pyreduce-astro 0.8a1__tar.gz → 0.8a2__tar.gz

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/CHANGELOG.md

@@ -1,6 +1,30 @@
 # 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

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/CLAUDE.md

@@ -31,11 +31,11 @@ pyreduce/
 ├── reduce.py            # Step class implementations
 ├── configuration.py     # Config loading (settings JSON)
 ├── extract.py           # Optimal extraction algorithm
-├── curvature_model.py   # SlitCurvature dataclass for curvature data
+├── 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
 │
@@ -71,6 +71,19 @@ This means:
 - **Traces** are polynomial functions of x, giving y-position
 - **`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
 
 The reduction pipeline consists of these steps (in typical order):
@@ -310,7 +323,8 @@ 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/curvature_model.py` | SlitCurvature dataclass, save/load |
+| `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_astro-0.8a1 → pyreduce_astro-0.8a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.8a1
+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

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/WhatsNew.md

@@ -1,3 +1,19 @@
+## 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

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/andes_riz.py

@@ -153,18 +153,15 @@ if __name__ == "__main__":
 
     print("\n=== Running pipeline ===")
     # pipe.trace(trace_files)
-    pipe.curvature(wavecal_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, column_range, *_ = results["trace"]
+        traces = results["trace"]  # list[Trace]
         print(f"Traces found: {len(traces)}")
-
-    if "trace_groups" in results and results["trace_groups"]:
-        group_traces, group_cr, group_heights = results["trace_groups"]
-        print(f"Fiber groups: {list(group_traces.keys())}")
-        for name, traces_dict in group_traces.items():
-            if isinstance(traces_dict, dict):
-                print(f"  {name}: orders {list(traces_dict.keys())}")
+        for t in traces[:3]:
+            print(f"  m={t.m}, group={t.group}, columns={t.column_range}")

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/andes_yjh_example.py

@@ -2,7 +2,8 @@
 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)
@@ -58,33 +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, heights = 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, group_heights = 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...")

pyreduce_astro-0.8a2/examples/debug_single_swath.py

@@ -0,0 +1,139 @@
+"""
+Debug script for extracting a single swath from a specific trace.
+
+Manually loads traces from FITS, cuts out one swath, runs extraction,
+and saves all intermediate outputs for inspection.
+"""
+
+import os
+from os.path import join
+
+import numpy as np
+from astropy.io import fits
+
+from pyreduce.cwrappers import slitfunc_curved
+from pyreduce.extract import fix_parameters, make_bins
+from pyreduce.trace_model import load_traces
+from pyreduce.util import make_index
+
+# === Configuration ===
+# Which trace and swath to extract
+TRACE_INDEX = 4  # 5th trace (0-indexed), i.e. 5th fiber bundle center
+SWATH_INDEX = 2  # 3rd swath (0-indexed)
+
+# Extraction parameters
+EXTRACTION_HEIGHT = 0.5  # fraction of order spacing
+OSAMPLE = 1
+LAMBDA_SF = 0.1
+LAMBDA_SP = 0
+MAXITER = 20
+GAIN = 1.0
+
+# === Data paths ===
+data_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
+base_dir = join(data_dir, "MOSAIC", "REF_E2E", "NIR")
+output_dir = join(data_dir, "MOSAIC", "reduced", "NIR")
+
+flat_file = join(
+    base_dir,
+    "E2E_FLAT_DIT_20s_MOSAIC_2Cam_c01",
+    "E2E_FLAT_DIT_20s_MOSAIC_2Cam_c01_STATIC_FOCAL_PLANE.fits",
+)
+trace_file = join(output_dir, "MOSAIC_NIR.traces.fits")
+
+
+def load_image(flat_file):
+    """Load the flat field image."""
+    with fits.open(flat_file) as hdu:
+        img = hdu[0].data.astype(float)
+    print(f"Loaded image: {img.shape}")
+    return img
+
+
+def main():
+    # Load data
+    img = load_image(flat_file)
+    nrow, ncol = img.shape
+
+    # Load traces from FITS file
+    trace_list, _ = load_traces(trace_file)
+    print(f"Loaded {len(trace_list)} traces from {trace_file}")
+
+    # Convert to arrays for fix_parameters
+    traces = np.array([t.pos for t in trace_list])
+    column_range = np.array([t.column_range for t in trace_list])
+    ntrace = len(traces)
+
+    # Get extraction parameters
+    xwd, cr = fix_parameters(
+        EXTRACTION_HEIGHT, column_range, traces, nrow, ncol, ntrace
+    )
+    print(f"Extraction heights: {xwd[TRACE_INDEX]}")
+    print(f"Column range: {cr[TRACE_INDEX]}")
+
+    # Select the trace
+    trace = traces[TRACE_INDEX]
+    xlow, xhigh = xwd[TRACE_INDEX]
+    ibeg, iend = cr[TRACE_INDEX]
+
+    # Calculate trace center positions
+    ix = np.arange(ncol)
+    ycen = np.polyval(trace, ix)
+    ycen_int = ycen.astype(int)
+
+    # Make swath bins
+    bins = make_bins(None, ibeg, iend, ycen)  # swath_width=None for default
+    print(f"Number of swaths: {len(bins) - 1}")
+    print(f"Swath boundaries: {bins}")
+
+    # Select one swath
+    swath_start = bins[SWATH_INDEX]
+    swath_end = bins[SWATH_INDEX + 1]
+    print(f"Processing swath {SWATH_INDEX}: columns {swath_start} to {swath_end}")
+
+    # Extract swath region
+    index = make_index(ycen_int - xlow, ycen_int + xhigh + 1, swath_start, swath_end)
+    swath_img = img[index]
+    swath_ycen = ycen[swath_start:swath_end] - ycen_int[swath_start:swath_end]
+
+    print(f"Swath image shape: {swath_img.shape}")
+    print(f"Swath ycen range: [{swath_ycen.min():.3f}, {swath_ycen.max():.3f}]")
+
+    # Save input for debugging
+    np.savetxt("debug_swath_img.txt", swath_img)
+    np.savetxt("debug_swath_ycen.txt", swath_ycen)
+    print("Saved debug_swath_img.txt and debug_swath_ycen.txt")
+
+    # Run extraction
+    print("\nRunning slitfunc_curved...")
+    result = slitfunc_curved(
+        swath_img,
+        swath_ycen,
+        0,  # p0 (tilt)
+        0,  # p1 (curvature)
+        LAMBDA_SF,
+        LAMBDA_SP,
+        osample=OSAMPLE,
+        maxiter=MAXITER,
+        gain=GAIN,
+        yrange=(int(xlow), int(xhigh)),
+    )
+
+    spec, slitf, model, unc, mask = result
+
+    # Save outputs
+    np.savetxt("debug_spectrum.txt", spec)
+    np.savetxt("debug_slitfunc.txt", slitf)
+    np.savetxt("debug_model.txt", model)
+    np.savetxt("debug_unc.txt", unc)
+    np.savetxt("debug_mask.txt", mask.astype(int))
+
+    print("\nResults saved:")
+    print(f"  Spectrum: {len(spec)} points, sum={spec.sum():.1f}")
+    print(f"  Slit function: {len(slitf)} points")
+    print(f"  Model: {model.shape}")
+    print(f"  Masked pixels: {mask.sum()} / {mask.size}")
+
+
+if __name__ == "__main__":
+    main()

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/harps_gridsearch.py

@@ -18,7 +18,7 @@ def func_wavecal(deg, thar, instrument, channel, **kwargs):
     kwargs["degree"] = deg
 
     module = WavelengthCalibrationModule(**kwargs)
-    wave, coef = module.execute(thar, linelist)
+    _wave, _coef, _linelist = module.execute(thar, linelist)
 
     return module.aic
 

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/just_one_swath.py

@@ -1,8 +1,15 @@
+"""
+Debug script for extracting a single swath from a specific trace.
+
+Demonstrates manual swath extraction using the trace_model interface.
+"""
+
 import matplotlib.pyplot as plt
 import numpy as np
 from astropy.io import fits
 
 from pyreduce import cwrappers, extract
+from pyreduce.trace_model import load_traces
 
 input_dir = "../DATA/datasets/UVES/reduced/2010-04-01/middle/"
 raw_dir = "../DATA/datasets/UVES/raw/"
@@ -11,30 +18,17 @@ hdu = fits.open(input_dir + "uves_middle.flat.fits")
 img = hdu[0].data
 nrow, ncol = img.shape
 
-import warnings
-
-data = np.load(input_dir + "uves_middle.traces.npz", allow_pickle=True)
-if "traces" in data:
-    traces = data["traces"]
-elif "orders" in data:
-    warnings.warn(
-        "Trace file uses old key 'orders'. Re-run the trace step to update.",
-        DeprecationWarning,
-        stacklevel=1,
-    )
-    traces = data["orders"]
-else:
-    raise KeyError("Trace file missing 'traces' key")
-column_range = data["column_range"]
+# Load traces from FITS file
+traces, _ = load_traces(input_dir + "uves_middle.traces.fits")
+print(f"Loaded {len(traces)} traces")
 
 i = 5
 ix = np.arange(ncol)
 
 ylow, yhigh = 50, 50
 ibeg, iend = 1500, 2000
-ycen = np.polyval(traces[i], ix)
+ycen = np.polyval(traces[i].pos, ix)
 ycen_int = ycen.astype(int)
-# yrange = extract.get_y_scale(ycen, [400, 600], [5, 5], nrow)
 
 index = extract.make_index(ycen_int - ylow, ycen_int + yhigh, ibeg, iend)
 swath_img = img[index]
@@ -44,8 +38,6 @@ osample = 10
 np.savetxt("image.txt", swath_img)
 np.savetxt("ycen.txt", swath_ycen)
 
-# return sp, sl, model, unc, mask
-# data1 = cwrappers.slitfunc(swath_img, swath_ycen, osample=osample)
 data2 = cwrappers.slitfunc_curved(
     swath_img, swath_ycen, 0, 0, 0.0, 0.5, osample=osample, yrange=(ylow, yhigh)
 )
@@ -84,17 +76,6 @@ for i in range(ncol):
         slitf,
     )
 
-    # plt.subplot(111)
-    # plt.plot(swath_img[:, i] / np.mean(swath_img[:, i]), label="Image")
-    # plt.plot(sf[:, i] / np.mean(sf[:, i]), label="Interpolated")
-    # plt.plot(np.linspace(-1, nrow, nsf), slitf / np.mean(slitf), label="Slitfunction")
-    # plt.legend()
-    # plt.show()
-
-# plt.subplot(122)
-# plt.imshow(swath_img / sf, aspect="auto", origin="lower")
-# plt.show()
-
 y = swath_img / sf
 y = y.ravel() * np.mean(spec) / np.mean(y)
 plt.plot(x, y, ".", label="Observation")

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/mosaic_nir.py

@@ -72,21 +72,17 @@ pipe = Pipeline(
 # - Groups 630 traces into 90 bundles of 7
 # - Selects center fiber from each bundle
 # - Uses grouped traces for curvature and science steps
-pipe.trace([flat_file])
+# pipe.trace([flat_file])
 # pipe.curvature([thar_file])
 # pipe.flat([flat_file])
 # pipe.normalize_flat()
-# pipe.extract([flat_file])
+pipe.extract([thar_file])
 
 print("\n=== Running Pipeline ===")
 results = pipe.run()
 
 print("\n=== Results ===")
-traces, column_range = results["trace"]
-print(f"Raw traces: {len(traces)}")
-
-if "trace_groups" in results and results["trace_groups"]:
-    group_traces, group_cr = results["trace_groups"]
-    print(
-        f"Fiber groups: {list(group_traces.keys())[:5]}... ({len(group_traces)} total)"
-    )
+traces = results["trace"]  # list[Trace]
+print(f"Traces: {len(traces)}")
+for t in traces[:3]:
+    print(f"  m={t.m}, fiber={t.fiber}, columns={t.column_range}")

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/mosaic_preset-slitfunc.py

@@ -13,6 +13,7 @@ import numpy as np
 from pyreduce import util
 from pyreduce.configuration import load_config
 from pyreduce.extract import extract
+from pyreduce.trace_model import load_traces
 
 # Parameters
 instrument_name = "MOSAIC"
@@ -64,18 +65,36 @@ prefix = "mosaic_nir"
 # Load saved results from previous pipeline run
 print("\n=== Loading saved results ===")
 
-trace_file = join(output_dir, f"{prefix}.traces.npz")
+trace_file = join(output_dir, f"{prefix}.traces.fits")
 norm_file = join(output_dir, f"{prefix}.flat_norm.npz")
-curve_file = join(output_dir, f"{prefix}.curve.npz")
 
-# Load trace (use grouped traces that norm_flat used)
-trace_data = np.load(trace_file)
-group_names = trace_data["group_names"]
-all_traces = [trace_data[f"group_{name}_traces"] for name in group_names]
-all_cr = [trace_data[f"group_{name}_cr"] for name in group_names]
-traces = np.vstack(all_traces)
-column_range = np.vstack(all_cr)
-print(f"Loaded {len(traces)} grouped traces from {trace_file}")
+# Load traces from FITS file (includes curvature if available)
+trace_list, _ = load_traces(trace_file)
+print(f"Loaded {len(trace_list)} traces from {trace_file}")
+
+# Convert to arrays for extract()
+traces = np.array([t.pos for t in trace_list])
+column_range = np.array([t.column_range for t in trace_list])
+
+# Get curvature from traces (if available)
+# The slit curvature is now stored in each Trace object
+has_curvature = trace_list[0].slit is not None
+if has_curvature:
+    # For the extract() function, we need p1, p2 as arrays (ntrace, 2)
+    # Extract the linear and quadratic curvature terms
+    p1 = np.zeros(len(trace_list))
+    p2 = np.zeros(len(trace_list))
+    for i, t in enumerate(trace_list):
+        if t.slit is not None and t.slit.shape[0] >= 2:
+            # slit[1, :] contains coefficients for the y^1 term (linear tilt)
+            # Take the constant term (value at x=0) as p1
+            p1[i] = t.slit[1, -1] if len(t.slit[1]) > 0 else 0
+            if t.slit.shape[0] >= 3:
+                p2[i] = t.slit[2, -1] if len(t.slit[2]) > 0 else 0
+    print(f"Loaded curvature from traces (p1 range: [{p1.min():.4f}, {p1.max():.4f}])")
+else:
+    p1, p2 = None, None
+    print("No curvature data in traces")
 
 # Load norm_flat (with slitfunc)
 norm_data = np.load(norm_file, allow_pickle=True)
@@ -84,37 +103,24 @@ slitfunc_meta = norm_data["slitfunc_meta"].item()
 print(f"Loaded {len(slitfunc_list)} slit functions from {norm_file}")
 print(f"Slitfunc meta: {slitfunc_meta}")
 
-# Load curvature if available
-if os.path.exists(curve_file):
-    curve_data = np.load(curve_file)
-    p1, p2 = curve_data["p1"], curve_data["p2"]
-    print(f"Loaded curvature from {curve_file}")
-else:
-    p1, p2 = None, None
-    print("No curvature file found, using p1=p2=None")
-
 # Now extract ThAr using preset slit function
 print("\n=== Extracting ThAr with preset slit function ===")
 
 # Load ThAr image
 thar_img, thar_head = instrument.load_fits(thar_file, channel)
 
-# Use the grouped traces (same as norm_flat)
-selected_traces = traces
-selected_cr = column_range
-
 # Extraction parameters from slitfunc_meta
 osample = slitfunc_meta["osample"]
 extraction_height = slitfunc_meta["extraction_height"]
 
-print(f"Extracting {len(selected_traces)} traces with preset slitfunc")
+print(f"Extracting {len(traces)} traces with preset slitfunc")
 print(f"  osample={osample}, extraction_height={extraction_height}")
 
 # Extract using the extract() function with preset_slitfunc
 spectrum, uncertainties, slitfunc_out, column_range_out = extract(
     thar_img,
-    selected_traces,
-    column_range=selected_cr,
+    traces,
+    column_range=column_range,
     extraction_type="optimal",
     extraction_height=extraction_height,
     p1=p1,

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/mosaic_vis.py

@@ -81,11 +81,7 @@ print("\n=== Running Pipeline ===")
 results = pipe.run()
 
 print("\n=== Results ===")
-traces, column_range = results["trace"]
-print(f"Raw traces: {len(traces)}")
-
-if "trace_groups" in results and results["trace_groups"]:
-    group_traces, group_cr = results["trace_groups"]
-    print(
-        f"Fiber groups: {list(group_traces.keys())[:5]}... ({len(group_traces)} total)"
-    )
+traces = results["trace"]  # list[Trace]
+print(f"Traces: {len(traces)}")
+for t in traces[:3]:
+    print(f"  m={t.m}, fiber={t.fiber}, columns={t.column_range}")

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/examples/uves_callfunc.py

@@ -148,11 +148,11 @@ wavecal_master = wavecal_master_step.run(
 wavecal_init_step = WavelengthCalibrationInitialize(
     *step_args, **step_config("wavecal_init")
 )
-wavecal_init = wavecal_init_step.load(config, wavecal_master)
+wavecal_init = wavecal_init_step.run(wavecal_master)
 
 wavecal_step = WavelengthCalibrationFinalize(*step_args, **step_config("wavecal"))
 wavecal = wavecal_step.run(wavecal_master, wavecal_init)
-wave, coef, linelist = wavecal
+# wavecal returns {group: linelist}; wavelengths are stored in traces
 
 # Step 8: Science extraction
 print("\n=== SCIENCE ===")
@@ -166,14 +166,14 @@ science = science_step.run(
     mask=mask,
 )
 
-# Step 9: Continuum normalization
+# Step 9: Continuum normalization (gets wavelengths from traces)
 print("\n=== CONTINUUM ===")
 continuum_step = ContinuumNormalization(*step_args, **step_config("continuum"))
-continuum = continuum_step.run(science, wave, norm_flat)
+continuum = continuum_step.run(science, norm_flat, traces)
 
-# Step 10: Finalize
+# Step 10: Finalize (gets wavelengths from traces)
 print("\n=== FINALIZE ===")
 finalize_step = Finalize(*step_args, **step_config("finalize"))
-finalize_step.run(continuum, wave, config)
+finalize_step.run(continuum, traces, config)
 
 print("\nDone!")

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyreduce-astro"
-version = "0.8a1"
+version = "0.8a2"
 requires-python = ">=3.13"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"

{pyreduce_astro-0.8a1 → pyreduce_astro-0.8a2}/pyreduce/cli.py

@@ -247,7 +247,7 @@ def run(config_file: str, steps: str, skip_existing: bool, plot: int):
         files:
           bias: /data/raw/bias/*.fits
           flat: /data/raw/flat/*.fits
-          wavecal: /data/raw/thar/*.fits
+          wavecal: /data/raw/wavecal/*.fits
           science: /data/raw/science/*.fits
         steps: [bias, flat, trace, wavecal, extract]
     """