isgri 0.5.1__tar.gz → 0.6.0__tar.gz

{isgri-0.5.1 → isgri-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: isgri
-Version: 0.5.1
+Version: 0.6.0
 Summary: Python package for INTEGRAL IBIS/ISGRI lightcurve analysis
 Author: Dominik Patryk Pacholski
 License: MIT
@@ -55,6 +55,9 @@ pip install isgri
 # Configure default paths (once)
 isgri config-set --catalog ~/data/scw_catalog.fits
 
+# Interactive method
+isgri query
+
 # Query by time range
 isgri query --tstart 2010-01-01 --tstop 2010-12-31
 
@@ -138,27 +141,4 @@ Local config file `isgri_config.toml` in current directory overrides global conf
 - **CLI Reference**: Run `isgri --help` or `isgri <command> --help`
 - **Catalog Tutorial**: [scwquery_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/scwquery_walkthrough.ipynb)
 - **Light Curve Tutorial**: [lightcurve_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/lightcurve_walkthrough.ipynb)
-- **API Reference**: Use `help()` in Python or see docstrings
-
-## Project Structure
-
-```
-isgri/
-├── catalog/          # SCW catalog query tools
-│   ├── scwquery.py   # Main query interface
-│   └── wcs.py        # Coordinate transformations
-├── utils/            # Light curve analysis utilities
-│   ├── lightcurve.py # Light curve class
-│   ├── quality.py    # Quality metrics
-│   ├── pif.py        # PIF tools
-│   ├── file_loaders.py
-│   └── time_conversion.py
-├── config.py         # Configuration management
-└── cli.py            # Command line interface
-```
-
-## Requirements
-
-- Python ≥ 3.10
-- astropy
-- numpy
+- **API Reference**: Use `help()` in Python or see docstrings

{isgri-0.5.1 → isgri-0.6.0}/README.md

@@ -39,6 +39,9 @@ pip install isgri
 # Configure default paths (once)
 isgri config-set --catalog ~/data/scw_catalog.fits
 
+# Interactive method
+isgri query
+
 # Query by time range
 isgri query --tstart 2010-01-01 --tstop 2010-12-31
 
@@ -122,27 +125,4 @@ Local config file `isgri_config.toml` in current directory overrides global conf
 - **CLI Reference**: Run `isgri --help` or `isgri <command> --help`
 - **Catalog Tutorial**: [scwquery_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/scwquery_walkthrough.ipynb)
 - **Light Curve Tutorial**: [lightcurve_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/lightcurve_walkthrough.ipynb)
-- **API Reference**: Use `help()` in Python or see docstrings
-
-## Project Structure
-
-```
-isgri/
-├── catalog/          # SCW catalog query tools
-│   ├── scwquery.py   # Main query interface
-│   └── wcs.py        # Coordinate transformations
-├── utils/            # Light curve analysis utilities
-│   ├── lightcurve.py # Light curve class
-│   ├── quality.py    # Quality metrics
-│   ├── pif.py        # PIF tools
-│   ├── file_loaders.py
-│   └── time_conversion.py
-├── config.py         # Configuration management
-└── cli.py            # Command line interface
-```
-
-## Requirements
-
-- Python ≥ 3.10
-- astropy
-- numpy
+- **API Reference**: Use `help()` in Python or see docstrings

{isgri-0.5.1 → isgri-0.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "isgri"
-version = "0.5.1"
+version = "0.6.0"
 authors = [{name = "Dominik Patryk Pacholski"}]
 license = {text = "MIT"}
 description = "Python package for INTEGRAL IBIS/ISGRI lightcurve analysis"
@@ -23,4 +23,4 @@ dependencies = [
 where = ["src"]
 
 [project.scripts]
-isgri = "isgri.cli:main"
+isgri = "isgri.cli.main:main"

isgri-0.6.0/src/isgri/__version__.py

@@ -0,0 +1 @@
+__version__ = "0.6.0"

{isgri-0.5.1 → isgri-0.6.0}/src/isgri/catalog/scwquery.py

@@ -344,6 +344,48 @@ class ScwQuery:
             combined_mask &= filt.mask
         return self.catalog[combined_mask]
 
+    def write(
+        self, output_path: Union[str, Path], swid_only: Optional[str] = False, overwrite: Optional[bool] = False
+    ):
+        """Write filtered catalog to the file.
+
+        Parameters
+        ----------
+        output_path : str or Path
+            Path to output file. Format auto-detected from extension:
+                - .txt: SWID list (one per line)
+                - .fits: FITS table
+                - .csv: CSV table
+        swid_only : bool, optional
+            If True, write only SWID list regardless of extension
+        overwrite : bool, optional
+            Whether to overwrite existing file, by default False
+
+        Raises
+        ------
+        FileExistsError
+            If file exists and overwrite=False
+
+        Examples
+        --------
+        >>> query.time(tstart=3000).write("filtered_scws.fits", overwrite=True)
+        >>> query.quality(max_chi=2.0).write("good_scws.txt", swid_only=True)
+        >>> query.write("scws.csv")
+        >>> query.write("output", swid_only=True)  # Force SWID list regardless of extension
+        """
+
+        results = self.get()
+        if isinstance(output_path, str):
+            output_path = Path(output_path)
+        if output_path.exists() and not overwrite:
+            raise FileExistsError(f"Output file already exists: {output_path}")
+        if swid_only or output_path.suffix == ".txt":
+            with open(output_path, "w") as f:
+                for swid in results["SWID"]:
+                    f.write(f"{swid}\n")
+        else:
+            results.write(output_path, overwrite=overwrite)
+
     def count(self) -> int:
         """
         Count SCWs matching current filters.

isgri-0.6.0/src/isgri/cli/__init__.py

@@ -0,0 +1 @@
+from .main import main

isgri-0.5.1/src/isgri/cli.py → isgri-0.6.0/src/isgri/cli/main.py

@@ -1,224 +1,168 @@
-import click
-from pathlib import Path
-from .catalog import ScwQuery
-from .__version__ import __version__
-from .config import Config
-
-
-@click.group()
-@click.version_option(version=__version__)
-def main():
-    """ISGRI - INTEGRAL/ISGRI data analysis toolkit."""
-    pass
-
-
-def parse_time(time_str):
-    """
-    Parse time string as IJD float or ISO date string.
-
-    Parameters
-    ----------
-    time_str : str or None
-        Time as "YYYY-MM-DD" or IJD number
-
-    Returns
-    -------
-    float or str or None
-        Parsed time value
-    """
-    if time_str is None:
-        return None
-
-    try:
-        return float(time_str)
-    except ValueError:
-        return time_str
-
-
-@main.command()
-@click.option("--catalog", type=click.Path(), help="Path to catalog FITS file. If not provided, uses config value.")
-@click.option("--tstart", help="Start time (YYYY-MM-DD or IJD)")
-@click.option("--tstop", help="Stop time (YYYY-MM-DD or IJD)")
-@click.option("--ra", type=float, help="Right ascension (degrees)")
-@click.option("--dec", type=float, help="Declination (degrees)")
-@click.option("--fov", type=click.Choice(["full", "any"]), default="any", help="Field of view mode")
-@click.option("--max-chi", type=float, help="Maximum chi-squared value")
-@click.option("--chi-type", type=click.Choice(["RAW", "CUT", "GTI"]), default="CUT", help="Type of chi-squared value")
-@click.option("--revolution", "-r", help="Revolution number")
-@click.option("--output", "-o", type=click.Path(), help="Output file (.fits or .csv)")
-@click.option("--list-swids", is_flag=True, help="Only output SWID list")
-@click.option("--count", is_flag=True, help="Only show count")
-def query(catalog, tstart, tstop, ra, dec, fov, max_chi, chi_type, revolution, output, list_swids, count):
-    """
-    Query INTEGRAL science window catalog.
-
-    If no catalog path is provided, uses the default from configuration.
-    Multiple filters can be combined.
-
-    Examples:
-        Query by time range (IJD):
-
-            isgri query --tstart 3000 --tstop 3100
-
-        Query by time range (ISO date):
-
-            isgri query --tstart 2010-01-01 --tstop 2010-12-31
-
-        Query by sky position:
-
-            isgri query --ra 83.63 --dec 22.01 --fov full
-
-        Query with quality cut:
-
-            isgri query --max-chi 2.0 --chi-type CUT
-
-        Save results to file:
-
-            isgri query --tstart 3000 --tstop 3100 --output results.fits
-
-        Get only SWID list:
-
-            isgri query --tstart 3000 --tstop 3100 --list-swids
-
-        Count matching science windows:
-
-            isgri query --ra 83.63 --dec 22.01 --count
-    """
-    try:
-        # Load catalog
-        q = ScwQuery(catalog)
-        initial_count = len(q.catalog)
-
-        # Parse times (handle both IJD and ISO)
-        tstart = parse_time(tstart)
-        tstop = parse_time(tstop)
-
-        # Apply filters
-        if tstart or tstop:
-            q = q.time(tstart=tstart, tstop=tstop)
-
-        if ra is not None and dec is not None:
-            q = q.position(ra=ra, dec=dec, fov_mode=fov)
-
-        if max_chi is not None:
-            q = q.quality(max_chi=max_chi, chi_type=chi_type)
-
-        if revolution:
-            q = q.revolution(revolution)
-
-        results = q.get()
-
-        if count:
-            click.echo(len(results))
-
-        elif list_swids:
-            for swid in results["SWID"]:
-                click.echo(swid)
-
-        elif output:
-            if output.endswith(".csv"):
-                results.write(output, format="ascii.csv", overwrite=True)
-            else:
-                results.write(output, format="fits", overwrite=True)
-            click.echo(f"Saved {len(results)} SCWs to {output}")
-
-        else:
-            click.echo(f"Found {len(results)}/{initial_count} SCWs")
-            if len(results) > 0:
-                display_cols = ["SWID", "TSTART", "TSTOP", "RA_SCX", "DEC_SCX"]
-                chi_col = f"{chi_type}_CHI" if chi_type != "RAW" else "CHI"
-                if chi_col in results.colnames:
-                    display_cols.append(chi_col)
-                click.echo(results[display_cols][:10])
-                if len(results) > 10:
-                    click.echo(f"... and {len(results) - 10} more")
-
-    except Exception as e:
-        click.echo(f"Error: {e}", err=True)
-        raise click.Abort()
-
-
-@main.command()
-def config():
-    """
-    Show current configuration.
-
-    Displays paths to config file, archive directory, and catalog file,
-    along with their existence status.
-    """
-    cfg = Config()
-
-    click.echo(f"Config file: {cfg.path}")
-    click.echo(f"  Exists: {cfg.path.exists()}")
-    click.echo()
-
-    archive = cfg.archive_path
-    click.echo(f"Archive path: {archive if archive else '(not set)'}")
-    if archive:
-        click.echo(f"  Exists: {archive.exists()}")
-
-    try:
-        catalog = cfg.catalog_path
-        click.echo(f"Catalog path: {catalog if catalog else '(not set)'}")
-        if catalog:
-            click.echo(f"  Exists: {catalog.exists()}")
-    except FileNotFoundError as e:
-        click.echo(f"Catalog path: (configured but file not found)")
-        click.echo(f"  Error: {e}")
-
-
-@main.command()
-@click.option("--archive", type=click.Path(), help="INTEGRAL archive directory path")
-@click.option("--catalog", type=click.Path(), help="Catalog FITS file path")
-def config_set(archive, catalog):
-    """
-    Set configuration values.
-
-    Set default paths for archive directory and/or catalog file.
-    Paths are expanded (~ becomes home directory) and resolved to absolute paths.
-    Warns if path doesn't exist but allows setting anyway.
-
-    Examples:
-
-        Set archive path:
-
-            isgri config-set --archive /anita/archivio/
-
-        Set catalog path:
-
-            isgri config-set --catalog ~/data/scw_catalog.fits
-
-        Set both at once:
-
-            isgri config-set --archive /anita/archivio/ --catalog ~/data/scw_catalog.fits
-    """
-    if not archive and not catalog:
-        click.echo("Error: Specify at least one option (--archive or --catalog)", err=True)
-        raise click.Abort()
-
-    cfg = Config()
-
-    if archive:
-        archive_path = Path(archive).expanduser().resolve()
-        if not archive_path.exists():
-            click.echo(f"Warning: Archive path does not exist: {archive_path}", err=True)
-            if not click.confirm("Set anyway?"):
-                raise click.Abort()
-        cfg.set(archive_path=archive_path)
-        click.echo(f"✓ Archive path set to: {archive_path}")
-
-    if catalog:
-        catalog_path = Path(catalog).expanduser().resolve()
-        if not catalog_path.exists():
-            click.echo(f"Warning: Catalog file does not exist: {catalog_path}", err=True)
-            if not click.confirm("Set anyway?"):
-                raise click.Abort()
-        cfg.set(catalog_path=catalog_path)
-        click.echo(f"✓ Catalog path set to: {catalog_path}")
-
-    click.echo()
-    click.echo(f"Configuration saved to: {cfg.path}")
-
-
-if __name__ == "__main__":
-    main()
+import click
+from pathlib import Path
+from ..catalog import ScwQuery
+from ..__version__ import __version__
+from ..config import Config
+from .query import query_direct, query_interactive
+
+
+@click.group()
+@click.version_option(version=__version__)
+def main():
+    """ISGRI - INTEGRAL/ISGRI data analysis toolkit."""
+    pass
+
+
+@main.command()
+@click.option("--catalog", type=click.Path(), help="Path to catalog FITS file. If not provided, uses config value.")
+@click.option("--tstart", help="Start time (YYYY-MM-DD or IJD)")
+@click.option("--tstop", help="Stop time (YYYY-MM-DD or IJD)")
+@click.option("--ra", help="Right ascension (degrees or HH:MM:SS)")
+@click.option("--dec", help="Declination (degrees or DD:MM:SS)")
+@click.option("--radius", type=float, help="Angular separation (degrees)")
+@click.option("--fov", type=click.Choice(["full", "any"]), default="any", help="Field of view mode")
+@click.option("--max-chi", type=float, help="Maximum chi-squared value")
+@click.option("--chi-type", type=click.Choice(["RAW", "CUT", "GTI"]), default="CUT", help="Type of chi-squared value")
+@click.option("--revolution", help="Revolution number")
+@click.option(
+    "--output", "-o", type=click.Path(), help="Output file (.fits or .csv or any if --list-swids or --count)"
+)
+@click.option("--list-swids", is_flag=True, help="Only output SWID list")
+@click.option("--count", is_flag=True, help="Only show count")
+def query(catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count):
+    """
+    Query INTEGRAL science window catalog.
+
+    If no catalog path is provided, uses the default from configuration.
+    Multiple filters can be combined.
+
+    Examples:
+        Query by time range (IJD):
+
+            isgri query --tstart 3000 --tstop 3100
+
+        Query by time range (ISO date):
+
+            isgri query --tstart 2010-01-01 --tstop 2010-12-31
+
+        Query by sky position:
+
+            isgri query --ra 83.63 --dec 22.01 --fov full
+            isgri query --ra 83.63 --dec 22.01 --radius 5.0
+
+        Query with quality cut:
+
+            isgri query --max-chi 2.0 --chi-type CUT
+
+        Save results to file:
+
+            isgri query --tstart 3000 --tstop 3100 --output results.fits
+
+        Get only SWID list:
+
+            isgri query --tstart 3000 --tstop 3100 --list-swids
+
+        Count matching science windows:
+
+            isgri query --ra 83.63 --dec 22.01 --count
+    """
+    if catalog is None:
+        cfg = Config()
+        catalog = cfg.catalog_path
+
+        if not catalog:
+            click.echo("Error: No catalog configured", err=True)
+            raise click.Abort()
+
+    if any(param is not None for param in [tstart, tstop, ra, dec, radius, max_chi, revolution]):
+        query_direct(
+            catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count
+        )
+    else:
+        query_interactive(catalog)
+
+
+@main.command()
+def config():
+    """
+    Show current configuration.
+
+    Displays paths to config file, archive directory, and catalog file,
+    along with their existence status.
+    """
+    cfg = Config()
+
+    click.echo(f"Config file: {cfg.path}")
+    click.echo(f"  Exists: {cfg.path.exists()}")
+    click.echo()
+
+    archive = cfg.archive_path
+    click.echo(f"Archive path: {archive if archive else '(not set)'}")
+    if archive:
+        click.echo(f"  Exists: {archive.exists()}")
+
+    try:
+        catalog = cfg.catalog_path
+        click.echo(f"Catalog path: {catalog if catalog else '(not set)'}")
+        if catalog:
+            click.echo(f"  Exists: {catalog.exists()}")
+    except FileNotFoundError as e:
+        click.echo(f"Catalog path: (configured but file not found)")
+        click.echo(f"  Error: {e}")
+
+
+@main.command()
+@click.option("--archive", type=click.Path(), help="INTEGRAL archive directory path")
+@click.option("--catalog", type=click.Path(), help="Catalog FITS file path")
+def config_set(archive, catalog):
+    """
+    Set configuration values.
+
+    Set default paths for archive directory and/or catalog file.
+    Paths are expanded (~ becomes home directory) and resolved to absolute paths.
+    Warns if path doesn't exist but allows setting anyway.
+
+    Examples:
+
+        Set archive path:
+
+            isgri config-set --archive /anita/archivio/
+
+        Set catalog path:
+
+            isgri config-set --catalog ~/data/scw_catalog.fits
+
+        Set both at once:
+
+            isgri config-set --archive /anita/archivio/ --catalog ~/data/scw_catalog.fits
+    """
+    if not archive and not catalog:
+        click.echo("Error: Specify at least one option (--archive or --catalog)", err=True)
+        raise click.Abort()
+
+    cfg = Config()
+
+    if archive:
+        archive_path = Path(archive).expanduser().resolve()
+        if not archive_path.exists():
+            click.echo(f"Warning: Archive path does not exist: {archive_path}", err=True)
+            if not click.confirm("Set anyway?"):
+                raise click.Abort()
+        cfg.set(archive_path=archive_path)
+        click.echo(f"✓ Archive path set to: {archive_path}")
+
+    if catalog:
+        catalog_path = Path(catalog).expanduser().resolve()
+        if not catalog_path.exists():
+            click.echo(f"Warning: Catalog file does not exist: {catalog_path}", err=True)
+            if not click.confirm("Set anyway?"):
+                raise click.Abort()
+        cfg.set(catalog_path=catalog_path)
+        click.echo(f"✓ Catalog path set to: {catalog_path}")
+
+    click.echo()
+    click.echo(f"Configuration saved to: {cfg.path}")
+
+
+if __name__ == "__main__":
+    main()

isgri-0.6.0/src/isgri/cli/query.py

@@ -0,0 +1,172 @@
+import click
+from pathlib import Path
+from ..catalog import ScwQuery
+from ..config import Config
+from ..__version__ import __version__
+
+
+def parse_time(time_str):
+    """
+    Parse time string as IJD float or ISO date string.
+
+    Parameters
+    ----------
+    time_str : str or None
+        Time as "YYYY-MM-DD" or IJD number
+
+    Returns
+    -------
+    float or str or None
+        Parsed time value
+    """
+    if time_str is None:
+        return None
+
+    try:
+        return float(time_str)
+    except ValueError:
+        return time_str
+
+
+def parse_coord(coord):
+    """
+    Parse RA and Dec strings as float degrees or sexagesimal strings.
+
+    Parameters
+    ----------
+    coord : str or None
+        Coordinate as float degrees or sexagesimal string
+    Returns
+    -------
+    float or str or None
+        Parsed coordinate value
+    """
+    if coord is None:
+        return None
+
+    try:
+        return float(coord)
+    except ValueError:
+        return coord
+
+
+def query_direct(
+    catalog_path, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count
+):
+    try:
+        q = ScwQuery(catalog_path)
+        initial_count = len(q.catalog)
+        # Parse times (handle both IJD and ISO)
+        tstart = parse_time(tstart)
+        tstop = parse_time(tstop)
+
+        # Apply filters
+        if tstart or tstop:
+            q = q.time(tstart=tstart, tstop=tstop)
+
+        if ra is not None and dec is not None:
+            ra = parse_coord(ra)
+            dec = parse_coord(dec)
+            if radius is not None:
+                q = q.position(ra=ra, dec=dec, radius=radius)
+            else:
+                q = q.position(ra=ra, dec=dec, fov_mode=fov)
+
+        if max_chi is not None:
+            q = q.quality(max_chi=max_chi, chi_type=chi_type)
+
+        if revolution:
+            q = q.revolution(revolution)
+
+        results = q.get()
+
+        if count:
+            click.echo(len(results))
+
+        elif list_swids:
+            for swid in results["SWID"]:
+                click.echo(swid)
+
+        elif output:
+            if output.endswith(".csv"):
+                results.write(output, format="ascii.csv", overwrite=True)
+            else:
+                results.write(output, format="fits", overwrite=True)
+            click.echo(f"Saved {len(results)} SCWs to {output}")
+
+        else:
+            click.echo(f"Found {len(results)}/{initial_count} SCWs")
+            if len(results) > 0:
+                display_cols = ["SWID", "TSTART", "TSTOP", "RA_SCX", "DEC_SCX"]
+                chi_col = f"{chi_type}_CHI" if chi_type != "RAW" else "CHI"
+                if chi_col in results.colnames:
+                    display_cols.append(chi_col)
+                click.echo(results[display_cols][:10])
+                if len(results) > 10:
+                    click.echo(f"... and {len(results) - 10} more")
+
+    except Exception as e:
+        click.echo(f"Error: {e}", err=True)
+        raise click.Abort()
+
+
+def query_interactive(catalog_path):
+    """Run interactive query session."""
+    click.echo("=== Interactive Query Mode ===\n")
+
+    q = ScwQuery(catalog_path)
+    click.echo(f"Loaded {len(q.catalog)} SCWs")
+    click.echo("Type 'help' for commands\n")
+
+    while True:
+        try:
+            cmd = click.prompt("query>", default="").strip().lower()
+
+            if cmd in ("exit", "quit", "q"):
+                break
+            elif cmd == "help":
+                click.echo("Commands: time, pos, quality, show, reset, save, exit")
+            elif cmd == "time":
+                tstart = click.prompt("Start", default="", show_default=False)
+                tstop = click.prompt("Stop", default="", show_default=False)
+                tstart = parse_time(tstart) if tstart else None
+                tstop = parse_time(tstop) if tstop else None
+                q = q.time(tstart=tstart or None, tstop=tstop or None)
+                click.echo(f"→ {q.count()} SCWs")
+            elif cmd == "pos":
+                ra = click.prompt("RA")
+                dec = click.prompt("Dec")
+                mode = click.prompt("Mode", type=click.Choice(["fov", "radius"]), default="fov")
+                if mode == "radius":
+                    radius = click.prompt("Radius (deg)", type=float, default=10.0)
+                    q = q.position(ra=parse_coord(ra), dec=parse_coord(dec), radius=radius)
+                else:
+                    fov_mode = click.prompt("FOV mode", type=click.Choice(["full", "any"]), default="any")
+                    q = q.position(ra=parse_coord(ra), dec=parse_coord(dec), fov_mode=fov_mode)
+                click.echo(f"→ {q.count()} SCWs")
+
+            elif cmd == "quality":
+                max_chi = click.prompt("Max chi-squared", type=float)
+                chi_type = click.prompt("Chi type", type=click.Choice(["RAW", "CUT", "GTI"]), default="CUT")
+                q = q.quality(max_chi=max_chi, chi_type=chi_type)
+                click.echo(f"→ {q.count()} SCWs")
+
+            elif cmd == "show":
+                results = q.get()
+                click.echo(f"\n{len(results)} SCWs:")
+                click.echo(results[["SWID", "TSTART", "TSTOP"]])
+            elif cmd == "reset":
+                q = q.reset()
+                click.echo(f"→ {len(q.catalog)} SCWs")
+            elif cmd == "save":
+                only_scws = click.confirm("Save only SWID list?", default=False)
+                path = click.prompt("File")
+                q.write(path, overwrite=True, swid_only=only_scws)
+                click.echo(f"✓ Saved")
+            else:
+                click.echo(f"Unknown: {cmd}")
+
+        except KeyboardInterrupt:
+            click.echo("\nUse 'exit' to quit")
+        except Exception as e:
+            click.echo(f"Error: {e}", err=True)

{isgri-0.5.1 → isgri-0.6.0}/tests/catalog/test_scwquery.py

@@ -377,31 +377,34 @@ def test_scwquery_uses_config(tmp_path, mock_catalog, monkeypatch):
     """Test ScwQuery uses config when no path provided."""
     config_path = tmp_path / "config.toml"
     cfg = Config(config_path)
-    cfg.set(catalog_path=mock_catalog) 
+    cfg.set(catalog_path=mock_catalog)
 
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
 
     query = ScwQuery()
     assert str(query.catalog_path) == mock_catalog
-    assert len(query.catalog) == 1000  
+    assert len(query.catalog) == 1000
+
 
 def test_scwquery_explicit_path_overrides_config(tmp_path, mock_catalog, monkeypatch):
     """Test explicit path overrides config."""
     # Create a second catalog
     n_scw = 50
-    other_catalog = Table({
-        "SWID": [f"{i:012d}" for i in range(n_scw)],
-        "REVOL": np.random.randint(100, 500, n_scw),
-        "TSTART": np.linspace(5000, 6000, n_scw),
-        "TSTOP": np.linspace(5001, 6001, n_scw),
-        "RA_SCX": np.random.uniform(0, 360, n_scw),
-        "DEC_SCX": np.random.uniform(-80, 80, n_scw),
-        "RA_SCZ": np.random.uniform(0, 360, n_scw),
-        "DEC_SCZ": np.random.uniform(-80, 80, n_scw),
-        "CHI": np.random.uniform(0.5, 5.0, n_scw),
-        "CUT_CHI": np.random.uniform(0.5, 5.0, n_scw),
-        "GTI_CHI": np.random.uniform(0.5, 5.0, n_scw),
-    })
+    other_catalog = Table(
+        {
+            "SWID": [f"{i:012d}" for i in range(n_scw)],
+            "REVOL": np.random.randint(100, 500, n_scw),
+            "TSTART": np.linspace(5000, 6000, n_scw),
+            "TSTOP": np.linspace(5001, 6001, n_scw),
+            "RA_SCX": np.random.uniform(0, 360, n_scw),
+            "DEC_SCX": np.random.uniform(-80, 80, n_scw),
+            "RA_SCZ": np.random.uniform(0, 360, n_scw),
+            "DEC_SCZ": np.random.uniform(-80, 80, n_scw),
+            "CHI": np.random.uniform(0.5, 5.0, n_scw),
+            "CUT_CHI": np.random.uniform(0.5, 5.0, n_scw),
+            "GTI_CHI": np.random.uniform(0.5, 5.0, n_scw),
+        }
+    )
     other_path = tmp_path / "other_catalog.fits"
     other_catalog.write(other_path, overwrite=True)
 
@@ -412,13 +415,12 @@ def test_scwquery_explicit_path_overrides_config(tmp_path, mock_catalog, monkeyp
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
     query = ScwQuery()
     assert query.catalog_path == Path(other_path)
-    assert len(query.catalog) == 50  
-
+    assert len(query.catalog) == 50
 
     # path should override config
     query = ScwQuery(mock_catalog)
     assert query.catalog_path == Path(mock_catalog)
-    assert len(query.catalog) == 1000  
+    assert len(query.catalog) == 1000
 
 
 def test_scwquery_no_config_raises(tmp_path, monkeypatch):
@@ -441,6 +443,104 @@ def test_scwquery_config_file_not_exists(tmp_path, monkeypatch):
 
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
 
-    # Should raise when file doesn't exist (in config.catalog_path property)
     with pytest.raises(FileNotFoundError, match="Catalog path does not exist"):
         ScwQuery()
+
+
+def test_write_fits(tmp_path, mock_catalog):
+    """Test writing to FITS file"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "results.fits"
+
+    query.time(tstart=3400, tstop=3600).write(output)
+
+    assert output.exists()
+    written = Table.read(output)
+    assert len(written) > 0
+    assert all(written["TSTOP"] >= 3400)
+    assert all(written["TSTART"] <= 3600)
+
+
+def test_write_csv(tmp_path, mock_catalog):
+    """Test writing to CSV file"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "results.csv"
+
+    query.quality(max_chi=2.0).write(output)
+
+    assert output.exists()
+    written = Table.read(output, format="ascii.csv")
+    assert len(written) > 0
+    assert all(written["CHI"] <= 2.0)
+
+
+def test_write_swid_list_txt(tmp_path, mock_catalog):
+    """Test writing SWID list to .txt file"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "swids.txt"
+
+    query.time(tstart=3500).write(output)
+
+    assert output.exists()
+    swids = output.read_text().strip().split("\n")
+    assert len(swids) > 0
+    assert all(len(swid) == 12 for swid in swids)
+
+
+def test_write_swid_only_flag(tmp_path, mock_catalog):
+    """Test swid_only flag forces SWID list"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "swids.fits"  # .fits extension but force SWID
+
+    query.time(tstart=3500).write(output, swid_only=True)
+
+    assert output.exists()
+    # Should be text file despite .fits extension
+    swids = output.read_text().strip().split("\n")
+    assert len(swids) > 0
+    assert all(len(swid) == 12 for swid in swids)
+
+
+def test_write_overwrite_false(tmp_path, mock_catalog):
+    """Test write raises when file exists and overwrite=False"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "results.fits"
+
+    # Write once
+    query.write(output)
+
+    # Try to write again without overwrite
+    with pytest.raises(FileExistsError, match="already exists"):
+        query.write(output, overwrite=False)
+
+
+def test_write_overwrite_true(tmp_path, mock_catalog):
+    """Test write overwrites when overwrite=True"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "results.fits"
+
+    # First write
+    query.time(tstart=3400, tstop=3600).write(output)
+    first_result = Table.read(output)
+
+    # Overwrite with different data
+    query.time(tstart=3700, tstop=3800).write(output, overwrite=True)
+    second_result = Table.read(output)
+
+    # Check different time ranges (data should be different)
+    assert all(first_result["TSTART"] <= 3600)
+    assert all(second_result["TSTOP"] >= 3700)
+    assert first_result != second_result
+
+
+def test_write_empty_result(tmp_path, mock_catalog):
+    """Test writing empty result set"""
+    query = ScwQuery(mock_catalog)
+    output = tmp_path / "empty.fits"
+
+    # Query that returns no results
+    query.time(tstart=10000).write(output)
+
+    assert output.exists()
+    result = Table.read(output)
+    assert len(result) == 0

isgri-0.5.1/tests/test_cli.py → isgri-0.6.0/tests/cli/test_main.py

@@ -17,98 +17,85 @@ def runner():
 def mock_catalog(tmp_path):
     """Create mock SCW catalog."""
     catalog_path = tmp_path / "test_catalog.fits"
-    
+
     n_scw = 100
     data = {
-        'SWID': [f"{i:012d}" for i in range(n_scw)],
-        'REVOL': np.random.randint(100, 500, n_scw),
-        'TSTART': np.linspace(3000, 4000, n_scw),
-        'TSTOP': np.linspace(3000.5, 4000.5, n_scw),
-        'RA_SCX': np.random.uniform(0, 360, n_scw),
-        'DEC_SCX': np.random.uniform(-80, 80, n_scw),
-        'RA_SCZ': np.random.uniform(0, 360, n_scw),
-        'DEC_SCZ': np.random.uniform(-80, 80, n_scw),
-        'CHI': np.random.uniform(0.5, 5.0, n_scw),
-        'CUT_CHI': np.random.uniform(0.5, 5.0, n_scw),
-        'GTI_CHI': np.random.uniform(0.5, 5.0, n_scw),
+        "SWID": [f"{i:012d}" for i in range(n_scw)],
+        "REVOL": np.random.randint(100, 500, n_scw),
+        "TSTART": np.linspace(3000, 4000, n_scw),
+        "TSTOP": np.linspace(3000.5, 4000.5, n_scw),
+        "RA_SCX": np.random.uniform(0, 360, n_scw),
+        "DEC_SCX": np.random.uniform(-80, 80, n_scw),
+        "RA_SCZ": np.random.uniform(0, 360, n_scw),
+        "DEC_SCZ": np.random.uniform(-80, 80, n_scw),
+        "CHI": np.random.uniform(0.5, 5.0, n_scw),
+        "CUT_CHI": np.random.uniform(0.5, 5.0, n_scw),
+        "GTI_CHI": np.random.uniform(0.5, 5.0, n_scw),
     }
     table = Table(data)
-    table.write(catalog_path, format='fits', overwrite=True)
-    
+    table.write(catalog_path, format="fits", overwrite=True)
+
     return catalog_path
 
 
 def test_cli_version(runner):
     """Test --version flag."""
-    result = runner.invoke(main, ['--version'])
+    result = runner.invoke(main, ["--version"])
     assert result.exit_code == 0
-    assert 'version' in result.output.lower()
+    assert "version" in result.output.lower()
 
 
 def test_cli_help(runner):
     """Test --help flag."""
-    result = runner.invoke(main, ['--help'])
+    result = runner.invoke(main, ["--help"])
     assert result.exit_code == 0
-    assert 'ISGRI' in result.output
+    assert "ISGRI" in result.output
 
 
 def test_query_with_catalog(runner, mock_catalog):
     """Test query command with explicit catalog."""
-    result = runner.invoke(main, ['query', '--catalog', str(mock_catalog)])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog), "--tstart", "3000", "--tstop", "4000"])
     assert result.exit_code == 0
-    assert 'Found' in result.output
-    assert '100' in result.output
+    assert "Found" in result.output
+    assert "100" in result.output
 
 
 def test_query_count(runner, mock_catalog):
     """Test query --count flag."""
-    result = runner.invoke(main, ['query', '--catalog', str(mock_catalog), '--count'])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog),"--tstart", "3000", "--count"])
     assert result.exit_code == 0
-    assert result.output.strip() == '100'
+    assert result.output.strip() == "100"
 
 
 def test_query_list_swids(runner, mock_catalog):
     """Test query --list-swids flag."""
-    result = runner.invoke(main, ['query', '--catalog', str(mock_catalog), '--list-swids'])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog), "--tstart", "3000","--list-swids"])
     assert result.exit_code == 0
-    lines = result.output.strip().split('\n')
+    lines = result.output.strip().split("\n")
     assert len(lines) == 100
     assert all(len(line) == 12 for line in lines)
 
 
 def test_query_with_filters(runner, mock_catalog):
     """Test query with time filters."""
-    result = runner.invoke(main, [
-        'query', 
-        '--catalog', str(mock_catalog),
-        '--tstart', '3000',
-        '--tstop', '3100'
-    ])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog), "--tstart", "3000", "--tstop", "3100"])
     assert result.exit_code == 0
-    assert 'Found' in result.output
+    assert "Found" in result.output
 
 
 def test_query_output_fits(runner, mock_catalog, tmp_path):
     """Test query with FITS output."""
     output_file = tmp_path / "results.fits"
-    result = runner.invoke(main, [
-        'query',
-        '--catalog', str(mock_catalog),
-        '--output', str(output_file)
-    ])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog),"--tstart", "3000", "--output", str(output_file)])
     assert result.exit_code == 0
     assert output_file.exists()
-    assert 'Saved' in result.output
+    assert "Saved" in result.output
 
 
 def test_query_output_csv(runner, mock_catalog, tmp_path):
     """Test query with CSV output."""
     output_file = tmp_path / "results.csv"
-    result = runner.invoke(main, [
-        'query',
-        '--catalog', str(mock_catalog),
-        '--output', str(output_file)
-    ])
+    result = runner.invoke(main, ["query", "--catalog", str(mock_catalog),"--tstart", "3000", "--output", str(output_file)])
     assert result.exit_code == 0
     assert output_file.exists()
 
@@ -117,10 +104,10 @@ def test_query_no_catalog_no_config(runner, tmp_path, monkeypatch):
     """Test query fails when no catalog and no config."""
     config_path = tmp_path / "config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, ['query'])
+
+    result = runner.invoke(main, ["query"])
     assert result.exit_code != 0
-    assert 'No catalog_path provided' in result.output
+    assert "No catalog configured" in result.output
 
 
 def test_query_uses_config(runner, mock_catalog, tmp_path, monkeypatch):
@@ -128,23 +115,23 @@ def test_query_uses_config(runner, mock_catalog, tmp_path, monkeypatch):
     config_path = tmp_path / "config.toml"
     cfg = Config(config_path)
     cfg.set(catalog_path=mock_catalog)
-    
+
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, ['query'])
+
+    result = runner.invoke(main, ["query","--tstart", "3000", ])
     assert result.exit_code == 0
-    assert 'Found 100' in result.output
+    assert "Found 100" in result.output
 
 
 def test_config_show_empty(runner, tmp_path, monkeypatch):
     """Test config command with empty config."""
     config_path = tmp_path / "config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, ['config'])
+
+    result = runner.invoke(main, ["config"])
     assert result.exit_code == 0
     assert str(config_path) in result.output
-    assert '(not set)' in result.output
+    assert "(not set)" in result.output
 
 
 def test_config_show_with_values(runner, tmp_path, mock_catalog, monkeypatch):
@@ -152,10 +139,10 @@ def test_config_show_with_values(runner, tmp_path, mock_catalog, monkeypatch):
     config_path = tmp_path / "config.toml"
     cfg = Config(config_path)
     cfg.set(archive_path=tmp_path, catalog_path=mock_catalog)
-    
+
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, ['config'])
+
+    result = runner.invoke(main, ["config"])
     assert result.exit_code == 0
     assert str(tmp_path) in result.output
     assert str(mock_catalog) in result.output
@@ -165,14 +152,14 @@ def test_config_set_archive(runner, tmp_path, monkeypatch):
     """Test config-set --archive."""
     config_path = tmp_path / "test_config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
+
     archive_path = tmp_path / "archive"
     archive_path.mkdir()
-    
-    result = runner.invoke(main, ['config-set', '--archive', str(archive_path)])
+
+    result = runner.invoke(main, ["config-set", "--archive", str(archive_path)])
     assert result.exit_code == 0
-    assert 'Archive path set' in result.output
-    
+    assert "Archive path set" in result.output
+
     cfg = Config(config_path)
     assert cfg.archive_path == archive_path
 
@@ -181,11 +168,11 @@ def test_config_set_catalog(runner, tmp_path, mock_catalog, monkeypatch):
     """Test config-set --catalog."""
     config_path = tmp_path / "test_config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, ['config-set', '--catalog', str(mock_catalog)])
+
+    result = runner.invoke(main, ["config-set", "--catalog", str(mock_catalog)])
     assert result.exit_code == 0
-    assert 'Catalog path set' in result.output
-    
+    assert "Catalog path set" in result.output
+
     cfg = Config(config_path)
     assert str(cfg.catalog_path) == str(mock_catalog)
 
@@ -194,50 +181,44 @@ def test_config_set_both(runner, tmp_path, mock_catalog, monkeypatch):
     """Test config-set with both options."""
     config_path = tmp_path / "test_config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
+
     archive_path = tmp_path / "archive"
     archive_path.mkdir()
-    
-    result = runner.invoke(main, [
-        'config-set',
-        '--archive', str(archive_path),
-        '--catalog', str(mock_catalog)
-    ])
+
+    result = runner.invoke(main, ["config-set", "--archive", str(archive_path), "--catalog", str(mock_catalog)])
     assert result.exit_code == 0
-    assert 'Archive path set' in result.output
-    assert 'Catalog path set' in result.output
+    assert "Archive path set" in result.output
+    assert "Catalog path set" in result.output
 
 
 def test_config_set_no_options(runner):
     """Test config-set with no options fails."""
-    result = runner.invoke(main, ['config-set'])
+    result = runner.invoke(main, ["config-set"])
     assert result.exit_code != 0
-    assert 'Specify at least one option' in result.output
+    assert "Specify at least one option" in result.output
 
 
 def test_config_set_nonexistent_path_abort(runner, tmp_path, monkeypatch):
     """Test config-set with non-existent path (user aborts)."""
     config_path = tmp_path / "test_config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, [
-        'config-set',
-        '--archive', '/nonexistent/path'
-    ], input='n\n')  # User says 'no' to confirmation
-    
+
+    result = runner.invoke(
+        main, ["config-set", "--archive", "/nonexistent/path"], input="n\n"
+    )  # User says 'no' to confirmation
+
     assert result.exit_code != 0
-    assert 'Warning' in result.output
+    assert "Warning" in result.output
 
 
 def test_config_set_nonexistent_path_confirm(runner, tmp_path, monkeypatch):
     """Test config-set with non-existent path (user confirms)."""
     config_path = tmp_path / "test_config.toml"
     monkeypatch.setattr(Config, "DEFAULT_PATH", config_path)
-    
-    result = runner.invoke(main, [
-        'config-set',
-        '--archive', '/nonexistent/path'
-    ], input='y\n')  # User says 'yes' to confirmation
-    
+
+    result = runner.invoke(
+        main, ["config-set", "--archive", "/nonexistent/path"], input="y\n"
+    )  # User says 'yes' to confirmation
+
     assert result.exit_code == 0
-    assert 'Archive path set' in result.output
+    assert "Archive path set" in result.output

isgri-0.5.1/src/isgri/__version__.py

@@ -1 +0,0 @@
-__version__ = "0.5.1"