Add ruff formating, support numpy 2

.pre-commit-config.yaml

@@ -16,45 +16,19 @@ repos:
  - id: mixed-line-ending
  args: ['--fix=no']
 
-- repo: https://github.com/PyCQA/flake8
- rev: 7.0.0
- hooks:
- - id: flake8
- additional_dependencies:
- - flake8-comprehensions
- - flake8-logging-format
- - flake8-builtins
- - flake8-eradicate
- - pep8-naming
- - flake8-pytest
- - flake8-docstrings
- - flake8-rst-docstrings
- - flake8-rst
- - flake8-copyright
-# - flake8-ownership
- - flake8-markdown
- - flake8-bugbear
- - flake8-comprehensions
- - flake8-print
-
-
-- repo: https://github.com/psf/black-pre-commit-mirror
- rev: 24.4.2
- hooks:
- - id: black
-
-- repo: https://github.com/PyCQA/isort
- rev: 5.13.2
- hooks:
- - id: isort
 
 - repo: https://github.com/pre-commit/pygrep-hooks
  rev: v1.10.0
  hooks:
  - id: rst-backticks
 
-- repo: https://github.com/asottile/pyupgrade
- rev: v3.16.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: v0.4.10
  hooks:
- - id: pyupgrade
- args: [--py38-plus]
+ # Run the linter.
+ - id: ruff
+ args: [--fix]
+
+ # Run the formatter.
+ - id: ruff-format

docs/conf.py

@@ -1,8 +1,8 @@
-# -*- coding: utf-8 -*-
-from __future__ import unicode_literals
+"""Configuration for docs."""
 
 import os
 from datetime import datetime
+
 from py21cmsense import __version__
 
 extensions = [
@@ -35,9 +35,9 @@
 source_suffix = ".rst"
 master_doc = "index"
 project = "21cmSense"
-year = str(datetime.now().year)
+year = str(datetime.now(tz=datetime.tzinfo).year)
 author = "Jonathan Pober and Steven Murray"
-copyright = "{0}, {1}".format(year, author)
+copyright = f"{year}, {author}"
 version = release = __version__
 templates_path = ["templates"]
 
@@ -68,9 +68,7 @@
 napoleon_use_rtype = False
 napoleon_use_param = False
 
-mathjax_path = (
- "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
-)
+mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
 
 exclude_patterns = [
  "_build",

pyproject.toml

@@ -30,7 +30,7 @@ dynamic = ['version']
 
 # Add here dependencies of your project (semicolon/line-separated), e.g.
 dependencies = [
- "numpy",
+ "numpy<2.0", # Restriction can be lifted once pyuvdata is good with numpy 2
  "scipy",
  "future",
  "click",
@@ -64,6 +64,7 @@ dev = [
  "21cmSense[docs,test]",
  "pre-commit",
  "commitizen",
+ "ruff"
 ]
 
 [project.scripts]
@@ -72,6 +73,61 @@ sense = "py21cmsense.cli:main"
 
 [tool.setuptools_scm]
 
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.ruff.lint]
+extend-select = [
+ "UP", # pyupgrade
+ "E", # pycodestyle
+ "W", # pycodestyle warning
+ "C90", # mccabe complexity
+ "I", # isort
+ "N", # pep8-naming
+ "D", # docstyle
+ "B", # bugbear
+ "A", # builtins
+ "C4", # comprehensions
+ "DTZ", # datetime
+ "FA", # future annotations
+ "PIE", # flake8-pie
+ "T", # print statements
+ "PT", # pytest-style
+ "Q", # quotes
+ "SIM", # simplify
+ # "PTH", # use Pathlib
+ "ERA", # kill commented code
+ "NPY", # numpy-specific rules
+ "PERF", # performance
+ "RUF", # ruff-specific rules
+]
+ignore = [
+ "DTZ007", # use %z in strptime
+ "A003", # class attribute shadows python builtin
+ "B008", # function call in argument defaults
+ "N802", # TODO: remove this (function name should be lower-case)
+ "B019", # no using lru_cache on methods
+ "G004", # logging uses f-string
+ "D107", # no docstring in __init__
+]
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = [
+ "D103", # ignore missing docstring in tests
+ "DTZ", # ignore datetime in tests
+ "T", # print statements
+]
+"docs/conf.py" = [
+ "A", # conf.py can shadow builtins
+ "ERA",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
+property-decorators = ['property', 'functools.cached_property']
+
+[tool.ruff.lint.mccabe]
+max-complexity = 15
 
 [tool.pytest.ini_options]
 # Options for py.test:

src/py21cmsense/__init__.py

@@ -9,6 +9,17 @@
 finally:
  del version, PackageNotFoundError
 
+__all__ = [
+ "data",
+ "theory",
+ "yaml",
+ "hera",
+ "BaselineRange",
+ "GaussianBeam",
+ "Observation",
+ "Observatory",
+ "PowerSpectrum",
+]
 from . import data, theory, yaml
 from .antpos import hera
 from .baseline_filters import BaselineRange

src/py21cmsense/_utils.py

@@ -6,8 +6,6 @@
 from astropy.time import Time
 from pyuvdata import utils as uvutils
 
-from . import config
-
 
 def between(xmin, xmax):
  """Return an attrs validation function that checks a number is within bounds."""
@@ -19,12 +17,18 @@ def validator(instance, att, val):
 
 
 def positive(instance, att, x):
- """An attrs validator that checks a value is positive."""
+ """Check that a value is positive.
+
+ This is an attrs validator.
+ """
  assert x > 0, "must be positive"
 
 
 def nonnegative(instance, att, x):
- """An attrs validator that checks a value is non-negative."""
+ """Check that a value is non-negative.
+
+ This is an attrs validator.
+ """
  assert x >= 0, "must be non-negative"
 
 

src/py21cmsense/antpos.py

@@ -9,7 +9,6 @@
 
 import numpy as np
 from astropy import units as un
-from typing import Sequence
 
 from . import units as tp
 from . import yaml
@@ -52,10 +51,7 @@ def hera(
 
  sep = separation.to_value("m")
 
- if row_separation is None:
- row_sep = sep * np.sqrt(3) / 2
- else:
- row_sep = row_separation.to_value("m")
+ row_sep = sep * np.sqrt(3) / 2 if row_separation is None else row_separation.to_value("m")
 
  # construct the main hexagon
  positions = []
@@ -97,11 +93,7 @@ def hera(
  exterior_hex_num = outriggers + 2
  for row in range(exterior_hex_num - 1, -exterior_hex_num, -1):
  for col in range(2 * exterior_hex_num - abs(row) - 1):
- x_pos = (
- ((2 - (2 * exterior_hex_num - abs(row))) / 2 + col)
- * sep
- * (hex_num - 1)
- )
+ x_pos = ((2 - (2 * exterior_hex_num - abs(row))) / 2 + col) * sep * (hex_num - 1)
  y_pos = row * (hex_num - 1) * row_sep
  theta = np.arctan2(y_pos, x_pos)
  if np.sqrt(x_pos**2 + y_pos**2) > sep * (hex_num + 1):

src/py21cmsense/baseline_filters.py

@@ -7,11 +7,10 @@
 """
 
 import abc
+
 import attr
 import numpy as np
-import warnings
 from astropy import units as un
-from pathlib import Path
 
 from . import units as tp
 
@@ -44,29 +43,22 @@ def __call__(self, bl: tp.Length) -> bool:
  bool
  True if the baseline should be included.
  """
- pass # pragma: no cover
+ # pragma: no cover
 
 
 @attr.define
 class BaselineRange(BaselineFilter):
  """Theory model from EOS2021 (https://arxiv.org/abs/2110.13919)."""
 
- bl_min: tp.Length = attr.field(
- default=0 * un.m, validator=tp.vld_physical_type("length")
- )
- bl_max: tp.Length = attr.field(
- default=np.inf * un.m, validator=tp.vld_physical_type("length")
- )
- direction: str = attr.field(
- default="mag", validator=attr.validators.in_(("ew", "ns", "mag"))
- )
+ bl_min: tp.Length = attr.field(default=0 * un.m, validator=tp.vld_physical_type("length"))
+ bl_max: tp.Length = attr.field(default=np.inf * un.m, validator=tp.vld_physical_type("length"))
+ direction: str = attr.field(default="mag", validator=attr.validators.in_(("ew", "ns", "mag")))
 
  @bl_max.validator
  def _bl_max_vld(self, att, val):
  if val <= self.bl_min:
  raise ValueError(
- "bl_max must be greater than bl_min, got "
- f"bl_min={self.bl_min} and bl_max={val}"
+ "bl_max must be greater than bl_min, got " f"bl_min={self.bl_min} and bl_max={val}"
  )
 
  def __call__(self, bl: tp.Length) -> bool:

src/py21cmsense/beam.py

@@ -2,8 +2,9 @@
 
 from __future__ import annotations
 
+from abc import ABCMeta, abstractmethod
+
 import attr
-from abc import ABCMeta, abstractmethod, abstractproperty
 from astropy import constants as cnst
 from astropy import units as un
 from hickleable import hickleable
@@ -37,25 +38,25 @@ def at(self, frequency: tp.Frequency) -> PrimaryBeam:
  """Get a copy of the object at a new frequency."""
  return attr.evolve(self, frequency=frequency)
 
- @abstractproperty
+ @property
+ @abstractmethod
  def area(self) -> un.Quantity[un.steradian]:
  """Beam area [units: sr]."""
- pass
 
- @abstractproperty
+ @property
+ @abstractmethod
  def width(self) -> un.Quantity[un.radians]:
  """Beam width [units: rad]."""
- pass
 
- @abstractproperty
+ @property
+ @abstractmethod
  def first_null(self) -> un.Quantity[un.radians]:
  """An approximation of the first null of the beam."""
- pass
 
- @abstractproperty
+ @property
+ @abstractmethod
  def sq_area(self) -> un.Quantity[un.steradian]:
  """The area of the beam^2."""
- pass
 
  @property
  def b_eff(self) -> un.Quantity[un.steradian]:
@@ -65,10 +66,10 @@ def b_eff(self) -> un.Quantity[un.steradian]:
  """
  return self.area**2 / self.sq_area
 
- @abstractproperty
+ @property
+ @abstractmethod
  def uv_resolution(self) -> un.Quantity[1 / un.radians]:
  """The UV footprint of the beam."""
- pass
 
  @classmethod
  def from_uvbeam(cls) -> PrimaryBeam:
@@ -91,9 +92,7 @@ class GaussianBeam(PrimaryBeam):
  otherwise defined. This generates the beam size.
  """
 
- dish_size: tp.Length = attr.ib(
- validator=(tp.vld_physical_type("length"), ut.positive)
- )
+ dish_size: tp.Length = attr.ib(validator=(tp.vld_physical_type("length"), ut.positive))
 
  @property
  def wavelength(self) -> un.Quantity[un.m]: