Specutils

------------------

Bug Fixes
^^^^^^^^^

- Fix JWST s3d loader. [866]

----------------

New Features
^^^^^^^^^^^^

- Allow overriding existing astropy registry elements. [861]

- ``Spectrum1D`` will now swap the spectral axis with the last axis on initialization
if it can be identified from the WCS and is not last, rather than erroring. [654, 822]

Bug Fixes
^^^^^^^^^

- Change loader priorities so survey loaders always override generic ones. [860]

- Handle "FLUX_ERROR" header keyword in addition to "ERROR" in JWST loader. [856]


Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- ``Spectrum1D`` now subclasses ``NDCube`` instead of ``NDDataRef``. [754, 822, 850]

------------------

New Features
^^^^^^^^^^^^

- Add ``SpectrumList`` loader for set of JWST _x1d files. [838]

Bug Fixes
^^^^^^^^^

- Handle new ``astropy.units.PhysicalType`` class added in astropy 4.3. [833]
- Handle case of WCS with None values in ``world_axis_physical_types`` when
initializing Spectrum1D. [839]
- Fix bug in apStar loader. [839]

Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- Improve continuum flux calculation in ``equivalent_width``. [843]

----------------

New Features
^^^^^^^^^^^^

- Added ability to slice ``Spectrum1D`` with spectral axis values. [790]

- Added ability to replace a section of a spectrum with a spline or model fit. [782]

Bug Fixes
^^^^^^^^^

- Fix infinite recursion when unpickling a ``QuantityModel``. [823]

- Changed positional to keyword arguments in ``fit_continuum``. [806]

Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- Fix inaccuracy about custom loading in docs. [819]

- Use non-root logger to prevent duplicate messages. [810]

- Removed unused astropy config code. [805]

----------------

New Features
^^^^^^^^^^^^

- Add support for reading IRAF MULTISPEC format with non-linear 2D WCS into
``SpectrumCollection`` to default_loaders. [708]

- ``SpectralRegion`` objects can now be created from the ``QTable``
object returned from the line finding rountines. [759]

- Include new 6dFGS loaders. [734]

- Include new OzDES loaders. [764]

- Include new GAMA survey loaders. [765]

- Include new GALAH loaders. [766]

- Include new WiggleZ loaders. [767]

- Include new 2dF/AAOmega loaders. [768]

- Add loader to handle IRAF MULTISPEC non-linear 2D WCS. [708]

- Add ability to extract minimum bounding regions of ``SpectralRegion`` objects. [755]

- Implement new moment analysis function for specutils objects. [758]

- Add new spectral slab extraction functionality. [753]

- Include new loaders for AAT and other Australian surveys. [719]

- Improve docstrings and intialization of ``SpectralRegion`` objects. [770]


Bug Fixes
^^^^^^^^^

- Fix ``extract_region`` behavior and slicing for ``Spectrum1D`` objects
that have multi-dimensional flux arrays. Extracting a region that extends
beyond the limits of the data no longer drops the last data point in the
returned spectrum. [724]

- Fixes to the jwst loaders. [759]

- Fix handling of ``SpectralCollection`` objects in moment calculations. [781]

- Fix issue with non-loadable x1d files. [775]

- Fix WCS handling in SDSS loaders. [738]

- Fix the property setters for radial velocity and redshift. [722]

- Fix line test errors and include python 3.9 in tests. [751]

- Fix smoothing functionality dropping spectrum meta information. [732]

- Fix region extraction for ``Spectrum1D`` objects with multi-dimensional fluxes. [724]

Documentation
^^^^^^^^^^^^^

- Update SDSS spectrum documentation examples. [778]

- Include new documentation on working with ``SpectralCube`` objects. [726, 784]

- Add documentation on spectral cube related functionality. [783]

Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- Improved error messages when creating ``SpectralRegion`` objects. [759]

- Update documentation favicons and ensure color consistency. [780]

- Remove fallback ``SpectralCoord`` code and rely on upstream. [786]

- Move remaining loaders to use utility functions for parsing files. [718]

- Remove unnecessary data reshaping in tabular fits writer. [730]

- Remove astropy helpers and CI helpers dependencies. [562]

----------------

New Features
^^^^^^^^^^^^

- Added writer to ``wcs1d-fits`` and support for multi-D flux arrays with
1D WCS (identical ``spectral_axis`` scale). [632]

- Implement ``SpectralCoord`` for ``SpectrumCollection`` objects. [619]

- Default loaders work with fits file-like objects. [637]

- Implement bin edge support on ``SpectralCoord`` objects using
``SpectralAxis`` subclass. [645]

- Implement new 6dFGS loader. [608]

- Implement uncertainty handling for ``line_flux``. [669]

- Implement new 2SLAQ-LRG loader. [633]

- Implement new 2dFGRS loader. [695]

- Default loaders now include WCS 1D (with multi-dimensional flux handling) writer. [632]

- Allow continuum fitting over multiple windows. [698]

- Have NaN-masked inputs automatically update the ``mask`` appropriately. [699]

Bug Fixes
^^^^^^^^^

- Fixed ``tabular-fits`` handling of 1D+2D spectra without WCS;
identification and parsing of metadata and units for ``apogee``
and ``muscles`` improved; enabled loading from file-like objects. [573]

- Fix ASDF handling of ``SpectralCoord``. [642]

- Preserve flux unit in ``resample1d`` for older versions of numpy. [649]

- Fix setting the doppler values on ``SpectralCoord`` instances. [657]

- Properly handle malformed distances in ``SkyCoord`` instances. [663]

- Restrict spectral equivalencies to contexts where it is required. [573]

- Fix ``from_center`` descending spectral axis handling. [656]

- Fix factor of two error in ``from_center`` method of ``SpectralRegion`` object. [710]

- Fix handling of multi-dimensional mask slicing. [704]

- Fix identifier for JWST 1D loader. [715]

Documentation
^^^^^^^^^^^^^

- Display supported loaders in specutils documentation. [675]

- Clarify inter-relation of specutils objects in relevant docstrings. [654]

Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- Remove pytest runtime dependency. [603]

- Change implementation of ``.quantity`` to ``.view`` in ``SpectralCoord``. [614]

- Ensure underlying references point to ``SpectralCoord`` object. [640]

- Deprecate ``spectral_axis_unit`` property. [618]

- Backport ``SpectralCoord`` from astropy core for versions <4.1. [674]

- Improve SDSS loaders and improve handling of extensions. [667]

- Remove spectral cube testing utilities. [683]

- Change local specutils directory creation behavior. [691]

- Ensure existing manipulation and analysis functions use ``mask`` attribute. [670]

- Improve mask handling in analysis functions. [701]