Update dependencies and use new jax random key (#569)

* Update dependency * chex version typo * fix typing * fix typing 2 * Revert "fix typing 2" This reverts commit 154e6b3. * jax.random.PRNGKey(...) -> jax.random.key(...)
blackjax-devs · Sep 20, 2023 · 8efb158 · 8efb158
1 parent 46d874d
commit 8efb158
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diff --git a/blackjax/types.py b/blackjax/types.py
@@ -13,7 +13,6 @@
 from typing import Any, Iterable, Mapping, Union
 
 import jax
-from jax import Array
 from jax.typing import ArrayLike
 
 """
@@ -36,10 +35,11 @@ class WelfordAlgorithmState(NamedTuple):
 (until we introduce shape annotation).
 """
 #: JAX PyTrees
-ArrayTree = Union[Array, Iterable["ArrayTree"], Mapping[Any, "ArrayTree"]]
+Array = jax.Array
+ArrayTree = Union[jax.Array, Iterable["ArrayTree"], Mapping[Any, "ArrayTree"]]
 ArrayLikeTree = Union[
     ArrayLike, Iterable["ArrayLikeTree"], Mapping[Any, "ArrayLikeTree"]
 ]
 
 #: JAX PRNGKey
-PRNGKey = jax.random.PRNGKeyArray
+PRNGKey = jax.Array
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,11 +31,11 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Mathematics",
 ]
 dependencies = [
-    "fastprogress>=0.2.0",
-    "jax>=0.3.13",
-    "jaxlib>=0.3.10",
-    "jaxopt>=0.5.5",
-    "optax",
+    "fastprogress>=1.0.0",
+    "jax>=0.4.16",
+    "jaxlib>=0.4.16",
+    "jaxopt>=0.8",
+    "optax>=0.1.7",
     "typing-extensions>=4.4.0",
 ]
 dynamic = ["version"]

diff --git a/requirements-doc.txt b/requirements-doc.txt
@@ -4,8 +4,8 @@ aesara>=2.8.8
 arviz
 flax
 ipython
-jax
-jaxlib
+jax>=0.4.16
+jaxlib>=0.4.16
 jaxopt
 jupytext
 myst_nb

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 -e ./
-chex
+chex>=0.1.83
 pre-commit
 pytest
 pytest-benchmark

diff --git a/tests/adaptation/test_step_size.py b/tests/adaptation/test_step_size.py
@@ -16,7 +16,7 @@ def test_reasonable_step_size(self):
         def logdensity_fn(x):
             return -jnp.sum(0.5 * x)
 
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         run_key0, run_key1 = jax.random.split(rng_key, 2)
 
         init_position = jnp.array([3.0])

diff --git a/tests/mcmc/test_latent_gaussian.py b/tests/mcmc/test_latent_gaussian.py
@@ -14,7 +14,7 @@ class GaussianTest(chex.TestCase):
     def test_gaussian(self, seed, mean):
         n_samples = 500_000
 
-        key = jax.random.PRNGKey(seed)
+        key = jax.random.key(seed)
         key1, key2, key3, key4, key5 = jax.random.split(key, 5)
 
         D = 5

diff --git a/tests/mcmc/test_metrics.py b/tests/mcmc/test_metrics.py
@@ -11,7 +11,7 @@
 class GaussianEuclideanMetricsTest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = random.PRNGKey(0)
+        self.key = random.key(0)
         self.dtype = "float32"
 
     @parameterized.named_parameters(

diff --git a/tests/mcmc/test_proposal.py b/tests/mcmc/test_proposal.py
@@ -10,7 +10,7 @@
 class TestNormalProposalDistribution(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(20220611)
+        self.key = jax.random.key(20220611)
 
     def test_normal_univariate(self):
         """

diff --git a/tests/mcmc/test_random_walk_without_chex.py b/tests/mcmc/test_random_walk_without_chex.py
@@ -21,7 +21,7 @@ def test_one_step_addition(self):
         Since the density == 1, the proposal is accepted.
         The random step may depend on the previous position
         """
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         initial_position = jnp.array([50.0])
 
         def random_step(key, position):
@@ -51,7 +51,7 @@ def test_logdensity_accepts(position):
 class IRMHTest(unittest.TestCase):
     def test_proposal_is_independent_of_position(self):
         """New position does not depend on previous"""
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         initial_position = jnp.array([50.0])
         other_position = jnp.array([15000.0])
 
@@ -99,7 +99,7 @@ def test_generate_reject(self):
         and given that the sampling rule rejects,
         the prev_state is proposed again
         """
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         prev_state = RWState(jnp.array([30.0]), 15.0)
 
@@ -118,7 +118,7 @@ def test_generate_reject(self):
         np.testing.assert_allclose(sampled_proposal.state.position, jnp.array([30.0]))
 
     def test_generate_accept(self):
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         prev_state = RWState(jnp.array([30.0]), 15.0)
 
         generate = rmh_proposal(

diff --git a/tests/mcmc/test_sampling.py b/tests/mcmc/test_sampling.py
@@ -71,7 +71,7 @@ class LinearRegressionTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(19)
+        self.key = jax.random.key(19)
 
     def regression_logprob(self, log_scale, coefs, preds, x):
         """Linear regression"""
@@ -229,7 +229,7 @@ class SGMCMCTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(19)
+        self.key = jax.random.key(19)
 
     def logprior_fn(self, position):
         return -0.5 * jnp.dot(position, position) * 0.01
@@ -379,7 +379,7 @@ class LatentGaussianTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(19)
+        self.key = jax.random.key(19)
         self.C = 2.0 * np.eye(1)
         self.delta = 5.0
         self.sampling_steps = 25_000
@@ -494,7 +494,7 @@ class UnivariateNormalTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(12)
+        self.key = jax.random.key(12)
 
     def normal_logprob(self, x):
         return stats.norm.logpdf(x, loc=1.0, scale=2.0)
@@ -572,7 +572,7 @@ class MonteCarloStandardErrorTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(20220203)
+        self.key = jax.random.key(20220203)
 
     def generate_multivariate_target(self, rng=None):
         """Genrate a Multivariate Normal distribution as target."""

diff --git a/tests/mcmc/test_trajectory.py b/tests/mcmc/test_trajectory.py
@@ -22,7 +22,7 @@ class TrajectoryTest(chex.TestCase):
     def test_dynamic_progressive_integration_divergence(
         self, step_size, should_diverge
     ):
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         logdensity_fn = jax.scipy.stats.norm.logpdf
 
@@ -74,7 +74,7 @@ def test_dynamic_progressive_integration_divergence(
         assert is_diverging.item() is should_diverge
 
     def test_dynamic_progressive_equal_recursive(self):
-        rng_key = jax.random.PRNGKey(23132)
+        rng_key = jax.random.key(23132)
 
         def logdensity_fn(x):
             return -((1.0 - x[0]) ** 2) - 1.5 * (x[1] - x[0] ** 2) ** 2
@@ -202,7 +202,7 @@ def logdensity_fn(x):
     def test_dynamic_progressive_expansion(
         self, step_size, should_diverge, should_turn, expected_doublings
     ):
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         def logdensity_fn(x):
             return -0.5 * x**2
@@ -260,7 +260,7 @@ def logdensity_fn(x):
         assert is_turning == should_turn
 
     def test_static_integration_variable_num_steps(self):
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         logdensity_fn = jax.scipy.stats.norm.logpdf
         position = 1.0

diff --git a/tests/optimizers/test_optimizers.py b/tests/optimizers/test_optimizers.py
@@ -23,7 +23,7 @@
 class OptimizerTest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(1)
+        self.key = jax.random.key(1)
 
     @chex.all_variants(with_pmap=False)
     def test_dual_averaging(self):

diff --git a/tests/optimizers/test_pathfinder.py b/tests/optimizers/test_pathfinder.py
@@ -14,7 +14,7 @@
 class PathfinderTest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(1)
+        self.key = jax.random.key(1)
 
     @chex.all_variants(without_device=False, with_pmap=False)
     @parameterized.parameters(

diff --git a/tests/smc/test_kernel_compatibility.py b/tests/smc/test_kernel_compatibility.py
@@ -17,7 +17,7 @@ class SMCAndMCMCIntegrationTest(unittest.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(42)
+        self.key = jax.random.key(42)
         self.initial_particles = jax.random.multivariate_normal(
             self.key, jnp.zeros(2), jnp.eye(2), (3,)
         )

diff --git a/tests/smc/test_resampling.py b/tests/smc/test_resampling.py
@@ -41,7 +41,7 @@ def test_resampling_methods(self, num_samples, method_name):
         x = jnp.array(np.random.randn(N), dtype="float32")
         w = w / w.sum()
 
-        resampling_keys = jax.random.split(jax.random.PRNGKey(42), batch_size)
+        resampling_keys = jax.random.split(jax.random.key(42), batch_size)
 
         resampling_idx = jax.vmap(
             self.variant(resampling_methods[method_name], static_argnums=(2,)),

diff --git a/tests/smc/test_smc.py b/tests/smc/test_smc.py
@@ -24,7 +24,7 @@ def _weighted_avg_and_std(values, weights):
 class SMCTest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(42)
+        self.key = jax.random.key(42)
 
     @chex.variants(with_jit=True)
     def test_smc(self):

diff --git a/tests/smc/test_tempered_smc.py b/tests/smc/test_tempered_smc.py
@@ -37,7 +37,7 @@ class TemperedSMCTest(chex.TestCase):
 
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(42)
+        self.key = jax.random.key(42)
 
     def logdensity_fn(self, log_scale, coefs, preds, x):
         """Linear regression"""
@@ -174,7 +174,7 @@ def test_normalizing_constant(self):
         num_particles = 200
         num_dim = 2
 
-        rng_key = jax.random.PRNGKey(2356)
+        rng_key = jax.random.key(2356)
         rng_key, cov_key = jax.random.split(rng_key, 2)
         chol_cov = jax.random.uniform(cov_key, shape=(num_dim, num_dim))
         iu = np.triu_indices(num_dim, 1)

diff --git a/tests/test_benchmarks.py b/tests/test_benchmarks.py
@@ -38,7 +38,7 @@ def one_step(state, rng_key):
 
 
 def run_regression(algorithm, **parameters):
-    key = jax.random.PRNGKey(0)
+    key = jax.random.key(0)
     rng_key, init_key0, init_key1 = jax.random.split(key, 3)
     x_data = jax.random.normal(init_key0, shape=(100_000, 1))
     y_data = 3 * x_data + jax.random.normal(init_key1, shape=x_data.shape)

diff --git a/tests/test_compilation.py b/tests/test_compilation.py
@@ -29,7 +29,7 @@ def logdensity_fn(x):
 
         chex.clear_trace_counter()
 
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         state = blackjax.hmc.init(1.0, logdensity_fn)
 
         kernel = blackjax.hmc(
@@ -58,7 +58,7 @@ def logdensity_fn(x):
 
         chex.clear_trace_counter()
 
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
         state = blackjax.nuts.init(1.0, logdensity_fn)
 
         kernel = blackjax.nuts(
@@ -83,7 +83,7 @@ def logdensity_fn(x):
 
         chex.clear_trace_counter()
 
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         warmup = blackjax.window_adaptation(
             algorithm=blackjax.hmc,
@@ -111,7 +111,7 @@ def logdensity_fn(x):
 
         chex.clear_trace_counter()
 
-        rng_key = jax.random.PRNGKey(0)
+        rng_key = jax.random.key(0)
 
         warmup = blackjax.window_adaptation(
             algorithm=blackjax.nuts,

diff --git a/tests/test_diagnostics.py b/tests/test_diagnostics.py
@@ -50,7 +50,7 @@ def setUp(self):
         itertools.product(test_cases, [1, 2, 10], [(), (3,), (5, 7)])
     )
     def test_rhat_ess(self, case, num_chains, event_shape):
-        rng_key = jax.random.PRNGKey(self.test_seed)
+        rng_key = jax.random.key(self.test_seed)
         sample_shape = list(event_shape)
         if case["chain_axis"] < case["sample_axis"]:
             sample_shape = insert_list(sample_shape, case["chain_axis"], num_chains)

diff --git a/tests/vi/test_meanfield_vi.py b/tests/vi/test_meanfield_vi.py
@@ -11,7 +11,7 @@
 class MFVITest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(42)
+        self.key = jax.random.key(42)
 
     def test_recover_posterior(self):
         ground_truth = [

diff --git a/tests/vi/test_svgd.py b/tests/vi/test_svgd.py
@@ -32,7 +32,7 @@ def svgd_training_loop(
 class SvgdTest(chex.TestCase):
     def setUp(self):
         super().setUp()
-        self.key = jax.random.PRNGKey(1)
+        self.key = jax.random.key(1)
 
     def test_recover_posterior(self):
         # TODO improve testing
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,8 +4,8 @@ aesara>=2.8.8 @@
     arviz
     flax
     ipython
-    jax
-    jaxlib
+    jax>=0.4.16
+    jaxlib>=0.4.16
     jaxopt
     jupytext
     myst_nb
@@ Expand Down @@