upgrade to specutils>2.0 (#106)

* upgrade to specutils2.1

* fix docstring

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: kelle

astrodbkit/spectra.py

@@ -8,7 +8,7 @@
 from astropy.nddata import StdDevUncertainty
 from astropy.units import Unit
 from astropy.wcs import WCS
-from specutils import Spectrum1D
+from specutils import Spectrum
 from specutils.io.parsing_utils import read_fileobj_or_hdulist
 from specutils.io.registers import data_loader
 
@@ -45,9 +45,9 @@ def identify_spex_prism(origin, *args, **kwargs):
         return is_spex
 
 
-@data_loader("Spex Prism", identifier=identify_spex_prism, extensions=["fits"], dtype=Spectrum1D)
+@data_loader("Spex Prism", identifier=identify_spex_prism, extensions=["fits"], dtype=Spectrum)
 def spex_prism_loader(filename, **kwargs):
-    """Open a SpeX Prism file and convert it to a Spectrum1D object"""
+    """Open a SpeX Prism file and convert it to a Spectrum object"""
 
     with fits.open(filename, **kwargs) as hdulist:
         header = hdulist[0].header
@@ -72,7 +72,7 @@ def spex_prism_loader(filename, **kwargs):
 
         meta = {"header": header}
 
-    return Spectrum1D(flux=data, spectral_axis=wave, uncertainty=uncertainty, meta=meta)
+    return Spectrum(flux=data, spectral_axis=wave, uncertainty=uncertainty, meta=meta)
 
 
 def identify_wcs1d_multispec(origin, *args, **kwargs):
@@ -92,7 +92,7 @@ def identify_wcs1d_multispec(origin, *args, **kwargs):
         )
 
 
-@data_loader("wcs1d-multispec", identifier=identify_wcs1d_multispec, extensions=["fits"], dtype=Spectrum1D, priority=10)
+@data_loader("wcs1d-multispec", identifier=identify_wcs1d_multispec, extensions=["fits"], dtype=Spectrum, priority=10)
 def wcs1d_multispec_loader(file_obj, flux_unit=None, hdu=0, verbose=False, **kwargs):
     """
     Loader for multiextension spectra as wcs1d. Adapted from wcs1d_fits_loader
@@ -115,7 +115,7 @@ def wcs1d_multispec_loader(file_obj, flux_unit=None, hdu=0, verbose=False, **kwa
 
     Returns
     -------
-    :class:`~specutils.Spectrum1D`
+    :class:`~specutils.Spectrum`
     """
 
     with read_fileobj_or_hdulist(file_obj, **kwargs) as hdulist:
@@ -178,7 +178,7 @@ def wcs1d_multispec_loader(file_obj, flux_unit=None, hdu=0, verbose=False, **kwa
     # Store header as metadata information
     meta = {"header": header}
 
-    return Spectrum1D(flux=flux_data, spectral_axis=spectral_axis, uncertainty=uncertainty, meta=meta)
+    return Spectrum(flux=flux_data, spectral_axis=spectral_axis, uncertainty=uncertainty, meta=meta)
 
 
 def load_spectrum(filename: str, spectra_format: str = None, raise_error: bool = False):
@@ -189,8 +189,8 @@ def load_spectrum(filename: str, spectra_format: str = None, raise_error: bool =
     filename
         Name of the file to read
     spectra_format
-        Optional file format, passed to Spectrum1D.read.
-        In its absense Spectrum1D.read will attempt to determine the format.
+        Optional file format, passed to Spectrum.read.
+        In its absense Spectrum.read will attempt to determine the format.
     raise_error
         Boolean to control if a failure to read the spectrum should raise an error.
     """
@@ -208,9 +208,9 @@ def load_spectrum(filename: str, spectra_format: str = None, raise_error: bool =
 
     try:
         if spectra_format is not None:
-            spec1d = Spectrum1D.read(filename, format=spectra_format)
+            spec1d = Spectrum.read(filename, format=spectra_format)
         else:
-            spec1d = Spectrum1D.read(filename)
+            spec1d = Spectrum.read(filename)
     except Exception as e:  # pylint: disable=broad-except, invalid-name
         msg = f"Error loading {filename}: {e}"
 

astrodbkit/tests/test_spectra.py

@@ -142,7 +142,7 @@ def test_wcs1d_multispec_loader(mock_fits_open, good_wcs1dmultispec, alt_wcs1dmu
     assert spectrum.wavelength.unit == Unit("Angstrom")
 
 
-@mock.patch("astrodbkit.spectra.Spectrum1D.read")
+@mock.patch("astrodbkit.spectra.Spectrum.read")
 def test_load_spectrum(mock_spectrum1d, monkeypatch):
     _ = load_spectrum("fake_file.txt")
     mock_spectrum1d.assert_called_with("fake_file.txt")

docs/index.rst

@@ -328,7 +328,7 @@ General Queries with Transformations
 ------------------------------------
 
 **AstrodbKit** can convert columns to special types.
-Currently, spectra transformations are implemented and the specified column would be converted to a `Spectrum1D` object
+Currently, spectra transformations are implemented and the specified column would be converted to a `Spectrum` object
 using the `specutils package <https://specutils.readthedocs.io/en/stable/>`_.
 To call this, users can supply the name of the column to convert
 (by default, none is converted, though .spectra assumes the column name is *spectrum*)::
@@ -338,7 +338,7 @@ To call this, users can supply the name of the column to convert
     db.query(db.Spectra).spectra(fmt='astropy')
 
 These three calls will return results from the Spectra table and will attempt to convert the *spectrum*
-column to a Spectrum1D object for each row. Multiple columns to convert can also be passed as a list.
+column to a Spectrum object for each row. Multiple columns to convert can also be passed as a list.
 The parameter `spectra_format` can be specified if **specutils** is having trouble determining the type of spectrum.
 
 Spectra need to be specified as either URL or paths relative to an environment variable,

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "sqlalchemy>=2.0.38",
     "pandas>=1.0.4",
     "packaging",
-    "specutils>=1.0",
+    "specutils>=2.0",
     "tqdm",
 ]