pyreduce-astro 0.7a7__tar.gz → 0.7b1__tar.gz

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/CHANGELOG.md

@@ -1,6 +1,28 @@
 # Changelog
 
 
+## [0.7b1] - 2026-01-06
+
+### Changed
+- **Curvature algorithm rewrite**: Replace 2D model fitting with row-tracking method for better robustness
+- Rename `make_shear.py` to `slit_curve.py`
+- Rename curvature coefficients: `tilt`/`shear` → `p1`/`p2` throughout codebase
+- Rename `arc_extraction` to `simple_extraction`
+- Split curvature `extraction_height` into separate `extraction_height` and `curve_height` parameters
+- Save file renamed from `.shear.npz` to `.curve.npz`
+
+### Added
+- `discover_channels()` for automatic channel detection from data files
+- CLI: `--target` is now optional; loops over all targets if not specified
+- CLI: Uses `$REDUCE_DATA` for base_dir, reads default input_dir from config
+- Comprehensive CLI test coverage
+
+### Fixed
+- Curvature step index error when traces are removed during processing
+- Validate base_dir and input_dir exist with clear error messages
+- File sorting to correctly loop over all nights when not specified
+- CLI dynamic dependency loading for step commands
+
 ## [0.7a7] - 2026-01-04
 
 ### Added

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/CLAUDE.md

@@ -74,7 +74,7 @@ The reduction pipeline consists of these steps (in typical order):
 | `bias` | `Bias` | Combine bias frames into master bias |
 | `flat` | `Flat` | Combine flat frames, subtract bias |
 | `trace` | `OrderTracing` | Trace echelle order positions on flat |
-| `curvature` | `SlitCurvatureDetermination` | Measure slit tilt/shear from arc lamp |
+| `curvature` | `SlitCurvatureDetermination` | Measure slit curvature from arc lamp |
 | `scatter` | `BackgroundScatter` | Model inter-order scattered light |
 | `norm_flat` | `NormalizeFlatField` | Normalize flat, extract blaze function |
 | `wavecal_master` | `WavelengthCalibrationMaster` | Extract wavelength calibration spectrum |
@@ -260,12 +260,16 @@ uv run reduce list-steps
 
 ```bash
 uv sync                              # Install dependencies
+uv run reduce-build                  # Compile C extensions
+uv run reduce-clean                  # Remove compiled extensions
 uv run pre-commit install            # Setup hooks (once)
 uv run pytest -m unit                # Fast unit tests
 uv run pytest --instrument=UVES      # Test single instrument
 uv run ruff check --fix .            # Lint and fix
 ```
 
+After a fresh clone or `rm -rf .venv`, run `uv sync && uv run reduce-build` to set up.
+
 ### Adding Instruments
 
 1. Create `pyreduce/instruments/name.yaml` with detector/header config

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a7
+Version: 0.7b1
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -37,7 +37,6 @@ Requires-Dist: scikit-image>=0.22.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: spectres>=2.2.0
 Requires-Dist: tqdm>=4.66.0
-Requires-Dist: wget>=3.2
 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)

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce
@@ -21,14 +21,14 @@ steps = (
     # "bias",
     # "flat",
     # "trace",
-    # "curvature",
+    "curvature",
     # "scatter",
     # "norm_flat",
     # "wavecal_master",
     # "wavecal_init",
     # "wavecal",
     # "freq_comb_master",
-    "freq_comb",
+    # "freq_comb",
     # "science",
     # "continuum",
     # "finalize",
@@ -48,6 +48,5 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    allow_calibration_only=True,
     # order_range=(0, 4),
 ).run()

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 import os.path
 

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce
@@ -17,9 +17,9 @@ night = None
 channel = ""
 steps = (
     "bias",
-    # "flat",
-    # "trace",
-    # "norm_flat",
+    "flat",
+    "trace",
+    "norm_flat",
     # "wavecal",
     # "curvature",
     "science",
@@ -42,5 +42,5 @@ Pipeline.from_instrument(
     input_dir=input_dir,
     output_dir=output_dir,
     # order_range=(0, 25),
-    plot=0,
+    plot=1,
 ).run()

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/metis_lss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/micado_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/neid_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 NEID reduction example

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/nirspec_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/toes_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 import numpy as np
 

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/uves_callfunc.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Example showing direct function calls for each step.

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/uves_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/examples/xshooter_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b1"]
 # ///
 """
 Simple usage example for PyReduce
@@ -41,7 +41,7 @@ input_dir = "raw"
 output_dir = "reduced"
 
 config = get_configuration_for_instrument(instrument)
-# config["science"]["extraction_method"] = "arc"
+# config["science"]["extraction_method"] = "simple"
 # config["science"]["extraction_cutoff"] = 0
 
 Pipeline.from_instrument(

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyreduce-astro"
-version = "0.7a7"
+version = "0.7b1"
 requires-python = ">=3.13"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"
@@ -42,7 +42,6 @@ dependencies = [
     "python-dateutil>=2.8.0",
     "scikit-image>=0.22.0",
     "tqdm>=4.66.0",
-    "wget>=3.2",
     "Pillow>=10.0.0",
 ]
 
@@ -55,6 +54,7 @@ dev = [
     "sphinx>=7.2.0",
     "ipython>=9.8.0",
     "myst-parser",
+    "setuptools",
 ]
 
 [project.urls]
@@ -65,6 +65,8 @@ Issues = "https://github.com/ivh/PyReduce/issues"
 
 [project.scripts]
 reduce = "pyreduce.__main__:main"
+reduce-build = "pyreduce.clib.build_extract:build"
+reduce-clean = "pyreduce.clib.build_extract:clean"
 
 [build-system]
 requires = ["hatchling>=1.25.0", "cffi>=1.17.1", "setuptools"]

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b1}/pyreduce/__main__.py

@@ -38,7 +38,7 @@ def cli():
 
 @cli.command()
 @click.argument("instrument")
-@click.argument("target")
+@click.option("--target", "-t", default=None, help="Target star name or regex pattern")
 @click.option("--night", "-n", default=None, help="Observation night (YYYY-MM-DD)")
 @click.option("--channel", "-c", default=None, help="Instrument channel")
 @click.option(
@@ -54,7 +54,7 @@ def cli():
     help="Base directory for data (default: $REDUCE_DATA or ~/REDUCE_DATA)",
 )
 @click.option(
-    "--input-dir", "-i", default="raw", help="Input directory relative to base"
+    "--input-dir", "-i", default=None, help="Input directory relative to base"
 )
 @click.option(
     "--output-dir", "-o", default="reduced", help="Output directory relative to base"
@@ -89,7 +89,6 @@ def run(
     """Run the reduction pipeline.
 
     INSTRUMENT: Name of the instrument (e.g., UVES, HARPS, XSHOOTER)
-    TARGET: Target star name or regex pattern
     """
     from .configuration import get_configuration_for_instrument, load_settings_override
     from .reduce import main as reduce_main
@@ -111,19 +110,22 @@ def run(
         config = load_settings_override(config, settings)
 
     # Run reduction
-    reduce_main(
-        instrument=instrument,
-        target=target,
-        night=night,
-        channels=channel,
-        steps=steps,
-        base_dir=base_dir or "",
-        input_dir=input_dir,
-        output_dir=output_dir,
-        configuration=config,
-        order_range=order_range,
-        plot=plot,
-    )
+    try:
+        reduce_main(
+            instrument=instrument,
+            target=target,
+            night=night,
+            channels=channel,
+            steps=steps,
+            base_dir=base_dir,
+            input_dir=input_dir,
+            output_dir=output_dir,
+            configuration=config,
+            order_range=order_range,
+            plot=plot,
+        )
+    except FileNotFoundError as e:
+        raise click.ClickException(str(e)) from None
 
 
 @cli.command()
@@ -345,31 +347,96 @@ def make_step_command(step_name):
             config = get_configuration_for_instrument(instrument)
             if settings:
                 config = load_settings_override(config, settings)
-            step_config = config.get(step_name, {})
-            step_config["plot"] = plot
 
-            # Get the step class
+            # Step classes that support --file (take raw files as input)
             step_classes = {
                 "bias": reduce_module.Bias,
                 "flat": reduce_module.Flat,
                 "trace": reduce_module.OrderTracing,
                 "curvature": reduce_module.SlitCurvatureDetermination,
                 "scatter": reduce_module.BackgroundScatter,
-                "norm_flat": reduce_module.NormalizeFlatField,
                 "wavecal_master": reduce_module.WavelengthCalibrationMaster,
-                "wavecal_init": reduce_module.WavelengthCalibrationInitialize,
-                "wavecal": reduce_module.WavelengthCalibrationFinalize,
                 "freq_comb_master": reduce_module.LaserFrequencyCombMaster,
-                "freq_comb": reduce_module.LaserFrequencyCombFinalize,
                 "science": reduce_module.ScienceExtraction,
-                "continuum": reduce_module.ContinuumNormalization,
             }
 
+            # Steps that don't take raw files - --file makes no sense
+            no_file_steps = {
+                "mask",
+                "norm_flat",
+                "wavecal_init",
+                "wavecal",
+                "freq_comb",
+                "continuum",
+                "finalize",
+                "rectify",
+            }
+
+            if step_name in no_file_steps:
+                raise click.ClickException(
+                    f"Step '{step_name}' does not accept raw files. "
+                    f"Run without --file to use the pipeline."
+                )
+
             if step_name not in step_classes:
                 raise click.ClickException(
                     f"Step '{step_name}' does not support --file option"
                 )
 
+            def make_step(name):
+                """Create a step instance."""
+                step_class = {
+                    "mask": reduce_module.Mask,
+                    "bias": reduce_module.Bias,
+                    "flat": reduce_module.Flat,
+                    "trace": reduce_module.OrderTracing,
+                    "curvature": reduce_module.SlitCurvatureDetermination,
+                    "scatter": reduce_module.BackgroundScatter,
+                    "norm_flat": reduce_module.NormalizeFlatField,
+                    "wavecal_master": reduce_module.WavelengthCalibrationMaster,
+                    "freq_comb_master": reduce_module.LaserFrequencyCombMaster,
+                    "science": reduce_module.ScienceExtraction,
+                }.get(name)
+                if not step_class:
+                    return None
+                step_config = config.get(name, {}).copy()
+                step_config["plot"] = 0  # No plots for dependency loading
+                return step_class(
+                    inst,
+                    channel,
+                    target=target or "",
+                    night=night,
+                    output_dir=output_dir_full,
+                    order_range=None,
+                    **step_config,
+                )
+
+            def load_dependency(name, loaded):
+                """Load a dependency from disk."""
+                if name in loaded:
+                    return loaded[name]
+                if name == "config":
+                    loaded["config"] = config
+                    return config
+                dep_step = make_step(name)
+                if dep_step is None:
+                    return None
+                # Load this step's dependencies first
+                for sub_dep in dep_step.loadDependsOn:
+                    load_dependency(sub_dep, loaded)
+                # Build kwargs for load()
+                load_kwargs = {
+                    d: loaded[d] for d in dep_step.loadDependsOn if d in loaded
+                }
+                try:
+                    loaded[name] = dep_step.load(**load_kwargs)
+                except FileNotFoundError:
+                    loaded[name] = None
+                return loaded[name]
+
+            # Create the target step
+            step_config = config.get(step_name, {}).copy()
+            step_config["plot"] = plot
             step_class = step_classes[step_name]
             step = step_class(
                 inst,
@@ -380,7 +447,17 @@ def make_step_command(step_name):
                 order_range=None,
                 **step_config,
             )
-            step.run(files=np.array([file]), mask=None, bias=None)
+
+            # Load all dependencies
+            loaded = {}
+            for dep in step.dependsOn:
+                load_dependency(dep, loaded)
+
+            # Build kwargs for run()
+            run_kwargs = {d: loaded.get(d) for d in step.dependsOn}
+            run_kwargs["files"] = np.array([file])
+
+            step.run(**run_kwargs)
         else:
             config = get_configuration_for_instrument(instrument)
             if settings:

pyreduce_astro-0.7b1/pyreduce/clib/build_extract.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+"""Build script for CFFI C extensions (development only).
+
+Usage:
+    uv run reduce-build    # compile extensions
+    uv run reduce-clean    # remove compiled files
+
+This compiles the C extraction libraries in-place for development.
+For production, extensions are built automatically during wheel creation
+via hatch_build.py.
+"""
+
+import glob
+import os
+
+from cffi import FFI
+
+CWD = os.path.dirname(__file__)
+CWD = os.path.abspath(CWD)
+release_path = os.path.join(CWD, "Release")
+
+
+def clean():
+    """Remove compiled extension files."""
+    patterns = ["*.so", "*.o", "*.pyd"]
+    removed = []
+    for pattern in patterns:
+        for f in glob.glob(os.path.join(CWD, pattern)):
+            os.remove(f)
+            removed.append(os.path.basename(f))
+    if removed:
+        print(f"Removed: {', '.join(removed)}")
+    else:
+        print("Nothing to clean.")
+
+
+def build():
+    """Build the C slitfunc libraries in-place."""
+    print("Building CFFI extensions for development...")
+    print(f"  Source dir: {CWD}")
+
+    old_cwd = os.getcwd()
+    os.chdir(CWD)
+
+    try:
+        # Vertical extraction
+        ffibuilder_vertical = FFI()
+        with open("slit_func_bd.h") as f:
+            ffibuilder_vertical.cdef(f.read())
+        with open("slit_func_bd.c") as f:
+            ffibuilder_vertical.set_source(
+                "_slitfunc_bd",
+                f.read(),
+                include_dirs=[CWD, release_path],
+                depends=["slit_func_bd.h"],
+            )
+        ffibuilder_vertical.compile(verbose=True)
+        print("[OK] _slitfunc_bd")
+
+        # Curved extraction
+        ffibuilder_curved = FFI()
+        with open("slit_func_2d_xi_zeta_bd.h") as f:
+            ffibuilder_curved.cdef(f.read())
+        with open("slit_func_2d_xi_zeta_bd.c") as f:
+            ffibuilder_curved.set_source(
+                "_slitfunc_2d",
+                f.read(),
+                include_dirs=[CWD, release_path],
+                depends=["slit_func_2d_xi_zeta_bd.h"],
+            )
+        ffibuilder_curved.compile(verbose=True)
+        print("[OK] _slitfunc_2d")
+
+        print("Done.")
+    finally:
+        os.chdir(old_cwd)
+
+
+if __name__ == "__main__":
+    build()