hooks now documented and working correctly

[0.6.0b2] - 2025-10-02

Changed

  • lazy imports
  • cosmetic fixes like version string

[0.6.0b1] - 2025-10-02

Changed

  • Modern build system using uv package manager
  • Minimum Python version now 3.11, default 3.13
  • Migrated build system from setuptools to Hatchling (PEP 517)
  • Replaced black, isort, flake8, and pyupgrade with Ruff
  • Improved code formatting across entire codebase using Ruff
  • Modernized GitHub Actions workflow (uv-based, Python 3.11-3.13 matrix)
  • Updated documentation to reflect modern installation with uv
  • Consolidated legacy build files (setup.py, requirements.txt) into pyproject.toml
  • Removed automatic PyPI publishing from GitHub Actions (now manual)
  • GitHub Actions tests now manual-only on master branch
  • Modernized ReadTheDocs build configuration

Fixed

  • Close FITS file handles after reading to prevent resource leaks (#28)
  • Store wavelength calibration in double precision instead of single (#30)
  • Add fallback value for E_ORIENT header keyword (#31)
  • Return final wavelength linelist with flags from calibration (#33)
  • Fix MaskedArray filling in normflat routine
  • Fix undefined TypeFilter import in NEID instrument
  • Fix Sphinx documentation build warnings
  • Fix pre-commit hook configuration issues

Documentation

  • Updated README badges for GitHub Actions and Python versions
  • Updated installation instructions to use uv instead of pip
  • Improved documentation build process
  • CLAUDE.md / AGENTS.md for AI-assisted development guidance
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