Version 3.1.1

This is a patch release that fixes some floating point comparison issues in our tests to enable conda releases.

Full details below and in our changelog:

What's Changed

• Set tolerances for floating point comparisons in tests by @bhazelton in #1492

Full Changelog: v3.1.0...v3.1.1

Version 3.1.0

This version has several additions, the most notable are:

• Adds new analytic beam objects.
• Adds a new BeamInterface object that unifies the interface for analytic and UVBeam objects.
• Adds a new pol_convention parameter on UVData and UVCal to specify the convention assumed for converting linear to stokes polarizations -- either "sum" or "avg". Also added to uvcalibrate to apply from the UVCal to the UVData.
• Adds a new optional spatial interpolation method, interpolation_function="az_za_map_coordinates"
  that improves the linear interpolation speed for data in az_za coordinates.

This version also fixes some bugs including:

• Fixes a bug in the MWA beam reader that resulted in the wrong polarization response.
• Fixes a bug in reading UVH5 files with antenna names saved as variable length strings that was introduced in v3.0.0.

There are a some new optional dependency version changes:

• lunarsky>=0.2.5
• pytest>=8.2.0

Full changes detailed below and in our changelog:

What's Changed

• Add UVData.get_enu_data_ants to get ENU positions for antennas with data by @bhazelton in #1457
• feat: add Telescope object to FastUVH5Meta by @steven-murray in #1456
• feat: ignore_telescope_param_update_warnings_for by @steven-murray in #1459
• Pol convention by @steven-murray in #1455
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1465
• Fix uvh5 ant names bug by @bhazelton in #1468
• Use Ruff for linting (replaces flake8, black and isort) by @bhazelton in #1466
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1471
• CalH5 Memo by @bhazelton in #1462
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1472
• Faster interpolation in UVBeam.interp by @tyler-a-cox in #1464
• Correctly pass spline_opts to new uvbeam interpolator by @tyler-a-cox in #1474
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1475
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1476
• CI fix: Mambaforge is deprecated and mamba in now the default installer by @bhazelton in #1478
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1479
• Benchmark by @mkolopanis in #1463
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1480
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1481
• Add AnalyticBeam objects and a unified interface for UVBeams and AnalyticBeams by @bhazelton in #1383
• Fix a bug in the MWA beams where the polarization responses were swapped by @bhazelton in #1485
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1489
• benchmark against the compiled extension explicitly by @mkolopanis in #1484
• Prepare for version 3.1.0 by @bhazelton in #1490

New Contributors

• @tyler-a-cox made their first contribution in #1464

Full Changelog: v3.0.0...v3.1.0

Version 3.0

This is a major new version with many new features and some breaking API changes. Highlights include:

Added/Changed:

• Telescope-related metadata (including antenna metadata) on UVData, UVCal and UVFlag objects have been refactored into a Telescope object (attached to these objects as the telescope attribute)
• Restructured utils.py into a new sub package utils with functions split among several submodules. Utility functions used widely are still available from pyuvdata.utils, although this access pattern is deprecated for some of them.
• Require keyword arguments rather than allowing for passing arguments by position for
  functions and methods with many parameters.

UVCal:

• Introduced CalH5, a new HDF5 based file format for calibration solutions.
• Add reading and writing calibration solutions from measurement sets.
• Improved support for calibration solutions that apply over a range of times, using the time_range parameter to give the start and stop times for each solutions instead of time_array (which is used for calibration solutions that are calculated per integration).
• Support for "flexible-Jones" UVCal objects -- where different spectral windows can contain different Jones vectors/polarization information -- has been added, along with methods for converting UVCal objects to and from flex-Jones format and reading and writing to and from measurement sets and CalH5 files.

UVData:

• Changed the way files are passed for reading FHD files to make it more similar to the API for reading FHD calibration solutions.
• Support for writing "MODEL_DATA" and "CORRECTED_DATA" columns has been added to the UVData.write_ms method.
• Improved performance for antpair2ind and _key2inds by using the blts_are_rectangular parameter, and also by caching the results. To improve performance of the cache, the resulting indices are returned as slices whenever possible.

Deprecated:

• The future_array_shapes attribute on UVBase objects has been deprecated, as pyuvdata now exclusively uses future array shapes.
• The use_future_array_shapes keyword in several different class methods, as well as the use_future_array_shapes method on UVBase objects.
• Accessing the telescope-related metadata through their old attribute names on UVData, UVCal and UVFlag rather than via their attributes on the attached Telescope object (e.g. UVData.telescope_name -> UVData.telescope.name and UVData.antenna_positions -> UVData.telescope.antenna_positions).
• Passing telescope-related metadata as separate parameters to UVData.new and UVCal.new rather than Telescope objects.
• The UVData.get_ENU_antpos method in favor of UVData.telescope.get_enu_antpos.
• The Telescope.telescope_location and Telescope.telescope_name attributes in favor of Telescope.location and Telescope.name.
• The get_telescope function in favor of the known_telescope_location function and the Telescope.from_known_telescopes classmethod.
• The KNOWN_TELESCOPE dict in favor of the known_telescope_location function and the Telescope.from_known_telescopes classmethod.

Removed:

• Support for current array shapes has been removed on UVData, UVCal, UVFlag, and UVBeam objects, as well as the use_current_array_shapes method for these classes.
• The flex_spw attribute has been removed on UVData and UVCal objects.
• Support for using the old phasing attributes (phase_center_ra, phase_center_dec, phase_center_frame, phase_center_epoch, phase_type, and object_name) in UVData.
• Support for handling of the input_flag_array parameter for UVCal objects.
• Support for 'unknown' cal type in UVCal objects.

Full details below and in our changelog:

What's Changed

• Prepare for version 3.0 by @bhazelton in #1444

Full Changelog: v2.4.5...v3.0.0

Version 2.4.5

This is the last release before version 3.0.

Primarily, it fixes compatibility with numpy v2.0.

It also fixed a bug in UVData.new() where in some corner cases the UVData.ant1_array and UVData.ant2_array were not correctly set as integer arrays.

Full details below and in our changelog:

What's Changed

• Numpy 2.0 compatibility by @pre-commit-ci in #1447
• fix: always cast antpairs to int by @steven-murray in #1448
• Prepare for v2.4.5 which adds compatibility with numpy 2.0 by @bhazelton in #1454

Full Changelog: v2.4.4...v2.4.5

Version 2.4.4

This fixes a few bugs and updates the following dependencies:

• cython >= 3.0
• astropy-healpix>=1.0.2

Full details below and in our changelog:

What's Changed

• Fix correct_cable_len default by @PyxieLouStar in #1419
• Increase astropy_healpix version to be compatible with astropy 6.0 by @bhazelton in #1423
• Cython3 by @mkolopanis in #1421
• Fix pyuvsim test CI for new package structure by @bhazelton in #1426
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1428
• Fixing bugs with extra catalog entries by @kartographer in #1429
• • docs/ref/uvh5_memo specify baseline direction by @radonnachie in #1427
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1432
• Dcp uvfits rdate fix by @telegraphic in #1439
• Prepare for v2.4.4 by @bhazelton in #1443

New Contributors

• @telegraphic made their first contribution in #1439

Full Changelog: v2.4.3...v2.4.4

Version 2.4.3

This version has several improvements, the most notable are:

• Adds support for the new lunar ellipsoids recently added to lunarsky.
• A significant speed up for reading MWA correlator FITS files.
• Support for v.6 of the MIR data format

There are a number of dependency version changes, pyuvdata now requires:

• python >= 3.10
• astropy>=6.0
• h5py>=3.4
• numpy>=1.23
• pyerfa>=2.0.1.1
• scipy>=1.7.3

And optional dependecy version changes include:

• hdf5plugin>=3.2.0
• pytest>=6.2.5
• pytest-cases>=3.8.3
• python-casacore>=3.5.2
• pyyaml>=5.4.1
• lunarsky>=0.2.2

Full changes detailed below and in our changelog:

Full Changelog: v2.4.3...v2.4.3

Version 2.4.2

This version has several improvements, the most notable are:

• Improvements to the MIR reader and interface.
• A new gridding-based baseline redundancy finding algorithm that is now used by default (the older algorithm is still available).
• A new UVBeam.new() method that creates a new, self-consistent UVBeam object from scratch from a set of flexible input parameters.
• Improvements for handling of telescopes on the moon.

Full changes detailed below and in our changelog:

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1350
• Better handing of discrepancies for LSTs and telescope position in check by @kartographer in #1356
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1358
• MS writer improvements by @kartographer in #1363
• Pyx datatypes by @mkolopanis in #1357
• Clean up freq_range and freq_array handling in UVCal by @bhazelton in #1361
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1366
• Drop python 3.8 support, add python 3.12 by @bhazelton in #1367
• Update flake8 plugin versions to match CI by @bhazelton in #1364
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1369
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1370
• Uvh5 memo updates by @bhazelton in #1368
• Updating antenna positions in UVData by @kartographer in #1372
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1373
• Run the tutorial plotting code in doctests by @bhazelton in #1374
• Replacing deprecated scipy simps method in MWA code by @kartographer in #1377
• Add a UVBeam.new() method similar to the ones on UVData and UVCal by @bhazelton in #1378
• Minor bug fix for tests.WarningChecker when IERS is down by @kartographer in #1382
• Miriad support (UVFITS and UV file writing) and MS write with legacy array shape by @kartographer in #1392
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1385
• Fix so that write_uvfits doesn't change the object, add loopback testing by @bhazelton in #1393
• Mcmf enu calc by @mkolopanis in #1376
• SMA/MirParser Improvements by @kartographer in #1371
• Add a changelog entry for small UVFlag bug fixed in a recent PR by @bhazelton in #1394
• Fix CI by @bhazelton in #1398
• Handle differently sorted ant metadata in UVFlag to_baseline and to_antenna by @bhazelton in #1397
• Minor fixes for handling of older SMA data by @kartographer in #1399
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1400
• Adding support for initializing MirParser from Path objects by @kartographer in #1405
• ignore warnings in hera_cal and hera_qm test runs by @bhazelton in #1402
• Add an option to use the HERA gridding algorithm to find redundancies by @bhazelton in #1403
• Prepare for v2.4.2 by @bhazelton in #1406

Full Changelog: v2.4.1...v2.4.2

Version 2.4.1

This version has several improvements, the most notable are:

• New uvw_track_generator utility method for calculating the expected uvws (and a few other values) without needing to instantiate a whole UVData object.
• Proper round-tripping of the telescope frame through UVH5, UVFITS and MS files.
• New options to UVFlag.read and UVFlag.__init__ to help with setting telescope metadata for old UVFlag files that are missing it.
• Support for recarrays in UVParameter objects and in UVBase.

Full changes detailed below and in our changelog:

What's Changed

• Fix bug in calc_app_coords by @kartographer in #1325
• Undo numpy pin on python 3.11 tests by @bhazelton in #1321
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1327
• Fix docstrings for shape of waterfall-type UVFlag objects by @jsdillon in #1326
• Add warnings in check if lst_array doesn't match expectations by @bhazelton in #1322
• Add options for astrometry library to object methods, round-trip telescope frame through UVH5, UVFITS and MS files by @bhazelton in #1329
• Fix write_ms handling of history by @kartographer in #1332
• Fix some ERFA calls by @bhazelton in #1331
• Update uvdata_tutorial.rst by @elillesk in #1337
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1338
• Add support for recarray UVParameters, needed for pyradiosky by @bhazelton in #1334
• Add external testing against SSINS by @bhazelton in #1335
• Add MWA antenna information by @bhazelton in #1340
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1345
• UVW helper utilities (for use on the moon and otherwise...) by @kartographer in #1292
• New version by @bhazelton in #1347

New Contributors

• @elillesk made their first contribution in #1337

Full Changelog: v2.4.0...v2.4.1

Version 2.4

This version has several improvements, the most notable are:

• More flexibility in the UVData.frequency_average method, including support for multiple spectral windows and better handling in when averaging by a number of channels that does not divide evenly into the number of channels in each spectral window.
• Fixed a bug in LST calculation that led to small discontinuities in LSTs calculated using the erfa (the default) or novas astrometry libraries.
• The quality_array on UVCal objects is no longer required.
• Fixed a bug in reading mwa_corr_fits files from the new MWAX correlator
• Added compatibility with Python 3.11

There are also a number of breaking changes, including changes associated with:

• Removing support for old style phasing
• Full support for multiple phase centers (so rephrasing when adding/concatenating is not required)
• A number of telescope metadata parameters are now required on UVFlag objects.

Full changes detailed below and in our changelog:

What's Changed

• Add testing against python 3.11 by @bhazelton in #1298
• small mwax metafits updates by @PyxieLouStar in #1299
• fix: error when setting freq_interp_kind to an integer by @steven-murray in #1304
• better error message if az_za_grid set but no az_array or za_array by @bhazelton in #1302
• Fix code that raises new numpy deprecation warnings by @bhazelton in #1308
• Make UVCal quality array optional by @bhazelton in #1301
• Deprecate sky_field parameter on UVCal by @bhazelton in #1312
• Fix LST discontinuities by @bhazelton in #1314
• Fix a few small CI issues by @bhazelton in #1316
• Support multiple spws in UVData.frequency_average by @bhazelton in #1307
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1320
• Prepare for version 2.4 by @bhazelton in #1319

Full Changelog: v2.3.3...v2.4.0

Version 2.3.3

This version adds many new features including:

• The UVCal.new and UVData.new methods to create self-consistent object from scratch from a set of flexible input parameters.
• A new fast_concat method on UVCal.
• A new generic read method on UVCal that supports all file types and a new UVCal.from_file class method.

A new required dependency, docstring_parser was also added.

Full changes detailed below and in our changelog:

What's Changed

• Transactional FastUVH5Meta by @steven-murray in #1285
• Add fast_concat, generic read, and from_file methods to UVCal by @bhazelton in #1271
• feat: new_uvdata function for simple initialization by @steven-murray in #1281
• fix: error when times or freqs are length 1 by @steven-murray in #1287
• Fix error on ntimes one by @steven-murray in #1289
• Deprecate the 'unknown' cal_type by @bhazelton in #1288
• Deprecate the input_flag_array attribute on UVCal by @bhazelton in #1275
• Cal init method by @steven-murray in #1284
• Update CI by @bhazelton in #1295
• Prepare for v2.3.3 release by @bhazelton in #1297

Full Changelog: v2.3.2...v2.3.3