Remove deprecated code, update changelog for version 2.3

CHANGELOG.md

@@ -3,6 +3,8 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [2.3.0] - 2023-03-13
+
 ### 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.
@@ -19,6 +21,7 @@ they are converted between types using UVData and UVCalobjects.
 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.
 
@@ -60,6 +63,10 @@ non-wide-band UVCal objects in version 3.0.
 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.
+
 ## [2.2.12] - 2022-12-07
 
 ### Changed

README.md

@@ -142,11 +142,11 @@ Note that as of v2.2, `pyuvdata` is only supported on python 3.7+.
 Required:
 
 * astropy >= 5.0.4
-* h5py >= 3.0
+* h5py >= 3.1
 * numpy >= 1.19
 * pyerfa >= 2.0
 * scipy >= 1.3
-* setuptools_scm
+* setuptools_scm <7.0|>=7.0.3
 
 Optional:
 

ci/pyuvdata_min_deps_tests.yml

@@ -5,7 +5,7 @@ dependencies:
   - astropy>=5.0.4
   - numpy>=1.19.*
   - scipy>=1.3
-  - h5py>=3.0
+  - h5py>=3.1
   - pyerfa>=2.0
   - coverage
   - pytest>=6.2.0

ci/pyuvdata_publish.yml

@@ -5,7 +5,7 @@ dependencies:
   - astropy>=5.0.4
   - numpy>=1.19.*
   - scipy>=1.3
-  - h5py>=3.0
+  - h5py>=3.1
   - pyerfa>=2.0
   - cython
   - setuptools_scm<7.0|>=7.0.3

ci/pyuvdata_tests.yml

@@ -5,7 +5,7 @@ dependencies:
   - astropy>=5.0.4
   - astropy-healpix>=0.6
   - astroquery>=0.4.4
-  - h5py>=3.0
+  - h5py>=3.1
   - hdf5plugin>=3.1.0
   - numpy>=1.19.*
   - pyerfa>=2.0

ci/pyuvdata_tests_windows.yml

@@ -5,7 +5,7 @@ dependencies:
   - astropy>=5.0.4
   - astropy-healpix>=0.6
   - astroquery>=0.4.4
-  - h5py>=3.0
+  - h5py>=3.1
   - hdf5>=1.12.0
   - hdf5plugin>=3.1.0
   - numpy>=1.19.*

ci/pyuvdata_warning_test.yml

@@ -5,7 +5,7 @@ dependencies:
   - astropy>=5.0.4
   - astropy-healpix>=0.6
   - astroquery>=0.4.4
-  - h5py>=3.0
+  - h5py>=3.1
   - hdf5plugin>=3.1.0
   - numpy>=1.19.*
   - pyerfa>=2.0

environment.yaml

@@ -7,7 +7,7 @@ dependencies:
   - astroquery>=0.4.4
   - coverage
   - cython>=0.23
-  - h5py>=3.0
+  - h5py>=3.1
   - hdf5plugin>=3.1.0
   - numpy>=1.19
   - pip

pyuvdata/uvcal/calfits.py

@@ -181,13 +181,12 @@ def write_calfits(
         # Conforming to fits format
         prihdr["SIMPLE"] = True
         prihdr["TELESCOP"] = self.telescope_name
-        if self.telescope_location is not None:
-            prihdr["ARRAYX"] = self.telescope_location[0]
-            prihdr["ARRAYY"] = self.telescope_location[1]
-            prihdr["ARRAYZ"] = self.telescope_location[2]
-            prihdr["LAT"] = self.telescope_location_lat_lon_alt_degrees[0]
-            prihdr["LON"] = self.telescope_location_lat_lon_alt_degrees[1]
-            prihdr["ALT"] = self.telescope_location_lat_lon_alt[2]
+        prihdr["ARRAYX"] = self.telescope_location[0]
+        prihdr["ARRAYY"] = self.telescope_location[1]
+        prihdr["ARRAYZ"] = self.telescope_location[2]
+        prihdr["LAT"] = self.telescope_location_lat_lon_alt_degrees[0]
+        prihdr["LON"] = self.telescope_location_lat_lon_alt_degrees[1]
+        prihdr["ALT"] = self.telescope_location_lat_lon_alt[2]
         prihdr["GNCONVEN"] = self.gain_convention
         prihdr["CALTYPE"] = self.cal_type
         prihdr["CALSTYLE"] = self.cal_style
@@ -491,11 +490,8 @@ def write_calfits(
                 self.ant_array, np.zeros(nants_add, dtype=np.int64) - 1
             )
             col3 = fits.Column(name="ANTARR", format="D", array=ant_array_use)
-        if self.antenna_positions is not None:
-            col4 = fits.Column(name="ANTXYZ", format="3D", array=self.antenna_positions)
-            cols = fits.ColDefs([col1, col2, col3, col4])
-        else:
-            cols = fits.ColDefs([col1, col2, col3])
+        col4 = fits.Column(name="ANTXYZ", format="3D", array=self.antenna_positions)
+        cols = fits.ColDefs([col1, col2, col3, col4])
         ant_hdu = fits.BinTableHDU.from_columns(cols)
         ant_hdu.header["EXTNAME"] = "ANTENNAS"
 

pyuvdata/uvcal/tests/test_fhd_cal.py

@@ -292,29 +292,21 @@ def test_break_read_fhdcal(cal_file, obs_file, layout_file, settings_file, nfile
         expected_history += " Combined data along time axis using pyuvdata."
     assert fhd_cal.history == expected_history
 
-    message_list = (
-        ["No layout file, antenna_postions will not be defined."] * nfiles
-        + ["UVParameter diffuse_model does not match"] * (nfiles - 1)
-        + [
-            "The antenna_positions parameter is not set. It will be a required "
-            "parameter starting in pyuvdata version 2.3"
-        ]
-        * (4 * nfiles - 3)
-    )
-
-    warning_list = [UserWarning] * (2 * nfiles - 1) + [DeprecationWarning] * (
-        4 * nfiles - 3
-    )
-    with uvtest.check_warnings(warning_list, message_list):
-        fhd_cal.read_fhd_cal(
-            cal_file,
-            obs_file,
-            settings_file=settings_file,
-            use_future_array_shapes=True,
-        )
+    message_list = [
+        "No layout file, antenna_postions will not be defined."
+    ] * nfiles + ["UVParameter diffuse_model does not match"] * (nfiles - 1)
 
-    # Check no antenna_positions
-    assert fhd_cal.antenna_positions is None
+    warning_list = [UserWarning] * (2 * nfiles - 1)
+    with pytest.raises(
+        ValueError, match="Required UVParameter _antenna_positions has not been set."
+    ):
+        with uvtest.check_warnings(warning_list, message_list):
+            fhd_cal.read_fhd_cal(
+                cal_file,
+                obs_file,
+                settings_file=settings_file,
+                use_future_array_shapes=True,
+            )
 
 
 def test_read_multi(tmp_path):

pyuvdata/uvcal/tests/test_uvcal.py

@@ -11,6 +11,8 @@
 
 import numpy as np
 import pytest
+from astropy.io import fits
+from astropy.table import Table
 
 import pyuvdata.tests as uvtest
 import pyuvdata.utils as uvutils
@@ -313,26 +315,6 @@ def test_check(gain_data):
     assert gain_data.check()
 
 
-def test_check_warnings(gain_data):
-    """Test that parameter checks run properly"""
-    gain_data.telescope_location = None
-    gain_data.lst_array = None
-    gain_data.antenna_positions = None
-
-    with uvtest.check_warnings(
-        DeprecationWarning,
-        [
-            "The telescope_location is not set. It will be a required "
-            "parameter starting in pyuvdata version 2.3",
-            "The antenna_positions parameter is not set. It will be a required "
-            "parameter starting in pyuvdata version 2.3",
-            "The lst_array is not set. It will be a required "
-            "parameter starting in pyuvdata version 2.3",
-        ],
-    ):
-        assert gain_data.check()
-
-
 def test_check_flag_array(gain_data):
     gain_data.flag_array = np.ones((gain_data.flag_array.shape), dtype=int)
 
@@ -492,30 +474,47 @@ def test_future_array_shape_errors(
 
 def test_unknown_telescopes(gain_data, tmp_path):
     calobj = gain_data
-    calobj.telescope_name = "foo"
-    calobj.telescope_location = None
-    calobj.lst_array = None
-    calobj.antenna_positions = None
 
-    write_file_calfits = str(tmp_path / "test.calfits")
-    deprecation_messages = [
-        "The telescope_location is not set. It will be a required "
-        "parameter starting in pyuvdata version 2.3",
-        "The antenna_positions parameter is not set. It will be a required "
-        "parameter starting in pyuvdata version 2.3",
-        "The lst_array is not set. It will be a required "
-        "parameter starting in pyuvdata version 2.3",
-    ]
-
-    with uvtest.check_warnings(DeprecationWarning, match=deprecation_messages):
-        calobj.write_calfits(write_file_calfits, clobber=True)
+    write_file = str(tmp_path / "test.calfits")
+    write_file2 = str(tmp_path / "test2.calfits")
+    calobj.write_calfits(write_file)
+    with fits.open(write_file, memmap=True) as hdu_list:
+        hdunames = uvutils._fits_indexhdus(hdu_list)
+        primary_hdu = hdu_list[0]
+        primary_hdr = primary_hdu.header.copy()
+        del primary_hdr["ARRAYX"]
+        del primary_hdr["ARRAYY"]
+        del primary_hdr["ARRAYZ"]
+        del primary_hdr["LAT"]
+        del primary_hdr["LON"]
+        del primary_hdr["ALT"]
+        primary_hdr["TELESCOP"] = "foo"
+        primary_hdu.header = primary_hdr
+
+        ant_hdu = hdu_list[hdunames["ANTENNAS"]]
+
+        table = Table(ant_hdu.data)
+        del table["ANTXYZ"]
+        ant_hdu = fits.BinTableHDU(table)
+        ant_hdu.header["EXTNAME"] = "ANTENNAS"
+
+        hdulist = fits.HDUList([primary_hdu, ant_hdu])
+
+        hdulist.writeto(write_file2)
+        hdulist.close()
 
     calobj2 = UVCal()
+    with pytest.raises(
+        ValueError, match="Required UVParameter _antenna_positions has not been set."
+    ):
+        with uvtest.check_warnings(
+            [UserWarning], match=["Telescope foo is not in known_telescopes"]
+        ):
+            calobj2.read_calfits(write_file2, use_future_array_shapes=True)
     with uvtest.check_warnings(
-        [UserWarning] + [DeprecationWarning] * 3,
-        match=["Telescope foo is not in known_telescopes"] + deprecation_messages,
+        [UserWarning], match=["Telescope foo is not in known_telescopes"]
     ):
-        calobj2.read_calfits(write_file_calfits, use_future_array_shapes=True)
+        calobj2.read_calfits(write_file2, use_future_array_shapes=True, run_check=False)
 
 
 def test_nants_data_telescope_larger(gain_data):
@@ -3348,21 +3347,29 @@ def test_match_antpos_antname(gain_data, antnamefix, tmp_path):
         ]
 
     # remove the antenna_positions to test matching them on read
-    gain_data2 = gain_data.copy()
-    gain_data2.antenna_positions = None
+    write_file = str(tmp_path / "test.calfits")
+    write_file2 = str(tmp_path / "test2.calfits")
+    gain_data.write_calfits(write_file)
+    with fits.open(write_file, memmap=True) as hdu_list:
+        hdunames = uvutils._fits_indexhdus(hdu_list)
+        primary_hdu = hdu_list[0]
+        ant_hdu = hdu_list[hdunames["ANTENNAS"]]
 
-    write_file_calfits = str(tmp_path / "test.calfits")
-    with uvtest.check_warnings(
-        DeprecationWarning,
-        match="The antenna_positions parameter is not set. It will be a required "
-        "parameter starting in pyuvdata version 2.3",
-    ):
-        gain_data2.write_calfits(write_file_calfits)
+        table = Table(ant_hdu.data)
+        del table["ANTXYZ"]
+        ant_hdu = fits.BinTableHDU(table)
+        ant_hdu.header["EXTNAME"] = "ANTENNAS"
+
+        hdulist = fits.HDUList([primary_hdu, ant_hdu])
 
+        hdulist.writeto(write_file2)
+        hdulist.close()
+
+    gain_data2 = UVCal()
     with uvtest.check_warnings(
         UserWarning, "antenna_positions is not set. Using known values for HERA."
     ):
-        gain_data2.read_calfits(write_file_calfits, use_future_array_shapes=True)
+        gain_data2.read_calfits(write_file2, use_future_array_shapes=True)
 
     assert gain_data2.antenna_positions is not None
     assert gain_data == gain_data2
@@ -3391,27 +3398,47 @@ def test_set_antpos_from_telescope_errors(gain_data, modtype, tmp_path):
         gain_data.antenna_numbers[1] = orig_num
 
     # remove the antenna_positions to test matching them on read
-    gain_data2 = gain_data.copy()
-    gain_data2.antenna_positions = None
+    write_file = str(tmp_path / "test.calfits")
+    write_file2 = str(tmp_path / "test2.calfits")
+    gain_data.write_calfits(write_file)
+    with fits.open(write_file, memmap=True) as hdu_list:
+        hdunames = uvutils._fits_indexhdus(hdu_list)
+        primary_hdu = hdu_list[0]
+        ant_hdu = hdu_list[hdunames["ANTENNAS"]]
 
-    write_file_calfits = str(tmp_path / "test.calfits")
-    with uvtest.check_warnings(
-        DeprecationWarning,
-        match="The antenna_positions parameter is not set. It will be a required "
-        "parameter starting in pyuvdata version 2.3",
+        table = Table(ant_hdu.data)
+        del table["ANTXYZ"]
+        ant_hdu = fits.BinTableHDU(table)
+        ant_hdu.header["EXTNAME"] = "ANTENNAS"
+
+        hdulist = fits.HDUList([primary_hdu, ant_hdu])
+
+        hdulist.writeto(write_file2)
+        hdulist.close()
+
+    gain_data2 = UVCal()
+    with pytest.raises(
+        ValueError, match="Required UVParameter _antenna_positions has not been set."
     ):
-        gain_data2.write_calfits(write_file_calfits)
+        with uvtest.check_warnings(
+            [UserWarning],
+            match=[
+                "Not all antennas have positions in the telescope object. "
+                "Not setting antenna_positions."
+            ],
+        ):
+            gain_data2.read_calfits(write_file2, use_future_array_shapes=True)
 
     with uvtest.check_warnings(
-        [UserWarning, DeprecationWarning],
+        UserWarning,
         match=[
             "Not all antennas have positions in the telescope object. "
-            "Not setting antenna_positions.",
-            "The antenna_positions parameter is not set. It will be a required "
-            "parameter starting in pyuvdata version 2.3",
+            "Not setting antenna_positions."
         ],
     ):
-        gain_data2.read_calfits(write_file_calfits, use_future_array_shapes=True)
+        gain_data2.read_calfits(
+            write_file2, use_future_array_shapes=True, run_check=False
+        )
 
     assert gain_data2.antenna_positions is None