pyreduce-astro 0.7a5__tar.gz → 0.7a6__tar.gz

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/.gitignore

@@ -20,3 +20,4 @@ docs/_build/
 .claude
 debug/
 idl/
+logs/

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/CHANGELOG.md

@@ -1,6 +1,18 @@
 # Changelog
 
 
+## [0.7a6] - 2026-01-03
+
+### Added
+- `--file` option for CLI step commands to bypass file discovery
+- NEID instrument with multi-amplifier support
+
+### Changed
+- Rename `orders` step to `trace` throughout codebase (CLI, API, configs)
+
+### Fixed
+- test_normflat to use column_range returned by extract
+
 ## [0.7a5] - 2025-12-30
 
 ### Changed

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/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,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 ```
 
 ## Package Structure
@@ -63,7 +63,7 @@ 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 |
-| `orders` | `OrderTracing` | Trace echelle order positions on flat |
+| `trace` | `OrderTracing` | Trace echelle order positions on flat |
 | `curvature` | `SlitCurvatureDetermination` | Measure slit tilt/shear from arc lamp |
 | `scatter` | `BackgroundScatter` | Model inter-order scattered light |
 | `norm_flat` | `NormalizeFlatField` | Normalize flat, extract blaze function |
@@ -138,7 +138,7 @@ Defines HOW to reduce - algorithm parameters per step:
   "bias": {
     "degree": 0
   },
-  "orders": {
+  "trace": {
     "degree": 4,
     "noise": 100,
     "min_cluster": 500,
@@ -176,7 +176,7 @@ result = Pipeline.from_instrument(
     target="HD132205",
     night="2010-04-01",
     channel="middle",
-    steps=("bias", "flat", "orders", "science"),
+    steps=("bias", "flat", "trace", "science"),
     base_dir="/data",
     plot=1,
 ).run()
@@ -221,11 +221,11 @@ pyreduce.reduce.main(
 
 ```bash
 # Full pipeline
-uv run reduce run UVES HD132205 --steps bias,flat,orders
+uv run reduce run UVES HD132205 --steps bias,flat,trace
 
 # Individual steps (top-level commands)
 uv run reduce bias UVES HD132205
-uv run reduce orders UVES HD132205
+uv run reduce trace UVES HD132205
 uv run reduce wavecal UVES HD132205
 
 # Combine reduced spectra

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a5
+Version: 0.7a6
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -76,7 +76,7 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
 uv run reduce bias UVES HD132205

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/README.md

@@ -34,7 +34,7 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
 uv run reduce bias UVES HD132205

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "J1228_det1"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -32,7 +32,7 @@ instrument.info["prescan_x"] = "PRESCAN X"
 # For loading the config we specify pyreduce as the source, since this is the default
 config = get_configuration_for_instrument("pyreduce")
 # Define your own configuration
-config["orders"]["degree"] = 5
+config["trace"]["degree"] = 5
 
 # Since we can't find the files ourselves (at least not without defining the criteria we are looking for)
 # We need to manually define which files go where
@@ -53,7 +53,7 @@ channel = ""
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "HARPN"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "norm_flat",
     # "wavecal_master",
     "wavecal",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "red"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 import os.path
 

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "LRS_SLITLESS"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "GR700XD"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = ""
 steps = (
     "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -19,7 +19,7 @@ channel = "CS23"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "IFU_NOMINAL"
 steps = (
     # "bias",
     # "flat",
-    "orders",
+    "trace",
     "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/metis_lss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "LSS_M"
 steps = (
     # "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/micado_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -17,7 +17,7 @@ channel = ""
 steps = (
     # "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     # # "scatter",
     # "norm_flat",
@@ -47,7 +47,7 @@ config = pyreduce.configuration.get_configuration_for_instrument(instrument)
 # Once you are satisfied with a certain parameter, you can update it in settings_MICADO.json.
 
 
-# config["orders"]["noise"] = 100
+# config["trace"]["noise"] = 100
 # config["curvature"]["extraction_width"] = 350 # curvature can still be improved with this and the following parameters
 # config["curvature"]["peak_threshold"] =10
 # config["curvature"]["peak_width"] =2 #CHECK 6 also works and detects one less line

pyreduce_astro-0.7a6/examples/neid_example.py

@@ -0,0 +1,65 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a6"]
+# ///
+"""
+NEID reduction example
+
+NEID is a fiber-fed, high-resolution (R~110,000) spectrograph on the
+WIYN 3.5m telescope at Kitt Peak. L0 data has 16 amplifiers that are
+automatically assembled during loading.
+
+This example reduces HD 4628 observations from night 2024-09-19.
+Note: Observations before 12:00 UTC belong to the previous night.
+"""
+
+import os
+
+from pyreduce.configuration import get_configuration_for_instrument
+from pyreduce.pipeline import Pipeline
+
+# Define parameters
+instrument = "NEID"
+target = "HD 4628"
+night = "2024-09-19"  # Observations before 12:00 UTC belong to previous night
+channel = "HR"
+
+# Reduction steps to run
+# Start with basic steps; add wavecal/science once calibration files are set up
+steps = (
+    "flat",
+    "trace",
+    # "curvature",
+    # "norm_flat",
+    # "wavecal_master",
+    # "wavecal_init",
+    # "wavecal",
+    # "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data paths
+# Set REDUCE_DATA environment variable or modify base_dir
+base_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
+base_dir = os.path.join(base_dir, "NEID")
+input_dir = ""  # Files directly in base_dir
+output_dir = "reduced"
+
+# Load default configuration
+config = get_configuration_for_instrument(instrument)
+
+# Run the pipeline
+if __name__ == "__main__":
+    Pipeline.from_instrument(
+        instrument,
+        target,
+        night=night,
+        channel=channel,
+        steps=steps,
+        base_dir=base_dir,
+        input_dir=input_dir,
+        output_dir=output_dir,
+        configuration=config,
+        plot=1,
+    ).run()

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/nirspec_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "NIRSPEC"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     "wavecal",
     "freq_comb",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/toes_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 import numpy as np
 
@@ -81,13 +81,13 @@ instrument.info["wavelength_range"] = [
 # For loading the config we specify pyreduce as the source, since this is the default
 config = get_configuration_for_instrument("pyreduce")
 # Define your own configuration
-config["orders"]["filter_y"] = 20  # smoothing along cross-dispersion
-config["orders"]["degree"] = 4
-config["orders"]["degree_before_merge"] = 2
-config["orders"]["noise"] = 5.5
-config["orders"]["min_cluster"] = 3000
-config["orders"]["min_width"] = 200
-config["orders"]["manual"] = True
+config["trace"]["filter_y"] = 20  # smoothing along cross-dispersion
+config["trace"]["degree"] = 4
+config["trace"]["degree_before_merge"] = 2
+config["trace"]["noise"] = 5.5
+config["trace"]["min_cluster"] = 3000
+config["trace"]["min_width"] = 200
+config["trace"]["manual"] = True
 config["norm_flat"]["oversampling"] = 8  # Subpixel scale for slit function modelling
 config["norm_flat"]["swath_width"] = 400  # Extraction swath width (columns)
 config["wavecal_master"]["extraction_width"] = 2
@@ -110,7 +110,7 @@ config["science"]["bias_scaling"] = "number_of_files"
 files = {
     "bias": ["Bias_0s_20240621_221716-%d.fit" % i for i in np.arange(1, 11)],
     "flat": ["Flat_5s_20240621_222912-%d.fit" % i for i in np.arange(1, 5)],
-    "orders": [flat_file],
+    "trace": [flat_file],
     "science": ["Vega_Object_25s_20240621_224908-%d.fit" % i for i in np.arange(1, 2)],
     "wavecal_master": [
         "Sun_Calibration_35s_20240621_184136-%d.fit" % i for i in np.arange(1, 2)
@@ -138,7 +138,7 @@ channel = ""
 steps = (
     #    "bias",
     #    "flat",
-    #    "orders",
+    #    "trace",
     #    "norm_flat",
     "wavecal_master",
     "wavecal",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/uves_callfunc.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Example showing direct function calls for each step.
@@ -77,12 +77,12 @@ settings, files = file_groups[0]
 print("Settings:", settings)
 
 # Files are now accessible as a dict with keys:
-#   bias, flat, orders, curvature, scatter, wavecal_master, freq_comb_master, science
+#   bias, flat, trace, curvature, scatter, wavecal_master, freq_comb_master, science
 # Each is a list/array of file paths
 
 bias_files = files.get("bias", [])
 flat_files = files.get("flat", [])
-order_files = files.get("orders", flat_files)  # Use flat if no dedicated order files
+order_files = files.get("trace", flat_files)  # Use flat if no dedicated order files
 curvature_files = files.get("curvature", files.get("wavecal_master", []))
 wavecal_files = files.get("wavecal_master", [])
 science_files = files.get("science", [])
@@ -119,8 +119,8 @@ flat_step = Flat(*step_args, **step_config("flat"))
 flat = flat_step.run(flat_files, bias, mask)
 
 # Step 4: Order tracing
-print("\n=== ORDERS ===")
-orders_step = OrderTracing(*step_args, **step_config("orders"))
+print("\n=== TRACE ===")
+orders_step = OrderTracing(*step_args, **step_config("trace"))
 orders = orders_step.run(order_files, mask, bias)
 
 # Step 5: Curvature

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/uves_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "middle"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     "curvature",
     "wavecal",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/examples/xshooter_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -19,7 +19,7 @@ channel = "NIR"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "scatter",
     # "norm_flat",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyreduce-astro"
-version = "0.7a5"
+version = "0.7a6"
 requires-python = ">=3.13"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"