From 883add6ebaa3be0b0cac05e9ac08787064132730 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Wed, 3 Apr 2024 14:05:32 +0200
Subject: [PATCH 01/13] fix: import blackmanharris from scipy.signal.windows

---
 hera_sim/sigchain.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hera_sim/sigchain.py b/hera_sim/sigchain.py
index 5774da86..f5f44b91 100644
--- a/hera_sim/sigchain.py
+++ b/hera_sim/sigchain.py
@@ -16,7 +16,7 @@
 from pyuvdata import UVBeam
 from pyuvsim import AnalyticBeam
 from scipy import stats
-from scipy.signal import blackmanharris
+from scipy.signal.windows import blackmanharris
 from typing import Callable
 
 from . import DATA_PATH, interpolators, utils

From 7b1b5cf492b19967afc3018a31e73a91857bc049 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Wed, 3 Apr 2024 14:31:40 +0200
Subject: [PATCH 02/13] refactor: fix some upcoming numpy 2 bugs

---
 hera_sim/cli_utils.py                               |  4 ++--
 .../tutorials_data/end_to_end/make_mock_catalog.py  |  7 +++++--
 hera_sim/foregrounds.py                             | 12 ++++++------
 hera_sim/interpolators.py                           |  4 ++--
 hera_sim/rfi.py                                     |  9 +++++----
 hera_sim/simulate.py                                | 12 ++++++------
 hera_sim/tests/test_simulator.py                    | 10 ++++------
 hera_sim/tests/test_utils.py                        |  4 ++--
 pyproject.toml                                      | 13 ++++++++++++-
 scripts/hera-sim-simulate.py                        |  2 +-
 10 files changed, 45 insertions(+), 32 deletions(-)

diff --git a/hera_sim/cli_utils.py b/hera_sim/cli_utils.py
index f1b95ed5..95181d66 100644
--- a/hera_sim/cli_utils.py
+++ b/hera_sim/cli_utils.py
@@ -61,7 +61,7 @@ def validate_config(config: dict):
         is not valid.
     """
     if config.get("defaults") is not None:
-        if type(config["defaults"]) is not str:
+        if not isinstance(config["defaults"], str):
             raise ValueError(
                 "Defaults in the CLI may only be specified using a string. "
                 "The string used may specify either a path to a configuration "
@@ -155,7 +155,7 @@ def write_calfits(
     # Update gain keys to conform to write_cal assumptions.
     # New Simulator gains have keys (ant, pol), so shouldn't need
     # special pre-processing.
-    if all(np.issctype(type(ant)) for ant in gains.keys()):
+    if all(issubclass(type(ant), np.generic) for ant in gains.keys()):
         # Old-style, single polarization assumption.
         gains = {(ant, "Jee"): gain for ant, gain in gains.items()}
 
diff --git a/hera_sim/data/tutorials_data/end_to_end/make_mock_catalog.py b/hera_sim/data/tutorials_data/end_to_end/make_mock_catalog.py
index 81d11705..ac568b65 100644
--- a/hera_sim/data/tutorials_data/end_to_end/make_mock_catalog.py
+++ b/hera_sim/data/tutorials_data/end_to_end/make_mock_catalog.py
@@ -18,9 +18,12 @@ def make_mock_catalog(
     sigma=5,
     index_low=-3,
     index_high=-1,
+    seed=None,
 ):
     """Generate and svae a mock point source catalog."""
     # Easiset to load the metadata this way.
+    rng = np.random.default_rng(seed)
+
     temp_uvdata = initialize_uvdata_from_params(str(obsparam_file))[0]
     center_time = np.mean(np.unique(temp_uvdata.time_array))
     ref_freq = np.mean(np.unique(temp_uvdata.freq_array))
@@ -38,11 +41,11 @@ def make_mock_catalog(
     decs = np.array([row[2] for row in sky_model_recarray])
 
     # Randomly assign fluxes (whether this is realistic or not).
-    ref_fluxes = np.random.lognormal(mean=1, sigma=sigma, size=len(ras))
+    ref_fluxes = rng.lognormal(mean=1, sigma=sigma, size=len(ras))
     # Don't include super bright sources.
     ref_fluxes[ref_fluxes > flux_cut] = 1 / ref_fluxes[ref_fluxes > flux_cut]
     # Assign spectral indices.
-    indices = np.random.uniform(low=index_low, high=index_high, size=len(ras))
+    indices = rng.uniform(low=index_low, high=index_high, size=len(ras))
 
     # Actually add in the spectral structure.
     freqs = np.unique(temp_uvdata.freq_array)
diff --git a/hera_sim/foregrounds.py b/hera_sim/foregrounds.py
index f8e54863..fdebad62 100644
--- a/hera_sim/foregrounds.py
+++ b/hera_sim/foregrounds.py
@@ -264,13 +264,13 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
         # get baseline length (it should already be in ns)
         bl_len_ns = np.linalg.norm(bl_vec)
 
+        rng = np.random.default_rng()
+
         # randomly generate source RAs
-        ras = np.random.uniform(0, 2 * np.pi, nsrcs)
+        ras = rng.uniform(0, 2 * np.pi, nsrcs)
 
         # draw spectral indices from normal distribution
-        spec_indices = np.random.normal(
-            spectral_index_mean, spectral_index_std, size=nsrcs
-        )
+        spec_indices = rng.normal(spectral_index_mean, spectral_index_std, size=nsrcs)
 
         # calculate beam width, hardcoded for HERA
         beam_width = (40 * 60) * (f0 / freqs) / units.sday.to("s") * 2 * np.pi
@@ -278,7 +278,7 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
         # draw flux densities from a power law
         alpha = beta + 1
         flux_densities = (
-            Smax**alpha + Smin**alpha * (1 - np.random.uniform(size=nsrcs))
+            Smax**alpha + Smin**alpha * (1 - rng.uniform(size=nsrcs))
         ) ** (1 / alpha)
 
         # initialize the visibility array
@@ -290,7 +290,7 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
             lst_ind = np.argmin(np.abs(utils.compute_ha(lsts, ra)))
 
             # slight offset in delay? why??
-            dtau = np.random.uniform(-1, 1) * 0.1 * bl_len_ns
+            dtau = rng.uniform(-1, 1) * 0.1 * bl_len_ns
 
             # fill in the corresponding region of the visibility array
             vis[lst_ind, :] += flux * (freqs / f0) ** index
diff --git a/hera_sim/interpolators.py b/hera_sim/interpolators.py
index 0ece1937..432e441a 100644
--- a/hera_sim/interpolators.py
+++ b/hera_sim/interpolators.py
@@ -316,8 +316,8 @@ def _check_format(self):
             )
             assert self._obj in self._data.keys() and "freqs" in self._data.keys(), (
                 "You've chosen to use an interp1d object for modeling the "
-                "{}. Please ensure that the `.npz` archive has the following "
-                "keys: 'freqs', '{}'".format(self._obj, self._obj)
+                f"{self._obj}. Please ensure that the `.npz` archive has the following "
+                f"keys: 'freqs', '{self._obj}'"
             )
         else:
             # we can relax this a bit and allow for users to also pass a npz
diff --git a/hera_sim/rfi.py b/hera_sim/rfi.py
index d800bf8a..a859232b 100644
--- a/hera_sim/rfi.py
+++ b/hera_sim/rfi.py
@@ -96,14 +96,15 @@ def __call__(self, lsts, freqs):
         ch2 = ch1 + 1 if self.f0 > freqs[ch1] else ch1 - 1
 
         # generate some random phases
-        phs1, phs2 = np.random.uniform(0, 2 * np.pi, size=2)
+        rng = np.random.default_rng()
+        phs1, phs2 = rng.uniform(0, 2 * np.pi, size=2)
 
         # find out when the station is broadcasting
         is_on = 0.999 * np.cos(lsts * u.sday.to("s") / self.timescale + phs1)
         is_on = is_on > (1 - 2 * self.duty_cycle)
 
         # generate a signal and filter it according to when it's on
-        signal = np.random.normal(self.strength, self.std, lsts.size)
+        signal = rng.normal(self.strength, self.std, lsts.size)
         signal = np.where(is_on, signal, 0) * np.exp(1j * phs2)
 
         # now add the signal to the rfi array
@@ -484,8 +485,8 @@ def _listify_params(self, bands, *args):
                     "values with the same length as the number of DTV "
                     "bands specified. For reference, the DTV bands you "
                     "specified have the following characteristics: \n"
-                    "f_min : {fmin} \nf_max : {fmax}\n N_bands : "
-                    "{Nchan}".format(fmin=bands[0], fmax=bands[-1], Nchan=Nchan)
+                    f"f_min : {bands[0]} \nf_max : {bands[-1]}\n N_bands : "
+                    f"{Nchan}"
                 )
 
             # everything should be in order now, so
diff --git a/hera_sim/simulate.py b/hera_sim/simulate.py
index 805e97f7..803f234a 100644
--- a/hera_sim/simulate.py
+++ b/hera_sim/simulate.py
@@ -727,7 +727,7 @@ def _apply_filter(vis_filter, ant1, ant2, pol):
                 return not pol == vis_filter[0]
             # Otherwise, assume that this specifies an antenna.
             else:
-                return not vis_filter[0] in (ant1, ant2)
+                return vis_filter[0] not in (ant1, ant2)
         elif len(vis_filter) == 2:
             # TODO: This will need to be updated when we support ant strings.
             # Three cases: two pols; an ant+pol; a baseline.
@@ -756,7 +756,7 @@ def _apply_filter(vis_filter, ant1, ant2, pol):
             for key in vis_filter:
                 if isinstance(key, str):
                     pols.append(key)
-                elif type(key) is int:
+                elif isinstance(key, int):
                     ants.append(key)
             # We want polarization and ant1 or ant2 in the filter.
             # This would be used in simulating e.g. a few feeds that have an
@@ -1228,7 +1228,7 @@ def _seed_rng(self, seed, model, ant1=None, ant2=None, pol=None):
         """
         if seed is None:
             return
-        if type(seed) is int:
+        if isinstance(seed, int):
             np.random.seed(seed)
             return seed
         if not isinstance(seed, str):
@@ -1390,7 +1390,7 @@ def _get_component(
         component: Union[str, type[SimulationComponent], SimulationComponent]
     ) -> Union[SimulationComponent, type[SimulationComponent]]:
         """Normalize a component to be either a class or instance."""
-        if np.issubclass_(component, SimulationComponent):
+        if issubclass(component, SimulationComponent):
             return component
         elif isinstance(component, str):
             try:
@@ -1435,7 +1435,7 @@ def _get_model_name(model):
         """Find out the (lowercase) name of a provided model."""
         if isinstance(model, str):
             return model.lower()
-        elif np.issubclass_(model, SimulationComponent):
+        elif issubclass(model, SimulationComponent):
             return model.__name__.lower()
         elif isinstance(model, SimulationComponent):
             return model.__class__.__name__.lower()
@@ -1472,7 +1472,7 @@ def _parse_key(self, key: Union[int, str, AntPair, AntPairPol]) -> AntPairPol:
                     "pair with a polarization string."
                 )
             if len(key) == 2:
-                if all(type(val) is int for val in key):
+                if all(isinstance(val, int) for val in key):
                     ant1, ant2 = key
                     pol = None
                 else:
diff --git a/hera_sim/tests/test_simulator.py b/hera_sim/tests/test_simulator.py
index 8f928bb7..aaa71223 100644
--- a/hera_sim/tests/test_simulator.py
+++ b/hera_sim/tests/test_simulator.py
@@ -418,10 +418,10 @@ def test_run_sim():
     # write something to it
     with open(tmp_sim_file, "w") as sim_file:
         sim_file.write(
-            """
+            f"""
             diffuse_foreground:
                 Tsky_mdl: !Tsky
-                    datafile: {}/HERA_Tsky_Reformatted.npz
+                    datafile: {DATA_PATH}/HERA_Tsky_Reformatted.npz
                     pol: yy
             pntsrc_foreground:
                 nsrcs: 500
@@ -436,16 +436,14 @@ def test_run_sim():
                 phs: 2.1123
             thermal_noise:
                 Tsky_mdl: !Tsky
-                    datafile: {}/HERA_Tsky_Reformatted.npz
+                    datafile: {DATA_PATH}/HERA_Tsky_Reformatted.npz
                     pol: xx
                 integration_time: 9.72
             rfi_scatter:
                 scatter_chance: 0.99
                 scatter_strength: 5.7
                 scatter_std: 2.2
-                """.format(
-                DATA_PATH, DATA_PATH
-            )
+                """
         )
     sim = create_sim(autos=True)
     sim.run_sim(tmp_sim_file)
diff --git a/hera_sim/tests/test_utils.py b/hera_sim/tests/test_utils.py
index 4ac51817..c00ad5f7 100644
--- a/hera_sim/tests/test_utils.py
+++ b/hera_sim/tests/test_utils.py
@@ -326,7 +326,7 @@ def test_use_pre_computed_filter(freqs, lsts, filter_type):
 @pytest.mark.parametrize("shape", [100, (100, 200)])
 def test_gen_white_noise_shape(shape):
     noise = utils.gen_white_noise(shape)
-    if type(shape) is int:
+    if isinstance(shape, int):
         shape = (shape,)
     assert noise.shape == shape
 
@@ -384,7 +384,7 @@ def test_Jy2T(freqs, omega_p):
 
 @pytest.mark.parametrize("obj", [1, (1, 2), "abc", np.array([13])])
 def test_listify(obj):
-    assert type(utils._listify(obj)) is list
+    assert isinstance(utils._listify(obj), list)
 
 
 @pytest.mark.parametrize("jit", [True, False])
diff --git a/pyproject.toml b/pyproject.toml
index fac1440f..8e595f40 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,6 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 88
-py36 = false
 exclude = '''
 /(
     \.eggs
@@ -21,3 +20,15 @@ exclude = '''
   | dist
 )/
 '''
+
+[tool.ruff]
+line-length = 88
+target-version = "py39"
+
+[tool.ruff.lint]
+select = [
+  "UP",   # pyupgrade
+  "E",    # pycodestyle
+  "W",    # pycodestyle warning
+  "NPY",  # numpy-specific rules
+]
diff --git a/scripts/hera-sim-simulate.py b/scripts/hera-sim-simulate.py
index d91e9136..2076114a 100644
--- a/scripts/hera-sim-simulate.py
+++ b/scripts/hera-sim-simulate.py
@@ -157,7 +157,7 @@
                 this_sim.data.data_array = data
             if bda_params:
                 this_sim.data = bda_tools.apply_bda(this_sim.data, **bda_params)
-            if type(data) is dict:
+            if isinstance(data, dict):
                 # The component is a gain-like term, so save as a calfits file.
                 ext = os.path.splitext(filename)[1]
                 if ext == "":

From 8b1b79d6be2c8e215e9b96c634445862a1208c19 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Wed, 3 Apr 2024 14:36:45 +0200
Subject: [PATCH 03/13] ci: add ruff check for npy

---
 .pre-commit-config.yaml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 360c3b90..d712b921 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -57,4 +57,12 @@ repos:
 - repo: https://github.com/asottile/setup-cfg-fmt
   rev: v2.5.0
   hooks:
-  - id: setup-cfg-fmt
\ No newline at end of file
+  - id: setup-cfg-fmt
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.4
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--fix]

From 80ab80a081387883799b331a51899d4de3196d3e Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Wed, 3 Apr 2024 16:33:53 +0200
Subject: [PATCH 04/13] fix: bugs in updating numpy stuff

---
 hera_sim/cli_utils.py               |  2 +-
 hera_sim/simulate.py                | 14 +++++++++-----
 hera_sim/visibilities/simulators.py | 14 ++++++++------
 3 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/hera_sim/cli_utils.py b/hera_sim/cli_utils.py
index 95181d66..1ea14a33 100644
--- a/hera_sim/cli_utils.py
+++ b/hera_sim/cli_utils.py
@@ -155,7 +155,7 @@ def write_calfits(
     # Update gain keys to conform to write_cal assumptions.
     # New Simulator gains have keys (ant, pol), so shouldn't need
     # special pre-processing.
-    if all(issubclass(type(ant), np.generic) for ant in gains.keys()):
+    if all(np.isscalar(ant) for ant in gains.keys()):
         # Old-style, single polarization assumption.
         gains = {(ant, "Jee"): gain for ant, gain in gains.items()}
 
diff --git a/hera_sim/simulate.py b/hera_sim/simulate.py
index 803f234a..e4ef5d3d 100644
--- a/hera_sim/simulate.py
+++ b/hera_sim/simulate.py
@@ -6,6 +6,7 @@
 :class:`Simulator`, please refer to the tutorials.
 """
 
+import contextlib
 import functools
 import inspect
 import numpy as np
@@ -1390,9 +1391,7 @@ def _get_component(
         component: Union[str, type[SimulationComponent], SimulationComponent]
     ) -> Union[SimulationComponent, type[SimulationComponent]]:
         """Normalize a component to be either a class or instance."""
-        if issubclass(component, SimulationComponent):
-            return component
-        elif isinstance(component, str):
+        if isinstance(component, str):
             try:
                 return get_model(component)
             except KeyError:
@@ -1403,6 +1402,9 @@ def _get_component(
         elif isinstance(component, SimulationComponent):
             return component
         else:
+            with contextlib.suppress(TypeError):
+                if issubclass(component, SimulationComponent):
+                    return component
             raise TypeError(
                 "The input type for the component was not understood. "
                 "Must be a string, or a class/instance of type 'SimulationComponent'. "
@@ -1435,11 +1437,13 @@ def _get_model_name(model):
         """Find out the (lowercase) name of a provided model."""
         if isinstance(model, str):
             return model.lower()
-        elif issubclass(model, SimulationComponent):
-            return model.__name__.lower()
         elif isinstance(model, SimulationComponent):
             return model.__class__.__name__.lower()
         else:
+            with contextlib.suppress(TypeError):
+                if issubclass(model, SimulationComponent):
+                    return model.__name__.lower()
+
             raise TypeError(
                 "You are trying to simulate an effect using a custom function. "
                 "Please refer to the tutorial for instructions regarding how "
diff --git a/hera_sim/visibilities/simulators.py b/hera_sim/visibilities/simulators.py
index 18f35b28..53f64a58 100644
--- a/hera_sim/visibilities/simulators.py
+++ b/hera_sim/visibilities/simulators.py
@@ -494,11 +494,13 @@ def load_simulator_from_yaml(config: Path | str) -> VisibilitySimulator:
         module = importlib.import_module(module)
         simulator_cls = getattr(module, simulator_cls.split(".")[-1])
 
-    if not issubclass(simulator_cls, VisibilitySimulator):
-        raise TypeError(
-            f"Specified simulator {simulator_cls} is not a subclass of"
-            "VisibilitySimulator!"
-        )
+    try:
+        if not issubclass(simulator_cls, VisibilitySimulator):
+            raise TypeError(
+                f"Specified simulator {simulator_cls} is not a subclass of"
+                "VisibilitySimulator!"
+            )
+    except TypeError as e:
+        raise TypeError(f"Specified simulator {simulator_cls} is not a class!") from e
 
-    assert issubclass(simulator_cls, VisibilitySimulator)
     return simulator_cls.from_yaml(cfg)

From 976c9173a27aa2c98eff74823c095c465a6321ea Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Fri, 19 Apr 2024 11:22:20 +0200
Subject: [PATCH 05/13] maint: revert rng changes

---
 hera_sim/foregrounds.py | 12 ++++++------
 hera_sim/rfi.py         |  5 ++---
 pyproject.toml          |  4 ++++
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/hera_sim/foregrounds.py b/hera_sim/foregrounds.py
index fdebad62..f8e54863 100644
--- a/hera_sim/foregrounds.py
+++ b/hera_sim/foregrounds.py
@@ -264,13 +264,13 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
         # get baseline length (it should already be in ns)
         bl_len_ns = np.linalg.norm(bl_vec)
 
-        rng = np.random.default_rng()
-
         # randomly generate source RAs
-        ras = rng.uniform(0, 2 * np.pi, nsrcs)
+        ras = np.random.uniform(0, 2 * np.pi, nsrcs)
 
         # draw spectral indices from normal distribution
-        spec_indices = rng.normal(spectral_index_mean, spectral_index_std, size=nsrcs)
+        spec_indices = np.random.normal(
+            spectral_index_mean, spectral_index_std, size=nsrcs
+        )
 
         # calculate beam width, hardcoded for HERA
         beam_width = (40 * 60) * (f0 / freqs) / units.sday.to("s") * 2 * np.pi
@@ -278,7 +278,7 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
         # draw flux densities from a power law
         alpha = beta + 1
         flux_densities = (
-            Smax**alpha + Smin**alpha * (1 - rng.uniform(size=nsrcs))
+            Smax**alpha + Smin**alpha * (1 - np.random.uniform(size=nsrcs))
         ) ** (1 / alpha)
 
         # initialize the visibility array
@@ -290,7 +290,7 @@ def __call__(self, lsts, freqs, bl_vec, **kwargs):
             lst_ind = np.argmin(np.abs(utils.compute_ha(lsts, ra)))
 
             # slight offset in delay? why??
-            dtau = rng.uniform(-1, 1) * 0.1 * bl_len_ns
+            dtau = np.random.uniform(-1, 1) * 0.1 * bl_len_ns
 
             # fill in the corresponding region of the visibility array
             vis[lst_ind, :] += flux * (freqs / f0) ** index
diff --git a/hera_sim/rfi.py b/hera_sim/rfi.py
index a859232b..b0d62996 100644
--- a/hera_sim/rfi.py
+++ b/hera_sim/rfi.py
@@ -96,15 +96,14 @@ def __call__(self, lsts, freqs):
         ch2 = ch1 + 1 if self.f0 > freqs[ch1] else ch1 - 1
 
         # generate some random phases
-        rng = np.random.default_rng()
-        phs1, phs2 = rng.uniform(0, 2 * np.pi, size=2)
+        phs1, phs2 = np.random.uniform(0, 2 * np.pi, size=2)
 
         # find out when the station is broadcasting
         is_on = 0.999 * np.cos(lsts * u.sday.to("s") / self.timescale + phs1)
         is_on = is_on > (1 - 2 * self.duty_cycle)
 
         # generate a signal and filter it according to when it's on
-        signal = rng.normal(self.strength, self.std, lsts.size)
+        signal = np.random.normal(self.strength, self.std, lsts.size)
         signal = np.where(is_on, signal, 0) * np.exp(1j * phs2)
 
         # now add the signal to the rfi array
diff --git a/pyproject.toml b/pyproject.toml
index 8e595f40..894995d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,3 +32,7 @@ select = [
   "W",    # pycodestyle warning
   "NPY",  # numpy-specific rules
 ]
+
+ignore = [
+  "NPY002",  # RNG -- fix soon!
+]

From 097636db0be65ce4f7efda2d4b620587f9001146 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 10:19:11 +0200
Subject: [PATCH 06/13] maint: drop 3.9, add 3.12

---
 .github/workflows/test_suite.yaml | 2 +-
 CHANGELOG.rst                     | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_suite.yaml b/.github/workflows/test_suite.yaml
index eb598903..dba2d54e 100644
--- a/.github/workflows/test_suite.yaml
+++ b/.github/workflows/test_suite.yaml
@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.9, "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@main
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 309bc491..de32cff9 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -5,6 +5,11 @@ Changelog
 dev
 ===
 
+Deprecated
+----------
+
+- Support for Python 3.9 has been dropped.
+
 Fixed
 -----
 - API calls for pyuvdata v2.4.0.

From e86694dc371206038dc55742e9a811d5b7712362 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 10:40:05 +0200
Subject: [PATCH 07/13] test: add tests of bad specification of simulator.yaml

---
 hera_sim/tests/test_vis.py          | 12 ++++++++++++
 hera_sim/visibilities/simulators.py |  4 ++--
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/hera_sim/tests/test_vis.py b/hera_sim/tests/test_vis.py
index 7cc13e47..a094c129 100644
--- a/hera_sim/tests/test_vis.py
+++ b/hera_sim/tests/test_vis.py
@@ -630,3 +630,15 @@ def test_bad_load(tmpdir):
 
     with pytest.raises(AttributeError, match="The given simulator"):
         load_simulator_from_yaml(tmpdir / "bad_sim.yaml")
+
+    with open(tmpdir / "bad_sim.yaml", "w") as fl:
+        fl.write("""simulator: hera_sim.foregrounds.DiffuseForeground\n""")
+
+    with pytest.raises(ValueError, match="is not a subclass of VisibilitySimulator"):
+        load_simulator_from_yaml(tmpdir / "bad_sim.yaml")
+
+    with open(tmpdir / "bad_sim.yaml", "w") as fl:
+        fl.write("""simulator: hera_sim.foregrounds.diffuse_foreground\n""")
+
+    with pytest.raises(TypeError, match="is not a class"):
+        load_simulator_from_yaml(tmpdir / "bad_sim.yaml")
diff --git a/hera_sim/visibilities/simulators.py b/hera_sim/visibilities/simulators.py
index 53f64a58..6d20ca64 100644
--- a/hera_sim/visibilities/simulators.py
+++ b/hera_sim/visibilities/simulators.py
@@ -496,8 +496,8 @@ def load_simulator_from_yaml(config: Path | str) -> VisibilitySimulator:
 
     try:
         if not issubclass(simulator_cls, VisibilitySimulator):
-            raise TypeError(
-                f"Specified simulator {simulator_cls} is not a subclass of"
+            raise ValueError(
+                f"Specified simulator {simulator_cls} is not a subclass of "
                 "VisibilitySimulator!"
             )
     except TypeError as e:

From c082fe1c759fcc8d829b2b10db37e5f748d82347 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 11:25:14 +0200
Subject: [PATCH 08/13] test: add tests of corner-cases

---
 hera_sim/simulate.py             | 19 +++++++++++--
 hera_sim/tests/test_simulator.py | 46 ++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 2 deletions(-)

diff --git a/hera_sim/simulate.py b/hera_sim/simulate.py
index e4ef5d3d..114ff3ef 100644
--- a/hera_sim/simulate.py
+++ b/hera_sim/simulate.py
@@ -19,6 +19,7 @@
 from deprecation import deprecated
 from pathlib import Path
 from pyuvdata import UVData
+from pyuvdata import utils as uvutils
 from typing import Optional, Union
 
 from . import __version__, io, utils
@@ -1464,16 +1465,30 @@ def _parse_key(self, key: Union[int, str, AntPair, AntPairPol]) -> AntPairPol:
         elif isinstance(key, str):
             if key.lower() in ("auto", "cross"):
                 raise NotImplementedError("Functionality not yet supported.")
+            if key.lower() not in {
+                **uvutils.POL_STR2NUM_DICT,
+                **uvutils.JONES_STR2NUM_DICT,
+                **uvutils.CONJ_POL_DICT,
+            }:
+                raise ValueError(f"Invalid polarization string: {key}.")
             ant1, ant2, pol = None, None, key
         else:
             try:
                 iter(key)
-                if len(key) not in (2, 3):
+                if len(key) not in (2, 3) or (
+                    len(key) == 3
+                    and not (
+                        isinstance(key[0], int)
+                        and isinstance(key[1], int)
+                        and isinstance(key[2], str)
+                    )
+                ):
                     raise TypeError
+
             except TypeError:
                 raise ValueError(
                     "Key must be an integer, string, antenna pair, or antenna "
-                    "pair with a polarization string."
+                    f"pair with a polarization string. Got {key}"
                 )
             if len(key) == 2:
                 if all(isinstance(val, int) for val in key):
diff --git a/hera_sim/tests/test_simulator.py b/hera_sim/tests/test_simulator.py
index aaa71223..24d37d93 100644
--- a/hera_sim/tests/test_simulator.py
+++ b/hera_sim/tests/test_simulator.py
@@ -702,3 +702,49 @@ def test_cached_filters():
     sim2.add("diffuse_foreground", seed=seed)
     defaults.deactivate()
     assert np.allclose(sim1.data.data_array, sim2.data.data_array)
+
+
+def test_get_model_name():
+    assert Simulator._get_model_name("noiselike_eor") == "noiselike_eor"
+    assert Simulator._get_model_name("NOISELIKE_EOR") == "noiselike_eor"
+
+    assert Simulator._get_model_name(DiffuseForeground) == "diffuseforeground"
+    assert Simulator._get_model_name(diffuse_foreground) == "diffuseforeground"
+
+    with pytest.raises(
+        TypeError, match="You are trying to simulate an effect using a custom function"
+    ):
+        Simulator._get_model_name(lambda x: x)
+
+    with pytest.raises(
+        TypeError, match="You are trying to simulate an effect using a custom function"
+    ):
+        Simulator._get_model_name(3)
+
+
+def test_parse_key(base_sim: Simulator):
+    assert base_sim._parse_key(None) == (None, None, None)
+    assert base_sim._parse_key(1) == (1, None, None)
+    assert base_sim._parse_key(
+        base_sim.data.baseline_array[-1]
+    ) == base_sim.data.baseline_to_antnums(base_sim.data.baseline_array[-1]) + (None,)
+
+    with pytest.raises(NotImplementedError, match="Functionality not yet supported"):
+        base_sim._parse_key("auto")
+
+    assert base_sim._parse_key("ee") == (None, None, "ee")
+
+    for badkey in [3.14, [1, 2, 3], (1,)]:
+        print(badkey)
+        with pytest.raises(
+            ValueError,
+            match="Key must be an integer, string, antenna pair, or antenna pair with",
+        ):
+            base_sim._parse_key(badkey)
+
+    with pytest.raises(ValueError, match="Invalid polarization string"):
+        base_sim._parse_key("bad_pol")
+
+    assert base_sim._parse_key((1, 2)) == (1, 2, None)
+    assert base_sim._parse_key((1, "Jee")) == (1, None, "Jee")
+    assert base_sim._parse_key((1, 2, "ee")) == (1, 2, "ee")

From 5c6f74bb80684eb5e5c406f1b83c2782442c5e54 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 11:37:33 +0200
Subject: [PATCH 09/13] fix: _parse_key for (int, int, None)

---
 hera_sim/simulate.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/hera_sim/simulate.py b/hera_sim/simulate.py
index 114ff3ef..88c66b52 100644
--- a/hera_sim/simulate.py
+++ b/hera_sim/simulate.py
@@ -1478,9 +1478,9 @@ def _parse_key(self, key: Union[int, str, AntPair, AntPairPol]) -> AntPairPol:
                 if len(key) not in (2, 3) or (
                     len(key) == 3
                     and not (
-                        isinstance(key[0], int)
-                        and isinstance(key[1], int)
-                        and isinstance(key[2], str)
+                        isinstance(key[0], (int, None))
+                        and isinstance(key[1], (int, None))
+                        and isinstance(key[2], (str, None))
                     )
                 ):
                     raise TypeError

From c23e390069687c2681eff3fff70f8202cface4df Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 15:41:18 +0200
Subject: [PATCH 10/13] fix: corner cases for _parse_key

---
 hera_sim/simulate.py | 65 +++++++++++++++++++++++++++-----------------
 1 file changed, 40 insertions(+), 25 deletions(-)

diff --git a/hera_sim/simulate.py b/hera_sim/simulate.py
index 88c66b52..9f10abd4 100644
--- a/hera_sim/simulate.py
+++ b/hera_sim/simulate.py
@@ -1453,6 +1453,28 @@ def _get_model_name(model):
 
     def _parse_key(self, key: Union[int, str, AntPair, AntPairPol]) -> AntPairPol:
         """Convert a key of at-most length-3 to an (ant1, ant2, pol) tuple."""
+        valid_pols = {
+            k.lower()
+            for k in {
+                **uvutils.POL_STR2NUM_DICT,
+                **uvutils.JONES_STR2NUM_DICT,
+                **uvutils.CONJ_POL_DICT,
+            }
+        }
+        valid_pols.update({"jee", "jen", "jne", "jnn"})
+
+        def checkpol(pol):
+            if pol is None:
+                return None
+
+            if not isinstance(pol, str):
+                raise TypeError(f"Invalid polarization type: {type(pol)}.")
+
+            if pol.lower() not in valid_pols:
+                raise ValueError(f"Invalid polarization string: {pol}.")
+
+            return pol
+
         if key is None:
             ant1, ant2, pol = None, None, None
         elif np.issubdtype(type(key), int):
@@ -1465,40 +1487,33 @@ def _parse_key(self, key: Union[int, str, AntPair, AntPairPol]) -> AntPairPol:
         elif isinstance(key, str):
             if key.lower() in ("auto", "cross"):
                 raise NotImplementedError("Functionality not yet supported.")
-            if key.lower() not in {
-                **uvutils.POL_STR2NUM_DICT,
-                **uvutils.JONES_STR2NUM_DICT,
-                **uvutils.CONJ_POL_DICT,
-            }:
-                raise ValueError(f"Invalid polarization string: {key}.")
+            key = checkpol(key)
             ant1, ant2, pol = None, None, key
         else:
+
+            def intify(x):
+                return x if x is None else int(x)
+
             try:
-                iter(key)
-                if len(key) not in (2, 3) or (
-                    len(key) == 3
-                    and not (
-                        isinstance(key[0], (int, None))
-                        and isinstance(key[1], (int, None))
-                        and isinstance(key[2], (str, None))
-                    )
-                ):
+                iter(key)  # ensure it's iterable
+                if len(key) not in (2, 3):
                     raise TypeError
 
+                if len(key) == 2:
+                    if all(isinstance(val, int) for val in key):
+                        ant1, ant2 = key
+                        pol = None
+                    else:
+                        ant1, pol = intify(key[0]), checkpol(key[1])
+                        ant2 = None
+                else:
+                    ant1, ant2, pol = intify(key[0]), intify(key[1]), checkpol(key[2])
+
             except TypeError:
                 raise ValueError(
                     "Key must be an integer, string, antenna pair, or antenna "
-                    f"pair with a polarization string. Got {key}"
+                    f"pair with a polarization string. Got {key}."
                 )
-            if len(key) == 2:
-                if all(isinstance(val, int) for val in key):
-                    ant1, ant2 = key
-                    pol = None
-                else:
-                    ant1, pol = key
-                    ant2 = None
-            else:
-                ant1, ant2, pol = key
         return ant1, ant2, pol
 
     def _sanity_check(self, model):

From e2729a609335845614ba5a417c747d4e8cb212d1 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 19:02:26 +0200
Subject: [PATCH 11/13] test: more resilient equality testing

---
 hera_sim/tests/test_simulator.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/hera_sim/tests/test_simulator.py b/hera_sim/tests/test_simulator.py
index 24d37d93..a15cd424 100644
--- a/hera_sim/tests/test_simulator.py
+++ b/hera_sim/tests/test_simulator.py
@@ -285,18 +285,19 @@ def test_get_multiplicative_effect(base_sim, pol, ant1):
     gains = base_sim.add("gains", seed="once", ret_vis=True)
     _gains = base_sim.get("gains", key=(ant1, pol))
     if pol is not None and ant1 is not None:
-        assert np.all(gains[(ant1, pol)] == _gains)
+        assert np.allclose(gains[(ant1, pol)] == _gains)
     elif pol is None and ant1 is not None:
         assert all(
-            np.all(gains[(ant1, _pol)] == _gains[(ant1, _pol)])
+            np.allclose(gains[(ant1, _pol)] == _gains[(ant1, _pol)])
             for _pol in base_sim.data.get_feedpols()
         )
     elif pol is not None and ant1 is None:
         assert all(
-            np.all(gains[(ant, pol)] == _gains[(ant, pol)]) for ant in base_sim.antpos
+            np.allclose(gains[(ant, pol)] == _gains[(ant, pol)])
+            for ant in base_sim.antpos
         )
     else:
-        assert all(np.all(gains[antpol] == _gains[antpol]) for antpol in gains)
+        assert all(np.allclose(gains[antpol] == _gains[antpol]) for antpol in gains)
 
 
 def test_not_add_vis(base_sim):

From 9455392c5c80e0dffa11aee9db39149353b4d195 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 19:52:29 +0200
Subject: [PATCH 12/13] test: more resilient equality testing

---
 hera_sim/tests/test_simulator.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/hera_sim/tests/test_simulator.py b/hera_sim/tests/test_simulator.py
index a15cd424..8905164e 100644
--- a/hera_sim/tests/test_simulator.py
+++ b/hera_sim/tests/test_simulator.py
@@ -285,19 +285,19 @@ def test_get_multiplicative_effect(base_sim, pol, ant1):
     gains = base_sim.add("gains", seed="once", ret_vis=True)
     _gains = base_sim.get("gains", key=(ant1, pol))
     if pol is not None and ant1 is not None:
-        assert np.allclose(gains[(ant1, pol)] == _gains)
+        assert np.allclose(gains[(ant1, pol)], _gains)
     elif pol is None and ant1 is not None:
         assert all(
-            np.allclose(gains[(ant1, _pol)] == _gains[(ant1, _pol)])
+            np.allclose(gains[(ant1, _pol)], _gains[(ant1, _pol)])
             for _pol in base_sim.data.get_feedpols()
         )
     elif pol is not None and ant1 is None:
         assert all(
-            np.allclose(gains[(ant, pol)] == _gains[(ant, pol)])
+            np.allclose(gains[(ant, pol)], _gains[(ant, pol)])
             for ant in base_sim.antpos
         )
     else:
-        assert all(np.allclose(gains[antpol] == _gains[antpol]) for antpol in gains)
+        assert all(np.allclose(gains[antpol], _gains[antpol]) for antpol in gains)
 
 
 def test_not_add_vis(base_sim):

From 921110aeb4f38b654a6469f724ba3fe42f2fe6e2 Mon Sep 17 00:00:00 2001
From: Steven Murray <steven.g.murray@asu.edu>
Date: Tue, 23 Apr 2024 22:16:02 +0200
Subject: [PATCH 13/13] style: pre-commit autoupdate

---
 .flake8                             | 2 ++
 .pre-commit-config.yaml             | 9 ++++-----
 hera_sim/tests/test_sim_red_data.py | 4 ++--
 hera_sim/visibilities/cli.py        | 4 ++--
 hera_sim/visibilities/matvis.py     | 2 +-
 5 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/.flake8 b/.flake8
index 267e45f2..04fb6718 100644
--- a/.flake8
+++ b/.flake8
@@ -17,6 +17,8 @@ ignore =
     G004,
     # Logging statement uses + (this makes no sense...)
     G003,
+    # Allow builtin module names
+    A005,
 max-line-length = 88
 # Should be 18.
 max-complexity = 35
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d712b921..4269a723 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: 'config.yaml|config_examples/.*.yaml|hera_sim/config/H1C.yaml|hera_sim/
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -25,7 +25,6 @@ repos:
           - flake8-rst-docstrings
           #- flake8-docstrings  # not available for flake8>5
           - flake8-builtins
-          - flake8-logging-format
           - flake8-rst-docstrings
           - flake8-rst
 #          - flake8-markdown    # not available for flake8>5 (check later...)
@@ -34,7 +33,7 @@ repos:
           - flake8-print
 
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 24.2.0
+  rev: 24.4.0
   hooks:
     - id: black
 
@@ -49,7 +48,7 @@ repos:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.1
+  rev: v3.15.2
   hooks:
   - id: pyupgrade
     args: [--py39-plus]
@@ -61,7 +60,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.4
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff
diff --git a/hera_sim/tests/test_sim_red_data.py b/hera_sim/tests/test_sim_red_data.py
index 4137ee7f..f4ee2806 100644
--- a/hera_sim/tests/test_sim_red_data.py
+++ b/hera_sim/tests/test_sim_red_data.py
@@ -58,13 +58,13 @@ def test_sim_red_data_4pol(antpos, gain_data):
         for pol in ["xx", "xy", "yx", "yy"]:
             ai, aj, pol = bl0
             ans0 = data[ai, aj, pol] / (
-                gains[(ai, f"J{pol[0]*2}")] * gains[(aj, f"J{pol[1]*2}")].conj()
+                gains[(ai, f"J{pol[0] * 2}")] * gains[(aj, f"J{pol[1] * 2}")].conj()
             )
 
             for bl in bls[1:]:
                 ai, aj, pol = bl
                 ans = data[ai, aj, pol] / (
-                    gains[(ai, f"J{pol[0]*2}")] * gains[(aj, f"J{pol[1]*2}")].conj()
+                    gains[(ai, f"J{pol[0] * 2}")] * gains[(aj, f"J{pol[1] * 2}")].conj()
                 )
 
                 # compare calibrated visibilities knowing the input gains
diff --git a/hera_sim/visibilities/cli.py b/hera_sim/visibilities/cli.py
index 1b035dba..fa9c005e 100644
--- a/hera_sim/visibilities/cli.py
+++ b/hera_sim/visibilities/cli.py
@@ -139,8 +139,8 @@ def run_vis_sim(args):
     ram_avail = psutil.virtual_memory().available / 1024**3
 
     cprint(
-        f"[bold {'red' if ram < 1.5*ram_avail else 'green'}] This simulation will use "
-        f"at least {ram:.2f}GB of RAM (Available: {ram_avail:.2f}GB).[/]"
+        f"[bold {'red' if ram < 1.5 * ram_avail else 'green'}] This simulation will use"
+        f" at least {ram:.2f}GB of RAM (Available: {ram_avail:.2f}GB).[/]"
     )
 
     if args.object_name is None:
diff --git a/hera_sim/visibilities/matvis.py b/hera_sim/visibilities/matvis.py
index fe7f54b2..e602e47e 100644
--- a/hera_sim/visibilities/matvis.py
+++ b/hera_sim/visibilities/matvis.py
@@ -378,7 +378,7 @@ def simulate(self, data_model):
             if self.mpi_comm is not None and i % nproc != myid:
                 continue
 
-            logger.info(f"Simulating Frequency {i+1}/{len(data_model.freqs)}")
+            logger.info(f"Simulating Frequency {i + 1}/{len(data_model.freqs)}")
 
             # Call matvis function to simulate visibilities
             vis = self._matvis(