pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/__init__.py

@@ -0,0 +1,67 @@
+try:
+    from importlib.metadata import PackageNotFoundError, version
+except ImportError:  # for Python<3.8
+    from importlib_metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("pyreduce-astro")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+
+# add logger to console
+import logging
+
+import tqdm
+
+
+# We need to use this to have logging messages handle properly with the progressbar
+class TqdmLoggingHandler(logging.Handler):
+    def __init__(self, level=logging.NOTSET):
+        super().__init__(level)
+
+    def emit(self, record):
+        try:
+            msg = self.format(record)
+            tqdm.tqdm.write(msg)
+            self.flush()
+        except (KeyboardInterrupt, SystemExit):
+            raise
+        except:
+            self.handleError(record)
+
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+logging.captureWarnings(True)
+
+console = TqdmLoggingHandler()
+console.setLevel(logging.INFO)
+
+try:
+    import colorlog
+
+    console.setFormatter(
+        colorlog.ColoredFormatter("%(log_color)s%(levelname)s - %(message)s")
+    )
+    del colorlog
+except ImportError:
+    console.setFormatter("%(levelname)s - %(message)s")
+    print("Install colorlog for colored logging output")
+
+logger.addHandler(console)
+
+del logging
+# do not del tqdm, it is needed in the Log Handler
+
+
+# Lazy loading for faster imports
+def __getattr__(name):
+    """Lazy load submodules on first access."""
+    if name in ("configuration", "datasets", "reduce", "util"):
+        import importlib
+
+        module = importlib.import_module(f".{name}", __name__)
+        globals()[name] = module
+        return module
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

pyreduce/__main__.py

@@ -0,0 +1,322 @@
+"""
+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
+
+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
+    """
+    from .configuration import get_configuration_for_instrument
+    from .reduce import main as reduce_main
+
+    # 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
+    """
+    from .tools.combine import combine as tools_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)
+    """
+    from . import datasets
+
+    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()
+@click.argument("filename", required=False)
+@click.option(
+    "--list", "-l", "list_examples", is_flag=True, help="List available examples"
+)
+@click.option("--all", "-a", "download_all", is_flag=True, help="Download all examples")
+@click.option("--run", "-r", is_flag=True, help="Run the example after downloading")
+@click.option("--output", "-o", default=".", help="Output directory")
+def examples(filename, list_examples, download_all, run, output):
+    """List, download, or run example scripts from GitHub.
+
+    Downloads examples matching your installed PyReduce version.
+
+    \b
+    Examples:
+        reduce examples                     # List available examples
+        reduce examples uves_example.py     # Download to current dir
+        reduce examples -r uves_example.py  # Download and run
+        reduce examples --all -o ~/scripts  # Download all to ~/scripts
+    """
+    import json
+    import os
+    import subprocess
+    import sys
+    import tempfile
+    import urllib.request
+    from urllib.error import HTTPError
+
+    from pyreduce import __version__
+
+    version = __version__.split("+")[0]
+    if version == "unknown":
+        raise click.ClickException(
+            "Cannot determine package version. Install from PyPI or a tagged release."
+        )
+
+    github_api = (
+        f"https://api.github.com/repos/ivh/PyReduce/contents/examples?ref=v{version}"
+    )
+    github_raw = f"https://raw.githubusercontent.com/ivh/PyReduce/v{version}/examples"
+
+    # Fetch list of examples from GitHub API
+    try:
+        with urllib.request.urlopen(github_api) as resp:
+            contents = json.loads(resp.read().decode())
+    except HTTPError as e:
+        if e.code == 404:
+            raise click.ClickException(
+                f"Tag v{version} not found on GitHub. "
+                "Try installing a released version."
+            ) from None
+        raise click.ClickException(f"GitHub API error: {e}") from None
+
+    example_files = sorted(f["name"] for f in contents if f["name"].endswith(".py"))
+
+    # List mode
+    if list_examples or (not filename and not download_all):
+        click.echo(f"Available examples for v{version}:")
+        for name in example_files:
+            click.echo(f"  {name}")
+        return
+
+    if run and download_all:
+        raise click.ClickException("Cannot use --run with --all")
+
+    # Run mode: download to temp and execute
+    if run:
+        if filename not in example_files:
+            raise click.ClickException(
+                f"Unknown example '{filename}'. Use 'reduce examples --list' to see available."
+            )
+        url = f"{github_raw}/{filename}"
+        with tempfile.NamedTemporaryFile(mode="w", suffix=".py", delete=False) as f:
+            try:
+                with urllib.request.urlopen(url) as resp:
+                    f.write(resp.read().decode())
+                temp_path = f.name
+            except HTTPError as e:
+                raise click.ClickException(
+                    f"Failed to download {filename}: {e}"
+                ) from None
+        try:
+            click.echo(f"Running {filename}...")
+            result = subprocess.run([sys.executable, temp_path], check=False)
+            sys.exit(result.returncode)
+        finally:
+            os.unlink(temp_path)
+
+    # Ensure output directory exists
+    os.makedirs(output, exist_ok=True)
+
+    def download_file(name):
+        url = f"{github_raw}/{name}"
+        dest = os.path.join(output, name)
+        try:
+            urllib.request.urlretrieve(url, dest)
+            click.echo(f"Downloaded: {dest}")
+        except HTTPError as e:
+            click.echo(f"Failed to download {name}: {e}", err=True)
+
+    if download_all:
+        for name in example_files:
+            download_file(name)
+    else:
+        if filename not in example_files:
+            raise click.ClickException(
+                f"Unknown example '{filename}'. Use 'reduce examples --list' to see available."
+            )
+        download_file(filename)
+
+
+@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):
+        from .configuration import get_configuration_for_instrument
+        from .reduce import main as reduce_main
+
+        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()