Pyuvsim

Added
- Support for writing out measurement set files.
- Support for unit tests parallelized with MPI.
- Require that future changes not drastically increase runtime for current capabilities.

Changed
- Require pyuvdata >= 2.1.5
- Use future array shapes on UVData objects.
- Use the replacements for the deprecated `SkyModel.source_cuts` method if the pyradiosky
version is new enough to have them.
- Use remote memory access to collect finished visibility data, without serialization.

Fixed
- `x_orientation` is now checked on UVBeam objects and flowed into the output UVData files.
- `SkyModel.name` is now coerced to an array.
- Bug MPI-enabled tests which caused failure on tests that wouldn't pass in serial mode.
- Fix bugs in reading catalogs using pyradiosky for `skyh5` files and files with unusual extension names.
- Corrects the distribution of random points for the random mock catalog.
- pixel interpolation was defaulting to az_za_simple for all beams, breaking healpix-coord UVBeams.

Added
- Diffuse models in mock catalogs, via the analytic_diffuse module.
- quantity_shared_bcast function to allow objects derived from astropy.units.Quantity to use shared memory broadcasting.
- SkyModelData class to replace recarray conversion in pyradiosky.
- quiet keyword for run_uvsim, to suppress stdout printing.
- Support for Moon-based observing -- keyword "world: moon" in telescope config.
- Option to pass along interpolating spline order to UVBeam from teleconfig file.
- Scripts for running / verifying reference simulations.
- Benchmarking tools.

Changed
- Switch to a new definition for the Counter class, without threading.
- Cleaned up unit tests
- Use `at_frequencies` method to enable support for all pyradiosky spectral types.
- Only do coherency calculation when the time changes
- Only do beam eval when time, freq, or beam type changes.
- The definition of the Airy beam now uses the exact value of c, not 3e8.

Fixed
- Keep a UVBeam with more than two frequencies for tests, so the (default) cubic interpolation works.
- Use pytest hooks to ensure the profiler tests run last.
- Switched to using a remote-memory-access based counter class. Appears to have fixed bug in the Counter test.
- Ensure that source positions, coherency matrices, and Jones matrices are updated at the right times.
- Error early if the task list is too long for gather.

Deprecated
- Support for pyradiosky versions <0.1.0.

Added
- BeamList class for handling the set of beams, and their string representations.
- Support for individual shape parameters for analytic beams.

Fixed
- Removed warning catch for astropy GLEAM read in tests -- new versions don't raise the warning.

Added
- A function for checking the memory usage on each Node

Changed
- Replaced init_uvdata_out function with complete_uvdata
- init_uvdata_out function is more modular.
- unit tests check error messages raised.
- Polarization selection is now allowed in setup. Will break if incorrect polarization is used in pyuvsim.
- Added functions to read healpix maps and added support for frequency axis

Fixed
- Fixed a serious bug with improper conversion of Angle to rad/deg in simsetup.py
- skymodel splitting was not working correctly to avoid running out of memory.
- Flush stderr in excepthook, so stack trace is printed when an exception is raised in MPI.
- No longer calling UVBeam.interp with freq_interp_kind, for updated pyuvdata.
- Circular-installation bug
- Bug in how integration_time array is set in setup
- Bug in how filepath is interpreted in setup

Added
- A parallelized counter that can track progress across all ranks.
- shared memory broadcast, which will create a shared memory window for a given object on each node
- Function to generate UVData object from keywords, optionally saving config files.
- Optionally, can skip having telescope_config file if there is no beam list.

Changed
- UVBeam frequency interpolation is cubic spline by default, not linear.
- Tasks are split over time, frequency, and baseline only (in that order).
- Tasks are split over the source axis if the estimated memory footprint exceeds available resources.
- The source class is replaced with SkyModel, which supports vectorized coordinate transformation and beam interpolation.

Fixed
- MPI.Init -> MPI.Init_thread(), for threaded applications.
- Progress steps now update in real time, accurately reflecting job progress.
- Analytic visibility calculation tests now also check analytic beams.
- Analytic beams are redefined so that off-diagonal Jones matrix terms are zero.
- parameter dicts are not modified by functions using them.

Deprecated
- Coarse horizon cuts are no longer performed. Should be restored in a future version.

Added
- More detailed comparison to other simulators in the documentation.
- Option to convert analytic beams from efield to pstokes
- Enabled Gaussian beams to be defined with power law widths.
- Enabled Gaussian beams to be defined from antenna diameter and have chromaticity
- Checking the beam kernel width makes sense for Airy beams

Changed
- Pending deprecation of gaussian beams defined from sigma parameter

Fixed
- pip installation instructions