Merge pull request #305 from HERA-Team/np-upgrade

fix: import blackmanharris from scipy.signal.windows

.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

.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

.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
 
@@ -49,12 +48,20 @@ repos:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.1
+  rev: v3.15.2
   hooks:
   - id: pyupgrade
     args: [--py39-plus]
 
 - repo: https://github.com/asottile/setup-cfg-fmt
   rev: v2.5.0
   hooks:
-  - id: setup-cfg-fmt
+  - id: setup-cfg-fmt
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.1
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--fix]

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.

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(np.isscalar(ant) for ant in gains.keys()):
         # Old-style, single polarization assumption.
         gains = {(ant, "Jee"): gain for ant, gain in gains.items()}
 

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)

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

hera_sim/rfi.py

@@ -484,8 +484,8 @@ 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

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

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
@@ -18,6 +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
@@ -727,7 +729,7 @@ 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 +758,7 @@ 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 +1230,7 @@ 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):
@@ -1390,9 +1392,7 @@ 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):
-            return component
-        elif isinstance(component, str):
+        if isinstance(component, str):
             try:
                 return get_model(component)
             except KeyError:
@@ -1403,6 +1403,9 @@ 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 +1438,13 @@ 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):
-            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 "
@@ -1448,6 +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):
@@ -1460,26 +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.")
+            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)
+                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 "
-                    "pair with a polarization string."
+                    f"pair with a polarization string. Got {key}."
                 )
-            if len(key) == 2:
-                if all(type(val) is 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):

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