Merge pull request #226 from HERA-Team/pypi-release

maint: remove all git repo deps

CHANGELOG.rst

@@ -5,15 +5,20 @@ Changelog
 dev-version
 ===========
 
+v2.3.4 [2022.06.08]
+===================
+
 Added
 -----
 - ``NotImplementedError`` raised when trying to simulate noise using an interpolated
   sky temperature and phase-wrapped LSTs.
+- More comparison tests of pyuvsim wrapper.
 
 Fixed
 -----
 - Inferred integration time in ``ThermalNoise`` when phase-wrapped LSTs are used.
-- Added **kwargs to ``PolyBeam.interp`` method to match UVBeam.
+- Added ``**kwargs`` to ``PolyBeam.interp`` method to match UVBeam.
+- healvis wrapper properly sets cross-pol visibilities to zero.
 
 Changed
 -------

ci/tests.yaml

@@ -24,11 +24,11 @@ dependencies:
   - git
   - pip:
     - cached-property
-    - pyuvsim[sim]>=1.2,<1.4
+    - pyuvsim[sim]>=1.2
     - vis_cpu>=0.2.2
     - deprecation
     - pyradiosky
-    - git+https://github.com/HERA-Team/uvtools.git
+    - uvtools
     - git+https://github.com/rasg-affiliates/healvis
-    - git+https://github.com/HERA-Team/hera_cal.git
-    - git+https://github.com/HERA-Team/baseline_dependent_averaging.git
+    - hera-calibration
+    - bda

docs/conf.py

@@ -56,6 +56,8 @@
 autosectionlabel_prefix_document = True
 autosummary_generate = True
 
+autodoc_mock_imports = ["healvis"]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

hera_sim/adjustment.py

@@ -23,7 +23,7 @@
     HERA_CAL = True
 except (ModuleNotFoundError, FileNotFoundError) as err:  # pragma: no cover
     if err is ModuleNotFoundError:
-        missing = "hera_cal"
+        missing = "hera-calibration"
     else:
         missing = "git"
     warn(f"{missing} is not installed. Rephasing tool unavailable.")
@@ -669,7 +669,7 @@ def rephase_to_reference(
     """
     if not HERA_CAL:  # pragma: no cover
         raise NotImplementedError(
-            "You must have ``hera_cal`` installed to use this function."
+            "You must have ``hera-calibration`` installed to use this function."
         )
 
     # Convert target to a HERAData object.

hera_sim/tests/test_vis.py

@@ -11,7 +11,6 @@
 from hera_sim import io
 from hera_sim.visibilities import (
     VisCPU,
-    HealVis,
     VisibilitySimulation,
     ModelData,
     UVSim,
@@ -25,7 +24,14 @@
 import copy
 from pathlib import Path
 
-SIMULATORS = (HealVis, VisCPU, UVSim)
+SIMULATORS = (VisCPU, UVSim)
+
+try:
+    from hera_sim.visibilities import HealVis
+
+    SIMULATORS = SIMULATORS + (HealVis,)
+except ImportError:
+    pass
 
 if HAVE_GPU:
 
@@ -111,6 +117,7 @@ def sky_modelJD(uvdataJD):
 
 
 def test_healvis_beam(uvdata, sky_model):
+    pytest.importorskip("healvis")
     sim = VisibilitySimulation(
         simulator=HealVis(),
         data_model=ModelData(
@@ -126,6 +133,7 @@ def test_healvis_beam(uvdata, sky_model):
 
 def test_healvis_beam_obsparams(tmpdir):
     # Now try creating with an obsparam file
+    pytest.importorskip("healvis")
     direc = tmpdir.mkdir("test_healvis_beam")
 
     with open(direc.join("catalog.txt"), "w") as fl:
@@ -210,6 +218,7 @@ def uvdata2():
         array_layout={0: (0, 0, 0), 1: (1, 1, 0)},
         start_time=2456658.5,
         conjugation="ant1<ant2",
+        polarization_array=["xx", "yy", "xy", "yx"],
     )
 
 
@@ -468,6 +477,7 @@ def align_src_to_healpix(ra, dec, nside=2**4):
     return ra, dec
 
 
+@pytest.mark.parametrize("simulator", SIMULATORS[1:])
 @pytest.mark.parametrize(
     "sky_model, beam_model",
     [
@@ -478,22 +488,22 @@ def align_src_to_healpix(ra, dec, nside=2**4):
         (half_sky_model, [AnalyticBeam("airy", diameter=1.75)]),
     ],
 )
-def test_comparison(uvdata2, sky_model, beam_model):
-    cpu = VisCPU()
-    healvis = HealVis()
-
+def test_comparison(simulator, uvdata2, sky_model, beam_model):
     model_data = ModelData(
         uvdata=uvdata2, sky_model=sky_model(uvdata2), beams=beam_model
     )
 
-    viscpu = VisibilitySimulation(data_model=model_data, simulator=cpu).simulate()
+    v0 = VisibilitySimulation(
+        data_model=model_data, simulator=SIMULATORS[0](), n_side=2**4
+    ).simulate()
 
-    healvis = VisibilitySimulation(
-        data_model=model_data, simulator=healvis, n_side=2**4
+    v1 = VisibilitySimulation(
+        data_model=model_data, simulator=simulator(), n_side=2**4
     ).simulate()
 
-    assert viscpu.shape == healvis.shape
-    np.testing.assert_allclose(viscpu, healvis, rtol=0.05)
+    assert v0.shape == v1.shape
+
+    np.testing.assert_allclose(v0, v1, rtol=0.05)
 
 
 def test_vis_cpu_pol_gpu(uvdata_linear):
@@ -662,13 +672,15 @@ def test_str_uvdata(uvdata, sky_model, tmp_path):
 
 
 def test_bad_healvis_skymodel(sky_model):
+    pytest.importorskip("healvis")
     hv = HealVis()
     sky_model.stokes *= units.sr  # something stupid
     with pytest.raises(ValueError, match="not compatible with healvis"):
         hv.get_sky_model(sky_model)
 
 
 def test_mK_healvis_skymodel(sky_model):
+    pytest.importorskip("healvis")
     hv = HealVis()
     sky_model.stokes = sky_model.stokes.value * units.mK
     sky_model.nside = 2**3

hera_sim/visibilities/healvis_wrapper.py

@@ -45,6 +45,14 @@ def __init__(self, fov=180, nprocesses=1, sky_ref_chan=0):
         if not HAVE_HEALVIS:
             raise ImportError("to use the healvis wrapper, you must install healvis!")
 
+        warnings.warn(
+            (
+                "The healvis package is deprecated. Please use pyuvsim instead. "
+                "The healvis wrapper will be removed from hera_sim in version 4",
+            ),
+            category=DeprecationWarning,
+        )
+
         self.fov = fov
         self._nprocs = nprocesses
         self._sky_ref_chan = sky_ref_chan
@@ -155,9 +163,15 @@ def simulate(self, data_model: ModelData):
 
         # Simulate the visibilities for each polarization.
         for pol in data_model.uvdata.get_pols():
-            visibility, _, baselines = obs.make_visibilities(
-                sky, Nprocs=self._nprocs, beam_pol=pol
-            )  # Shape (Nblts, Nskies, Nfreqs)
+            if pol in ["xx", "yy"]:
+                visibility, _, baselines = obs.make_visibilities(
+                    sky, Nprocs=self._nprocs, beam_pol=pol
+                )  # Shape (Nblts, Nskies, Nfreqs)
+            else:
+                # healvis doesn't support polarization
+                visibility = np.zeros(
+                    (data_model.uvdata.Nblts, 1, data_model.uvdata.Nfreqs)
+                )
 
             # AnalyticBeams do not use polarization at all in healvis, and are
             # equivalent to "pI" polarization. To match our definition of linear pols

setup.cfg

@@ -54,32 +54,31 @@ exclude =
 
 [options.extras_require]
 bda =
-    bda @ git+https://github.com/HERA-Team/baseline_dependent_averaging
+    bda
 gpu =
-    hera_gpu @ git+https://github.com/hera-team/hera_gpu
+    pycuda
+    scikit-cuda
 cal =
-    hera_cal @ git+https://github.com/hera-team/hera_cal
+    hera-calibration
 docs =
     sphinx>=1.8
     nbsphinx
     ipython
     sphinx_autorun
     numpydoc>=0.8
     nbsphinx
-    vis_cpu>=0.4.1<1.0
-    healvis @ git+https://github.com/RASG-Affiliates/healvis
+    vis_cpu>=0.4.1
     pyradiosky>=0.1.2
 tests =
     coverage>=4.5.1
     pytest>=3.5.1
     pytest-cov>=2.5.1
     pre-commit
     matplotlib>=3.4.2
-    uvtools @ git+https://github.com/HERA-Team/uvtools.git
-    hera_cal @ git+https://github.com/hera-team/hera_cal
-    healvis @ git+https://github.com/rasg-affiliates/healvis
-    bda @ git+https://github.com/HERA-Team/baseline_dependent_averaging.git
-    vis_cpu>=0.4.1<1.0
+    uvtools
+    hera-calibration
+    bda
+    vis_cpu>=0.4.1
 dev =
     sphinx>=1.8
     numpydoc>=0.8.0
@@ -89,14 +88,12 @@ dev =
     pytest>=3.5.1
     pytest-cov>=2.5.1
     pre-commit
-    uvtools @ git+https://github.com/HERA-Team/uvtools.git
-    healvis @ git+https://github.com/rasg-affiliates/healvis
-    hera_cal @ git+https://github.com/hera-team/hera_cal
-    bda @ git+https://github.com/HERA-Team/baseline_dependent_averaging.git
-    vis_cpu>=0.4.1<1.0
+    uvtools
+    hera-calibration
+    bda
+    vis_cpu>=0.4.1
 vis =
-    vis_cpu>=0.4.1<1.0
-    healvis @ git+https://github.com/RASG-Affiliates/healvis
+    vis_cpu>=0.4.1
     pyradiosky>=0.1.2
     mpi4py