pyreduce-astro 0.7__tar.gz → 0.7a1__tar.gz

{pyreduce_astro-0.7 → pyreduce_astro-0.7a1}/.gitignore

@@ -20,7 +20,3 @@ docs/_build/
 .claude
 debug/
 idl/
-logs/
-*.ipynb
-tmp/*
-.obsidian/

{pyreduce_astro-0.7 → pyreduce_astro-0.7a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7
+Version: 0.7a1
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -15,10 +15,12 @@ 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: >=3.13
+Requires-Python: >=3.11
 Requires-Dist: astropy>=5.3.0
 Requires-Dist: cffi>=1.17.1
 Requires-Dist: click>=8.1.0
@@ -37,15 +39,20 @@ 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
+Provides-Extra: dev
+Requires-Dist: myst-parser>=3.0.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.5.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
+Requires-Dist: pytest>=7.4.0; extra == 'dev'
+Requires-Dist: ruff>=0.8.0; extra == 'dev'
+Requires-Dist: setuptools; extra == 'dev'
+Requires-Dist: sphinx>=7.2.0; extra == 'dev'
 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 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
-
-# What's new?
-
-Version 0.7 is a major overhaul with many improvements, please see [WhatsNew.md](WhatsNew.md) for the highlights. If the update breaks your existing setup, you are very welcome to file an issue, so we can assist you.
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
 
 # PyReduce
 
@@ -79,11 +86,11 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES -t HD132205 --steps bias,flat,trace,science
+uv run reduce run UVES HD132205 --steps bias,flat,orders,science
 
 # Or run individual steps
-uv run reduce bias UVES -t HD132205
-uv run reduce flat UVES -t HD132205
+uv run reduce bias UVES HD132205
+uv run reduce flat UVES HD132205
 ```
 
 Or use the Python API:
@@ -94,28 +101,14 @@ Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    channel="middle",
+    arm="middle",
 ).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/).
 
 ## Output
 
-PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7 → pyreduce_astro-0.7a1}/README.md

@@ -1,10 +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 3.13+](https://img.shields.io/badge/python-3.13+-blue.svg)](https://www.python.org/downloads/)
-
-# What's new?
-
-Version 0.7 is a major overhaul with many improvements, please see [WhatsNew.md](WhatsNew.md) for the highlights. If the update breaks your existing setup, you are very welcome to file an issue, so we can assist you.
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
 
 # PyReduce
 
@@ -38,11 +34,11 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES -t HD132205 --steps bias,flat,trace,science
+uv run reduce run UVES HD132205 --steps bias,flat,orders,science
 
 # Or run individual steps
-uv run reduce bias UVES -t HD132205
-uv run reduce flat UVES -t HD132205
+uv run reduce bias UVES HD132205
+uv run reduce flat UVES HD132205
 ```
 
 Or use the Python API:
@@ -53,28 +49,14 @@ Pipeline.from_instrument(
     instrument="UVES",
     target="HD132205",
     night="2010-04-01",
-    channel="middle",
+    arm="middle",
 ).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/).
 
 ## Output
 
-PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7 → pyreduce_astro-0.7a1}/pyproject.toml

@@ -1,7 +1,11 @@
+[build-system]
+requires = ["hatchling>=1.25.0", "cffi>=1.17.1", "setuptools"]
+build-backend = "hatchling.build"
+
 [project]
 name = "pyreduce-astro"
-version = "0.7"
-requires-python = ">=3.13"
+version = "0.7a1"
+requires-python = ">=3.11"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"
 authors = [
@@ -19,6 +23,8 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Programming Language :: C",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Astronomy",
@@ -42,25 +48,19 @@ dependencies = [
     "python-dateutil>=2.8.0",
     "scikit-image>=0.22.0",
     "tqdm>=4.66.0",
+    "wget>=3.2",
     "Pillow>=10.0.0",
 ]
 
-[dependency-groups]
+[project.optional-dependencies]
 dev = [
     "ruff>=0.8.0",
     "pre-commit>=3.5.0",
     "pytest>=7.4.0",
     "pytest-cov>=4.1.0",
     "sphinx>=7.2.0",
-    "ipython>=9.8.0",
-    "myst-parser",
-    "setuptools",
-]
-ipynb = [
-    "ipykernel>=7.1.0",
-    "jupyter-client>=8.8.0",
-    "jupytext>=1.18.1",
-    "nbconvert>=7.16.6",
+    "myst-parser>=3.0.0",
+    "setuptools",  # Required for CFFI compilation in tests (Python 3.12+)
 ]
 
 [project.urls]
@@ -71,19 +71,15 @@ 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"]
-build-backend = "hatchling.build"
 
+# Hatch build configuration
 [tool.hatch.build]
+packages = ["pyreduce"]
 exclude = [
     "/.git",
     "/.github",
     "/docs",
-    "/test",
+    "/tests",
     "*.pyc",
     "__pycache__",
 ]
@@ -177,13 +173,13 @@ markers = [
 ]
 filterwarnings = [
     "ignore:The following header keyword is invalid:astropy.utils.exceptions.AstropyUserWarning",
-    "ignore::astropy.io.fits.verify.VerifyWarning",
+    "ignore:Invalid 'BLANK' keyword:astropy.io.fits.verify.VerifyWarning",
 ]
 
 # Coverage configuration
 [tool.coverage.run]
 source = ["pyreduce"]
-omit = ["*/test/*", "*/test_*.py"]
+omit = ["*/tests/*", "*/test_*.py"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -197,9 +193,20 @@ exclude_lines = [
     "@(abc\\.)?abstractmethod",
 ]
 
+# Development dependency groups
+[dependency-groups]
+dev = [
+    "ruff>=0.8.0",
+    "pre-commit>=3.5.0",
+    "pytest>=7.4.0",
+    "pytest-cov>=4.1.0",
+    "sphinx>=7.2.0",
+    "ipython>=9.8.0",
+]
+
 # cibuildwheel configuration for building platform-specific wheels
 [tool.cibuildwheel]
-build = "cp313-* cp314-*"
+build = "cp311-* cp312-* cp313-* cp314-*"
 skip = "*-musllinux_* *-win32 *-manylinux_i686"
 test-command = "pytest {project}/test -m unit"
 test-requires = ["pytest"]

pyreduce_astro-0.7a1/pyreduce/__main__.py

@@ -0,0 +1,206 @@
+"""
+PyReduce command-line interface.
+
+Usage:
+    uv run reduce --help
+    uv run reduce run UVES HD132205 --night 2010-04-01
+    uv run reduce run UVES HD132205 --steps bias,flat,orders
+    uv run reduce bias UVES HD132205
+    uv run reduce combine --output combined.fits *.final.fits
+"""
+
+import click
+
+from . import datasets
+from .configuration import get_configuration_for_instrument
+from .reduce import main as reduce_main
+from .tools.combine import combine as tools_combine
+
+ALL_STEPS = (
+    "bias",
+    "flat",
+    "orders",
+    "curvature",
+    "scatter",
+    "norm_flat",
+    "wavecal_master",
+    "wavecal_init",
+    "wavecal",
+    "freq_comb_master",
+    "freq_comb",
+    "science",
+    "continuum",
+    "finalize",
+)
+
+
+@click.group()
+@click.version_option(package_name="pyreduce-astro")
+def cli():
+    """PyReduce - Echelle spectrograph data reduction pipeline."""
+    pass
+
+
+@cli.command()
+@click.argument("instrument")
+@click.argument("target")
+@click.option("--night", "-n", default=None, help="Observation night (YYYY-MM-DD)")
+@click.option("--arm", "-a", default=None, help="Instrument arm/detector")
+@click.option(
+    "--steps",
+    "-s",
+    default=None,
+    help="Comma-separated steps to run (default: all)",
+)
+@click.option(
+    "--base-dir",
+    "-b",
+    default=None,
+    help="Base directory for data (default: $REDUCE_DATA or ~/REDUCE_DATA)",
+)
+@click.option(
+    "--input-dir", "-i", default="raw", help="Input directory relative to base"
+)
+@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=save, 2=interactive)"
+)
+@click.option(
+    "--order-range",
+    default=None,
+    help="Order range to process (e.g., '1,21')",
+)
+def run(
+    instrument,
+    target,
+    night,
+    arm,
+    steps,
+    base_dir,
+    input_dir,
+    output_dir,
+    plot,
+    order_range,
+):
+    """Run the reduction pipeline.
+
+    INSTRUMENT: Name of the instrument (e.g., UVES, HARPS, XSHOOTER)
+    TARGET: Target star name or regex pattern
+    """
+    # Parse steps
+    if steps:
+        steps = tuple(s.strip() for s in steps.split(","))
+    else:
+        steps = "all"
+
+    # Parse order range
+    if order_range:
+        parts = order_range.split(",")
+        order_range = (int(parts[0]), int(parts[1]))
+
+    # Load configuration
+    config = get_configuration_for_instrument(instrument)
+
+    # Run reduction
+    reduce_main(
+        instrument=instrument,
+        target=target,
+        night=night,
+        arms=arm,
+        steps=steps,
+        base_dir=base_dir or "",
+        input_dir=input_dir,
+        output_dir=output_dir,
+        configuration=config,
+        order_range=order_range,
+        plot=plot,
+    )
+
+
+@cli.command()
+@click.argument("files", nargs=-1, required=True)
+@click.option("--output", "-o", default="combined.fits", help="Output filename")
+@click.option("--plot", "-p", default=None, type=int, help="Plot specific order")
+def combine(files, output, plot):
+    """Combine multiple reduced spectra.
+
+    FILES: Input .final.fits files to combine
+    """
+    tools_combine(list(files), output, plot=plot)
+
+
+@cli.command()
+@click.argument("instrument")
+def download(instrument):
+    """Download sample dataset for an instrument.
+
+    INSTRUMENT: Name of the instrument (e.g., UVES, HARPS)
+    """
+    instrument = instrument.upper()
+    dataset_func = getattr(datasets, instrument, None)
+    if dataset_func is None:
+        available = [
+            name
+            for name in dir(datasets)
+            if name.isupper() and not name.startswith("_")
+        ]
+        raise click.ClickException(
+            f"Unknown instrument '{instrument}'. Available: {', '.join(available)}"
+        )
+    path = dataset_func()
+    click.echo(f"Dataset downloaded to: {path}")
+
+
+@cli.command("list-steps")
+def list_steps():
+    """List all available reduction steps."""
+    click.echo("Available reduction steps:")
+    for step in ALL_STEPS:
+        click.echo(f"  - {step}")
+
+
+def make_step_command(step_name):
+    """Factory to create a command for a single step."""
+
+    @click.command(name=step_name)
+    @click.argument("instrument")
+    @click.argument("target")
+    @click.option("--night", "-n", default=None, help="Observation night")
+    @click.option("--arm", "-a", default=None, help="Instrument arm")
+    @click.option("--base-dir", "-b", default=None, help="Base directory")
+    @click.option("--input-dir", "-i", default="raw", help="Input directory")
+    @click.option("--output-dir", "-o", default="reduced", help="Output directory")
+    @click.option("--plot", "-p", default=0, help="Plot level")
+    def cmd(instrument, target, night, arm, base_dir, input_dir, output_dir, plot):
+        config = get_configuration_for_instrument(instrument)
+        reduce_main(
+            instrument=instrument,
+            target=target,
+            night=night,
+            arms=arm,
+            steps=(step_name,),
+            base_dir=base_dir or "",
+            input_dir=input_dir,
+            output_dir=output_dir,
+            configuration=config,
+            plot=plot,
+        )
+
+    cmd.__doc__ = f"Run the '{step_name}' step."
+    return cmd
+
+
+# Register individual step commands
+for _step in ALL_STEPS:
+    cli.add_command(make_step_command(_step))
+
+
+def main():
+    """Entry point for the CLI."""
+    cli()
+
+
+if __name__ == "__main__":
+    main()

{pyreduce_astro-0.7 → pyreduce_astro-0.7a1}/pyreduce/cli.py

@@ -155,7 +155,7 @@ def trace(instrument: str, files: tuple[str, ...], output: str, mode: str, plot:
     pipe = Pipeline(inst, output, mode=mode, plot=plot)
     if file_list:
         pipe = pipe.flat(file_list)
-    pipe.trace(file_list).run()
+    pipe.trace_orders(file_list).run()
     click.echo(f"Order trace saved to {output}")
 
 
@@ -287,8 +287,8 @@ def run(config_file: str, steps: str, skip_existing: bool, plot: int):
         pipe = pipe.flat(_expand_globs(files["flat"]))
 
     if "trace" in config_steps:
-        trace_files = files.get("trace") or files.get("flat")
-        pipe = pipe.trace(_expand_globs(trace_files) if trace_files else None)
+        trace_files = files.get("orders") or files.get("flat")
+        pipe = pipe.trace_orders(_expand_globs(trace_files) if trace_files else None)
 
     if "scatter" in config_steps:
         pipe = pipe.scatter()

pyreduce_astro-0.7a1/pyreduce/clib/build_extract.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+"""Builds the C library that contains the extraction algorithm
+
+This module prepares and builds the C libary containing the curved
+(and vertical) extraction algorithm using CFFI.
+It also prepares the ffibuilder objects for setup.py,
+so that the library is compiled on installation.
+
+
+The user can also call the Module as a script to compile the
+C libraries again.
+
+Attributes
+----------
+ffi_builder_vertical : FFI
+    CFFI Builder for the vertical extraction algorithm
+ffi_builder_curved : FFI
+    CFFI Builder for the curved extraction algorithm
+"""
+
+import logging
+import os
+
+from cffi import FFI
+
+logger = logging.getLogger(__name__)
+
+
+CWD = os.path.dirname(__file__)
+CWD = os.path.abspath(CWD)
+release_path = os.path.join(CWD, "Release")
+
+print("Include dir: ", CWD)
+print("Release dir: ", release_path)
+
+
+ffibuilder_vertical = FFI()
+with open(os.path.join(CWD, "slit_func_bd.h")) as f:
+    ffibuilder_vertical.cdef(f.read())
+with open(os.path.join(CWD, "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_curved = FFI()
+with open(os.path.join(CWD, "slit_func_2d_xi_zeta_bd.h")) as f:
+    ffibuilder_curved.cdef(f.read())
+with open(os.path.join(CWD, "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"],
+    )
+
+
+def build():
+    """Builds the C slitfunc library"""
+    logger.info("Building required C libraries, this might take a few seconds")
+
+    old_cwd = os.getcwd()
+    path = os.path.abspath(CWD)
+    os.chdir(path)
+
+    ffibuilder_vertical.compile(verbose=True, debug=False)
+    ffibuilder_curved.compile(verbose=True, debug=False)
+
+    os.chdir(old_cwd)
+
+
+if __name__ == "__main__":  # pragma: no cover
+    build()