pyreduce-astro 0.7b2__tar.gz → 0.7b3__tar.gz

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/.gitignore

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

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/CHANGELOG.md

@@ -1,6 +1,22 @@
 # 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

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/CLAUDE.md

@@ -257,8 +257,11 @@ 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`
+
+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
 

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7b2
+Version: 0.7b3
 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-0.7b3}/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-0.7b2 → pyreduce_astro-0.7b3}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 import os.path
 

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/metis_lss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/micado_example.py

@@ -1,13 +1,14 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce
 Loads a ScopeSim simulated MICADO dataset (with updated spectral layout and updated line lists), and runs the full extraction.
 """
 
-import pyreduce
+from pyreduce.configuration import get_configuration_for_instrument
+from pyreduce.pipeline import Pipeline
 
 # define parameters
 instrument = "MICADO"
@@ -40,7 +41,7 @@ base_dir = "/media/data/Dropbox/Dropbox/WORKING/iMICADO/Working/WORKING_PyReduce
 input_dir = "raw_new/HK/"
 output_dir = "reduced_new/"
 
-config = pyreduce.configuration.get_configuration_for_instrument(instrument)
+config = get_configuration_for_instrument(instrument)
 
 
 # Configuring parameters of individual steps here overwrites those defined  in the settings_MICADO.json file.
@@ -56,19 +57,16 @@ config = pyreduce.configuration.get_configuration_for_instrument(instrument)
 
 # NOTE: micado.thar_master.fits (created and controlled by wavecal_master) is NOT overwritten if any parameter in the steps in or before it are changed. Thus it has to be deleted before running PyReduce again.
 
-pyreduce.reduce.main(
+Pipeline.from_instrument(
     instrument,
     target,
-    night,
-    channel,
-    steps,
+    night=night,
+    channel=channel,
+    steps=steps,
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
     configuration=config,
-    order_range=(
-        3,
-        4,
-    ),  # for MICADO, when one order is on the detector (currently detector 5 of the HK band)
+    order_range=(3, 4),
     plot=1,
-)
+).run()

pyreduce_astro-0.7b3/examples/mosaic_example.py

@@ -0,0 +1,171 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7b3"]
+# ///
+"""
+MOSAIC NIR spectrograph example.
+
+Demonstrates fiber bundle tracing and extraction on simulated E2E data.
+After tracing all fibers, identifies the central fiber in each group of 7
+and extracts only those 90 traces.
+"""
+
+import os
+from os.path import join
+
+import numpy as np
+
+from pyreduce import util
+from pyreduce.configuration import load_config
+from pyreduce.instruments.instrument_info import load_instrument
+from pyreduce.reduce import (
+    OrderTracing,
+    ScienceExtraction,
+    SlitCurvatureDetermination,
+)
+
+# Parameters
+instrument_name = "MOSAIC"
+target = "MOSAIC_NIR"
+night = ""
+channel = "NIR"
+order_range = None
+plot = 1
+
+# Handle plot environment variables
+if "PYREDUCE_PLOT" in os.environ:
+    plot = int(os.environ["PYREDUCE_PLOT"])
+plot_dir = os.environ.get("PYREDUCE_PLOT_DIR")
+util.set_plot_dir(plot_dir)
+
+# Data location
+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")
+
+os.makedirs(output_dir, exist_ok=True)
+
+# File paths (simulated data)
+flat_file = join(
+    base_dir,
+    "E2E_FLAT_DIT_20s_MOSAIC_2Cam_c01",
+    "E2E_FLAT_DIT_20s_MOSAIC_2Cam_c01_STATIC_FOCAL_PLANE.fits",
+)
+thar_file = join(
+    base_dir,
+    "E2E_ThAr_DIT_20s_MOSAIC_2Cam_c01",
+    "E2E_ThAr_DIT_20s_MOSAIC_2Cam_c01_STATIC_FOCAL_PLANE.fits",
+)
+
+# Verify files exist
+for fpath in [flat_file, thar_file]:
+    if not os.path.exists(fpath):
+        raise FileNotFoundError(f"Data file not found: {fpath}")
+
+print(f"FLAT: {flat_file}")
+print(f"ThAr: {thar_file}")
+
+# Load instrument and configuration
+instrument = load_instrument(instrument_name)
+config = load_config(None, instrument_name, 0)
+
+# Common step arguments
+step_args = (instrument, channel, target, night, output_dir, order_range)
+
+
+def step_config(name):
+    """Get step config with plot level override."""
+    cfg = config.get(name, {}).copy()
+    cfg["plot"] = plot
+    return cfg
+
+
+print("\n=== TRACE ===")
+trace_step = OrderTracing(*step_args, **step_config("trace"))
+# traces, column_range = trace_step.run([flat_file])
+traces, column_range = trace_step.load()
+print(f"Found {len(traces)} traces (expected ~630)")
+
+# --- STEP 3: Identify group centers from gap pattern ---
+print("\n=== IDENTIFY GROUP CENTERS ===")
+
+# Evaluate all traces at detector center (x=2048)
+x_center = 2048
+traced_y = np.array([np.polyval(o, x_center) for o in traces])
+print(f"Traced y-positions at x={x_center}: {traced_y[0]:.1f} to {traced_y[-1]:.1f}")
+
+# Sort traces by y position
+sort_idx = np.argsort(traced_y)
+sorted_y = traced_y[sort_idx]
+
+# Compute gaps between consecutive traces
+gaps = np.diff(sorted_y)
+
+# Inter-group gaps are ~2x larger than intra-group gaps.
+# Use median gap as the intra-group spacing estimate (robust to outliers).
+median_gap = np.median(gaps)
+threshold = 1.5 * median_gap  # Between 1x (intra) and 2x (inter)
+print(f"Median gap: {median_gap:.2f} px, threshold: {threshold:.2f} px")
+
+# Find group boundaries (where gap exceeds threshold)
+is_group_boundary = gaps > threshold
+
+# Assign group IDs: increment at each boundary
+group_ids = np.zeros(len(sorted_y), dtype=int)
+group_ids[1:] = np.cumsum(is_group_boundary)
+
+n_groups = group_ids.max() + 1
+print(f"Identified {n_groups} groups")
+
+# For each group, find the center trace (middle element)
+center_trace_indices = []
+group_sizes = []
+
+for g in range(n_groups):
+    group_mask = group_ids == g
+    group_orig_indices = sort_idx[group_mask]
+    group_y_values = traced_y[group_orig_indices]
+
+    # Sort by y within group to find center
+    within_sort = np.argsort(group_y_values)
+    center_idx = len(within_sort) // 2  # Middle element
+    center_trace_indices.append(group_orig_indices[within_sort[center_idx]])
+    group_sizes.append(len(group_orig_indices))
+
+center_trace_indices = np.array(center_trace_indices)
+group_sizes = np.array(group_sizes)
+
+# Report group size distribution
+size_counts = {sz: (group_sizes == sz).sum() for sz in sorted(set(group_sizes))}
+print(f"Group sizes: {size_counts}")
+
+# Extract only the center traces
+center_traces = traces[center_trace_indices]
+center_column_range = column_range[center_trace_indices]
+print(f"\nUsing {len(center_traces)} group center traces for extraction")
+
+center_trace = (center_traces, center_column_range)
+
+print("\n=== CURVATURE ===")
+curve_step = SlitCurvatureDetermination(*step_args, **step_config("curvature"))
+# curvature = curve_step.run([thar_file], center_trace)
+curvature = curve_step.load()
+print("Curvature determination complete")
+
+science_step = ScienceExtraction(*step_args, **step_config("science"))
+
+print("\n=== EXTRACT ThAr ===")
+try:
+    thar_spec = science_step.run([thar_file], center_trace, curvature=curvature)
+    print("ThAr extraction complete")
+except Exception as e:
+    print(f"ThAr extraction failed: {e}")
+    thar_spec = None
+
+print("\n=== EXTRACT FLAT ===")
+try:
+    flat_spec = science_step.run([flat_file], center_trace, curvature=curvature)
+    print("FLAT extraction complete")
+except Exception as e:
+    print(f"FLAT extraction failed: {e}")
+    flat_spec = None

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/neid_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 NEID reduction example

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/nirspec_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/toes_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 import numpy as np
 

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/uves_callfunc.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Example showing direct function calls for each step.
@@ -111,28 +111,27 @@ mask = mask_step.run()
 # Step 2: Bias
 print("\n=== BIAS ===")
 bias_step = Bias(*step_args, **step_config("bias"))
-bias = bias_step.run(bias_files, mask)
+bias = bias_step.run(bias_files, mask=mask)
 
 # Step 3: Flat
 print("\n=== FLAT ===")
 flat_step = Flat(*step_args, **step_config("flat"))
-flat = flat_step.run(flat_files, bias, mask)
+flat = flat_step.run(flat_files, bias=bias, mask=mask)
 
 # Step 4: Order tracing
 print("\n=== TRACE ===")
 orders_step = OrderTracing(*step_args, **step_config("trace"))
-orders = orders_step.run(order_files, mask, bias)
+orders = orders_step.run(order_files, mask=mask, bias=bias)
 
 # Step 5: Curvature
 print("\n=== CURVATURE ===")
 curvature_step = SlitCurvatureDetermination(*step_args, **step_config("curvature"))
-curvature = curvature_step.run(curvature_files, orders, mask, bias)
+curvature = curvature_step.run(curvature_files, orders, mask=mask, bias=bias)
 
 # Step 6: Normalize flat
 print("\n=== NORM_FLAT ===")
 norm_flat_step = NormalizeFlatField(*step_args, **step_config("norm_flat"))
-scatter = None  # Optional background scatter
-norm_flat = norm_flat_step.run(flat, orders, scatter, curvature)
+norm_flat = norm_flat_step.run(flat, orders)
 
 # Step 7: Wavelength calibration (three sub-steps)
 print("\n=== WAVECAL ===")
@@ -140,7 +139,12 @@ wavecal_master_step = WavelengthCalibrationMaster(
     *step_args, **step_config("wavecal_master")
 )
 wavecal_master = wavecal_master_step.run(
-    wavecal_files, orders, mask, curvature, bias, norm_flat
+    wavecal_files,
+    orders,
+    mask=mask,
+    curvature=curvature,
+    bias=bias,
+    norm_flat=norm_flat,
 )
 
 # wavecal_init: load existing linelist (from instrument defaults or previous run)
@@ -158,7 +162,12 @@ wave, coef, linelist = wavecal
 print("\n=== SCIENCE ===")
 science_step = ScienceExtraction(*step_args, **step_config("science"))
 science = science_step.run(
-    science_files, bias, orders, norm_flat, curvature, scatter, mask
+    science_files,
+    orders,
+    bias=bias,
+    norm_flat=norm_flat,
+    curvature=curvature,
+    mask=mask,
 )
 
 # Step 9: Continuum normalization

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/uves_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/examples/xshooter_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7b2"]
+# dependencies = ["pyreduce-astro>=0.7b3"]
 # ///
 """
 Simple usage example for PyReduce
@@ -19,10 +19,10 @@ channel = "NIR"
 steps = (
     # "bias",
     # "flat",
-    # "trace",
-    # "scatter",
-    # "norm_flat",
-    # "curvature",
+    "trace",
+    "scatter",
+    "norm_flat",
+    "curvature",
     "wavecal",
     "science",
     # "continuum",

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyreduce-astro"
-version = "0.7b2"
+version = "0.7b3"
 requires-python = ">=3.13"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"
@@ -56,6 +56,12 @@ dev = [
     "myst-parser",
     "setuptools",
 ]
+ipynb = [
+    "ipykernel>=7.1.0",
+    "jupyter-client>=8.8.0",
+    "jupytext>=1.18.1",
+    "nbconvert>=7.16.6",
+]
 
 [project.urls]
 Homepage = "https://github.com/ivh/PyReduce"

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/pyreduce/__main__.py

@@ -59,8 +59,17 @@ def cli():
 @click.option(
     "--output-dir", "-o", default="reduced", help="Output directory relative to base"
 )
+@click.option("--plot", "-p", default=0, help="Plot level: 0=none, 1=basic, 2=detailed")
 @click.option(
-    "--plot", "-p", default=0, help="Plot level (0=none, 1=save, 2=interactive)"
+    "--plot-dir",
+    default=None,
+    help="Save plots to this directory as PNG files",
+)
+@click.option(
+    "--plot-show",
+    type=click.Choice(["block", "defer", "off"]),
+    default=None,
+    help="Display mode: block (interactive), defer (show all at end), off",
 )
 @click.option(
     "--order-range",
@@ -83,6 +92,8 @@ def run(
     input_dir,
     output_dir,
     plot,
+    plot_dir,
+    plot_show,
     order_range,
     settings,
 ):
@@ -90,9 +101,15 @@ def run(
 
     INSTRUMENT: Name of the instrument (e.g., UVES, HARPS, XSHOOTER)
     """
+    import os
+
     from .configuration import get_configuration_for_instrument, load_settings_override
     from .reduce import main as reduce_main
 
+    # CLI args override env vars for plot settings
+    if plot_show is not None:
+        os.environ["PYREDUCE_PLOT_SHOW"] = plot_show
+
     # Parse steps
     if steps:
         steps = tuple(s.strip() for s in steps.split(","))
@@ -123,6 +140,7 @@ def run(
             configuration=config,
             order_range=order_range,
             plot=plot,
+            plot_dir=plot_dir,
         )
     except FileNotFoundError as e:
         raise click.ClickException(str(e)) from None

{pyreduce_astro-0.7b2 → pyreduce_astro-0.7b3}/pyreduce/combine_frames.py

@@ -630,6 +630,7 @@ def combine_calibrate(
             )
 
     if plot:  # pragma: no cover
+        plt.figure()
         title = "Master"
         if plot_title is not None:
             title = f"{plot_title}\n{title}"
@@ -695,6 +696,7 @@ def combine_polynomial(
     bhead["EXPTIME"] = np.sum(exptimes)
 
     if plot:
+        plt.figure()
         title = "Master"
         if plot_title is not None:
             title = f"{plot_title}\n{title}"
@@ -844,6 +846,7 @@ def combine_bias(
         nbad = 0
 
     if plot:  # pragma: no cover
+        plt.figure()
         title = "Master Bias"
         if plot_title is not None:
             title = f"{plot_title}\n{title}"