theme update and doc fixes (#473)

* theme update and doc fixes

* configure search and use pypi release

Author: OriolAbril

.gitignore

@@ -11,6 +11,7 @@ tmtags
 tags
 .DS_Store
 .cache
+_version.py
 # IntelliJ IDE
 .idea
 *.iml

.readthedocs.yaml

@@ -17,3 +17,14 @@ python:
 sphinx:
   fail_on_warning: false
   configuration: docs/conf.py
+
+search:
+  ranking:
+    _sources/*: -10
+    _modules/*: -5
+    genindex.html: -9
+
+  ignore:
+    - 404.html
+    - search.html
+    - index.html

docs/conf.py

@@ -26,23 +26,18 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
-import sys
-
-import pymc_extras  # isort:skip
-
-sys.path.insert(0, os.path.abspath("../"))
+import pymc_extras
 
 # -- Project information -----------------------------------------------------
 
 project = "pymc_extras"
 copyright = "2022, pymc-devs"
 author = "pymc-devs"
 
-# The short X.Y version
-version = pymc_extras.__version__
 # The full version, including alpha/beta/rc tags
-release = version
+release = pymc_extras.__version__
+# The short X.Y version
+version = release.split("+")[0] if "+" in release else release
 
 
 # -- General configuration ---------------------------------------------------
@@ -112,9 +107,16 @@
     "collapse_navigation": True,
     "show_toc_level": 2,
     "navigation_depth": 4,
-    "search_bar_text": "Search the docs...",
-    "use_search_override": False,
+    "search_bar_text": "Search within PyMC-extras...",
+    "use_search_override": True,
     "logo": {"text": project},
+    "icon_links": [
+        {
+            "url": "https://github.com/pymc-devs/pymc-extras",
+            "icon": "fa-brands fa-github",
+            "name": "GitHub",
+        },
+    ],
 }
 html_context = {
     "github_user": "pymc-devs",
@@ -128,7 +130,7 @@
 # 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 = ["../_static"]
+# html_static_path = ["../_static"]
 
 # -- Options for HTMLHelp output ---------------------------------------------
 

docs/index.rst

@@ -21,7 +21,7 @@ Where we grow the next batch of cool PyMC features
 Installation
 ============
 
-To install the latest release on [PyPI](https://pypi.org/project/pymc-extras/), you can use a package manager like pip:
+To install the latest release on `PyPI <https://pypi.org/project/pymc-extras/>`_, you can use a package manager like pip:
 
 .. code-block:: bash
 

pymc_extras/distributions/continuous.py

@@ -81,7 +81,7 @@ class GenExtreme(Continuous):
 
         \left\{x: 1 + \xi\left(\frac{x-\mu}{\sigma}\right) > 0 \right\}.
 
-    Note that this parametrization is per Coles (2001), and differs from that of
+    Note that this parametrization is per Coles (2001) [1]_, and differs from that of
     Scipy in the sign of the shape parameter, :math:`\xi`.
 
     .. plot::
@@ -132,7 +132,7 @@ class GenExtreme(Continuous):
 
     References
     ----------
-    .. [Coles2001] Coles, S.G. (2001).
+    .. [1] Coles, S.G. (2001).
         An Introduction to the Statistical Modeling of Extreme Values
         Springer-Verlag, London
 
@@ -260,6 +260,7 @@ class Chi:
     Examples
     --------
     .. code-block:: python
+
         import pymc as pm
         from pymc_extras.distributions import Chi
 

pymc_extras/distributions/discrete.py

@@ -116,6 +116,7 @@ class GeneralizedPoisson(pm.distributions.Discrete):
 
     .. math:: f(x \mid \mu, \lambda) =
                   \frac{\mu (\mu + \lambda x)^{x-1} e^{-\mu - \lambda x}}{x!}
+
     ========  ======================================
     Support   :math:`x \in \mathbb{N}_0`
     Mean      :math:`\frac{\mu}{1 - \lambda}`
@@ -135,9 +136,10 @@ class GeneralizedPoisson(pm.distributions.Discrete):
     When lam < 0, the mean is greater than the variance (underdispersion).
     When lam > 0, the mean is less than the variance (overdispersion).
 
+    The PMF is taken from [1]_ and the random generator function is adapted from [2]_.
+
     References
     ----------
-    The PMF is taken from [1] and the random generator function is adapted from [2].
     .. [1] Consul, PoC, and Felix Famoye. "Generalized Poisson regression model."
        Communications in Statistics-Theory and Methods 21.1 (1992): 89-109.
     .. [2] Famoye, Felix. "Generalized Poisson random variate generation." American

pyproject.toml

@@ -53,9 +53,8 @@ dev = [
 ]
 docs = [
   "nbsphinx>=0.4.2",
-  "pydata-sphinx-theme>=0.6.3",
   "sphinx>=4.0",
-  "pymc-sphinx-theme@git+https://github.com/pymc-devs/pymc-sphinx-theme",
+  "pymc-sphinx-theme>=0.16",
 ]
 dask_histogram = [
   "dask[complete]<2025.1.1",