Pyuvdata

Added
- The `catalog_name` keyword has been added to the `UVData.read` and `UVData.select`
methods to allow users to select on source name.

Changed
- The keywords for `UVData.read` have been changed for MIR-specific values to more
generally match those founds with other data types.
- The `UVData.read_mir` method has been overhauled to mak reading in of MIR data more
efficiency in memory/processor usage.

Fixed
- Frequency frame information for MS datasets is now correctly recorded as "TOPO".

Added
- A new `FastUVH5Meta` object that enables quick partial reading of uvh5 file metadata.
This is used by default in the `UVData.read_uvh5` method to initialize a `UVData`
object, without any apparent change for the user. To get the benefits of the new class,
use it directly to interface with the metadata portion of a `.uvh5` file.

Changed
- Updated numpy requirements to `>=1.20`.
- Updated scipy requirements to `>=1.5`.

Fixed
- Handling of antenna_names and antenna_numbers in `read_fhd` and `read_fhd_cal`.

Added
- A new `interpolation_function` parameter to `UVBeam.interp` and `UVBeam.to_healpix`
to allow the function name to be passed into the methods, with sensible defaulting.
- Support for selecting on phase center IDs, including on read.
- Several new attributes to UVFlag: `telescope_name`, `telescope_location`,
`antenna_names`, `antenna_numbers`, `antenna_positions`, `channel_width`, `spw_array`,
`flex_spw_id_array`, enabling support for flexible spectral windows. All of these except
`flex_spw_id_array` will eventually be required for all UVFlag object types, as will
`Nspws` (which used to only be required for baseline and antenna types). These
parameters all already exist on UVData and UVCal objects and UVFlag objects initialized
from them will inherit them. UVFlag objects will also inherit these parameters when
they are converted between types using UVData and UVCalobjects.
- The `UVFlag.set_telescope_params` method, similar to the ones on UVData and UVCal,
to set several of these new parameters.

Changed
- Increases the h5py minimum version to 3.1.
- Increase the minimum compatible version for lunarsky to 0.2.1 to fix astropy
deprecation warnings.

Fixed
- Fixed some bugs related to handling of the `UVCal.time_range` parameter in
`UVCal.__add__` and other methods. Ensured that it is a list when
`UVCal.future_array_shapes` is False.
- Fixed a bug in `UVCal.__add__` when data are sorted differently along any axis or
interleaved along an axis.
- Fixed a bug in reading MS files with non-UTC time scales.
- Fixed some bugs in UVData, UVFlag and UVCal `__add__` and `select` methods for objects
with only one spectral window and `flex_spw_id_array` defined. Also fixed some handling
in those methods on UVFlag for objects with multiple spectral windows.
- Fix a bug when reading FHD files into UVData objects when the layout file was not
passed but the antenna_positions are in the known telescopes.
- Fixed a bug where the beamfits partial read parameters were not available in the
`UVBeam.from_file` class method and were not passed properly when reading multiple files.
- Fixed a bug where objects created from scratch with the old phase attributes weren't
properly getting converted to the new `phase_center_catalog` representation. That
conversion now happens in the check so will happen before any `write`. There could still
be errors if some methods are called before a check is done (or if the check is turned
off).
- Fix a bug in how `frame_pa` was calculated in `phase` and `_set_app_coords_helper` for
multi_phase_center objects (it was using the old `phase_center_frame` attribute).
- Fix a bug where trying to select lsts or lst_ranges on read didn't work for some file
types.
- Severe performance hit when calling `polnum2str` and its variants for many baselines.

Deprecated
- Reading files into objects without setting `use_future_array_shapes` now results in
deprecation warnings.
- The utility functions `phase_uvw` and `unphase_uvw` associated with the deprecated
old phasing method.
- The `flex_spw_id_array` will be required on all UVData and UVFlag and all
non-wide-band UVCal objects in version 3.0.
- Deprecated the `interpolation_function` attribute on UVBeams.
- Deprecated the older phase attributes (`phase_type`, `phase_center_ra`,
`phase_center_dec`, `phase_center_frame`, `phase_center_epoch`, `object_name`) in favor
of the `phase_center_catalog`. The older phase attributes will be removed in version 3.0.
- The `lst_from_uv` function in the uvflag module.

Removed
- Removed deprecated handling for UVCal objects without `telescope_location`,
`antenna_positions` and `lst_array` parameters defined.

Changed
- Updated how wheels for PyPI are built.

Added
- A frame attribute to the telescope_location parameters on UVData, UVCal and UVFlag
objects to support observatories on the moon (or anywhere not on earth).

Fixed
- A bug in `UVData.read_uvh5` where `multi_phase_center` was being used to imply the
existence of the `phase_center_catalog` header item, rather than checking for the
presence of that item. This conflicted with the uvh5 memo.

Added
- A new subclass of UVParameter for SkyCoord objects, needed in pyradiosky.
- Added `UVData.convert_to_flex_pol` method to enable writing uvh5 files with the
polarization axis changing slowest as desired by HERA. Also updated
`UVData.remove_flex_pol` to properly undo the `UVData.convert_to_flex_pol` operation.
- Added an option to `UVData.read` and `UVData.from_file` methods when reading uvh5
type files to call `remove_flex_pol` as part of the read. This is defaulted to `True`
so that when HERA data is written with flex_pol the change will not disrupt users, but
other users of uvh5 may want to set it to `False`.
- Added support to make bitshuffle compression easier when writing UVData objects to
uvh5 files
- Support for partial reads on beamfits files. This can be done on frequency, azimuth
or zenith angle (if beam is in az/za coordinates).
- Logging statements (INFO level) in `UVData.check`.

Changed
- Significantly increased uvh5 reading and writing speed.
- Added `use_future_array_shapes` method to UVBeam to allow users to convert to using
the future array shapes now, with support throughout UVBeam methods and related utility
functions. Also added `use_current_array_shapes` to revert to the standard shapes.
- Major performance improvement in the `UVBeam.to_healpix` method.
- Performance improvement when doing a `UVData.select` using the `bls` parameter (~70%
improvement in the `_select_preprocess` function)

Fixed
- A bug in `UVData.check` when `check_autos` is True and the object is a flex pol object.