Merge branch 'main' into add-astra-loader

.github/workflows/ci_cron_weekly.yml

@@ -39,11 +39,11 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3  # v5.2.0
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b  # v5.3.0
       with:
         python-version: ${{ matrix.python }}
     - name: Install Python dependencies

.github/workflows/ci_workflows.yml

@@ -49,11 +49,11 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3  # v5.2.0
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b  # v5.3.0
       with:
         python-version: ${{ matrix.python }}
     - name: Install Python dependencies
@@ -63,7 +63,7 @@ jobs:
     # TODO: Do we need --gcov-glob "*cextern*" ?
     - name: Upload coverage to artifacts
       if: ${{ contains(matrix.toxenv,'-cov') }}
-      uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9  # v4.4.1
+      uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882  # v4.4.3
       with:
         name: coverage_${{ matrix.toxenv }}.xml
         path: coverage.xml
@@ -112,11 +112,11 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871  # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3  # v5.2.0
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b  # v5.3.0
       with:
         python-version: ${{ matrix.python }}
     - name: Install Python dependencies

CHANGES.rst

@@ -1,4 +1,4 @@
-1.19.0 (unreleased)
+1.20.0 (unreleased)
 -------------------
 
 New Features
@@ -10,6 +10,25 @@ Bug Fixes
 Other Changes and Additions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+1.19.0 (2024-11-05)
+-------------------
+
+Bug Fixes
+^^^^^^^^^
+
+- Fixed ``mwmVisit`` SDSS-V ``Spectrum1D`` and ``SpectrumList`` default loader
+  being unable to load files containing only BOSS instrument spectra. [#1185]
+
+- Fixed automatic format detection for SDSS-V ``SpectrumList`` default loaders. [#1185]
+
+- Fixed ``SplineInterpolatedResampler`` when input and output spectral axes are different
+  physical types, e.g. wavelength and velocity. [#1190]
+
+Other Changes and Additions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- "Multi" loaders have been removed from SDSS-V ``SpectrumList`` default loaders. [#1185]
+
 1.18.0 (2024-10-16)
 -------------------
 

docs/spectral_regions.rst

@@ -327,6 +327,11 @@ to create a new `~specutils.SpectralRegion` using the ``read`` class method:
 
     >>> spec_reg = SpectralRegion.read("spectral_region.ecsv")
 
+.. testcleanup::
+
+    >>> import os
+    >>> os.remove("spectral_region.ecsv")
+
 The `~astropy.table.QTable` created to write out the `~specutils.SpectralRegion` to file can also be accessed
 directly with the ``as_table`` method, and a `~specutils.SpectralRegion` can be created directly from a `~astropy.table.QTable`
 with the appropriate columns (minimally ``lower_bound`` and ``upper_bound``) using the ``from_qtable`` class method.

specutils/io/default_loaders/jwst_reader.py

@@ -479,7 +479,11 @@ def _jwst_s2d_loader(filename, **kwargs):
 
             # Get the wavelength array from the GWCS object which returns a
             # tuple of (RA, Dec, lambda)
-            grid = grid_from_bounding_box(wcs.bounding_box)
+            with warnings.catch_warnings():
+                # https://github.com/spacetelescope/gwcs/pull/522
+                warnings.filterwarnings(
+                    "ignore", message="The bounding_box was set in C order.*")
+                grid = grid_from_bounding_box(wcs.bounding_box)
             _, _, lam = wcs(*grid)
             _, _, lam_unit = wcs.output_frame.unit
 
@@ -587,7 +591,11 @@ def _jwst_s3d_loader(filename, **kwargs):
             # tuple of (RA, Dec, lambda).
             # Since the spatial and spectral axes are orthogonal in s3d data,
             # it is much faster to compute a slice down the spectral axis.
-            grid = grid_from_bounding_box(wcs.bounding_box)[:, :, 0, 0]
+            with warnings.catch_warnings():
+                # https://github.com/spacetelescope/gwcs/pull/522
+                warnings.filterwarnings(
+                    "ignore", message="The bounding_box was set in C order.*")
+                grid = grid_from_bounding_box(wcs.bounding_box)[:, :, 0, 0]
             _, _, wavelength_array = wcs(*grid)
             _, _, wavelength_unit = wcs.output_frame.unit
 

specutils/io/default_loaders/sdss_v.py

@@ -763,17 +763,17 @@ def _load_astra_hdu(hdulist: HDUList, hdu: int, **kwargs):
 
     # collapse shape if 1D spectra in 2D array, makes readout easier
     if flux.shape[0] == 1:
-        flux = flux[0]
-        e_flux = e_flux[0]
-        mask = mask[0]
+        flux = np.ravel(flux)
+        e_flux = e_flux[0]  # different class
+        mask = np.ravel(mask)
 
     # Create metadata
     meta = dict()
     meta["header"] = hdulist[0].header
 
     # Add identifiers (obj, telescope, mjd, datatype)
     meta["telescope"] = hdulist[hdu].data["telescope"]
-    meta['instrument'] = 'BOSS' if hdu <= 2 else 'APOGEE'
+    meta["instrument"] = hdulist[hdu].header.get("INSTRMNT")
     try:  # get obj if exists
         meta["obj"] = hdulist[hdu].data["obj"]
     except KeyError:
@@ -791,6 +791,7 @@ def _load_astra_hdu(hdulist: HDUList, hdu: int, **kwargs):
         meta["name"] = hdulist[hdu].name
         meta["sdss_id"] = hdulist[hdu].data['sdss_id']
 
+    # drop back a list of Spectrum1Ds to unpack
     return Spectrum1D(
         spectral_axis=spectral_axis,
         flux=flux,

specutils/manipulation/resample.py

@@ -461,7 +461,7 @@ def resample1d(self, orig_spectrum, fin_spec_axis):
         if self.extrapolation_treatment == 'zero_fill':
             fill_val = 0
 
-        orig_edges = orig_spectrum.spectral_axis.bin_edges
+        orig_edges = orig_axis_in_new.bin_edges
         off_edges = (fin_spec_axis < np.min(orig_edges)) | (np.max(orig_edges) < fin_spec_axis)
         out_flux_val[off_edges] = fill_val
         if new_unc is not None:

specutils/tests/test_regions.py

@@ -191,10 +191,11 @@ def test_from_list_list():
         assert_quantity_allclose(reg, (spec_reg[i].lower, spec_reg[i].upper))
 
 
-def test_read_write():
+def test_read_write(tmp_path):
+    path = tmp_path / "test_sr.ecsv"
     sr = SpectralRegion([(0.45*u.um, 0.6*u.um), (0.8*u.um, 0.9*u.um)])
-    sr.write("test_sr.ecsv")
-    sr2 = SpectralRegion.read("test_sr.ecsv")
+    sr.write(str(path))
+    sr2 = SpectralRegion.read(path)
     assert list(sr2.as_table().columns) == ["lower_bound", "upper_bound"]
 
     sr3 = SpectralRegion.from_qtable(sr2.as_table())

specutils/tests/test_resample.py

@@ -4,7 +4,7 @@
 from astropy.nddata import VarianceUncertainty, InverseVariance, StdDevUncertainty
 from astropy.tests.helper import assert_quantity_allclose
 
-from ..spectra.spectrum1d import Spectrum1D
+from ..spectra.spectrum1d import Spectrum1D, SpectralAxis
 from ..manipulation.resample import FluxConservingResampler, LinearInterpolatedResampler, SplineInterpolatedResampler
 
 
@@ -214,6 +214,22 @@ def test_resample_different_units(all_resamplers):
     resampled = resampler(input_spectrum, resamp_grid)
     assert not np.any(np.isnan(resampled.flux))
 
+    resamp_grid = [550, 650]*u.nm
+    resampled = resampler(input_spectrum, resamp_grid)
+
+    # Test conversion to velocity grid
+    rest_wavelength = 656.2 * u.nm
+    wavelengths = np.linspace(640, 672, 10) * u.nm
+    flux = np.ones(10) * u.mJy
+    spec1d = Spectrum1D(spectral_axis=wavelengths, velocity_convention="optical", flux=flux)
+    spec1d.spectral_axis.doppler_rest = rest_wavelength
+
+    velocities = np.linspace(-1000, 1000, 5) * u.km/u.s
+    velocity_grid = SpectralAxis(velocities, doppler_rest=rest_wavelength,
+                                 doppler_convention="optical")
+    velocity_binned = resampler(spec1d, velocity_grid)
+    assert not np.any(np.isnan(velocity_binned.flux))
+
 
 def test_resample_uncs(all_resamplers):
     sdunc = StdDevUncertainty([0.1, 0.2, 0.3]*u.mJy)

specutils/tests/test_spectrum1d.py

@@ -318,15 +318,19 @@ def test_wcs_transformations():
     spec = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm,
                       flux=np.ones(49) * u.Jy)
 
-    pix_axis = spec.wcs.world_to_pixel(np.arange(20, 30) * u.nm)
+    # After spacetelescope/gwcs#457 is merged and released, this can be changed to
+    # pix_axis = spec.wcs.world_to_pixel_values(np.arange(20, 30) * u.nm)
+    pix_axis = spec.wcs.world_to_pixel(SpectralCoord(np.arange(20, 30) * u.nm))
     disp_axis = spec.wcs.pixel_to_world(np.arange(20, 30))
 
     assert isinstance(pix_axis, np.ndarray)
     assert isinstance(disp_axis, u.Quantity)
 
     # Test transform with different unit
     with u.set_enabled_equivalencies(u.spectral()):
-        spec.wcs.world_to_pixel(np.arange(20, 30) * u.GHz)
+        # After spacetelescope/gwcs#457 is merged and released, this can be changed to
+        # spec.wcs.world_to_pixel_values(np.arange(20, 30) * u.GHz)
+        spec.wcs.world_to_pixel(SpectralCoord(np.arange(20, 30) * u.GHz))
 
     # Test with a FITS WCS
     my_wcs = fitswcs.WCS(header={'CDELT1': 1, 'CRVAL1': 6562.8, 'CUNIT1': 'Angstrom',