pyreduce-astro 0.6.0b5__tar.gz → 0.7a1__tar.gz

{pyreduce_astro-0.6.0b5 → pyreduce_astro-0.7a1}/.gitignore

@@ -17,3 +17,6 @@ esorex.log
 pyesorex.log
 test/test_outputs
 docs/_build/
+.claude
+debug/
+idl/

pyreduce_astro-0.7a1/PKG-INFO

@@ -0,0 +1,114 @@
+Metadata-Version: 2.4
+Name: pyreduce-astro
+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
+Project-URL: Repository, https://github.com/ivh/PyReduce
+Project-URL: Issues, https://github.com/ivh/PyReduce/issues
+Author: Nikolai Piskunov, Thomas Marquart, Ansgar Wehrhahn
+Maintainer-email: Thomas Marquart <thomas.marquart@astro.uu.se>
+License: GPL-3.0-or-later
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+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-Dist: astropy>=5.3.0
+Requires-Dist: cffi>=1.17.1
+Requires-Dist: click>=8.1.0
+Requires-Dist: colorlog>=6.8.0
+Requires-Dist: corner>=2.2.0
+Requires-Dist: emcee>=3.1.0
+Requires-Dist: joblib>=1.3.0
+Requires-Dist: jsonschema>=4.20.0
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: pillow>=10.0.0
+Requires-Dist: pydantic>=2.5.0
+Requires-Dist: python-dateutil>=2.8.0
+Requires-Dist: pyyaml>=6.0.0
+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 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+
+# PyReduce
+
+A data reduction pipeline for echelle spectrographs (HARPS, UVES, XSHOOTER, CRIRES+, JWST/NIRISS, and more).
+
+Based on the [REDUCE](http://www.astro.uu.se/~piskunov/RESEARCH/REDUCE/) package. See the papers:
+- Piskunov & Valenti (2001) [doi:10.1051/0004-6361:20020175](https://doi.org/10.1051/0004-6361:20020175)
+- Piskunov, Wehrhahn & Marquart (2021) [doi:10.1051/0004-6361/202038293](https://doi.org/10.1051/0004-6361/202038293)
+
+## Installation
+
+```bash
+# Using uv (recommended)
+uv add pyreduce-astro
+
+# Or pip
+pip install pyreduce-astro
+```
+
+For development:
+```bash
+git clone https://github.com/ivh/PyReduce
+cd PyReduce
+uv sync
+```
+
+## Quick Start
+
+```bash
+# Download sample data
+uv run reduce download UVES
+
+# Run reduction
+uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+
+# Or run individual steps
+uv run reduce bias UVES HD132205
+uv run reduce flat UVES HD132205
+```
+
+Or use the Python API:
+```python
+from pyreduce.pipeline import Pipeline
+
+Pipeline.from_instrument(
+    instrument="UVES",
+    target="HD132205",
+    night="2010-04-01",
+    arm="middle",
+).run()
+```
+
+## Documentation
+
+Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
+
+## Output
+
+PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

pyreduce_astro-0.7a1/README.md

@@ -0,0 +1,62 @@
+[![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/)
+
+# PyReduce
+
+A data reduction pipeline for echelle spectrographs (HARPS, UVES, XSHOOTER, CRIRES+, JWST/NIRISS, and more).
+
+Based on the [REDUCE](http://www.astro.uu.se/~piskunov/RESEARCH/REDUCE/) package. See the papers:
+- Piskunov & Valenti (2001) [doi:10.1051/0004-6361:20020175](https://doi.org/10.1051/0004-6361:20020175)
+- Piskunov, Wehrhahn & Marquart (2021) [doi:10.1051/0004-6361/202038293](https://doi.org/10.1051/0004-6361/202038293)
+
+## Installation
+
+```bash
+# Using uv (recommended)
+uv add pyreduce-astro
+
+# Or pip
+pip install pyreduce-astro
+```
+
+For development:
+```bash
+git clone https://github.com/ivh/PyReduce
+cd PyReduce
+uv sync
+```
+
+## Quick Start
+
+```bash
+# Download sample data
+uv run reduce download UVES
+
+# Run reduction
+uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+
+# Or run individual steps
+uv run reduce bias UVES HD132205
+uv run reduce flat UVES HD132205
+```
+
+Or use the Python API:
+```python
+from pyreduce.pipeline import Pipeline
+
+Pipeline.from_instrument(
+    instrument="UVES",
+    target="HD132205",
+    night="2010-04-01",
+    arm="middle",
+).run()
+```
+
+## Documentation
+
+Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
+
+## Output
+
+PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.6.0b5 → pyreduce_astro-0.7a1}/pyproject.toml

@@ -4,15 +4,18 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pyreduce-astro"
-version = "0.6.0b5"
+version = "0.7a1"
 requires-python = ">=3.11"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"
 authors = [
-    {name = "Thomas Marquart", email = "thomas.marquart@astro.uu.se"},
     {name = "Nikolai Piskunov"},
+    {name = "Thomas Marquart"},
     {name = "Ansgar Wehrhahn"}
 ]
+maintainers = [
+    {name = "Thomas Marquart", email = "thomas.marquart@astro.uu.se"}
+]
 license = {text = "GPL-3.0-or-later"}
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -23,10 +26,12 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Astronomy",
 ]
 
 dependencies = [
+    "click>=8.1.0",
     "cffi>=1.17.1",
     "numpy>=1.26.0",
     "matplotlib>=3.8.0",
@@ -37,6 +42,8 @@ dependencies = [
     "emcee>=3.1.0",
     "joblib>=1.3.0",
     "jsonschema>=4.20.0",
+    "pyyaml>=6.0.0",
+    "pydantic>=2.5.0",
     "spectres>=2.2.0",
     "python-dateutil>=2.8.0",
     "scikit-image>=0.22.0",
@@ -52,6 +59,7 @@ dev = [
     "pytest>=7.4.0",
     "pytest-cov>=4.1.0",
     "sphinx>=7.2.0",
+    "myst-parser>=3.0.0",
     "setuptools",  # Required for CFFI compilation in tests (Python 3.12+)
 ]
 
@@ -61,6 +69,9 @@ Documentation = "https://pyreduce-astro.readthedocs.io"
 Repository = "https://github.com/ivh/PyReduce"
 Issues = "https://github.com/ivh/PyReduce/issues"
 
+[project.scripts]
+reduce = "pyreduce.__main__:main"
+
 # Hatch build configuration
 [tool.hatch.build]
 packages = ["pyreduce"]
@@ -160,6 +171,10 @@ markers = [
     "slow: Tests taking >5 seconds",
     "downloads: Tests that download sample datasets",
 ]
+filterwarnings = [
+    "ignore:The following header keyword is invalid:astropy.utils.exceptions.AstropyUserWarning",
+    "ignore:Invalid 'BLANK' keyword:astropy.io.fits.verify.VerifyWarning",
+]
 
 # Coverage configuration
 [tool.coverage.run]
@@ -186,16 +201,21 @@ dev = [
     "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 for Python 3.11, 3.12, 3.13 on common platforms
-build = "cp311-* cp312-* cp313-*"
-
-# Skip musllinux (use manylinux instead) and 32-bit builds
+build = "cp311-* cp312-* cp313-* cp314-*"
 skip = "*-musllinux_* *-win32 *-manylinux_i686"
-
-# Test the built wheels
 test-command = "pytest {project}/test -m unit"
 test-requires = ["pytest"]
+
+[tool.cibuildwheel.linux]
+archs = ["x86_64"]
+
+[tool.cibuildwheel.macos]
+archs = ["arm64"]
+
+[tool.cibuildwheel.windows]
+archs = ["AMD64"]

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()