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# CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
## Project Overview
Specreduce is an Astropy coordinated package providing Python utilities for reducing and calibrating spectroscopic data. It offers modular, composable building blocks for spectral reduction workflows.
## Common Commands
### Testing
```bash
# Run all tests via tox
tox -e py314-test
# Run tests with coverage
pytest --pyargs specreduce docs --cov specreduce --cov-config=pyproject.toml
# Run a specific test file
pytest specreduce/tests/test_background.py -v
# Run tests with all optional dependencies
tox -e py314-test-alldeps-cov
```
### Code Style
```bash
# Check code style
tox -e codestyle
# Direct flake8
flake8 specreduce --count --extend-ignore E203
```
### Documentation
```bash
# Build HTML docs
cd docs && make html
# Or with sphinx directly
sphinx-build -b html docs docs/_build/html
```
### Development Setup
```bash
pip install -e ".[test,docs,all]"
```
## Architecture
The reduction workflow follows a modular pipeline: **Trace → Background → Extract → Wavelength Calibration → Flux Calibration**
### Core Modules
- **core.py**: Base class `SpecreduceOperation` and `_ImageParser` for image format coercion. Handles Spectrum1D, CCDData, NDData, Quantity, and ndarray inputs. Defines `MaskingOption` enum and masking strategies.
- **tracing.py**: Trace determination classes
- `Trace`: Base trace (center of image)
- `FlatTrace`: Constant position trace
- `ArrayTrace`: Custom trace from array
- `FitTrace`: Fit trace to image features using peak detection (median, gaussian, centroid methods)
- **background.py**: `Background` class with `two_sided()` and `one_sided()` methods for background estimation. Supports multiple traces and custom aperture definitions.
- **extract.py**: 1D spectrum extraction
- `BoxcarExtract`: Simple aperture extraction
- `HorneExtract`/`OptimalExtract`: Optimal extraction with spatial profile fitting and variance propagation
- **wavecal1d.py**: Current wavelength calibration implementation using `WavelengthCalibration1D`. Supports automated line matching, template matching, and produces GWCS-based WCS objects.
- **wavelength_calibration.py**: Legacy wavelength calibration (deprecated in v1.7.0, removal in v2.0)
- **fluxcal.py**: `FluxCalibration` class for flux calibration with magnitude-to-flux conversion and airmass extinction correction
- **calibration_data.py**: Spectrophotometric standards and line lists
- **utils/synth_data.py**: Synthetic spectroscopic data generation for testing
- **compat.py**: Compatibility layer for specutils v1.x and v2.x
### Key Design Patterns
1. **Image Format Flexibility**: All operations accept multiple input formats via `_ImageParser`
2. **Masking Strategies**: Seven masking options defined in `MaskingOption` enum
3. **Astropy Integration**: Uses Astropy models, units, and conventions throughout
4. **GWCS Support**: Wavelength calibration produces proper WCS objects
## Dependencies
- Python ≥3.11
- Core: numpy≥1.24, astropy≥5.3, scipy≥1.10, specutils≥1.9.1, matplotlib≥3.10, gwcs
- Optional: photutils≥1.0 (stellar profile fitting), synphot (synthetic photometry)
## Code Style
- Line length: 100 characters (flake8 and black)
- Black formatter targeting Python 3.11+
- Ignore E203 (whitespace before ':')
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