test cleanup and improvements

pyuvsim/analyticbeam.py

@@ -176,7 +176,9 @@ def interp(
             interp_basis_vector = None
         elif self.type == 'gaussian':
             if (self.diameter is None) and (self.sigma is None):
-                raise ValueError("Dish diameter needed for gaussian beam -- units: meters")
+                raise ValueError(
+                    "Antenna diameter (meters) or sigma (radians) needed for gaussian beams."
+                )
             interp_data = np.zeros((2, 2, freq_array.size, az_array.size), dtype=float)
             # gaussian beam only depends on Zenith Angle (symmetric is azimuth)
             # standard deviation of sigma is referring to the standard deviation of e-field beam!
@@ -191,7 +193,7 @@ def interp(
             interp_basis_vector = None
         elif self.type == 'airy':
             if self.diameter is None:
-                raise ValueError("Dish diameter needed for airy beam -- units: meters")
+                raise ValueError("Antenna diameter needed for airy beam -- units: meters")
             interp_data = np.zeros((2, 2, freq_array.size, az_array.size), dtype=float)
             za_grid, f_grid = np.meshgrid(za_array, freq_array)
             xvals = self.diameter / 2. * np.sin(za_grid) * 2. * np.pi * f_grid / c_ms

pyuvsim/antenna.py

@@ -147,7 +147,6 @@ def get_beam_jones(
         jones_matrix = np.zeros((2, 2, Ncomponents), dtype=complex)
 
         # first axis is feed, second axis is theta, phi (opposite order of beam!)
-        print(interp_data.shape)
         jones_matrix[0, 0] = interp_data[1, 0, 0, :]
         jones_matrix[1, 1] = interp_data[0, 1, 0, :]
         jones_matrix[0, 1] = interp_data[0, 0, 0, :]

pyuvsim/data/test_config/28m_triangle_10time_10chan.yaml

@@ -10,4 +10,4 @@ beam_paths:
     type: airy
     diameter: 14.6
 telescope_location: (-30.721527777777847, 21.428305555555557, 1073.0000000046566)
-telescope_name: HERA
+telescope_name: Triangle

pyuvsim/data/test_config/28m_triangle_10time_10chan_gaussnoshape.yaml

@@ -8,4 +8,4 @@ beam_paths:
   3:
     type: gaussian
 telescope_location: (-30.721527777777847, 21.428305555555557, 1073.0000000046566)
-telescope_name: HERA
+telescope_name: Triangle

pyuvsim/data/test_config/28m_triangle_10time_10chan_nodiameter.yaml

@@ -9,4 +9,4 @@ beam_paths:
   3:
     type: airy
 telescope_location: (-30.721527777777847, 21.428305555555557, 1073.0000000046566)
-telescope_name: HERA
+telescope_name: Triangle

pyuvsim/data/test_config/28m_triangle_10time_10chan_nofile.yaml

@@ -10,4 +10,4 @@ beam_paths:
     type: airy
     diameter: 14.6
 telescope_location: (-30.721527777777847, 21.428305555555557, 1073.0000000046566)
-telescope_name: HERA
+telescope_name: Triangle

pyuvsim/profiling.py

@@ -76,7 +76,7 @@ def set_profiler(func_list=default_profile_funcs, rank=0, outfile_prefix='time_p
         return
 
     prof = LineProfiler()
-    if mpi is None or prof is None:  # pragma: no cover
+    if mpi is None or prof is None:
         raise ImportError("You need mpi4py and line_profiler to use the "
                           "profiling module. Install them both by running pip "
                           "install pyuvsim[all].")

pyuvsim/simsetup.py

@@ -856,16 +856,16 @@ def initialize_catalog_from_params(
 
     Returns
     -------
-    skydata: :class:`pyradiosky.SkyModel`
+    sky: :class:`pyradiosky.SkyModel`
         Source catalog filled with data.
     source_list_name: str
         Catalog identifier for metadata. Only returned if return_catname is True.
 
     """
     if return_catname is None:
         warnings.warn(
-            "The return_catname parameter currently defaults to True, but starting in"
-            "version 1.4 it will default to False.",
+            "The return_catname parameter currently defaults to True, but "
+            "starting in version 1.4 it will default to False.",
             DeprecationWarning
         )
         return_catname = True
@@ -1218,12 +1218,13 @@ def parse_telescope_params(tele_params, config_path='', freq_range=None, force_b
     if 'array_layout' not in tele_params:
         raise KeyError('array_layout must be provided.')
     array_layout = tele_params.pop('array_layout')
+    assert isinstance(array_layout, (str, dict)), "array_layout must be a string or a dict"
     if isinstance(array_layout, str):
         # Interpet as file path to layout csv file.
         layout_csv = array_layout
         # if array layout is a str, parse it as .csv filepath
         if isinstance(layout_csv, str):
-            if not os.path.exists(layout_csv):
+            if not os.path.exists(layout_csv) and isinstance(config_path, str):
                 layout_csv = os.path.join(config_path, layout_csv)
                 if not os.path.exists(layout_csv):
                     raise ValueError(
@@ -2015,9 +2016,16 @@ def initialize_uvdata_from_keywords(
     arrfile = antenna_layout_filepath is not None
     outfile = output_layout_filename is not None
 
-    if write_files:
+    if array_layout is None and antenna_layout_filepath is None:
+        raise ValueError(
+            "Either array_layout or antenna_layout_filepath must be passed."
+        )
+
+    if array_layout is None or isinstance(array_layout, str) or write_files:
         if path_out is None:
             path_out = '.'
+
+    if write_files:
         if not outfile:
             if not arrfile:
                 output_layout_filename = 'antenna_layout.csv'
@@ -2057,7 +2065,7 @@ def initialize_uvdata_from_keywords(
             )
 
     if array_layout is None:
-        if outfile:
+        if write_files and output_layout_filename is not None:
             array_layout = output_layout_filename
         else:
             array_layout = antenna_layout_filepath

pyuvsim/tests/test_analyticbeam.py

@@ -3,6 +3,7 @@
 # Licensed under the 3-clause BSD License
 
 import os
+import re
 
 import numpy as np
 import pytest
@@ -48,13 +49,13 @@ def test_uniform_beam(heratext_posfreq):
     nsrcs = az_vals.size
     n_freqs = freqs.size
 
-    interpolated_beam, interp_basis_vector = beam.interp(
+    interpolated_beam, _ = beam.interp(
         az_array=az_vals, za_array=za_vals, freq_array=freqs
     )
     expected_data = np.zeros((2, 2, n_freqs, nsrcs), dtype=float)
     expected_data[1, 0, :, :] = 1
     expected_data[0, 1, :, :] = 1
-    assert np.allclose(interpolated_beam, expected_data)
+    np.testing.assert_allclose(interpolated_beam, expected_data)
 
 
 def test_airy_beam_values(heratext_posfreq):
@@ -64,7 +65,7 @@ def test_airy_beam_values(heratext_posfreq):
 
     az_vals, za_vals, freq_vals = heratext_posfreq
 
-    interpolated_beam, interp_basis_vector = beam.interp(
+    interpolated_beam, _ = beam.interp(
         az_array=az_vals, za_array=za_vals, freq_array=freq_vals
     )
 
@@ -79,7 +80,7 @@ def test_airy_beam_values(heratext_posfreq):
     expected_data[1, 0, :, :] = airy_values
     expected_data[0, 1, :, :] = airy_values
 
-    assert np.allclose(interpolated_beam, expected_data)
+    np.testing.assert_allclose(interpolated_beam, expected_data)
 
 
 def test_interp_errors(heratext_posfreq):
@@ -164,7 +165,7 @@ def test_achromatic_gaussian_beam(heratext_posfreq):
     expected_data[1, 0, :, :] = gaussian_vals
     expected_data[0, 1, :, :] = gaussian_vals
 
-    assert np.allclose(interpolated_beam, expected_data)
+    np.testing.assert_allclose(interpolated_beam, expected_data)
 
 
 @pytest.mark.filterwarnings("ignore:UVW orientation appears to be flipped")
@@ -186,7 +187,7 @@ def test_gaussbeam_values():
 
     time = Time(hera_uv.time_array[0], scale='utc', format='jd')
 
-    catalog, mock_keywords = pyuvsim.create_mock_catalog(
+    catalog, _ = pyuvsim.create_mock_catalog(
         time=time, arrangement='long-line', Nsrcs=41, min_alt=80., array_location=array_location
     )
 
@@ -237,16 +238,11 @@ def test_chromatic_gaussian():
     az = np.zeros(Npix)
     za = np.linspace(0, np.pi / 2., Npix)
 
-    # Error if trying to define chromatic beam without a reference frequency
-    with pytest.raises(ValueError,
-                       match='ref_freq must be set for nonzero gaussian beam spectral index'):
-        pyuvsim.AnalyticBeam('gaussian', sigma=sigma, spectral_index=alpha)
-
-    A = pyuvsim.AnalyticBeam('gaussian', sigma=sigma, ref_freq=freqs[0], spectral_index=alpha)
+    gauss = pyuvsim.AnalyticBeam('gaussian', sigma=sigma, ref_freq=freqs[0], spectral_index=alpha)
 
     # Get the widths at each frequency.
 
-    vals, _ = A.interp(az, za, freqs)
+    vals, _ = gauss.interp(az, za, freqs)
 
     vals = vals[0, 1]
 
@@ -256,6 +252,13 @@ def test_chromatic_gaussian():
         assert np.isclose(sig_f, 2 * hwhm / 2.355, atol=1e-3)
 
 
+def test_chromatic_gaussian_error():
+    # Error if trying to define chromatic beam without a reference frequency
+    with pytest.raises(ValueError,
+                       match='ref_freq must be set for nonzero gaussian beam spectral index'):
+        pyuvsim.AnalyticBeam('gaussian', sigma=np.radians(15.0), spectral_index=-1.5)
+
+
 def test_power_analytic_beam():
     # Check that power beam evaluation matches electric field amp**2 for analytic beams.
     freqs = np.arange(120e6, 160e6, 4e6)
@@ -271,12 +274,7 @@ def test_power_analytic_beam():
         pb.efield_to_power()
         evals = eb.interp(az, za, freqs)[0][0, 1]
         pvals = pb.interp(az, za, freqs)[0][0, 0]
-        assert np.allclose(evals**2, pvals)
-
-    # Ensure uniform beam works
-    pb = pyuvsim.AnalyticBeam('uniform')
-    pb.efield_to_power()
-    pb.interp(az, za, freqs)
+        np.testing.assert_allclose(evals**2, pvals)
 
 
 def test_comparison():
@@ -292,25 +290,39 @@ def test_comparison():
     assert beam2 != beam1
 
 
-def test_beamerrs():
+def test_beam_init_errs():
     """
     Error cases.
     """
     with pytest.raises(ValueError, match='type not recognized'):
         pyuvsim.AnalyticBeam('unsupported_type')
 
-    beam = pyuvsim.AnalyticBeam('gaussian')
+
+@pytest.mark.parametrize(
+    ("beam_type", "error_msg"),
+    [
+        (
+            "gaussian",
+            re.escape(
+                "Antenna diameter (meters) or sigma (radians) needed for gaussian beams."
+            ),
+        ),
+        ("airy", "Antenna diameter needed for airy beam"),
+        ("noninterpolable", "no interp for this type: noninterpolable"),
+    ]
+)
+def test_beam_interp_errs(beam_type, error_msg):
+    if beam_type == "noninterpolable":
+        beam = pyuvsim.AnalyticBeam("uniform")
+        beam.type = "noninterpolable"
+    else:
+        beam = pyuvsim.AnalyticBeam(beam_type)
     az, za = np.random.uniform(0.0, np.pi, (2, 5))
     freq_arr = np.linspace(1e8, 1.5e8, 10)
-    with pytest.raises(ValueError, match='Dish diameter needed for gaussian beam'):
-        beam.interp(az, za, freq_arr)
-
-    beam.type = 'airy'
-    with pytest.raises(ValueError, match='Dish diameter needed for airy beam'):
-        beam.interp(az, za, freq_arr)
-
-    beam.type = 'noninterpolable'
-    with pytest.raises(ValueError, match='no interp for this type: noninterpolable'):
+    with pytest.raises(
+        ValueError,
+        match=error_msg
+    ):
         beam.interp(az, za, freq_arr)
 
 

pyuvsim/tests/test_antenna.py

@@ -1,6 +1,7 @@
 # -*- mode: python; coding: utf-8 -*
 # Copyright (c) 2021 Radio Astronomy Software Group
 # Licensed under the 3-clause BSD License
+import copy
 import os
 
 import numpy as np
@@ -47,7 +48,38 @@ def test_jones_set_spline(cst_beam, hera_loc):
     altaz[:, 0] = alts.flatten()
     altaz[:, 1] = azs.flatten()
 
-    antenna.get_beam_jones(array, altaz, 150e6, interpolation_function='az_za_simple')
+    jones_matrix = antenna.get_beam_jones(
+        array, altaz, 150e6, interpolation_function='az_za_simple'
+    )
+
+    # These are just values from a run, so this just tests for unexpected changes.
+    expected_jones = np.array(
+        [
+            [
+                [
+                    -4.57061296e-04 - 3.88626249e-04j,
+                    -7.28285993e-05 - 1.45479743e-04j,
+                    -7.28285993e-05 - 1.45479743e-04j
+                ], [
+                    -3.35886569e-02 - 1.83636844e-02j,
+                    -3.36205621e-02 - 1.84105336e-02j,
+                    -3.36205621e-02 - 1.84105336e-02j
+                ],
+            ], [
+                [
+                    -1.04000784e-02 - 1.11629186e-02j,
+                    -1.03973090e-02 - 1.11516998e-02j,
+                    -1.03973090e-02 - 1.11516998e-02j
+                ], [
+                    5.32870283e-04 + 1.16831373e-04j,
+                    1.26946128e-06 - 1.22843330e-06j,
+                    1.26946128e-06 - 1.22843330e-06j
+                ],
+            ],
+        ]
+    )
+
+    np.testing.assert_allclose(expected_jones, jones_matrix)
 
 
 def test_jones_set_interp(cst_beam, hera_loc):
@@ -102,3 +134,19 @@ def test_set_interps(cst_beam, hera_loc):
 
     if interp_function_attr:
         assert beam.interpolation_function == 'az_za_simple'
+
+
+def test_ant_comparison():
+    antenna1 = pyuvsim.Antenna('ant1', 1, np.array([0, 10, 0]), 1)
+    antenna2 = pyuvsim.Antenna('ant2', 2, np.array([0, 20, 0]), 1)
+
+    ant1_copy = copy.deepcopy(antenna1)
+
+    assert antenna1 < antenna2
+    assert antenna1 <= antenna2
+    assert antenna1 <= antenna1
+    assert antenna1 == ant1_copy
+
+    assert antenna2 > antenna1
+    assert antenna2 >= antenna2
+    assert antenna1 >= antenna1

pyuvsim/tests/test_baseline.py

@@ -0,0 +1,27 @@
+# -*- mode: python; coding: utf-8 -*
+# Copyright (c) 2024 Radio Astronomy Software Group
+# Licensed under the 3-clause BSD License
+import copy
+
+import numpy as np
+
+import pyuvsim
+
+
+def test_baseline_comparison():
+    antenna1 = pyuvsim.Antenna('ant1', 1, np.array([0, 10, 0]), 1)
+    antenna2 = pyuvsim.Antenna('ant2', 2, np.array([0, 20, 0]), 1)
+
+    baseline12 = pyuvsim.Baseline(antenna1, antenna2)
+    baseline21 = pyuvsim.Baseline(antenna2, antenna1)
+
+    bl12_copy = copy.deepcopy(baseline12)
+
+    assert baseline12 < baseline21
+    assert baseline12 <= baseline21
+    assert baseline12 <= baseline12
+    assert baseline12 == bl12_copy
+
+    assert baseline21 > baseline12
+    assert baseline21 >= baseline21
+    assert baseline21 >= baseline12