isgri 0.5.0__tar.gz → 0.6.0__tar.gz

{isgri-0.5.0 → isgri-0.6.0}/.gitignore

@@ -213,4 +213,6 @@ marimo/_lsp/
 __marimo__/
 
 # Streamlit
-.streamlit/secrets.toml
+.streamlit/secrets.toml
+
+docs/**

isgri-0.6.0/.python-version

@@ -0,0 +1 @@
+3.9

{isgri-0.5.0 → isgri-0.6.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: isgri
-Version: 0.5.0
+Version: 0.6.0
 Summary: Python package for INTEGRAL IBIS/ISGRI lightcurve analysis
 Author: Dominik Patryk Pacholski
 License: MIT
 License-File: LICENSE
-Requires-Python: >=3.10
+Requires-Python: >=3.9
 Requires-Dist: astropy
 Requires-Dist: click
 Requires-Dist: numpy
@@ -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-0.5.0 → 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-0.5.0 → isgri-0.6.0}/pyproject.toml

@@ -4,12 +4,12 @@ build-backend = "hatchling.build"
 
 [project]
 name = "isgri"
-version = "0.5.0"
+version = "0.6.0"
 authors = [{name = "Dominik Patryk Pacholski"}]
 license = {text = "MIT"}
 description = "Python package for INTEGRAL IBIS/ISGRI lightcurve analysis"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 dependencies = [
     "numpy",
     "astropy",
@@ -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-0.5.0 → isgri-0.6.0}/src/isgri/catalog/builder.py

@@ -86,5 +86,5 @@ class CatalogBuilder:
     def _find_scws(self) -> tuple[np.ndarray[str], np.ndarray[str]]:
         # Find all SCW files in the archive
         scws_files = subprocess.run(
-            ["find", "-L", self.archive_path, "-name", "isgri_events.fits.gz"], capture_output=True, text=True
+            ["ls", f"{self.archive_path}/*", "|", "isgri_events.fits.gz"], capture_output=True, text=True
         )

{isgri-0.5.0 → 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-0.5.0/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()