flake8: fix B028 errors

.flake8

@@ -1,14 +1,14 @@
 [flake8]
 ignore =
     # No space before colon
-    E203, 
+    E203,
     W503,
     # Ignore using dict() function.
     C408,
     # Missing docstring in __init__ (we do it in the class)
     D107,
     # "First line should be in imperative mood" -- this doesn't work for properties, see https://github.com/PyCQA/pydocstyle/issues/301
-    D401, 
+    D401,
     # allow method names to be the same as python builtins
     A003,
     # inline strong start-string without end-string. This is OK in the case of **kwargs in parameters.

CHANGELOG.rst

@@ -5,6 +5,14 @@ Changelog
 dev-version
 ===========
 
+v3.1.1 [2023.02.23]
+===================
+
+Changed
+-------
+- Coupling matrix calculation in :class:`~.sigchain.MutualCoupling` has been updated
+  to correctly calculate the coupling coefficients from the provided E-field beam.
+
 v3.1.0 [2023.01.17]
 ===================
 

hera_sim/__yaml_constructors.py

@@ -41,7 +41,10 @@ def astropy_unit_constructor(loader, node):
     if value is None:
         return None
     elif units is None:
-        warnings.warn("You have not specified the units for this item. Returning None.")
+        warnings.warn(
+            "You have not specified the units for this item. Returning None.",
+            stacklevel=2,
+        )
         return None
     else:
         try:

hera_sim/cli_utils.py

@@ -137,7 +137,8 @@ def write_calfits(
         if sim_x_orientation is None:
             warnings.warn(
                 "x_orientation not specified in simulation object."
-                "Assuming that the x-direction points north."
+                "Assuming that the x-direction points north.",
+                stacklevel=1,
             )
         else:
             x_orientation = sim_x_orientation

hera_sim/defaults.py

@@ -295,7 +295,7 @@ def _check_config(self):
                 "Please check your configuration, as only the last "
                 "value specified for each parameter will be used."
             )
-            warnings.warn(warning)
+            warnings.warn(warning, stacklevel=1)
 
     def _handler(self, func, *args, **kwargs):
         """Decorator for applying new function parameter defaults."""

hera_sim/interpolators.py

@@ -181,7 +181,8 @@ def _interpolator(self):
             warnings.warn(
                 "The provided LSTs do not sufficiently cover [0, 2*pi). "
                 "The interpolated sky temperature may have unexpected behavior "
-                "near 0 and 2*pi."
+                "near 0 and 2*pi.",
+                stacklevel=1,
             )
 
         lsts = np.concatenate(

hera_sim/io.py

@@ -69,7 +69,8 @@ def empty_uvdata(
             "deprecated and will be removed in the future. Please "
             "update your code to use the Nfreqs, Ntimes, and "
             "array_layout parameters instead.",
-            DeprecationWarning,
+            category=DeprecationWarning,
+            stacklevel=2,
         )
 
     # for backwards compatability

hera_sim/noise.py

@@ -243,5 +243,9 @@ def white_noise(*args, **kwargs):
 
     Deprecated. Use ``utils.gen_white_noise`` instead.
     """
-    warnings.warn("white_noise is being deprecated. Use utils.gen_white_noise instead.")
+    warnings.warn(
+        "white_noise is being deprecated. Use utils.gen_white_noise instead.",
+        category=DeprecationWarning,
+        stacklevel=2,
+    )
     return utils.gen_white_noise(*args, **kwargs)

hera_sim/rfi.py

@@ -164,7 +164,10 @@ def __call__(self, lsts, freqs, **kwargs):
         rfi = np.zeros((lsts.size, freqs.size), dtype=complex)
 
         if stations is None:
-            warnings.warn("You did not specify any stations to simulate.")
+            warnings.warn(
+                "You did not specify any stations to simulate.",
+                stacklevel=2,
+            )
             return rfi
         elif isinstance(stations, (str, Path)):
             # assume that it's a path to a npy file
@@ -410,7 +413,8 @@ def __call__(self, lsts, freqs, **kwargs):
             warnings.warn(
                 "The DTV band does not overlap with any of the passed "
                 "frequencies. Please ensure that you are passing the "
-                "correct set of parameters."
+                "correct set of parameters.",
+                stacklevel=2,
             )
 
         # define an iterator, just to keep things neat

hera_sim/simulate.py

@@ -289,7 +289,8 @@ def add(
         if seed is None and add_vis:
             warnings.warn(
                 "You have not specified how to seed the random state. "
-                "This effect might not be exactly recoverable."
+                "This effect might not be exactly recoverable.",
+                stacklevel=2,
             )
 
         # Simulate the effect by iterating over baselines and polarizations.
@@ -1007,7 +1008,8 @@ def _iteratively_apply(
             warnings.warn(
                 "You have chosen to neither add nor return the effect "
                 "you are trying to simulate, so nothing will be "
-                f"computed. This warning was raised for the model: {model}"
+                f"computed. This warning was raised for the model: {model}",
+                stacklevel=2,
             )
             return
 
@@ -1030,7 +1032,8 @@ def _iteratively_apply(
                 "You are attempting to compute a component but have "
                 "not specified an ``is_multiplicative`` attribute for "
                 "the component. The component will be added under "
-                "the assumption that it is *not* multiplicative."
+                "the assumption that it is *not* multiplicative.",
+                stacklevel=2,
             )
             is_multiplicative = False
 
@@ -1487,14 +1490,14 @@ def _sanity_check(self, model):
         if is_multiplicative and not has_data:
             warnings.warn(
                 "You are trying to compute a multiplicative "
-                "effect, but no visibilities have been "
-                "simulated yet."
+                "effect, but no visibilities have been simulated yet.",
+                stacklevel=1,
             )
         elif not is_multiplicative and contains_multiplicative_effect:
             warnings.warn(
                 "You are adding visibilities to a data array "
-                "*after* multiplicative effects have been "
-                "introduced."
+                "*after* multiplicative effects have been introduced.",
+                stacklevel=1,
             )
 
     def _update_history(self, model, **kwargs):

hera_sim/utils.py

@@ -471,8 +471,8 @@ def Jy2T(freqs, omega_p):
     Deprecated in v1.0.0. Will be removed in v1.1.0
     """
     warnings.warn(
-        "The function Jy2T has been renamed 'jansky_to_kelvin'. It will be removed in "
-        "v1.1."
+        "This function has been deprecated. Please use `jansky_to_kelvin` instead.",
+        stacklevel=1,
     )
     return jansky_to_kelvin(freqs, omega_p)
 

hera_sim/visibilities/healvis_wrapper.py

@@ -46,11 +46,10 @@ def __init__(self, fov=180, nprocesses=1, sky_ref_chan=0):
             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",
-            ),
+            "The healvis package is deprecated. Please use pyuvsim instead. "
+            "The healvis wrapper will be removed from hera_sim in version 4",
             category=DeprecationWarning,
+            stacklevel=2,
         )
 
         self.fov = fov
@@ -72,7 +71,8 @@ def validate(self, model_data: ModelData):
             warnings.warn(
                 "Using pyuvsim.AnalyticBeam for healvis is not really supported. "
                 "model_data.beams is being automatically modified to be a single "
-                "healvis.AnalyticBeam of the same type."
+                "healvis.AnalyticBeam of the same type.",
+                stacklevel=1,
             )
             old_args = model_data.beams[0].__dict__
 

hera_sim/visibilities/pyuvsim_wrapper.py

@@ -34,7 +34,8 @@ def simulate(self, data_model: ModelData):
             data_model.sky_model.name = np.array(data_model.sky_model.name)
 
         warnings.warn(
-            "UVSim requires time-ordered data. Ensuring that order in UVData..."
+            "UVSim requires time-ordered data. Ensuring that order in UVData...",
+            stacklevel=1,
         )
         data_model.uvdata.reorder_blts("time")
 
@@ -44,7 +45,8 @@ def simulate(self, data_model: ModelData):
         # at least check whether reordering is necessary once uvdata has that ability.
         if np.any(data_model.uvdata.polarization_array != np.array([-5, -6, -7, -8])):
             warnings.warn(
-                "In UVSim, polarization array must be in AIPS order. Reordering..."
+                "In UVSim, polarization array must be in AIPS order. Reordering...",
+                stacklevel=1,
             )
             data_model.uvdata.reorder_pols("AIPS")