pyreduce-astro 0.7b4__tar.gz → 0.8a2__tar.gz

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/.gitignore

@@ -23,3 +23,5 @@ idl/
 logs/
 *.ipynb
 tmp/*
+.obsidian/
+uv.toml

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/CHANGELOG.md

@@ -1,6 +1,72 @@
 # 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

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/CLAUDE.md

@@ -19,7 +19,7 @@ uv run reduce download UVES
 PYREDUCE_PLOT=0 uv run python examples/uves_example.py
 
 # Or use CLI
-uv run reduce run UVES HD132205 --steps bias,flat,trace,science
+uv run reduce run UVES -t HD132205 --steps bias,flat,trace,science
 ```
 
 ## Package Structure
@@ -31,10 +31,11 @@ pyreduce/
 ├── reduce.py            # Step class implementations
 ├── configuration.py     # Config loading (settings JSON)
 ├── extract.py           # Optimal extraction algorithm
+├── trace_model.py       # Trace dataclass (geometry, curvature, wavelength)
+├── spectra.py           # Spectrum/Spectra classes for I/O
 ├── trace.py             # Order detection and tracing
 ├── wavelength_calibration.py  # Wavelength solution fitting
 ├── combine_frames.py    # Frame combination/calibration
-├── echelle.py           # Echelle spectrum I/O
 ├── util.py              # Utilities, plotting helpers
 ├── cwrappers.py         # CFFI C extension wrappers
 │
@@ -68,7 +69,20 @@ This means:
 - **Columns (x)** = wavelength/dispersion direction
 - **Rows (y)** = spatial/cross-dispersion direction
 - **Traces** are polynomial functions of x, giving y-position
-- **`extraction_height`** refers to pixels above/below each trace (in y)
+- **`extraction_height`** is the extraction aperture size (fraction of order separation, or pixels if >1.5)
+
+## Spectral Order Numbers (Trace.m)
+
+Each `Trace` has an `m` attribute representing the physical spectral (diffraction) order number - not a sequential index. Higher order numbers = shorter wavelengths.
+
+**Assignment priority:**
+1. `order_centers_{channel}.yaml` in instrument directory - traces matched by y-position during detection
+2. `obase` from linelist file (`wavecal_*.npz`) - assigned as `m = obase + trace_index` during wavecal
+3. Sequential fallback (legacy/MOSAIC mode)
+
+**Why it matters:** The 2D wavelength polynomial fits `wavelength = P(x, m)`. Using physical order numbers enables accurate interpolation between orders. `Trace.wlen(x)` evaluates this polynomial at the trace's order number.
+
+See `docs/wavecal_linelist.md` for details on wavelength calibration and order numbering.
 
 ## Pipeline Steps
 
@@ -79,8 +93,8 @@ The reduction pipeline consists of these steps (in typical order):
 | `mask` | `Mask` | Load bad pixel mask for detector |
 | `bias` | `Bias` | Combine bias frames into master bias |
 | `flat` | `Flat` | Combine flat frames, subtract bias |
-| `trace` | `OrderTracing` | Trace echelle order positions on flat |
-| `curvature` | `SlitCurvatureDetermination` | Measure slit curvature from arc lamp |
+| `trace` | `Trace` | Trace echelle order positions on flat |
+| `curvature` | `SlitCurvatureDetermination` | Measure slit curvature (polynomial degree 1-5) |
 | `scatter` | `BackgroundScatter` | Model inter-order scattered light |
 | `norm_flat` | `NormalizeFlatField` | Normalize flat, extract blaze function |
 | `wavecal_master` | `WavelengthCalibrationMaster` | Extract wavelength calibration spectrum |
@@ -237,12 +251,12 @@ pyreduce.reduce.main(
 
 ```bash
 # Full pipeline
-uv run reduce run UVES HD132205 --steps bias,flat,trace
+uv run reduce run UVES -t HD132205 --steps bias,flat,trace
 
 # Individual steps (top-level commands)
-uv run reduce bias UVES HD132205
-uv run reduce trace UVES HD132205
-uv run reduce wavecal UVES HD132205
+uv run reduce bias UVES -t HD132205
+uv run reduce trace UVES -t HD132205
+uv run reduce wavecal UVES -t HD132205
 
 # Combine reduced spectra
 uv run reduce combine --output combined.fits *.final.fits
@@ -261,15 +275,21 @@ uv run reduce list-steps
 - `PYREDUCE_PLOT_DIR` - Save plots to directory as PNG files
 - `PYREDUCE_PLOT_SHOW` - Display mode: `block` (default), `defer`, or `off`
 - `PYREDUCE_PLOT_ANIMATION_SPEED` - Frame delay in seconds for extraction animation (default: 0.3)
+- `PYREDUCE_USE_CHARSLIT` - Use charslit extraction backend instead of CFFI (default: 0)
+- `PYREDUCE_USE_DELTAS` - Enable slitdelta correction with charslit backend (default: 1)
 
 Plot modes: `block` shows each plot interactively; `defer` accumulates all plots and shows at end (useful with webagg backend); `off` disables display. Save and display are independent.
 
+The charslit backend supports higher-degree curvature polynomials (up to degree 5) and per-row slitdelta corrections. It requires the optional `charslit` dependency.
+
 ## Development
 
 ### Commands
 
 ```bash
 uv sync                              # Install dependencies
+uv sync --extra charslit             # Include charslit backend (from GitHub)
+uv pip install -e ../CharSlit.git    # Overlay local editable charslit for dev
 uv run reduce-build                  # Compile C extensions
 uv run reduce-clean                  # Remove compiled extensions
 uv run pre-commit install            # Setup hooks (once)
@@ -303,6 +323,9 @@ After a fresh clone or `rm -rf .venv`, run `uv sync && uv run reduce-build` to s
 | `pyreduce/pipeline.py` | Fluent Pipeline API, `from_instrument()` |
 | `pyreduce/reduce.py` | Step class implementations |
 | `pyreduce/extract.py` | Optimal extraction algorithm |
+| `pyreduce/trace_model.py` | Trace dataclass (pos, slit, wave, column_range) |
+| `pyreduce/spectra.py` | Spectrum/Spectra classes for FITS I/O |
+| `pyreduce/slit_curve.py` | Slit curvature fitting (degree 1-5) |
 | `pyreduce/wavelength_calibration.py` | Wavelength solution fitting |
 | `pyreduce/trace.py` | Order detection and tracing |
 | `pyreduce/instruments/common.py` | Base Instrument class |
@@ -326,17 +349,15 @@ To release a new version (e.g., `0.7a6`):
 
 3a. **sync** - run `uv sync` to get the new version into uv.lock
 
-4. **Update example headers** - all `examples/*.py` have PEP 723 metadata:
-   ```python
-   # /// script
-   # dependencies = ["pyreduce-astro>=0.7a6"]
-   # ///
+4. **Run unit tests** to catch issues before release:
+   ```bash
+   uv run pytest -m unit
    ```
 
 5. **Commit, tag, and push**:
    ```bash
-   git add -A && git commit -m "Release v0.7a6"
-   git tag v0.7a6
+   git add -A && git commit -m "Release v0.8a1"
+   git tag v0.8a1
    git push && git push --tags
    ```
 

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7b4
+Version: 0.8a2
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -37,12 +37,18 @@ Requires-Dist: scikit-image>=0.22.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: spectres>=2.2.0
 Requires-Dist: tqdm>=4.66.0
+Provides-Extra: charslit
+Requires-Dist: charslit>=0.1.0; extra == 'charslit'
 Description-Content-Type: text/markdown
 
 [![CI](https://github.com/ivh/PyReduce/actions/workflows/python-publish.yml/badge.svg)](https://github.com/ivh/PyReduce/actions/workflows/python-publish.yml)
 [![Documentation Status](https://readthedocs.org/projects/pyreduce-astro/badge/?version=latest)](https://pyreduce-astro.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
 
+# What's new?
+
+Version 0.7 is a major overhaul with many improvements, please see [WhatsNew.md](WhatsNew.md) for the highlights. If the update breaks your existing setup, you are very welcome to file an issue, so we can assist you.
+
 # PyReduce
 
 A data reduction pipeline for echelle spectrographs (HARPS, UVES, XSHOOTER, CRIRES+, JWST/NIRISS, and more).
@@ -75,11 +81,11 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,trace,science
+uv run reduce run UVES -t HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
-uv run reduce bias UVES HD132205
-uv run reduce flat UVES HD132205
+uv run reduce bias UVES -t HD132205
+uv run reduce flat UVES -t HD132205
 ```
 
 Or use the Python API:

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/README.md

@@ -2,6 +2,10 @@
 [![Documentation Status](https://readthedocs.org/projects/pyreduce-astro/badge/?version=latest)](https://pyreduce-astro.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
 
+# What's new?
+
+Version 0.7 is a major overhaul with many improvements, please see [WhatsNew.md](WhatsNew.md) for the highlights. If the update breaks your existing setup, you are very welcome to file an issue, so we can assist you.
+
 # PyReduce
 
 A data reduction pipeline for echelle spectrographs (HARPS, UVES, XSHOOTER, CRIRES+, JWST/NIRISS, and more).
@@ -34,11 +38,11 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,trace,science
+uv run reduce run UVES -t HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
-uv run reduce bias UVES HD132205
-uv run reduce flat UVES HD132205
+uv run reduce bias UVES -t HD132205
+uv run reduce flat UVES -t HD132205
 ```
 
 Or use the Python API:

pyreduce_astro-0.8a2/WhatsNew.md

@@ -0,0 +1,94 @@
+## 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](docs/redesign.md) for details.
+
+### 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](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](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](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](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
+
+```python
+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](docs/examples.md) for more.
+
+### New CLI
+
+The old argparse CLI is replaced with a cleaner Click-based interface. See [docs/cli.md](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 3.11+** required (3.13 recommended)
+- Build system migrated from setuptools to Hatchling
+
+See [docs/installation.md](docs/installation.md) for details.

pyreduce_astro-0.8a2/examples/andes_riz.py

@@ -0,0 +1,167 @@
+"""
+ANDES_RIZ instrument example: Step-by-step pipeline execution.
+
+This example demonstrates running individual pipeline steps for the ANDES R-band
+instrument with simulated PSF comparison data. Files are distinguished by:
+- HDFMODEL header: selects channel (R0, R1, R2 = different optical models)
+- SIMTYPE header: file type (flat_field, lfc, spectrum)
+- FIBMODE header: even/odd fiber illumination pattern
+
+Usage:
+    PYREDUCE_PLOT=1 uv run python examples/andes_riz.py
+
+Or import and run steps interactively:
+    from examples.andes_riz import pipe, flat_files, lfc_files
+    pipe.trace(flat_files)
+    pipe.run()
+"""
+
+import os
+from os.path import join
+
+from astropy.io import fits
+
+from pyreduce import util
+from pyreduce.combine_frames import combine_calibrate
+from pyreduce.configuration import load_config
+from pyreduce.instruments import instrument_info
+from pyreduce.pipeline import Pipeline
+
+# --- Configuration ---
+instrument_name = "ANDES_RIZ"
+target = "psf_comp"
+night = ""
+channel = "R0"  # R0, R1, or R2 (different optical models)
+
+# Plot settings
+plot = int(os.environ.get("PYREDUCE_PLOT", "1"))
+plot_dir = os.environ.get("PYREDUCE_PLOT_DIR")
+if plot_dir:
+    util.set_plot_dir(plot_dir)
+
+# Data location
+data_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
+raw_dir = join(data_dir, "ANDES", "psf_comp_R")
+output_dir = join(data_dir, "ANDES", "reduced", f"psf_comp_{channel}")
+
+# --- Discover files ---
+print(f"Discovering files in {raw_dir}...")
+sorted_files = instrument_info.sort_files(
+    input_dir=raw_dir,
+    target=target,
+    night=night,
+    instrument=instrument_name,
+    channel=channel,
+)
+
+if not sorted_files:
+    raise RuntimeError(f"No files found for channel {channel}")
+
+# Extract file lists from sorted results
+setting, files = sorted_files[0]
+flat_files = list(files.get("flat", []))
+trace_files = list(files.get("trace", []))
+wavecal_files = list(files.get("wavecal_master", []))
+
+print(f"Channel: {channel} ({setting['channel']})")
+print(f"Flat files: {[os.path.basename(f) for f in flat_files]}")
+print(f"Trace files: {[os.path.basename(f) for f in trace_files]}")
+print(f"Wavecal files: {[os.path.basename(f) for f in wavecal_files]}")
+
+# --- Create Pipeline ---
+config = load_config(None, instrument_name, channel=channel)
+pipe = Pipeline(
+    instrument=instrument_name,
+    output_dir=output_dir,
+    target=target,
+    channel=channel,
+    night=night,
+    config=config,
+    plot=plot,
+)
+
+print(f"\nInstrument: {pipe.instrument.name}")
+print(f"Output: {output_dir}")
+
+# Show fiber config if present
+if pipe.instrument.config.fibers:
+    fc = pipe.instrument.config.fibers
+    print(f"Fibers per order: {fc.fibers_per_order}")
+    print(f"Groups: {list(fc.groups.keys())}")
+
+
+def combine_lfc_with_flats(lfc_files, flat_files, output_path):
+    """Combine LFC files with flat-field frames to add continuum."""
+    import numpy as np
+
+    print(f"Combining {len(lfc_files)} LFC + {len(flat_files)} flat files...")
+
+    # Combine LFC files
+    lfc_combined, head = combine_calibrate(
+        lfc_files,
+        pipe.instrument,
+        channel,
+        mask=None,
+    )
+    lfc_data = np.asarray(
+        lfc_combined.filled(0) if hasattr(lfc_combined, "filled") else lfc_combined
+    )
+
+    if flat_files:
+        # Combine flat files
+        flat_combined, _ = combine_calibrate(
+            flat_files,
+            pipe.instrument,
+            channel,
+            mask=None,
+        )
+        flat_data = np.asarray(
+            flat_combined.filled(0)
+            if hasattr(flat_combined, "filled")
+            else flat_combined
+        )
+
+        # Add flat continuum to LFC (scale flat to ~10% of LFC peak to not overwhelm lines)
+        lfc_peak = (
+            np.percentile(lfc_data[lfc_data > 0], 95) if np.any(lfc_data > 0) else 1
+        )
+        flat_peak = (
+            np.percentile(flat_data[flat_data > 0], 95) if np.any(flat_data > 0) else 1
+        )
+        scale = 0.1 * lfc_peak / flat_peak
+        combined = lfc_data + flat_data * scale
+        print(
+            f"  LFC peak: {lfc_peak:.0f}, flat peak: {flat_peak:.0f}, scale: {scale:.4f}"
+        )
+    else:
+        combined = lfc_data
+        print("  No flats available, using LFC only")
+
+    fits.writeto(output_path, combined.astype(np.float32), head, overwrite=True)
+    print(f"Saved combined LFC+flat: {output_path}")
+    return output_path
+
+
+if __name__ == "__main__":
+    # Combine LFC + flat files before extraction
+    lfc_combined_path = join(output_dir, "lfc_combined.fits")
+    if wavecal_files and flat_files:
+        combine_lfc_with_flats(wavecal_files, flat_files, lfc_combined_path)
+    elif wavecal_files:
+        # Fallback to LFC only if no flats
+        combine_lfc_with_flats(wavecal_files, [], lfc_combined_path)
+
+    print("\n=== Running pipeline ===")
+    # pipe.trace(trace_files)
+    # pipe.curvature(wavecal_files)
+    # Full wavecal: master -> init (MCMC line matching) -> finalize
+    pipe.wavelength_calibration([lfc_combined_path])
+    pipe.extract([lfc_combined_path])
+
+    results = pipe.run()
+
+    if "trace" in results:
+        traces = results["trace"]  # list[Trace]
+        print(f"Traces found: {len(traces)}")
+        for t in traces[:3]:
+            print(f"  m={t.m}, group={t.group}, columns={t.column_range}")

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/examples/andes_yjh_example.py

@@ -1,12 +1,9 @@
-# /// script
-# requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b4"]
-# ///
 """
 ANDES_YJH instrument example: Multi-fiber tracing with Pipeline API.
 
 Demonstrates tracing fibers illuminated in separate flat field images
-(even/odd pattern) using the Pipeline's trace_raw() and organize() methods.
+(even/odd pattern). The Pipeline trace() step handles merging traces
+from multiple files.
 
 The fiber config in ANDES_YJH/config.yaml handles:
 - order_centers_file: assigns traces to spectral orders by y-position (channel-specific)
@@ -62,33 +59,25 @@ LOAD_TRACE = True  # Set True to load traces from previous run
 
 if LOAD_TRACE:
     print("\nLoading traces from previous run...")
-    traces, column_range = pipe._run_step("trace", None, load_only=True)
-    print(f"  Loaded {len(traces)} traces")
-
-    # Re-run organize with current config (picks up any config changes)
-    print("\nRe-organizing traces with current config...")
-    pipe.organize(traces, column_range)
+    trace_objects = pipe._run_step("trace", None, load_only=True)  # list[Trace]
+    print(f"  Loaded {len(trace_objects)} traces")
 else:
-    # Trace each flat independently
-    print(f"\nTracing even fibers from {os.path.basename(file_even)}...")
-    traces_even, cr_even = pipe.trace_raw([file_even])
-    print(f"  Found {len(traces_even)} traces")
-
-    print(f"\nTracing odd fibers from {os.path.basename(file_odd)}...")
-    traces_odd, cr_odd = pipe.trace_raw([file_odd])
-    print(f"  Found {len(traces_odd)} traces")
-
-    # Organize into fiber groups
-    print("\nOrganizing traces into fiber groups...")
-    pipe.organize(traces_even, cr_even, traces_odd, cr_odd)
-
-# Access organized groups
-if "trace_groups" in pipe._data and pipe._data["trace_groups"][0]:
-    group_traces, group_cr = pipe._data["trace_groups"]
-    print("Fiber groups:")
-    for name, traces_dict in group_traces.items():
-        n_traces = len(traces_dict)
-        print(f"  {name}: {n_traces} traces")
+    # Trace both files together - the pipeline will organize by fiber config
+    print(
+        f"\nTracing fibers from {os.path.basename(file_even)} and {os.path.basename(file_odd)}..."
+    )
+    pipe.trace([file_even, file_odd])
+    results = pipe.run()
+    trace_objects = results["trace"]  # list[Trace]
+    print(f"  Found {len(trace_objects)} traces")
+
+# Show trace info
+print("\nTraces:")
+fibers = {t.fiber for t in trace_objects}
+print(f"  Fibers: {sorted(fibers)}")
+for fiber in sorted(fibers)[:3]:
+    count = sum(1 for t in trace_objects if t.fiber == fiber)
+    print(f"  {fiber}: {count} traces")
 
 # --- Create combined flat for extraction ---
 print("\nCombining even/odd flats...")
@@ -108,6 +97,5 @@ print(f"  Saved combined flat: {combined_file}")
 
 # --- Extract using the science step ---
 print("\nExtracting spectra (group A from fiber config)...")
-pipe.instrument.config.fibers.use["science"] = ["ring1"]
-pipe.config["science"]["extraction_height"] = 60
+pipe.instrument.config.fibers.use["science"] = ["ring2"]
 pipe.extract([combined_file]).run()

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/examples/crires_plus_example.py

@@ -1,7 +1,3 @@
-# /// script
-# requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b4"]
-# ///
 """
 Simple usage example for PyReduce
 Loads a CRIRES+ dataset, and runs the extraction

{pyreduce_astro-0.7b4 → pyreduce_astro-0.8a2}/examples/custom_instrument_example.py

@@ -1,7 +1,3 @@
-# /// script
-# requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b4"]
-# ///
 """
 Simple usage example for PyReduce
 Loads a sample UVES dataset, and runs the full extraction