Release v0.8a2

Changelog

[0.8a2] - 2026-02-03

Added

• Trace dataclass (trace_model.py) for unified trace data model
• Spectrum/Spectra classes (spectra.py) replacing legacy Echelle format
• Trace.wlen(x) method to evaluate wavelength polynomial
• Per-group wavelength calibration support
• LFC wavecal support for ANDES_RIZ
• docs/output_formats.md documenting new file formats

Changed

• All pipeline steps use list[Trace] interface instead of array-based
• extract() takes list[Trace], returns list[Spectrum]
• Renamed nord/iord to ntrace/idx for clarity
• Renamed Trace.fiber to Trace.group, added fiber_idx for per-fiber wavecal
• File format: traces.npz -> traces.fits (unified FITS format)
• Wavelength calibration stored in traces.fits instead of separate wavecal.npz
• Spectra use NaN masking instead of COLUMNS+MASK redundancy

Removed

• curvature_model.py (curvature now stored in Trace)
• echelle.py functionality (deprecated, use spectra.py)
• Dead code from util.py

[0.8a1] - 2026-02-03

Added

• Charslit extraction backend with degree 1-5 curvature support
• ANDES_RIZ instrument configuration and settings
• trace_by config for separate tracing of illumination groups
• HDF-to-wavecal tool and reference files for ANDES_RIZ
• ANDES spectra plotting tool

Changed

• Curvature: use literal pixel extraction_height, not fractional
• Simplify extraction_height to single full-height value
• Move fiber selection default from hardcoded to config
• Update METIS_IFU for dynamic wavelength-based channels
• Use git URL for charslit optional dependency

Removed

• PEP 723 inline metadata from examples (caused confusion with uv run)

Fixed

• Fix curve_height to use new full-height format in plot_comparison
• Fix extraction_height to give exactly N rows
• Fix CRIRES_PLUS docstring (was incorrectly HARPS)

[0.7] - 2026-01-25

First stable release of the 0.7 series!

Changed

• Rename OrderTracing class to Trace, save file from .orders.npz to .traces.npz
• Store per-trace extraction heights in traces.npz
• Compute extraction heights for fiber bundles automatically
• CLI: consistent -t/--target option across all commands
• Allow explicit paths in settings __inherits__ directive

Fixed

• Limit trace overlay to column_range in science step plot

Documentation

• Add WhatsNew.md summarizing 0.7 series improvements
• Update docs for traces.npz rename and mask convention

[0.7b4] - 2026-01-22

Added

• Per-channel settings support via settings_{channel}.json files
• Fiber grouping configuration for multi-fiber instruments (bundle_centers, fiber_groups)
• preset_slitfunc parameter for single-pass extraction using pre-computed slit function
• noise_relative parameter for trace threshold scaling
• extraction_reject threshold parameter for outlier rejection
• ANDES_YJH instrument with multi-channel support
• MOSAIC VIS quadrant support (VIS1-VIS4 channels) and NIR settings
• HARPN fiber B wavecal file
• Extraction residual panel in ProgressPlot
• tools/plot_swath_debug.py for analyzing extraction debug data

Changed

• Mask convention: Switch to numpy convention (True/1=bad) on Python side; C code uses inverted (1=good)
• Extraction convergence now based on spectrum change with global RMS for rejection
• Improved outlier rejection using 6*sigma instead of MAD in 2D extraction
• Norm_flat step saves slit function with metadata for reuse
• Refactor Pipeline trace API: add trace_raw() and organize() methods
• Remove extraction_cutoff parameter (dead code)

Fixed

• smooth_spectrum normalization (port from cr2res)
• Masked array handling in swath debug plotting
• Minimum 4 iterations enforced in curved extraction

[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....

Release v0.8a1

Changelog

[0.8a1] - 2026-02-03

Added

• Charslit extraction backend with degree 1-5 curvature support
• ANDES_RIZ instrument configuration and settings
• trace_by config for separate tracing of illumination groups
• HDF-to-wavecal tool and reference files for ANDES_RIZ
• ANDES spectra plotting tool

Changed

• Curvature: use literal pixel extraction_height, not fractional
• Simplify extraction_height to single full-height value
• Move fiber selection default from hardcoded to config
• Update METIS_IFU for dynamic wavelength-based channels
• Use git URL for charslit optional dependency

Removed

• PEP 723 inline metadata from examples (caused confusion with uv run)

Fixed

• Fix curve_height to use new full-height format in plot_comparison
• Fix extraction_height to give exactly N rows
• Fix CRIRES_PLUS docstring (was incorrectly HARPS)

[0.7] - 2026-01-25

First stable release of the 0.7 series!

Changed

• Rename OrderTracing class to Trace, save file from .orders.npz to .traces.npz
• Store per-trace extraction heights in traces.npz
• Compute extraction heights for fiber bundles automatically
• CLI: consistent -t/--target option across all commands
• Allow explicit paths in settings __inherits__ directive

Fixed

• Limit trace overlay to column_range in science step plot

Documentation

• Add WhatsNew.md summarizing 0.7 series improvements
• Update docs for traces.npz rename and mask convention

[0.7b4] - 2026-01-22

Added

• Per-channel settings support via settings_{channel}.json files
• Fiber grouping configuration for multi-fiber instruments (bundle_centers, fiber_groups)
• preset_slitfunc parameter for single-pass extraction using pre-computed slit function
• noise_relative parameter for trace threshold scaling
• extraction_reject threshold parameter for outlier rejection
• ANDES_YJH instrument with multi-channel support
• MOSAIC VIS quadrant support (VIS1-VIS4 channels) and NIR settings
• HARPN fiber B wavecal file
• Extraction residual panel in ProgressPlot
• tools/plot_swath_debug.py for analyzing extraction debug data

Changed

• Mask convention: Switch to numpy convention (True/1=bad) on Python side; C code uses inverted (1=good)
• Extraction convergence now based on spectrum change with global RMS for rejection
• Improved outlier rejection using 6*sigma instead of MAD in 2D extraction
• Norm_flat step saves slit function with metadata for reuse
• Refactor Pipeline trace API: add trace_raw() and organize() methods
• Remove extraction_cutoff parameter (dead code)

Fixed

• smooth_spectrum normalization (port from cr2res)
• Masked array handling in swath debug plotting
• Minimum 4 iterations enforced in curved extraction

[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...

Release v0.7

Changelog

[0.7] - 2026-01-25

First stable release of the 0.7 series!

Changed

• Rename OrderTracing class to Trace, save file from .orders.npz to .traces.npz
• Store per-trace extraction heights in traces.npz
• Compute extraction heights for fiber bundles automatically
• CLI: consistent -t/--target option across all commands
• Allow explicit paths in settings __inherits__ directive

Fixed

• Limit trace overlay to column_range in science step plot

Documentation

• Add WhatsNew.md summarizing 0.7 series improvements
• Update docs for traces.npz rename and mask convention

[0.7b4] - 2026-01-22

Added

• Per-channel settings support via settings_{channel}.json files
• Fiber grouping configuration for multi-fiber instruments (bundle_centers, fiber_groups)
• preset_slitfunc parameter for single-pass extraction using pre-computed slit function
• noise_relative parameter for trace threshold scaling
• extraction_reject threshold parameter for outlier rejection
• ANDES_YJH instrument with multi-channel support
• MOSAIC VIS quadrant support (VIS1-VIS4 channels) and NIR settings
• HARPN fiber B wavecal file
• Extraction residual panel in ProgressPlot
• tools/plot_swath_debug.py for analyzing extraction debug data

Changed

• Mask convention: Switch to numpy convention (True/1=bad) on Python side; C code uses inverted (1=good)
• Extraction convergence now based on spectrum change with global RMS for rejection
• Improved outlier rejection using 6*sigma instead of MAD in 2D extraction
• Norm_flat step saves slit function with metadata for reuse
• Refactor Pipeline trace API: add trace_raw() and organize() methods
• Remove extraction_cutoff parameter (dead code)

Fixed

• smooth_spectrum normalization (port from cr2res)
• Masked array handling in swath debug plotting
• Minimum 4 iterations enforced in curved extraction

[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

Release v0.7b4

Changelog

[0.7b4] - 2026-01-22

Added

• Per-channel settings support via settings_{channel}.json files
• Fiber grouping configuration for multi-fiber instruments (bundle_centers, fiber_groups)
• preset_slitfunc parameter for single-pass extraction using pre-computed slit function
• noise_relative parameter for trace threshold scaling
• extraction_reject threshold parameter for outlier rejection
• ANDES_YJH instrument with multi-channel support
• MOSAIC VIS quadrant support (VIS1-VIS4 channels) and NIR settings
• HARPN fiber B wavecal file
• Extraction residual panel in ProgressPlot
• tools/plot_swath_debug.py for analyzing extraction debug data

Changed

• Mask convention: Switch to numpy convention (True/1=bad) on Python side; C code uses inverted (1=good)
• Extraction convergence now based on spectrum change with global RMS for rejection
• Improved outlier rejection using 6*sigma instead of MAD in 2D extraction
• Norm_flat step saves slit function with metadata for reuse
• Refactor Pipeline trace API: add trace_raw() and organize() methods
• Remove extraction_cutoff parameter (dead code)

Fixed

• smooth_spectrum normalization (port from cr2res)
• Masked array handling in swath debug plotting
• Minimum 4 iterations enforced in curved extraction

[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

Release v0.7b3

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

Release v0.7b2

Changelog

[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

Release v0.7b1

Changelog

[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

Release v0.7a7

Changelog

[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

Release v0.7a6

Changelog

[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

Release v0.7a5

Changelog

[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