Merge pull request #443 from lnccbrown/442-jax-has-deprecated-the-jax…

…config-module-from-0429

Update reference to jax.config

docs/tutorials/main_tutorial.ipynb

@@ -407,21 +407,20 @@
     "import os\n",
     "import sys\n",
     "import time\n",
-    "from matplotlib import pyplot as plt\n",
+    "\n",
     "import arviz as az  # Visualization\n",
-    "import pytensor  # Graph-based tensor library\n",
-    "import hssm\n",
+    "import bambi as bmb\n",
     "\n",
     "# import ssms.basic_simulators # Model simulators\n",
     "import hddm_wfpt\n",
-    "import bambi as bmb\n",
+    "import hssm\n",
+    "import jax\n",
+    "import pytensor  # Graph-based tensor library\n",
+    "from matplotlib import pyplot as plt\n",
     "\n",
     "# Setting float precision in pytensor\n",
     "pytensor.config.floatX = \"float32\"\n",
-    "\n",
-    "from jax.config import config\n",
-    "\n",
-    "config.update(\"jax_enable_x64\", False)"
+    "jax.config.update(\"jax_enable_x64\", False)"
    ]
   },
   {
@@ -4004,9 +4003,7 @@
     }
    ],
    "source": [
-    "from jax.config import config\n",
-    "\n",
-    "config.update(\"jax_enable_x64\", False)\n",
+    "jax.config.update(\"jax_enable_x64\", False)\n",
     "infer_data_angle = model_angle.sample(\n",
     "    sampler=\"nuts_numpyro\",\n",
     "    chains=2,\n",
@@ -10117,9 +10114,7 @@
     }
    ],
    "source": [
-    "from jax.config import config\n",
-    "\n",
-    "config.update(\"jax_enable_x64\", False)\n",
+    "jax.config.update(\"jax_enable_x64\", False)\n",
     "model_reg_v_angle_hier.sample(\n",
     "    sampler=\"nuts_numpyro\", chains=2, cores=1, draws=1000, tune=1000\n",
     ")"

pyproject.toml

@@ -25,7 +25,7 @@ bambi = "^0.13.0"
 numpyro = "^0.15.0"
 hddm-wfpt = "^0.1.4"
 seaborn = "^0.13.2"
-jax = { version = ">=0.4.23,<0.4.28", extras = ["cuda12"], optional = true }
+jax = { version = "^0.4.25", extras = ["cuda12"], optional = true }
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.2.0"

src/hssm/utils.py

@@ -13,13 +13,13 @@
 from typing import Any, Iterable, Literal, NewType
 
 import bambi as bmb
+import jax
 import numpy as np
 import pandas as pd
 import pytensor
 import xarray as xr
 from bambi.terms import CommonTerm, GroupSpecificTerm, HSGPTerm, OffsetTerm
 from huggingface_hub import hf_hub_download
-from jax import config
 from pymc.model_graph import ModelGraph
 from pytensor import function
 
@@ -258,7 +258,7 @@ def make_graph(
         return graph
 
 
-def set_floatX(dtype: Literal["float32", "float64"], jax: bool = True):
+def set_floatX(dtype: Literal["float32", "float64"], update_jax: bool = True):
     """Set float types for pytensor and Jax.
 
     Often we wish to work with a specific type of float in both PyTensor and JAX.
@@ -268,7 +268,7 @@ def set_floatX(dtype: Literal["float32", "float64"], jax: bool = True):
     ----------
     dtype
         Either `float32` or `float64`. Float type for pytensor (and jax if `jax=True`).
-    jax : optional
+    update_jax : optional
         Whether this function also sets float type for JAX by changing the
         `jax_enable_x64` setting in JAX config. Defaults to True.
     """
@@ -278,9 +278,9 @@ def set_floatX(dtype: Literal["float32", "float64"], jax: bool = True):
     pytensor.config.floatX = dtype
     _logger.info("Setting PyTensor floatX type to %s.", dtype)
 
-    if jax:
+    if update_jax:
         jax_enable_x64 = dtype == "float64"
-        config.update("jax_enable_x64", jax_enable_x64)
+        jax.config.update("jax_enable_x64", jax_enable_x64)
 
         _logger.info(
             'Setting "jax_enable_x64" to %s. '

tests/slow/test_mcmc.py

@@ -10,7 +10,7 @@
 
 from hssm.utils import _rearrange_data
 
-hssm.set_floatX("float32", jax=True)
+hssm.set_floatX("float32", update_jax=True)
 
 # AF-TODO: Include more tests that use different link functions!
 

tests/test_hssm.py

@@ -7,7 +7,7 @@
 from hssm.utils import download_hf
 from hssm.likelihoods import DDM, logp_ddm
 
-hssm.set_floatX("float32", jax=True)
+hssm.set_floatX("float32", update_jax=True)
 
 param_v = {
     "name": "v",