Fix ruff not format the changes (#1761)

* fix ruff did not format previously

* further ruff format

Makefile

@@ -1,14 +1,15 @@
 all: test
 
 lint: FORCE
-	ruff .
+	ruff check .
+	ruff format . --check
 	python scripts/update_headers.py --check
 
 license: FORCE
 	python scripts/update_headers.py
 
 format: license FORCE
-	ruff . --fix
+	ruff format .
 
 install: FORCE
 	pip install -e .[dev,doc,test,examples]

examples/hmm_enum.py

@@ -303,8 +303,13 @@ def transition_fn(carry, y):
         with numpyro.plate("sequences", num_sequences, dim=-2):
             with mask(mask=(t < lengths)[..., None]):
                 probs_x_t = Vindex(probs_x)[x_prev, x_curr]
-                x_prev, x_curr = x_curr, numpyro.sample(
-                    "x", dist.Categorical(probs_x_t), infer={"enumerate": "parallel"}
+                x_prev, x_curr = (
+                    x_curr,
+                    numpyro.sample(
+                        "x",
+                        dist.Categorical(probs_x_t),
+                        infer={"enumerate": "parallel"},
+                    ),
                 )
                 with numpyro.plate("tones", data_dim, dim=-1):
                     probs_y_t = probs_y[x_curr.squeeze(-1)]

examples/hsgp.py

@@ -46,6 +46,7 @@
 
 
 """
+
 import argparse
 import os
 

examples/prodlda.py

@@ -30,6 +30,7 @@
 .. image:: ../_static/img/examples/prodlda.png
     :align: center
 """
+
 import argparse
 
 import matplotlib.pyplot as plt

examples/proportion_test.py

@@ -16,7 +16,6 @@
 density interval for the effect of making a call.
 """
 
-
 import argparse
 import os
 

examples/stein_dmm.py

@@ -18,6 +18,7 @@
 .. image:: ../_static/img/examples/stein_dmm.png
     :align: center
 """
+
 import argparse
 
 import numpy as np

numpyro/compat/infer.py

@@ -126,7 +126,7 @@ def __init__(
         loss_and_grads=None,
         num_samples=10,
         num_steps=0,
-        **kwargs
+        **kwargs,
     ):
         super(SVI, self).__init__(model=model, guide=guide, optim=optim, loss=loss)
         self.svi_state = None

numpyro/contrib/ecs_proxies.py

@@ -185,7 +185,6 @@ def log_likelihood_sum(params_flat, subsample_indices=None):
             ref_sum_log_lik_hessians = hessian(log_likelihood_sum)(ref_params_flat)
 
         def gibbs_init(rng_key, gibbs_sites):
-
             ref_subsamples_taylor = [
                 log_likelihood(ref_params_flat, gibbs_sites),
                 jacobian(log_likelihood)(ref_params_flat, gibbs_sites),

numpyro/contrib/einstein/steinvi.py

@@ -217,13 +217,11 @@ def local_trace(key):
 
     def _svgd_loss_and_grads(self, rng_key, unconstr_params, *args, **kwargs):
         # 0. Separate model and guide parameters, since only guide parameters are updated using Stein
-        non_mixture_uparams = (
-            {  # Includes any marked guide parameters and all model parameters
-                p: v
-                for p, v in unconstr_params.items()
-                if p not in self.guide_sites or self.non_mixture_params_fn(p)
-            }
-        )
+        non_mixture_uparams = {  # Includes any marked guide parameters and all model parameters
+            p: v
+            for p, v in unconstr_params.items()
+            if p not in self.guide_sites or self.non_mixture_params_fn(p)
+        }
         stein_uparams = {
             p: v for p, v in unconstr_params.items() if p not in non_mixture_uparams
         }

numpyro/contrib/module.py

@@ -254,7 +254,7 @@ def random_flax_module(
     input_shape=None,
     apply_rng=None,
     mutable=None,
-    **kwargs
+    **kwargs,
 ):
     """
     A primitive to place a prior over the parameters of the Flax module `nn_module`.
@@ -372,7 +372,7 @@ def __call__(self, x):
         input_shape=input_shape,
         apply_rng=apply_rng,
         mutable=mutable,
-        **kwargs
+        **kwargs,
     )
     params = nn.args[0]
     new_params = deepcopy(params)

numpyro/contrib/tfp/distributions.py

@@ -314,9 +314,7 @@ def kl_divergence(p, q):  # noqa: F811
     _PyroDist.__doc__ = """
     Wraps `{}.{} <https://www.tensorflow.org/probability/api_docs/python/tfp/substrates/jax/distributions/{}>`_
     with :class:`~numpyro.contrib.tfp.distributions.TFPDistribution`.
-    """.format(
-        _Dist.__module__, _Dist.__name__, _Dist.__name__
-    )
+    """.format(_Dist.__module__, _Dist.__name__, _Dist.__name__)
 
     __all__.append(_name)
 
@@ -328,9 +326,7 @@ def kl_divergence(p, q):  # noqa: F811
     {0}
     ----------------------------------------------------------------
     .. autoclass:: numpyro.contrib.tfp.distributions.{0}
-    """.format(
-            _name
-        )
+    """.format(_name)
         for _name in __all__[:_len_all]
     ]
 )

numpyro/contrib/tfp/mcmc.py

@@ -236,9 +236,7 @@ def sample(self, state, model_args, model_kwargs):
     Wraps `{}.{} <https://www.tensorflow.org/probability/api_docs/python/tfp/substrates/jax/mcmc/{}>`_
     with :class:`~numpyro.contrib.tfp.mcmc.TFPKernel`. The first argument `target_log_prob_fn`
     in TFP kernel construction is replaced by either `model` or `potential_fn`.
-    """.format(
-        _Kernel.__module__, _Kernel.__name__, _Kernel.__name__
-    )
+    """.format(_Kernel.__module__, _Kernel.__name__, _Kernel.__name__)
 
     __all__.append(_name)
 
@@ -250,9 +248,7 @@ def sample(self, state, model_args, model_kwargs):
     {0}
     ----------------------------------------------------------------
     .. autoclass:: numpyro.contrib.tfp.mcmc.{0}
-    """.format(
-            _name
-        )
+    """.format(_name)
         for _name in __all__[:1] + sorted(__all__[1:])
     ]
 )

numpyro/distributions/conjugate.py

@@ -36,6 +36,7 @@ class BetaBinomial(Distribution):
         Beta distribution.
     :param numpy.ndarray total_count: number of Bernoulli trials.
     """
+
     arg_constraints = {
         "concentration1": constraints.positive,
         "concentration0": constraints.positive,
@@ -107,6 +108,7 @@ class DirichletMultinomial(Distribution):
         Dirichlet distribution.
     :param numpy.ndarray total_count: number of Categorical trials.
     """
+
     arg_constraints = {
         "concentration": constraints.independent(constraints.positive, 1),
         "total_count": constraints.nonnegative_integer,
@@ -182,6 +184,7 @@ class GammaPoisson(Distribution):
     :param numpy.ndarray concentration: shape parameter (alpha) of the Gamma distribution.
     :param numpy.ndarray rate: rate parameter (beta) for the Gamma distribution.
     """
+
     arg_constraints = {
         "concentration": constraints.positive,
         "rate": constraints.positive,

numpyro/distributions/continuous.py

@@ -284,9 +284,7 @@ def mean(self):
     @property
     def variance(self):
         con0 = jnp.sum(self.concentration, axis=-1, keepdims=True)
-        return (
-            self.concentration * (con0 - self.concentration) / (con0**2 * (con0 + 1))
-        )
+        return self.concentration * (con0 - self.concentration) / (con0**2 * (con0 + 1))
 
     @staticmethod
     def infer_shapes(concentration):
@@ -909,6 +907,7 @@ def model(y):  # y has dimension N x d
     [1] `Generating random correlation matrices based on vines and extended onion method`,
     Daniel Lewandowski, Dorota Kurowicka, Harry Joe
     """
+
     arg_constraints = {"concentration": constraints.positive}
     reparametrized_params = ["concentration"]
     support = constraints.corr_matrix
@@ -985,6 +984,7 @@ def model(y):  # y has dimension N x d
     [1] `Generating random correlation matrices based on vines and extended onion method`,
     Daniel Lewandowski, Dorota Kurowicka, Harry Joe
     """
+
     arg_constraints = {"concentration": constraints.positive}
     reparametrized_params = ["concentration"]
     support = constraints.corr_cholesky
@@ -1961,9 +1961,10 @@ def scale_tril(self):
 
     @lazy_property
     def covariance_matrix(self):
-        covariance_matrix = add_diag(jnp.matmul(
-            self.cov_factor, jnp.swapaxes(self.cov_factor, -1, -2)
-        ), self.cov_diag)
+        covariance_matrix = add_diag(
+            jnp.matmul(self.cov_factor, jnp.swapaxes(self.cov_factor, -1, -2)),
+            self.cov_diag,
+        )
         return covariance_matrix
 
     @lazy_property
@@ -1976,7 +1977,7 @@ def precision_matrix(self):
         )
         A = solve_triangular(Wt_Dinv, self._capacitance_tril, lower=True)
         inverse_cov_diag = jnp.reciprocal(self.cov_diag)
-        return add_diag(- jnp.matmul(jnp.swapaxes(A, -1, -2), A), inverse_cov_diag)
+        return add_diag(-jnp.matmul(jnp.swapaxes(A, -1, -2), A), inverse_cov_diag)
 
     def sample(self, key, sample_shape=()):
         assert is_prng_key(key)
@@ -2068,8 +2069,9 @@ class Pareto(TransformedDistribution):
     def __init__(self, scale, alpha, *, validate_args=None):
         self.scale, self.alpha = promote_shapes(scale, alpha)
         batch_shape = lax.broadcast_shapes(jnp.shape(scale), jnp.shape(alpha))
-        scale, alpha = jnp.broadcast_to(scale, batch_shape), jnp.broadcast_to(
-            alpha, batch_shape
+        scale, alpha = (
+            jnp.broadcast_to(scale, batch_shape),
+            jnp.broadcast_to(alpha, batch_shape),
         )
         base_dist = Exponential(alpha)
         transforms = [ExpTransform(), AffineTransform(loc=0, scale=scale)]

numpyro/distributions/discrete.py

@@ -679,6 +679,7 @@ class Poisson(Distribution):
     :param bool is_sparse: Whether to assume value is mostly zero when computing
         :meth:`log_prob`, which can speed up computation when data is sparse.
     """
+
     arg_constraints = {"rate": constraints.positive}
     support = constraints.nonnegative_integer
     pytree_aux_fields = ("is_sparse",)

numpyro/distributions/transforms.py

@@ -400,6 +400,7 @@ class CholeskyTransform(ParameterFreeTransform):
     Transform via the mapping :math:`y = cholesky(x)`, where `x` is a
     positive definite matrix.
     """
+
     domain = constraints.positive_definite
     codomain = constraints.lower_cholesky
 
@@ -444,6 +445,7 @@ class :class:`StickBreakingTransform` to transform :math:`X_i` into a
             c. Applies :math:`s_i = StickBreakingTransform(z_i)`.
             d. Transforms back into signed domain: :math:`y_i = (sign(r_i), 1) * \sqrt{s_i}`.
     """
+
     domain = constraints.real_vector
     codomain = constraints.corr_cholesky
 
@@ -493,6 +495,7 @@ class CorrMatrixCholeskyTransform(CholeskyTransform):
     Transform via the mapping :math:`y = cholesky(x)`, where `x` is a
     correlation matrix.
     """
+
     domain = constraints.corr_matrix
     codomain = constraints.corr_cholesky
 
@@ -624,6 +627,7 @@ class L1BallTransform(ParameterFreeTransform):
     r"""
     Transforms a uncontrained real vector :math:`x` into the unit L1 ball.
     """
+
     domain = constraints.real_vector
     codomain = constraints.l1_ball
 
@@ -687,6 +691,7 @@ class LowerCholeskyAffine(Transform):
        >>> affine(base)
        Array([0.3, 1.5], dtype=float32)
     """
+
     domain = constraints.real_vector
     codomain = constraints.real_vector
 
@@ -786,6 +791,7 @@ class ScaledUnitLowerCholeskyTransform(LowerCholeskyTransform):
     and :math:`scale\_diag` is a diagonal matrix with all positive
     entries that is parameterized with a softplus transform.
     """
+
     domain = constraints.real_vector
     codomain = constraints.scaled_unit_lower_cholesky
 
@@ -995,6 +1001,7 @@ class SoftplusTransform(ParameterFreeTransform):
     Transform from unconstrained space to positive domain via softplus :math:`y = \log(1 + \exp(x))`.
     The inverse is computed as :math:`x = \log(\exp(y) - 1)`.
     """
+
     domain = constraints.real
     codomain = constraints.softplus_positive
 
@@ -1200,7 +1207,6 @@ def __eq__(self, other):
         )
 
 
-
 ##########################################################
 # CONSTRAINT_REGISTRY
 ##########################################################

numpyro/distributions/truncated.py

@@ -263,9 +263,7 @@ def mean(self):
         if isinstance(self.base_dist, Normal):
             low_prob = jnp.exp(self.log_prob(self.low))
             high_prob = jnp.exp(self.log_prob(self.high))
-            return (
-                self.base_dist.loc + (low_prob - high_prob) * self.base_dist.scale**2
-            )
+            return self.base_dist.loc + (low_prob - high_prob) * self.base_dist.scale**2
         elif isinstance(self.base_dist, Cauchy):
             return jnp.full(self.batch_shape, jnp.nan)
         else:

numpyro/infer/autoguide.py

@@ -1858,7 +1858,7 @@ def _setup_prototype(self, *args, **kwargs):
                         f"Expected {self.batch_ndim} batch dimensions, but site "
                         f"`{site['name']}` only has shape {shape}."
                     )
-                shape = shape[:self.batch_ndim]
+                shape = shape[: self.batch_ndim]
                 if batch_shape is None:
                     batch_shape = shape
                 elif shape != batch_shape:
@@ -1884,7 +1884,9 @@ def _get_posterior(self):
         )
 
     def _get_reshape_transform(self) -> ReshapeTransform:
-        return ReshapeTransform((self.latent_dim,), self._batch_shape + self._event_shape)
+        return ReshapeTransform(
+            (self.latent_dim,), self._batch_shape + self._event_shape
+        )
 
 
 class AutoBatchedMultivariateNormal(AutoBatchedMixin, AutoContinuous):
@@ -1914,7 +1916,10 @@ def __init__(
             raise ValueError("Expected init_scale > 0. but got {}".format(init_scale))
         self._init_scale = init_scale
         super().__init__(
-            model, prefix=prefix, init_loc_fn=init_loc_fn, batch_ndim=batch_ndim,
+            model,
+            prefix=prefix,
+            init_loc_fn=init_loc_fn,
+            batch_ndim=batch_ndim,
         )
 
     def _get_batched_posterior(self):
@@ -2044,16 +2049,21 @@ def __init__(
         self._init_scale = init_scale
         self.rank = rank
         super().__init__(
-            model, prefix=prefix, init_loc_fn=init_loc_fn, batch_ndim=batch_ndim,
+            model,
+            prefix=prefix,
+            init_loc_fn=init_loc_fn,
+            batch_ndim=batch_ndim,
         )
 
     def _get_batched_posterior(self):
-        rank = int(round(self._event_shape[0]**0.5)) if self.rank is None else self.rank
+        rank = (
+            int(round(self._event_shape[0] ** 0.5)) if self.rank is None else self.rank
+        )
         init_latent = self._init_latent.reshape(self._batch_shape + self._event_shape)
         loc = numpyro.param("{}_loc".format(self.prefix), init_latent)
         cov_factor = numpyro.param(
             "{}_cov_factor".format(self.prefix),
-            jnp.zeros(self._batch_shape + self._event_shape + (rank,))
+            jnp.zeros(self._batch_shape + self._event_shape + (rank,)),
         )
         scale = numpyro.param(
             "{}_scale".format(self.prefix),