Merge pull request #319 from lnccbrown/292-graphing-quantile-probabil…

…ity-plot

First attempt at Quantile probability plot

.pre-commit-config.yaml

@@ -5,12 +5,12 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.278
+    rev: v0.1.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.10.1
     hooks:
       - id: black-jupyter
         args:
@@ -29,7 +29,7 @@ repos:
             build|
             dist"""
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1 # Use the sha / tag you want to point at
+    rev: v1.6.1 # Use the sha / tag you want to point at
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]

pyproject.toml

@@ -30,17 +30,18 @@ bambi = "^0.12.0"
 numpyro = "^0.12.1"
 hddm-wfpt = "^0.1.1"
 seaborn = "^0.13.0"
+xhistogram = "^0.3.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"
-black = { extras = ["jupyter"], version = "^23.7.0" }
-mypy = "^1.4.1"
+black = { extras = ["jupyter"], version = "^23.10.1" }
+mypy = "^1.6.1"
 pre-commit = "^2.20.0"
 jupyterlab = "^4.0.2"
 ipykernel = "^6.16.0"
 ipywidgets = "^8.0.3"
 graphviz = "^0.20.1"
-ruff = "^0.0.272"
+ruff = "^0.1.3"
 mkdocs = "^1.4.3"
 mkdocs-material = "^9.1.17"
 mkdocstrings-python = "^1.1.2"
@@ -159,6 +160,8 @@ ignore = [
     "PLR2004",
     # Consider `elif` instead of `else` then `if` to remove indentation level
     "PLR5501",
+    # Ignore "Use `float` instead of `int | float`."
+    "PYI041",
     # Allow importing from parent modules
     "TID252",
 ]

src/hssm/datasets.py

@@ -5,14 +5,20 @@
 """
 
 import os
-from collections import namedtuple
-from typing import Optional, Union
+from typing import NamedTuple, Optional, Union
 
 import pandas as pd
 
 base_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 
-FileMetadata = namedtuple("FileMetadata", ["filename", "path", "description"])
+
+class FileMetadata(NamedTuple):
+    """Typing for dataset metadata."""
+
+    filename: str
+    path: str
+    description: str
+
 
 DATASETS = {
     "cavanagh_theta": FileMetadata(

src/hssm/defaults.py

@@ -123,7 +123,13 @@ class DefaultConfig(TypedDict):
             "approx_differentiable": {
                 "loglik": "ddm_sdv.onnx",
                 "backend": "jax",
-                "default_priors": {},
+                "default_priors": {
+                    "t": {
+                        "name": "HalfNormal",
+                        "sigma": 2.0,
+                        "initval": 0.1,
+                    },
+                },
                 "bounds": {
                     "v": (-3.0, 3.0),
                     "a": (0.3, 2.5),

src/hssm/distribution_utils/dist.py

@@ -7,7 +7,7 @@
 
 import logging
 from os import PathLike
-from typing import Any, Callable, Iterable, Type
+from typing import Any, Callable, Type
 
 import bambi as bmb
 import numpy as np
@@ -279,19 +279,24 @@ def rng_fn(
                 )
                 out_shape = sims_out.shape[:-1]
                 replace = rng.binomial(n=1, p=p_outlier, size=out_shape).astype(bool)
-                replace = np.stack([replace, replace], axis=-1)
-                n_draws = np.prod(out_shape)
+                replace_n = int(np.sum(replace, axis=None))
+                if replace_n == 0:
+                    return sims_out
+                replace_shape = (*out_shape[:-1], replace_n)
+                replace_mask = np.stack([replace, replace], axis=-1)
+                n_draws = np.prod(replace_shape)
                 lapse_rt = pm.draw(
                     get_distribution_from_prior(cls._lapse).dist(**cls._lapse.args),
                     n_draws,
                     random_seed=rng,
-                ).reshape(out_shape)
-                lapse_response = rng.binomial(n=1, p=0.5, size=out_shape)
+                ).reshape(replace_shape)
+                lapse_response = rng.binomial(n=1, p=0.5, size=replace_shape)
+                lapse_response = np.where(lapse_response == 1, 1, -1)
                 lapse_output = np.stack(
                     [lapse_rt, lapse_response],
                     axis=-1,
                 )
-                np.putmask(sims_out, replace, lapse_output)
+                np.putmask(sims_out, replace_mask, lapse_output)
 
             return sims_out
 
@@ -379,7 +384,7 @@ def dist(cls, **kwargs):  # pylint: disable=arguments-renamed
 
         def logp(data, *dist_params):  # pylint: disable=E0213
             num_params = len(list_params)
-            extra_fields: Iterable[np.ndarray] = []
+            extra_fields = []
 
             if num_params < len(dist_params):
                 extra_fields = dist_params[num_params:]

src/hssm/distribution_utils/onnx/onnx2pt.py

@@ -52,7 +52,7 @@ def pt_interpret_onnx(graph, *args):
     """
     vals = dict(
         {n.name: a for n, a in zip(graph.input, args)},
-        **{n.name: _asarray(n) for n in graph.initializer}
+        **{n.name: _asarray(n) for n in graph.initializer},
     )
     for node in graph.node:
         args = (vals[name] for name in node.input)

src/hssm/distribution_utils/onnx/onnx2xla.py

@@ -151,7 +151,7 @@ def interpret_onnx(graph, *args):
     """
     vals = dict(
         {n.name: a for n, a in zip(graph.input, args)},
-        **{n.name: _asarray(n) for n in graph.initializer}
+        **{n.name: _asarray(n) for n in graph.initializer},
     )
     for node in graph.node:
         args = (vals[name] for name in node.input)

src/hssm/plotting/__init__.py

@@ -1,5 +1,6 @@
 """Plotting functionalities for HSSM."""
 
 from .posterior_predictive import plot_posterior_predictive
+from .quantile_probability import plot_quantile_probability
 
-__all__ = ["plot_posterior_predictive"]
+__all__ = ["plot_posterior_predictive", "plot_quantile_probability"]