Pyuvdata

Added
- Support for reading the MWA full embedded element beam into a UVBeam object.
- New `time_range` keyword to `select` so exact times don't need to be specified (also added to `read` methods for select on read).
- Support for rephasing phased data including on `read`, `__add__` and `fast_concat` so that files with different phasing can be read in together.
- `sum_vis` and `diff_vis` for summing or differencing visibilities in the data_array.
- `read_mwa_corr_fits` for reading in MWA correlator gpubox files and applying cable corrections.
- `eq_coeffs` for storing equalization coefficients and `remove_eq_coeffs` for removing them.
- `utils.apply_uvflag` for applying UVFlag objects to UVData objects

Fixed
- Fixed `utils.uvcalibrate` to handle `x_orientation` attribute
- Arrays of file names can now be passed to `read` (not just lists).
- run_check is no longer turned off in `read_uvfits` and `read_uvh5` when `read_data` is False.
- Redundancy finder will now error if any baselines appear in multiple groups.
- A bug in `UVCal` objects that prevented them from properly getting data with `ee`/`nn`-style polarizations.
- a bug in `UVFlag` where `x_orientation` was not set during initialization.
- A bug in `UVCal.read_fhd_cal` that caused calibration solutions to be approximately doubled.
- A bug in UVFlag where polarization array states were not updated when using `force_pol` keyword in `to_antenna` and `to_baseline`
- A bug in UVFlag.to_baseline() where force_pol kwarg did not work for UVData Npols > 1
- `UVData.read_uvfits` no longer breaks if there are non-ascii bytes in antenna names (which CASA sometimes writes).

Deprecated
- Reading in multiple files (or file sets) using file-type specific read methods (e.g. `read_uvfits`) in favor of the generic `read` method.
- The `phase_center` and `phase_data` keywords to `read_mwa_corr_fits` in favor of `phase_to_pointing_center` and the `phase_center_radec` keyword in the generic `read` method.
- Support for reading only the header (not all the metadata) of uvfits files.
- The `read_uvfits_metadata` and `read_uvfits_data` methods on the UVFITS object.
- The `read_miriad_metadata` method on the Mirad object.

Added
- `copy` method for `UVData`, which can optionally make a copy of just metadata
- `upsample_in_time`, `downsample_in_time`, and `resample_in_time` methods on `UVData` objects
- `utils.uvcalibrate(.., undo=True)` kwarg for undo-ing a calibration.
- `utils.uvcalibrate` updates `UVData.vis_units` if `UVCal.gain_scale` is set.
- `UVCal.gain_scale` non-required attribute
- UVData.get_redundancies method to replace old get_baseline_redundancies and get_antenna_redundancies.
- option for `UVBeam.interp` to return a new beam object.
- `UVFlag` information on Read The Docs

Changed
- `UVData.phase_to_time` now accepts a float as an input. Assumes float represents a JD.
- Added optional acceptability check for `utils.LatLonAlt_from_XYZ`
- Use `astropy_healpix` rather than `healpy` for HEALPix functionality because `healpy` has a GPL license which is incompatible with ours.
- `h5py` is now a required package instead of an optional one.
- Phasing now supports metadata only `UVData` objects
- utils.get_baseline_redundancies uses scipy pdist functions instead of for loops (faster)
- UVData.get_antenna_redundancies will no longer automatically conjugate baselines.
- UVData.get_baseline_redundancies and UVData.get_antenna_redundancies have been combined.
- `UVFlag` inherits from `UVBase` object.
- `UVFlag` objects can now convert from antenna type to baseline type
- `UVFlag` objects can now be initialized without inputs

Fixed
- A bug in UVBeam._interp_freq where kind parameter was not passed for real-only beams
- A bug in get_antenna_redundancies for nearly N-S baselines.
- A bug where `conj_pol` could not handle cardinal direction polarizations.
- A bug that gave the wrong error message when calling `UVData.phase_to_time` without an Astropy Time object.

Deprecated
- UVData.get_baseline_redundancies and UVData.get_antenna_redundancies will be deprecated in version 1.6.1

Added
- `metadata_only` property on `UVData` to automatically detect if data-like arrays are present
- support for combining metadata only objects and reading in multiple files as metadata only
- `utils.uvcalibrate` flag propagation bug fix
- `UVCal.ant2ind` indexing bug fix
- `UVCal.get_*` methods for accessing data arrays with antenna-polarization keys
- `utils.uvcalibrate` for automated calibration of `UVData` by `UVCal`

Fixed
- Fixed a bug in select that caused bls and antenna_names/numbers to be or'ed rather than and'ed together.
- Fixed a bug where `baseline_to_antnums` could accept a numpy array as input but not other array_like objects.

Changed
- removed `new_object` keyword from `UVBeam._interp_freq` in favor of new functionality in `UVBeam.interp`

Added
- Option in UVBase.check() to ignore whether required parameters are set.
- made an option to not save the `lst_array` to uvfits files.
- `conjugate_bls` option to `UVData.get_antenna_redundancies`
- `UVData.conjugate_bls` method to conjugate baselines to get the desired baseline directions.
- `UVData.reorder_blts` method to reorder the data along the blt axis (and optionally also conjugate baselines), and a new `blt_order` optional parameter on UVData objects to track the ordering (including through read/writes).
- `lst_array` is now saved to UVFITS files (even though it's not a standard parameter) so that it doesn't have to be recalculated

Fixed
- Fixed init logic in UVFlag.
- Fixed a bug in how FHD uvw vectors were oriented (and visibilities were conjugated)
- Fixed a bug in `UVData.inflate_by_redundancy` when Nblts is not equal to Nbls * Ntimes.
- Fixed a bug in UVData when reading in an FHD file with a single time integration.
- Fixed a bug in how the longitudinal branch cut was handled in beam interpolation
- Changed the way interpolation splines are saved in UVBeam to fix errors related to polarization selections.
- Python 3: `np.string_` call now uses `keepdims=True` to guard against `antenna_names` being cast as an array.

Changed
- Testing framework changed from `nose` to `pytest`.
- `uvdata.set_lsts_from_time_array` only calculates lsts for unique elements in `time_array`.

Added
- Optional `x_orientation` parameter to utils functions polstr2num, polnum2str, jstr2num and jnum2str to allow for E/N based polarization strings (rather than just x/y based ones)
- New optional `x_orientation` parameter on UVBeam (paralleling UVData and UVCal), with read/write support in beamfits
- Added `x_orientation` as an optional parameter in read_cst_beam and in cst settings yaml files.
- All str2num or num2str calls on UVData and UVBeam pass the object's x_orientation
- New `UVData.fast_concat` method to allow fast concatenation of UVData objects (or files) along a particular axis.
- Added preliminary `UVFlag` module from hera_qm to pyuvdata. Will eventually promote to `UVBase` object, but for now this is undocumented functionality.

Deprecated
- Defined 'east' and 'north' as the allowed 'x_orientation' values in UVData and UVCal, Backwards compatiblity support exists for 'E' and 'N' values
- `UVData.order_pols` method in favor of `UVData.reorder_pols`.

Fixed
- Building pyuvdata on macOS now targets minimum macOS 10.9 if run on macOS 10.9 or above
- Possible bug where `check_variables` dictionary can change size during `read_miriad` call

Added
- Added `add_to_history` kwarg to UVH5.write_uvh5_part
- `_healpix_interp_bilinear` as a new interpolation method in `UVBeam`
- `freq_interpolation_kind` added as an attribute to `UVBeam`
- `tol` added as keyword argument to `UVBeam._interp_freq` which allows for a fast return of `data_array` slice if nearest-neighbor frequencies are all within the distance tolerance.
- `polarizations` added as keyword argument to `UVBeam` interpolation methods.
- Support for a yaml settings file to collect and propagate metadata for CST beam files.

Changed
- `UVBeam._interp_freq` returns both `interp_data` and `interp_bandpass`, instead of just the former.

Fixed
- Combining overlapping data along multiple axes (most common when reading in multiple files) no longer errors.