Merge pull request #299 from hpparvi/specutils2

Dropping Specutils v1 support.

Author: hpparvi

docs/conf.py

@@ -208,7 +208,6 @@
 nitpick_ignore = [
     ("py:class", "ArrayLike"),
     ("py:class", "numpy._typing.ArrayLike"),
-    ("py:class", "specutils.spectra.spectrum1d.Spectrum1D"),
 ]
 
 # Ignore complex type annotations that can't be cross-referenced

docs/specphot_standards.rst

@@ -8,7 +8,7 @@ Introduction
 
 Instrument sensitivity as a function of wavelength is calibrated using observations of
 spectrophotometric standard stars. `specreduce <https://specreduce.readthedocs.io/en/stable/index.html>`_ offers some
-convenience functions for accessing some databases of commonly used standard stars and loading the data into `~specutils.Spectrum1D`
+convenience functions for accessing some databases of commonly used standard stars and loading the data into `~specutils.Spectrum`
 instances.
 
 Supported Databases
@@ -43,7 +43,7 @@ The bulk of them are inherited from IRAF's `onedstds <https://github.com/iraf-co
 some more recently curated datasets from `ESO <https://www.eso.org/sci/observing/tools/standards/spectra/stanlis.html>`_, the
 `Nearby Supernova Factory <https://snfactory.lbl.gov/>`_, and `Gemini
 <https://github.com/GeminiDRSoftware/DRAGONS/tree/master/geminidr/gemini/lookups/spectrophotometric_standards>`_ are included as well. The
-`~specreduce.calibration_data.load_onedstds` function is provided to load these data into `~specutils.Spectrum1D`
+`~specreduce.calibration_data.load_onedstds` function is provided to load these data into `~specutils.Spectrum`
 instances. If `specreduce_data <https://github.com/astropy/specreduce-data/>`_ is not installed, the data will be downloaded from the GitHub
 `repository <https://github.com/astropy/specreduce-data/tree/main/specreduce_data/reference_data/onedstds>`_. The available
 database names and their descriptions are listed here. Please refer to the `specreduce-data repository

docs/terms.rst

@@ -65,7 +65,7 @@ Extraction
 ==========
 
 - The process of converting raw spectrum data on 2D image into flux versus
-  spectral axis or pixel (i.e. Spectrum1D), not necessarily flux or spectral
+  spectral axis or pixel (i.e. Spectrum), not necessarily flux or spectral
   calibration.
 
 Rectified ND spectrum
@@ -227,8 +227,8 @@ MOS (Multi-Object Spectroscopy)
 - Also used as a shorthand for “the not spectral unit part of a 1D spectrum”
   (would that be the “dependent variable”?)
 - Oftentimes used to mean “flux density”
-- `Spectrum1D
-  <https://specutils.readthedocs.io/en/stable/api/specutils.Spectrum1D.html#specutils.Spectrum1D>`__
+- `Spectrum
+  <https://specutils.readthedocs.io/en/stable/api/specutils.Spectrum.html#specutils.Spectrum>`__
   uses the attribute 'flux'. Should this be renamed to 'flux_density'?
 
     - The intent in specutils was to not agonize over this but just accept that
@@ -246,7 +246,7 @@ Flux Density
 
 - Collection of 1D spectra in a 2D array (image?), one spectrum per row.
 - Shared spectral axis.
-- This is the format of specutils.Spectrum1D when it's a “vector” spectrum1D
+- This is the format of specutils.Spectrum when it's a “vector” spectrum1D
 
 *Data cube*
 ===========
@@ -280,12 +280,12 @@ Data Structures
 
 - Python Data structures, which are Python classes.
 
-    - NDData/NDCube/SpectrumCollection, Spectrum1D etc.  
+    - NDData/NDCube/SpectrumCollection, Spectrum etc.  
     - CCDData. Subclass of NDData
     - AstroData - from DRAGONS (collection of NDData-like objects, mapped to a
       file, plus metadata abstraction etc.)
     - Lots of classes to represent spectra
-    - Link to issue about renaming Spectrum1D class in specutils.
+    - Link to issue about renaming Spectrum class in specutils.
     - arrays
 
 *Data Model*
@@ -439,7 +439,7 @@ API
 *Spectral class*
 ================
 
-- E.g., Spectrum1D
+- E.g., Spectrum
 - In SDSS, 'class' is short for 'classification'.
 - DESI uses SPECTYPE for spectral type (QSO, GALAXY, STAR)
 

pyproject.toml

@@ -10,9 +10,9 @@ readme = "README.rst"
 requires-python = ">=3.11"
 dependencies = [
     "numpy>=1.24",
-    "astropy>=5.3",
-    "scipy>=1.10",
-    "specutils>=1.9.1",
+    "astropy>=6.0",
+    "scipy>=1.14",
+    "specutils>=2.0",
     "matplotlib>=3.10",
     "gwcs",
 ]
@@ -28,13 +28,13 @@ docs = [
     "sphinx-copybutton",
     "sphinx-design",
     "matplotlib>=3.7",
-    "photutils>=1.0",
+    "photutils>=1.11",
     "synphot",
     "nbsphinx",
     "ipykernel"
 ]
 all = [
-    "photutils>=1.0",
+    "photutils>=1.11",
     "synphot",
 ]
 
@@ -89,7 +89,6 @@ filterwarnings = [
     "ignore:.*utcfromtimestamp:DeprecationWarning",
     # DeprecationWarning from gwcs 0.18.3 in oldestdeps
     "ignore:.*pkg_resources.*:DeprecationWarning",
-    "ignore:The Spectrum1D class is deprecated and may be removed",
     # DeprecationWarning from gwcs in devdeps
     "ignore:The isiterable function is deprecated and may be removed",
 ]

specreduce/background.py

@@ -9,7 +9,7 @@
 from astropy.stats import sigma_clip
 from astropy.utils.decorators import deprecated_attribute
 
-from specreduce.compat import SPECUTILS_LT_2, Spectrum
+from specutils import Spectrum
 from specreduce.core import _ImageParser, MaskingOption, ImageLike
 from specreduce.extract import _ap_weight_image
 from specreduce.tracing import Trace, FlatTrace
@@ -375,12 +375,9 @@ def bkg_image(self, image=None) -> Spectrum:
             self._orig_uncty_type
         )
 
-        if SPECUTILS_LT_2:
-            kwargs = {}
-        else:
-            kwargs = {"spectral_axis_index": arr.ndim - 1}
         return Spectrum(
-            arr * image.unit, spectral_axis=image.spectral_axis, uncertainty=uncertainty, **kwargs
+            arr * image.unit, spectral_axis=image.spectral_axis, uncertainty=uncertainty,
+            spectral_axis_index=arr.ndim - 1
         )
 
     def bkg_spectrum(self, image=None, bkg_statistic=None) -> Spectrum:
@@ -400,7 +397,7 @@ def bkg_spectrum(self, image=None, bkg_statistic=None) -> Spectrum:
 
         Returns
         -------
-        `~specutils.Spectrum1D`
+        `~specutils.Spectrum`
             The background 1D spectrum, with flux and uncertainty expressed
             in the same units as the input image (or DN if none were provided).
         """
@@ -436,17 +433,7 @@ def sub_image(self, image=None) -> Spectrum:
             uncertainty.
         """
         image = self._parse_image(image)
-
-        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 {}
-
-        # https://docs.astropy.org/en/stable/nddata/mixins/ndarithmetic.html
-        return image.subtract(self.bkg_image(image), **kwargs)
+        return image - self.bkg_image(image)
 
     def sub_spectrum(self, image=None) -> Spectrum:
         """

specreduce/calibration_data.py

@@ -14,7 +14,7 @@
 from astropy.coordinates import SpectralCoord
 from specutils.utils.wcs_utils import vac_to_air
 
-from specreduce.compat import Spectrum
+from specutils import Spectrum
 
 __all__ = [
     'get_available_line_catalogs',

specreduce/compat.py

@@ -8,7 +8,7 @@
 from astropy.utils.data import get_pkg_data_filename
 from specutils import SpectralAxis
 
-from specreduce.compat import SPECUTILS_LT_2, Spectrum
+from specutils import Spectrum
 
 try:
     from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
@@ -33,11 +33,7 @@ def _mk_test_data(imgtype, nrows=30, ncols=10):
         flux = image * u.DN
         uncert = VarianceUncertainty(image_ones)
         if imgtype == "spec_no_axis":
-            if SPECUTILS_LT_2:
-                kwargs = {}
-            else:
-                kwargs = {"spectral_axis_index": image.ndim - 1}
-            image = Spectrum(flux, uncertainty=uncert, **kwargs)
+            image = Spectrum(flux, uncertainty=uncert, spectral_axis_index=image.ndim - 1)
         else:  # "spec"
             image = Spectrum(flux, spectral_axis=np.arange(ncols) * u.um, uncertainty=uncert)
     return image
@@ -77,15 +73,10 @@ def all_images():
     sax = SpectralAxis(np.linspace(14.377, 3.677, flux.shape[-1]) * u.um)
     unc = VarianceUncertainty(np.random.rand(*flux.shape))
 
-    if SPECUTILS_LT_2:
-        kwargs = {}
-    else:
-        kwargs = {"spectral_axis_index": img.ndim - 1}
-
     all_images = {}
     all_images['arr'] = img
     all_images['s1d'] = Spectrum(flux, spectral_axis=sax, uncertainty=unc)
-    all_images['s1d_pix'] = Spectrum(flux, uncertainty=unc, **kwargs)
+    all_images['s1d_pix'] = Spectrum(flux, uncertainty=unc, spectral_axis_index=img.ndim - 1)
     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

specreduce/conftest.py

@@ -9,7 +9,7 @@
 from astropy import units as u
 from astropy.nddata import VarianceUncertainty, NDData
 
-from specreduce.compat import SPECUTILS_LT_2, Spectrum
+from specutils import Spectrum
 
 __all__ = ["SpecreduceOperation"]
 
@@ -29,7 +29,7 @@ class _ImageParser:
     that are missing in the provided image with generic values.
     Accepted image types are:
 
-        - `~specutils.Spectrum1D` (preferred)
+        - `~specutils.Spectrum` (preferred)
         - `~astropy.nddata.ccddata.CCDData`
         - `~astropy.nddata.ndddata.NDDData`
         - `~astropy.units.quantity.Quantity`
@@ -148,13 +148,9 @@ def _get_data_from_image(
 
         spectral_axis = getattr(image, "spectral_axis", np.arange(img.shape[disp_axis]) * u.pix)
 
-        if SPECUTILS_LT_2:
-            kwargs = {}
-        else:
-            kwargs = {"spectral_axis_index": img.ndim - 1}
         img = Spectrum(
             img * unit, spectral_axis=spectral_axis, uncertainty=uncertainty, mask=mask,
-            **kwargs
+            spectral_axis_index=img.ndim - 1
         )
         return img
 

specreduce/core.py

@@ -11,7 +11,7 @@
 from scipy.integrate import trapezoid
 from scipy.interpolate import RectBivariateSpline
 
-from specreduce.compat import Spectrum
+from specutils import Spectrum
 from specreduce.core import SpecreduceOperation, ImageLike, MaskingOption
 from specreduce.tracing import Trace, FlatTrace
 
@@ -169,7 +169,7 @@ class BoxcarExtract(SpecreduceOperation):
 
     Returns
     -------
-    spec : `~specutils.Spectrum1D`
+    spec : `~specutils.Spectrum`
         The extracted 1d spectrum expressed in DN and pixel units
     """
 
@@ -666,7 +666,7 @@ def __call__(
 
         Returns
         -------
-        spec_1d : `~specutils.Spectrum1D`
+        spec_1d : `~specutils.Spectrum`
             The final, Horne extracted 1D spectrum.
         """
         image = image if image is not None else self.image