Replace deprecated AsdfInFits

setup.cfg

@@ -33,12 +33,14 @@ test =
     graphviz
     coverage
     spectral-cube
+    stdatamodels>=1.1.0
 docs =
-    # TODO: Remove numpy pinning when astropy v5.2.1 is released.
-    numpy<1.24
     sphinx-astropy
     matplotlib
     graphviz
+    # TODO: Remove pinning when ndcube fixed
+    # See https://github.com/astropy/specutils/issues/1028
+    ndcube<2.1
 
 [options.package_data]
 specutils = data/*

specutils/io/default_loaders/tests/test_jwst_reader.py

@@ -1,27 +1,25 @@
-import warnings
+import gwcs.coordinate_frames as cf
 import numpy as np
+import pytest
+from astropy import coordinates as coord
+from astropy import units as u
 from astropy.io import fits
-from astropy.table import Table
-import astropy.units as u
 from astropy.io.registry import IORegistryError
-from astropy.utils.exceptions import AstropyUserWarning
 from astropy.modeling import models
-from astropy import coordinates as coord
-import gwcs.coordinate_frames as cf
+from astropy.table import Table
+from astropy.utils.exceptions import AstropyUserWarning
 from gwcs.wcs import WCS
-import pytest
-
-from asdf.exceptions import AsdfDeprecationWarning
-with warnings.catch_warnings():
-    warnings.filterwarnings(
-        "ignore",
-        category=AsdfDeprecationWarning,
-        message=r"AsdfInFits has been deprecated.*",
-    )
-    from asdf import fits_embed
 
 from specutils import Spectrum1D, SpectrumList
 
+# ASDF_LT_2_14_1
+try:
+    from stdatamodels import asdf_in_fits
+except ImportError:
+    HAS_STDATAMODELS = False
+else:
+    HAS_STDATAMODELS = True
+
 
 # The c1d/x1d reader tests --------------------------
 
@@ -398,33 +396,36 @@ def create_image_hdu(name='SCI', data=None, shape=None, hdrs=[], ndim=3):
 
 
 @pytest.fixture(scope='function')
-def cube(tmpdir, tmp_asdf):
+def cube(tmp_path, tmp_asdf):
     """ Mock a JWST s3d cube """
-    hdulist = fits.HDUList()
-    hdulist.append(fits.PrimaryHDU())
-    hdulist["PRIMARY"].header["TELESCOP"] = ("JWST", "comment")
-    hdulist["PRIMARY"].header["FLUXEXT"] = ("ERR", "comment")
-    hdulist["PRIMARY"].header["ERREXT"] = ("ERR", "comment")
-    hdulist["PRIMARY"].header["MASKEXT"] = ("DQ", "comment")
+    prihdu = fits.PrimaryHDU()
+    prihdu.header["TELESCOP"] = ("JWST", "comment")
+    prihdu.header["FLUXEXT"] = ("ERR", "comment")
+    prihdu.header["ERREXT"] = ("ERR", "comment")
+    prihdu.header["MASKEXT"] = ("DQ", "comment")
+    hdulist = fits.HDUList([prihdu])
+
     # Add ImageHDU for cubes
-    shape = [30, 10, 10]
+    shape = (30, 10, 10)
     hdulist.append(create_image_hdu(name='SCI', shape=shape, hdrs=[("BUNIT", 'MJy')]))
     hdulist.append(create_image_hdu(name='ERR', shape=shape,
                                     hdrs=[("BUNIT", 'MJy'), ('ERRTYPE', 'ERR')]))
     hdulist.append(create_image_hdu(name='DQ', shape=shape))
 
     # Mock the ASDF extension
     hdulist.append(fits.BinTableHDU(name='ASDF'))
-    ff = fits_embed.AsdfInFits(hdulist, tmp_asdf)
-    tmpfile = str(tmpdir.join('jwst_embedded_asdf.fits'))
-    ff.write_to(tmpfile)
+
+    if HAS_STDATAMODELS:
+        tmpfile = str(tmp_path / 'jwst_embedded_asdf.fits')
+        asdf_in_fits.write(tmpfile, tmp_asdf, hdulist=hdulist, overwrite=True)
 
     return hdulist
 
 
-def test_jwst_s3d_single(tmpdir, cube):
+@pytest.mark.skipif(not HAS_STDATAMODELS, reason="requires stdatamodels")
+def test_jwst_s3d_single(tmp_path, cube):
     """Test Spectrum1D.read for JWST x1d data"""
-    tmpfile = str(tmpdir.join('jwst_s3d.fits'))
+    tmpfile = str(tmp_path / 'jwst_s3d.fits')
     cube.writeto(tmpfile)
 
     data = Spectrum1D.read(tmpfile, format='JWST s3d')

specutils/tests/test_io.py

@@ -32,8 +32,8 @@ def test_generic_spectrum_from_table(recwarn):
     assert spectrum.spectral_axis.unit == table['wave'].unit
     assert spectrum.flux.unit == table['flux'].unit
     assert spectrum.spectral_axis.unit == table['wave'].unit
-    assert np.alltrue(spectrum.spectral_axis == table['wave'])
-    assert np.alltrue(spectrum.flux == table['flux'])
+    assert np.all(spectrum.spectral_axis == table['wave'])
+    assert np.all(spectrum.flux == table['flux'])
 
     # Add uncertainties and retest
     err = 0.01*flux
@@ -43,9 +43,9 @@ def test_generic_spectrum_from_table(recwarn):
     assert spectrum.flux.unit == table['flux'].unit
     assert spectrum.uncertainty.unit == table['err'].unit
     assert spectrum.spectral_axis.unit == table['wave'].unit
-    assert np.alltrue(spectrum.spectral_axis == table['wave'])
-    assert np.alltrue(spectrum.flux == table['flux'])
-    assert np.alltrue(spectrum.uncertainty.array == table['err'])
+    assert np.all(spectrum.spectral_axis == table['wave'])
+    assert np.all(spectrum.flux == table['flux'])
+    assert np.all(spectrum.uncertainty.array == table['err'])
 
     # Test for warning if standard deviation is zero or negative
     err[0] = 0.

specutils/tests/test_loaders.py

@@ -105,9 +105,9 @@ def test_generic_ecsv_reader(tmpdir):
     assert spectrum.flux.unit == table['flux'].unit
     assert spectrum.uncertainty.unit == table['uncertainty'].unit
     assert spectrum.spectral_axis.unit == table['wave'].unit
-    assert np.alltrue(spectrum.spectral_axis == table['wave'])
-    assert np.alltrue(spectrum.flux == table['flux'])
-    assert np.alltrue(spectrum.uncertainty.array == table['uncertainty'])
+    assert np.all(spectrum.spectral_axis == table['wave'])
+    assert np.all(spectrum.flux == table['flux'])
+    assert np.all(spectrum.uncertainty.array == table['uncertainty'])
 
 
 @remote_access([{'id': '1481119', 'filename': 'COS_FUV.fits'},

tox.ini

@@ -53,11 +53,6 @@ deps =
     devdeps: scipy>=0.0.dev0
     devdeps: git+https://github.com/spacetelescope/gwcs.git#egg=gwcs
 
-    # While nice to test in principle, we cannot enable this in CI
-    # because this will generate AsdfWarning and AstropyDeprecationWarning
-    # so this setting is not used.
-    external: jwst
-
 # The following indicates which extras_require from setup.cfg will be installed
 extras =
     test