Merge branch 'pymc-devs:main' into flaky_eulermaruyama_tests

Author: williambdean

conda-envs/environment-dev.yml

@@ -27,7 +27,6 @@ dependencies:
 - myst-nb
 - numpydoc
 - pre-commit>=2.8.0
-- pydata-sphinx-theme>=0.11.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - sphinx-copybutton
@@ -38,5 +37,7 @@ dependencies:
 - watermark
 - polyagamma
 - sphinx-remove-toctrees
-- mypy=0.982
+- mypy=0.990
 - types-cachetools
+- pip:
+  - git+https://github.com/pymc-devs/pymc-sphinx-theme

conda-envs/environment-test.yml

@@ -27,5 +27,5 @@ dependencies:
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
-- mypy=0.982
+- mypy=0.990
 - types-cachetools

conda-envs/windows-environment-dev.yml

@@ -25,7 +25,6 @@ dependencies:
 - myst-nb
 - numpydoc
 - pre-commit>=2.8.0
-- pydata-sphinx-theme>=0.11.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - sphinx-autobuild>=0.7
@@ -35,5 +34,7 @@ dependencies:
 - sphinx>=1.5
 - watermark
 - sphinx-remove-toctrees
-- mypy=0.982
+- mypy=0.990
 - types-cachetools
+- pip:
+  - git+https://github.com/pymc-devs/pymc-sphinx-theme

conda-envs/windows-environment-test.yml

@@ -28,5 +28,5 @@ dependencies:
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
-- mypy=0.982
+- mypy=0.990
 - types-cachetools

docs/source/_static/custom.css

@@ -17,7 +17,6 @@
 # serve to show the default.
 
 import os
-import sys
 from pathlib import Path
 
 import pymc  # isort:skip
@@ -110,8 +109,12 @@
 version = pymc.__version__
 if os.environ.get("READTHEDOCS", False):
     rtd_version = os.environ.get("READTHEDOCS_VERSION", "")
-    if "." not in rtd_version and rtd_version.lower() != "stable":
+    if rtd_version.lower() == "stable":
+        version = pymc.__version__.split("+")[0]
+    elif rtd_version.lower() == "latest":
         version = "dev"
+    else:
+        version = rtd_version
 else:
     rtd_version = "local"
 # The full version, including alpha/beta/rc tags.
@@ -222,47 +225,17 @@ def setup(app):
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "pydata_sphinx_theme"
+html_theme = "pymc_sphinx_theme"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 
 html_theme_options = {
-    "icon_links": [
-        {
-            "name": "GitHub",
-            "url": "https://github.com/pymc-devs/pymc",
-            "icon": "fab fa-github-square",
-        },
-        {
-            "name": "Twitter",
-            "url": "https://twitter.com/pymc_devs",
-            "icon": "fab fa-twitter-square",
-        },
-        {
-            "name": "YouTube",
-            "url": "https://www.youtube.com/c/PyMCDevelopers",
-            "icon": "fab fa-youtube",
-        },
-        {
-            "name": "Discourse",
-            "url": "https://discourse.pymc.io",
-            "icon": "fab fa-discourse",
-        },
-    ],
     "logo": {
         "link": "https://www.pymc.io",
     },
-    "show_prev_next": False,
-    "navbar_start": ["navbar-logo", "navbar-version"],
-    "navbar_end": ["navbar-icon-links.html"],
-    "page_sidebar_items": ["page-toc", "edit-this-page", "donate"],
-    "header_links_before_dropdown": 6,
-    "search_bar_text": "Search...",
-    "use_edit_page_button": True,
-    "google_analytics_id": "UA-176578023-1",
 }
 html_context = {
     "github_user": "pymc-devs",
@@ -294,8 +267,7 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["../logos", "_static"]
-html_css_files = ["custom.css"]
+html_static_path = ["../logos"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -311,9 +283,6 @@ def setup(app):
 # html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {
-    "**": ["sidebar-nav-bs.html"],
-}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

docs/source/_templates/donate.html

@@ -26,14 +26,11 @@
 import pymc
 
 from pymc.aesaraf import extract_obs_data
-from pymc.model import modelcontext
+from pymc.model import Model, modelcontext
 from pymc.util import get_default_varnames
 
 if TYPE_CHECKING:
-    from typing import Set  # pylint: disable=ungrouped-imports
-
     from pymc.backends.base import MultiTrace  # pylint: disable=invalid-name
-    from pymc.model import Model
 
 ___all__ = [""]
 
@@ -145,12 +142,10 @@ def insert(self, k: str, v, idx: int):
 class InferenceDataConverter:  # pylint: disable=too-many-instance-attributes
     """Encapsulate InferenceData specific logic."""
 
-    model = None  # type: Optional[Model]
-    nchains = None  # type: int
-    ndraws = None  # type: int
-    posterior_predictive = None  # Type: Optional[Mapping[str, np.ndarray]]
-    predictions = None  # Type: Optional[Mapping[str, np.ndarray]]
-    prior = None  # Type: Optional[Mapping[str, np.ndarray]]
+    model: Optional[Model] = None
+    posterior_predictive: Optional[Mapping[str, np.ndarray]] = None
+    predictions: Optional[Mapping[str, np.ndarray]] = None
+    prior: Optional[Mapping[str, np.ndarray]] = None
 
     def __init__(
         self,

docs/source/_templates/edit-this-page.html

@@ -85,7 +85,7 @@ def setup(self, draws, chain, sampler_vars=None) -> None:
         if self._stats is None:
             self._stats = []
             for sampler in sampler_vars:
-                data = dict()  # type: Dict[str, np.ndarray]
+                data: Dict[str, np.ndarray] = dict()
                 self._stats.append(data)
                 for varname, dtype in sampler.items():
                     data[varname] = np.zeros(draws, dtype=dtype)

docs/source/_templates/footer.html

@@ -15,7 +15,7 @@
 import dataclasses
 import logging
 
-from typing import Optional
+from typing import Dict, List, Optional
 
 import arviz
 
@@ -32,7 +32,7 @@
 class SamplerReport:
     """Bundle warnings, convergence stats and metadata of a sampling run."""
 
-    def __init__(self):
+    def __init__(self) -> None:
         self._chain_warnings: Dict[int, List[SamplerWarning]] = {}
         self._global_warnings: List[SamplerWarning] = []
         self._n_tune = None

docs/source/_templates/layout.html

@@ -17,10 +17,10 @@
 
 Classes for working with subsets of parameters.
 """
-import collections
+from __future__ import annotations
 
 from functools import partial
-from typing import Callable, Dict, Generic, Optional, TypeVar
+from typing import Callable, Dict, Generic, NamedTuple, TypeVar
 
 import numpy as np
 
@@ -32,7 +32,9 @@
 
 # `point_map_info` is a tuple of tuples containing `(name, shape, dtype)` for
 # each of the raveled variables.
-RaveledVars = collections.namedtuple("RaveledVars", "data, point_map_info")
+class RaveledVars(NamedTuple):
+    data: np.ndarray
+    point_map_info: tuple[tuple[str, tuple[int, ...], np.dtype], ...]
 
 
 class Compose(Generic[T]):
@@ -69,7 +71,7 @@ def map(var_dict: PointType) -> RaveledVars:
     @staticmethod
     def rmap(
         array: RaveledVars,
-        start_point: Optional[PointType] = None,
+        start_point: PointType | None = None,
     ) -> PointType:
         """Map 1D concatenated array to a dictionary of variables in their original spaces.
 
@@ -100,7 +102,7 @@ def rmap(
 
     @classmethod
     def mapf(
-        cls, f: Callable[[PointType], T], start_point: Optional[PointType] = None
+        cls, f: Callable[[PointType], T], start_point: PointType | None = None
     ) -> Callable[[RaveledVars], T]:
         """Create a callable that first maps back to ``dict`` inputs and then applies a function.
 

docs/source/_templates/navbar-version.html

@@ -301,7 +301,7 @@ class Minibatch(TensorVariable):
         >>> assert x.eval().shape == (2, 20, 20, 40, 10)
     """
 
-    RNG = collections.defaultdict(list)  # type: Dict[str, List[Any]]
+    RNG: Dict[str, List[Any]] = collections.defaultdict(list)
 
     @aesara.config.change_flags(compute_test_value="raise")
     def __init__(
@@ -708,7 +708,7 @@ def Data(
             xshape = x.shape
         # Register new dimension lengths
         for d, dname in enumerate(dims):
-            if not dname in model.dim_lengths:
+            if dname not in model.dim_lengths:
                 model.add_coord(
                     name=dname,
                     # Note: Coordinate values can't be taken from