Compatibility with specutils 2.0

.github/workflows/tox-tests.yml

@@ -50,5 +50,6 @@ jobs:
           posargs: --remote-data=any
 
         - name: (Allowed Failure) Python 3.13 on Linux with dev dependencies
-          linux: py313-test-devdeps
+          linux: py313-test-devdeps-cov
+          coverage: codecov
           toxargs: -v

CHANGES.rst

@@ -15,6 +15,7 @@ Bug Fixes
 Other changes
 ^^^^^^^^^^^^^
 
+- Compatibility with specutils 2.0. [#260]
 
 1.5.1 (2024-03-08)
 ------------------

conftest.py

@@ -1,12 +1,4 @@
-# This file is used to configure the behavior of pytest
-
-import numpy as np
-import pytest
-from astropy import units as u
-from astropy.io import fits
-from astropy.nddata import CCDData, NDData, VarianceUncertainty
-from astropy.utils.data import get_pkg_data_filename
-from specutils import Spectrum1D, SpectralAxis
+# Root level conftest.py is only for nice pytest header when using tox.
 
 try:
     from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
@@ -15,103 +7,6 @@
     ASTROPY_HEADER = False
 
 
-# Test image is comprised of 30 rows with 10 columns each. Row content
-# is row index itself. This makes it easy to predict what should be the
-# value extracted from a region centered at any arbitrary Y position.
-def _mk_test_data(imgtype, nrows=30, ncols=10):
-    image_ones = np.ones(shape=(nrows, ncols))
-    image = image_ones.copy()
-    for j in range(nrows):
-        image[j, ::] *= j
-    if imgtype == "raw":
-        pass  # no extra processing
-    elif imgtype == "ccddata":
-        image = CCDData(image, unit=u.Jy)
-    else:  # spectrum
-        flux = image * u.DN
-        uncert = VarianceUncertainty(image_ones)
-        if imgtype == "spec_no_axis":
-            image = Spectrum1D(flux, uncertainty=uncert)
-        else:  # "spec"
-            image = Spectrum1D(flux, spectral_axis=np.arange(ncols) * u.um, uncertainty=uncert)
-    return image
-
-
-@pytest.fixture
-def mk_test_img_raw():
-    return _mk_test_data("raw")
-
-
-@pytest.fixture
-def mk_test_img():
-    return _mk_test_data("ccddata")
-
-
-@pytest.fixture
-def mk_test_spec_no_spectral_axis():
-    return _mk_test_data("spec_no_axis")
-
-
-@pytest.fixture
-def mk_test_spec_with_spectral_axis():
-    return _mk_test_data("spec")
-
-
-# Test data file already transposed like this:
-# fn = download_file('https://stsci.box.com/shared/static/exnkul627fcuhy5akf2gswytud5tazmw.fits', cache=True)  # noqa: E501
-# img = fits.getdata(fn).T
-@pytest.fixture
-def all_images():
-    np.random.seed(7)
-
-    filename = get_pkg_data_filename(
-        "data/transposed_det_image_seq5_MIRIMAGE_P750Lexp1_s2d.fits", package="specreduce.tests")
-    img = fits.getdata(filename)
-    flux = img * (u.MJy / u.sr)
-    sax = SpectralAxis(np.linspace(14.377, 3.677, flux.shape[-1]) * u.um)
-    unc = VarianceUncertainty(np.random.rand(*flux.shape))
-
-    all_images = {}
-    all_images['arr'] = img
-    all_images['s1d'] = Spectrum1D(flux, spectral_axis=sax, uncertainty=unc)
-    all_images['s1d_pix'] = Spectrum1D(flux, uncertainty=unc)
-    all_images['ccd'] = CCDData(img, uncertainty=unc, unit=flux.unit)
-    all_images['ndd'] = NDData(img, uncertainty=unc, unit=flux.unit)
-    all_images['qnt'] = img * flux.unit
-    return all_images
-
-
-@pytest.fixture
-def spec1d():
-    np.random.seed(7)
-    flux = np.random.random(50)*u.Jy
-    sa = np.arange(0, 50)*u.pix
-    spec = Spectrum1D(flux, spectral_axis=sa)
-    return spec
-
-
-@pytest.fixture
-def spec1d_with_emission_line():
-    np.random.seed(7)
-    sa = np.arange(0, 200)*u.pix
-    flux = (np.random.randn(200) +
-            10*np.exp(-0.01*((sa.value-130)**2)) +
-            sa.value/100) * u.Jy
-    spec = Spectrum1D(flux, spectral_axis=sa)
-    return spec
-
-
-@pytest.fixture
-def spec1d_with_absorption_line():
-    np.random.seed(7)
-    sa = np.arange(0, 200)*u.pix
-    flux = (np.random.randn(200) -
-            10*np.exp(-0.01*((sa.value-130)**2)) +
-            sa.value/100) * u.Jy
-    spec = Spectrum1D(flux, spectral_axis=sa)
-    return spec
-
-
 def pytest_configure(config):
 
     if ASTROPY_HEADER:

notebook_sandbox/apo05.ipynb

@@ -24,7 +24,7 @@
     "from astropy import units as u\n",
     "\n",
     "from astropy.nddata import CCDData, StdDevUncertainty\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from ccdproc import trim_image, Combiner\n",
     "\n",
     "# need to get import to work in notebook w/o global package install\n",

notebook_sandbox/fluxcal_demo.ipynb

@@ -14,7 +14,7 @@
     "from ccdproc import trim_image\n",
     "from astropy import units as u\n",
     "\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from astropy.nddata import StdDevUncertainty\n",
     "\n",
     "# need to get import to work in notebook w/o global package install\n",

notebook_sandbox/wavecal_demo.ipynb

@@ -17,7 +17,7 @@
     "from astropy.nddata import StdDevUncertainty\n",
     "import astropy.units as u\n",
     "\n",
-    "from specutils import Spectrum1D\n",
+    "from specreduce.compat import Spectrum as Spectrum1D\n",
     "from specutils.fitting import fit_generic_continuum\n",
     "\n",
     "from specreduce.calibration_data import load_pypeit_calibration_lines\n",

specreduce/background.py

@@ -6,8 +6,8 @@
 import numpy as np
 from astropy import units as u
 from astropy.utils.decorators import deprecated_attribute
-from specutils import Spectrum1D
 
+from specreduce.compat import SPECUTILS_LT_2, Spectrum
 from specreduce.core import _ImageParser, MaskingOption, ImageLike
 from specreduce.extract import _ap_weight_image
 from specreduce.tracing import Trace, FlatTrace
@@ -84,7 +84,7 @@
         "apply_nan_only",
     )
 
-    # TO-DO: update bkg_array with Spectrum1D alternative (is bkg_image enough?)
+    # TO-DO: update bkg_array with Spectrum alternative (is bkg_image enough?)
     bkg_array = deprecated_attribute("bkg_array", "1.3")
 
     def __post_init__(self):
@@ -303,12 +303,18 @@
 
         Returns
         -------
-        `~specutils.Spectrum1D` object with same shape as ``image``.
+        spec : `~specutils.Spectrum1D`
+            Spectrum object with same shape as ``image``.
         """
         image = self._parse_image(image)
-        return Spectrum1D(
-            np.tile(self._bkg_array, (image.shape[0], 1)) * image.unit,
-            spectral_axis=image.spectral_axis,
+        arr = np.tile(self._bkg_array, (image.shape[0], 1))
+        if SPECUTILS_LT_2:
+            kwargs = {}
+        else:
+            kwargs = {"spectral_axis_index": arr.ndim - 1}
+        return Spectrum(
+            arr * image.unit,
+            spectral_axis=image.spectral_axis, **kwargs
         )
 
     def bkg_spectrum(self, image=None, bkg_statistic="sum"):
@@ -355,7 +361,7 @@
             # can't collapse with a spectral axis in pixels because
             # SpectralCoord only allows frequency/wavelength equivalent units...
             ext1d = statistic_function(bkg_image.flux, axis=self.crossdisp_axis)
-            return Spectrum1D(ext1d, bkg_image.spectral_axis)
+            return Spectrum(ext1d, bkg_image.spectral_axis)
 
     def sub_image(self, image=None):
         """
@@ -369,11 +375,15 @@
 
         Returns
         -------
-        `~specutils.Spectrum1D` object with same shape as ``image``.
+        spec : `~specutils.Spectrum1D`
+            Spectrum object with same shape as ``image``.
         """
         image = self._parse_image(image)
 
-        # a compare_wcs argument is needed for Spectrum1D.subtract() in order to
+        if not SPECUTILS_LT_2:
+            return image - self.bkg_image(image)
+
+        # a compare_wcs argument is needed for Spectrum.subtract() in order to
         # avoid a TypeError from SpectralCoord when image's spectral axis is in
         # pixels. it is not needed when image's spectral axis has physical units
         kwargs = {"compare_wcs": None} if image.spectral_axis.unit == u.pix else {}
@@ -406,7 +416,7 @@
             # can't collapse with a spectral axis in pixels because
             # SpectralCoord only allows frequency/wavelength equivalent units...
             ext1d = np.nansum(sub_image.flux, axis=self.crossdisp_axis)
-            return Spectrum1D(ext1d, spectral_axis=sub_image.spectral_axis)
+            return Spectrum(ext1d, spectral_axis=sub_image.spectral_axis)
 
     def __rsub__(self, image):
         """

specreduce/calibration_data.py

@@ -12,10 +12,10 @@
 from astropy.utils.data import download_file
 from astropy.utils.exceptions import AstropyUserWarning
 from astropy.coordinates import SpectralCoord
-
-from specutils import Spectrum1D
 from specutils.utils.wcs_utils import vac_to_air
 
+from specreduce.compat import Spectrum
+
 __all__ = [
     'get_available_line_catalogs',
     'load_pypeit_calibration_lines',
@@ -187,7 +187,7 @@ def load_MAST_calspec(
         filename: str | Path,
         cache: bool | Literal['update'] = True,
         show_progress: bool = False
-) -> Spectrum1D | None:
+) -> Spectrum | None:
     """
     Load a standard star spectrum from the ``calspec`` database at MAST. These spectra are provided
     in FITS format and are described in detail at:
@@ -238,7 +238,7 @@ def load_MAST_calspec(
         # supported directly by astropy.units. mJy is chosen since it's the JWST
         # standard and can easily be converted to/from AB magnitudes.
         flux_mjy = synphot.units.convert_flux(wave, flux, u.mJy)
-        spectrum = Spectrum1D(spectral_axis=wave, flux=flux_mjy)
+        spectrum = Spectrum(spectral_axis=wave, flux=flux_mjy)
         return spectrum
 
 
@@ -247,7 +247,7 @@ def load_onedstds(
         specfile: str = "EG131.dat",
         cache: bool | Literal['update'] = True,
         show_progress: bool = False
-) -> Spectrum1D | None:
+) -> Spectrum | None:
     """
     This is a convenience function for loading a standard star spectrum from the 'onedstds'
     dataset in the ``specreduce_data`` package. They will be downloaded from the
@@ -290,11 +290,11 @@ def load_onedstds(
     # the specreduce_data standard star spectra all provide fluxes in AB mag
     flux = t['ABmag'].data * u.ABmag
     flux = flux.to(u.mJy)  # convert to linear flux units
-    spectrum = Spectrum1D(spectral_axis=spectral_axis, flux=flux)
+    spectrum = Spectrum(spectral_axis=spectral_axis, flux=flux)
     return spectrum
 
 
-class AtmosphericExtinction(Spectrum1D):
+class AtmosphericExtinction(Spectrum):
     """
     Spectrum container for atmospheric extinction in magnitudes as a function of wavelength.
     If extinction and spectral_axis are provided, this will use them to build a custom model.
@@ -353,7 +353,7 @@ def __init__(
                 extinction = u.Magnitude(
                     extinction,
                     u.MagUnit(u.dimensionless_unscaled)
-                ).to(u.dimensionless_unscaled)  # Spectrum1D wants this to be linear
+                ).to(u.dimensionless_unscaled)  # Spectrum wants this to be linear
             elif isinstance(extinction, (u.LogUnit, u.Magnitude)) or extinction.unit == u.mag:
                 # if in log or magnitudes, recast into Magnitude with dimensionless physical units
                 extinction = u.Magnitude(

specreduce/compat.py

@@ -0,0 +1,11 @@
+import specutils
+from astropy.utils import minversion
+
+__all__ = []
+
+SPECUTILS_LT_2 = not minversion(specutils, "2.0.dev")
+
+if SPECUTILS_LT_2:
+    from specutils import Spectrum1D as Spectrum
+else:
+    from specutils import Spectrum  # noqa: F401