Make imports work with current and future pyuvdata, fix compatibility with numpy 2.0

CHANGELOG.md

@@ -2,10 +2,14 @@
 
 ## [Unreleased]
 
+### Changed
+- pyuvdata utils imports to ensure compatibility with version 3.0.
+- `numpy.string_` calls to `numpy.bytes_`, `np.in1d` to `np.isin` and a few other
+changes for numpy 2.0 compatibility.
+
 ### Fixed
 - An error when Skymodel.concat was called serially.
 
-
 ## [1.0.0] - 2024-05-09
 
 ### Changed

docs/tutorial.rst

@@ -1166,6 +1166,7 @@ d) Other time and position related attributes and methods
   ...     Latitude,
   ...     Galactic)
   >>> from astropy.time import Time
+  >>> from astropy.units import Quantity
 
   >>> # Create a couple sources near zenith
   >>> array_location = EarthLocation(lat="-30d43m17.5s", lon="21d25m41.9s", height=1073.0)
@@ -1191,14 +1192,15 @@ d) Other time and position related attributes and methods
   >>> sm.update_positions(time, array_location)
   >>> print(sm.time)
   2015-03-01 00:00:00.000
-  >>> print(sm.telescope_location)
-  (5109342.76037543, 2005241.90402741, -3239939.46926403) m
+  >>> with np.printoptions(precision=3):
+  ...   print(Quantity(sm.telescope_location.geocentric).to_value("m"))
+  [ 5109342.76   2005241.904 -3239939.469]
 
   >>> # Limit the precision for testing on different platforms
-  >>> with np.printoptions(precision=3):
+  >>> with np.printoptions(precision=2):
   ...   print(sm.alt_az)
-  [[1.571 1.396]
-   [1.73  0.175]]
+  [[1.57 1.4 ]
+   [1.73 0.17]]
 
   >>> # Can directly access direction cosines of the sources
   >>> with np.printoptions(precision=1):

src/pyradiosky/skymodel.py

@@ -10,7 +10,6 @@
 import astropy.units as units
 import h5py
 import numpy as np
-import pyuvdata.utils as uvutils
 import scipy.io
 from astropy.coordinates import (
     AltAz,
@@ -34,6 +33,15 @@
 from . import spherical_coords_transforms as sct
 from . import utils as skyutils
 
+try:  # pragma: no cover  # This pragma can be removed once pyuvdata v3 is released.
+    import pyuvdata.utils.history as history_utils
+    import pyuvdata.utils.tools as uvutils
+except ImportError:
+    # this can be removed once we require pyuvdata >= v3.0
+    import pyuvdata.utils as uvutils
+    import pyuvdata.utils as history_utils
+
+
 __all__ = ["hasmoon", "SkyModel"]
 
 try:
@@ -263,7 +271,7 @@
         if isinstance(value, (list, np.ndarray)):
             group[name] = np.asarray(value, dtype="bytes")
         else:
-            group[name] = np.string_(value)
+            group[name] = np.bytes_(value)
     else:
         group[name] = value
 
@@ -1049,7 +1057,7 @@
                 self._filename.form = (len(filename_use),)
 
             self.history = history
-            if not uvutils._check_history_version(
+            if not history_utils._check_history_version(
                 self.history, self.pyradiosky_version_str
             ):
                 self.history += self.pyradiosky_version_str
@@ -2157,7 +2165,7 @@
                     new_stokes[:, :, wh_non_nan] = finterp(at_freq_arr)
 
                 if nan_handling == "propagate":
-                    new_stokes[:, :, wh_nan] = np.NaN
+                    new_stokes[:, :, wh_nan] = np.nan
                 else:
                     wh_all_nan = []
                     wh_nan_high = []
@@ -2168,7 +2176,7 @@
                             np.all(~np.isnan(stokes_arr[:, :, comp]), axis=0)
                         )[0]
                         if freq_inds_use.size == 0:
-                            new_stokes[:, :, comp] = np.NaN
+                            new_stokes[:, :, comp] = np.nan
                             wh_all_nan.append(comp)
                             continue
                         at_freq_inds_use = np.arange(freqs.size)
@@ -2182,7 +2190,7 @@
                             )[0]
                             wh_nan_high.append(comp)
                             if nan_handling == "interp":
-                                new_stokes[:, at_freqs_large, comp] = np.NaN
+                                new_stokes[:, at_freqs_large, comp] = np.nan
                             else:  # clip
                                 large_inds_use = np.full(
                                     (at_freqs_large.size), freq_inds_use[-1]
@@ -2203,7 +2211,7 @@
                             )[0]
                             wh_nan_low.append(comp)
                             if nan_handling == "interp":
-                                new_stokes[:, at_freqs_small, comp] = np.NaN
+                                new_stokes[:, at_freqs_small, comp] = np.nan
                             else:  # clip
                                 small_inds_use = np.full(
                                     (at_freqs_small.size), freq_inds_use[0]
@@ -2603,7 +2611,7 @@
 
             # This is a boolean array of length len(above_horizon)
             # that identifies polarized sources above the horizon.
-            pol_over_hor = np.in1d(
+            pol_over_hor = np.isin(
                 np.arange(self.Ncomponents)[above_horizon], self._polarized
             )
 
@@ -2897,14 +2905,14 @@
         history_update_string = (
             " Combined skymodels along the component axis using pyradiosky."
         )
-        histories_match = uvutils._check_histories(this.history, other.history)
+        histories_match = history_utils._check_histories(this.history, other.history)
 
         this.history += history_update_string
         if not histories_match:
             if verbose_history:
                 this.history += " Next object history follows. " + other.history
             else:
-                extra_history = uvutils._combine_history_addition(
+                extra_history = history_utils._combine_history_addition(
                     this.history, other.history
                 )
                 if extra_history is not None:
@@ -4906,7 +4914,7 @@
         if self.history is None:
             self.history = self.pyradiosky_version_str
         else:
-            if not uvutils._check_history_version(
+            if not history_utils._check_history_version(
                 self.history, self.pyradiosky_version_str
             ):
                 self.history += self.pyradiosky_version_str

tests/test_skymodel.py

@@ -13,12 +13,13 @@
 import pytest
 
 try:
+    import pyuvdata.utils.history as history_utils
     from pyuvdata.testing import check_warnings
 except ImportError:
     # this can be removed once we require pyuvdata >= v3.0
     from pyuvdata.tests import check_warnings
+    import pyuvdata.utils as history_utils
 
-import pyuvdata.utils as uvutils
 import scipy.io
 from astropy import units
 from astropy.coordinates import (
@@ -1628,7 +1629,7 @@ def test_concat(comp_type, spec_type, healpix_disk_new):
         + " Combined skymodels along the component axis using pyradiosky."
         + " Combined skymodels along the component axis using pyradiosky."
     )
-    assert uvutils._check_histories(skyobj_new.history, expected_history)
+    assert history_utils._check_histories(skyobj_new.history, expected_history)
 
     skyobj_new.history = skyobj_full.history
     assert skyobj_new == skyobj_full
@@ -1650,7 +1651,7 @@ def test_concat(comp_type, spec_type, healpix_disk_new):
     skyobj_new = skyobj1.concat(skyobj2, inplace=False, run_check=False)
     skyobj_new.concat(skyobj3)
     assert skyobj_new.history != skyobj_full.history
-    assert uvutils._check_histories(skyobj_new.history, expected_history)
+    assert history_utils._check_histories(skyobj_new.history, expected_history)
 
     skyobj_new = skyobj1.concat(skyobj2, inplace=False, verbose_history=True)
     skyobj_new.concat(skyobj3, verbose_history=True)
@@ -1665,7 +1666,7 @@ def test_concat(comp_type, spec_type, healpix_disk_new):
         + "Next object history follows. "
         + skyobj3.history
     )
-    assert uvutils._check_histories(skyobj_new.history, expected_history)
+    assert history_utils._check_histories(skyobj_new.history, expected_history)
 
 
 @pytest.mark.parametrize(
@@ -2135,12 +2136,12 @@ def test_flux_source_cuts():
     expected_history2 = (
         skyobj.history + "  Downselected to specific components using pyradiosky."
     )
-    assert uvutils._check_histories(skyobj2.history, expected_history2)
+    assert history_utils._check_histories(skyobj2.history, expected_history2)
 
     expected_history3 = (
         skyobj.history + "  Downselected to specific components using pyradiosky."
     )
-    assert uvutils._check_histories(skyobj3.history, expected_history3)
+    assert history_utils._check_histories(skyobj3.history, expected_history3)
 
     skyobj2.history = skyobj3.history
 
@@ -3073,7 +3074,7 @@ def test_point_catalog_reader():
     with open(catfile, "r") as fileobj:
         header = fileobj.readline()
     header = [h.strip() for h in header.split()]
-    dt = np.format_parser(
+    dt = np.rec.format_parser(
         ["U10", "f8", "f8", "f8", "f8"],
         ["source_id", "ra_j2000", "dec_j2000", "flux_density", "frequency"],
         header,
@@ -3433,7 +3434,7 @@ def test_at_frequencies_interp_errors(mock_point_skies):
     ):
         sky.at_frequencies(sky.freq_array - 10 * units.Hz)
 
-    sky.stokes[0, 0, 0] = np.NaN
+    sky.stokes[0, 0, 0] = np.nan
     with pytest.raises(ValueError, match="nan_handling must be one of "):
         sky.at_frequencies(sky.freq_array, nan_handling="foo")
 
@@ -3465,14 +3466,14 @@ def test_at_frequencies_nan_handling(nan_handling):
 
     skyobj2 = skyobj.copy()
     # add some NaNs. These exist in full GLEAM catalog but not in our small test file
-    skyobj2.stokes[0, 0:2, 0] = np.NaN  # no low freq support
-    skyobj2.stokes[0, 10:11, 1] = np.NaN  # missing freqs in middle
-    skyobj2.stokes[0, -2:, 2] = np.NaN  # no high freq support
-    skyobj2.stokes[0, :, 3] = np.NaN  # all NaNs
-    skyobj2.stokes[0, 1:-2, 4] = np.NaN  # only 2 good freqs
-    skyobj2.stokes[0, 0, 5] = np.NaN  # no low or high frequency support
-    skyobj2.stokes[0, -1, 5] = np.NaN  # no low or high frequency support
-    skyobj2.stokes[0, 1:, 6] = np.NaN  # only 1 good freqs
+    skyobj2.stokes[0, 0:2, 0] = np.nan  # no low freq support
+    skyobj2.stokes[0, 10:11, 1] = np.nan  # missing freqs in middle
+    skyobj2.stokes[0, -2:, 2] = np.nan  # no high freq support
+    skyobj2.stokes[0, :, 3] = np.nan  # all NaNs
+    skyobj2.stokes[0, 1:-2, 4] = np.nan  # only 2 good freqs
+    skyobj2.stokes[0, 0, 5] = np.nan  # no low or high frequency support
+    skyobj2.stokes[0, -1, 5] = np.nan  # no low or high frequency support
+    skyobj2.stokes[0, 1:, 6] = np.nan  # only 1 good freqs
 
     message = ["Some stokes values are NaNs."]
     if nan_handling == "propagate":
@@ -3624,7 +3625,7 @@ def test_at_frequencies_nan_handling_allsrc(nan_handling):
 
     skyobj2 = skyobj.copy()
     # add some NaNs to all sources
-    skyobj2.stokes[0, 10:11, :] = np.NaN
+    skyobj2.stokes[0, 10:11, :] = np.nan
     message = ["Some stokes values are NaNs."]
     if nan_handling == "propagate":
         message[
@@ -3866,7 +3867,7 @@ def test_skyh5_backwards_compatibility_healpix(healpix_disk_new, tmpdir):
 
     with h5py.File(testfile, "r+") as h5f:
         del h5f["/Header/hpx_frame"]
-        h5f["/Header/hpx_frame"] = np.string_(sky.hpx_frame.name)
+        h5f["/Header/hpx_frame"] = np.bytes_(sky.hpx_frame.name)
 
     sky2 = SkyModel.from_file(testfile)
     assert sky == sky2