pyreduce-astro 0.7a4__tar.gz → 0.7a6__tar.gz

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/.gitignore

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

pyreduce_astro-0.7a6/.python-version

@@ -0,0 +1 @@
+3.14

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/CHANGELOG.md

@@ -1,6 +1,25 @@
 # 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
+- Rename `arm` to `channel` throughout codebase (API, CLI, configs)
+- Remove decker from CRIRES+ channel format (`J1228_det1` instead of `J1228_Open_det1`)
+- Example scripts now use `$REDUCE_DATA` env var instead of hardcoded paths
+
 ## [0.7a4] - 2025-12-23
 
 ### Added
@@ -41,7 +60,7 @@
 - `filter_x` and `filter_type` options for order tracing
 
 ### Changed
-- Rename `mode` to `arm` terminology throughout
+- Rename `mode` to `channel` terminology throughout
 - Output extension changed from `.ech` to `.fits`
 - Documentation converted from RST to Markdown
 - Trace detection parameters renamed (`opower` -> `degree`, `filter_size` -> `filter_y`)

{pyreduce_astro-0.7a4 → 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 |
@@ -95,7 +95,7 @@ Defines what the instrument IS - hardware properties and header mappings:
 # Basic identification
 instrument: HARPS
 telescope: ESO-3.6m
-arms: [red, blue]
+channels: [red, blue]
 
 # Detector properties
 naxis: [4096, 4096]
@@ -138,7 +138,7 @@ Defines HOW to reduce - algorithm parameters per step:
   "bias": {
     "degree": 0
   },
-  "orders": {
+  "trace": {
     "degree": 4,
     "noise": 100,
     "min_cluster": 500,
@@ -175,8 +175,8 @@ result = Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    arm="middle",
-    steps=("bias", "flat", "orders", "science"),
+    channel="middle",
+    steps=("bias", "flat", "trace", "science"),
     base_dir="/data",
     plot=1,
 ).run()
@@ -196,7 +196,7 @@ from pyreduce.pipeline import Pipeline
 pipe = Pipeline(
     instrument="UVES",
     output_dir="/output",
-    arm="middle",
+    channel="middle",
     plot=0,
 )
 pipe.bias(bias_files)
@@ -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-0.7a4 → pyreduce_astro-0.7a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a4
+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
@@ -15,12 +15,10 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Programming Language :: C
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Astronomy
-Requires-Python: >=3.11
+Requires-Python: >=3.13
 Requires-Dist: astropy>=5.3.0
 Requires-Dist: cffi>=1.17.1
 Requires-Dist: click>=8.1.0
@@ -44,7 +42,7 @@ 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 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
 
 # PyReduce
 
@@ -78,7 +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
@@ -93,7 +91,7 @@ Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    arm="middle",
+    channel="middle",
 ).run()
 ```
 

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/README.md

@@ -1,6 +1,6 @@
 [![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 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
 
 # PyReduce
 
@@ -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
@@ -49,7 +49,7 @@ Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    arm="middle",
+    channel="middle",
 ).run()
 ```
 

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.
@@ -79,16 +79,16 @@ logical_fibers = {
 
 # --- Load instrument ---
 instrument = load_instrument(instrument_name)
-arm = instrument.info["arms"][0]  # Use first arm
-print(f"Instrument: {instrument.name}, arm: {arm}")
+channel = instrument.info["channels"][0]  # Use first channel
+print(f"Instrument: {instrument.name}, channel: {channel}")
 
 # --- Step 1: Load images using instrument class ---
 print(f"\nLoading {file_even}...")
-img_even, head_even = instrument.load_fits(file_even, arm=arm, extension=0)
+img_even, head_even = instrument.load_fits(file_even, channel=channel, extension=0)
 print(f"  Shape: {img_even.shape}, dtype: {img_even.dtype}")
 
 print(f"Loading {file_odd}...")
-img_odd, head_odd = instrument.load_fits(file_odd, arm=arm, extension=0)
+img_odd, head_odd = instrument.load_fits(file_odd, channel=channel, extension=0)
 
 # --- Step 2: Trace each flat independently ---
 print("\nTracing even-illuminated fibers...")

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/crires_plus_example.py

@@ -1,24 +1,26 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
 Loads a CRIRES+ dataset, and runs the extraction
 """
 
-from pyreduce.configuration import get_configuration_for_instrument
+import os
+
+from pyreduce import datasets
 from pyreduce.pipeline import Pipeline
 
 # define parameters
-instrument = "Crires_plus"
+instrument = "CRIRES_PLUS"
 target = ""
 night = ""
-arm = "J1228_Open_det1"
+channel = "J1228_det1"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     # "scatter",
     # "norm_flat",
@@ -32,32 +34,20 @@ steps = (
     # "finalize",
 )
 
-# some basic settings
-# Expected Folder Structure: base_dir/datasets/HD132205/*.fits.gz
-# Feel free to change this to your own preference, values in curly brackets will be replaced with the actual values {}
-
-# load dataset (and save the location)
-base_dir = "/DATA/datasets/CRIRES"
-input_dir = base_dir
-output_dir = base_dir + "/reduced/"
-
-# Path to the configuration parameters, that are to be used for this reduction
-
-config = get_configuration_for_instrument(
-    instrument,
-    plot=1,
-)
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = os.path.join(datasets.get_data_dir(), "CRIRES")
+input_dir = ""
+output_dir = "reduced"
 
 Pipeline.from_instrument(
     instrument,
     target,
     night=night,
-    arm=arm,
+    channel=channel,
     steps=steps,
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    configuration=config,
     allow_calibration_only=True,
     # order_range=(0, 4),
 ).run()

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# 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
@@ -49,11 +49,11 @@ start_logging(log_file)
 # Define other parameter for PyReduce
 target = ""
 night = "2019-07-21"
-arm = ""
+channel = ""
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",
@@ -70,7 +70,7 @@ pipe = Pipeline.from_files(
     output_dir=output_dir,
     target=target,
     instrument=instrument,
-    arm=arm,
+    channel=channel,
     night=night,
     config=config,
     # order_range=order_range,

pyreduce_astro-0.7a6/examples/harpn_example.py

@@ -0,0 +1,48 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a6"]
+# ///
+"""
+Simple usage example for PyReduce
+Loads a HARPS-N dataset, and runs the extraction
+"""
+
+import os
+
+from pyreduce import datasets
+from pyreduce.pipeline import Pipeline
+
+# define parameters
+instrument = "HARPN"
+target = ""
+night = ""
+channel = "HARPN"
+steps = (
+    # "bias",
+    # "flat",
+    # "trace",
+    # "norm_flat",
+    # "wavecal_master",
+    "wavecal",
+    # "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = os.path.join(datasets.get_data_dir(), "HARPN")
+input_dir = "raw"
+output_dir = "reduced/{channel}"
+
+Pipeline.from_instrument(
+    instrument,
+    target,
+    night=night,
+    channel=channel,
+    steps=steps,
+    base_dir=base_dir,
+    input_dir=input_dir,
+    output_dir=output_dir,
+    # order_range=(0, 25),
+    plot=1,
+).run()

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -14,11 +14,11 @@ from pyreduce.pipeline import Pipeline
 instrument = "HARPS"
 target = "HD109200"
 night = None
-arm = "red"
+channel = "red"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",
@@ -36,13 +36,13 @@ steps = (
 # load dataset (and save the location)
 base_dir = datasets.HARPS()  # Uses $REDUCE_DATA or ~/REDUCE_DATA
 input_dir = "raw"
-output_dir = "reduced_{arm}"
+output_dir = "reduced_{channel}"
 
 Pipeline.from_instrument(
     instrument,
     target,
     night=night,
-    arm=arm,
+    channel=channel,
     steps=steps,
     base_dir=base_dir,
     input_dir=input_dir,

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 import os.path
 
@@ -13,9 +13,9 @@ from pyreduce.wavelength_calibration import (
 )
 
 
-def func_wavecal(deg, thar, instrument, arm, **kwargs):
+def func_wavecal(deg, thar, instrument, channel, **kwargs):
     reference = instruments.instrument_info.get_wavecal_filename(
-        None, instrument, arm, polarimetry=False
+        None, instrument, channel, polarimetry=False
     )
     reference = np.load(reference, allow_pickle=True)
     linelist = reference["cs_lines"]
@@ -40,7 +40,7 @@ def func_freq_comb(deg, comb, wave, **kwargs):
 instrument = "HARPS"
 target = "HD109200"
 night = "2015-04-09"
-arm = "red"
+channel = "red"
 
 # some basic settings
 # Expected Folder Structure: base_dir/datasets/HD132205/*.fits.gz
@@ -49,7 +49,7 @@ arm = "red"
 # load dataset (and save the location)
 base_dir = datasets.HARPS()  # Uses $REDUCE_DATA or ~/REDUCE_DATA
 input_dir = "raw"
-output_dir = f"reduced_{arm}"
+output_dir = f"reduced_{channel}"
 
 config = configuration.get_configuration_for_instrument(instrument)
 
@@ -82,10 +82,10 @@ for i in np.ndindex(shape):
     grid[i] += 1
 
 # aic = func_freq_comb((3, 6), comb, wave, **kwargs_comb)
-# aic = func_wavecal((3, 6), thar, instrument, arm, **kwargs)
+# aic = func_wavecal((3, 6), thar, instrument, channel, **kwargs)
 
 # matrix = util.gridsearch(
-#     func_wavecal, grid, args=(thar, instrument, arm), kwargs=kwargs
+#     func_wavecal, grid, args=(thar, instrument, channel), kwargs=kwargs
 # )
 # np.save(f"matrix_{ndim}D.npy", matrix)
 # matrix = np.load(f"matrix_{ndim}D.npy")

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/just_one_swath.py

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

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/jwst_miri_example.py

@@ -1,24 +1,24 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
 Loads a JWST MIRI dataset, and runs the extraction
 """
 
-from pyreduce.configuration import get_configuration_for_instrument
+from pyreduce import datasets
 from pyreduce.pipeline import Pipeline
 
 # define parameters
 instrument = "JWST_MIRI"
 target = None
 night = None
-arm = "LRS_SLITLESS"
+channel = "LRS_SLITLESS"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     # "wavecal",
     # "curvature",
@@ -27,28 +27,20 @@ steps = (
     # "finalize",
 )
 
-# some basic settings
-# Expected Folder Structure: base_dir/datasets/HD132205/*.fits.gz
-# Feel free to change this to your own preference, values in curly brackets will be replaced with the actual values {}
-
-# load dataset (and save the location)
-base_dir = "/DATA/JWST/MIRI/MIRIsim/"
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = datasets.JWST_MIRI()
 input_dir = "raw"
 output_dir = "reduced"
 
-# Path to the configuration parameters, that are to be used for this reduction
-config = get_configuration_for_instrument(instrument)
-
 Pipeline.from_instrument(
     instrument,
     target,
     night=night,
-    arm=arm,
+    channel=channel,
     steps=steps,
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    configuration=config,
     # order_range=(0, 25),
     plot=1,
 ).run()

pyreduce_astro-0.7a6/examples/jwst_niriss_example.py

@@ -0,0 +1,46 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a6"]
+# ///
+"""
+Simple usage example for PyReduce
+Loads a sample JWST NIRISS dataset, and runs the extraction
+"""
+
+from pyreduce import datasets
+from pyreduce.pipeline import Pipeline
+
+# define parameters
+instrument = "JWST_NIRISS"
+target = None
+night = None
+channel = "GR700XD"
+steps = (
+    "bias",
+    "flat",
+    "trace",
+    "norm_flat",
+    # "wavecal",
+    # "curvature",
+    "science",
+    "continuum",
+    "finalize",
+)
+
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = datasets.JWST_NIRISS()
+input_dir = "raw"
+output_dir = "reduced"
+
+Pipeline.from_instrument(
+    instrument,
+    target,
+    night=night,
+    channel=channel,
+    steps=steps,
+    base_dir=base_dir,
+    input_dir=input_dir,
+    output_dir=output_dir,
+    # order_range=(0, 25),
+    plot=0,
+).run()

pyreduce_astro-0.7a6/examples/lick_apf_example.py

@@ -0,0 +1,46 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a6"]
+# ///
+"""
+Simple usage example for PyReduce
+Loads a Lick APF dataset, and runs the extraction
+"""
+
+from pyreduce import datasets
+from pyreduce.pipeline import Pipeline
+
+# define parameters
+instrument = "LICK_APF"
+target = "KIC05005618"
+night = None
+channel = ""
+steps = (
+    "bias",
+    # "flat",
+    # "trace",
+    # "norm_flat",
+    # "wavecal",
+    # "curvature",
+    "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = datasets.LICK_APF()
+input_dir = "raw"
+output_dir = "reduced"
+
+Pipeline.from_instrument(
+    instrument,
+    target,
+    night=night,
+    channel=channel,
+    steps=steps,
+    base_dir=base_dir,
+    input_dir=input_dir,
+    output_dir=output_dir,
+    # order_range=(0, 25),
+    plot=0,
+).run()

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a6}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a6"]
 # ///
 """
 Simple usage example for PyReduce
@@ -15,11 +15,11 @@ from pyreduce.pipeline import Pipeline
 instrument = "McDonald"
 target = "Vega"
 night = None
-arm = "CS23"
+channel = "CS23"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     "scatter",
     # "norm_flat",
@@ -46,7 +46,7 @@ Pipeline.from_instrument(
     instrument,
     target,
     night=night,
-    arm=arm,
+    channel=channel,
     steps=steps,
     base_dir=base_dir,
     input_dir=input_dir,