pyreduce-astro 0.7b2__tar.gz → 0.7b4__tar.gz

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/.gitignore

@@ -21,3 +21,5 @@ docs/_build/
 debug/
 idl/
 logs/
+*.ipynb
+tmp/*

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/CHANGELOG.md

@@ -1,6 +1,49 @@
 # 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

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/CLAUDE.md

@@ -31,7 +31,7 @@ pyreduce/
 ├── reduce.py            # Step class implementations
 ├── configuration.py     # Config loading (settings JSON)
 ├── extract.py           # Optimal extraction algorithm
-├── trace_orders.py      # Order detection and tracing
+├── trace.py             # Order detection and tracing
 ├── wavelength_calibration.py  # Wavelength solution fitting
 ├── combine_frames.py    # Frame combination/calibration
 ├── echelle.py           # Echelle spectrum I/O
@@ -158,7 +158,7 @@ Defines HOW to reduce - algorithm parameters per step:
     "degree": 4,
     "noise": 100,
     "min_cluster": 500,
-    "filter_size": 120
+    "filter_y": 120
   },
   "norm_flat": {
     "extraction_height": 0.5,
@@ -217,7 +217,7 @@ pipe = Pipeline(
 )
 pipe.bias(bias_files)
 pipe.flat(flat_files)
-pipe.trace_orders()
+pipe.trace()
 pipe.extract(science_files)
 result = pipe.run()
 ```
@@ -257,8 +257,12 @@ uv run reduce list-steps
 ## Environment Variables
 
 - `REDUCE_DATA` - Base data directory (default: `~/REDUCE_DATA`)
-- `PYREDUCE_PLOT` - Override plot level (0, 1, 2)
-- `PYREDUCE_PLOT_DIR` - Save plots to directory instead of displaying
+- `PYREDUCE_PLOT` - Override plot level (0=off, 1=basic, 2=detailed)
+- `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)
+
+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.
 
 ## Development
 
@@ -300,7 +304,7 @@ After a fresh clone or `rm -rf .venv`, run `uv sync && uv run reduce-build` to s
 | `pyreduce/reduce.py` | Step class implementations |
 | `pyreduce/extract.py` | Optimal extraction algorithm |
 | `pyreduce/wavelength_calibration.py` | Wavelength solution fitting |
-| `pyreduce/trace_orders.py` | Order detection and tracing |
+| `pyreduce/trace.py` | Order detection and tracing |
 | `pyreduce/instruments/common.py` | Base Instrument class |
 | `pyreduce/instruments/models.py` | Pydantic config models |
 | `pyreduce/clib/*.c` | C code for slit function decomposition |

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7b2
+Version: 0.7b4
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -94,6 +94,20 @@ Pipeline.from_instrument(
 ).run()
 ```
 
+## Plotting
+
+Control plotting with environment variables:
+
+```bash
+# Save plots to files (headless/CI)
+PYREDUCE_PLOT=1 PYREDUCE_PLOT_DIR=/tmp/plots PYREDUCE_PLOT_SHOW=off uv run reduce run ...
+
+# Show all plots at end (browser via webagg)
+MPLBACKEND=webagg PYREDUCE_PLOT=1 PYREDUCE_PLOT_SHOW=defer uv run reduce run ...
+```
+
+See [How To](https://pyreduce-astro.readthedocs.io/en/latest/howto.html#plot-modes) for details.
+
 ## Documentation
 
 Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/README.md

@@ -53,6 +53,20 @@ Pipeline.from_instrument(
 ).run()
 ```
 
+## Plotting
+
+Control plotting with environment variables:
+
+```bash
+# Save plots to files (headless/CI)
+PYREDUCE_PLOT=1 PYREDUCE_PLOT_DIR=/tmp/plots PYREDUCE_PLOT_SHOW=off uv run reduce run ...
+
+# Show all plots at end (browser via webagg)
+MPLBACKEND=webagg PYREDUCE_PLOT=1 PYREDUCE_PLOT_SHOW=defer uv run reduce run ...
+```
+
+See [How To](https://pyreduce-astro.readthedocs.io/en/latest/howto.html#plot-modes) for details.
+
 ## Documentation
 
 Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).

pyreduce_astro-0.7b4/examples/andes_yjh_example.py

@@ -0,0 +1,113 @@
+# /// 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.
+
+The fiber config in ANDES_YJH/config.yaml handles:
+- order_centers_file: assigns traces to spectral orders by y-position (channel-specific)
+- groups: organizes fibers into logical groups (A, cal, B) within each order
+- merge: average - averages fiber traces within each group
+
+ANDES_YJH has three channels: Y, J, H (selected by BAND header in files).
+"""
+
+import os
+
+import numpy as np
+
+from pyreduce.configuration import load_config
+from pyreduce.pipeline import Pipeline
+
+# --- Configuration ---
+instrument_name = "ANDES_YJH"
+channel = "J"  # Y, J, or H
+data_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
+raw_dir = os.path.join(data_dir, "ANDES", channel)
+output_dir = os.path.join(data_dir, "ANDES", "reduced", channel)
+
+# Input files (even and odd illuminated flats)
+# File selection is header-based:
+#   BAND header determines channel (Y, J, H)
+#   SIMTYPE='flat_field' → flat, SIMTYPE='spectrum' → science
+#   FIBMODE='even' → even flat, FIBMODE='odd' → odd flat
+file_even = os.path.join(raw_dir, f"{channel}_FF_even_1s.fits")
+file_odd = os.path.join(raw_dir, f"{channel}_FF_odd_1s.fits")
+
+# Plot settings
+plot = int(os.environ.get("PYREDUCE_PLOT", "1"))
+
+# --- Create Pipeline ---
+config = load_config(None, instrument_name)
+pipe = Pipeline(
+    instrument=instrument_name,
+    channel=channel,
+    output_dir=output_dir,
+    target="ANDES_fiber_test",
+    config=config,
+    plot=plot,
+)
+
+print(f"Instrument: {pipe.instrument.name}")
+fibers_config = pipe.instrument.config.fibers
+print(f"Per-order grouping: {fibers_config.per_order}")
+print(f"Groups: {list(fibers_config.groups.keys())}")
+
+# --- Trace or load from previous run ---
+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)
+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")
+
+# --- Create combined flat for extraction ---
+print("\nCombining even/odd flats...")
+img_even, head = pipe.instrument.load_fits(file_even, channel=channel, extension=0)
+img_odd, _ = pipe.instrument.load_fits(file_odd, channel=channel, extension=0)
+img_combined = np.asarray(img_even, dtype=np.float64) + np.asarray(
+    img_odd, dtype=np.float64
+)
+
+# Save combined flat to file for the science step
+from astropy.io import fits
+
+combined_file = os.path.join(output_dir, "combined_flat.fits")
+os.makedirs(output_dir, exist_ok=True)
+fits.writeto(combined_file, img_combined.astype(np.float32), head, overwrite=True)
+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.extract([combined_file]).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -48,5 +48,5 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    # order_range=(0, 4),
+    # trace_range=(0, 4),
 ).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -73,7 +73,7 @@ pipe = Pipeline.from_files(
     channel=channel,
     night=night,
     config=config,
-    # order_range=order_range,
+    # trace_range=trace_range,
     steps=steps,
     plot=1,
 )

pyreduce_astro-0.7b4/examples/debug_single_swath.py

@@ -0,0 +1,233 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7b4"]
+# ///
+"""
+Debug script for extracting a single swath from a specific trace.
+
+Manually loads traces from NPZ, 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.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.ord_default.npz")
+
+
+def load_traces(trace_file):
+    """Load traces and column ranges from NPZ."""
+    import warnings
+
+    data = np.load(trace_file, allow_pickle=True)
+    if "traces" in data:
+        traces = data["traces"]
+    elif "orders" in data:
+        warnings.warn(
+            f"Trace file {trace_file} uses old key 'orders'. "
+            "Re-run the trace step to update the file format.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        traces = data["orders"]
+    else:
+        raise KeyError("Trace file missing 'traces' key")
+    column_range = data["column_range"]
+    print(f"Loaded {len(traces)} traces from {trace_file}")
+    return traces, column_range
+
+
+def load_image(flat_file):
+    """Load and prepare the flat field image."""
+    with fits.open(flat_file) as hdul:
+        img = hdul[0].data.astype(float)
+    print(f"Loaded image {img.shape} from {flat_file}")
+    return img
+
+
+def extract_single_swath(
+    img,
+    trace_coef,
+    column_range,
+    swath_index,
+    extraction_height,
+    p1=None,
+    p2=None,
+):
+    """
+    Extract a single swath from one trace.
+
+    Returns the swath image, extraction results, and metadata.
+    """
+    nrow, ncol = img.shape
+    xlow, xhigh = column_range
+
+    # Evaluate trace polynomial
+    x = np.arange(ncol)
+    ycen = np.polyval(trace_coef, x)
+
+    # Get extraction height in pixels
+    ylow, yhigh = extraction_height
+
+    # Create swath bins
+    nbin, bins_start, bins_end = make_bins(None, xlow, xhigh, ycen)
+    nswath = 2 * nbin - 1
+    print(f"Order has {nswath} swaths, extracting swath {swath_index}")
+
+    if swath_index >= nswath:
+        raise ValueError(f"Swath index {swath_index} >= number of swaths {nswath}")
+
+    # Get this swath's column range
+    ibeg = bins_start[swath_index]
+    iend = bins_end[swath_index]
+    print(f"Swath columns: {ibeg} - {iend} (width={iend - ibeg})")
+
+    # Cut out swath from image
+    ycen_int = np.floor(ycen).astype(int)
+    index = make_index(ycen_int - ylow, ycen_int + yhigh, ibeg, iend)
+    swath_img = img[index].copy()
+    swath_ycen = ycen[ibeg:iend]
+
+    # Fractional y offset within each pixel
+    swath_ycen_frac = swath_ycen - np.floor(swath_ycen)
+
+    print(f"Swath image shape: {swath_img.shape}")
+    print(f"Swath ycen range: {swath_ycen.min():.1f} - {swath_ycen.max():.1f}")
+
+    # Get curvature for this swath
+    swath_p1 = p1[ibeg:iend] if p1 is not None else 0
+    swath_p2 = p2[ibeg:iend] if p2 is not None else 0
+
+    # Run extraction
+    yrange = (ylow, yhigh)
+    spec, slitf, model, unc, mask, info = slitfunc_curved(
+        swath_img,
+        swath_ycen_frac,
+        swath_p1,
+        swath_p2,
+        lambda_sp=LAMBDA_SP,
+        lambda_sf=LAMBDA_SF,
+        osample=OSAMPLE,
+        yrange=yrange,
+        maxiter=MAXITER,
+        gain=GAIN,
+    )
+
+    return {
+        "swath_img": swath_img,
+        "spec": spec,
+        "slitf": slitf,
+        "model": model,
+        "unc": unc,
+        "mask": mask,
+        "info": info,
+        "ycen": swath_ycen_frac,
+        "ibeg": ibeg,
+        "iend": iend,
+        "yrange": yrange,
+    }
+
+
+def main():
+    # Check files exist
+    for fpath in [flat_file, trace_file]:
+        if not os.path.exists(fpath):
+            raise FileNotFoundError(f"File not found: {fpath}")
+
+    # Load data
+    img = load_image(flat_file)
+    traces, column_range = load_traces(trace_file)
+    nrow, ncol = img.shape
+    ntrace = len(traces)
+
+    print(f"\nImage: {nrow} x {ncol}")
+    print(f"Traces: {ntrace}")
+    print(f"Extracting trace {TRACE_INDEX}, swath {SWATH_INDEX}\n")
+
+    # Fix extraction parameters
+    xwd, cr, traces = fix_parameters(
+        EXTRACTION_HEIGHT, column_range, traces, nrow, ncol, ntrace
+    )
+
+    # Get the specific trace
+    trace_coef = traces[TRACE_INDEX]
+    trace_cr = cr[TRACE_INDEX]
+    trace_xwd = xwd[TRACE_INDEX]
+
+    print(f"Trace {TRACE_INDEX}:")
+    print(f"  Column range: {trace_cr}")
+    print(f"  Extraction height: {trace_xwd} (below, above)")
+
+    # Extract single swath
+    result = extract_single_swath(
+        img,
+        trace_coef,
+        trace_cr,
+        SWATH_INDEX,
+        trace_xwd,
+        p1=None,  # No curvature correction
+        p2=None,
+    )
+
+    # Save outputs
+    out_file = join(output_dir, f"debug_swath_t{TRACE_INDEX}_s{SWATH_INDEX}.npz")
+    os.makedirs(output_dir, exist_ok=True)
+    np.savez(
+        out_file,
+        swath_img=result["swath_img"],
+        spec=result["spec"],
+        slitf=result["slitf"],
+        model=result["model"],
+        unc=result["unc"],
+        mask=result["mask"],
+        ycen=result["ycen"],
+        ibeg=result["ibeg"],
+        iend=result["iend"],
+        yrange=result["yrange"],
+        trace_index=TRACE_INDEX,
+        swath_index=SWATH_INDEX,
+    )
+    print(f"\nSaved results to: {out_file}")
+
+    # Print summary
+    print("\n=== Extraction Results ===")
+    print(f"Spectrum shape: {result['spec'].shape}")
+    print(f"Slitfunction shape: {result['slitf'].shape}")
+    print(f"Model shape: {result['model'].shape}")
+    print(f"Chi-squared: {result['info'][1]:.3f}")
+    print(f"Iterations: {result['info'][0]}")
+    print(f"Masked pixels: {result['mask'].sum()}")
+
+
+if __name__ == "__main__":
+    main()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -43,6 +43,6 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    # order_range=(0, 25),
+    # trace_range=(0, 25),
     plot=1,
 ).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 import os.path
 
@@ -71,7 +71,7 @@ kwargs_comb["nstep"] = 0
 kwargs["plot"] = False
 
 
-for key in ["extraction_method", "extraction_height", "extraction_cutoff"]:
+for key in ["extraction_method", "extraction_height"]:
     del kwargs_comb[key]
     del kwargs[key]
 

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np
@@ -15,8 +15,20 @@ 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.ord_default.npz", allow_pickle=True)
-orders = data["orders"]
+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"]
 
 i = 5
@@ -24,7 +36,7 @@ ix = np.arange(ncol)
 
 ylow, yhigh = 50, 50
 ibeg, iend = 1500, 2000
-ycen = np.polyval(orders[i], ix)
+ycen = np.polyval(traces[i], ix)
 ycen_int = ycen.astype(int)
 # yrange = extract.get_y_scale(ycen, [400, 600], [5, 5], nrow)
 

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -41,6 +41,6 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    # order_range=(0, 25),
+    # trace_range=(0, 25),
     plot=1,
 ).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -41,6 +41,6 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    # order_range=(0, 25),
+    # trace_range=(0, 25),
     plot=0,
 ).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -41,6 +41,6 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    # order_range=(0, 25),
+    # trace_range=(0, 25),
     plot=1,
 ).run()

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b4}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b4"]
 # ///
 """
 Simple usage example for PyReduce
@@ -52,6 +52,6 @@ Pipeline.from_instrument(
     input_dir=input_dir,
     output_dir=output_dir,
     configuration=config,
-    # order_range=(0, 25),
+    # trace_range=(0, 25),
     plot=2,
 ).run()