Move to ruff

.pre-commit-config.yaml

@@ -13,26 +13,6 @@ repos:
  - id: requirements-txt-fixer
  - id: trailing-whitespace
 
-- repo: https://github.com/asottile/pyupgrade
- rev: v2.29.1
- hooks:
- - id: pyupgrade
- args: [--py38-plus]
-
-- repo: https://github.com/psf/black
- rev: 24.2.0
- hooks:
- - id: black
- args: ["--config=pyproject.toml"]
- files: "(sbijax|examples)"
-
-- repo: https://github.com/pycqa/isort
- rev: 5.12.0
- hooks:
- - id: isort
- args: ["--settings-path=pyproject.toml"]
- files: "(sbijax|examples)"
-
 - repo: https://github.com/pycqa/bandit
  rev: 1.7.1
  hooks:
@@ -44,24 +24,16 @@ repos:
  additional_dependencies: ["toml"]
  files: "(sbijax|examples)"
 
-- repo: https://github.com/PyCQA/flake8
- rev: 5.0.1
- hooks:
- - id: flake8
- additional_dependencies: [
- flake8-typing-imports==1.14.0,
- flake8-pyproject==1.1.0.post0
- ]
-
 - repo: https://github.com/pre-commit/mirrors-mypy
  rev: v0.910-1
  hooks:
  - id: mypy
  args: ["--ignore-missing-imports"]
  files: "(sbijax|examples)"
 
-- repo: https://github.com/pycqa/pydocstyle
- rev: 6.1.1
+- repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.3.0
  hooks:
- - id: pydocstyle
- additional_dependencies: ["toml"]
+ - id: ruff
+ args: [ --fix ]
+ - id: ruff-format

pyproject.toml

@@ -11,7 +11,7 @@ license = "Apache-2.0"
 homepage = "https://github.com/dirmeier/sbijax"
 keywords = ["abc", "simulation-based inference", "approximate Bayesian computation", "normalizing flows", "smc-abc"]
 classifiers = [
- "Development Status :: 1 - Planning",
+ "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: Apache Software License",
  "Programming Language :: Python :: 3",
@@ -57,54 +57,27 @@ dependencies = [
 
 [tool.hatch.envs.test]
 dependencies = [
- "pylint>=2.15.10",
+ "ruff>=0.3.0",
  "pytest>=7.2.0",
  "pytest-cov>=4.0.0"
 ]
 
 [tool.hatch.envs.test.scripts]
-lint = 'pylint sbijax'
+lint = 'ruff check sbijax'
 test = 'pytest -v --cov=./sbijax --cov-report=xml sbijax'
 
-[tool.black]
-line-length = 80
-target-version = ['py311']
-exclude = '''
-/(
- \.eggs
- | \.git
- | \.hg
- | \.mypy_cache
- | \.tox
- | \.venv
- | _build
- | buck-out
- | build
- | dist
-)/
-'''
-
+[tool.bandit]
+skips = ["B101"]
 
-[tool.isort]
-profile = "black"
-line_length = 80
-include_trailing_comma = true
+[tool.ruff]
+line-length = 80
+exclude = ["*_test.py", "docs/**", "examples/**"]
 
-[tool.flake8]
-max-line-length = 80
-extend-ignore = ["E203", "W503", "E731", "E231"]
-per-file-ignores = [
- '__init__.py:F401',
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F"]
+extend-select = [
+ "UP", "D", "I", "PL", "S"
 ]
 
-[tool.pylint.messages_control]
-disable = """
-invalid-name,missing-module-docstring,R0801,E0633
-"""
-
-[tool.bandit]
-skips = ["B101"]
-
-[tool.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention= 'google'
-match = '^sbijax/.*/((?!_test).)*\.py'

sbijax/__init__.py

@@ -1,10 +1,7 @@
-"""
-sbijax: Simulation-based inference in JAX
-"""
+"""sbijax: Simulation-based inference in JAX."""
 
 __version__ = "0.2.0"
 
-
 from sbijax._src.abc.smc_abc import SMCABC
 from sbijax._src.scmpe import SCMPE
 from sbijax._src.sfmpe import SFMPE
@@ -13,3 +10,5 @@
 from sbijax._src.snl import SNL
 from sbijax._src.snp import SNP
 from sbijax._src.snr import SNR
+
+__all__ = ["SMCABC", "SCMPE", "SFMPE", "SNASS", "SNASSS", "SNL", "SNP", "SNR"]

sbijax/_src/_sne_base.py

@@ -10,8 +10,7 @@
 from sbijax._src.util.dataloader import as_batch_iterators, named_dataset
 
 
-# pylint: disable=too-many-arguments,unused-argument
-# pylint: disable=too-many-function-args,arguments-differ
+# ruff: noqa: PLR0913
 class SNE(SBI, ABC):
  """Sequential neural estimation base class."""
 

sbijax/_src/abc/smc_abc.py

@@ -12,8 +12,7 @@
 from sbijax._src._sbi_base import SBI
 
 
-# pylint: disable=arguments-differ,too-many-function-args,too-many-locals
-# pylint: disable=too-few-public-methods
+# ruff: noqa: PLR0913
 class SMCABC(SBI):
  """Sequential Monte Carlo approximate Bayesian computation.
 
@@ -38,7 +37,6 @@ def __init__(self, model_fns, summary_fn, distance_fn):
  self.summarized_observed: chex.Array
  self.n_total_simulations = 0
 
- # pylint: disable=too-many-arguments,arguments-differ
  def sample_posterior(
  self,
  rng_key,
@@ -53,9 +51,10 @@ def sample_posterior(
  r"""Sample from the approximate posterior.
 
  Args:
+ rng_key: a jax random
  n_rounds: max number of SMC rounds
  observable: the observation to condition on
- n_round: number of rounds of SMC
+ n_rounds: number of rounds of SMC
  n_particles: number of n_particles to draw for each parameter
  n_simulations_per_theta: number of simulations for each paramrter
  sample

sbijax/_src/mcmc/__init__.py

@@ -4,3 +4,12 @@
 from sbijax._src.mcmc.nuts import sample_with_nuts
 from sbijax._src.mcmc.rmh import sample_with_rmh
 from sbijax._src.mcmc.slice import sample_with_slice
+
+__all__ = [
+ "mcmc_diagnostics",
+ "sample_with_slice",
+ "sample_with_nuts",
+ "sample_with_mala",
+ "sample_with_rmh",
+ "sample_with_imh",
+]

sbijax/_src/mcmc/irmh.py

@@ -4,14 +4,14 @@
 from jax import random as jr
 
 
-# pylint: disable=too-many-arguments,unused-argument
+# ruff: noqa: PLR0913,D417
 def sample_with_imh(
  rng_key, lp, prior, *, n_chains=4, n_samples=2_000, n_warmup=1_000, **kwargs
 ):
  r"""Draw samples using the indepdendent Metropolis-Hastings sampler.
 
  Args:
- rng_seq: a hk.PRNGSequence
+ rng_key: a jax random key
  lp: the logdensity you wish to sample from
  prior: a function that returns a prior sample
  n_chains: number of chains to sample

sbijax/_src/mcmc/mala.py

@@ -4,7 +4,7 @@
 from jax import random as jr
 
 
-# pylint: disable=too-many-arguments,unused-argument
+# ruff: noqa: PLR0913,D417
 def sample_with_mala(
  rng_key, lp, prior, *, n_chains=4, n_samples=2_000, n_warmup=1_000, **kwargs
 ):

sbijax/_src/mcmc/nuts.py

@@ -4,7 +4,7 @@
 from jax import random as jr
 
 
-# pylint: disable=too-many-arguments,unused-argument
+# ruff: noqa: PLR0913,D417
 def sample_with_nuts(
  rng_key, lp, prior, *, n_chains=4, n_samples=2_000, n_warmup=1_000, **kwargs
 ):

sbijax/_src/mcmc/rmh.py

@@ -5,7 +5,7 @@
 from jax import random as jr
 
 
-# pylint: disable=too-many-arguments,unused-argument
+# ruff: noqa: PLR0913,D417
 def sample_with_rmh(
  rng_key, lp, prior, *, n_chains=4, n_samples=2_000, n_warmup=1_000, **kwargs
 ):

sbijax/_src/mcmc/slice.py

@@ -3,7 +3,7 @@
 from jax import random as jr
 
 
-# pylint: disable=too-many-arguments,unused-argument
+# ruff: noqa: PLR0913,D417
 def sample_with_slice(
  rng_key,
  lp,
@@ -20,7 +20,7 @@ def sample_with_slice(
  r"""Sample from a distribution using the No-U-Turn sampler.
 
  Args:
- rng_seq: a hk.PRNGSequence
+ rng_key: a jax random key
  lp: the logdensity you wish to sample from
  prior: a function that returns a prior sample
  n_chains: number of chains to sample

sbijax/_src/nn/consistency_model.py

@@ -10,6 +10,7 @@
 __all__ = ["ConsistencyModel", "make_consistency_model"]
 
 
+# ruff: noqa: PLR0913,D417
 class ConsistencyModel(hk.Module):
  """A consistency model.
 
@@ -161,6 +162,7 @@ def _c_out(self, time):
  )
 
 
+# ruff: noqa: PLR0913
 def make_consistency_model(
  n_dimension: int,
  n_layers: int = 2,

sbijax/_src/nn/continuous_normalizing_flow.py

@@ -10,6 +10,7 @@
 __all__ = ["CCNF", "make_ccnf"]
 
 
+# ruff: noqa: PLR0913,D417
 class CCNF(hk.Module):
  """Conditional continuous normalizing flow.
 
@@ -180,6 +181,7 @@ def __call__(self, theta, time, context, is_training=False, **kwargs):
  return outputs
 
 
+# ruff: noqa: PLR0913
 def make_ccnf(
  n_dimension: int,
  n_layers: int = 2,

sbijax/_src/nn/make_flows.py

@@ -1,4 +1,5 @@
-from typing import Callable, Iterable
+from collections.abc import Iterable
+from typing import Callable
 
 import distrax
 import haiku as hk
@@ -11,8 +12,7 @@
  Permutation,
  TransformedDistribution,
 )
-from surjectors._src.conditioners.mlp import make_mlp
-from surjectors._src.conditioners.nn.made import MADE
+from surjectors.nn import MADE, make_mlp
 from surjectors.util import unstack
 
 

sbijax/_src/nn/make_resnet.py

@@ -39,7 +39,7 @@ def __call__(self, inputs, is_training=False):
  return outputs + inputs
 
 
-# pylint: disable=too-many-arguments
+# ruff: noqa: PLR0913
 class _Resnet(hk.Module):
  """A simplified 1-d residual network."""
 

sbijax/_src/nn/make_snass_networks.py

@@ -1,4 +1,5 @@
-from typing import Callable, Iterable
+from collections.abc import Iterable
+from typing import Callable
 
 import haiku as hk
 import jax

sbijax/_src/nn/snass_net.py

@@ -1,12 +1,12 @@
-from typing import Callable, Iterable
+from collections.abc import Iterable
+from typing import Callable
 
 import haiku as hk
 import jax
 from jax import numpy as jnp
 
 
-# pylint: disable=missing-function-docstring,missing-class-docstring
-# pydocstyle: disable=D102
+# ruff: noqa: PLR0913,S101
 class SNASSNet(hk.Module):
  """A network for SNASS."""
 

sbijax/_src/nn/snasss_net.py

@@ -1,4 +1,5 @@
-from typing import Callable, Iterable
+from collections.abc import Iterable
+from typing import Callable
 
 import haiku as hk
 import jax
@@ -7,8 +8,7 @@
 from sbijax._src.nn.snass_net import SNASSNet
 
 
-# pylint: disable=missing-function-docstring,missing-class-docstring
-# pylint: disable=too-many-arguments
+# ruff: noqa: PLR0913,S101
 class SNASSSNet(SNASSNet):
  """A network for SNASSS."""
 

sbijax/_src/scmpe.py

@@ -87,7 +87,7 @@ def _consistency_loss(
  return jnp.mean(loss)
 
 
-# pylint: disable=too-many-arguments,unused-argument,useless-parent-delegation
+# ruff: noqa: PLR0913
 class SCMPE(SFMPE):
  r"""Sequential consistency model posterior estimation.
 

sbijax/_src/sfmpe.py

@@ -57,7 +57,7 @@ def _cfm_loss(
  return loss
 
 
-# pylint: disable=too-many-arguments,unused-argument,useless-parent-delegation
+# ruff: noqa: PLR0913
 class SFMPE(SNE):
  r"""Sequential flow matching posterior estimation.
 
@@ -106,7 +106,7 @@ def __init__(self, model_fns, density_estimator):
  """
  super().__init__(model_fns, density_estimator)
 
- # pylint: disable=arguments-differ,too-many-locals
+ # ruff: noqa: D417
  def fit(
  self,
  rng_key,
@@ -233,6 +233,7 @@ def body_fn(batch_key, **batch):
  loss += body_fn(val_key, **batch)
  return loss
 
+ # ruff: noqa: D417
  def sample_posterior(
  self, rng_key, params, observable, *, n_samples=4_000, **kwargs
  ):