pyreduce-astro 0.7a4__tar.gz → 0.7a5__tar.gz

pyreduce_astro-0.7a5/.python-version

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

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a5}/CHANGELOG.md

@@ -1,6 +1,13 @@
 # Changelog
 
 
+## [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 +48,7 @@
 - `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-0.7a5}/CLAUDE.md

@@ -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]
@@ -175,7 +175,7 @@ result = Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    arm="middle",
+    channel="middle",
     steps=("bias", "flat", "orders", "science"),
     base_dir="/data",
     plot=1,
@@ -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)

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a4
+Version: 0.7a5
 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
 
@@ -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-0.7a5}/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
 
@@ -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-0.7a5}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 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-0.7a5}/examples/crires_plus_example.py

@@ -1,20 +1,22 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 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",
@@ -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-0.7a5}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 Simple usage example for PyReduce
@@ -49,7 +49,7 @@ start_logging(log_file)
 # Define other parameter for PyReduce
 target = ""
 night = "2019-07-21"
-arm = ""
+channel = ""
 steps = (
     "bias",
     "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-0.7a5/examples/harpn_example.py

@@ -0,0 +1,48 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a5"]
+# ///
+"""
+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",
+    # "orders",
+    # "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-0.7a5}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 Simple usage example for PyReduce
@@ -14,7 +14,7 @@ from pyreduce.pipeline import Pipeline
 instrument = "HARPS"
 target = "HD109200"
 night = None
-arm = "red"
+channel = "red"
 steps = (
     "bias",
     "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-0.7a5}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 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-0.7a5}/examples/just_one_swath.py

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

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a5}/examples/jwst_miri_example.py

@@ -1,20 +1,20 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 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",
@@ -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-0.7a4 → pyreduce_astro-0.7a5}/examples/jwst_niriss_example.py

@@ -1,23 +1,20 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 Simple usage example for PyReduce
 Loads a sample JWST NIRISS dataset, and runs the extraction
 """
 
-import os.path
-
 from pyreduce import datasets
-from pyreduce.configuration import get_configuration_for_instrument
 from pyreduce.pipeline import Pipeline
 
 # define parameters
 instrument = "JWST_NIRISS"
 target = None
 night = None
-arm = "GR700XD"
+channel = "GR700XD"
 steps = (
     "bias",
     "flat",
@@ -30,28 +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 = datasets.JWST_NIRISS(os.path.expanduser("~") + "/PyReduce/DATA")
-input_dir = "awesimsoss"
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = datasets.JWST_NIRISS()
+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=0,
 ).run()

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a5}/examples/lick_apf_example.py

@@ -1,20 +1,20 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 Simple usage example for PyReduce
 Loads a Lick APF 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 = "Lick_APF"
+instrument = "LICK_APF"
 target = "KIC05005618"
 night = None
-arm = ""
+channel = ""
 steps = (
     "bias",
     # "flat",
@@ -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/Lick/APF/"
-input_dir = "Raw"
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = datasets.LICK_APF()
+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=0,
 ).run()

{pyreduce_astro-0.7a4 → pyreduce_astro-0.7a5}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7"]
+# dependencies = ["pyreduce-astro>=0.7a5"]
 # ///
 """
 Simple usage example for PyReduce
@@ -15,7 +15,7 @@ from pyreduce.pipeline import Pipeline
 instrument = "McDonald"
 target = "Vega"
 night = None
-arm = "CS23"
+channel = "CS23"
 steps = (
     # "bias",
     # "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,

pyreduce_astro-0.7a5/examples/metis_ifu_example.py

@@ -0,0 +1,52 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a5"]
+# ///
+"""
+Simple usage example for PyReduce
+Loads a simulated METIS dataset, and runs the full extraction
+"""
+
+import os
+
+from pyreduce import datasets
+from pyreduce.pipeline import Pipeline
+
+# define parameters
+instrument = "METIS_IFU"
+target = ""
+night = ""
+channel = "IFU_NOMINAL"
+steps = (
+    # "bias",
+    # "flat",
+    "orders",
+    "curvature",
+    # "scatter",
+    # "norm_flat",
+    # "wavecal_master",
+    # "wavecal_init",
+    # "wavecal",
+    # "rectify",
+    # "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = os.path.join(datasets.get_data_dir(), "METIS")
+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=(16, 17),
+    plot=1,
+).run()

pyreduce_astro-0.7a5/examples/metis_lss_example.py

@@ -0,0 +1,52 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a5"]
+# ///
+"""
+Simple usage example for PyReduce
+Loads a simulated METIS dataset, and runs the full extraction
+"""
+
+import os
+
+from pyreduce import datasets
+from pyreduce.pipeline import Pipeline
+
+# define parameters
+instrument = "METIS_LSS"
+target = ""
+night = ""
+channel = "LSS_M"
+steps = (
+    # "bias",
+    "flat",
+    "orders",
+    "curvature",
+    # "scatter",
+    # "norm_flat",
+    "wavecal_master",
+    # "wavecal_init",
+    "wavecal",
+    # "rectify",
+    # "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data location: uses $REDUCE_DATA or ~/REDUCE_DATA
+base_dir = os.path.join(datasets.get_data_dir(), "METIS")
+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=(16, 17),
+    plot=1,
+).run()